From 9615791ae1fe62569d72f256c33c0f986fa490e7 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 20 May 2024 14:35:39 +0200 Subject: [PATCH 01/25] wip --- builder/README.md | 4 +- builder/fairgraph_module_template.py.txt | 25 +- builder/update_openminds.py | 9 +- fairgraph/__init__.py | 3 +- fairgraph/base.py | 434 +----------------- fairgraph/client.py | 7 +- fairgraph/embedded.py | 5 +- fairgraph/kgobject.py | 16 +- fairgraph/kgproxy.py | 3 +- fairgraph/kgquery.py | 5 +- fairgraph/node.py | 438 ++++++++++++++++++ fairgraph/properties.py | 542 ----------------------- fairgraph/queries.py | 218 ++++++++- fairgraph/registry.py | 107 +---- fairgraph/utility.py | 11 +- test/test_base.py | 24 +- test/test_openminds_core.py | 11 +- test/test_properties.py | 9 +- test/test_registry.py | 7 +- test/utils.py | 3 +- 20 files changed, 753 insertions(+), 1128 deletions(-) create mode 100644 fairgraph/node.py delete mode 100644 fairgraph/properties.py diff --git a/builder/README.md b/builder/README.md index 30916bdf..eeadae7e 100644 --- a/builder/README.md +++ b/builder/README.md @@ -3,10 +3,10 @@ To update the `fairgraph.openminds` module, run: ``` -python update_openminds.py /path/to/openMINDS +python update_openminds.py /path/to/openMINDS/schemas/latest ``` -Where the various submodules have already been cloned and the desired version branches checked out. +Where /path/to/openMINDS is a clone of the main branch of https://github.com/openMetadataInitiative/openMINDS.git Before committing the resulting generated files, check that any changed introduced seem correct. Currently a few changes are applied by hand on top of the generated files, be sure not to overwrite these. diff --git a/builder/fairgraph_module_template.py.txt b/builder/fairgraph_module_template.py.txt index 5385ce2b..2711f7d3 100644 --- a/builder/fairgraph_module_template.py.txt +++ b/builder/fairgraph_module_template.py.txt @@ -4,35 +4,20 @@ # this file was auto-generated -from fairgraph import {{ base_class }}, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.{{ module_name }} import {{ class_name }} +from fairgraph import {{ base_class }} {{preamble}} -class {{ class_name }}({{ base_class }}): +class {{ class_name }}({{ class_name }}, {{ base_class }}): """ {{ docstring }} """ {%- if default_space %} default_space = "{{ default_space }}" {%- endif %} - type_ = "{{ openminds_type }}" - context = { - "schema": "http://schema.org/", - "kg": "https://kg.ebrains.eu/api/instances/", - "vocab": "https://openminds.ebrains.eu/vocab/", - "terms": "https://openminds.ebrains.eu/controlledTerms/", - "core": "https://openminds.ebrains.eu/core/" - } - properties = [ - {% for prop in properties -%} - Property("{{prop.name}}", {{prop.type_str}}, "{{prop.iri}}", - {%- if prop.allow_multiple %}multiple={{prop.allow_multiple}},{% endif -%} - {%- if prop.required %}required={{prop.required}},{% endif -%} - doc="{{prop.doc}}"), - {% endfor %} - ] reverse_properties = [ {% for prop in reverse_properties -%} Property( @@ -49,7 +34,7 @@ class {{ class_name }}({{ base_class }}): {% endif -%} {%- if prop.allow_multiple %}multiple={{prop.allow_multiple}},{% endif -%} {%- if prop.required %}, required={{prop.required}},{% endif -%} - doc="{{prop.doc}}"), + description="{{prop.doc}}"), {% endfor %} ] {%- if aliases %} diff --git a/builder/update_openminds.py b/builder/update_openminds.py index ce89bc3a..e0275e44 100644 --- a/builder/update_openminds.py +++ b/builder/update_openminds.py @@ -489,7 +489,7 @@ def generate_class_name(iri): parts = iri.split("/")[-2:] for i in range(len(parts) - 1): parts[i] = generate_python_name(parts[i]) - return "openminds." + ".".join(parts) + return "openminds.latest." + ".".join(parts) def get_controlled_terms_table(type_): @@ -713,7 +713,7 @@ def get_type(prop): (forward_link_name,) = unique_forward_link_names (forward_link_name_plural,) = set(linked_from[reverse_link_name][1]) _forward_link_name_python = generate_python_name(forward_link_name_plural) - iri = f"^vocab:{forward_link_name}" + iri = forward_link_name doc = f"reverse of '{forward_link_name}'" # use _plural? types_str = sorted(types_str) if len(types_str) == 1: @@ -730,7 +730,7 @@ def get_type(prop): forward_link_name = linked_from[reverse_link_name][0] forward_link_name_plural = linked_from[reverse_link_name][1] _forward_link_name_python = [generate_python_name(name) for name in forward_link_name_plural] - iri = [f"^vocab:{name}" for name in forward_link_name] + iri = [name for name in forward_link_name] doc = "reverse of " + ", ".join(name for name in forward_link_name) # use _plural? reverse_name_python = generate_python_name(reverse_link_name) if reverse_name_python in forward_property_names: @@ -761,6 +761,7 @@ def get_type(prop): "docstring": self._schema_payload.get("description", ""), "base_class": base_class, "preamble": preamble.get(class_name, ""), # default value, may be updated below + "module_name": module_name, "class_name": class_name, "default_space": default_space, "openminds_type": self._schema_payload["_type"], @@ -780,7 +781,7 @@ def get_type(prop): "date": "from datetime import date", "datetime": "from datetime import datetime", "time": "from datetime import time", - "IRI": "from fairgraph.base import IRI", + "IRI": "from openminds import IRI", "[datetime, time]": "from datetime import datetime, time", } extra_imports = set() diff --git a/fairgraph/__init__.py b/fairgraph/__init__.py index f1360601..05e0b7ee 100644 --- a/fairgraph/__init__.py +++ b/fairgraph/__init__.py @@ -19,12 +19,13 @@ limitations under the License. """ +from openminds import IRI from .client import KGClient from .kgobject import KGObject from .embedded import EmbeddedMetadata from .kgproxy import KGProxy from .kgquery import KGQuery -from .base import IRI + __version__ = "0.12.0" diff --git a/fairgraph/base.py b/fairgraph/base.py index 64c52d0b..b588974c 100644 --- a/fairgraph/base.py +++ b/fairgraph/base.py @@ -19,27 +19,15 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Optional, Dict, List, Union, Any -from typing_extensions import TypeAlias -from copy import copy +from typing import TYPE_CHECKING, Optional, Dict, List, Any from enum import Enum import logging from warnings import warn -from .registry import Registry -from .queries import QueryProperty -from .errors import ResolutionFailure, AuthorizationError, CannotBuildExistenceQuery -from .utility import ( - as_list, # temporary for backwards compatibility (a lot of code imports it from here) - expand_uri, - normalize_data, - invert_dict -) +from .errors import AuthorizationError if TYPE_CHECKING: from .client import KGClient - from .properties import Property - from .utility import ActivityLog logger = logging.getLogger("fairgraph") @@ -73,401 +61,6 @@ def resolve( pass -class ContainsMetadata(Resolvable, metaclass=Registry): # KGObject and EmbeddedMetadata - properties: List[Property] - reverse_properties: List[Property] - context: Dict[str, str] - type_: str - scope: Optional[str] - space: Union[str, None] - default_space: Union[str, None] - remote_data: Optional[JSONdict] - aliases: Dict[str, str] = {} - - def __init__(self, data: Optional[Dict] = None, **properties): - properties_copy = copy(properties) - for prop in self.__class__.all_properties: - try: - val = properties[prop.name] - except KeyError: - if prop.required: - msg = "Property '{}' is required.".format(prop.name) - ErrorHandling.handle_violation(prop.error_handling, msg) - val = None - else: - properties_copy.pop(prop.name) - if val is None: - val = prop.default - if callable(val): - val = val() - elif isinstance(val, (list, tuple)) and len(val) == 0: # empty list - val = None - setattr(self, prop.name, val) - for name_, alias_ in self.aliases.items(): - # the trailing underscores are because 'name' and 'alias' can be keys in 'properties' - if name_ in properties_copy: - val = properties_copy.pop(name_) - if val is not None: - if properties.get(alias_, None): - raise ValueError(f"'{name_}' is an alias for '{alias_}', you cannot specify both") - setattr(self, alias_, val) - if len(properties_copy) > 0: - if len(properties_copy) == 1: - raise NameError(f'{self.__class__.__name__} does not have a property named "{list(properties_copy)[0]}".') - else: - raise NameError( - f"""{self.__class__.__name__} does not have properties named "{'", "'.join(properties_copy)}".""" - ) - - # we store the original remote data in `_raw_remote_data` - # and a normalized version in `remote_data` - self._raw_remote_data = data # for debugging - self.remote_data = {} - if data: - self.remote_data = self.to_jsonld(include_empty_properties=True, follow_links=False) - - def __getattribute__(self, name): - try: - return object.__getattribute__(self, name) - except AttributeError: - if name in self.aliases: - return object.__getattribute__(self, self.aliases[name]) - else: - raise - - def __setattr__(self, name, value): - try: - prop = self._property_lookup[name] - except KeyError: - if name in self.aliases: - setattr(self, self.aliases[name], value) - else: - super().__setattr__(name, value) - else: - prop.check_value(value) - super().__setattr__(name, value) - - def to_jsonld( - self, - normalized: bool = True, - follow_links: bool = False, - include_empty_properties: bool = False, - include_reverse_properties: bool = False, - ): - """ - Return a JSON-LD representation of this metadata object - - Args: - normalized (bool): Whether to expand all URIs. Defaults to True. - follow_links (bool, optional): Whether to represent linked objects just by their "@id" - or to include their full metadata. Defaults to False. - include_empty_properties (bool, optional): Whether to include empty properties (with value "null"). - Defaults to False. - - """ - if self.properties: - data: JSONdict = {"@type": [self.type_]} - if hasattr(self, "id") and self.id: - data["@id"] = self.id - for prop in self.__class__.all_properties: - if prop.intrinsic or include_reverse_properties: - expanded_path = prop.expanded_path - value = getattr(self, prop.name) - if include_empty_properties or prop.required or value is not None: - serialized = prop.serialize(value, follow_links=follow_links) - if expanded_path in data: - if isinstance(data[expanded_path], list): - data[expanded_path].append(serialized) - else: - data[expanded_path] = [data[expanded_path], serialized] - else: - data[expanded_path] = serialized - if normalized: - return normalize_data(data, self.context) - else: - return data - else: - raise NotImplementedError("to be implemented by child classes") - - @classmethod - def from_jsonld(cls, data: JSONdict, client: KGClient, scope: Optional[str] = None): - """ - Create an instance of the class from a JSON-LD document. - """ - if scope: - return cls.from_kg_instance(data, client, scope) - else: - return cls.from_kg_instance(data, client) - - @classmethod - def from_kg_instance(cls, data: JSONdict, client: KGClient, scope: Optional[str] = None) -> ContainsMetadata: - pass - - def save( - self, - client: KGClient, - space: Optional[str] = None, - recursive: bool = True, - activity_log: Optional[ActivityLog] = None, - replace: bool = False, - ignore_auth_errors: bool = False, - ): - pass - - @classmethod - def set_error_handling( - cls, value: Union[ErrorHandling, None], property_names: Optional[Union[str, List[str]]] = None - ): - """ - Control validation for this class. - - Args: - value (str): action to follow when there is a validation failure. - (e.g. if a required property is not provided). - Possible values: "error", "warning", "log", None - property_names (str or list of str, optional): If not provided, the error handling - mode will be applied to all properties. If a property name or list of names is given, - the mode will be applied only to those properties. - """ - if value is None: - value = ErrorHandling.none - else: - value = ErrorHandling(value) - if property_names: - for property_name in as_list(property_names): - try: - prop = cls._property_lookup[property_name] - except KeyError: - raise ValueError("No such property: {}".format(property_name)) - else: - prop.error_handling = value - else: - for prop in cls.all_properties: - prop.error_handling = value - - @classmethod - def normalize_filter(cls, filter_dict: Dict[str, Any]) -> Dict[str, Any]: - """ - Normalize a dict containing filter key:value pairs so that it can be used - in a call to the KG query API. - - Example: - >>> import fairgraph.openminds.core as omcore - >>> person = omcore.Person.from_uuid("045f846f-f010-4db8-97b9-b95b20970bf2", kg_client) - >>> filter_dict = {"custodians": person, "name": "Virtual"} - >>> omcore.Dataset.normalize_filter(filter_dict) - {'name': 'Virtual', - 'custodians': 'https://kg.ebrains.eu/api/instances/045f846f-f010-4db8-97b9-b95b20970bf2'} - """ - normalized = {} - filter_dict_copy = filter_dict.copy() - - # handle aliases - for name_, alias_ in cls.aliases.items(): - if name_ in filter_dict_copy: - filter_dict_copy[alias_] = filter_dict_copy.pop(name_) - - for prop in cls.all_properties: - if prop.name in filter_dict_copy: - value = filter_dict_copy[prop.name] - if isinstance(value, dict): - normalized[prop.name] = {} - for child_cls in prop.types: - normalized[prop.name].update(child_cls.normalize_filter(value)) - else: - normalized[prop.name] = prop.get_filter_value(value) - return normalized - - @classmethod - def generate_query_properties(cls, follow_links: Optional[Dict[str, Any]] = None): - """ - Generate a list of QueryProperty instances for this class - for use in constructing a KG query definition. - - Args: - follow_links (dict): The links in the graph to follow when constructing the query. Defaults to None. - """ - properties = [QueryProperty("@type")] - reverse_aliases = invert_dict(cls.aliases) - for prop in cls.all_properties: - if prop.is_link and follow_links: - if prop.name in follow_links: - properties.extend(prop.get_query_properties(follow_links[prop.name])) - elif reverse_aliases.get(prop.name, None) in follow_links: - properties.extend(prop.get_query_properties(follow_links[reverse_aliases[prop.name]])) - else: - properties.extend(prop.get_query_properties()) - else: - properties.extend(prop.get_query_properties()) - return properties - - @classmethod - def generate_query_filter_properties( - cls, - filters: Optional[Dict[str, Any]] = None, - ): - """ - - Args: - filters (dict, optional): A dict containing search parameters for the query. - """ - if filters is None: - filters = {} - properties = [] - for prop in cls.all_properties: - if prop.name in filters: - properties.append(prop.get_query_filter_property(filters[prop.name])) - return properties - - @classmethod - def _deserialize_data(cls, data: JSONdict, client: KGClient, include_id: bool = False): - # normalize data by expanding keys - D = {"@type": data["@type"]} - if include_id: - D["@id"] = data["@id"] - for key, value in data.items(): - if "__" in key: - key, type_filter = key.split("__") - normalised_key = expand_uri(key, cls.context) - value = [item for item in as_list(value) if item["@type"][0].endswith(type_filter)] - if normalised_key in D: - D[normalised_key].extend(value) - else: - D[normalised_key] = value - elif key.startswith("Q"): # for 'Q' properties in data from queries - D[key] = value - elif key[0] != "@": - normalised_key = expand_uri(key, cls.context) - D[normalised_key] = value - if cls.type_ not in D["@type"]: - raise TypeError("type mismatch {} - {}".format(cls.type_, D["@type"])) - - def _get_type_from_data(data_item): - type_ = data_item.get("@type", None) - if type_: - return type_[0] - else: - return None - - deserialized_data = {} - for prop in cls.all_properties: - expanded_path = expand_uri(prop.path, cls.context) - data_item = D.get(expanded_path) - if data_item is not None and prop.reverse: - # for reverse properties, more than one property can have the same path - # so we extract only those sub-items whose types match - try: - data_item = [ - part for part in as_list(data_item) - if _get_type_from_data(part) in [t.type_ for t in prop.types] - ] - except AttributeError: - # problem when a forward and reverse path both given the same expanded path - # e.g. for Configuration - data_item = None - # sometimes queries put single items in a list, this removes the enclosing list - if (not prop.multiple) and isinstance(data_item, (list, tuple)) and len(data_item) == 1: - data_item = data_item[0] - deserialized_data[prop.name] = prop.deserialize(data_item, client, belongs_to=data.get("@id", None)) - return deserialized_data - - def resolve( - self, - client: KGClient, - scope: Optional[str] = None, - use_cache: bool = True, - follow_links: Optional[Dict[str, Any]] = None, - ): - """ - Resolve properties that are represented by KGProxy objects. - - Args: - client: KGClient object that handles the communication with the KG. - scope (str): The scope of instances to include in the response. - Valid values are 'released', 'in progress', 'any'. - use_cache (bool): whether to use cached data if they exist. Defaults to True. - follow_links (dict): The links in the graph to follow. Defaults to None. - - Note: a real (non-proxy) object resolves to itself. - """ - use_scope = scope or self.scope or "released" - if follow_links: - reverse_aliases = invert_dict(self.__class__.aliases) - for prop in self.__class__.all_properties: - if prop.is_link: - follow_name = None - if prop.name in follow_links: - follow_name = prop.name - elif reverse_aliases.get(prop.name, None) in follow_links: - follow_name = reverse_aliases[prop.name] - - if follow_name: - if issubclass(prop.types[0], ContainsMetadata): - values = getattr(self, prop.name) - resolved_values: List[Any] = [] - for value in as_list(values): - if isinstance(value, Resolvable): - if isinstance(value, ContainsMetadata) and isinstance(value, RepresentsSingleObject): - # i.e. isinstance(value, KGObject) - already resolved - resolved_values.append(value) - else: - try: - resolved_value = value.resolve( - client, - scope=use_scope, - use_cache=use_cache, - follow_links=follow_links[follow_name], - ) - except ResolutionFailure as err: - warn(str(err)) - resolved_values.append(value) - else: - resolved_values.append(resolved_value) - if isinstance(values, RepresentsSingleObject): - assert len(resolved_values) == 1 - setattr(self, prop.name, resolved_values[0]) - elif values is None: - assert len(resolved_values) == 0 - setattr(self, prop.name, None) - else: - setattr(self, prop.name, resolved_values) - return self - - def _build_existence_query(self) -> Union[None, Dict[str, Any]]: - """ - Generate a KG query definition (as a JSON-LD document) that can be used to - check whether a locally-defined object (with no ID) already exists in the KG. - """ - if self.existence_query_properties is None: - return None - - query_properties = [] - for property_name in self.existence_query_properties: - for property in self.__class__.all_properties: - if property.name == property_name: - query_properties.append(property) - break - if len(query_properties) < 1: - raise CannotBuildExistenceQuery("Empty existence query for class {}".format(self.__class__.__name__)) - query = {} - for property in query_properties: - query_property_name = property.name - value = getattr(self, property.name) - if isinstance(value, ContainsMetadata): - if hasattr(value, "id") and value.id: - query[query_property_name] = value.id - else: - sub_query = value._build_existence_query() - query.update({f"{query_property_name}__{key}": val for key, val in sub_query.items()}) - elif isinstance(value, (list, tuple)): - raise CannotBuildExistenceQuery("not implemented yet") - else: - query_val = property.serialize(getattr(self, property.name), follow_links=False) - if query_val is None: - raise CannotBuildExistenceQuery("Required value is missing") - query[query_property_name] = query_val - return query - class RepresentsSingleObject(Resolvable): # KGObject, KGProxy id: Optional[str] remote_data: Optional[JSONdict] @@ -507,26 +100,3 @@ def unrelease(self, client: KGClient, with_children: bool = False): class SupportsQuerying: # KGObject, KGQuery pass - - -class IRI: - def __init__(self, value: Union[str, IRI]): - if isinstance(value, IRI): - iri = value.value - else: - iri = value - if not iri.startswith("http"): - raise ValueError("Invalid IRI") - self.value: str = iri - - def __eq__(self, other): - return self.__class__ == other.__class__ and self.value == other.value - - def __repr__(self): - return f"IRI({self.value})" - - def __str__(self): - return self.value - - def to_jsonld(self): - return self.value diff --git a/fairgraph/client.py b/fairgraph/client.py index 657e9791..706e886b 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -114,7 +114,12 @@ def __init__( try: self._kg_client_builder = kg(host).with_token(os.environ["KG_AUTH_TOKEN"]) except KeyError: - raise AuthenticationError("Need to provide either token or client id/secret.") + iam_config_url = "https://iam.ebrains.eu/auth/realms/hbp/.well-known/openid-configuration" + self._kg_client_builder = kg(host).with_device_flow( + client_id="kg-core-python", + open_id_configuration_url=iam_config_url + ) + #raise AuthenticationError("Need to provide either token or client id/secret.") self._kg_client = self._kg_client_builder.build() self.__kg_admin_client = None self.host = host diff --git a/fairgraph/embedded.py b/fairgraph/embedded.py index a1a8c598..4b6e7432 100644 --- a/fairgraph/embedded.py +++ b/fairgraph/embedded.py @@ -24,7 +24,8 @@ from warnings import warn from .utility import as_list, ActivityLog -from .base import Resolvable, ContainsMetadata, JSONdict +from .base import Resolvable, JSONdict +from .node import ContainsMetadata if TYPE_CHECKING: from .client import KGClient @@ -67,7 +68,7 @@ def __repr__(self): return template.format(self=self) def __eq__(self, other): - return isinstance(other, self.__class__) and self.to_jsonld() == other.to_jsonld() + return isinstance(other, self.__class__) and self.to_jsonld(embed_linked_nodes=False) == other.to_jsonld(embed_linked_nodes=False) @classmethod def from_kg_instance(cls, data: JSONdict, client: KGClient) -> Union[None, EmbeddedMetadata]: diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index 44a2c7de..89087102 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -33,12 +33,16 @@ have_tabulate = True except ImportError: have_tabulate = False + +from openminds.registry import lookup_type +from openminds import IRI + from .utility import expand_uri, as_list, expand_filter, ActivityLog -from .registry import lookup_type from .queries import Query from .errors import AuthorizationError, ResourceExistsError, CannotBuildExistenceQuery from .caching import object_cache, save_cache, generate_cache_key -from .base import RepresentsSingleObject, ContainsMetadata, SupportsQuerying, IRI, JSONdict +from .base import RepresentsSingleObject, SupportsQuerying, JSONdict +from .node import ContainsMetadata from .kgproxy import KGProxy from .kgquery import KGQuery @@ -528,7 +532,7 @@ def modified_data(self) -> JSONdict: Return a dict containing the properties that have been modified locally from the values originally obtained from the Knowledge Graph. """ - current_data = self.to_jsonld(include_empty_properties=True, follow_links=False) + current_data = self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) modified_data = {} for key, current_value in current_data.items(): if not key.startswith("@"): @@ -614,7 +618,7 @@ def save( activity_log.update(item=self, delta=None, space=space, entry_type="no-op") else: # update - local_data = self.to_jsonld() + local_data = self.to_jsonld(embed_linked_nodes=False) if replace: logger.info(f" - replacing - {self.__class__.__name__}(id={self.id})") if activity_log: @@ -667,7 +671,7 @@ def save( activity_log.update(item=self, delta=None, space=space, entry_type="no-op") else: # create new - local_data = self.to_jsonld() + local_data = self.to_jsonld(embed_linked_nodes=False) logger.info(" - creating instance with data {}".format(local_data)) try: instance_data = client.create_new_instance( @@ -693,7 +697,7 @@ def save( activity_log.update(item=self, delta=instance_data, space=self.space, entry_type="create") # not handled yet: save existing object to new space - requires changing uuid if self.id: - logger.debug("Updating cache for object {}. Current state: {}".format(self.id, self.to_jsonld())) + logger.debug("Updating cache for object {}. Current state: {}".format(self.id, self.to_jsonld(embed_linked_nodes=False))) object_cache[self.id] = self else: logger.warning("Object has no id - see log for the underlying error") diff --git a/fairgraph/kgproxy.py b/fairgraph/kgproxy.py index 09bcfeb9..8a0a4a73 100644 --- a/fairgraph/kgproxy.py +++ b/fairgraph/kgproxy.py @@ -22,7 +22,8 @@ import logging from typing import List, Optional, Tuple, Union, Dict, Any, TYPE_CHECKING -from .registry import lookup +from openminds.registry import lookup + from .errors import ResolutionFailure from .caching import object_cache from .base import RepresentsSingleObject diff --git a/fairgraph/kgquery.py b/fairgraph/kgquery.py index a48a97f9..86de93e7 100644 --- a/fairgraph/kgquery.py +++ b/fairgraph/kgquery.py @@ -22,10 +22,11 @@ import logging from typing import Dict, List, Optional, Union, Any, TYPE_CHECKING +from openminds.registry import lookup + from .utility import as_list, expand_filter -from .registry import lookup from .caching import object_cache -from .base import Resolvable, SupportsQuerying, ContainsMetadata +from .base import Resolvable, SupportsQuerying if TYPE_CHECKING: from .client import KGClient diff --git a/fairgraph/node.py b/fairgraph/node.py new file mode 100644 index 00000000..423cef09 --- /dev/null +++ b/fairgraph/node.py @@ -0,0 +1,438 @@ +from __future__ import annotations +from typing import TYPE_CHECKING, Optional, Dict, List, Union, Any +from copy import copy +import logging +from warnings import warn + +from openminds.base import value_to_jsonld +from openminds.properties import Property + +from .registry import Node +from .base import Resolvable, ErrorHandling, RepresentsSingleObject +from .kgquery import KGQuery +from .queries import ( + QueryProperty, + get_query_properties, + get_query_filter_property, + get_filter_value +) +from .errors import ResolutionFailure, CannotBuildExistenceQuery +from .utility import ( + as_list, # temporary for backwards compatibility (a lot of code imports it from here) + expand_uri, + invert_dict +) + +if TYPE_CHECKING: + from .client import KGClient + from .utility import ActivityLog + +logger = logging.getLogger("fairgraph") + +JSONdict = Dict[str, Any] # see https://github.com/python/typing/issues/182 for some possible improvements + + + +class ContainsMetadata(Resolvable, metaclass=Node): # KGObject and EmbeddedMetadata + properties: List[Property] = [] + reverse_properties: List[Property] = [] + context: Dict[str, str] + type_: str + scope: Optional[str] + space: Union[str, None] + default_space: Union[str, None] + remote_data: Optional[JSONdict] + aliases: Dict[str, str] = {} + + def __init__(self, data: Optional[Dict] = None, **properties): + properties_copy = copy(properties) + for prop in self.__class__.all_properties: + try: + val = properties[prop.name] + except KeyError: + if prop.required: + msg = "Property '{}' is required.".format(prop.name) + ErrorHandling.handle_violation(prop.error_handling, msg) + val = None + else: + properties_copy.pop(prop.name) + if isinstance(val, (list, tuple)) and len(val) == 0: # empty list + val = None + setattr(self, prop.name, val) + for name_, alias_ in self.aliases.items(): + # the trailing underscores are because 'name' and 'alias' can be keys in 'properties' + if name_ in properties_copy: + val = properties_copy.pop(name_) + if val is not None: + if properties.get(alias_, None): + raise ValueError(f"'{name_}' is an alias for '{alias_}', you cannot specify both") + setattr(self, alias_, val) + if len(properties_copy) > 0: + if len(properties_copy) == 1: + raise NameError(f'{self.__class__.__name__} does not have a property named "{list(properties_copy)[0]}".') + else: + raise NameError( + f"""{self.__class__.__name__} does not have properties named "{'", "'.join(properties_copy)}".""" + ) + + # we store the original remote data in `_raw_remote_data` + # and a normalized version in `remote_data` + self._raw_remote_data = data # for debugging + self.remote_data = {} + if data: + self.remote_data = self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) + + def __getattribute__(self, name): + try: + return object.__getattribute__(self, name) + except AttributeError: + if name in self.aliases: + return object.__getattribute__(self, self.aliases[name]) + else: + raise + + def __setattr__(self, name, value): + try: + prop = self._property_lookup[name] + except KeyError: + if name in self.aliases: + setattr(self, self.aliases[name], value) + else: + super().__setattr__(name, value) + else: + failures = prop.validate(value) + if failures: + raise Exception("TODO") # ErrorHandling.handle_violation(self.error_handling, errmsg) + super().__setattr__(name, value) + + # def to_jsonld( + # self, + # normalized: bool = True, + # follow_links: bool = False, + # include_empty_properties: bool = False, + # include_reverse_properties: bool = False, + # ): + # """ + # Return a JSON-LD representation of this metadata object + + # Args: + # normalized (bool): Whether to expand all URIs. Defaults to True. + # follow_links (bool, optional): Whether to represent linked objects just by their "@id" + # or to include their full metadata. Defaults to False. + # include_empty_properties (bool, optional): Whether to include empty properties (with value "null"). + # Defaults to False. + + # """ + # if self.properties: + # data: JSONdict = {"@type": [self.type_]} + # if hasattr(self, "id") and self.id: + # data["@id"] = self.id + # for prop in self.__class__.all_properties: + # if prop.intrinsic or include_reverse_properties: + # expanded_path = prop.expanded_path + # value = getattr(self, prop.name) + # if include_empty_properties or prop.required or value is not None: + # serialized = prop.serialize(value, follow_links=follow_links) + # if expanded_path in data: + # if isinstance(data[expanded_path], list): + # data[expanded_path].append(serialized) + # else: + # data[expanded_path] = [data[expanded_path], serialized] + # else: + # data[expanded_path] = serialized + # if normalized: + # return normalize_data(data, self.context) + # else: + # return data + # else: + # raise NotImplementedError("to be implemented by child classes") + + @classmethod + def from_jsonld(cls, data: JSONdict, client: KGClient, scope: Optional[str] = None): + """ + Create an instance of the class from a JSON-LD document. + """ + if scope: + return cls.from_kg_instance(data, client, scope) + else: + return cls.from_kg_instance(data, client) + + @classmethod + def from_kg_instance(cls, data: JSONdict, client: KGClient, scope: Optional[str] = None) -> ContainsMetadata: + pass + + def save( + self, + client: KGClient, + space: Optional[str] = None, + recursive: bool = True, + activity_log: Optional[ActivityLog] = None, + replace: bool = False, + ignore_auth_errors: bool = False, + ): + pass + + @classmethod + def set_error_handling( + cls, value: Union[ErrorHandling, None], property_names: Optional[Union[str, List[str]]] = None + ): + """ + Control validation for this class. + + Args: + value (str): action to follow when there is a validation failure. + (e.g. if a required property is not provided). + Possible values: "error", "warning", "log", None + property_names (str or list of str, optional): If not provided, the error handling + mode will be applied to all properties. If a property name or list of names is given, + the mode will be applied only to those properties. + """ + if value is None: + value = ErrorHandling.none + else: + value = ErrorHandling(value) + if property_names: + for property_name in as_list(property_names): + try: + prop = cls._property_lookup[property_name] + except KeyError: + raise ValueError("No such property: {}".format(property_name)) + else: + prop.error_handling = value + else: + for prop in cls.all_properties: + prop.error_handling = value + + @classmethod + def normalize_filter(cls, filter_dict: Dict[str, Any]) -> Dict[str, Any]: + """ + Normalize a dict containing filter key:value pairs so that it can be used + in a call to the KG query API. + + Example: + >>> import fairgraph.openminds.core as omcore + >>> person = omcore.Person.from_uuid("045f846f-f010-4db8-97b9-b95b20970bf2", kg_client) + >>> filter_dict = {"custodians": person, "name": "Virtual"} + >>> omcore.Dataset.normalize_filter(filter_dict) + {'name': 'Virtual', + 'custodians': 'https://kg.ebrains.eu/api/instances/045f846f-f010-4db8-97b9-b95b20970bf2'} + """ + normalized = {} + filter_dict_copy = filter_dict.copy() + + # handle aliases + for name_, alias_ in cls.aliases.items(): + if name_ in filter_dict_copy: + filter_dict_copy[alias_] = filter_dict_copy.pop(name_) + + for prop in cls.all_properties: + if prop.name in filter_dict_copy: + value = filter_dict_copy[prop.name] + if isinstance(value, dict): + normalized[prop.name] = {} + for child_cls in prop.types: + normalized[prop.name].update(child_cls.normalize_filter(value)) + else: + normalized[prop.name] = get_filter_value(prop, value) + return normalized + + @classmethod + def generate_query_properties(cls, follow_links: Optional[Dict[str, Any]] = None): + """ + Generate a list of QueryProperty instances for this class + for use in constructing a KG query definition. + + Args: + follow_links (dict): The links in the graph to follow when constructing the query. Defaults to None. + """ + properties = [QueryProperty("@type")] + reverse_aliases = invert_dict(cls.aliases) + for prop in cls.all_properties: + if prop.is_link and follow_links: + if prop.name in follow_links: + properties.extend(get_query_properties(prop, follow_links[prop.name])) + elif reverse_aliases.get(prop.name, None) in follow_links: + properties.extend(get_query_properties(prop, follow_links[reverse_aliases[prop.name]])) + else: + properties.extend(get_query_properties(prop)) + else: + properties.extend(get_query_properties(prop)) + return properties + + @classmethod + def generate_query_filter_properties( + cls, + filters: Optional[Dict[str, Any]] = None, + ): + """ + + Args: + filters (dict, optional): A dict containing search parameters for the query. + """ + if filters is None: + filters = {} + properties = [] + for prop in cls.all_properties: + if prop.name in filters: + properties.append(get_query_filter_property(prop, filters[prop.name])) + return properties + + @classmethod + def _deserialize_data(cls, data: JSONdict, client: KGClient, include_id: bool = False): + # normalize data by expanding keys + D = {"@type": data["@type"]} + if include_id: + D["@id"] = data["@id"] + for key, value in data.items(): + if "__" in key: + key, type_filter = key.split("__") + normalised_key = expand_uri(key, cls.context) + value = [item for item in as_list(value) if item["@type"][0].endswith(type_filter)] + if normalised_key in D: + D[normalised_key].extend(value) + else: + D[normalised_key] = value + elif key.startswith("Q"): # for 'Q' properties in data from queries + D[key] = value + elif key[0] != "@": + normalised_key = expand_uri(key, cls.context) + D[normalised_key] = value + if cls.type_ not in D["@type"]: + raise TypeError("type mismatch {} - {}".format(cls.type_, D["@type"])) + + def _get_type_from_data(data_item): + type_ = data_item.get("@type", None) + if type_: + return type_[0] + else: + return None + + deserialized_data = {} + for prop in cls.all_properties: + expanded_path = expand_uri(prop.path, cls.context) + data_item = D.get(expanded_path) + if data_item is not None and prop.reverse: + # for reverse properties, more than one property can have the same path + # so we extract only those sub-items whose types match + try: + data_item = [ + part for part in as_list(data_item) + if _get_type_from_data(part) in [t.type_ for t in prop.types] + ] + except AttributeError: + # problem when a forward and reverse path both given the same expanded path + # e.g. for Configuration + data_item = None + # sometimes queries put single items in a list, this removes the enclosing list + if (not prop.multiple) and isinstance(data_item, (list, tuple)) and len(data_item) == 1: + data_item = data_item[0] + if data_item is None: + if prop.reverse and "@id" in data: + if isinstance(prop.reverse, list): + # todo: handle all possible reverses + # for now, we just take the first + deserialized_data[prop.name] = KGQuery(prop.types, {prop.reverse[0]: data["@id"]}) + else: + deserialized_data[prop.name] = KGQuery(prop.types, {prop.reverse: data["@id"]}) + else: + deserialized_data[prop.name] = None + else: + deserialized_data[prop.name] = prop.deserialize(data_item) + return deserialized_data + + def resolve( + self, + client: KGClient, + scope: Optional[str] = None, + use_cache: bool = True, + follow_links: Optional[Dict[str, Any]] = None, + ): + """ + Resolve properties that are represented by KGProxy objects. + + Args: + client: KGClient object that handles the communication with the KG. + scope (str): The scope of instances to include in the response. + Valid values are 'released', 'in progress', 'any'. + use_cache (bool): whether to use cached data if they exist. Defaults to True. + follow_links (dict): The links in the graph to follow. Defaults to None. + + Note: a real (non-proxy) object resolves to itself. + """ + use_scope = scope or self.scope or "released" + if follow_links: + reverse_aliases = invert_dict(self.__class__.aliases) + for prop in self.__class__.all_properties: + if prop.is_link: + follow_name = None + if prop.name in follow_links: + follow_name = prop.name + elif reverse_aliases.get(prop.name, None) in follow_links: + follow_name = reverse_aliases[prop.name] + + if follow_name: + if issubclass(prop.types[0], ContainsMetadata): + values = getattr(self, prop.name) + resolved_values: List[Any] = [] + for value in as_list(values): + if isinstance(value, Resolvable): + if isinstance(value, ContainsMetadata) and isinstance(value, RepresentsSingleObject): + # i.e. isinstance(value, KGObject) - already resolved + resolved_values.append(value) + else: + try: + resolved_value = value.resolve( + client, + scope=use_scope, + use_cache=use_cache, + follow_links=follow_links[follow_name], + ) + except ResolutionFailure as err: + warn(str(err)) + resolved_values.append(value) + else: + resolved_values.append(resolved_value) + if isinstance(values, RepresentsSingleObject): + assert len(resolved_values) == 1 + setattr(self, prop.name, resolved_values[0]) + elif values is None: + assert len(resolved_values) == 0 + setattr(self, prop.name, None) + else: + setattr(self, prop.name, resolved_values) + return self + + def _build_existence_query(self) -> Union[None, Dict[str, Any]]: + """ + Generate a KG query definition (as a JSON-LD document) that can be used to + check whether a locally-defined object (with no ID) already exists in the KG. + """ + if self.existence_query_properties is None: + return None + + query_properties = [] + for property_name in self.existence_query_properties: + for property in self.__class__.all_properties: + if property.name == property_name: + query_properties.append(property) + break + if len(query_properties) < 1: + raise CannotBuildExistenceQuery("Empty existence query for class {}".format(self.__class__.__name__)) + query = {} + for property in query_properties: + query_property_name = property.name + value = getattr(self, property.name) + if isinstance(value, ContainsMetadata): + if hasattr(value, "id") and value.id: + query[query_property_name] = value.id + else: + sub_query = value._build_existence_query() + query.update({f"{query_property_name}__{key}": val for key, val in sub_query.items()}) + elif isinstance(value, (list, tuple)): + raise CannotBuildExistenceQuery("not implemented yet") + else: + query_val = value_to_jsonld(value, include_empty_properties=False, embed_linked_nodes=False) + if query_val is None: + raise CannotBuildExistenceQuery("Required value is missing") + query[query_property_name] = query_val + return query diff --git a/fairgraph/properties.py b/fairgraph/properties.py deleted file mode 100644 index 5298dd58..00000000 --- a/fairgraph/properties.py +++ /dev/null @@ -1,542 +0,0 @@ -""" -Representations of metadata properties. -""" - -# Copyright 2018-2024 CNRS - -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at - -# http://www.apache.org/licenses/LICENSE-2.0 - -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from __future__ import annotations -import logging -from datetime import date, datetime -from collections.abc import Iterable, Mapping -from typing import Any, Dict, List, Optional, Tuple, TYPE_CHECKING, Union -from uuid import UUID -from warnings import warn - -if TYPE_CHECKING: - from .client import KGClient - -from dateutil import parser as date_parser - -from .registry import lookup, lookup_type -from .utility import as_list -from .base import IRI, JSONdict, ContainsMetadata, ErrorHandling -from .kgproxy import KGProxy -from .kgquery import KGQuery -from .kgobject import KGObject -from .embedded import EmbeddedMetadata -from .utility import expand_uri -from .queries import Filter, QueryProperty - - -logger = logging.getLogger("fairgraph") - - -global_context = { - "vocab": "https://openminds.ebrains.eu/vocab/", -} - - -def is_resolved(item: JSONdict) -> bool: - return set(item.keys()) not in (set(["@id", "@type"]), set(["@id"])) - - -def build_kg_object( - possible_classes: Iterable[Union[EmbeddedMetadata, KGObject]], - data: Optional[Union[JSONdict, List[JSONdict]]], - client: Optional[KGClient] = None, -) -> Union[EmbeddedMetadata, KGObject, KGProxy, None, List[Union[EmbeddedMetadata, KGObject, KGProxy]]]: - """ - Build a KGObject, an EmbeddedMetadata, a KGProxy, or a list of such, based on the data provided. - - This takes care of the JSON-LD quirk that you get a list if there are multiple - objects, but you get the object directly if there is only one. - - Returns `None` if data is None. - """ - if data is None: - return None - if not isinstance(data, list): - if not isinstance(data, dict): - raise ValueError("data must be a list or dict") - if "@list" in data: - assert len(data) == 1 - data = data["@list"] - else: - data = [data] - assert isinstance(data, list) - - objects = [] - for item in data: - if item is None: - logger.error(f"Unexpected null. possible_classes={possible_classes} data={data}") - continue - logger.debug(f"Building {possible_classes} from {item.get('@id', 'not a node')}") - if possible_classes is None: - raise NotImplementedError - - assert isinstance(possible_classes, (list, tuple)) - assert all(issubclass(item, KGObject) for item in possible_classes) or all( - issubclass(item, EmbeddedMetadata) for item in possible_classes - ) - if len(possible_classes) > 1: - if "@type" in item: - for cls in possible_classes: - if item["@type"] == [cls.type_]: - kg_cls = cls - break - else: - kg_cls = possible_classes - - else: - kg_cls = possible_classes[0] - - if "@id" in item: - # the following line is only relevant to test data, - # for real data it is always an expanded uri - item["@id"] = expand_uri(item["@id"], {"kg": "https://kg.ebrains.eu/api/instances/"}) - if is_resolved(item): - try: - obj = kg_cls.from_kg_instance(item, client) - except (ValueError, KeyError) as err: - # to add: emit a warning - logger.warning("Error in building {}: {}".format(kg_cls.__name__, err)) - obj = KGProxy(kg_cls, item["@id"]).resolve(client) - # todo: provide space and scope - else: - if "@type" in item and item["@type"] is not None and kg_cls not in as_list(lookup_type(item["@type"][0])): - raise Exception(f"mismatched types: {kg_cls} <> {item['@type']} (id: {item['@id']})") - obj = None - else: - obj = KGProxy(kg_cls, item["@id"]) - elif "@type" in item: # Embedded metadata - obj = kg_cls.from_kg_instance(item, client) - else: - # todo: add a logger.warning that we have dud data - obj = None - - if obj is not None: - objects.append(obj) - if len(objects) == 1: - return objects[0] - else: - return objects - - -class Property(object): - """ - Representation of a metadata property. - - Args: - name (str): The name of the property. - types (str, date, datetime, int, KGObject, EmbeddedMetadata): The types of values that the property can take. - path (URI): The globally unique identifier of this property. - required (bool, optional): Whether the property is required or not. Defaults to False. - default (Any, optional): The default value of the property if it is not provided. - multiple (bool, optional): Whether the property can have multiple values or not. Defaults to False. - error_handling (str, optional): How to handle errors, such as the wrong type of value being provided. - One of "error", "warning", "log", "none". Defaults to "warning". - reverse (str, optional): The name of the reverse property, if any. - doc (str, optional): The documentation of the property. - - The class also contains machinery for serialization into JSON-LD of values stored in properties in - KGObjects and EmbeddedMetadata instances, and for de-serialization from JSON-LD into Python objects. - """ - - def __init__( - self, - name: str, - types: Union[ - str, - type, - KGObject, - EmbeddedMetadata, - Iterable[Union[str, type, KGObject, EmbeddedMetadata]], - ], - path: str, - required: bool = False, - default: Any = None, - multiple: bool = False, - error_handling: ErrorHandling = ErrorHandling.log, - reverse: Optional[str] = None, - doc: str = "", - ): - self.name = name - self._types: Tuple[Union[str, type, KGObject, EmbeddedMetadata], ...] - if isinstance(types, (type, str)): - self._types = (types,) - else: - assert isinstance(types, Iterable) - self._types = tuple(types) - self._resolved_types = False - # later, may need to use lookup() to turn strings into classes - self.path = path - self.required = required - self.default = default - self.multiple = multiple - self.error_handling = error_handling - self.reverse = reverse - self.doc = doc - - def __repr__(self): - return "Property(name='{}', types={}, path='{}', required={}, multiple={})".format( - self.name, self._types, self.path, self.required, self.multiple - ) - - @property - def types(self): - if not self._resolved_types: - self._types = tuple([lookup(obj) if isinstance(obj, str) else obj for obj in self._types]) - self._resolved_types = True - return self._types - - def check_value(self, value): - def check_single(item): - if not isinstance(item, self.types): - if not ( - isinstance(item, (KGProxy, KGQuery, EmbeddedMetadata)) - and any(issubclass(cls, _type) for _type in self.types for cls in item.classes) - ): - if item is None and self.required: - errmsg = "Property '{}' is required but was not provided.".format(self.name) - else: - errmsg = "Property '{}' should be of type {}, not {}".format(self.name, self.types, type(item)) - ErrorHandling.handle_violation(self.error_handling, errmsg) - - if self.required or value is not None: - if self.multiple and isinstance(value, Iterable) and not isinstance(value, Mapping): - for item in value: - check_single(item) - else: - check_single(value) - - @property - def intrinsic(self): - """ - Return True If the prop contains data that is directly stored in the instance, - False if the prop contains data that is obtained through a query - """ - return not self.reverse - - @property - def is_link(self) -> bool: - return issubclass(self.types[0], (KGObject, EmbeddedMetadata)) - - @property - def expanded_path(self) -> str: - return expand_uri(self.path, global_context) - - def serialize(self, value: Any, follow_links: bool = False): - """ - Serialize a value to JSON-LD. - - Args: - value (any): The value to be serialized. - follow_links (bool): If the value contains graph links, these links - will be represented using "@id" (follow_links=False) or fully - serialized recursively (follow_links=True). - """ - - def serialize_single(value): - if isinstance(value, (str, int, float, dict)): - return value - elif isinstance(value, EmbeddedMetadata): - return value.to_jsonld(follow_links=follow_links) - elif isinstance(value, IRI): - return value.to_jsonld() - elif isinstance(value, KGObject): - if follow_links or value.id is None: - return value.to_jsonld(follow_links=follow_links) - else: - return {"@id": value.id} - elif isinstance(value, KGProxy): - return {"@id": value.id} - elif isinstance(value, (datetime, date)): - return value.isoformat() - elif value is None: - return None - else: - raise ValueError("don't know how to serialize this value") - - if isinstance(value, (list, tuple)): - if self.multiple or self.error_handling != ErrorHandling.error: - value = [serialize_single(item) for item in value] - if len(value) == 1: - return value[0] - else: - return value - elif len(value) == 1: - return serialize_single(value[0]) - elif self.error_handling != ErrorHandling.none: - errmsg = f"Single item expected for prop {self.name} but received multiple" - ErrorHandling.handle_violation(self.error_handling, errmsg) - else: - return value - else: - return serialize_single(value) - - def deserialize(self, data: Union[JSONdict, List[JSONdict]], client: KGClient, belongs_to: Optional[str] = None): - """ - Deserialize a JSON-LD data structure into Python objects. - - Args: - data: the JSON-LD data - client: a KG client - belongs_to: the ID of the object this property belongs to - """ - if data == []: - return None - elif data is None: - if self.reverse: - if isinstance(self.reverse, list): - # todo: handle all possible reverses - # for now, we just take the first - return KGQuery(self.types, {self.reverse[0]: belongs_to}) - else: - return KGQuery(self.types, {self.reverse: belongs_to}) - else: - return None - try: - if issubclass(self.types[0], (KGObject, EmbeddedMetadata)): - return build_kg_object(self.types, data, client=client) - elif self.types[0] in (datetime, date): - if isinstance(data, str): - if data == "": # seems like the KG Editor puts empty strings here rather than None? - return None - return date_parser.parse(data) - elif isinstance(data, Iterable): - return [date_parser.parse(item) for item in data] - else: - raise ValueError("expecting a string or list") - elif self.types[0] == int: - if isinstance(data, str): - return int(data) - elif isinstance(data, Iterable): - return [int(item) for item in data] - else: - return int(data) - elif self.types[0] == IRI: - return IRI(data) - else: - return data - except Exception as err: - ErrorHandling.handle_violation(self.error_handling, str(err)) - return None - - def _get_query_property_name(self, possible_classes): - if isinstance(self.path, str): - property_name = self.path - else: - assert isinstance(self.path, list) - found_match = False - for cls in possible_classes: - for path in self.path: - assert path.startswith("^") - for prop in cls.all_properties: - if path[1:] == prop.path: - property_name = path - found_match = True - break - if found_match: - break - if found_match: - break - assert found_match - if property_name.startswith("^"): - assert self.reverse - property_name = property_name[1:] - return property_name - - def get_query_properties(self, follow_links: Optional[Dict[str, Any]] = None) -> List[QueryProperty]: - """ - Generate one or more QueryProperty instances for this property, - for use in constructing a KG query definition. - """ - - properties = [] - if any(issubclass(_type, EmbeddedMetadata) for _type in self.types): - if not all(issubclass(_type, EmbeddedMetadata) for _type in self.types): - warn(f"Mixed types in {self}") - return properties - for cls in self.types: - if len(self.types) > 1: - property_name = f"{self.path}__{cls.__name__}" - type_filter = cls.type_ - else: - property_name = self.path - type_filter = None - if property_name.startswith("^"): - # used to mark reverse properties. Maybe not necessary? - assert self.reverse - property_name = property_name[1:] - properties.append( - QueryProperty( - self.expanded_path, - name=property_name, - reverse=self.reverse, - type_filter=type_filter, - ensure_order=self.multiple, - properties=cls.generate_query_properties(follow_links), - ) - ) - elif any(issubclass(_type, KGObject) for _type in self.types): - assert all(issubclass(_type, KGObject) for _type in self.types) - if follow_links is not None: - for cls in self.types: - property_name = self._get_query_property_name(possible_classes=[cls]) - if len(self.types) > 1: - property_name = f"{property_name}__{cls.__name__}" - type_filter = cls.type_ - else: - type_filter = None - properties.append( - QueryProperty( - self.expanded_path, - name=property_name, - reverse=self.reverse, - type_filter=type_filter, - ensure_order=self.multiple, - properties=[QueryProperty("@id"), *cls.generate_query_properties(follow_links)], - ) - ) - else: - if isinstance(self.path, str): - property_name = self.path - if property_name.startswith("^"): - assert self.reverse - property_name = property_name[1:] - properties.append( - QueryProperty( - self.expanded_path, - name=property_name, - reverse=self.reverse, - type_filter=None, - ensure_order=self.multiple, - properties=[ - QueryProperty("@id"), - QueryProperty("@type"), - ], - ) - ) - else: - assert isinstance(self.path, list) - logger.warning(f"Cannot yet handle case where self.path is a list: {self}") - else: - assert not self.reverse - properties.append( - QueryProperty( - self.expanded_path, - name=self.path, - reverse=self.reverse, - ensure_order=self.multiple, - ) - ) - return properties - - def get_query_filter_property(self, filter: Any) -> QueryProperty: - """ - Generate a QueryProperty instance containing a filter, - for use in constructing a KG query definition. - """ - assert filter is not None - if isinstance(filter, dict): - # we pass the filter through to the next level - filter_obj = None - else: - # we have a filter value for this property - if self.types[0] in (int, float, bool, datetime, date): - op = "EQUALS" - else: - op = "CONTAINS" - filter_obj = Filter(op, value=filter) - - if any(issubclass(_type, ContainsMetadata) for _type in self.types): - assert all(issubclass(_type, ContainsMetadata) for _type in self.types) - prop = QueryProperty(self.expanded_path, name=f"Q{self.name}", required=True, reverse=self.reverse) - if filter_obj: - prop.properties.append(QueryProperty("@id", filter=filter_obj)) - else: - for cls in self.types: - child_properties = cls.generate_query_filter_properties(filter) - if child_properties: - # if the class has properties with the appropriate name - # we add them, then break to avoid adding the same - # prop twice - prop.properties.extend(child_properties) - break - else: - prop = QueryProperty(self.expanded_path, name=f"Q{self.name}", filter=filter_obj, required=True) - return prop - - def get_filter_value(self, value: Any) -> Union[str, List[str]]: - """ - Normalize a value for use in a KG query - - Example: - >>> import fairgraph.openminds.core as omcore - >>> person = omcore.Person.from_uuid("045f846f-f010-4db8-97b9-b95b20970bf2", kg_client) - >>> prop = Property(name='custodians', types=(omcore.Organization, omcore.Person), - ... path="vocab:custodian", multiple=True) - >>> prop.get_filter_value(person) - https://kg.ebrains.eu/api/instances/045f846f-f010-4db8-97b9-b95b20970bf2 - """ - - def is_valid(val): - if isinstance(val, str): - try: - val = UUID(val) - except ValueError: - pass - return isinstance(val, (IRI, UUID, *self.types)) or (isinstance(val, KGProxy) and val.cls in self.types) - - if isinstance(value, list) and len(value) > 0: - valid_type = all(is_valid(item) for item in value) - have_multiple = True - else: - valid_type = is_valid(value) - have_multiple = False - if not valid_type: - if self.name == "hash": # bit of a hack - filter_value = value - elif isinstance(value, str) and value.startswith("http"): # for @id - filter_value = value - else: - raise TypeError("{} must be of type {}, not {}".format(self.name, self.types, type(value))) - - filter_items = [] - for item in as_list(value): - if isinstance(item, IRI): - filter_item = item.value - elif isinstance(item, (date, datetime)): - filter_item = item.isoformat() - elif hasattr(item, "id"): - filter_item = item.id - elif isinstance(item, UUID): - # todo: consider using client.uri_from_uuid() - # would require passing client as arg - filter_item = f"https://kg.ebrains.eu/api/instances/{item}" - elif isinstance(item, str) and "+" in item: # workaround for KG bug - invalid_char_index = item.index("+") - if invalid_char_index < 3: - raise ValueError(f"Cannot use {item} as filter, contains invalid characters") - filter_item = item[:invalid_char_index] - warn(f"Truncating filter value {item} --> {filter_item}") - else: - filter_item = item - filter_items.append(filter_item) - - if have_multiple: - return filter_items - else: - return filter_items[0] diff --git a/fairgraph/queries.py b/fairgraph/queries.py index c6748fa7..af477149 100644 --- a/fairgraph/queries.py +++ b/fairgraph/queries.py @@ -17,7 +17,18 @@ # limitations under the License. from __future__ import annotations -from typing import Optional, List, Any, Dict +from typing import Optional, List, Any, Dict, Union +from uuid import UUID +from datetime import date, datetime +import logging +from warnings import warn + +from openminds.base import IRI, EmbeddedMetadata, LinkedMetadata, Node + +from .utility import as_list, expand_uri + + +logger = logging.getLogger("fairgraph") class Filter: @@ -246,3 +257,208 @@ def serialize(self) -> Dict[str, Any]: # todo: I think only one property can have "sort": True - need to check this + + + +def _get_query_property_name(property, possible_classes): + if isinstance(property.path, str): + property_name = property.path + else: + assert isinstance(property.path, list) + found_match = False + for cls in possible_classes: + for path in property.path: + for prop in cls.properties: + if path == prop.path: + property_name = path + found_match = True + break + if found_match: + break + if found_match: + break + assert found_match + return property_name + + +def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None) -> List[QueryProperty]: + """ + Generate one or more QueryProperty instances for this property, + for use in constructing a KG query definition. + """ + expanded_path = expand_uri(property.path, {"@vocab": "https://openminds.ebrains.eu/vocab/"}) + properties = [] + if any(issubclass(_type, EmbeddedMetadata) for _type in property.types): + if not all(issubclass(_type, EmbeddedMetadata) for _type in property.types): + warn(f"Mixed types in {property}") + return properties + for cls in property.types: + if len(property.types) > 1: + property_name = f"{property.path}__{cls.__name__}" + type_filter = cls.type_[0] + else: + property_name = property.path + type_filter = None + properties.append( + QueryProperty( + expanded_path, + name=property_name, + reverse=property.reverse, + type_filter=type_filter, + ensure_order=property.multiple, + properties=cls.generate_query_properties(follow_links), + ) + ) + elif any(issubclass(_type, LinkedMetadata) for _type in property.types): + assert all(issubclass(_type, LinkedMetadata) for _type in property.types) + if follow_links is not None: + for cls in property.types: + property_name = _get_query_property_name(property, possible_classes=[cls]) + if len(property.types) > 1: + property_name = f"{property_name}__{cls.__name__}" + type_filter = cls.type_[0] + else: + type_filter = None + + properties.append( + QueryProperty( + expanded_path, + name=property_name, + reverse=property.reverse, + type_filter=type_filter, + ensure_order=property.multiple, + properties=[QueryProperty("@id"), *cls.generate_query_properties(follow_links)], + ) + ) + else: + if isinstance(property.path, str): + property_name = property.path + properties.append( + QueryProperty( + expanded_path, + name=property_name, + reverse=property.reverse, + type_filter=None, + ensure_order=property.multiple, + properties=[ + QueryProperty("@id"), + QueryProperty("@type"), + ], + ) + ) + else: + assert isinstance(property.path, list) + logger.warning(f"Cannot yet handle case where property.path is a list: {property}") + else: + assert not property.reverse + properties.append( + QueryProperty( + expanded_path, + name=property.path, + reverse=property.reverse, + ensure_order=property.multiple, + ) + ) + return properties + + +def get_query_filter_property(property, filter: Any) -> QueryProperty: + """ + Generate a QueryProperty instance containing a filter, + for use in constructing a KG query definition. + """ + assert filter is not None + if isinstance(filter, dict): + # we pass the filter through to the next level + filter_obj = None + else: + # we have a filter value for this property + if property.types[0] in (int, float, bool, datetime, date): + op = "EQUALS" + else: + op = "CONTAINS" + filter_obj = Filter(op, value=filter) + + expanded_path = expand_uri(property.path, {"@vocab": "https://openminds.ebrains.eu/vocab/"}) + + if any(issubclass(_type, Node) for _type in property.types): + assert all(issubclass(_type, Node) for _type in property.types) + prop = QueryProperty(expanded_path, name=f"Q{property.name}", required=True, reverse=property.reverse) + if filter_obj: + prop.properties.append(QueryProperty("@id", filter=filter_obj)) + else: + for cls in property.types: + child_properties = cls.generate_query_filter_properties(filter) + if child_properties: + # if the class has properties with the appropriate name + # we add them, then break to avoid adding the same + # prop twice + prop.properties.extend(child_properties) + break + else: + prop = QueryProperty(expanded_path, name=f"Q{property.name}", filter=filter_obj, required=True) + return prop + + +def get_filter_value(property, value: Any) -> Union[str, List[str]]: + """ + Normalize a value for use in a KG query + + Example: + >>> import fairgraph.openminds.core as omcore + >>> person = omcore.Person.from_uuid("045f846f-f010-4db8-97b9-b95b20970bf2", kg_client) + >>> prop = Property(name='custodians', types=(omcore.Organization, omcore.Person), + ... path="vocab:custodian", multiple=True) + >>> get_filter_value(prop, person) + https://kg.ebrains.eu/api/instances/045f846f-f010-4db8-97b9-b95b20970bf2 + """ + from .kgproxy import KGProxy + + def is_valid(val): + if isinstance(val, str): + try: + val = UUID(val) + except ValueError: + pass + return isinstance(val, (IRI, UUID, *property.types)) or (isinstance(val, KGProxy) and val.cls in property.types) + + if isinstance(value, list) and len(value) > 0: + valid_type = all(is_valid(item) for item in value) + have_multiple = True + else: + valid_type = is_valid(value) + have_multiple = False + if not valid_type: + if property.name == "hash": # bit of a hack + filter_value = value + elif isinstance(value, str) and value.startswith("http"): # for @id + filter_value = value + else: + raise TypeError("{} must be of type {}, not {}".format(property.name, property.types, type(value))) + + filter_items = [] + for item in as_list(value): + if isinstance(item, IRI): + filter_item = item.value + elif isinstance(item, (date, datetime)): + filter_item = item.isoformat() + elif hasattr(item, "id"): + filter_item = item.id + elif isinstance(item, UUID): + # todo: consider using client.uri_from_uuid() + # would require passing client as arg + filter_item = f"https://kg.ebrains.eu/api/instances/{item}" + elif isinstance(item, str) and "+" in item: # workaround for KG bug + invalid_char_index = item.index("+") + if invalid_char_index < 3: + raise ValueError(f"Cannot use {item} as filter, contains invalid characters") + filter_item = item[:invalid_char_index] + warn(f"Truncating filter value {item} --> {filter_item}") + else: + filter_item = item + filter_items.append(filter_item) + + if have_multiple: + return filter_items + else: + return filter_items[0] diff --git a/fairgraph/registry.py b/fairgraph/registry.py index 200e0da6..ad504fe2 100644 --- a/fairgraph/registry.py +++ b/fairgraph/registry.py @@ -6,104 +6,37 @@ from __future__ import annotations from itertools import chain -from typing import TYPE_CHECKING, Union, List +import logging +from typing import TYPE_CHECKING, Union, List, Dict from warnings import warn -if TYPE_CHECKING: - from .base import ContainsMetadata - -registry: dict = {"names": {}, "types": {}} - - -def register_class(target_class: ContainsMetadata): - """Add a class to the registry""" - if "openminds" in target_class.__module__: - parts = target_class.__module__.split(".") - name = ".".join(parts[1:3] + [target_class.__name__]) # e.g. openminds.core.Dataset - else: - name = target_class.__module__.split(".")[-1] + "." + target_class.__name__ - - registry["names"][name] = target_class - if hasattr(target_class, "type_"): - assert isinstance(target_class.type_, str) - type_ = target_class.type_ - if type_ in registry["types"]: - if isinstance(registry["types"][type_], list): - registry["types"][type_].append(target_class) - else: - registry["types"][type_] = [registry["types"][type_], target_class] - else: - registry["types"][type_] = target_class - - -def lookup(class_name: str) -> ContainsMetadata: - """Return the class whose name is given.""" - return registry["names"][class_name] - - -def lookup_type(class_type: Union[str, List[str]]) -> ContainsMetadata: - """Return the class whose global type identifier (a URI) is given.""" - if isinstance(class_type, str): - if class_type in registry["types"]: - return registry["types"][class_type] - else: - return registry["types"][(class_type,)] - else: - return registry["types"][tuple(sorted(class_type))] - - -docstring_template = """ -{base} - -Args ----- -{args} +from openminds.properties import Property +from openminds.registry import Registry -""" +if TYPE_CHECKING: + from .node import ContainsMetadata -class Registry(type): +class Node(Registry): """Metaclass for registering Knowledge Graph classes.""" - properties = [] - reverse_properties = [] - aliases = {} + properties: List[Property] = [] + type_: Union[str, List[str]] + context: Dict[str, str] + _base_docstring: str def __new__(meta, name, bases, class_dict): - cls = type.__new__(meta, name, bases, class_dict) - cls._base_docstring = class_dict.get("__doc__", "").strip() - cls._property_lookup = { - prop.name: prop for prop in (cls.properties + cls.reverse_properties) - } - register_class(cls) + # set class_name so that the fairgraph class replaces the equivalent openminds class + # in the registry + # e.g. 'fairgraph.openminds.sands.miscellaneous.anatomical_target_position' + # --> 'openminds.latest.sands.AnatomicalTargetPosition' + class_dict["class_name"] = ".".join( + class_dict["__module__"].replace("fairgraph.openminds", "openminds.latest").split(".")[:3] + [name] + ) + cls = Registry.__new__(meta, name, bases, class_dict) + cls._property_lookup = {prop.name: prop for prop in (cls.properties + cls.reverse_properties)} return cls - def _get_doc(cls) -> str: - """Dynamically generate docstrings""" - property_docs = [] - if hasattr(cls, "properties"): - - def gen_path(type_): - if type_.__module__ == "builtins": - return type_.__name__ - else: - return "~{}.{}".format(type_.__module__, type_.__name__) - - for prop in cls.all_properties: - doc = "{} : {}\n {}".format(prop.name, ", ".join(gen_path(t) for t in prop.types), prop.doc) - property_docs.append(doc) - return docstring_template.format(base=cls._base_docstring, args="\n".join(property_docs)) - - __doc__ = property(_get_doc) - - @property - def property_names(cls) -> List[str]: - return list(cls._property_lookup.keys()) - - @property - def required_property_names(cls) -> List[str]: - return [f.name for f in cls.properties if f.required] - @property def all_properties(cls): return chain(cls.properties, cls.reverse_properties) diff --git a/fairgraph/utility.py b/fairgraph/utility.py index 41ed36cf..0310ffa7 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -94,11 +94,14 @@ def expand_uri(uri_list: Union[str, List[str]], context: Dict[str, Any]) -> Unio if uri.startswith("http") or uri.startswith("@"): expanded_uris.append(uri) else: - prefix, identifier = uri.split(":") - if prefix.startswith("^"): # used to indicate a reverse connection - prefix = prefix[1:] + parts = uri.split(":") + if len(parts) == 1: + prefix = "@vocab" + identifier = uri + else: + prefix, identifier = parts if prefix not in context: - raise ValueError("prefix {prefix} not found in context") + raise ValueError(f"prefix {prefix} not found in context") base_url = context[prefix] if not base_url.endswith("/"): base_url.append("/") diff --git a/test/test_base.py b/test/test_base.py index 3f882048..2cc89d18 100644 --- a/test/test_base.py +++ b/test/test_base.py @@ -4,16 +4,18 @@ """ from datetime import date, datetime +from openminds.base import Node +from openminds.properties import Property from fairgraph.embedded import EmbeddedMetadata from fairgraph.kgobject import KGObject from fairgraph.kgproxy import KGProxy -from fairgraph.properties import Property from fairgraph.caching import generate_cache_key import pytest -class MockEmbeddedObject(EmbeddedMetadata): +class MockEmbeddedObject(EmbeddedMetadata, Node): type_ = "https://openminds.ebrains.eu/mock/MockEmbeddedObject" + schema_version = "latest" context = { "schema": "http://schema.org/", "kg": "https://kg.ebrains.eu/api/instances/", @@ -47,9 +49,10 @@ class MockEmbeddedObject(EmbeddedMetadata): existence_query_properties = ("a_number",) -class MockKGObject2(KGObject): +class MockKGObject2(KGObject, Node): default_space = "mock" type_ = "https://openminds.ebrains.eu/mock/MockKGObject2" + schema_version = "latest" context = { "schema": "http://schema.org/", "kg": "https://kg.ebrains.eu/api/instances/", @@ -60,9 +63,10 @@ class MockKGObject2(KGObject): reverse_properties = [] -class MockKGObject(KGObject): +class MockKGObject(KGObject, Node): default_space = "mock" type_ = "https://openminds.ebrains.eu/mock/MockKGObject" + schema_version = "latest" context = { "schema": "http://schema.org/", "kg": "https://kg.ebrains.eu/api/instances/", @@ -128,14 +132,14 @@ class MockKGObject(KGObject): ), Property( "a_required_linked_object", - ["test_base.MockKGObject", MockKGObject2], + ["test.test_base.MockKGObject", MockKGObject2], "https://openminds.ebrains.eu/vocab/aRequiredLinkedObject", multiple=False, required=True, ), Property( "a_required_list_of_linked_objects", - ["test_base.MockKGObject", MockKGObject2], + ["test.test_base.MockKGObject", MockKGObject2], "https://openminds.ebrains.eu/vocab/aRequiredListOfLinkedObjects", multiple=True, required=True, @@ -149,7 +153,7 @@ class MockKGObject(KGObject): ), Property( "an_optional_list_of_linked_objects", - ["test_base.MockKGObject", MockKGObject2], + ["test.test_base.MockKGObject", MockKGObject2], "https://openminds.ebrains.eu/vocab/anOptionalListOfLinkedObjects", multiple=True, required=False, @@ -443,7 +447,7 @@ def test_build_data_all_properties(self): "https://openminds.ebrains.eu/vocab/anOptionalListOfStrings": "plum, peach, apricot", "https://openminds.ebrains.eu/vocab/anOptionalString": "melon", } - assert obj.to_jsonld(include_empty_properties=True) == expected + assert obj.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) == expected def test_modified_data(self): obj = self._construct_object_all_properties() @@ -491,7 +495,7 @@ def test_exists__it_does_exist(self): class MockClient: def instance_from_full_uri(self, id, use_cache=True, scope="in progress", require_full_data=True): - data = orig_object.to_jsonld(include_empty_properties=True) + data = orig_object.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) data["https://core.kg.ebrains.eu/vocab/meta/space"] = "collab-foobar" data["@id"] = orig_object.id data["@context"] = orig_object.context @@ -593,7 +597,7 @@ def test_initialization_with_class(self): def test_initialization_with_string(self): uri = "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000001234" - proxy = KGProxy("test_base.MockKGObject", uri) + proxy = KGProxy("test.test_base.MockKGObject", uri) assert proxy.cls is MockKGObject assert proxy.id == uri diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index 918fe17d..22526115 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -10,8 +10,9 @@ import pytest +from openminds import IRI + from fairgraph.utility import as_list -from fairgraph.base import IRI from fairgraph.kgproxy import KGProxy from fairgraph.kgquery import KGQuery from fairgraph.kgobject import KGObject @@ -479,8 +480,8 @@ def test_to_jsonld(): "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield", "https://openminds.ebrains.eu/vocab/givenName": "Thorin", } - assert person1.to_jsonld(follow_links=True) == expected1 - assert person1.to_jsonld(follow_links=False) == expected1 + assert person1.to_jsonld(embed_linked_nodes=True) == expected1 + assert person1.to_jsonld(embed_linked_nodes=False) == expected1 person2 = omcore.Person( id="0000", @@ -512,8 +513,8 @@ def test_to_jsonld(): "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield", "https://openminds.ebrains.eu/vocab/givenName": "Thorin", } - assert person2.to_jsonld(follow_links=True) == expected2a - assert person2.to_jsonld(follow_links=False) == expected2b + assert person2.to_jsonld(embed_linked_nodes=True) == expected2a + assert person2.to_jsonld(embed_linked_nodes=False) == expected2b @skip_if_using_production_server diff --git a/test/test_properties.py b/test/test_properties.py index cd7c3e07..700d59b2 100644 --- a/test/test_properties.py +++ b/test/test_properties.py @@ -1,10 +1,11 @@ from datetime import date from uuid import uuid4 +from openminds.properties import Property from fairgraph.base import ErrorHandling -from fairgraph.properties import Property from fairgraph.kgobject import KGObject from fairgraph.embedded import EmbeddedMetadata from fairgraph.kgproxy import KGProxy +from fairgraph.queries import get_filter_value import pytest @@ -158,11 +159,11 @@ def test_deserialize(): def test_get_filter_value(): date_property = Property("the_date", date, "TheDate", error_handling=ErrorHandling.error) - assert date_property.get_filter_value(date(2023, 6, 2)) == "2023-06-02" + assert get_filter_value(date_property, date(2023, 6, 2)) == "2023-06-02" integer_property = Property("the_number", int, "TheNumber", error_handling=ErrorHandling.error) - assert integer_property.get_filter_value(42) == 42 + assert get_filter_value(integer_property, 42) == 42 object_property = Property("the_object", SomeOrganization, "TheObject", error_handling=ErrorHandling.error) obj = SomeOrganization(name="The University", alias="TU", id="https://kg.ebrains.eu/api/instances/the_id") - assert object_property.get_filter_value(obj) == "https://kg.ebrains.eu/api/instances/the_id" + assert get_filter_value(object_property, obj) == "https://kg.ebrains.eu/api/instances/the_id" diff --git a/test/test_registry.py b/test/test_registry.py index 0ba0a82c..412bb5d7 100644 --- a/test/test_registry.py +++ b/test/test_registry.py @@ -1,9 +1,10 @@ -from fairgraph.registry import Registry -from fairgraph.properties import Property +from openminds.properties import Property + +from fairgraph.registry import Node def test_docstring_generation(): - class Foo(metaclass=Registry): + class Foo(metaclass=Node): """This is the base docstring""" properties = [Property("foo", str, "Foo", doc="foo-foo")] diff --git a/test/utils.py b/test/utils.py index db72af97..1b0f857c 100644 --- a/test/utils.py +++ b/test/utils.py @@ -6,7 +6,8 @@ import pytest -kg_host = "core.kg-ppd.ebrains.eu" # don't use production for testing +#kg_host = "core.kg-ppd.ebrains.eu" # don't use production for testing +kg_host = "core.kg.ebrains.eu" # don't use production for testing have_kg_connection = False no_kg_err_msg = "No KG connection - have you set the environment variable KG_AUTH_TOKEN?" From 7b3835bb4035dd15b34b961097fe9d13dd5723b4 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 16 Jul 2025 17:45:26 +0200 Subject: [PATCH 02/25] adapt tests --- test/test_base.py | 58 ++++++++++++++++++++++++----------------- test/test_properties.py | 55 ++++++++++++++++++-------------------- 2 files changed, 59 insertions(+), 54 deletions(-) diff --git a/test/test_base.py b/test/test_base.py index f622d3be..d203ac68 100644 --- a/test/test_base.py +++ b/test/test_base.py @@ -5,7 +5,7 @@ from datetime import date, datetime from numbers import Real -from openminds.base import Node +from openminds.base import LinkedMetadata, EmbeddedMetadata as OMEmbeddedMetadata from openminds.properties import Property from fairgraph.embedded import EmbeddedMetadata from fairgraph.kgobject import KGObject @@ -17,9 +17,10 @@ import pytest -class MockEmbeddedObject(EmbeddedMetadata, Node): +class MockEmbeddedObject(EmbeddedMetadata, OMEmbeddedMetadata): type_ = "https://openminds.ebrains.eu/mock/MockEmbeddedObject" schema_version = "latest" + preferred_import_path = "test.test_base.MockEmbeddedObject" context = { "schema": "http://schema.org/", "kg": "https://kg.ebrains.eu/api/instances/", @@ -53,10 +54,11 @@ class MockEmbeddedObject(EmbeddedMetadata, Node): existence_query_properties = ("a_number",) -class MockKGObject2(KGObject, Node): +class MockKGObject2(KGObject, LinkedMetadata): default_space = "mock" type_ = "https://openminds.ebrains.eu/mock/MockKGObject2" schema_version = "latest" + preferred_import_path = "test.test_base.MockKGObject2" context = { "schema": "http://schema.org/", "kg": "https://kg.ebrains.eu/api/instances/", @@ -67,10 +69,11 @@ class MockKGObject2(KGObject, Node): reverse_properties = [] -class MockKGObject(KGObject, Node): +class MockKGObject(KGObject, LinkedMetadata): default_space = "mock" type_ = "https://openminds.ebrains.eu/mock/MockKGObject" schema_version = "latest" + preferred_import_path = "test.test_base.MockKGObject" context = { "schema": "http://schema.org/", "kg": "https://kg.ebrains.eu/api/instances/", @@ -207,7 +210,7 @@ class TestKGObject(object): object_counter = 0 def _construct_embedded_object_required_properties(self, n): - return MockEmbeddedObject(a_number=float(n)) + return MockEmbeddedObject(a_number=n) def _construct_object_required_properties(self): data = { @@ -324,7 +327,7 @@ def _construct_object_all_properties(self): {"@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000001234"}, {"@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000000002"}, ], - "https://openminds.ebrains.eu/vocab/anOptionalListOfStrings": "plum, peach, apricot", + "https://openminds.ebrains.eu/vocab/anOptionalListOfStrings": ["plum, peach, apricot"], "https://openminds.ebrains.eu/vocab/anOptionalString": "melon", } return MockKGObject( @@ -333,7 +336,7 @@ def _construct_object_all_properties(self): a_required_string="apple", a_required_list_of_strings=["banana", "pear"], an_optional_string="melon", - an_optional_list_of_strings=["plum, peach, apricot"], + an_optional_list_of_strings=["plum, peach, apricot"], # note that this is a single string containing commas a_required_datetime=datetime(1789, 7, 14), a_required_list_of_datetimes=[datetime(1900, 1, 1), datetime(2000, 1, 1)], an_optional_datetime=datetime(1605, 11, 5), @@ -394,23 +397,26 @@ def test_build_existence_query_with_missing_properties(self): prop_name = MockKGObject.existence_query_properties[0] obj.id = None prop = obj._property_lookup[prop_name] - orig_error_handling = prop.error_handling - prop.error_handling = ErrorHandling.none + orig_error_handling = obj.__class__.error_handling + obj.__class__.error_handling = ErrorHandling.none setattr(obj, prop_name, None) # remove a required property with pytest.raises(CannotBuildExistenceQuery) as exc_info: obj._build_existence_query() assert exc_info.value.args[0] == f"Required value for '{prop_name}' is missing" - prop.error_handling = orig_error_handling + obj.__class__.error_handling = orig_error_handling def test_build_data_all_properties(self): obj = self._construct_object_all_properties() expected = { + "@context": { + "@vocab": "https://openminds.ebrains.eu/vocab/", + }, "@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000000001", - "@type": ["https://openminds.ebrains.eu/mock/MockKGObject"], + "@type": "https://openminds.ebrains.eu/mock/MockKGObject", "https://openminds.ebrains.eu/vocab/aRequiredDateTime": "1789-07-14T00:00:00", "https://openminds.ebrains.eu/vocab/aRequiredEmbeddedObject": { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": -1.0, }, "https://openminds.ebrains.eu/vocab/aRequiredLinkedObject": { @@ -422,11 +428,11 @@ def test_build_data_all_properties(self): ], "https://openminds.ebrains.eu/vocab/aRequiredListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 100.0, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 200.0, }, ], @@ -438,7 +444,7 @@ def test_build_data_all_properties(self): "https://openminds.ebrains.eu/vocab/aRequiredString": "apple", "https://openminds.ebrains.eu/vocab/anOptionalDateTime": "1605-11-05T00:00:00", "https://openminds.ebrains.eu/vocab/anOptionalEmbeddedObject": { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 17.0, }, "https://openminds.ebrains.eu/vocab/anOptionalLinkedObject": { @@ -450,11 +456,11 @@ def test_build_data_all_properties(self): ], "https://openminds.ebrains.eu/vocab/anOptionalListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 18.0, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 19.0, }, ], @@ -462,10 +468,10 @@ def test_build_data_all_properties(self): {"@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000001234"}, {"@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000000002"}, ], - "https://openminds.ebrains.eu/vocab/anOptionalListOfStrings": "plum, peach, apricot", + "https://openminds.ebrains.eu/vocab/anOptionalListOfStrings": ["plum, peach, apricot"], "https://openminds.ebrains.eu/vocab/anOptionalString": "melon", } - assert obj.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) == expected + assert obj.to_jsonld(include_empty_properties=False, embed_linked_nodes=False) == expected def test_modified_data(self): obj = self._construct_object_all_properties() @@ -481,12 +487,16 @@ def test_modified_data(self): "https://openminds.ebrains.eu/vocab/aRequiredString": "pomme", "https://openminds.ebrains.eu/vocab/anOptionalListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", + "https://openminds.ebrains.eu/vocab/aDate": None, "https://openminds.ebrains.eu/vocab/aNumber": -18, + "https://openminds.ebrains.eu/vocab/aString": None, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", + "https://openminds.ebrains.eu/vocab/aDate": None, "https://openminds.ebrains.eu/vocab/aNumber": 19, + "https://openminds.ebrains.eu/vocab/aString": None, }, ], } @@ -586,12 +596,12 @@ def test_exists_insufficient_query_properties(self): obj = self._construct_object_required_properties() obj.id = None prop = obj._property_lookup[prop_name] - orig_error_handling = prop.error_handling - prop.error_handling = ErrorHandling.none + orig_error_handling = obj.__class__.error_handling + obj.__class__.error_handling = ErrorHandling.none setattr(obj, prop_name, None) # remove a required property exists = obj.exists(client=None) assert not exists - prop.error_handling = orig_error_handling + obj.__class__.error_handling = orig_error_handling def test_exists__it_does_not_exist(self): pass diff --git a/test/test_properties.py b/test/test_properties.py index d37be950..aba8bc31 100644 --- a/test/test_properties.py +++ b/test/test_properties.py @@ -76,8 +76,7 @@ def test_serialize_no_multiple(): (SomeContactInformation,), "vocab:contactInformation", multiple=False, - required=False, - error_handling=ErrorHandling.error, + required=False ) client = None @@ -95,17 +94,15 @@ def test_serialize_no_multiple(): expected = {"@id": test_info.id} assert result == expected - # two objects, strict - property_no_multiple.error_handling = ErrorHandling.error - test_info = [ - SomeContactInformation(email="someone@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - SomeContactInformation(email="sameperson@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - ] - with pytest.raises(ValueError): - result = property_no_multiple.serialize(test_info, follow_links=False) + # # two objects, strict + # test_info = [ + # SomeContactInformation(email="someone@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), + # SomeContactInformation(email="sameperson@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), + # ] + # with pytest.raises(ValueError): + # result = property_no_multiple.serialize(test_info, follow_links=False) # two objects, not strict - property_no_multiple.error_handling = ErrorHandling.none test_info = [ SomeContactInformation(email="someone@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), SomeContactInformation(email="sameperson@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), @@ -115,7 +112,6 @@ def test_serialize_no_multiple(): assert result == expected # two proxies, not strict - property_no_multiple.error_handling = ErrorHandling.none test_info = [ KGProxy(SomeContactInformation, f"https://kg.ebrains.eu/api/instances/{uuid4()}"), KGProxy(SomeContactInformation, f"https://kg.ebrains.eu/api/instances/{uuid4()}"), @@ -132,34 +128,33 @@ def test_serialize_unknown(): "vocab:contactInformation", multiple=False, required=False, - error_handling=ErrorHandling.error, ) client = None - # single object - test_info = complex(1, -1) - with pytest.raises(ValueError) as excinfo: - result = some_property.serialize(test_info, follow_links=False) - expected_error_message = ( - "fairgraph cannot serialize a value of type " - "(for property 'contact_information')" - ) - assert excinfo.value.args[0] == expected_error_message + # # single object + # test_info = complex(1, -1) + # with pytest.raises(ValueError) as excinfo: + # result = some_property.serialize(test_info, follow_links=False) + # expected_error_message = ( + # "fairgraph cannot serialize a value of type " + # "(for property 'contact_information')" + # ) + # assert excinfo.value.args[0] == expected_error_message def test_deserialize(): - date_property = Property("the_date", date, "TheDate", error_handling=ErrorHandling.error) - with pytest.raises(ValueError): - date_property.deserialize(42, client=None) + date_property = Property("the_date", date, "TheDate") + # with pytest.raises(ValueError): + # date_property.deserialize(42, client=None) - integer_property = Property("the_number", int, "TheNumber", error_handling=ErrorHandling.error) + integer_property = Property("the_number", int, "TheNumber") assert integer_property.deserialize(42, client=None) == 42 assert integer_property.deserialize(42.0, client=None) == 42 assert integer_property.deserialize("42", client=None) == 42 assert integer_property.deserialize([42, 42, 42], client=None) == [42, 42, 42] assert integer_property.deserialize(["42", 42, "42"], client=None) == [42, 42, 42] - object_property = Property("the_object", SomeOrganization, "TheObject", error_handling=ErrorHandling.error) + object_property = Property("the_object", SomeOrganization, "TheObject") obj_data = { "@id": "https://kg.ebrains.eu/api/instances/the_id", "@type": SomeOrganization.type_, @@ -180,12 +175,12 @@ def test_deserialize(): def test_get_filter_value(): - date_property = Property("the_date", date, "TheDate", error_handling=ErrorHandling.error) + date_property = Property("the_date", date, "TheDate") assert get_filter_value(date_property, date(2023, 6, 2)) == "2023-06-02" - integer_property = Property("the_number", int, "TheNumber", error_handling=ErrorHandling.error) + integer_property = Property("the_number", int, "TheNumber") assert get_filter_value(integer_property, 42) == 42 - object_property = Property("the_object", SomeOrganization, "TheObject", error_handling=ErrorHandling.error) + object_property = Property("the_object", SomeOrganization, "TheObject") obj = SomeOrganization(name="The University", alias="TU", id="https://kg.ebrains.eu/api/instances/the_id") assert get_filter_value(object_property, obj) == "https://kg.ebrains.eu/api/instances/the_id" From 7852125d6e84e0a10138818573af1b8cd12c11d7 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Thu, 17 Jul 2025 12:41:53 +0200 Subject: [PATCH 03/25] rename `from_kg_instance()` to `from_json_ld()` for consistency with openMINDS-Python. --- fairgraph/embedded.py | 4 ++-- fairgraph/kgobject.py | 18 +++++++++--------- fairgraph/kgquery.py | 2 +- fairgraph/node.py | 13 +++---------- test/test_base.py | 2 +- test/test_openminds_core.py | 7 +++---- test/test_properties.py | 20 ++++++++++---------- 7 files changed, 29 insertions(+), 37 deletions(-) diff --git a/fairgraph/embedded.py b/fairgraph/embedded.py index 78b86901..88c9c0d0 100644 --- a/fairgraph/embedded.py +++ b/fairgraph/embedded.py @@ -71,12 +71,12 @@ def __eq__(self, other): return isinstance(other, self.__class__) and self.to_jsonld(embed_linked_nodes=False) == other.to_jsonld(embed_linked_nodes=False) @classmethod - def from_kg_instance(cls, data: JSONdict, client: KGClient) -> Union[None, EmbeddedMetadata]: + def from_json_ld(cls, data: JSONdict) -> Union[None, EmbeddedMetadata]: """Create an instance of the class from a JSON-LD document.""" if "@id" in data: warn("Expected embedded metadata, but received @id") return None - deserialized_data = cls._deserialize_data(data, client) + deserialized_data = cls._deserialize_data(data) return cls(data=data, **deserialized_data) def save( diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index 6571e207..75933eaf 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -107,9 +107,9 @@ def space(self) -> Union[str, None]: return self._space @classmethod - def from_kg_instance(cls, data: JSONdict, client: KGClient, scope: Optional[str] = None): + def from_jsonld(cls, data: JSONdict, scope: Optional[str] = None) -> KGObject: """Create an instance of the class from a JSON-LD document.""" - deserialized_data = cls._deserialize_data(data, client, include_id=True) + deserialized_data = cls._deserialize_data(data, include_id=True) return cls(id=data["@id"], data=data, scope=scope, **deserialized_data) # @classmethod @@ -165,7 +165,7 @@ def from_uri( if data is None: return None else: - return cls.from_kg_instance(data, client, scope=scope) + return cls.from_jsonld(data, client, scope=scope) @classmethod def from_uuid( @@ -238,7 +238,7 @@ def from_id( raise NotImplementedError data = client.instance_from_full_uri(uri, use_cache=use_cache, scope=scope) cls_from_data = lookup_type(data["@type"][0]) - return cls_from_data.from_kg_instance(data, client, scope=scope) + return cls_from_data.from_jsonld(data, client, scope=scope) @classmethod def from_alias( @@ -377,7 +377,7 @@ def list( else: raise ValueError("'api' must be either 'query', 'core', or 'auto'") - return [cls.from_kg_instance(instance, client, scope=scope) for instance in instances] + return [cls.from_jsonld(instance, client, scope=scope) for instance in instances] @classmethod def count( @@ -428,10 +428,10 @@ def count( response = client.list(cls.type_, space=space, scope=scope, from_index=0, size=1) return response.total - def _update_empty_properties(self, data: JSONdict, client: KGClient): + def _update_empty_properties(self, data: JSONdict): """Replace any empty properties (value None) with the supplied data""" cls = self.__class__ - deserialized_data = cls._deserialize_data(data, client, include_id=True) + deserialized_data = cls._deserialize_data(data, include_id=True) for prop in cls.all_properties: current_value = getattr(self, prop.name, None) if current_value is None: @@ -496,7 +496,7 @@ def exists( self._raw_remote_data = data obj_exists = bool(data) if obj_exists: - self._update_empty_properties(data, client) # also updates `remote_data` + self._update_empty_properties(data) # also updates `remote_data` return obj_exists else: try: @@ -543,7 +543,7 @@ def exists( self.id = instance["@id"] assert isinstance(self.id, str) save_cache[self.__class__][query_cache_key] = self.id - self._update_empty_properties(instance, client) # also updates `remote_data` + self._update_empty_properties(instance) # also updates `remote_data` return bool(instances) def modified_data(self) -> JSONdict: diff --git a/fairgraph/kgquery.py b/fairgraph/kgquery.py index 1001334d..f6bed9f8 100644 --- a/fairgraph/kgquery.py +++ b/fairgraph/kgquery.py @@ -117,7 +117,7 @@ def resolve( from_index=from_index, scope=scope, ).data - objects.extend(cls.from_kg_instance(instance_data, client) for instance_data in instances) + objects.extend(cls.from_jsonld(instance_data, client) for instance_data in instances) for obj in objects: object_cache[obj.id] = obj diff --git a/fairgraph/node.py b/fairgraph/node.py index 1c426f38..e228e22f 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -120,17 +120,10 @@ def get_property(cls, name): return cls._property_lookup[name] @classmethod - def from_jsonld(cls, data: JSONdict, client: KGClient, scope: Optional[str] = None): + def from_jsonld(cls, data: JSONdict, scope: Optional[str] = None) -> ContainsMetadata: """ Create an instance of the class from a JSON-LD document. """ - if scope: - return cls.from_kg_instance(data, client, scope) - else: - return cls.from_kg_instance(data, client) - - @classmethod - def from_kg_instance(cls, data: JSONdict, client: KGClient, scope: Optional[str] = None) -> ContainsMetadata: pass def save( @@ -246,7 +239,7 @@ def generate_query_filter_properties( return properties @classmethod - def _deserialize_data(cls, data: JSONdict, client: KGClient, include_id: bool = False): + def _deserialize_data(cls, data: JSONdict, include_id: bool = False): # check types match if cls.type_ not in data["@type"]: if types_match(cls.type_, data["@type"][0]): @@ -314,7 +307,7 @@ def _get_type_from_data(data_item): else: deserialized_data[prop.name] = None else: - deserialized_data[prop.name] = prop.deserialize(data_item, client) + deserialized_data[prop.name] = prop.deserialize(data_item) return deserialized_data def resolve( diff --git a/test/test_base.py b/test/test_base.py index d203ac68..f7158ee7 100644 --- a/test/test_base.py +++ b/test/test_base.py @@ -511,7 +511,7 @@ def test_update(self): "https://openminds.ebrains.eu/vocab/aRequiredListOfStrings": ["kumquat", "bilberry"], "https://openminds.ebrains.eu/vocab/anOptionalDateTime": "1789-07-14T00:00:00", } - obj._update_empty_properties(new_data, client=None) + obj._update_empty_properties(new_data) assert obj.a_required_list_of_strings == [ "banana", "pear", diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index a85e65d4..a0eb65c4 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -430,8 +430,7 @@ def test__update(): "https://openminds.ebrains.eu/vocab/familyName": "Bianchi", "https://openminds.ebrains.eu/vocab/givenName": "Daniela", } - client = None - person = omcore.Person.from_kg_instance(example_data, client=client, scope="in progress") + person = omcore.Person.from_jsonld(example_data, scope="in progress") for key in ( "http://schema.org/identifier", "https://core.kg.ebrains.eu/vocab/meta/revision", @@ -848,7 +847,7 @@ def test_with_new_namespace_from_core(): "https://core.kg.ebrains.eu/vocab/meta/lastReleasedAt": "2023-03-23T10:09:30.130Z", } orig_type = omcore.Model.type_ - obj = omcore.Model.from_kg_instance(data, client=None, scope="released") + obj = omcore.Model.from_jsonld(data, scope="released") assert obj.abstraction_level assert len(obj.developers) == 5 omcore.Model.type_ = orig_type @@ -938,7 +937,7 @@ def test_with_new_namespace_from_query(): } #omcore.set_error_handling("error") orig_types = (omcore.Model.type_, omcore.Person.type_) - obj = omcore.Model.from_kg_instance(data, client=None, scope="released") + obj = omcore.Model.from_jsonld(data, scope="released") assert obj.abstraction_level assert len(obj.developers) == 5 omcore.Model.type_, omcore.Person.type_ = orig_types diff --git a/test/test_properties.py b/test/test_properties.py index aba8bc31..40a7250d 100644 --- a/test/test_properties.py +++ b/test/test_properties.py @@ -145,14 +145,14 @@ def test_serialize_unknown(): def test_deserialize(): date_property = Property("the_date", date, "TheDate") # with pytest.raises(ValueError): - # date_property.deserialize(42, client=None) + # date_property.deserialize(42) integer_property = Property("the_number", int, "TheNumber") - assert integer_property.deserialize(42, client=None) == 42 - assert integer_property.deserialize(42.0, client=None) == 42 - assert integer_property.deserialize("42", client=None) == 42 - assert integer_property.deserialize([42, 42, 42], client=None) == [42, 42, 42] - assert integer_property.deserialize(["42", 42, "42"], client=None) == [42, 42, 42] + assert integer_property.deserialize(42) == 42 + assert integer_property.deserialize(42.0) == 42 + assert integer_property.deserialize("42") == 42 + assert integer_property.deserialize([42, 42, 42]) == [42, 42, 42] + assert integer_property.deserialize(["42", 42, "42"]) == [42, 42, 42] object_property = Property("the_object", SomeOrganization, "TheObject") obj_data = { @@ -162,13 +162,13 @@ def test_deserialize(): "https://openminds.ebrains.eu/vocab/shortName": "TU", } expected_obj = SomeOrganization(name="The University", alias="TU", id="https://kg.ebrains.eu/api/instances/the_id") - assert object_property.deserialize(obj_data, client=None) == expected_obj + assert object_property.deserialize(obj_data) == expected_obj - assert object_property.deserialize(None, client=None) is None + assert object_property.deserialize(None) is None - assert object_property.deserialize([None, obj_data, None, obj_data], client=None) == [expected_obj, expected_obj] + assert object_property.deserialize([None, obj_data, None, obj_data]) == [expected_obj, expected_obj] - assert object_property.deserialize({"@list": [None, obj_data, None, obj_data]}, client=None) == [ + assert object_property.deserialize({"@list": [None, obj_data, None, obj_data]}) == [ expected_obj, expected_obj, ] From 2843b75c90c14f7c4ba3464b3e8e1997db2d0c6c Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Thu, 17 Jul 2025 14:10:27 +0200 Subject: [PATCH 04/25] Apply changes from [0b889480] --- fairgraph/node.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/fairgraph/node.py b/fairgraph/node.py index e228e22f..3f619425 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -247,10 +247,11 @@ def _deserialize_data(cls, data: JSONdict, include_id: bool = False): else: raise TypeError("type mismatch {} - {}".format(cls.type_, data["@type"])) # normalize data by expanding keys + context = copy(cls.context) if "om-i.org" in cls.type_: - cls.context = default_context["v4"] + context = default_context["v4"] else: - cls.context = default_context["v3"] + context = default_context["v3"] D = {"@type": data["@type"]} if include_id: @@ -258,7 +259,7 @@ def _deserialize_data(cls, data: JSONdict, include_id: bool = False): for key, value in data.items(): if "__" in key: key, type_filter = key.split("__") - normalised_key = expand_uri(key, cls.context) + normalised_key = expand_uri(key, context) value = [item for item in as_list(value) if item["@type"][0].endswith(type_filter)] if normalised_key in D: D[normalised_key].extend(value) @@ -267,7 +268,7 @@ def _deserialize_data(cls, data: JSONdict, include_id: bool = False): elif key.startswith("Q"): # for 'Q' properties in data from queries D[key] = value elif key[0] != "@": - normalised_key = expand_uri(key, cls.context) + normalised_key = expand_uri(key, context) D[normalised_key] = value def _get_type_from_data(data_item): @@ -279,7 +280,7 @@ def _get_type_from_data(data_item): deserialized_data = {} for prop in cls.all_properties: - expanded_path = expand_uri(prop.path, cls.context) + expanded_path = expand_uri(prop.path, context) data_item = D.get(expanded_path) if data_item is not None and prop.reverse: # for reverse properties, more than one property can have the same path From 946470d1009040eb1ea00979aaf26cbea94e5b57 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Fri, 18 Jul 2025 16:43:25 +0200 Subject: [PATCH 05/25] bug fixes and improvements --- fairgraph/embedded.py | 2 +- fairgraph/kgobject.py | 21 +++++++++++++++++++-- fairgraph/node.py | 7 ++++--- test/test_base.py | 41 +++++++++++++++++++++++++++-------------- 4 files changed, 51 insertions(+), 20 deletions(-) diff --git a/fairgraph/embedded.py b/fairgraph/embedded.py index 88c9c0d0..1b2c9e35 100644 --- a/fairgraph/embedded.py +++ b/fairgraph/embedded.py @@ -71,7 +71,7 @@ def __eq__(self, other): return isinstance(other, self.__class__) and self.to_jsonld(embed_linked_nodes=False) == other.to_jsonld(embed_linked_nodes=False) @classmethod - def from_json_ld(cls, data: JSONdict) -> Union[None, EmbeddedMetadata]: + def from_jsonld(cls, data: JSONdict) -> Union[None, EmbeddedMetadata]: """Create an instance of the class from a JSON-LD document.""" if "@id" in data: warn("Expected embedded metadata, but received @id") diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index 75933eaf..bf5a1677 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -436,7 +436,8 @@ def _update_empty_properties(self, data: JSONdict): current_value = getattr(self, prop.name, None) if current_value is None: value = deserialized_data[prop.name] - setattr(self, prop.name, value) + if value is not None: + setattr(self, prop.name, value) assert self.remote_data is not None for key, value in data.items(): if not key.startswith("Q"): @@ -551,6 +552,19 @@ def modified_data(self) -> JSONdict: Return a dict containing the properties that have been modified locally from the values originally obtained from the Knowledge Graph. """ + + def values_are_equal(local, remote): + if type(local) != type(remote): + return False + if isinstance(local, list): + if len(local) != len(remote): + return False + return all(values_are_equal(a, b) for a, b in zip(local, remote)) + elif isinstance(local, dict): + return all(values_are_equal(local[key], remote.get(key, None)) for key in local.keys() if not (local[key] is None and key not in remote)) + else: + return local == remote + current_data = self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) modified_data = {} for key, current_value in current_data.items(): @@ -558,7 +572,7 @@ def modified_data(self) -> JSONdict: assert key.startswith("http") # keys should all be expanded by this point assert self.remote_data is not None remote_value = self.remote_data.get(key, None) - if current_value != remote_value: + if not values_are_equal(current_value, remote_value): modified_data[key] = current_value return modified_data @@ -671,6 +685,9 @@ def save( activity_log.update(item=self, delta=None, space=space, entry_type="no-op") else: try: + # Note: if modified_data includes embedded objects + # then _all_ fields of the embedded objects must be provided, + # not only those that have changed. client.update_instance(self.uuid, modified_data) except AuthorizationError as err: if ignore_auth_errors: diff --git a/fairgraph/node.py b/fairgraph/node.py index 3f619425..cb00fd0c 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -4,11 +4,12 @@ import logging from warnings import warn -from openminds.base import value_to_jsonld +from openminds.base import value_to_jsonld, Link from openminds.properties import Property from .registry import Node from .base import Resolvable, ErrorHandling, RepresentsSingleObject +from .kgproxy import KGProxy from .kgquery import KGQuery from .queries import ( QueryProperty, @@ -124,7 +125,7 @@ def from_jsonld(cls, data: JSONdict, scope: Optional[str] = None) -> ContainsMet """ Create an instance of the class from a JSON-LD document. """ - pass + raise NotImplementedError("This should be implemented by subclasses") def save( self, @@ -136,7 +137,7 @@ def save( ignore_auth_errors: bool = False, ignore_duplicates: bool = False ): - pass + raise NotImplementedError("This should be implemented by subclasses") @classmethod def set_error_handling( diff --git a/test/test_base.py b/test/test_base.py index f7158ee7..75ee94ae 100644 --- a/test/test_base.py +++ b/test/test_base.py @@ -523,7 +523,7 @@ def test_exists__it_does_exist(self): class MockClient: def instance_from_full_uri(self, id, use_cache=True, scope="in progress", require_full_data=True): - data = orig_object.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) + data = orig_object.to_jsonld(include_empty_properties=False, embed_linked_nodes=False) data["https://core.kg.ebrains.eu/vocab/meta/space"] = "collab-foobar" data["@id"] = orig_object.id data["@context"] = orig_object.context @@ -531,17 +531,22 @@ def instance_from_full_uri(self, id, use_cache=True, scope="in progress", requir return data MockKGObject.set_error_handling("none") # stop the constructor from complaining - new_obj = MockKGObject(id=orig_object.id, a_required_list_of_strings=["coconut"], an_optional_string="lime") + new_obj = MockKGObject( + id=orig_object.id, + a_required_list_of_strings=["coconut"], + an_optional_string="lime", + a_required_embedded_object=MockEmbeddedObject(a_number=41, a_string="forty one") + ) MockKGObject.set_error_handling("error") assert new_obj.a_required_list_of_strings == ["coconut"] assert new_obj.remote_data == {} - assert new_obj.a_required_embedded_object == None + assert new_obj.a_required_embedded_object.a_string == "forty one" assert ( new_obj.exists(MockClient()) and new_obj.space == "collab-foobar" ) # has the side-effect of setting .remote_data - assert new_obj.a_required_embedded_object == MockEmbeddedObject(a_number=41.0) + # check that all the metadata for the existing instance have been retrieved expected = { "@context": MockKGObject.context, "@id": orig_object.id, @@ -549,8 +554,8 @@ def instance_from_full_uri(self, id, use_cache=True, scope="in progress", requir "https://core.kg.ebrains.eu/vocab/meta/space": "collab-foobar", "https://openminds.ebrains.eu/vocab/aRequiredDateTime": "1789-07-14T00:00:00", "https://openminds.ebrains.eu/vocab/aRequiredEmbeddedObject": { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], - "https://openminds.ebrains.eu/vocab/aNumber": 41.0, + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", + "https://openminds.ebrains.eu/vocab/aNumber": 41 }, "https://openminds.ebrains.eu/vocab/aRequiredLinkedObject": { "@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000001234" @@ -561,12 +566,12 @@ def instance_from_full_uri(self, id, use_cache=True, scope="in progress", requir ], "https://openminds.ebrains.eu/vocab/aRequiredListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], - "https://openminds.ebrains.eu/vocab/aNumber": 42.0, + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", + "https://openminds.ebrains.eu/vocab/aNumber": 42, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], - "https://openminds.ebrains.eu/vocab/aNumber": 43.0, + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", + "https://openminds.ebrains.eu/vocab/aNumber": 43, }, ], "https://openminds.ebrains.eu/vocab/aRequiredListOfLinkedObjects": [ @@ -585,8 +590,16 @@ def instance_from_full_uri(self, id, use_cache=True, scope="in progress", requir assert new_obj.a_required_datetime == datetime(1789, 7, 14) expected = { - "https://openminds.ebrains.eu/vocab/aRequiredListOfStrings": "coconut", # note no square brackets, single item in list. Is this desired? + "https://openminds.ebrains.eu/vocab/aRequiredListOfStrings": ["coconut"], "https://openminds.ebrains.eu/vocab/anOptionalString": "lime", + "https://openminds.ebrains.eu/vocab/aRequiredEmbeddedObject": { + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", + # modified embedded metadata needs to include _all_ properties, + # not just those that have changed + "https://openminds.ebrains.eu/vocab/aNumber": 41, + "https://openminds.ebrains.eu/vocab/aString": "forty one", + "https://openminds.ebrains.eu/vocab/aDate": None, + }, } assert new_obj.modified_data() == expected @@ -617,9 +630,9 @@ def test_repr(self): "a_required_list_of_linked_objects=[MockKGObject2(a=2345, space=None, " "id=https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000002345), " "MockKGObject2(a=3456, space=None, id=https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000003456)], " - "a_required_embedded_object=MockEmbeddedObject(a_number=41.0), " - "a_required_list_of_embedded_objects=[MockEmbeddedObject(a_number=42.0), " - "MockEmbeddedObject(a_number=43.0)], space=None, " + "a_required_embedded_object=MockEmbeddedObject(a_number=41), " + "a_required_list_of_embedded_objects=[MockEmbeddedObject(a_number=42), " + "MockEmbeddedObject(a_number=43)], space=None, " "id=https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000000002)" ) From 50f465a7994714b907e3bd1740590f0e59be1c30 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 30 Jul 2025 15:04:44 +0200 Subject: [PATCH 06/25] Use `@vocab` in contexts; fix method resolution order by re-ordering parent classes --- builder/fairgraph_module_template.py.txt | 5 +- builder/update_openminds.py | 2 +- fairgraph/embedded.py | 2 - fairgraph/kgobject.py | 28 +- fairgraph/kgproxy.py | 68 ++--- fairgraph/node.py | 89 ++++-- fairgraph/queries.py | 13 +- fairgraph/registry.py | 39 +++ fairgraph/utility.py | 15 +- test/test_base.py | 14 +- test/test_client.py | 6 +- .../core/accountinformation_simple_query.json | 9 +- .../core/behavioralprotocol_simple_query.json | 16 +- .../openminds/core/comment_simple_query.json | 14 +- .../core/configuration_simple_query.json | 13 +- .../core/consortium_simple_query.json | 38 +-- .../core/contactinformation_simple_query.json | 4 +- .../core/contenttype_simple_query.json | 24 +- .../core/contenttypepattern_simple_query.json | 11 +- .../openminds/core/dataset_simple_query.json | 27 +- .../core/dataset_simple_query_v4.json | 25 +- .../core/datasetversion_simple_query.json | 117 ++++---- .../openminds/core/doi_simple_query.json | 8 +- .../experimentalactivity_simple_query.json | 30 +-- .../openminds/core/file_simple_query.json | 70 ++--- .../core/filearchive_simple_query.json | 13 +- .../core/filebundle_simple_query.json | 60 +++-- .../core/filerepository_simple_query.json | 60 +++-- .../filerepositorystructure_simple_query.json | 10 +- .../openminds/core/funding_simple_query.json | 13 +- .../openminds/core/gridid_simple_query.json | 4 +- .../openminds/core/handle_simple_query.json | 4 +- .../identifiersdotorgid_simple_query.json | 4 +- .../openminds/core/isbn_simple_query.json | 8 +- .../openminds/core/issn_simple_query.json | 6 +- .../openminds/core/license_simple_query.json | 10 +- .../core/metadatamodel_simple_query.json | 27 +- .../metadatamodelversion_simple_query.json | 97 ++++--- .../openminds/core/model_simple_query.json | 39 +-- .../core/modelversion_simple_query.json | 106 ++++---- .../openminds/core/orcid_simple_query.json | 4 +- .../core/organization_simple_query.json | 52 ++-- .../openminds/core/person_newstyle_query.json | 199 +++++++------- .../core/person_newstyle_query_alt.json | 68 ++--- .../core/person_resolved-1_query.json | 160 +++++------ .../core/person_resolved-2_query.json | 130 ++++----- .../openminds/core/person_simple_query.json | 48 ++-- .../openminds/core/project_simple_query.json | 12 +- .../core/propertyvaluelist_simple_query.json | 48 ++-- .../openminds/core/protocol_simple_query.json | 15 +- .../core/protocolexecution_simple_query.json | 255 ++++++++++-------- .../quantitativevaluearray_simple_query.json | 16 +- .../researchproductgroup_simple_query.json | 4 +- .../openminds/core/rorid_simple_query.json | 4 +- .../openminds/core/rrid_simple_query.json | 4 +- .../core/servicelink_simple_query.json | 19 +- .../openminds/core/setup_simple_query.json | 16 +- .../openminds/core/software_simple_query.json | 27 +- .../core/softwareversion_simple_query.json | 111 ++++---- .../core/stimulation_simple_query.json | 18 +- .../openminds/core/strain_simple_query.json | 54 ++-- .../openminds/core/subject_simple_query.json | 24 +- .../core/subjectgroup_simple_query.json | 22 +- .../core/subjectgroupstate_simple_query.json | 143 +++++----- .../core/subjectstate_simple_query.json | 151 ++++++----- .../openminds/core/swhid_simple_query.json | 4 +- .../core/tissuesample_simple_query.json | 38 +-- .../tissuesamplecollection_simple_query.json | 30 +-- ...suesamplecollectionstate_simple_query.json | 136 ++++++---- .../core/tissuesamplestate_simple_query.json | 138 +++++----- .../openminds/core/url_simple_query.json | 4 +- .../core/webresource_simple_query.json | 19 +- .../core/webservice_simple_query.json | 26 +- .../core/webserviceversion_simple_query.json | 86 +++--- test/test_openminds_computation.py | 14 +- test/test_openminds_core.py | 120 +++++---- test/test_properties.py | 186 ------------- test/test_queries.py | 100 +++---- test/test_registry.py | 12 - test/test_utility.py | 36 ++- 80 files changed, 1938 insertions(+), 1763 deletions(-) delete mode 100644 test/test_properties.py delete mode 100644 test/test_registry.py diff --git a/builder/fairgraph_module_template.py.txt b/builder/fairgraph_module_template.py.txt index 3904b29e..c0c025ba 100644 --- a/builder/fairgraph_module_template.py.txt +++ b/builder/fairgraph_module_template.py.txt @@ -11,10 +11,11 @@ from fairgraph import {{ base_class }} {{preamble}} -class {{ class_name }}({{ class_name }}, {{ base_class }}): +class {{ class_name }}({{base_class}}, {{ class_name }}): """ {{ docstring }} """ + type_ = "{{ openminds_type }}" {%- if default_space %} default_space = "{{ default_space }}" {%- endif %} @@ -46,5 +47,5 @@ class {{ class_name }}({{ class_name }}, {{ base_class }}): {%- endif %} def __init__(self {%- for arg in constructor_arguments -%}, {{arg}}=None{%- endfor -%}, id=None, data=None, space=None, scope=None): - return super().__init__({{ standard_init_properties }}data=data {%- for arg in constructor_arguments -%}, {{arg}}={{arg}}{%- endfor -%}) + return {{ base_class }}.__init__(self, {{ standard_init_properties }}data=data {%- for arg in constructor_arguments -%}, {{arg}}={{arg}}{%- endfor -%}) {{ additional_methods }} diff --git a/builder/update_openminds.py b/builder/update_openminds.py index c0124369..dc8045ff 100644 --- a/builder/update_openminds.py +++ b/builder/update_openminds.py @@ -697,7 +697,7 @@ def get_type(prop): { "name": python_name, "type_str": get_type(prop), # compress using JSON-LD context - "iri": f"vocab:{prop['name']}", + "iri": f"{prop['name']}", "allow_multiple": allow_multiple, "required": iri in self._schema_payload.get("required", []), "doc": generate_doc(prop, class_name), diff --git a/fairgraph/embedded.py b/fairgraph/embedded.py index 1b2c9e35..b35c6bf3 100644 --- a/fairgraph/embedded.py +++ b/fairgraph/embedded.py @@ -43,8 +43,6 @@ class EmbeddedMetadata(ContainsMetadata, Resolvable): properties: the metadata properties (property names and values) """ - properties = [] - def __init__(self, data: Optional[JSONdict] = None, **properties): super().__init__(data=data, **properties) diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index bf5a1677..092e1028 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -37,7 +37,7 @@ from openminds.registry import lookup_type from openminds import IRI -from .utility import expand_uri, as_list, expand_filter, ActivityLog +from .utility import expand_uri, as_list, expand_filter, ActivityLog, normalize_data from .queries import Query, QueryProperty from .errors import AuthorizationError, ResourceExistsError, CannotBuildExistenceQuery from .caching import object_cache, save_cache, generate_cache_key @@ -61,7 +61,6 @@ class KGObject(ContainsMetadata, RepresentsSingleObject, SupportsQuerying): Should not be instantiated directly, intended to be subclassed. """ - properties: List[Property] = [] existence_query_properties: Tuple[str, ...] = ("name",) # Note that this default value of existence_query_properties should in # many cases be over-ridden. @@ -165,7 +164,7 @@ def from_uri( if data is None: return None else: - return cls.from_jsonld(data, client, scope=scope) + return cls.from_jsonld(data, scope=scope) @classmethod def from_uuid( @@ -238,7 +237,7 @@ def from_id( raise NotImplementedError data = client.instance_from_full_uri(uri, use_cache=use_cache, scope=scope) cls_from_data = lookup_type(data["@type"][0]) - return cls_from_data.from_jsonld(data, client, scope=scope) + return cls_from_data.from_jsonld(data, scope=scope) @classmethod def from_alias( @@ -376,8 +375,7 @@ def list( instances = client.list(cls.type_, space=space, from_index=from_index, size=size, scope=scope).data else: raise ValueError("'api' must be either 'query', 'core', or 'auto'") - - return [cls.from_jsonld(instance, client, scope=scope) for instance in instances] + return [cls.from_jsonld(data=instance, scope=scope) for instance in instances] @classmethod def count( @@ -454,10 +452,11 @@ def __ne__(self, other): if self.id and other.id and self.id != other.id: return True for prop in self.properties: - assert prop.intrinsic val_self = getattr(self, prop.name) val_other = getattr(other, prop.name) if val_self != val_other: + #if self.uuid == "ab532423-1fd7-4255-8c6f-f99dc6df814f": + # raise Exception("breakpoint") return True return False @@ -472,7 +471,6 @@ def diff(self, other): if self.id != other.id: differences["id"] = (self.id, other.id) for prop in self.properties: - assert prop.intrinsic val_self = getattr(self, prop.name) val_other = getattr(other, prop.name) if val_self != val_other: @@ -565,7 +563,10 @@ def values_are_equal(local, remote): else: return local == remote - current_data = self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) + current_data = normalize_data( + self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False), + self.context + ) modified_data = {} for key, current_value in current_data.items(): if not key.startswith("@"): @@ -606,7 +607,6 @@ def save( """ if recursive: for prop in self.properties: - assert prop.intrinsic # we do not save reverse properties, those objects must be saved separately # this could be revisited, but we'll have to be careful about loops # if saving recursively @@ -653,7 +653,7 @@ def save( activity_log.update(item=self, delta=None, space=space, entry_type="no-op") else: # update - local_data = self.to_jsonld(embed_linked_nodes=False) + local_data = normalize_data(self.to_jsonld(embed_linked_nodes=False), self.context) if replace: logger.info(f" - replacing - {self.__class__.__name__}(id={self.id})") if activity_log: @@ -675,9 +675,9 @@ def save( f" - updating - {self.__class__.__name__}(id={self.id}) - properties changed: {modified_data.keys()}" ) skip_update = False - if "vocab:storageSize" in modified_data: + if "storageSize" in modified_data: warn("Removing storage size from update because this prop is currently locked by the KG") - modified_data.pop("vocab:storageSize") + modified_data.pop("storageSize") skip_update = len(modified_data) == 0 if skip_update: @@ -864,7 +864,7 @@ def generate_query( query.properties.extend(cls.generate_query_filter_properties(normalized_filters)) # third pass, we add sorting, which can only happen at the top level for prop in query.properties: - if prop.name in ("vocab:name", "vocab:fullName", "vocab:lookupLabel"): + if prop.name in ("name", "fullName", "lookupLabel"): prop.sorted = True # implementation note: the three-pass approach generates queries that are sometimes more verbose # than necessary, but it makes the logic easier to understand. diff --git a/fairgraph/kgproxy.py b/fairgraph/kgproxy.py index 8a0a4a73..6d96c7b3 100644 --- a/fairgraph/kgproxy.py +++ b/fairgraph/kgproxy.py @@ -38,11 +38,11 @@ class KGProxy(RepresentsSingleObject): """ - Representation of an KGObject whose type and identifier are known but whose + Representation of an KGObject whose identifier, and possibly type, are known but whose other metadata have not been retrieved from the KG. Args: - cls (str, KGObject): the type of the associated KG object, defined by a KGObject subclass + cls (str, KGObject, List[KGObject]): the possible types of the associated KG object, defined by a KGObject subclass or by the name of the subclass. uri (URI): The global identifier of the KG object. preferred_scope (str, optional): The preferred scope used to resolve the proxy. @@ -60,17 +60,24 @@ class KGProxy(RepresentsSingleObject): # todo: rename uri to id, for consistency? - def __init__(self, cls: Union[str, KGObject], uri: str, preferred_scope: str = "released"): - self.cls: KGObject - if isinstance(cls, str): - resolved_cls = lookup(cls) + def __init__( + self, + classes: Union[str, KGObject, List[KGObject], Tuple[KGObject]], + uri: str, + preferred_scope: str = "released" + ): + self.classes: List[KGObject] # todo: make this a set? + if isinstance(classes, str): + resolved_cls = lookup(classes) if TYPE_CHECKING: assert isinstance(resolved_cls, KGObject) - self.cls = resolved_cls + self.classes = [resolved_cls] + elif isinstance(classes, (list, tuple)): + self.classes = list(classes) else: - self.cls = cls + self.classes = [classes] if TYPE_CHECKING: - assert isinstance(self.cls, KGObject) + assert all(isinstance(cls, KGObject) for cls in self.classes) self.id = uri self.preferred_scope = preferred_scope self.remote_data = None @@ -81,21 +88,24 @@ def type(self) -> List[str]: Provide the global identifiers of the object type (as a list of URIs). """ try: - return self.cls.type_ + return [cls.type_ for cls in self.classes] except AttributeError as err: - raise AttributeError(f"{err} self.cls={self.cls}") + raise AttributeError(f"{err} self.classes={self.classes}") @property - def classes(self) -> Union[Tuple[KGObject], List[KGObject]]: + def cls(self): """ - Provide the metadata class associated with this object in a list. - - This is provided for consistency with the KGQuery interface. + For backwards compatibility """ - if isinstance(self.cls, (list, tuple)): - return self.cls + if len(self.classes) == 1: + return self.classes[0] else: - return [self.cls] + raise AttributeError("This KGProxy has multiple possible types, use the 'classes' attribute instead") + + def to_jsonld(self, **kwargs): + return { + "@id": self.id + } def resolve( self, @@ -121,19 +131,17 @@ def resolve( obj = object_cache[self.id] else: scope = scope or self.preferred_scope - if len(self.classes) > 1: - obj = None - for cls in self.classes: - try: - obj = cls.from_uri(self.id, client, scope=scope) - except TypeError: - pass - else: - break - else: - obj = self.cls.from_uri(self.id, client, scope=scope) + obj = None + for cls in self.classes: + # this is inefficient, we should just get the data from the id, then get the correct type from the data + try: + obj = cls.from_uri(self.id, client, scope=scope) + except TypeError: + pass + else: + break if obj is None: - raise ResolutionFailure(f"Cannot resolve proxy object of type {self.cls} with id {self.uuid}") + raise ResolutionFailure(f"Cannot resolve proxy object of type {self.classes} with id {self.uuid}") object_cache[self.id] = obj if follow_links: return obj.resolve(client, scope=scope, use_cache=use_cache, follow_links=follow_links) diff --git a/fairgraph/node.py b/fairgraph/node.py index cb00fd0c..f7cf6331 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -21,7 +21,9 @@ from .utility import ( as_list, # temporary for backwards compatibility (a lot of code imports it from here) expand_uri, - invert_dict + invert_dict, + normalize_data, + types_match ) if TYPE_CHECKING: @@ -34,16 +36,15 @@ default_context = { "v3": { - "vocab": "https://openminds.ebrains.eu/vocab/", + "@vocab": "https://openminds.ebrains.eu/vocab/", }, "v4": { - "vocab": "https://openminds.om-i.org/props/" + "@vocab": "https://openminds.om-i.org/props/" } } class ContainsMetadata(Resolvable, metaclass=Node): # KGObject and EmbeddedMetadata - properties: List[Property] = [] reverse_properties: List[Property] = [] context: Dict[str, str] = default_context["v3"] type_: str @@ -90,7 +91,10 @@ def __init__(self, data: Optional[Dict] = None, **properties): self._raw_remote_data = data # for debugging self.remote_data = {} if data: - self.remote_data = self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False) + self.remote_data = normalize_data( + self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False), + self.context + ) def __getattribute__(self, name): try: @@ -241,27 +245,48 @@ def generate_query_filter_properties( @classmethod def _deserialize_data(cls, data: JSONdict, include_id: bool = False): - # check types match - if cls.type_ not in data["@type"]: - if types_match(cls.type_, data["@type"][0]): - cls.type_ = data["@type"][0] + + def _get_type_from_data(data_item): + # KG returns a list of types, openMINDS expects only a single string + if isinstance(data_item, dict) and "@type" in data_item: + if isinstance(data_item["@type"], list): + assert len(data_item["@type"]) == 1 + return data_item["@type"][0] + else: + return data_item["@type"] else: - raise TypeError("type mismatch {} - {}".format(cls.type_, data["@type"])) + return None + + def _normalize_type(data_item): + # replace @type as list with @type as string + if isinstance(data_item, (list, tuple)): + data_item = [_normalize_type(part) for part in data_item] + else: + type_from_data_item = _get_type_from_data(data_item) + if type_from_data_item: + data_item = data_item.copy() + data_item["@type"] = type_from_data_item + return data_item + + type_from_data = _get_type_from_data(data) + # check types match + if not types_match(cls.type_, type_from_data): + raise TypeError("type mismatch {} - {}".format(cls.type_, type_from_data)) + # normalize data by expanding keys - context = copy(cls.context) - if "om-i.org" in cls.type_: + if "om-i.org" in type_from_data: context = default_context["v4"] else: context = default_context["v3"] - D = {"@type": data["@type"]} + D = {"@type": type_from_data} if include_id: D["@id"] = data["@id"] for key, value in data.items(): if "__" in key: key, type_filter = key.split("__") normalised_key = expand_uri(key, context) - value = [item for item in as_list(value) if item["@type"][0].endswith(type_filter)] + value = [item for item in as_list(value) if _get_type_from_data(item).endswith(type_filter)] if normalised_key in D: D[normalised_key].extend(value) else: @@ -272,17 +297,11 @@ def _deserialize_data(cls, data: JSONdict, include_id: bool = False): normalised_key = expand_uri(key, context) D[normalised_key] = value - def _get_type_from_data(data_item): - type_ = data_item.get("@type", None) - if type_: - return type_[0] - else: - return None - deserialized_data = {} for prop in cls.all_properties: expanded_path = expand_uri(prop.path, context) - data_item = D.get(expanded_path) + data_item = _normalize_type(D.get(expanded_path)) + if data_item is not None and prop.reverse: # for reverse properties, more than one property can have the same path # so we extract only those sub-items whose types match @@ -295,21 +314,39 @@ def _get_type_from_data(data_item): # problem when a forward and reverse path both given the same expanded path # e.g. for Configuration data_item = None + # sometimes queries put single items in a list, this removes the enclosing list if (not prop.multiple) and isinstance(data_item, (list, tuple)) and len(data_item) == 1: data_item = data_item[0] + + # deal with property names that conflict with kwargs in fairgraph + prop_name = prop.name + if prop_name == "scope": + prop_name = "model_scope" + if data_item is None: if prop.reverse and "@id" in data: if isinstance(prop.reverse, list): # todo: handle all possible reverses # for now, we just take the first - deserialized_data[prop.name] = KGQuery(prop.types, {prop.reverse[0]: data["@id"]}) + deserialized_data[prop_name] = KGQuery(prop.types, {prop.reverse[0]: data["@id"]}) else: - deserialized_data[prop.name] = KGQuery(prop.types, {prop.reverse: data["@id"]}) + deserialized_data[prop_name] = KGQuery(prop.types, {prop.reverse: data["@id"]}) else: - deserialized_data[prop.name] = None + deserialized_data[prop_name] = None else: - deserialized_data[prop.name] = prop.deserialize(data_item) + try: + value = prop.deserialize(data_item) + except ValueError as err: + ErrorHandling.handle_violation(cls.error_handling, str(err)) + else: + if isinstance(value, Link) and value.allowed_types is not None: + value = KGProxy(value.allowed_types, value.identifier) + elif isinstance(value, list) and len(value) > 0 and isinstance(value[0], Link): + # here we assume that if the first item is a Link, they all are + value = [KGProxy(item.allowed_types, item.identifier) for item in value] + deserialized_data[prop_name] = value + return deserialized_data def resolve( diff --git a/fairgraph/queries.py b/fairgraph/queries.py index b8d64bcb..1c9be049 100644 --- a/fairgraph/queries.py +++ b/fairgraph/queries.py @@ -303,6 +303,7 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None """ expanded_path = expand_uri(property.path, {"@vocab": "https://openminds.ebrains.eu/vocab/"}) properties = [] + if any(issubclass(_type, EmbeddedMetadata) for _type in property.types): if not all(issubclass(_type, EmbeddedMetadata) for _type in property.types): warn(f"Mixed types in {property}") @@ -310,7 +311,8 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None for cls in property.types: if len(property.types) > 1: property_name = f"{property.path}__{cls.__name__}" - type_filter = cls.type_[0] + assert isinstance(cls.type_, str) + type_filter = cls.type_ else: property_name = property.path type_filter = None @@ -321,6 +323,7 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None reverse=property.reverse, type_filter=type_filter, ensure_order=property.multiple, + expect_single=property.is_link and not property.multiple, properties=cls.generate_query_properties(follow_links), ) ) @@ -331,7 +334,8 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None property_name = _get_query_property_name(property, possible_classes=[cls]) if len(property.types) > 1: property_name = f"{property_name}__{cls.__name__}" - type_filter = cls.type_[0] + assert isinstance(cls.type_, str) + type_filter = cls.type_ else: type_filter = None @@ -342,6 +346,7 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None reverse=property.reverse, type_filter=type_filter, ensure_order=property.multiple, + expect_single=property.is_link and not property.multiple, properties=[QueryProperty("@id"), *cls.generate_query_properties(follow_links)], ) ) @@ -355,6 +360,7 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None reverse=property.reverse, type_filter=None, ensure_order=property.multiple, + expect_single=property.is_link and not property.multiple, properties=[ QueryProperty("@id"), QueryProperty("@type"), @@ -372,6 +378,7 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None name=property.path, reverse=property.reverse, ensure_order=property.multiple, + expect_single=property.is_link and not property.multiple, ) ) return properties @@ -435,7 +442,7 @@ def is_valid(val): val = UUID(val) except ValueError: pass - return isinstance(val, (IRI, UUID, *property.types)) or (isinstance(val, KGProxy) and val.cls in property.types) + return isinstance(val, (IRI, UUID, *property.types)) or (isinstance(val, KGProxy) and not set(val.classes).isdisjoint(property.types)) if isinstance(value, list) and len(value) > 0: valid_type = all(is_valid(item) for item in value) diff --git a/fairgraph/registry.py b/fairgraph/registry.py index ad504fe2..5e323065 100644 --- a/fairgraph/registry.py +++ b/fairgraph/registry.py @@ -17,6 +17,16 @@ from .node import ContainsMetadata +docstring_template = """ +{base} + +Args +---- +{args} + +""" + + class Node(Registry): """Metaclass for registering Knowledge Graph classes.""" @@ -33,14 +43,43 @@ def __new__(meta, name, bases, class_dict): class_dict["class_name"] = ".".join( class_dict["__module__"].replace("fairgraph.openminds", "openminds.latest").split(".")[:3] + [name] ) + class_dict["preferred_import_path"] = class_dict["class_name"] cls = Registry.__new__(meta, name, bases, class_dict) cls._property_lookup = {prop.name: prop for prop in (cls.properties + cls.reverse_properties)} return cls + def _get_doc(cls) -> str: + """Dynamically generate docstrings""" + # todo: consider generating the docstring in the build pipeline, + # avoiding all this run-time messing about + field_docs = [] + if hasattr(cls, "properties"): + + def gen_path(type_): + if type_.__module__ == "builtins": + return type_.__name__ + else: + return "~{}.{}".format(type_.__module__, type_.__name__) + + for property in cls.all_properties: + doc = "{} : {}\n {}".format( + property.name, ", ".join(gen_path(t) for t in property.types), property.description + ) + # todo: add property.instructions if present + field_docs.append(doc) + # todo: also document id, data, space, scope + return docstring_template.format(base=cls._base_docstring, args="\n".join(field_docs)) + + __doc__ = property(_get_doc) # type: ignore[assignment] + @property def all_properties(cls): return chain(cls.properties, cls.reverse_properties) + @property + def reverse_property_names(cls): + return [p.name for p in cls.reverse_properties] + @property def fields(cls): warn( diff --git a/fairgraph/utility.py b/fairgraph/utility.py index 90679811..f2311975 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -198,19 +198,26 @@ def normalize_data(data: Union[None, JSONdict], context: Dict[str, Any]) -> Unio normalized: JSONdict = {} for key, value in data.items(): assert isinstance(key, str) - if key.startswith("Q"): + if key == "@context": + continue + elif key.startswith("Q"): expanded_key = key else: result = expand_uri(key, context) assert isinstance(result, str) # for type checking expanded_key = result assert expanded_key.startswith("http") or expanded_key.startswith("@") or expanded_key.startswith("Q") + if hasattr(value, "__len__") and len(value) == 0: pass elif value is None: pass - elif isinstance(value, (list, tuple)) and key != "@type": - # note that we special-case "@type" for now + elif expanded_key == "@type": + if isinstance(value, str): + # KG makes @type a list + value = [value] + normalized[expanded_key] = value + elif isinstance(value, (list, tuple)): normalized[expanded_key] = [] for item in value: if isinstance(item, dict): @@ -219,7 +226,7 @@ def normalize_data(data: Union[None, JSONdict], context: Dict[str, Any]) -> Unio normalized[expanded_key].append(item) if len(value) == 1: normalized[expanded_key] = normalized[expanded_key][0] - elif isinstance(value, dict) and expanded_key != "@context": + elif isinstance(value, dict): normalized[expanded_key] = normalize_data(value, context) else: normalized[expanded_key] = value diff --git a/test/test_base.py b/test/test_base.py index 75ee94ae..119825ef 100644 --- a/test/test_base.py +++ b/test/test_base.py @@ -487,16 +487,12 @@ def test_modified_data(self): "https://openminds.ebrains.eu/vocab/aRequiredString": "pomme", "https://openminds.ebrains.eu/vocab/anOptionalListOfEmbeddedObjects": [ { - "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aDate": None, + "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], "https://openminds.ebrains.eu/vocab/aNumber": -18, - "https://openminds.ebrains.eu/vocab/aString": None, }, { - "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aDate": None, + "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], "https://openminds.ebrains.eu/vocab/aNumber": 19, - "https://openminds.ebrains.eu/vocab/aString": None, }, ], } @@ -646,19 +642,19 @@ class TestKGProxy: def test_initialization_with_class(self): uri = "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000001234" proxy = KGProxy(MockKGObject, uri) - assert proxy.cls is MockKGObject + assert proxy.classes[0] is MockKGObject assert proxy.id == uri def test_initialization_with_string(self): uri = "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000001234" proxy = KGProxy("test.test_base.MockKGObject", uri) - assert proxy.cls is MockKGObject + assert proxy.classes[0] is MockKGObject assert proxy.id == uri def test_properties(self): uri = "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000001234" proxy = KGProxy(MockKGObject, uri) - assert proxy.type == "https://openminds.ebrains.eu/mock/MockKGObject" + assert proxy.type == ["https://openminds.ebrains.eu/mock/MockKGObject"] assert proxy.classes == [MockKGObject] assert proxy.uuid == "00000000-0000-0000-0000-000000001234" diff --git a/test/test_client.py b/test/test_client.py index 60dea174..8515933b 100644 --- a/test/test_client.py +++ b/test/test_client.py @@ -54,19 +54,19 @@ def test_query_filter_by_space(kg_client): ), QueryProperty( "https://openminds.ebrains.eu/vocab/fullName", - name="vocab:fullName", + name="fullName", filter=Filter("CONTAINS", parameter="name"), sorted=True, required=True, ), QueryProperty( "https://openminds.ebrains.eu/vocab/custodian", - name="vocab:custodian", + name="custodian", type_filter="https://openminds.ebrains.eu/core/Person", properties=[ QueryProperty( "https://openminds.ebrains.eu/vocab/familyName", - name="vocab:familyName", + name="familyName", ), ], ), diff --git a/test/test_data/queries/openminds/core/accountinformation_simple_query.json b/test/test_data/queries/openminds/core/accountinformation_simple_query.json index f7097c04..fdef1e90 100644 --- a/test/test_data/queries/openminds/core/accountinformation_simple_query.json +++ b/test/test_data/queries/openminds/core/accountinformation_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/service", - "propertyName": "vocab:service", + "propertyName": "service", "structure": [ { "path": "@id" @@ -48,18 +48,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/userName", - "propertyName": "vocab:userName" + "propertyName": "userName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/associatedAccount", "reverse": true }, - "propertyName": "vocab:associatedAccount", + "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json b/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json index dd92bdf3..048c90ad 100644 --- a/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json +++ b/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/describedIn", - "propertyName": "vocab:describedIn", + "propertyName": "describedIn", "ensureOrder": true, "structure": [ { @@ -53,20 +53,20 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/stimulation", - "propertyName": "vocab:stimulation", + "propertyName": "stimulation", "ensureOrder": true, "structure": [ { @@ -79,7 +79,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/stimulusType", - "propertyName": "vocab:stimulusType", + "propertyName": "stimulusType", "ensureOrder": true, "structure": [ { @@ -95,7 +95,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -111,7 +111,7 @@ "@id": "https://openminds.ebrains.eu/vocab/behavioralProtocol", "reverse": true }, - "propertyName": "vocab:behavioralProtocol", + "propertyName": "behavioralProtocol", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/comment_simple_query.json b/test/test_data/queries/openminds/core/comment_simple_query.json index 40085385..31faf675 100644 --- a/test/test_data/queries/openminds/core/comment_simple_query.json +++ b/test/test_data/queries/openminds/core/comment_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/about", - "propertyName": "vocab:about", + "propertyName": "about", "structure": [ { "path": "@id" @@ -48,15 +48,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/comment", - "propertyName": "vocab:comment" + "propertyName": "comment" }, { "path": "https://openminds.ebrains.eu/vocab/commenter", - "propertyName": "vocab:commenter", + "propertyName": "commenter", "structure": [ { "path": "@id" @@ -64,11 +65,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/timestamp", - "propertyName": "vocab:timestamp" + "propertyName": "timestamp" } ] } \ No newline at end of file diff --git a/test/test_data/queries/openminds/core/configuration_simple_query.json b/test/test_data/queries/openminds/core/configuration_simple_query.json index ed031fe3..92e453d7 100644 --- a/test/test_data/queries/openminds/core/configuration_simple_query.json +++ b/test/test_data/queries/openminds/core/configuration_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/configuration", - "propertyName": "vocab:configuration" + "propertyName": "configuration" }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ { "path": "@id" @@ -52,11 +52,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { @@ -64,7 +65,7 @@ "@id": "https://openminds.ebrains.eu/vocab/configuration", "reverse": true }, - "propertyName": "vocab:configuration", + "propertyName": "configuration", "ensureOrder": true, "structure": [ { @@ -80,7 +81,7 @@ "@id": "https://openminds.ebrains.eu/vocab/specification", "reverse": true }, - "propertyName": "vocab:specification", + "propertyName": "specification", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/consortium_simple_query.json b/test/test_data/queries/openminds/core/consortium_simple_query.json index 1d9dd4d0..ec5fab28 100644 --- a/test/test_data/queries/openminds/core/consortium_simple_query.json +++ b/test/test_data/queries/openminds/core/consortium_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -48,27 +48,28 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -84,7 +85,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -100,7 +101,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -116,7 +117,7 @@ "@id": "https://openminds.ebrains.eu/vocab/memberOf", "reverse": true }, - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "ensureOrder": true, "structure": [ { @@ -124,11 +125,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -136,11 +137,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -149,7 +151,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -165,7 +167,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -181,7 +183,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -197,7 +199,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -213,7 +215,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/contactinformation_simple_query.json b/test/test_data/queries/openminds/core/contactinformation_simple_query.json index 3559e8f9..6c96b297 100644 --- a/test/test_data/queries/openminds/core/contactinformation_simple_query.json +++ b/test/test_data/queries/openminds/core/contactinformation_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/email", - "propertyName": "vocab:email" + "propertyName": "email" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/contactInformation", "reverse": true }, - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/contenttype_simple_query.json b/test/test_data/queries/openminds/core/contenttype_simple_query.json index f21c85b7..cc7ba6a1 100644 --- a/test/test_data/queries/openminds/core/contenttype_simple_query.json +++ b/test/test_data/queries/openminds/core/contenttype_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/dataType", - "propertyName": "vocab:dataType", + "propertyName": "dataType", "ensureOrder": true, "structure": [ { @@ -53,33 +53,33 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/displayLabel", - "propertyName": "vocab:displayLabel" + "propertyName": "displayLabel" }, { "path": "https://openminds.ebrains.eu/vocab/fileExtension", - "propertyName": "vocab:fileExtension", + "propertyName": "fileExtension", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/relatedMediaType", - "propertyName": "vocab:relatedMediaType" + "propertyName": "relatedMediaType" }, { "path": "https://openminds.ebrains.eu/vocab/specification", - "propertyName": "vocab:specification" + "propertyName": "specification" }, { "path": "https://openminds.ebrains.eu/vocab/synonym", - "propertyName": "vocab:synonym", + "propertyName": "synonym", "ensureOrder": true }, { @@ -87,7 +87,7 @@ "@id": "https://openminds.ebrains.eu/vocab/contentType", "reverse": true }, - "propertyName": "vocab:contentType", + "propertyName": "contentType", "ensureOrder": true, "structure": [ { @@ -103,7 +103,7 @@ "@id": "https://openminds.ebrains.eu/vocab/format", "reverse": true }, - "propertyName": "vocab:format", + "propertyName": "format", "ensureOrder": true, "structure": [ { @@ -119,7 +119,7 @@ "@id": "https://openminds.ebrains.eu/vocab/outputFormat", "reverse": true }, - "propertyName": "vocab:outputFormat", + "propertyName": "outputFormat", "ensureOrder": true, "structure": [ { @@ -135,7 +135,7 @@ "@id": "https://openminds.ebrains.eu/vocab/specificationFormat", "reverse": true }, - "propertyName": "vocab:specificationFormat", + "propertyName": "specificationFormat", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json b/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json index 0cd6dbcf..60cf2e8d 100644 --- a/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json +++ b/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contentType", - "propertyName": "vocab:contentType", + "propertyName": "contentType", "structure": [ { "path": "@id" @@ -48,23 +48,24 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/regex", - "propertyName": "vocab:regex" + "propertyName": "regex" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/contentTypePattern", "reverse": true }, - "propertyName": "vocab:contentTypePattern", + "propertyName": "contentTypePattern", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/dataset_simple_query.json b/test/test_data/queries/openminds/core/dataset_simple_query.json index b5d1faed..08f5a4be 100644 --- a/test/test_data/queries/openminds/core/dataset_simple_query.json +++ b/test/test_data/queries/openminds/core/dataset_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/author", - "propertyName": "vocab:author", + "propertyName": "author", "ensureOrder": true, "structure": [ { @@ -53,7 +53,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -66,11 +66,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -78,16 +78,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/hasVersion", - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -100,22 +101,22 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -131,7 +132,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -147,7 +148,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/dataset_simple_query_v4.json b/test/test_data/queries/openminds/core/dataset_simple_query_v4.json index 1350b946..2174c2b5 100644 --- a/test/test_data/queries/openminds/core/dataset_simple_query_v4.json +++ b/test/test_data/queries/openminds/core/dataset_simple_query_v4.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.om-i.org/props/author", - "propertyName": "vocab:author", + "propertyName": "author", "ensureOrder": true, "structure": [ { @@ -53,7 +53,7 @@ }, { "path": "https://openminds.om-i.org/props/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -66,11 +66,12 @@ }, { "path": "https://openminds.om-i.org/props/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.om-i.org/props/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", + "singleValue": "FIRST", "structure": [ { "path": "@id" @@ -82,12 +83,12 @@ }, { "path": "https://openminds.om-i.org/props/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.om-i.org/props/hasVersion", - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -100,22 +101,22 @@ }, { "path": "https://openminds.om-i.org/props/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.om-i.org/props/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.om-i.org/props/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.om-i.org/props/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -131,7 +132,7 @@ "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -147,7 +148,7 @@ "@id": "https://openminds.om-i.org/props/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/datasetversion_simple_query.json b/test/test_data/queries/openminds/core/datasetversion_simple_query.json index 105fbe31..17e55b11 100644 --- a/test/test_data/queries/openminds/core/datasetversion_simple_query.json +++ b/test/test_data/queries/openminds/core/datasetversion_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/accessibility", - "propertyName": "vocab:accessibility", + "propertyName": "accessibility", "structure": [ { "path": "@id" @@ -48,11 +48,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/author", - "propertyName": "vocab:author", + "propertyName": "author", "ensureOrder": true, "structure": [ { @@ -65,7 +66,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/behavioralProtocol", - "propertyName": "vocab:behavioralProtocol", + "propertyName": "behavioralProtocol", "ensureOrder": true, "structure": [ { @@ -78,14 +79,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/copyright", - "propertyName": "vocab:copyright", + "propertyName": "copyright", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/holder", - "propertyName": "vocab:holder", + "propertyName": "holder", "ensureOrder": true, "structure": [ { @@ -98,14 +99,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/year", - "propertyName": "vocab:year", + "propertyName": "year", "ensureOrder": true } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -118,7 +120,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/dataType", - "propertyName": "vocab:dataType", + "propertyName": "dataType", "ensureOrder": true, "structure": [ { @@ -131,11 +133,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -143,11 +145,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/ethicsAssessment", - "propertyName": "vocab:ethicsAssessment", + "propertyName": "ethicsAssessment", "structure": [ { "path": "@id" @@ -155,11 +158,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/experimentalApproach", - "propertyName": "vocab:experimentalApproach", + "propertyName": "experimentalApproach", "ensureOrder": true, "structure": [ { @@ -172,7 +176,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", - "propertyName": "vocab:fullDocumentation", + "propertyName": "fullDocumentation", "structure": [ { "path": "@id" @@ -180,16 +184,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/funding", - "propertyName": "vocab:funding", + "propertyName": "funding", "ensureOrder": true, "structure": [ { @@ -202,15 +207,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/inputData", - "propertyName": "vocab:inputData", + "propertyName": "inputData", "ensureOrder": true, "structure": [ { @@ -223,7 +228,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", - "propertyName": "vocab:isAlternativeVersionOf", + "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ { @@ -236,7 +241,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "structure": [ { "path": "@id" @@ -244,11 +249,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/keyword", - "propertyName": "vocab:keyword", + "propertyName": "keyword", "ensureOrder": true, "structure": [ { @@ -261,7 +267,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/license", - "propertyName": "vocab:license", + "propertyName": "license", "structure": [ { "path": "@id" @@ -269,11 +275,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/otherContribution", - "propertyName": "vocab:otherContribution", + "propertyName": "otherContribution", "ensureOrder": true, "structure": [ { @@ -281,7 +288,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contributor", - "propertyName": "vocab:contributor", + "propertyName": "contributor", "structure": [ { "path": "@id" @@ -289,11 +296,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "ensureOrder": true, "structure": [ { @@ -308,7 +316,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/preparationDesign", - "propertyName": "vocab:preparationDesign", + "propertyName": "preparationDesign", "ensureOrder": true, "structure": [ { @@ -321,7 +329,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/protocol", - "propertyName": "vocab:protocol", + "propertyName": "protocol", "ensureOrder": true, "structure": [ { @@ -334,7 +342,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/relatedPublication", - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { @@ -347,11 +355,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/releaseDate", - "propertyName": "vocab:releaseDate" + "propertyName": "releaseDate" }, { "path": "https://openminds.ebrains.eu/vocab/repository", - "propertyName": "vocab:repository", + "propertyName": "repository", "structure": [ { "path": "@id" @@ -359,15 +367,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/studiedSpecimen", - "propertyName": "vocab:studiedSpecimen", + "propertyName": "studiedSpecimen", "ensureOrder": true, "structure": [ { @@ -380,7 +389,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/studyTarget", - "propertyName": "vocab:studyTarget", + "propertyName": "studyTarget", "ensureOrder": true, "structure": [ { @@ -393,12 +402,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/supportChannel", - "propertyName": "vocab:supportChannel", + "propertyName": "supportChannel", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/technique", - "propertyName": "vocab:technique", + "propertyName": "technique", "ensureOrder": true, "structure": [ { @@ -411,18 +420,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", - "propertyName": "vocab:versionIdentifier" + "propertyName": "versionIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/versionInnovation", - "propertyName": "vocab:versionInnovation" + "propertyName": "versionInnovation" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -438,7 +447,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isPartOf", "reverse": true }, - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { @@ -454,7 +463,7 @@ "@id": "https://openminds.ebrains.eu/vocab/input", "reverse": true }, - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -470,7 +479,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", "reverse": true }, - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "ensureOrder": true, "structure": [ { @@ -486,7 +495,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -502,7 +511,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasVersion", "reverse": true }, - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -518,7 +527,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -534,7 +543,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/doi_simple_query.json b/test/test_data/queries/openminds/core/doi_simple_query.json index 6ff55a4e..fca0fc36 100644 --- a/test/test_data/queries/openminds/core/doi_simple_query.json +++ b/test/test_data/queries/openminds/core/doi_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/describedIn", "reverse": true }, - "propertyName": "vocab:describedIn", + "propertyName": "describedIn", "ensureOrder": true, "structure": [ { @@ -63,7 +63,7 @@ "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -79,7 +79,7 @@ "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", "reverse": true }, - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/experimentalactivity_simple_query.json b/test/test_data/queries/openminds/core/experimentalactivity_simple_query.json index d484b19b..ce102988 100644 --- a/test/test_data/queries/openminds/core/experimentalactivity_simple_query.json +++ b/test/test_data/queries/openminds/core/experimentalactivity_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel" + "propertyName": "lookupLabel" }, { "path": "https://openminds.ebrains.eu/vocab/customPropertySet", - "propertyName": "vocab:customPropertySet", + "propertyName": "customPropertySet", "filter": { "op": "CONTAINS", "parameter": "custom_property_sets" @@ -56,11 +56,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/context", - "propertyName": "vocab:context" + "propertyName": "context" }, { "path": "https://openminds.ebrains.eu/vocab/definedIn", - "propertyName": "vocab:definedIn", + "propertyName": "definedIn", "structure": [ { "path": "@id" @@ -72,7 +72,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/relevantFor", - "propertyName": "vocab:relevantFor", + "propertyName": "relevantFor", "structure": [ { "path": "@id" @@ -86,15 +86,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/endedAtTime", - "propertyName": "vocab:endedAtTime" + "propertyName": "endedAtTime" }, { "path": "https://openminds.ebrains.eu/vocab/input", - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -107,7 +107,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isPartOf", - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "structure": [ { "path": "@id" @@ -119,7 +119,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/output", - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { @@ -132,7 +132,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/performedBy", - "propertyName": "vocab:performedBy", + "propertyName": "performedBy", "ensureOrder": true, "structure": [ { @@ -145,7 +145,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/preparationDesign", - "propertyName": "vocab:preparationDesign", + "propertyName": "preparationDesign", "structure": [ { "path": "@id" @@ -157,7 +157,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/protocol", - "propertyName": "vocab:protocol", + "propertyName": "protocol", "ensureOrder": true, "structure": [ { @@ -170,11 +170,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/startedAtTime", - "propertyName": "vocab:startedAtTime" + "propertyName": "startedAtTime" }, { "path": "https://openminds.ebrains.eu/vocab/studyTarget", - "propertyName": "vocab:studyTarget", + "propertyName": "studyTarget", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/file_simple_query.json b/test/test_data/queries/openminds/core/file_simple_query.json index d708214b..39ce1045 100644 --- a/test/test_data/queries/openminds/core/file_simple_query.json +++ b/test/test_data/queries/openminds/core/file_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contentDescription", - "propertyName": "vocab:contentDescription" + "propertyName": "contentDescription" }, { "path": "https://openminds.ebrains.eu/vocab/dataType", - "propertyName": "vocab:dataType", + "propertyName": "dataType", "ensureOrder": true, "structure": [ { @@ -57,7 +57,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fileRepository", - "propertyName": "vocab:fileRepository", + "propertyName": "fileRepository", "structure": [ { "path": "@id" @@ -65,11 +65,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ { "path": "@id" @@ -77,11 +78,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/hash", - "propertyName": "vocab:hash", + "propertyName": "hash", "ensureOrder": true, "structure": [ { @@ -89,21 +91,21 @@ }, { "path": "https://openminds.ebrains.eu/vocab/algorithm", - "propertyName": "vocab:algorithm" + "propertyName": "algorithm" }, { "path": "https://openminds.ebrains.eu/vocab/digest", - "propertyName": "vocab:digest" + "propertyName": "digest" } ] }, { "path": "https://openminds.ebrains.eu/vocab/IRI", - "propertyName": "vocab:IRI" + "propertyName": "IRI" }, { "path": "https://openminds.ebrains.eu/vocab/isPartOf", - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { @@ -116,12 +118,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/specialUsageRole", - "propertyName": "vocab:specialUsageRole", + "propertyName": "specialUsageRole", "structure": [ { "path": "@id" @@ -129,18 +131,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/storageSize", - "propertyName": "vocab:storageSize", + "propertyName": "storageSize", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -148,16 +151,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -165,20 +169,22 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/fullDocumentation", "reverse": true }, - "propertyName": "vocab:fullDocumentation", + "propertyName": "fullDocumentation", "ensureOrder": true, "structure": [ { @@ -194,7 +200,7 @@ "@id": "https://openminds.ebrains.eu/vocab/copyOf", "reverse": true }, - "propertyName": "vocab:copyOf", + "propertyName": "copyOf", "ensureOrder": true, "structure": [ { @@ -210,7 +216,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -226,7 +232,7 @@ "@id": "https://openminds.ebrains.eu/vocab/configuration", "reverse": true }, - "propertyName": "vocab:configuration", + "propertyName": "configuration", "ensureOrder": true, "structure": [ { @@ -242,7 +248,7 @@ "@id": "https://openminds.ebrains.eu/vocab/defaultImage", "reverse": true }, - "propertyName": "vocab:defaultImage", + "propertyName": "defaultImage", "ensureOrder": true, "structure": [ { @@ -258,7 +264,7 @@ "@id": "https://openminds.ebrains.eu/vocab/inputData", "reverse": true }, - "propertyName": "vocab:inputData", + "propertyName": "inputData", "ensureOrder": true, "structure": [ { @@ -274,7 +280,7 @@ "@id": "https://openminds.ebrains.eu/vocab/previewImage", "reverse": true }, - "propertyName": "vocab:previewImage", + "propertyName": "previewImage", "ensureOrder": true, "structure": [ { @@ -290,7 +296,7 @@ "@id": "https://openminds.ebrains.eu/vocab/referenceData", "reverse": true }, - "propertyName": "vocab:referenceData", + "propertyName": "referenceData", "ensureOrder": true, "structure": [ { @@ -306,7 +312,7 @@ "@id": "https://openminds.ebrains.eu/vocab/sourceData", "reverse": true }, - "propertyName": "vocab:sourceData", + "propertyName": "sourceData", "ensureOrder": true, "structure": [ { @@ -322,7 +328,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/filearchive_simple_query.json b/test/test_data/queries/openminds/core/filearchive_simple_query.json index d6ac9e9d..aa16ef7f 100644 --- a/test/test_data/queries/openminds/core/filearchive_simple_query.json +++ b/test/test_data/queries/openminds/core/filearchive_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ { "path": "@id" @@ -48,15 +48,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/IRI", - "propertyName": "vocab:IRI" + "propertyName": "IRI" }, { "path": "https://openminds.ebrains.eu/vocab/sourceData", - "propertyName": "vocab:sourceData", + "propertyName": "sourceData", "ensureOrder": true, "structure": [ { @@ -72,7 +73,7 @@ "@id": "https://openminds.ebrains.eu/vocab/dataLocation", "reverse": true }, - "propertyName": "vocab:dataLocation", + "propertyName": "dataLocation", "ensureOrder": true, "structure": [ { @@ -88,7 +89,7 @@ "@id": "https://openminds.ebrains.eu/vocab/output", "reverse": true }, - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/filebundle_simple_query.json b/test/test_data/queries/openminds/core/filebundle_simple_query.json index 5bc92186..d902c0c3 100644 --- a/test/test_data/queries/openminds/core/filebundle_simple_query.json +++ b/test/test_data/queries/openminds/core/filebundle_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contentDescription", - "propertyName": "vocab:contentDescription" + "propertyName": "contentDescription" }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ { "path": "@id" @@ -52,11 +52,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/groupedBy", - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -69,7 +70,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/groupingType", - "propertyName": "vocab:groupingType", + "propertyName": "groupingType", "ensureOrder": true, "structure": [ { @@ -82,24 +83,25 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hash", - "propertyName": "vocab:hash", + "propertyName": "hash", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/algorithm", - "propertyName": "vocab:algorithm" + "propertyName": "algorithm" }, { "path": "https://openminds.ebrains.eu/vocab/digest", - "propertyName": "vocab:digest" + "propertyName": "digest" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/isPartOf", - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "structure": [ { "path": "@id" @@ -107,23 +109,24 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/storageSize", - "propertyName": "vocab:storageSize", + "propertyName": "storageSize", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -131,16 +134,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -148,20 +152,22 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/metadataLocation", "reverse": true }, - "propertyName": "vocab:metadataLocation", + "propertyName": "metadataLocation", "ensureOrder": true, "structure": [ { @@ -177,7 +183,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isPartOf", "reverse": true }, - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { @@ -193,7 +199,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -209,7 +215,7 @@ "@id": "https://openminds.ebrains.eu/vocab/inputData", "reverse": true }, - "propertyName": "vocab:inputData", + "propertyName": "inputData", "ensureOrder": true, "structure": [ { @@ -225,7 +231,7 @@ "@id": "https://openminds.ebrains.eu/vocab/dataLocation", "reverse": true }, - "propertyName": "vocab:dataLocation", + "propertyName": "dataLocation", "ensureOrder": true, "structure": [ { @@ -241,7 +247,7 @@ "@id": "https://openminds.ebrains.eu/vocab/referenceData", "reverse": true }, - "propertyName": "vocab:referenceData", + "propertyName": "referenceData", "ensureOrder": true, "structure": [ { @@ -257,7 +263,7 @@ "@id": "https://openminds.ebrains.eu/vocab/specification", "reverse": true }, - "propertyName": "vocab:specification", + "propertyName": "specification", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/filerepository_simple_query.json b/test/test_data/queries/openminds/core/filerepository_simple_query.json index daa14666..44f5d7ff 100644 --- a/test/test_data/queries/openminds/core/filerepository_simple_query.json +++ b/test/test_data/queries/openminds/core/filerepository_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contentTypePattern", - "propertyName": "vocab:contentTypePattern", + "propertyName": "contentTypePattern", "ensureOrder": true, "structure": [ { @@ -53,7 +53,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ { "path": "@id" @@ -61,28 +61,30 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/hash", - "propertyName": "vocab:hash", + "propertyName": "hash", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/algorithm", - "propertyName": "vocab:algorithm" + "propertyName": "algorithm" }, { "path": "https://openminds.ebrains.eu/vocab/digest", - "propertyName": "vocab:digest" + "propertyName": "digest" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/hostedBy", - "propertyName": "vocab:hostedBy", + "propertyName": "hostedBy", "structure": [ { "path": "@id" @@ -90,27 +92,28 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/IRI", - "propertyName": "vocab:IRI" + "propertyName": "IRI" }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/storageSize", - "propertyName": "vocab:storageSize", + "propertyName": "storageSize", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -118,16 +121,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -135,17 +139,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/structurePattern", - "propertyName": "vocab:structurePattern", + "propertyName": "structurePattern", "structure": [ { "path": "@id" @@ -153,11 +159,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "structure": [ { "path": "@id" @@ -165,14 +172,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/repository", "reverse": true }, - "propertyName": "vocab:repository", + "propertyName": "repository", "ensureOrder": true, "structure": [ { @@ -188,7 +196,7 @@ "@id": "https://openminds.ebrains.eu/vocab/fileRepository", "reverse": true }, - "propertyName": "vocab:fileRepository", + "propertyName": "fileRepository", "ensureOrder": true, "structure": [ { @@ -204,7 +212,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isPartOf", "reverse": true }, - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json b/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json index 41236e9c..59b619e3 100644 --- a/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json +++ b/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/filePathPattern", - "propertyName": "vocab:filePathPattern", + "propertyName": "filePathPattern", "ensureOrder": true, "structure": [ { @@ -48,7 +48,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/groupingType", - "propertyName": "vocab:groupingType", + "propertyName": "groupingType", "ensureOrder": true, "structure": [ { @@ -61,13 +61,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/regex", - "propertyName": "vocab:regex" + "propertyName": "regex" } ] }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { @@ -75,7 +75,7 @@ "@id": "https://openminds.ebrains.eu/vocab/structurePattern", "reverse": true }, - "propertyName": "vocab:structurePattern", + "propertyName": "structurePattern", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/funding_simple_query.json b/test/test_data/queries/openminds/core/funding_simple_query.json index 3690dccd..035671df 100644 --- a/test/test_data/queries/openminds/core/funding_simple_query.json +++ b/test/test_data/queries/openminds/core/funding_simple_query.json @@ -40,19 +40,19 @@ }, { "path": "https://openminds.ebrains.eu/vocab/acknowledgement", - "propertyName": "vocab:acknowledgement" + "propertyName": "acknowledgement" }, { "path": "https://openminds.ebrains.eu/vocab/awardNumber", - "propertyName": "vocab:awardNumber" + "propertyName": "awardNumber" }, { "path": "https://openminds.ebrains.eu/vocab/awardTitle", - "propertyName": "vocab:awardTitle" + "propertyName": "awardTitle" }, { "path": "https://openminds.ebrains.eu/vocab/funder", - "propertyName": "vocab:funder", + "propertyName": "funder", "structure": [ { "path": "@id" @@ -60,14 +60,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/funding", "reverse": true }, - "propertyName": "vocab:funding", + "propertyName": "funding", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/gridid_simple_query.json b/test/test_data/queries/openminds/core/gridid_simple_query.json index ca7c2995..42919def 100644 --- a/test/test_data/queries/openminds/core/gridid_simple_query.json +++ b/test/test_data/queries/openminds/core/gridid_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/handle_simple_query.json b/test/test_data/queries/openminds/core/handle_simple_query.json index 991f3fd1..82aa4d13 100644 --- a/test/test_data/queries/openminds/core/handle_simple_query.json +++ b/test/test_data/queries/openminds/core/handle_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", "reverse": true }, - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json b/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json index 9499f7e4..bac1a184 100644 --- a/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json +++ b/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/isbn_simple_query.json b/test/test_data/queries/openminds/core/isbn_simple_query.json index 5d09aaf0..d56b3024 100644 --- a/test/test_data/queries/openminds/core/isbn_simple_query.json +++ b/test/test_data/queries/openminds/core/isbn_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/citedPublication", "reverse": true }, - "propertyName": "vocab:citedPublication", + "propertyName": "citedPublication", "ensureOrder": true, "structure": [ { @@ -63,7 +63,7 @@ "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -79,7 +79,7 @@ "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", "reverse": true }, - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/issn_simple_query.json b/test/test_data/queries/openminds/core/issn_simple_query.json index 0e809500..43922e23 100644 --- a/test/test_data/queries/openminds/core/issn_simple_query.json +++ b/test/test_data/queries/openminds/core/issn_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -63,7 +63,7 @@ "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", "reverse": true }, - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/license_simple_query.json b/test/test_data/queries/openminds/core/license_simple_query.json index bbd033bf..1bb1fd0a 100644 --- a/test/test_data/queries/openminds/core/license_simple_query.json +++ b/test/test_data/queries/openminds/core/license_simple_query.json @@ -40,20 +40,20 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/legalCode", - "propertyName": "vocab:legalCode" + "propertyName": "legalCode" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/webpage", - "propertyName": "vocab:webpage", + "propertyName": "webpage", "ensureOrder": true }, { @@ -61,7 +61,7 @@ "@id": "https://openminds.ebrains.eu/vocab/license", "reverse": true }, - "propertyName": "vocab:license", + "propertyName": "license", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/metadatamodel_simple_query.json b/test/test_data/queries/openminds/core/metadatamodel_simple_query.json index e494eb3d..73276d87 100644 --- a/test/test_data/queries/openminds/core/metadatamodel_simple_query.json +++ b/test/test_data/queries/openminds/core/metadatamodel_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -53,11 +53,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -70,7 +70,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -78,16 +78,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/hasVersion", - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -100,22 +101,22 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -131,7 +132,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -147,7 +148,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json b/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json index 76ac65f2..ba4c03ad 100644 --- a/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json +++ b/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/accessibility", - "propertyName": "vocab:accessibility", + "propertyName": "accessibility", "structure": [ { "path": "@id" @@ -48,18 +48,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/copyright", - "propertyName": "vocab:copyright", + "propertyName": "copyright", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/holder", - "propertyName": "vocab:holder", + "propertyName": "holder", "ensureOrder": true, "structure": [ { @@ -72,14 +73,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/year", - "propertyName": "vocab:year", + "propertyName": "year", "ensureOrder": true } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -92,11 +94,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -109,7 +111,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -117,11 +119,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", - "propertyName": "vocab:fullDocumentation", + "propertyName": "fullDocumentation", "structure": [ { "path": "@id" @@ -129,16 +132,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/funding", - "propertyName": "vocab:funding", + "propertyName": "funding", "ensureOrder": true, "structure": [ { @@ -151,15 +155,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", - "propertyName": "vocab:isAlternativeVersionOf", + "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ { @@ -172,7 +176,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "structure": [ { "path": "@id" @@ -180,11 +184,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/keyword", - "propertyName": "vocab:keyword", + "propertyName": "keyword", "ensureOrder": true, "structure": [ { @@ -197,7 +202,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/license", - "propertyName": "vocab:license", + "propertyName": "license", "structure": [ { "path": "@id" @@ -205,11 +210,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/otherContribution", - "propertyName": "vocab:otherContribution", + "propertyName": "otherContribution", "ensureOrder": true, "structure": [ { @@ -217,7 +223,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contributor", - "propertyName": "vocab:contributor", + "propertyName": "contributor", "structure": [ { "path": "@id" @@ -225,11 +231,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "ensureOrder": true, "structure": [ { @@ -244,7 +251,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/relatedPublication", - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { @@ -257,11 +264,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/releaseDate", - "propertyName": "vocab:releaseDate" + "propertyName": "releaseDate" }, { "path": "https://openminds.ebrains.eu/vocab/repository", - "propertyName": "vocab:repository", + "propertyName": "repository", "structure": [ { "path": "@id" @@ -269,11 +276,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/serializationFormat", - "propertyName": "vocab:serializationFormat", + "propertyName": "serializationFormat", "ensureOrder": true, "structure": [ { @@ -286,11 +294,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/specificationFormat", - "propertyName": "vocab:specificationFormat", + "propertyName": "specificationFormat", "ensureOrder": true, "structure": [ { @@ -303,12 +311,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/supportChannel", - "propertyName": "vocab:supportChannel", + "propertyName": "supportChannel", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "structure": [ { "path": "@id" @@ -316,22 +324,23 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", - "propertyName": "vocab:versionIdentifier" + "propertyName": "versionIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/versionInnovation", - "propertyName": "vocab:versionInnovation" + "propertyName": "versionInnovation" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -347,7 +356,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", "reverse": true }, - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "ensureOrder": true, "structure": [ { @@ -363,7 +372,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -379,7 +388,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasVersion", "reverse": true }, - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -395,7 +404,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/model_simple_query.json b/test/test_data/queries/openminds/core/model_simple_query.json index 9edb6bf4..6dad9d6a 100644 --- a/test/test_data/queries/openminds/core/model_simple_query.json +++ b/test/test_data/queries/openminds/core/model_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/abstractionLevel", - "propertyName": "vocab:abstractionLevel", + "propertyName": "abstractionLevel", "structure": [ { "path": "@id" @@ -48,11 +48,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -65,11 +66,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -82,7 +83,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -90,16 +91,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/hasVersion", - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -112,15 +114,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/scope", - "propertyName": "vocab:scope", + "propertyName": "scope", "structure": [ { "path": "@id" @@ -128,15 +130,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/studyTarget", - "propertyName": "vocab:studyTarget", + "propertyName": "studyTarget", "ensureOrder": true, "structure": [ { @@ -152,7 +155,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -168,7 +171,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -184,7 +187,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/modelversion_simple_query.json b/test/test_data/queries/openminds/core/modelversion_simple_query.json index fa6562bb..63380f4b 100644 --- a/test/test_data/queries/openminds/core/modelversion_simple_query.json +++ b/test/test_data/queries/openminds/core/modelversion_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/accessibility", - "propertyName": "vocab:accessibility", + "propertyName": "accessibility", "structure": [ { "path": "@id" @@ -48,11 +48,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/configuration", - "propertyName": "vocab:configuration", + "propertyName": "configuration", "structure": [ { "path": "@id" @@ -60,18 +61,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/copyright", - "propertyName": "vocab:copyright", + "propertyName": "copyright", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/holder", - "propertyName": "vocab:holder", + "propertyName": "holder", "ensureOrder": true, "structure": [ { @@ -84,14 +86,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/year", - "propertyName": "vocab:year", + "propertyName": "year", "ensureOrder": true } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -104,11 +107,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -121,7 +124,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -129,15 +132,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/entryPoint", - "propertyName": "vocab:entryPoint" + "propertyName": "entryPoint" }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "ensureOrder": true, "structure": [ { @@ -150,7 +154,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", - "propertyName": "vocab:fullDocumentation", + "propertyName": "fullDocumentation", "structure": [ { "path": "@id" @@ -158,16 +162,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/funding", - "propertyName": "vocab:funding", + "propertyName": "funding", "ensureOrder": true, "structure": [ { @@ -180,15 +185,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/inputData", - "propertyName": "vocab:inputData", + "propertyName": "inputData", "ensureOrder": true, "structure": [ { @@ -201,7 +206,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", - "propertyName": "vocab:isAlternativeVersionOf", + "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ { @@ -214,7 +219,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "structure": [ { "path": "@id" @@ -222,11 +227,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/keyword", - "propertyName": "vocab:keyword", + "propertyName": "keyword", "ensureOrder": true, "structure": [ { @@ -239,7 +245,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/license", - "propertyName": "vocab:license", + "propertyName": "license", "ensureOrder": true, "structure": [ { @@ -252,7 +258,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/otherContribution", - "propertyName": "vocab:otherContribution", + "propertyName": "otherContribution", "ensureOrder": true, "structure": [ { @@ -260,7 +266,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contributor", - "propertyName": "vocab:contributor", + "propertyName": "contributor", "structure": [ { "path": "@id" @@ -268,11 +274,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "ensureOrder": true, "structure": [ { @@ -287,7 +294,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/outputData", - "propertyName": "vocab:outputData", + "propertyName": "outputData", "ensureOrder": true, "structure": [ { @@ -300,7 +307,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/relatedPublication", - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { @@ -313,11 +320,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/releaseDate", - "propertyName": "vocab:releaseDate" + "propertyName": "releaseDate" }, { "path": "https://openminds.ebrains.eu/vocab/repository", - "propertyName": "vocab:repository", + "propertyName": "repository", "structure": [ { "path": "@id" @@ -325,31 +332,32 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/supportChannel", - "propertyName": "vocab:supportChannel", + "propertyName": "supportChannel", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", - "propertyName": "vocab:versionIdentifier" + "propertyName": "versionIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/versionInnovation", - "propertyName": "vocab:versionInnovation" + "propertyName": "versionInnovation" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -365,7 +373,7 @@ "@id": "https://openminds.ebrains.eu/vocab/input", "reverse": true }, - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -381,7 +389,7 @@ "@id": "https://openminds.ebrains.eu/vocab/dataLocation", "reverse": true }, - "propertyName": "vocab:dataLocation", + "propertyName": "dataLocation", "ensureOrder": true, "structure": [ { @@ -397,7 +405,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", "reverse": true }, - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "ensureOrder": true, "structure": [ { @@ -413,7 +421,7 @@ "@id": "https://openminds.ebrains.eu/vocab/output", "reverse": true }, - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { @@ -429,7 +437,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -445,7 +453,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasVersion", "reverse": true }, - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -461,7 +469,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -477,7 +485,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/orcid_simple_query.json b/test/test_data/queries/openminds/core/orcid_simple_query.json index ce9f71ce..42159fb8 100644 --- a/test/test_data/queries/openminds/core/orcid_simple_query.json +++ b/test/test_data/queries/openminds/core/orcid_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/organization_simple_query.json b/test/test_data/queries/openminds/core/organization_simple_query.json index af1dab7b..e0b33697 100644 --- a/test/test_data/queries/openminds/core/organization_simple_query.json +++ b/test/test_data/queries/openminds/core/organization_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -48,11 +48,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -60,17 +60,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -83,12 +84,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -101,18 +102,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -128,7 +129,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -144,7 +145,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -160,7 +161,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasParent", "reverse": true }, - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -176,7 +177,7 @@ "@id": "https://openminds.ebrains.eu/vocab/memberOf", "reverse": true }, - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "ensureOrder": true, "structure": [ { @@ -184,11 +185,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -196,11 +197,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -209,7 +211,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hostedBy", "reverse": true }, - "propertyName": "vocab:hostedBy", + "propertyName": "hostedBy", "ensureOrder": true, "structure": [ { @@ -225,7 +227,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -241,7 +243,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -257,7 +259,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -273,7 +275,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -289,7 +291,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/person_newstyle_query.json b/test/test_data/queries/openminds/core/person_newstyle_query.json index fa44783a..afd6dc62 100644 --- a/test/test_data/queries/openminds/core/person_newstyle_query.json +++ b/test/test_data/queries/openminds/core/person_newstyle_query.json @@ -36,7 +36,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -44,7 +44,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": { @@ -53,7 +53,7 @@ "@id": "https://openminds.ebrains.eu/core/Consortium" } }, - "propertyName": "vocab:memberOf__Consortium", + "propertyName": "memberOf__Consortium", "structure": [ { "path": "@id" @@ -67,7 +67,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -75,26 +75,27 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName" + "propertyName": "fullName" }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -110,7 +111,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -126,7 +127,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -142,7 +143,7 @@ "@id": "https://openminds.ebrains.eu/vocab/memberOf", "reverse": true }, - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "ensureOrder": true, "structure": [ { @@ -150,11 +151,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -162,11 +163,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -175,7 +177,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -191,7 +193,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -207,7 +209,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -223,7 +225,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -239,7 +241,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -250,7 +252,8 @@ } ] } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -259,7 +262,7 @@ "@id": "https://openminds.ebrains.eu/core/Organization" } }, - "propertyName": "vocab:memberOf__Organization", + "propertyName": "memberOf__Organization", "structure": [ { "path": "@id" @@ -273,7 +276,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -281,11 +284,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -293,17 +296,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -316,11 +320,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName" + "propertyName": "fullName" }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -335,7 +339,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -343,11 +347,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -355,17 +359,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -378,11 +383,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName" + "propertyName": "fullName" }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -395,18 +400,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -422,7 +427,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -438,7 +443,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -454,7 +459,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasParent", "reverse": true }, - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -470,7 +475,7 @@ "@id": "https://openminds.ebrains.eu/vocab/memberOf", "reverse": true }, - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "ensureOrder": true, "structure": [ { @@ -478,11 +483,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -490,11 +495,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -503,7 +509,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hostedBy", "reverse": true }, - "propertyName": "vocab:hostedBy", + "propertyName": "hostedBy", "ensureOrder": true, "structure": [ { @@ -519,7 +525,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -535,7 +541,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -551,7 +557,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -567,7 +573,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -583,7 +589,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -598,18 +604,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -625,7 +631,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -641,7 +647,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -657,7 +663,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasParent", "reverse": true }, - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -673,7 +679,7 @@ "@id": "https://openminds.ebrains.eu/vocab/memberOf", "reverse": true }, - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "ensureOrder": true, "structure": [ { @@ -681,11 +687,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -693,11 +699,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -706,7 +713,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hostedBy", "reverse": true }, - "propertyName": "vocab:hostedBy", + "propertyName": "hostedBy", "ensureOrder": true, "structure": [ { @@ -722,7 +729,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -738,7 +745,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -754,7 +761,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -770,7 +777,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -786,7 +793,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -797,22 +804,23 @@ } ] } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/alternateName", - "propertyName": "vocab:alternateName", + "propertyName": "alternateName", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/associatedAccount", - "propertyName": "vocab:associatedAccount", + "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ { @@ -825,7 +833,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -839,14 +847,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/email", - "propertyName": "vocab:email" + "propertyName": "email" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/contactInformation", "reverse": true }, - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "ensureOrder": true, "structure": [ { @@ -857,11 +865,12 @@ } ] } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -874,18 +883,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/familyName", - "propertyName": "vocab:familyName" + "propertyName": "familyName" }, { "path": "https://openminds.ebrains.eu/vocab/givenName", - "propertyName": "vocab:givenName" + "propertyName": "givenName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/performedBy", "reverse": true }, - "propertyName": "vocab:performedBy", + "propertyName": "performedBy", "ensureOrder": true, "structure": [ { @@ -901,7 +910,7 @@ "@id": "https://openminds.ebrains.eu/vocab/commenter", "reverse": true }, - "propertyName": "vocab:commenter", + "propertyName": "commenter", "ensureOrder": true, "structure": [ { @@ -917,7 +926,7 @@ "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -933,7 +942,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -949,7 +958,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -965,7 +974,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -981,7 +990,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -997,7 +1006,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -1013,7 +1022,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -1029,7 +1038,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -1045,7 +1054,7 @@ "@id": "https://openminds.ebrains.eu/vocab/startedBy", "reverse": true }, - "propertyName": "vocab:startedBy", + "propertyName": "startedBy", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/person_newstyle_query_alt.json b/test/test_data/queries/openminds/core/person_newstyle_query_alt.json index 2c477b07..20bfe758 100644 --- a/test/test_data/queries/openminds/core/person_newstyle_query_alt.json +++ b/test/test_data/queries/openminds/core/person_newstyle_query_alt.json @@ -36,7 +36,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -44,7 +44,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": { @@ -53,7 +53,7 @@ "@id": "https://openminds.ebrains.eu/core/Consortium" } }, - "propertyName": "vocab:memberOf__Consortium", + "propertyName": "memberOf__Consortium", "structure": [ { "path": "@id" @@ -63,16 +63,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -84,7 +84,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, @@ -95,7 +95,7 @@ "@id": "https://openminds.ebrains.eu/core/Organization" } }, - "propertyName": "vocab:memberOf__Organization", + "propertyName": "memberOf__Organization", "structure": [ { "path": "@id" @@ -105,16 +105,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -122,11 +122,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -138,13 +138,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -157,7 +157,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -168,16 +168,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -185,11 +185,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -201,13 +201,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -220,7 +220,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -233,30 +233,30 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/alternateName", - "propertyName": "vocab:alternateName", + "propertyName": "alternateName", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/associatedAccount", - "propertyName": "vocab:associatedAccount", + "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ { @@ -269,7 +269,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -279,13 +279,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/email", - "propertyName": "vocab:email" + "propertyName": "email" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -298,11 +298,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/familyName", - "propertyName": "vocab:familyName" + "propertyName": "familyName" }, { "path": "https://openminds.ebrains.eu/vocab/givenName", - "propertyName": "vocab:givenName" + "propertyName": "givenName" }, { "path": [ diff --git a/test/test_data/queries/openminds/core/person_resolved-1_query.json b/test/test_data/queries/openminds/core/person_resolved-1_query.json index 69cc0297..916eafd7 100644 --- a/test/test_data/queries/openminds/core/person_resolved-1_query.json +++ b/test/test_data/queries/openminds/core/person_resolved-1_query.json @@ -36,7 +36,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -44,7 +44,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": { @@ -53,7 +53,7 @@ "@id": "https://openminds.ebrains.eu/core/Consortium" } }, - "propertyName": "vocab:memberOf__Consortium", + "propertyName": "memberOf__Consortium", "structure": [ { "path": "@id" @@ -67,7 +67,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -75,26 +75,27 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName" + "propertyName": "fullName" }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -110,7 +111,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -126,7 +127,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -142,7 +143,7 @@ "@id": "https://openminds.ebrains.eu/vocab/memberOf", "reverse": true }, - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "ensureOrder": true, "structure": [ { @@ -150,11 +151,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -162,11 +163,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -175,7 +177,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -191,7 +193,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -207,7 +209,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -223,7 +225,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -239,7 +241,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -250,7 +252,8 @@ } ] } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -259,7 +262,7 @@ "@id": "https://openminds.ebrains.eu/core/Organization" } }, - "propertyName": "vocab:memberOf__Organization", + "propertyName": "memberOf__Organization", "structure": [ { "path": "@id" @@ -273,7 +276,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -281,11 +284,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -293,17 +296,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -316,11 +320,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName" + "propertyName": "fullName" }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -333,18 +337,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -360,7 +364,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -376,7 +380,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -392,7 +396,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasParent", "reverse": true }, - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -408,7 +412,7 @@ "@id": "https://openminds.ebrains.eu/vocab/memberOf", "reverse": true }, - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "ensureOrder": true, "structure": [ { @@ -416,11 +420,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -428,11 +432,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -441,7 +446,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hostedBy", "reverse": true }, - "propertyName": "vocab:hostedBy", + "propertyName": "hostedBy", "ensureOrder": true, "structure": [ { @@ -457,7 +462,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -473,7 +478,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -489,7 +494,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -505,7 +510,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -521,7 +526,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -532,22 +537,23 @@ } ] } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/alternateName", - "propertyName": "vocab:alternateName", + "propertyName": "alternateName", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/associatedAccount", - "propertyName": "vocab:associatedAccount", + "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ { @@ -562,7 +568,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/service", - "propertyName": "vocab:service", + "propertyName": "service", "structure": [ { "path": "@id" @@ -570,18 +576,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/userName", - "propertyName": "vocab:userName" + "propertyName": "userName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/associatedAccount", "reverse": true }, - "propertyName": "vocab:associatedAccount", + "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ { @@ -596,7 +603,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -610,14 +617,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/email", - "propertyName": "vocab:email" + "propertyName": "email" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/contactInformation", "reverse": true }, - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "ensureOrder": true, "structure": [ { @@ -628,11 +635,12 @@ } ] } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -647,14 +655,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -669,18 +677,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/familyName", - "propertyName": "vocab:familyName" + "propertyName": "familyName" }, { "path": "https://openminds.ebrains.eu/vocab/givenName", - "propertyName": "vocab:givenName" + "propertyName": "givenName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/performedBy", "reverse": true }, - "propertyName": "vocab:performedBy", + "propertyName": "performedBy", "ensureOrder": true, "structure": [ { @@ -696,7 +704,7 @@ "@id": "https://openminds.ebrains.eu/vocab/commenter", "reverse": true }, - "propertyName": "vocab:commenter", + "propertyName": "commenter", "ensureOrder": true, "structure": [ { @@ -712,7 +720,7 @@ "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -728,7 +736,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -744,7 +752,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -760,7 +768,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -776,7 +784,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -792,7 +800,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -808,7 +816,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -824,7 +832,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -840,7 +848,7 @@ "@id": "https://openminds.ebrains.eu/vocab/startedBy", "reverse": true }, - "propertyName": "vocab:startedBy", + "propertyName": "startedBy", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/person_resolved-2_query.json b/test/test_data/queries/openminds/core/person_resolved-2_query.json index cb9a1b5d..d6f5ee7c 100644 --- a/test/test_data/queries/openminds/core/person_resolved-2_query.json +++ b/test/test_data/queries/openminds/core/person_resolved-2_query.json @@ -36,7 +36,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -44,7 +44,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": { @@ -53,7 +53,7 @@ "@id": "https://openminds.ebrains.eu/core/Consortium" } }, - "propertyName": "vocab:memberOf__Consortium", + "propertyName": "memberOf__Consortium", "structure": [ { "path": "@id" @@ -63,16 +63,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -82,13 +82,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/email", - "propertyName": "vocab:email" + "propertyName": "email" } ] }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, @@ -99,7 +99,7 @@ "@id": "https://openminds.ebrains.eu/core/Organization" } }, - "propertyName": "vocab:memberOf__Organization", + "propertyName": "memberOf__Organization", "structure": [ { "path": "@id" @@ -109,16 +109,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -126,7 +126,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": { @@ -135,7 +135,7 @@ "@id": "https://openminds.ebrains.eu/core/Consortium" } }, - "propertyName": "vocab:memberOf__Consortium", + "propertyName": "memberOf__Consortium", "structure": [ { "path": "@id" @@ -145,16 +145,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -166,7 +166,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, @@ -177,7 +177,7 @@ "@id": "https://openminds.ebrains.eu/core/Organization" } }, - "propertyName": "vocab:memberOf__Organization", + "propertyName": "memberOf__Organization", "structure": [ { "path": "@id" @@ -187,16 +187,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -204,11 +204,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -220,13 +220,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -239,7 +239,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -252,13 +252,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, @@ -269,7 +269,7 @@ "@id": "https://openminds.ebrains.eu/core/GRIDID" } }, - "propertyName": "vocab:digitalIdentifier__GRIDID", + "propertyName": "digitalIdentifier__GRIDID", "ensureOrder": true, "structure": [ { @@ -280,7 +280,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" } ] }, @@ -291,7 +291,7 @@ "@id": "https://openminds.ebrains.eu/core/RORID" } }, - "propertyName": "vocab:digitalIdentifier__RORID", + "propertyName": "digitalIdentifier__RORID", "ensureOrder": true, "structure": [ { @@ -302,7 +302,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" } ] }, @@ -313,7 +313,7 @@ "@id": "https://openminds.ebrains.eu/core/RRID" } }, - "propertyName": "vocab:digitalIdentifier__RRID", + "propertyName": "digitalIdentifier__RRID", "ensureOrder": true, "structure": [ { @@ -324,13 +324,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" } ] }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -341,16 +341,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -358,11 +358,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -374,13 +374,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -393,7 +393,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hasParent", - "propertyName": "vocab:hasParent", + "propertyName": "hasParent", "ensureOrder": true, "structure": [ { @@ -406,30 +406,30 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" } ] }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/alternateName", - "propertyName": "vocab:alternateName", + "propertyName": "alternateName", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/associatedAccount", - "propertyName": "vocab:associatedAccount", + "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ { @@ -440,7 +440,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/service", - "propertyName": "vocab:service", + "propertyName": "service", "structure": [ { "path": "@id" @@ -450,16 +450,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -472,11 +472,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -489,7 +489,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hasVersion", - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -502,23 +502,23 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" } ] }, { "path": "https://openminds.ebrains.eu/vocab/userName", - "propertyName": "vocab:userName" + "propertyName": "userName" } ] }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -528,13 +528,13 @@ }, { "path": "https://openminds.ebrains.eu/vocab/email", - "propertyName": "vocab:email" + "propertyName": "email" } ] }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -545,17 +545,17 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" } ] }, { "path": "https://openminds.ebrains.eu/vocab/familyName", - "propertyName": "vocab:familyName" + "propertyName": "familyName" }, { "path": "https://openminds.ebrains.eu/vocab/givenName", - "propertyName": "vocab:givenName" + "propertyName": "givenName" } ] } \ No newline at end of file diff --git a/test/test_data/queries/openminds/core/person_simple_query.json b/test/test_data/queries/openminds/core/person_simple_query.json index ce1a0495..53e9b929 100644 --- a/test/test_data/queries/openminds/core/person_simple_query.json +++ b/test/test_data/queries/openminds/core/person_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "ensureOrder": true, "structure": [ { @@ -48,11 +48,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/endDate", - "propertyName": "vocab:endDate" + "propertyName": "endDate" }, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [ { "path": "@id" @@ -60,22 +60,23 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate" + "propertyName": "startDate" } ] }, { "path": "https://openminds.ebrains.eu/vocab/alternateName", - "propertyName": "vocab:alternateName", + "propertyName": "alternateName", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/associatedAccount", - "propertyName": "vocab:associatedAccount", + "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ { @@ -88,7 +89,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contactInformation", - "propertyName": "vocab:contactInformation", + "propertyName": "contactInformation", "structure": [ { "path": "@id" @@ -96,11 +97,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { @@ -113,18 +115,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/familyName", - "propertyName": "vocab:familyName" + "propertyName": "familyName" }, { "path": "https://openminds.ebrains.eu/vocab/givenName", - "propertyName": "vocab:givenName" + "propertyName": "givenName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/performedBy", "reverse": true }, - "propertyName": "vocab:performedBy", + "propertyName": "performedBy", "ensureOrder": true, "structure": [ { @@ -140,7 +142,7 @@ "@id": "https://openminds.ebrains.eu/vocab/commenter", "reverse": true }, - "propertyName": "vocab:commenter", + "propertyName": "commenter", "ensureOrder": true, "structure": [ { @@ -156,7 +158,7 @@ "@id": "https://openminds.ebrains.eu/vocab/coordinator", "reverse": true }, - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -172,7 +174,7 @@ "@id": "https://openminds.ebrains.eu/vocab/developer", "reverse": true }, - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -188,7 +190,7 @@ "@id": "https://openminds.ebrains.eu/vocab/funder", "reverse": true }, - "propertyName": "vocab:funder", + "propertyName": "funder", "ensureOrder": true, "structure": [ { @@ -204,7 +206,7 @@ "@id": "https://openminds.ebrains.eu/vocab/custodian", "reverse": true }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -220,7 +222,7 @@ "@id": "https://openminds.ebrains.eu/vocab/owner", "reverse": true }, - "propertyName": "vocab:owner", + "propertyName": "owner", "ensureOrder": true, "structure": [ { @@ -236,7 +238,7 @@ "@id": "https://openminds.ebrains.eu/vocab/provider", "reverse": true }, - "propertyName": "vocab:provider", + "propertyName": "provider", "ensureOrder": true, "structure": [ { @@ -252,7 +254,7 @@ "@id": "https://openminds.ebrains.eu/vocab/manufacturer", "reverse": true }, - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -268,7 +270,7 @@ "@id": "https://openminds.ebrains.eu/vocab/publisher", "reverse": true }, - "propertyName": "vocab:publisher", + "propertyName": "publisher", "ensureOrder": true, "structure": [ { @@ -284,7 +286,7 @@ "@id": "https://openminds.ebrains.eu/vocab/startedBy", "reverse": true }, - "propertyName": "vocab:startedBy", + "propertyName": "startedBy", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/project_simple_query.json b/test/test_data/queries/openminds/core/project_simple_query.json index 2c85cdec..bc21b1bd 100644 --- a/test/test_data/queries/openminds/core/project_simple_query.json +++ b/test/test_data/queries/openminds/core/project_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/coordinator", - "propertyName": "vocab:coordinator", + "propertyName": "coordinator", "ensureOrder": true, "structure": [ { @@ -53,16 +53,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/hasPart", - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -75,11 +75,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" } ] } \ No newline at end of file diff --git a/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json b/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json index aacc43ca..8157ff31 100644 --- a/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json +++ b/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { @@ -50,7 +50,7 @@ "@id": "https://openminds.ebrains.eu/core/NumericalProperty" } }, - "propertyName": "vocab:propertyValuePair__NumericalProperty", + "propertyName": "propertyValuePair__NumericalProperty", "ensureOrder": true, "structure": [ { @@ -58,7 +58,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name" + "propertyName": "name" }, { "path": { @@ -67,7 +67,7 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:value__QuantitativeValue", + "propertyName": "value__QuantitativeValue", "ensureOrder": true, "structure": [ { @@ -75,7 +75,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -83,16 +83,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -100,11 +101,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] }, @@ -115,7 +117,7 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:value__QuantitativeValueRange", + "propertyName": "value__QuantitativeValueRange", "ensureOrder": true, "structure": [ { @@ -123,11 +125,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -135,15 +137,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -151,7 +154,8 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } ] } @@ -164,7 +168,7 @@ "@id": "https://openminds.ebrains.eu/core/StringProperty" } }, - "propertyName": "vocab:propertyValuePair__StringProperty", + "propertyName": "propertyValuePair__StringProperty", "ensureOrder": true, "structure": [ { @@ -172,11 +176,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name" + "propertyName": "name" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] }, @@ -185,7 +189,7 @@ "@id": "https://openminds.ebrains.eu/vocab/environmentVariable", "reverse": true }, - "propertyName": "vocab:environmentVariable", + "propertyName": "environmentVariable", "ensureOrder": true, "structure": [ { @@ -201,7 +205,7 @@ "@id": "https://openminds.ebrains.eu/vocab/configuration", "reverse": true }, - "propertyName": "vocab:configuration", + "propertyName": "configuration", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/protocol_simple_query.json b/test/test_data/queries/openminds/core/protocol_simple_query.json index bb0a8af3..5ac62482 100644 --- a/test/test_data/queries/openminds/core/protocol_simple_query.json +++ b/test/test_data/queries/openminds/core/protocol_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/describedIn", - "propertyName": "vocab:describedIn", + "propertyName": "describedIn", "structure": [ { "path": "@id" @@ -48,20 +48,21 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/stimulusType", - "propertyName": "vocab:stimulusType", + "propertyName": "stimulusType", "ensureOrder": true, "structure": [ { @@ -74,7 +75,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/technique", - "propertyName": "vocab:technique", + "propertyName": "technique", "ensureOrder": true, "structure": [ { @@ -90,7 +91,7 @@ "@id": "https://openminds.ebrains.eu/vocab/protocol", "reverse": true }, - "propertyName": "vocab:protocol", + "propertyName": "protocol", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/protocolexecution_simple_query.json b/test/test_data/queries/openminds/core/protocolexecution_simple_query.json index f6d04e70..623fc446 100644 --- a/test/test_data/queries/openminds/core/protocolexecution_simple_query.json +++ b/test/test_data/queries/openminds/core/protocolexecution_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/behavioralProtocol", - "propertyName": "vocab:behavioralProtocol", + "propertyName": "behavioralProtocol", "ensureOrder": true, "structure": [ { @@ -53,7 +53,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/customPropertySet", - "propertyName": "vocab:customPropertySet", + "propertyName": "customPropertySet", "ensureOrder": true, "structure": [ { @@ -61,11 +61,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/context", - "propertyName": "vocab:context" + "propertyName": "context" }, { "path": "https://openminds.ebrains.eu/vocab/dataLocation", - "propertyName": "vocab:dataLocation", + "propertyName": "dataLocation", "structure": [ { "path": "@id" @@ -73,11 +73,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/relevantFor", - "propertyName": "vocab:relevantFor", + "propertyName": "relevantFor", "structure": [ { "path": "@id" @@ -85,21 +86,22 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } ] }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/endTime", - "propertyName": "vocab:endTime" + "propertyName": "endTime" }, { "path": "https://openminds.ebrains.eu/vocab/input", - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -112,7 +114,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isPartOf", - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "structure": [ { "path": "@id" @@ -120,16 +122,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/output", - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { @@ -142,7 +145,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/performedBy", - "propertyName": "vocab:performedBy", + "propertyName": "performedBy", "ensureOrder": true, "structure": [ { @@ -155,7 +158,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/preparationDesign", - "propertyName": "vocab:preparationDesign", + "propertyName": "preparationDesign", "structure": [ { "path": "@id" @@ -163,11 +166,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/protocol", - "propertyName": "vocab:protocol", + "propertyName": "protocol", "ensureOrder": true, "structure": [ { @@ -180,11 +184,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/startTime", - "propertyName": "vocab:startTime" + "propertyName": "startTime" }, { "path": "https://openminds.ebrains.eu/vocab/studyTarget", - "propertyName": "vocab:studyTarget", + "propertyName": "studyTarget", "ensureOrder": true, "structure": [ { @@ -203,7 +207,7 @@ }, "reverse": true }, - "propertyName": "vocab:criteria__AtlasAnnotation", + "propertyName": "criteria__AtlasAnnotation", "ensureOrder": true, "structure": [ { @@ -211,7 +215,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/anchorPoint", - "propertyName": "vocab:anchorPoint", + "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ { @@ -219,7 +223,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -227,16 +231,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -244,17 +249,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] }, { "path": "https://openminds.ebrains.eu/vocab/criteria", - "propertyName": "vocab:criteria", + "propertyName": "criteria", "structure": [ { "path": "@id" @@ -262,11 +268,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/criteriaQualityType", - "propertyName": "vocab:criteriaQualityType", + "propertyName": "criteriaQualityType", "structure": [ { "path": "@id" @@ -274,11 +281,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/criteriaType", - "propertyName": "vocab:criteriaType", + "propertyName": "criteriaType", "structure": [ { "path": "@id" @@ -286,11 +294,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/inspiredBy", - "propertyName": "vocab:inspiredBy", + "propertyName": "inspiredBy", "ensureOrder": true, "structure": [ { @@ -303,11 +312,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/laterality", - "propertyName": "vocab:laterality", + "propertyName": "laterality", "ensureOrder": true, "structure": [ { @@ -320,18 +329,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/preferredVisualization", - "propertyName": "vocab:preferredVisualization", + "propertyName": "preferredVisualization", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": "https://openminds.ebrains.eu/vocab/anchorPoint", - "propertyName": "vocab:anchorPoint", + "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ { @@ -339,7 +348,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -347,16 +356,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -364,24 +374,25 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] }, { "path": "https://openminds.ebrains.eu/vocab/cameraPosition", - "propertyName": "vocab:cameraPosition", + "propertyName": "cameraPosition", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/coordinateSpace", - "propertyName": "vocab:coordinateSpace", + "propertyName": "coordinateSpace", "structure": [ { "path": "@id" @@ -389,11 +400,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/coordinates", - "propertyName": "vocab:coordinates", + "propertyName": "coordinates", "ensureOrder": true, "structure": [ { @@ -401,7 +413,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -409,16 +421,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -426,19 +439,21 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/preferredDisplayColor", - "propertyName": "vocab:preferredDisplayColor", + "propertyName": "preferredDisplayColor", "structure": [ { "path": "@id" @@ -446,13 +461,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/specification", - "propertyName": "vocab:specification", + "propertyName": "specification", "structure": [ { "path": "@id" @@ -460,11 +477,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "structure": [ { "path": "@id" @@ -472,7 +490,8 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } ] }, @@ -484,7 +503,7 @@ }, "reverse": true }, - "propertyName": "vocab:criteria__CustomAnnotation", + "propertyName": "criteria__CustomAnnotation", "ensureOrder": true, "structure": [ { @@ -492,7 +511,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/anchorPoint", - "propertyName": "vocab:anchorPoint", + "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ { @@ -500,7 +519,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -508,16 +527,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -525,17 +545,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] }, { "path": "https://openminds.ebrains.eu/vocab/coordinateSpace", - "propertyName": "vocab:coordinateSpace", + "propertyName": "coordinateSpace", "structure": [ { "path": "@id" @@ -543,11 +564,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/criteria", - "propertyName": "vocab:criteria", + "propertyName": "criteria", "structure": [ { "path": "@id" @@ -555,11 +577,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/criteriaQualityType", - "propertyName": "vocab:criteriaQualityType", + "propertyName": "criteriaQualityType", "structure": [ { "path": "@id" @@ -567,11 +590,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/criteriaType", - "propertyName": "vocab:criteriaType", + "propertyName": "criteriaType", "structure": [ { "path": "@id" @@ -579,11 +603,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/inspiredBy", - "propertyName": "vocab:inspiredBy", + "propertyName": "inspiredBy", "ensureOrder": true, "structure": [ { @@ -596,11 +621,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/laterality", - "propertyName": "vocab:laterality", + "propertyName": "laterality", "ensureOrder": true, "structure": [ { @@ -613,18 +638,18 @@ }, { "path": "https://openminds.ebrains.eu/vocab/preferredVisualization", - "propertyName": "vocab:preferredVisualization", + "propertyName": "preferredVisualization", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": "https://openminds.ebrains.eu/vocab/anchorPoint", - "propertyName": "vocab:anchorPoint", + "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ { @@ -632,7 +657,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -640,16 +665,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -657,24 +683,25 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] }, { "path": "https://openminds.ebrains.eu/vocab/cameraPosition", - "propertyName": "vocab:cameraPosition", + "propertyName": "cameraPosition", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/coordinateSpace", - "propertyName": "vocab:coordinateSpace", + "propertyName": "coordinateSpace", "structure": [ { "path": "@id" @@ -682,11 +709,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/coordinates", - "propertyName": "vocab:coordinates", + "propertyName": "coordinates", "ensureOrder": true, "structure": [ { @@ -694,7 +722,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -702,16 +730,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -719,19 +748,21 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } ] } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/preferredDisplayColor", - "propertyName": "vocab:preferredDisplayColor", + "propertyName": "preferredDisplayColor", "structure": [ { "path": "@id" @@ -739,13 +770,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/specification", - "propertyName": "vocab:specification", + "propertyName": "specification", "structure": [ { "path": "@id" @@ -753,11 +786,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "structure": [ { "path": "@id" @@ -765,7 +799,8 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } ] } diff --git a/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json b/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json index ea6e3c3a..153db241 100644 --- a/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json +++ b/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json @@ -40,17 +40,17 @@ }, { "path": "https://openminds.ebrains.eu/vocab/negativeUncertainties", - "propertyName": "vocab:negativeUncertainties", + "propertyName": "negativeUncertainties", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/positiveUncertainties", - "propertyName": "vocab:positiveUncertainties", + "propertyName": "positiveUncertainties", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -58,11 +58,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -70,11 +71,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/values", - "propertyName": "vocab:values", + "propertyName": "values", "ensureOrder": true } ] diff --git a/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json b/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json index 1967de3f..c2521385 100644 --- a/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json +++ b/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/context", - "propertyName": "vocab:context" + "propertyName": "context" }, { "path": "https://openminds.ebrains.eu/vocab/hasPart", - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/rorid_simple_query.json b/test/test_data/queries/openminds/core/rorid_simple_query.json index b99e0316..023053d0 100644 --- a/test/test_data/queries/openminds/core/rorid_simple_query.json +++ b/test/test_data/queries/openminds/core/rorid_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/rrid_simple_query.json b/test/test_data/queries/openminds/core/rrid_simple_query.json index ca53084c..fe3073ac 100644 --- a/test/test_data/queries/openminds/core/rrid_simple_query.json +++ b/test/test_data/queries/openminds/core/rrid_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/servicelink_simple_query.json b/test/test_data/queries/openminds/core/servicelink_simple_query.json index 8f0f5fe2..6fd03f4b 100644 --- a/test/test_data/queries/openminds/core/servicelink_simple_query.json +++ b/test/test_data/queries/openminds/core/servicelink_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/dataLocation", - "propertyName": "vocab:dataLocation", + "propertyName": "dataLocation", "structure": [ { "path": "@id" @@ -48,19 +48,20 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/displayLabel", - "propertyName": "vocab:displayLabel" + "propertyName": "displayLabel" }, { "path": "https://openminds.ebrains.eu/vocab/openDataIn", - "propertyName": "vocab:openDataIn" + "propertyName": "openDataIn" }, { "path": "https://openminds.ebrains.eu/vocab/previewImage", - "propertyName": "vocab:previewImage", + "propertyName": "previewImage", "structure": [ { "path": "@id" @@ -68,11 +69,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/service", - "propertyName": "vocab:service", + "propertyName": "service", "structure": [ { "path": "@id" @@ -80,7 +82,8 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } ] } \ No newline at end of file diff --git a/test/test_data/queries/openminds/core/setup_simple_query.json b/test/test_data/queries/openminds/core/setup_simple_query.json index adffe2d6..08549beb 100644 --- a/test/test_data/queries/openminds/core/setup_simple_query.json +++ b/test/test_data/queries/openminds/core/setup_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/hasPart", - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -57,11 +57,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/location", - "propertyName": "vocab:location" + "propertyName": "location" }, { "path": "https://openminds.ebrains.eu/vocab/manufacturer", - "propertyName": "vocab:manufacturer", + "propertyName": "manufacturer", "ensureOrder": true, "structure": [ { @@ -74,12 +74,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "ensureOrder": true, "structure": [ { @@ -95,7 +95,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -111,7 +111,7 @@ "@id": "https://openminds.ebrains.eu/vocab/setup", "reverse": true }, - "propertyName": "vocab:setup", + "propertyName": "setup", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/software_simple_query.json b/test/test_data/queries/openminds/core/software_simple_query.json index 053d92a3..add69c5b 100644 --- a/test/test_data/queries/openminds/core/software_simple_query.json +++ b/test/test_data/queries/openminds/core/software_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -53,11 +53,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -70,7 +70,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -78,16 +78,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/hasVersion", - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -100,22 +101,22 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -131,7 +132,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -147,7 +148,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/softwareversion_simple_query.json b/test/test_data/queries/openminds/core/softwareversion_simple_query.json index 59a8485b..20410699 100644 --- a/test/test_data/queries/openminds/core/softwareversion_simple_query.json +++ b/test/test_data/queries/openminds/core/softwareversion_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/accessibility", - "propertyName": "vocab:accessibility", + "propertyName": "accessibility", "structure": [ { "path": "@id" @@ -48,11 +48,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/applicationCategory", - "propertyName": "vocab:applicationCategory", + "propertyName": "applicationCategory", "ensureOrder": true, "structure": [ { @@ -65,14 +66,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/copyright", - "propertyName": "vocab:copyright", + "propertyName": "copyright", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/holder", - "propertyName": "vocab:holder", + "propertyName": "holder", "ensureOrder": true, "structure": [ { @@ -85,14 +86,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/year", - "propertyName": "vocab:year", + "propertyName": "year", "ensureOrder": true } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -105,11 +107,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -122,7 +124,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/device", - "propertyName": "vocab:device", + "propertyName": "device", "ensureOrder": true, "structure": [ { @@ -135,7 +137,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -143,11 +145,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/feature", - "propertyName": "vocab:feature", + "propertyName": "feature", "ensureOrder": true, "structure": [ { @@ -160,7 +163,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", - "propertyName": "vocab:fullDocumentation", + "propertyName": "fullDocumentation", "structure": [ { "path": "@id" @@ -168,16 +171,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/funding", - "propertyName": "vocab:funding", + "propertyName": "funding", "ensureOrder": true, "structure": [ { @@ -190,7 +194,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hasPart", - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -203,15 +207,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/inputFormat", - "propertyName": "vocab:inputFormat", + "propertyName": "inputFormat", "ensureOrder": true, "structure": [ { @@ -224,7 +228,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", - "propertyName": "vocab:isAlternativeVersionOf", + "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ { @@ -237,7 +241,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "structure": [ { "path": "@id" @@ -245,11 +249,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/keyword", - "propertyName": "vocab:keyword", + "propertyName": "keyword", "ensureOrder": true, "structure": [ { @@ -262,7 +267,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/language", - "propertyName": "vocab:language", + "propertyName": "language", "ensureOrder": true, "structure": [ { @@ -275,7 +280,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/license", - "propertyName": "vocab:license", + "propertyName": "license", "ensureOrder": true, "structure": [ { @@ -288,7 +293,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/operatingSystem", - "propertyName": "vocab:operatingSystem", + "propertyName": "operatingSystem", "ensureOrder": true, "structure": [ { @@ -301,7 +306,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/otherContribution", - "propertyName": "vocab:otherContribution", + "propertyName": "otherContribution", "ensureOrder": true, "structure": [ { @@ -309,7 +314,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contributor", - "propertyName": "vocab:contributor", + "propertyName": "contributor", "structure": [ { "path": "@id" @@ -317,11 +322,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "ensureOrder": true, "structure": [ { @@ -336,7 +342,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/outputFormat", - "propertyName": "vocab:outputFormat", + "propertyName": "outputFormat", "ensureOrder": true, "structure": [ { @@ -349,7 +355,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/programmingLanguage", - "propertyName": "vocab:programmingLanguage", + "propertyName": "programmingLanguage", "ensureOrder": true, "structure": [ { @@ -362,7 +368,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/relatedPublication", - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { @@ -375,11 +381,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/releaseDate", - "propertyName": "vocab:releaseDate" + "propertyName": "releaseDate" }, { "path": "https://openminds.ebrains.eu/vocab/repository", - "propertyName": "vocab:repository", + "propertyName": "repository", "structure": [ { "path": "@id" @@ -387,36 +393,37 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/requirement", - "propertyName": "vocab:requirement", + "propertyName": "requirement", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/supportChannel", - "propertyName": "vocab:supportChannel", + "propertyName": "supportChannel", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", - "propertyName": "vocab:versionIdentifier" + "propertyName": "versionIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/versionInnovation", - "propertyName": "vocab:versionInnovation" + "propertyName": "versionInnovation" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -432,7 +439,7 @@ "@id": "https://openminds.ebrains.eu/vocab/input", "reverse": true }, - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -448,7 +455,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", "reverse": true }, - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "ensureOrder": true, "structure": [ { @@ -464,7 +471,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -480,7 +487,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasVersion", "reverse": true }, - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -496,7 +503,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -512,7 +519,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -528,7 +535,7 @@ "@id": "https://openminds.ebrains.eu/vocab/software", "reverse": true }, - "propertyName": "vocab:software", + "propertyName": "software", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/stimulation_simple_query.json b/test/test_data/queries/openminds/core/stimulation_simple_query.json index 520476b7..2d906f4b 100644 --- a/test/test_data/queries/openminds/core/stimulation_simple_query.json +++ b/test/test_data/queries/openminds/core/stimulation_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel" + "propertyName": "lookupLabel" }, { "path": "https://openminds.ebrains.eu/vocab/customPropertySet", - "propertyName": "vocab:customPropertySet", + "propertyName": "customPropertySet", "filter": { "op": "CONTAINS", "parameter": "custom_property_sets" @@ -56,11 +56,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/context", - "propertyName": "vocab:context" + "propertyName": "context" }, { "path": "https://openminds.ebrains.eu/vocab/definedIn", - "propertyName": "vocab:definedIn", + "propertyName": "definedIn", "structure": [ { "path": "@id" @@ -72,7 +72,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/relevantFor", - "propertyName": "vocab:relevantFor", + "propertyName": "relevantFor", "structure": [ { "path": "@id" @@ -86,7 +86,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/dataLocation", - "propertyName": "vocab:dataLocation", + "propertyName": "dataLocation", "ensureOrder": true, "structure": [ { @@ -99,11 +99,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/stimulationApproach", - "propertyName": "vocab:stimulationApproach", + "propertyName": "stimulationApproach", "structure": [ { "path": "@id" @@ -115,7 +115,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/stimulusType", - "propertyName": "vocab:stimulusType", + "propertyName": "stimulusType", "structure": [ { "path": "@id" diff --git a/test/test_data/queries/openminds/core/strain_simple_query.json b/test/test_data/queries/openminds/core/strain_simple_query.json index 8817af3b..0886db65 100644 --- a/test/test_data/queries/openminds/core/strain_simple_query.json +++ b/test/test_data/queries/openminds/core/strain_simple_query.json @@ -40,12 +40,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/alternateIdentifier", - "propertyName": "vocab:alternateIdentifier", + "propertyName": "alternateIdentifier", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/backgroundStrain", - "propertyName": "vocab:backgroundStrain", + "propertyName": "backgroundStrain", "ensureOrder": true, "structure": [ { @@ -58,7 +58,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/breedingType", - "propertyName": "vocab:breedingType", + "propertyName": "breedingType", "structure": [ { "path": "@id" @@ -66,15 +66,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "structure": [ { "path": "@id" @@ -82,11 +83,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/diseaseModel", - "propertyName": "vocab:diseaseModel", + "propertyName": "diseaseModel", "ensureOrder": true, "structure": [ { @@ -99,7 +101,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/geneticStrainType", - "propertyName": "vocab:geneticStrainType", + "propertyName": "geneticStrainType", "structure": [ { "path": "@id" @@ -107,29 +109,30 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/laboratoryCode", - "propertyName": "vocab:laboratoryCode" + "propertyName": "laboratoryCode" }, { "path": "https://openminds.ebrains.eu/vocab/name", - "propertyName": "vocab:name", + "propertyName": "name", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/ontologyIdentifier", - "propertyName": "vocab:ontologyIdentifier", + "propertyName": "ontologyIdentifier", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/phenotype", - "propertyName": "vocab:phenotype" + "propertyName": "phenotype" }, { "path": "https://openminds.ebrains.eu/vocab/species", - "propertyName": "vocab:species", + "propertyName": "species", "structure": [ { "path": "@id" @@ -137,22 +140,23 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/stockNumber", - "propertyName": "vocab:stockNumber", + "propertyName": "stockNumber", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": "https://openminds.ebrains.eu/vocab/vendor", - "propertyName": "vocab:vendor", + "propertyName": "vendor", "structure": [ { "path": "@id" @@ -160,13 +164,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/synonym", - "propertyName": "vocab:synonym", + "propertyName": "synonym", "ensureOrder": true }, { @@ -174,7 +180,7 @@ "@id": "https://openminds.ebrains.eu/vocab/backgroundStrain", "reverse": true }, - "propertyName": "vocab:backgroundStrain", + "propertyName": "backgroundStrain", "ensureOrder": true, "structure": [ { @@ -190,7 +196,7 @@ "@id": "https://openminds.ebrains.eu/vocab/species", "reverse": true }, - "propertyName": "vocab:species", + "propertyName": "species", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/subject_simple_query.json b/test/test_data/queries/openminds/core/subject_simple_query.json index 71c0f4c4..ee5e1eac 100644 --- a/test/test_data/queries/openminds/core/subject_simple_query.json +++ b/test/test_data/queries/openminds/core/subject_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/biologicalSex", - "propertyName": "vocab:biologicalSex", + "propertyName": "biologicalSex", "structure": [ { "path": "@id" @@ -48,15 +48,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/isPartOf", - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { @@ -69,12 +70,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/species", - "propertyName": "vocab:species", + "propertyName": "species", "structure": [ { "path": "@id" @@ -82,11 +83,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/studiedState", - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -102,7 +104,7 @@ "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", "reverse": true }, - "propertyName": "vocab:studiedSpecimen", + "propertyName": "studiedSpecimen", "ensureOrder": true, "structure": [ { @@ -118,7 +120,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -134,7 +136,7 @@ "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", "reverse": true }, - "propertyName": "vocab:usedSpecimen", + "propertyName": "usedSpecimen", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/subjectgroup_simple_query.json b/test/test_data/queries/openminds/core/subjectgroup_simple_query.json index 7faf0e0c..c44ec337 100644 --- a/test/test_data/queries/openminds/core/subjectgroup_simple_query.json +++ b/test/test_data/queries/openminds/core/subjectgroup_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": "https://openminds.ebrains.eu/vocab/biologicalSex", - "propertyName": "vocab:biologicalSex", + "propertyName": "biologicalSex", "ensureOrder": true, "structure": [ { @@ -57,20 +57,20 @@ }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/numberOfSubjects", - "propertyName": "vocab:numberOfSubjects" + "propertyName": "numberOfSubjects" }, { "path": "https://openminds.ebrains.eu/vocab/species", - "propertyName": "vocab:species", + "propertyName": "species", "ensureOrder": true, "structure": [ { @@ -83,7 +83,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/studiedState", - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -99,7 +99,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isPartOf", "reverse": true }, - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { @@ -115,7 +115,7 @@ "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", "reverse": true }, - "propertyName": "vocab:studiedSpecimen", + "propertyName": "studiedSpecimen", "ensureOrder": true, "structure": [ { @@ -131,7 +131,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -147,7 +147,7 @@ "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", "reverse": true }, - "propertyName": "vocab:usedSpecimen", + "propertyName": "usedSpecimen", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json b/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json index 4b03eaf8..5b842d7e 100644 --- a/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json +++ b/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": { @@ -49,14 +49,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:age__QuantitativeValue", + "propertyName": "age__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -64,16 +64,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -81,13 +82,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -96,18 +99,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:age__QuantitativeValueRange", + "propertyName": "age__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -115,15 +118,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -131,13 +135,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/ageCategory", - "propertyName": "vocab:ageCategory", + "propertyName": "ageCategory", "ensureOrder": true, "structure": [ { @@ -150,7 +156,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/attribute", - "propertyName": "vocab:attribute", + "propertyName": "attribute", "ensureOrder": true, "structure": [ { @@ -163,7 +169,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/descendedFrom", - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "structure": [ { "path": "@id" @@ -171,11 +177,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/handedness", - "propertyName": "vocab:handedness", + "propertyName": "handedness", "ensureOrder": true, "structure": [ { @@ -188,16 +195,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/pathology", - "propertyName": "vocab:pathology", + "propertyName": "pathology", "ensureOrder": true, "structure": [ { @@ -215,14 +222,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValue", + "propertyName": "relativeTimeIndication__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -230,16 +237,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -247,13 +255,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -262,18 +272,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValueRange", + "propertyName": "relativeTimeIndication__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -281,15 +291,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -297,9 +308,11 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -308,14 +321,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:weight__QuantitativeValue", + "propertyName": "weight__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -323,16 +336,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -340,13 +354,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -355,18 +371,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:weight__QuantitativeValueRange", + "propertyName": "weight__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -374,15 +390,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -390,16 +407,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", "reverse": true }, - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ { @@ -415,7 +434,7 @@ "@id": "https://openminds.ebrains.eu/vocab/input", "reverse": true }, - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -431,7 +450,7 @@ "@id": "https://openminds.ebrains.eu/vocab/output", "reverse": true }, - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { @@ -447,7 +466,7 @@ "@id": "https://openminds.ebrains.eu/vocab/studiedState", "reverse": true }, - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -463,7 +482,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/subjectstate_simple_query.json b/test/test_data/queries/openminds/core/subjectstate_simple_query.json index cfc65389..e2b6d7f0 100644 --- a/test/test_data/queries/openminds/core/subjectstate_simple_query.json +++ b/test/test_data/queries/openminds/core/subjectstate_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": { @@ -49,14 +49,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:age__QuantitativeValue", + "propertyName": "age__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -64,16 +64,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -81,13 +82,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -96,18 +99,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:age__QuantitativeValueRange", + "propertyName": "age__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -115,15 +118,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -131,13 +135,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/ageCategory", - "propertyName": "vocab:ageCategory", + "propertyName": "ageCategory", "structure": [ { "path": "@id" @@ -145,11 +151,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/attribute", - "propertyName": "vocab:attribute", + "propertyName": "attribute", "ensureOrder": true, "structure": [ { @@ -162,7 +169,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/descendedFrom", - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "structure": [ { "path": "@id" @@ -170,11 +177,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/handedness", - "propertyName": "vocab:handedness", + "propertyName": "handedness", "structure": [ { "path": "@id" @@ -182,20 +190,21 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/pathology", - "propertyName": "vocab:pathology", + "propertyName": "pathology", "ensureOrder": true, "structure": [ { @@ -213,14 +222,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValue", + "propertyName": "relativeTimeIndication__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -228,16 +237,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -245,13 +255,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -260,18 +272,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValueRange", + "propertyName": "relativeTimeIndication__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -279,15 +291,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -295,9 +308,11 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -306,14 +321,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:weight__QuantitativeValue", + "propertyName": "weight__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -321,16 +336,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -338,13 +354,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -353,18 +371,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:weight__QuantitativeValueRange", + "propertyName": "weight__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -372,15 +390,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -388,16 +407,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", "reverse": true }, - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ { @@ -413,7 +434,7 @@ "@id": "https://openminds.ebrains.eu/vocab/input", "reverse": true }, - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -429,7 +450,7 @@ "@id": "https://openminds.ebrains.eu/vocab/output", "reverse": true }, - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { @@ -445,7 +466,7 @@ "@id": "https://openminds.ebrains.eu/vocab/studiedState", "reverse": true }, - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -461,7 +482,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -477,7 +498,7 @@ "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", "reverse": true }, - "propertyName": "vocab:usedSpecimen", + "propertyName": "usedSpecimen", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/swhid_simple_query.json b/test/test_data/queries/openminds/core/swhid_simple_query.json index 5d988de3..00d78bb5 100644 --- a/test/test_data/queries/openminds/core/swhid_simple_query.json +++ b/test/test_data/queries/openminds/core/swhid_simple_query.json @@ -40,14 +40,14 @@ }, { "path": "https://openminds.ebrains.eu/vocab/identifier", - "propertyName": "vocab:identifier" + "propertyName": "identifier" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", "reverse": true }, - "propertyName": "vocab:digitalIdentifier", + "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/tissuesample_simple_query.json b/test/test_data/queries/openminds/core/tissuesample_simple_query.json index 6c3c9c72..1612e22f 100644 --- a/test/test_data/queries/openminds/core/tissuesample_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesample_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/anatomicalLocation", - "propertyName": "vocab:anatomicalLocation", + "propertyName": "anatomicalLocation", "ensureOrder": true, "structure": [ { @@ -53,7 +53,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/biologicalSex", - "propertyName": "vocab:biologicalSex", + "propertyName": "biologicalSex", "structure": [ { "path": "@id" @@ -61,15 +61,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/isPartOf", - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { @@ -82,7 +83,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/laterality", - "propertyName": "vocab:laterality", + "propertyName": "laterality", "ensureOrder": true, "structure": [ { @@ -95,12 +96,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/origin", - "propertyName": "vocab:origin", + "propertyName": "origin", "structure": [ { "path": "@id" @@ -108,11 +109,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/species", - "propertyName": "vocab:species", + "propertyName": "species", "structure": [ { "path": "@id" @@ -120,11 +122,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/studiedState", - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -137,7 +140,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "structure": [ { "path": "@id" @@ -145,14 +148,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", "reverse": true }, - "propertyName": "vocab:studiedSpecimen", + "propertyName": "studiedSpecimen", "ensureOrder": true, "structure": [ { @@ -168,7 +172,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -184,7 +188,7 @@ "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", "reverse": true }, - "propertyName": "vocab:usedSpecimen", + "propertyName": "usedSpecimen", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json b/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json index 78a39ec6..9360af19 100644 --- a/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": "https://openminds.ebrains.eu/vocab/anatomicalLocation", - "propertyName": "vocab:anatomicalLocation", + "propertyName": "anatomicalLocation", "ensureOrder": true, "structure": [ { @@ -57,7 +57,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/biologicalSex", - "propertyName": "vocab:biologicalSex", + "propertyName": "biologicalSex", "ensureOrder": true, "structure": [ { @@ -70,11 +70,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/laterality", - "propertyName": "vocab:laterality", + "propertyName": "laterality", "ensureOrder": true, "structure": [ { @@ -87,16 +87,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/numberOfTissueSamples", - "propertyName": "vocab:numberOfTissueSamples" + "propertyName": "numberOfTissueSamples" }, { "path": "https://openminds.ebrains.eu/vocab/origin", - "propertyName": "vocab:origin", + "propertyName": "origin", "ensureOrder": true, "structure": [ { @@ -109,7 +109,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/species", - "propertyName": "vocab:species", + "propertyName": "species", "ensureOrder": true, "structure": [ { @@ -122,7 +122,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/studiedState", - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -135,7 +135,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "ensureOrder": true, "structure": [ { @@ -151,7 +151,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isPartOf", "reverse": true }, - "propertyName": "vocab:isPartOf", + "propertyName": "isPartOf", "ensureOrder": true, "structure": [ { @@ -167,7 +167,7 @@ "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", "reverse": true }, - "propertyName": "vocab:studiedSpecimen", + "propertyName": "studiedSpecimen", "ensureOrder": true, "structure": [ { @@ -183,7 +183,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -199,7 +199,7 @@ "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", "reverse": true }, - "propertyName": "vocab:usedSpecimen", + "propertyName": "usedSpecimen", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json b/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json index ea8b9c0c..5a0308e4 100644 --- a/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": { @@ -49,14 +49,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:age__QuantitativeValue", + "propertyName": "age__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -64,16 +64,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -81,13 +82,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -96,18 +99,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:age__QuantitativeValueRange", + "propertyName": "age__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -115,15 +118,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -131,13 +135,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/attribute", - "propertyName": "vocab:attribute", + "propertyName": "attribute", "ensureOrder": true, "structure": [ { @@ -150,7 +156,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/descendedFrom", - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ { @@ -163,16 +169,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/pathology", - "propertyName": "vocab:pathology", + "propertyName": "pathology", "ensureOrder": true, "structure": [ { @@ -190,14 +196,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValue", + "propertyName": "relativeTimeIndication__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -205,16 +211,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -222,13 +229,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -237,18 +246,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValueRange", + "propertyName": "relativeTimeIndication__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -256,15 +265,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -272,9 +282,11 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -283,14 +295,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:weight__QuantitativeValue", + "propertyName": "weight__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -298,16 +310,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -315,13 +328,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -330,18 +345,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:weight__QuantitativeValueRange", + "propertyName": "weight__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -349,15 +364,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -365,16 +381,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", "reverse": true }, - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ { @@ -390,7 +408,7 @@ "@id": "https://openminds.ebrains.eu/vocab/input", "reverse": true }, - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -406,7 +424,7 @@ "@id": "https://openminds.ebrains.eu/vocab/output", "reverse": true }, - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { @@ -422,7 +440,7 @@ "@id": "https://openminds.ebrains.eu/vocab/studiedState", "reverse": true }, - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -438,7 +456,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json b/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json index 7aeb92f7..674cd480 100644 --- a/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", - "propertyName": "vocab:additionalRemarks" + "propertyName": "additionalRemarks" }, { "path": { @@ -49,14 +49,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:age__QuantitativeValue", + "propertyName": "age__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -64,16 +64,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -81,13 +82,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -96,18 +99,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:age__QuantitativeValueRange", + "propertyName": "age__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -115,15 +118,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -131,13 +135,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/attribute", - "propertyName": "vocab:attribute", + "propertyName": "attribute", "ensureOrder": true, "structure": [ { @@ -150,7 +156,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/descendedFrom", - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ { @@ -163,16 +169,16 @@ }, { "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", - "propertyName": "vocab:internalIdentifier" + "propertyName": "internalIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/lookupLabel", - "propertyName": "vocab:lookupLabel", + "propertyName": "lookupLabel", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/pathology", - "propertyName": "vocab:pathology", + "propertyName": "pathology", "ensureOrder": true, "structure": [ { @@ -190,14 +196,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValue", + "propertyName": "relativeTimeIndication__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -205,16 +211,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -222,13 +229,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -237,18 +246,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:relativeTimeIndication__QuantitativeValueRange", + "propertyName": "relativeTimeIndication__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -256,15 +265,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -272,9 +282,11 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -283,14 +295,14 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" } }, - "propertyName": "vocab:weight__QuantitativeValue", + "propertyName": "weight__QuantitativeValue", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", - "propertyName": "vocab:typeOfUncertainty", + "propertyName": "typeOfUncertainty", "structure": [ { "path": "@id" @@ -298,16 +310,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/uncertainty", - "propertyName": "vocab:uncertainty", + "propertyName": "uncertainty", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/unit", - "propertyName": "vocab:unit", + "propertyName": "unit", "structure": [ { "path": "@id" @@ -315,13 +328,15 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/value", - "propertyName": "vocab:value" + "propertyName": "value" } - ] + ], + "singleValue": "FIRST" }, { "path": { @@ -330,18 +345,18 @@ "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" } }, - "propertyName": "vocab:weight__QuantitativeValueRange", + "propertyName": "weight__QuantitativeValueRange", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/maxValue", - "propertyName": "vocab:maxValue" + "propertyName": "maxValue" }, { "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", - "propertyName": "vocab:maxValueUnit", + "propertyName": "maxValueUnit", "structure": [ { "path": "@id" @@ -349,15 +364,16 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/minValue", - "propertyName": "vocab:minValue" + "propertyName": "minValue" }, { "path": "https://openminds.ebrains.eu/vocab/minValueUnit", - "propertyName": "vocab:minValueUnit", + "propertyName": "minValueUnit", "structure": [ { "path": "@id" @@ -365,16 +381,18 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" } - ] + ], + "singleValue": "FIRST" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", "reverse": true }, - "propertyName": "vocab:descendedFrom", + "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ { @@ -390,7 +408,7 @@ "@id": "https://openminds.ebrains.eu/vocab/input", "reverse": true }, - "propertyName": "vocab:input", + "propertyName": "input", "ensureOrder": true, "structure": [ { @@ -406,7 +424,7 @@ "@id": "https://openminds.ebrains.eu/vocab/output", "reverse": true }, - "propertyName": "vocab:output", + "propertyName": "output", "ensureOrder": true, "structure": [ { @@ -422,7 +440,7 @@ "@id": "https://openminds.ebrains.eu/vocab/studiedState", "reverse": true }, - "propertyName": "vocab:studiedState", + "propertyName": "studiedState", "ensureOrder": true, "structure": [ { @@ -438,7 +456,7 @@ "@id": "https://openminds.ebrains.eu/vocab/groupedBy", "reverse": true }, - "propertyName": "vocab:groupedBy", + "propertyName": "groupedBy", "ensureOrder": true, "structure": [ { @@ -454,7 +472,7 @@ "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", "reverse": true }, - "propertyName": "vocab:usedSpecimen", + "propertyName": "usedSpecimen", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/url_simple_query.json b/test/test_data/queries/openminds/core/url_simple_query.json index 72a691de..2ccf20c8 100644 --- a/test/test_data/queries/openminds/core/url_simple_query.json +++ b/test/test_data/queries/openminds/core/url_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/URL", - "propertyName": "vocab:URL" + "propertyName": "URL" }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ { "path": "@id" diff --git a/test/test_data/queries/openminds/core/webresource_simple_query.json b/test/test_data/queries/openminds/core/webresource_simple_query.json index 09b4d5f4..06196a4c 100644 --- a/test/test_data/queries/openminds/core/webresource_simple_query.json +++ b/test/test_data/queries/openminds/core/webresource_simple_query.json @@ -40,11 +40,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contentDescription", - "propertyName": "vocab:contentDescription" + "propertyName": "contentDescription" }, { "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ { "path": "@id" @@ -52,18 +52,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/IRI", - "propertyName": "vocab:IRI" + "propertyName": "IRI" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/describedIn", "reverse": true }, - "propertyName": "vocab:describedIn", + "propertyName": "describedIn", "ensureOrder": true, "structure": [ { @@ -79,7 +80,7 @@ "@id": "https://openminds.ebrains.eu/vocab/fullDocumentation", "reverse": true }, - "propertyName": "vocab:fullDocumentation", + "propertyName": "fullDocumentation", "ensureOrder": true, "structure": [ { @@ -95,7 +96,7 @@ "@id": "https://openminds.ebrains.eu/vocab/license", "reverse": true }, - "propertyName": "vocab:license", + "propertyName": "license", "ensureOrder": true, "structure": [ { @@ -111,7 +112,7 @@ "@id": "https://openminds.ebrains.eu/vocab/outputData", "reverse": true }, - "propertyName": "vocab:outputData", + "propertyName": "outputData", "ensureOrder": true, "structure": [ { @@ -127,7 +128,7 @@ "@id": "https://openminds.ebrains.eu/vocab/referenceData", "reverse": true }, - "propertyName": "vocab:referenceData", + "propertyName": "referenceData", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/webservice_simple_query.json b/test/test_data/queries/openminds/core/webservice_simple_query.json index 23c43eb9..d4999f43 100644 --- a/test/test_data/queries/openminds/core/webservice_simple_query.json +++ b/test/test_data/queries/openminds/core/webservice_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -53,11 +53,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -70,12 +70,12 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/hasVersion", - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -88,22 +88,22 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -119,7 +119,7 @@ "@id": "https://openminds.ebrains.eu/vocab/service", "reverse": true }, - "propertyName": "vocab:service", + "propertyName": "service", "ensureOrder": true, "structure": [ { @@ -135,7 +135,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hostedBy", "reverse": true }, - "propertyName": "vocab:hostedBy", + "propertyName": "hostedBy", "ensureOrder": true, "structure": [ { @@ -151,7 +151,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -167,7 +167,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { diff --git a/test/test_data/queries/openminds/core/webserviceversion_simple_query.json b/test/test_data/queries/openminds/core/webserviceversion_simple_query.json index 64d1292f..f1d7473b 100644 --- a/test/test_data/queries/openminds/core/webserviceversion_simple_query.json +++ b/test/test_data/queries/openminds/core/webserviceversion_simple_query.json @@ -40,7 +40,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/accessibility", - "propertyName": "vocab:accessibility", + "propertyName": "accessibility", "structure": [ { "path": "@id" @@ -48,18 +48,19 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/copyright", - "propertyName": "vocab:copyright", + "propertyName": "copyright", "structure": [ { "path": "@type" }, { "path": "https://openminds.ebrains.eu/vocab/holder", - "propertyName": "vocab:holder", + "propertyName": "holder", "ensureOrder": true, "structure": [ { @@ -72,14 +73,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/year", - "propertyName": "vocab:year", + "propertyName": "year", "ensureOrder": true } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/custodian", - "propertyName": "vocab:custodian", + "propertyName": "custodian", "ensureOrder": true, "structure": [ { @@ -92,11 +94,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/description", - "propertyName": "vocab:description" + "propertyName": "description" }, { "path": "https://openminds.ebrains.eu/vocab/developer", - "propertyName": "vocab:developer", + "propertyName": "developer", "ensureOrder": true, "structure": [ { @@ -109,7 +111,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", - "propertyName": "vocab:fullDocumentation", + "propertyName": "fullDocumentation", "structure": [ { "path": "@id" @@ -117,16 +119,17 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "sort": true }, { "path": "https://openminds.ebrains.eu/vocab/funding", - "propertyName": "vocab:funding", + "propertyName": "funding", "ensureOrder": true, "structure": [ { @@ -139,7 +142,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/hasPart", - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -152,15 +155,15 @@ }, { "path": "https://openminds.ebrains.eu/vocab/homepage", - "propertyName": "vocab:homepage" + "propertyName": "homepage" }, { "path": "https://openminds.ebrains.eu/vocab/howToCite", - "propertyName": "vocab:howToCite" + "propertyName": "howToCite" }, { "path": "https://openminds.ebrains.eu/vocab/inputFormat", - "propertyName": "vocab:inputFormat", + "propertyName": "inputFormat", "ensureOrder": true, "structure": [ { @@ -173,7 +176,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", - "propertyName": "vocab:isAlternativeVersionOf", + "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ { @@ -186,7 +189,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "structure": [ { "path": "@id" @@ -194,11 +197,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/keyword", - "propertyName": "vocab:keyword", + "propertyName": "keyword", "ensureOrder": true, "structure": [ { @@ -211,7 +215,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/otherContribution", - "propertyName": "vocab:otherContribution", + "propertyName": "otherContribution", "ensureOrder": true, "structure": [ { @@ -219,7 +223,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/contributor", - "propertyName": "vocab:contributor", + "propertyName": "contributor", "structure": [ { "path": "@id" @@ -227,11 +231,12 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/type", - "propertyName": "vocab:type", + "propertyName": "type", "ensureOrder": true, "structure": [ { @@ -246,7 +251,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/outputFormat", - "propertyName": "vocab:outputFormat", + "propertyName": "outputFormat", "ensureOrder": true, "structure": [ { @@ -259,7 +264,7 @@ }, { "path": "https://openminds.ebrains.eu/vocab/relatedPublication", - "propertyName": "vocab:relatedPublication", + "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ { @@ -272,11 +277,11 @@ }, { "path": "https://openminds.ebrains.eu/vocab/releaseDate", - "propertyName": "vocab:releaseDate" + "propertyName": "releaseDate" }, { "path": "https://openminds.ebrains.eu/vocab/repository", - "propertyName": "vocab:repository", + "propertyName": "repository", "structure": [ { "path": "@id" @@ -284,31 +289,32 @@ { "path": "@type" } - ] + ], + "singleValue": "FIRST" }, { "path": "https://openminds.ebrains.eu/vocab/shortName", - "propertyName": "vocab:shortName" + "propertyName": "shortName" }, { "path": "https://openminds.ebrains.eu/vocab/supportChannel", - "propertyName": "vocab:supportChannel", + "propertyName": "supportChannel", "ensureOrder": true }, { "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", - "propertyName": "vocab:versionIdentifier" + "propertyName": "versionIdentifier" }, { "path": "https://openminds.ebrains.eu/vocab/versionInnovation", - "propertyName": "vocab:versionInnovation" + "propertyName": "versionInnovation" }, { "path": { "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -324,7 +330,7 @@ "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", "reverse": true }, - "propertyName": "vocab:isNewVersionOf", + "propertyName": "isNewVersionOf", "ensureOrder": true, "structure": [ { @@ -340,7 +346,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasPart", "reverse": true }, - "propertyName": "vocab:hasPart", + "propertyName": "hasPart", "ensureOrder": true, "structure": [ { @@ -356,7 +362,7 @@ "@id": "https://openminds.ebrains.eu/vocab/hasVersion", "reverse": true }, - "propertyName": "vocab:hasVersion", + "propertyName": "hasVersion", "ensureOrder": true, "structure": [ { @@ -372,7 +378,7 @@ "@id": "https://openminds.ebrains.eu/vocab/about", "reverse": true }, - "propertyName": "vocab:about", + "propertyName": "about", "ensureOrder": true, "structure": [ { @@ -388,7 +394,7 @@ "@id": "https://openminds.ebrains.eu/vocab/environment", "reverse": true }, - "propertyName": "vocab:environment", + "propertyName": "environment", "ensureOrder": true, "structure": [ { diff --git a/test/test_openminds_computation.py b/test/test_openminds_computation.py index da96acdb..c3cb0519 100644 --- a/test/test_openminds_computation.py +++ b/test/test_openminds_computation.py @@ -38,25 +38,27 @@ def test_generate_query(self, mock_client): {"path": "@type"}, { "path": "https://openminds.ebrains.eu/vocab/configuration", - "propertyName": "vocab:configuration", + "propertyName": "configuration", + "singleValue": "FIRST", "structure": [{"path": "@id"}, {"path": "@type"}], }, - {"path": "https://openminds.ebrains.eu/vocab/description", "propertyName": "vocab:description"}, + {"path": "https://openminds.ebrains.eu/vocab/description", "propertyName": "description"}, { "path": "https://openminds.ebrains.eu/vocab/hardware", - "propertyName": "vocab:hardware", + "propertyName": "hardware", + "singleValue": "FIRST", "structure": [{"path": "@id"}, {"path": "@type"}], }, - {"path": "https://openminds.ebrains.eu/vocab/name", "propertyName": "vocab:name", "sort": True}, + {"path": "https://openminds.ebrains.eu/vocab/name", "propertyName": "name", "sort": True}, { "path": "https://openminds.ebrains.eu/vocab/software", - "propertyName": "vocab:software", + "propertyName": "software", "ensureOrder": True, "structure": [{"path": "@id"}, {"path": "@type"}], }, { "path": {"@id": "https://openminds.ebrains.eu/vocab/environment", "reverse": True}, - "propertyName": "vocab:environment", + "propertyName": "environment", "ensureOrder": True, "structure": [{"path": "@id"}, {"path": "@type"}], }, diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index a0eb65c4..28ab19e3 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -200,10 +200,11 @@ def test_retrieve_released_model_versions_no_follow(kg_client): assert isinstance(ct_proxy, KGProxy) assert ct_proxy.classes == [omcore.ContentType] if api == "query": - assert isinstance(ver.is_version_of, KGProxy) + assert isinstance(ver.is_version_of[0], KGProxy) + assert ver.is_version_of[0].classes == [omcore.Model] else: assert isinstance(ver.is_version_of, KGQuery) - assert ver.is_version_of.classes == [omcore.Model] + assert ver.is_version_of.classes == [omcore.Model] @skip_if_no_connection @@ -233,7 +234,7 @@ def test_retrieve_released_model_versions_follow_reverse_links(kg_client): for fmt in as_list(ver.formats): assert isinstance(fmt, omcore.ContentType) # check first level reverse links have been resolved - model = ver.is_version_of + model = ver.is_version_of[0] assert isinstance(model, omcore.Model) # check forward links from first level reverse links assert ver.id in [ver2.id for ver2 in as_list(model.versions)] @@ -335,7 +336,7 @@ def test_query_across_reverse_links(kg_client): assert len(versions) < 100 for version in versions: orgs = [] - model = version.is_version_of + model = version.is_version_of[0] for dev in as_list(model.developers): for affil in as_list(dev.affiliations): if affil.member_of: @@ -474,20 +475,25 @@ def test_to_jsonld(): affiliations=omcore.Affiliation(member_of=omcore.Organization(name="The Lonely Mountain")), ) expected1 = { + "@context": { + "@vocab": "https://openminds.ebrains.eu/vocab/" + }, "@id": "0000", - "@type": ["https://openminds.ebrains.eu/core/Person"], - "https://openminds.ebrains.eu/vocab/affiliation": { - "@type": ["https://openminds.ebrains.eu/core/Affiliation"], - "https://openminds.ebrains.eu/vocab/memberOf": { - "@type": ["https://openminds.ebrains.eu/core/Organization"], - "https://openminds.ebrains.eu/vocab/fullName": "The Lonely Mountain", + "@type": "https://openminds.ebrains.eu/core/Person", + "affiliation": [{ + "@type": "https://openminds.ebrains.eu/core/Affiliation", + "memberOf": { + "@type": "https://openminds.ebrains.eu/core/Organization", + "fullName": "The Lonely Mountain", }, - }, - "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield", - "https://openminds.ebrains.eu/vocab/givenName": "Thorin", + }], + "familyName": "Oakenshield", + "givenName": "Thorin", } - assert person1.to_jsonld(embed_linked_nodes=True) == expected1 - assert person1.to_jsonld(embed_linked_nodes=False) == expected1 + assert person1.to_jsonld(embed_linked_nodes=True, include_empty_properties=False) == expected1 + with pytest.raises(ValueError) as err: + person1.to_jsonld(embed_linked_nodes=False, include_empty_properties=False) + assert "Exporting as a stand-alone JSON-LD document requires @id to be defined" in err person2 = omcore.Person( id="0000", @@ -496,31 +502,37 @@ def test_to_jsonld(): affiliations=omcore.Affiliation(member_of=omcore.Organization(id="1111", name="The Lonely Mountain")), ) expected2a = { + "@context": { + "@vocab": "https://openminds.ebrains.eu/vocab/" + }, "@id": "0000", - "@type": ["https://openminds.ebrains.eu/core/Person"], - "https://openminds.ebrains.eu/vocab/affiliation": { - "@type": ["https://openminds.ebrains.eu/core/Affiliation"], - "https://openminds.ebrains.eu/vocab/memberOf": { + "@type": "https://openminds.ebrains.eu/core/Person", + "affiliation": [{ + "@type": "https://openminds.ebrains.eu/core/Affiliation", + "memberOf": { "@id": "1111", - "@type": ["https://openminds.ebrains.eu/core/Organization"], - "https://openminds.ebrains.eu/vocab/fullName": "The Lonely Mountain", + "@type": "https://openminds.ebrains.eu/core/Organization", + "fullName": "The Lonely Mountain", }, - }, - "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield", - "https://openminds.ebrains.eu/vocab/givenName": "Thorin", + }], + "familyName": "Oakenshield", + "givenName": "Thorin", } expected2b = { - "@id": "0000", - "@type": ["https://openminds.ebrains.eu/core/Person"], - "https://openminds.ebrains.eu/vocab/affiliation": { - "@type": ["https://openminds.ebrains.eu/core/Affiliation"], - "https://openminds.ebrains.eu/vocab/memberOf": {"@id": "1111"}, + "@context": { + "@vocab": "https://openminds.ebrains.eu/vocab/" }, - "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield", - "https://openminds.ebrains.eu/vocab/givenName": "Thorin", + "@id": "0000", + "@type": "https://openminds.ebrains.eu/core/Person", + "affiliation": [{ + "@type": "https://openminds.ebrains.eu/core/Affiliation", + "memberOf": {"@id": "1111"}, + }], + "familyName": "Oakenshield", + "givenName": "Thorin", } - assert person2.to_jsonld(embed_linked_nodes=True) == expected2a - assert person2.to_jsonld(embed_linked_nodes=False) == expected2b + assert person2.to_jsonld(embed_linked_nodes=True, include_empty_properties=False) == expected2a + assert person2.to_jsonld(embed_linked_nodes=False, include_empty_properties=False) == expected2b @skip_if_using_production_server @@ -696,7 +708,9 @@ def test_property_names(): "contact_information", "digital_identifiers", "family_name", - "given_name", + "given_name" + ] + assert omcore.Person.reverse_property_names == [ "activities", "comments", "coordinated_projects", @@ -717,20 +731,20 @@ def test_diff(): id="0000", given_name="Thorin", family_name="Oakenshield", - affiliations=omcore.Affiliation(member_of=omcore.Organization(name="The Lonely Mountain")), + affiliations=omcore.Affiliation(member_of=omcore.Organization(id="1000", name="The Lonely Mountain")), ) person2 = omcore.Person( given_name="Thorin son of Thráin", family_name="Oakenshield", - affiliations=omcore.Affiliation(member_of=omcore.Organization(name="Erebor")), + affiliations=omcore.Affiliation(member_of=omcore.Organization(id="1001", name="Erebor")), ) expected = { "id": ("0000", None), "properties": { "given_name": ("Thorin", "Thorin son of Thráin"), "affiliations": ( - omcore.Affiliation(member_of=omcore.Organization(name="The Lonely Mountain")), - omcore.Affiliation(member_of=omcore.Organization(name="Erebor")), + omcore.Affiliation(member_of=omcore.Organization(id="1000", name="The Lonely Mountain")), + omcore.Affiliation(member_of=omcore.Organization(id="1001", name="Erebor")), ), }, } @@ -858,8 +872,8 @@ def test_with_new_namespace_from_query(): "@id": "https://kg.ebrains.eu/api/instances/708024f7-9dd7-4c92-ae95-936db23c6d99", "https://schema.hbp.eu/myQuery/space": "model", "@type": ["https://openminds.om-i.org/types/Model"], - "vocab:abstractionLevel": {"@id": "https://kg.ebrains.eu/api/instances/57becc19-f0a1-4d23-99bb-eb3b7d3cdb9a"}, - "vocab:custodian": [ + "abstractionLevel": {"@id": "https://kg.ebrains.eu/api/instances/57becc19-f0a1-4d23-99bb-eb3b7d3cdb9a"}, + "custodian": [ { "@id": "https://kg.ebrains.eu/api/instances/2905ce6c-bc89-4c99-b8b0-0fa9a17d1897", "@type": ["https://openminds.om-i.org/types/Person"], @@ -881,8 +895,8 @@ def test_with_new_namespace_from_query(): "@type": ["https://openminds.om-i.org/types/Person"], }, ], - "vocab:description": "The scaffolding procedure has been enhanced compared to version 1.0. It's able to generate a scalable cerebellar structure, embedding specific 3D positions for each neuron and specific pair connections. Customized placement strategies allow to match layered density and encumbrance for each neuron type. Customized connection strategies allow to match anisotropic geometrical fields of intersection, and statistical convergence and divergence ratios.\nThe scaffold can host different neuron models. Several input stimulation patterns can be used to investigate network complex dynamics, revealing the relationships between structural constraints and underlying neuron mechanisms with the cerebellar circuit functioning, over space and time.\n\nMain link to Sonata conversion can be found here:\nhttps://github.com/SelezioneCasuale/scaffold/tree/sonata-version/scaffold", - "vocab:developer": [ + "description": "The scaffolding procedure has been enhanced compared to version 1.0. It's able to generate a scalable cerebellar structure, embedding specific 3D positions for each neuron and specific pair connections. Customized placement strategies allow to match layered density and encumbrance for each neuron type. Customized connection strategies allow to match anisotropic geometrical fields of intersection, and statistical convergence and divergence ratios.\nThe scaffold can host different neuron models. Several input stimulation patterns can be used to investigate network complex dynamics, revealing the relationships between structural constraints and underlying neuron mechanisms with the cerebellar circuit functioning, over space and time.\n\nMain link to Sonata conversion can be found here:\nhttps://github.com/SelezioneCasuale/scaffold/tree/sonata-version/scaffold", + "developer": [ { "@id": "https://kg.ebrains.eu/api/instances/2905ce6c-bc89-4c99-b8b0-0fa9a17d1897", "@type": ["https://openminds.om-i.org/types/Person"], @@ -904,24 +918,24 @@ def test_with_new_namespace_from_query(): "@type": ["https://openminds.om-i.org/types/Person"], }, ], - "vocab:digitalIdentifier": [], - "vocab:fullName": "Scaffold Model of Cerebellum microcircuit version 2.0", - "vocab:hasVersion": [ + "digitalIdentifier": [], + "fullName": "Scaffold Model of Cerebellum microcircuit version 2.0", + "hasVersion": [ { "@id": "https://kg.ebrains.eu/api/instances/7035d53f-1597-4a45-9f72-23c2c933ec66", "@type": ["https://openminds.om-i.org/types/ModelVersion"], } ], - "vocab:homepage": None, - "vocab:howToCite": None, - "vocab:scope": [ + "homepage": None, + "howToCite": None, + "scope": [ { "@id": "https://kg.ebrains.eu/api/instances/6c678004-b8e0-4339-90c5-824e66503eb9", "@type": ["https://openminds.om-i.org/types/ModelScope"], } ], - "vocab:shortName": None, - "vocab:studyTarget": [ + "shortName": None, + "studyTarget": [ { "@id": "https://kg.ebrains.eu/api/instances/ab532423-1fd7-4255-8c6f-f99dc6df814f", "@type": ["https://openminds.om-i.org/types/Species"], @@ -931,9 +945,9 @@ def test_with_new_namespace_from_query(): "@type": ["https://openminds.om-i.org/types/UBERONParcellation"], }, ], - "vocab:about": [], - "vocab:hasPart": [], - "@context": {"vocab": "https://openminds.om-i.org/props/"}, + "about": [], + "hasPart": [], + "@context": {"@vocab": "https://openminds.om-i.org/props/"}, } #omcore.set_error_handling("error") orig_types = (omcore.Model.type_, omcore.Person.type_) diff --git a/test/test_properties.py b/test/test_properties.py deleted file mode 100644 index 40a7250d..00000000 --- a/test/test_properties.py +++ /dev/null @@ -1,186 +0,0 @@ -from datetime import date -from uuid import uuid4 -from openminds.properties import Property -from fairgraph.base import ErrorHandling -from fairgraph.kgobject import KGObject -from fairgraph.embedded import EmbeddedMetadata -from fairgraph.kgproxy import KGProxy -from fairgraph.queries import get_filter_value -import pytest - - -class SomeOrganization(KGObject): - default_space = "common" - type_ = "https://openminds.ebrains.eu/test/Organization" - context = { - "vocab": "https://openminds.ebrains.eu/vocab/", - } - properties = [ - Property("name", str, "vocab:fullName", multiple=False, required=True), - Property("alias", str, "vocab:shortName", multiple=False, required=False), - ] - reverse_properties = [] - existence_query_properties = ("name",) - - -class SomeAffiliation(EmbeddedMetadata): - type_ = "https://openminds.ebrains.eu/test/Affiliation" - context = { - "vocab": "https://openminds.ebrains.eu/vocab/", - } - properties = [ - Property("end_date", date, "vocab:endDate", multiple=False, required=False), - Property("member_of", (SomeOrganization,), "vocab:memberOf", multiple=False, required=False), - Property("start_date", date, "vocab:startDate", multiple=False, required=False), - ] - reverse_properties = [] - - -class SomeContactInformation(KGObject): - default_space = "restricted" - type_ = "https://openminds.ebrains.eu/test/ContactInformation" - context = { - "vocab": "https://openminds.ebrains.eu/vocab/", - } - properties = [Property("email", str, "vocab:email", multiple=False, required=True)] - reverse_properties = [] - existence_query_properties = ("email",) - - -def test_serialize_embedded(): - property_embedded_metadata = Property( - "affiliations", (SomeAffiliation,), "vocab:affiliation", multiple=True, required=False - ) - - client = None - test_affiliation = SomeAffiliation( - start_date=date(2023, 1, 1), - member_of=SomeOrganization( - name="Acme Corporation", - alias="acme", - id=f"https://kg.ebrains.eu/api/instances/{uuid4()}", - ), - ) - result = property_embedded_metadata.serialize(test_affiliation, follow_links=False) - expected = { - "@type": [SomeAffiliation.type_], - "https://openminds.ebrains.eu/vocab/memberOf": {"@id": test_affiliation.member_of.id}, - "https://openminds.ebrains.eu/vocab/startDate": "2023-01-01", - } - assert result == expected - - -def test_serialize_no_multiple(): - property_no_multiple = Property( - "contact_information", - (SomeContactInformation,), - "vocab:contactInformation", - multiple=False, - required=False - ) - client = None - - # single object - test_info = SomeContactInformation( - email="someone@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}" - ) - result = property_no_multiple.serialize(test_info, follow_links=False) - expected = {"@id": test_info.id} - assert result == expected - - # single proxy - test_info = KGProxy(SomeContactInformation, f"https://kg.ebrains.eu/api/instances/{uuid4()}") - result = property_no_multiple.serialize(test_info, follow_links=False) - expected = {"@id": test_info.id} - assert result == expected - - # # two objects, strict - # test_info = [ - # SomeContactInformation(email="someone@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - # SomeContactInformation(email="sameperson@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - # ] - # with pytest.raises(ValueError): - # result = property_no_multiple.serialize(test_info, follow_links=False) - - # two objects, not strict - test_info = [ - SomeContactInformation(email="someone@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - SomeContactInformation(email="sameperson@example.com", id=f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - ] - result = property_no_multiple.serialize(test_info, follow_links=False) - expected = [{"@id": test_info[0].id}, {"@id": test_info[1].id}] - assert result == expected - - # two proxies, not strict - test_info = [ - KGProxy(SomeContactInformation, f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - KGProxy(SomeContactInformation, f"https://kg.ebrains.eu/api/instances/{uuid4()}"), - ] - result = property_no_multiple.serialize(test_info, follow_links=False) - expected = [{"@id": test_info[0].id}, {"@id": test_info[1].id}] - assert result == expected - - -def test_serialize_unknown(): - some_property = Property( - "contact_information", - (SomeContactInformation,), - "vocab:contactInformation", - multiple=False, - required=False, - ) - client = None - - # # single object - # test_info = complex(1, -1) - # with pytest.raises(ValueError) as excinfo: - # result = some_property.serialize(test_info, follow_links=False) - # expected_error_message = ( - # "fairgraph cannot serialize a value of type " - # "(for property 'contact_information')" - # ) - # assert excinfo.value.args[0] == expected_error_message - - -def test_deserialize(): - date_property = Property("the_date", date, "TheDate") - # with pytest.raises(ValueError): - # date_property.deserialize(42) - - integer_property = Property("the_number", int, "TheNumber") - assert integer_property.deserialize(42) == 42 - assert integer_property.deserialize(42.0) == 42 - assert integer_property.deserialize("42") == 42 - assert integer_property.deserialize([42, 42, 42]) == [42, 42, 42] - assert integer_property.deserialize(["42", 42, "42"]) == [42, 42, 42] - - object_property = Property("the_object", SomeOrganization, "TheObject") - obj_data = { - "@id": "https://kg.ebrains.eu/api/instances/the_id", - "@type": SomeOrganization.type_, - "https://openminds.ebrains.eu/vocab/fullName": "The University", - "https://openminds.ebrains.eu/vocab/shortName": "TU", - } - expected_obj = SomeOrganization(name="The University", alias="TU", id="https://kg.ebrains.eu/api/instances/the_id") - assert object_property.deserialize(obj_data) == expected_obj - - assert object_property.deserialize(None) is None - - assert object_property.deserialize([None, obj_data, None, obj_data]) == [expected_obj, expected_obj] - - assert object_property.deserialize({"@list": [None, obj_data, None, obj_data]}) == [ - expected_obj, - expected_obj, - ] - - -def test_get_filter_value(): - date_property = Property("the_date", date, "TheDate") - assert get_filter_value(date_property, date(2023, 6, 2)) == "2023-06-02" - - integer_property = Property("the_number", int, "TheNumber") - assert get_filter_value(integer_property, 42) == 42 - - object_property = Property("the_object", SomeOrganization, "TheObject") - obj = SomeOrganization(name="The University", alias="TU", id="https://kg.ebrains.eu/api/instances/the_id") - assert get_filter_value(object_property, obj) == "https://kg.ebrains.eu/api/instances/the_id" diff --git a/test/test_queries.py b/test/test_queries.py index 25fc7ab9..1630abd2 100644 --- a/test/test_queries.py +++ b/test/test_queries.py @@ -21,20 +21,20 @@ def example_query_model_version(): QueryProperty("@type"), QueryProperty( "https://openminds.ebrains.eu/vocab/fullName", - name="vocab:fullName", + name="fullName", filter=Filter("CONTAINS", parameter="name"), sorted=True, required=True, ), QueryProperty( "https://openminds.ebrains.eu/vocab/versionIdentifier", - name="vocab:versionIdentifier", + name="versionIdentifier", filter=Filter("EQUALS", parameter="version"), required=True, ), QueryProperty( "https://openminds.ebrains.eu/vocab/format", - name="vocab:format", + name="format", ensure_order=True, properties=[ QueryProperty("@id", filter=Filter("EQUALS", parameter="format")), @@ -43,24 +43,24 @@ def example_query_model_version(): ), QueryProperty( "https://openminds.ebrains.eu/vocab/custodian", - name="vocab:custodian", + name="custodian", ensure_order=True, type_filter="https://openminds.ebrains.eu/core/Person", properties=[ QueryProperty("@id", filter=Filter("EQUALS", parameter="custodian")), QueryProperty( "https://openminds.ebrains.eu/vocab/affiliation", - name="vocab:affiliation", + name="affiliation", properties=[ QueryProperty("@type"), QueryProperty( "https://openminds.ebrains.eu/vocab/memberOf", - name="vocab:memberOf", + name="memberOf", properties=[QueryProperty("@id")], ), QueryProperty( "https://openminds.ebrains.eu/vocab/startDate", - name="vocab:startDate", + name="startDate", ), ], ), @@ -84,32 +84,32 @@ def example_query_model(): QueryProperty("@type"), QueryProperty( "https://openminds.ebrains.eu/vocab/fullName", - name="vocab:fullName", + name="fullName", filter=Filter("CONTAINS", parameter="name"), sorted=True, required=True, ), QueryProperty( "https://openminds.ebrains.eu/vocab/custodian", - name="vocab:custodian", + name="custodian", type_filter="https://openminds.ebrains.eu/core/Person", properties=[ # QueryProperty("@type"), QueryProperty( "https://openminds.ebrains.eu/vocab/familyName", - name="vocab:familyName", + name="familyName", ), ], ), QueryProperty( "https://openminds.ebrains.eu/vocab/custodian", - name="vocab:organization", + name="organization", type_filter="https://openminds.ebrains.eu/core/Organization", properties=[ # QueryProperty("@type"), QueryProperty( "https://openminds.ebrains.eu/vocab/shortName", - name="vocab:shortName", + name="shortName", ), ], ), @@ -219,20 +219,20 @@ def test_query_builder(example_query_model_version): { "filter": {"op": "CONTAINS", "parameter": "name"}, "path": "https://openminds.ebrains.eu/vocab/fullName", - "propertyName": "vocab:fullName", + "propertyName": "fullName", "required": True, "sort": True, }, { "filter": {"op": "EQUALS", "parameter": "version"}, "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", - "propertyName": "vocab:versionIdentifier", + "propertyName": "versionIdentifier", "required": True, }, { "ensureOrder": True, "path": "https://openminds.ebrains.eu/vocab/format", - "propertyName": "vocab:format", + "propertyName": "format", "structure": [ {"filter": {"op": "EQUALS", "parameter": "format"}, "path": "@id"}, {"path": "@type"}, @@ -244,7 +244,7 @@ def test_query_builder(example_query_model_version): "@id": "https://openminds.ebrains.eu/vocab/custodian", "typeFilter": {"@id": "https://openminds.ebrains.eu/core/Person"}, }, - "propertyName": "vocab:custodian", + "propertyName": "custodian", "structure": [ { "filter": {"op": "EQUALS", "parameter": "custodian"}, @@ -252,17 +252,17 @@ def test_query_builder(example_query_model_version): }, { "path": "https://openminds.ebrains.eu/vocab/affiliation", - "propertyName": "vocab:affiliation", + "propertyName": "affiliation", "structure": [ {"path": "@type"}, { "path": "https://openminds.ebrains.eu/vocab/memberOf", - "propertyName": "vocab:memberOf", + "propertyName": "memberOf", "structure": [{"path": "@id"}], }, { "path": "https://openminds.ebrains.eu/vocab/startDate", - "propertyName": "vocab:startDate", + "propertyName": "startDate", }, ], }, @@ -382,21 +382,21 @@ def test_execute_query(kg_client, example_query_model_version): "@id", "@type", "https://schema.hbp.eu/myQuery/space", - "vocab:custodian", - "vocab:format", - "vocab:versionIdentifier", - "vocab:fullName", + "custodian", + "format", + "versionIdentifier", + "fullName", ] ) data0 = data[0] assert set(data0.keys()) == expected_keys - if data0["vocab:custodian"]: - custodian0 = data0["vocab:custodian"][0] - assert set(custodian0.keys()) == set(["@id", "vocab:affiliation"]) - if custodian0["vocab:affiliation"]: - affil0 = custodian0["vocab:affiliation"][0] - assert set(affil0.keys()) == set(["@type", "vocab:memberOf", "vocab:startDate"]) + if data0["custodian"]: + custodian0 = data0["custodian"][0] + assert set(custodian0.keys()) == set(["@id", "affiliation"]) + if custodian0["affiliation"]: + affil0 = custodian0["affiliation"][0] + assert set(affil0.keys()) == set(["@type", "memberOf", "startDate"]) @skip_if_no_connection @@ -410,9 +410,9 @@ def test_execute_query_with_id_filter(kg_client, example_query_model): ) data = response.data assert len(data) == 1 - assert data[0]["vocab:fullName"] == "AdEx Neuron Models with PyNN" - assert data[0]["vocab:custodian"][0]["vocab:familyName"] == "Destexhe" - # assert data[0]["vocab:organization"][0]["vocab:shortName"] == "Destexhe Lab" + assert data[0]["fullName"] == "AdEx Neuron Models with PyNN" + assert data[0]["custodian"][0]["familyName"] == "Destexhe" + # assert data[0]["organization"][0]["shortName"] == "Destexhe Lab" @skip_if_no_connection @@ -483,20 +483,20 @@ def test_generate_query_with_follow_one_link(mock_client): "core", f"{cls.__name__.lower()}_resolved-1_query.json", ) + generated = cls.generate_query( + space=None, + client=mock_client, + filters=None, + follow_links={ + "affiliations": {"member_of": {}}, + "associated_accounts": {}, + "contact_information": {}, + "digital_identifiers": {}, + }, + ) with open(path_expected) as fp: - generated = cls.generate_query( - space=None, - client=mock_client, - filters=None, - follow_links={ - "affiliations": {"member_of": {}}, - "associated_accounts": {}, - "contact_information": {}, - "digital_identifiers": {}, - }, - ) expected = json.load(fp) - assert generated == expected + assert generated == expected def test_generate_query_with_follow_named_links(mock_client): @@ -509,13 +509,13 @@ def test_generate_query_with_follow_named_links(mock_client): "core", f"{cls.__name__.lower()}_newstyle_query.json", ) + generated = cls.generate_query( + space=None, + client=mock_client, + filters={"affiliations__member_of__has_parents__alias": "FZJ"}, + follow_links={"affiliations": {"member_of": {"has_parents": {}}}, "contact_information": {}}, + ) with open(path_expected) as fp: - generated = cls.generate_query( - space=None, - client=mock_client, - filters={"affiliations__member_of__has_parents__alias": "FZJ"}, - follow_links={"affiliations": {"member_of": {"has_parents": {}}}, "contact_information": {}}, - ) expected = json.load(fp) assert generated == expected diff --git a/test/test_registry.py b/test/test_registry.py deleted file mode 100644 index 412bb5d7..00000000 --- a/test/test_registry.py +++ /dev/null @@ -1,12 +0,0 @@ -from openminds.properties import Property - -from fairgraph.registry import Node - - -def test_docstring_generation(): - class Foo(metaclass=Node): - """This is the base docstring""" - - properties = [Property("foo", str, "Foo", doc="foo-foo")] - - assert Foo.__doc__ == "\nThis is the base docstring\n\nArgs\n----\nfoo : str\n foo-foo\n\n" diff --git a/test/test_utility.py b/test/test_utility.py index 617f2d00..2a3a237e 100644 --- a/test/test_utility.py +++ b/test/test_utility.py @@ -1,7 +1,7 @@ import os import tempfile import pytest -from fairgraph.utility import expand_filter, compact_uri, in_notebook, accepted_terms_of_use, sha1sum +from fairgraph.utility import (expand_filter, compact_uri, in_notebook, accepted_terms_of_use, sha1sum, normalize_data) from .utils import kg_client, skip_if_no_connection @@ -57,3 +57,37 @@ def test_sha1sum(): fp.close() assert sha1sum(fp.name) == "80a963e503e9ed478c2cc528fd344d58122929c2" os.remove(fp.name) + + +def test_normalize_data(): + data = { + "@context": { + "@vocab": "https://openminds.ebrains.eu/vocab/" + }, + "@id": "0000", + "@type": "https://openminds.ebrains.eu/core/Person", + "affiliation": { + "@type": "https://openminds.ebrains.eu/core/Affiliation", + "memberOf": { + "@type": "https://openminds.ebrains.eu/core/Organization", + "fullName": "The Lonely Mountain", + }, + }, + "familyName": "Oakenshield", + "givenName": "Thorin", + } + context = data.pop("@context") + expected = { + "@id": "0000", + "@type": ["https://openminds.ebrains.eu/core/Person"], + "https://openminds.ebrains.eu/vocab/affiliation": { + "@type": ["https://openminds.ebrains.eu/core/Affiliation"], + "https://openminds.ebrains.eu/vocab/memberOf": { + "@type": ["https://openminds.ebrains.eu/core/Organization"], + "https://openminds.ebrains.eu/vocab/fullName": "The Lonely Mountain", + }, + }, + "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield", + "https://openminds.ebrains.eu/vocab/givenName": "Thorin", + } + assert normalize_data(data, context) == expected From ba49cea8c6a34018597ac227bd96989a03cba0df Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 30 Jul 2025 15:05:48 +0200 Subject: [PATCH 07/25] Changes to openminds module due to recent builder changes --- .../openminds/chemicals/amount_of_chemical.py | 24 +- .../openminds/chemicals/chemical_mixture.py | 70 +-- .../openminds/chemicals/chemical_substance.py | 57 +-- .../openminds/chemicals/product_source.py | 42 +- .../openminds/computation/data_analysis.py | 180 +------- fairgraph/openminds/computation/data_copy.py | 176 +------ .../openminds/computation/environment.py | 65 +-- .../computation/generic_computation.py | 178 +------ .../openminds/computation/hardware_system.py | 40 +- .../computation/launch_configuration.py | 53 +-- fairgraph/openminds/computation/local_file.py | 80 +--- .../openminds/computation/model_validation.py | 176 +------ .../openminds/computation/optimization.py | 179 +------ fairgraph/openminds/computation/simulation.py | 179 +------ .../openminds/computation/software_agent.py | 72 ++- .../openminds/computation/validation_test.py | 142 +----- .../computation/validation_test_version.py | 314 ++----------- .../openminds/computation/visualization.py | 178 +------ .../computation/workflow_execution.py | 46 +- .../openminds/computation/workflow_recipe.py | 92 +--- .../computation/workflow_recipe_version.py | 321 ++----------- .../controlled_terms/action_status_type.py | 111 ++--- .../controlled_terms/age_category.py | 99 ++-- .../controlled_terms/analysis_technique.py | 119 ++--- .../anatomical_axes_orientation.py | 99 ++-- .../anatomical_identification_type.py | 99 ++-- .../controlled_terms/anatomical_plane.py | 99 ++-- .../annotation_criteria_type.py | 99 ++-- .../controlled_terms/annotation_type.py | 99 ++-- .../openminds/controlled_terms/atlas_type.py | 97 ++-- .../auditory_stimulus_type.py | 143 ++---- .../controlled_terms/biological_order.py | 137 ++---- .../controlled_terms/biological_process.py | 93 +--- .../controlled_terms/biological_sex.py | 149 +++--- .../controlled_terms/breeding_type.py | 143 ++---- .../controlled_terms/cell_culture_type.py | 137 ++---- .../openminds/controlled_terms/cell_type.py | 159 +++---- .../controlled_terms/chemical_mixture_type.py | 99 ++-- .../openminds/controlled_terms/colormap.py | 93 +--- .../controlled_terms/contribution_type.py | 93 +--- .../cranial_window_construction_type.py | 99 ++-- .../cranial_window_reinforcement_type.py | 99 ++-- .../controlled_terms/criteria_quality_type.py | 99 ++-- .../openminds/controlled_terms/data_type.py | 103 ++--- .../openminds/controlled_terms/device_type.py | 105 ++--- .../controlled_terms/difference_measure.py | 99 ++-- .../openminds/controlled_terms/disease.py | 155 +++---- .../controlled_terms/disease_model.py | 155 +++---- .../controlled_terms/educational_level.py | 93 +--- .../electrical_stimulus_type.py | 149 +++--- .../controlled_terms/ethics_assessment.py | 93 +--- .../controlled_terms/experimental_approach.py | 93 +--- .../controlled_terms/file_bundle_grouping.py | 105 ++--- .../controlled_terms/file_repository_type.py | 99 ++-- .../controlled_terms/file_usage_role.py | 99 ++-- .../controlled_terms/genetic_strain_type.py | 143 ++---- .../gustatory_stimulus_type.py | 143 ++---- .../openminds/controlled_terms/handedness.py | 143 ++---- .../openminds/controlled_terms/language.py | 97 ++-- .../openminds/controlled_terms/laterality.py | 105 ++--- .../learning_resource_type.py | 97 ++-- .../controlled_terms/measured_quantity.py | 99 ++-- .../controlled_terms/measured_signal_type.py | 93 +--- .../controlled_terms/meta_data_model_type.py | 97 ++-- .../model_abstraction_level.py | 99 ++-- .../openminds/controlled_terms/model_scope.py | 99 ++-- .../controlled_terms/molecular_entity.py | 155 +++---- .../controlled_terms/mr_acquisition_type.py | 93 +--- .../controlled_terms/mri_pulse_sequence.py | 103 ++--- .../controlled_terms/mri_weighting.py | 103 ++--- .../olfactory_stimulus_type.py | 143 ++---- .../controlled_terms/operating_device.py | 93 +--- .../controlled_terms/operating_system.py | 97 ++-- .../controlled_terms/optical_stimulus_type.py | 143 ++---- fairgraph/openminds/controlled_terms/organ.py | 165 +++---- .../controlled_terms/organism_substance.py | 159 +++---- .../controlled_terms/organism_system.py | 137 ++---- .../controlled_terms/patch_clamp_variation.py | 99 ++-- .../controlled_terms/preparation_type.py | 113 ++--- .../controlled_terms/product_accessibility.py | 93 +--- .../controlled_terms/programming_language.py | 97 ++-- .../controlled_terms/qualitative_overlap.py | 93 +--- .../controlled_terms/semantic_data_type.py | 93 +--- .../openminds/controlled_terms/service.py | 105 ++--- .../openminds/controlled_terms/setup_type.py | 99 ++-- .../software_application_category.py | 93 +--- .../controlled_terms/software_feature.py | 93 +--- .../openminds/controlled_terms/species.py | 157 +++---- .../controlled_terms/stimulation_approach.py | 107 ++--- .../controlled_terms/stimulation_technique.py | 107 ++--- .../controlled_terms/subcellular_entity.py | 157 +++---- .../controlled_terms/subject_attribute.py | 99 ++-- .../controlled_terms/tactile_stimulus_type.py | 143 ++---- .../openminds/controlled_terms/technique.py | 109 ++--- .../controlled_terms/term_suggestion.py | 149 ++---- .../openminds/controlled_terms/terminology.py | 99 ++-- .../tissue_sample_attribute.py | 99 ++-- .../controlled_terms/tissue_sample_type.py | 143 ++---- .../controlled_terms/type_of_uncertainty.py | 99 ++-- .../controlled_terms/uberon_parcellation.py | 163 +++---- .../controlled_terms/unit_of_measurement.py | 110 ++--- .../controlled_terms/visual_stimulus_type.py | 143 ++---- .../core/actors/account_information.py | 33 +- .../openminds/core/actors/affiliation.py | 33 +- fairgraph/openminds/core/actors/consortium.py | 130 +++--- .../core/actors/contact_information.py | 28 +- .../openminds/core/actors/contribution.py | 27 +- .../openminds/core/actors/organization.py | 157 +++---- fairgraph/openminds/core/actors/person.py | 193 ++++---- fairgraph/openminds/core/data/content_type.py | 106 ++--- .../core/data/content_type_pattern.py | 30 +- fairgraph/openminds/core/data/copyright.py | 28 +- fairgraph/openminds/core/data/file.py | 202 +++----- fairgraph/openminds/core/data/file_archive.py | 52 +-- fairgraph/openminds/core/data/file_bundle.py | 186 ++------ .../openminds/core/data/file_path_pattern.py | 21 +- .../openminds/core/data/file_repository.py | 111 ++--- .../core/data/file_repository_structure.py | 30 +- fairgraph/openminds/core/data/hash.py | 22 +- fairgraph/openminds/core/data/license.py | 69 +-- fairgraph/openminds/core/data/measurement.py | 46 +- fairgraph/openminds/core/data/service_link.py | 41 +- .../openminds/core/digital_identifier/doi.py | 84 ++-- .../core/digital_identifier/gridid.py | 25 +- .../core/digital_identifier/handle.py | 43 +- .../identifiers_dot_org_id.py | 29 +- .../openminds/core/digital_identifier/isbn.py | 60 +-- .../openminds/core/digital_identifier/issn.py | 46 +- .../core/digital_identifier/orcid.py | 23 +- .../core/digital_identifier/rorid.py | 23 +- .../openminds/core/digital_identifier/rrid.py | 47 +- .../core/digital_identifier/stock_number.py | 18 +- .../core/digital_identifier/swhid.py | 33 +- .../openminds/core/miscellaneous/comment.py | 48 +- .../openminds/core/miscellaneous/funding.py | 72 +-- .../core/miscellaneous/quantitative_value.py | 39 +- .../miscellaneous/quantitative_value_array.py | 42 +- .../miscellaneous/quantitative_value_range.py | 27 +- .../miscellaneous/research_product_group.py | 46 +- .../core/miscellaneous/web_resource.py | 73 ++- fairgraph/openminds/core/products/dataset.py | 86 +--- .../core/products/dataset_version.py | 436 ++---------------- .../core/products/meta_data_model.py | 92 +--- .../core/products/meta_data_model_version.py | 303 +----------- fairgraph/openminds/core/products/model.py | 137 +----- .../openminds/core/products/model_version.py | 347 ++------------ fairgraph/openminds/core/products/project.py | 69 +-- fairgraph/openminds/core/products/setup.py | 71 +-- fairgraph/openminds/core/products/software.py | 88 +--- .../core/products/software_version.py | 400 ++-------------- .../openminds/core/products/web_service.py | 94 +--- .../core/products/web_service_version.py | 306 ++---------- .../core/research/behavioral_protocol.py | 76 +-- .../openminds/core/research/configuration.py | 42 +- .../core/research/custom_property_set.py | 36 +- .../core/research/numerical_property.py | 27 +- .../core/research/property_value_list.py | 42 +- fairgraph/openminds/core/research/protocol.py | 87 +--- .../core/research/protocol_execution.py | 140 +----- fairgraph/openminds/core/research/strain.py | 106 +---- .../core/research/string_property.py | 20 +- fairgraph/openminds/core/research/subject.py | 68 +-- .../openminds/core/research/subject_group.py | 76 +-- .../core/research/subject_group_state.py | 112 +---- .../openminds/core/research/subject_state.py | 134 ++---- .../openminds/core/research/tissue_sample.py | 109 +---- .../core/research/tissue_sample_collection.py | 119 +---- .../tissue_sample_collection_state.py | 106 +---- .../core/research/tissue_sample_state.py | 124 ++--- .../openminds/ephys/activity/cell_patching.py | 148 +----- .../ephys/activity/electrode_placement.py | 130 +----- .../ephys/activity/recording_activity.py | 129 +----- fairgraph/openminds/ephys/device/electrode.py | 101 +--- .../openminds/ephys/device/electrode_array.py | 112 +---- .../ephys/device/electrode_array_usage.py | 113 +---- .../openminds/ephys/device/electrode_usage.py | 93 +--- fairgraph/openminds/ephys/device/pipette.py | 97 +--- .../openminds/ephys/device/pipette_usage.py | 153 +----- fairgraph/openminds/ephys/entity/channel.py | 26 +- fairgraph/openminds/ephys/entity/recording.py | 79 +--- fairgraph/openminds/publications/book.py | 212 +-------- fairgraph/openminds/publications/chapter.py | 215 +-------- .../publications/learning_resource.py | 233 +--------- .../openminds/publications/live_paper.py | 88 +--- .../publications/live_paper_resource_item.py | 51 +- .../publications/live_paper_section.py | 49 +- .../publications/live_paper_version.py | 295 ++---------- .../openminds/publications/periodical.py | 35 +- .../publications/publication_issue.py | 29 +- .../publications/publication_volume.py | 29 +- .../publications/scholarly_article.py | 215 +-------- .../openminds/sands/atlas/atlas_annotation.py | 79 +--- .../openminds/sands/atlas/brain_atlas.py | 111 +---- .../sands/atlas/brain_atlas_version.py | 334 ++------------ .../sands/atlas/common_coordinate_space.py | 118 +---- .../atlas/common_coordinate_space_version.py | 359 ++------------ .../sands/atlas/parcellation_entity.py | 130 ++---- .../atlas/parcellation_entity_version.py | 159 ++----- .../sands/atlas/parcellation_terminology.py | 35 +- .../atlas/parcellation_terminology_version.py | 35 +- .../sands/mathematical_shapes/circle.py | 15 +- .../sands/mathematical_shapes/ellipse.py | 28 +- .../sands/mathematical_shapes/rectangle.py | 18 +- .../anatomical_target_position.py | 50 +- .../sands/miscellaneous/coordinate_point.py | 27 +- .../qualitative_relation_assessment.py | 38 +- .../quantitative_relation_assessment.py | 38 +- .../sands/miscellaneous/single_color.py | 15 +- .../miscellaneous/viewer_specification.py | 39 +- .../non_atlas/custom_anatomical_entity.py | 108 ++--- .../sands/non_atlas/custom_annotation.py | 86 +--- .../non_atlas/custom_coordinate_space.py | 63 +-- .../activity/cranial_window_preparation.py | 130 +----- .../activity/tissue_culture_preparation.py | 130 +----- .../activity/tissue_sample_slicing.py | 134 +----- .../specimen_prep/device/slicing_device.py | 69 +-- .../device/slicing_device_usage.py | 108 ++--- .../activity/stimulation_activity.py | 132 +----- .../stimulation/stimulus/ephys_stimulus.py | 76 +-- 219 files changed, 5509 insertions(+), 17907 deletions(-) diff --git a/fairgraph/openminds/chemicals/amount_of_chemical.py b/fairgraph/openminds/chemicals/amount_of_chemical.py index fe1db33a..f4e11536 100644 --- a/fairgraph/openminds/chemicals/amount_of_chemical.py +++ b/fairgraph/openminds/chemicals/amount_of_chemical.py @@ -4,31 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.chemicals import AmountOfChemical +from fairgraph import EmbeddedMetadata -class AmountOfChemical(EmbeddedMetadata): +class AmountOfChemical(EmbeddedMetadata, AmountOfChemical): """ Structured information about the amount of a given chemical that was used. """ type_ = "https://openminds.ebrains.eu/chemicals/AmountOfChemical" - properties = [ - Property("amount", "openminds.core.QuantitativeValue", "vocab:amount", doc="no description available"), - Property( - "chemical_product", - [ - "openminds.chemicals.ChemicalMixture", - "openminds.chemicals.ChemicalSubstance", - "openminds.controlled_terms.MolecularEntity", - ], - "vocab:chemicalProduct", - required=True, - doc="no description available", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, amount=None, chemical_product=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, amount=amount, chemical_product=chemical_product) + return EmbeddedMetadata.__init__(self, data=data, amount=amount, chemical_product=chemical_product) diff --git a/fairgraph/openminds/chemicals/chemical_mixture.py b/fairgraph/openminds/chemicals/chemical_mixture.py index 7af22ca5..7435385f 100644 --- a/fairgraph/openminds/chemicals/chemical_mixture.py +++ b/fairgraph/openminds/chemicals/chemical_mixture.py @@ -4,73 +4,44 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.chemicals import ChemicalMixture +from fairgraph import KGObject -class ChemicalMixture(KGObject): +class ChemicalMixture(KGObject, ChemicalMixture): """ Structured information about a mixture of chemical substances. """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/chemicals/ChemicalMixture" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "has_parts", - "openminds.chemicals.AmountOfChemical", - "vocab:hasPart", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - doc="Word or phrase that constitutes the distinctive designation of the chemical mixture.", - ), - Property( - "product_source", - "openminds.chemicals.ProductSource", - "vocab:productSource", - doc="no description available", - ), - Property( - "type", - "openminds.controlled_terms.ChemicalMixtureType", - "vocab:type", - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "composes", - ["openminds.ephys.Electrode", "openminds.ephys.ElectrodeArray", "openminds.ephys.Pipette"], - ["^vocab:insulatorMaterial", "^vocab:material"], + [ + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + ], + ["insulatorMaterial", "material"], reverse=["insulator_material", "material"], multiple=True, - doc="reverse of insulator_material, material", + description="reverse of insulator_material, material", ), Property( "used_in", [ - "openminds.ephys.CellPatching", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.PipetteUsage", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", ], - ["^vocab:cultureMedium", "^vocab:pipetteSolution", "^vocab:tissueBathSolution"], + ["cultureMedium", "pipetteSolution", "tissueBathSolution"], reverse=["culture_medium", "pipette_solution", "tissue_bath_solution"], multiple=True, - doc="reverse of culture_medium, pipette_solution, tissue_bath_solution", + description="reverse of culture_medium, pipette_solution, tissue_bath_solution", ), ] existence_query_properties = ("has_parts", "type") @@ -89,7 +60,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/chemicals/chemical_substance.py b/fairgraph/openminds/chemicals/chemical_substance.py index 68882461..8c9fdabd 100644 --- a/fairgraph/openminds/chemicals/chemical_substance.py +++ b/fairgraph/openminds/chemicals/chemical_substance.py @@ -4,61 +4,39 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.chemicals import ChemicalSubstance +from fairgraph import KGObject -class ChemicalSubstance(KGObject): +class ChemicalSubstance(KGObject, ChemicalSubstance): """ Structured information about a chemical substance. """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/chemicals/ChemicalSubstance" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "molecular_entity", - "openminds.controlled_terms.MolecularEntity", - "vocab:molecularEntity", - required=True, - doc="no description available", - ), - Property( - "product_source", - "openminds.chemicals.ProductSource", - "vocab:productSource", - doc="no description available", - ), - Property( - "purity", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:purity", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "composes", - ["openminds.ephys.Electrode", "openminds.ephys.ElectrodeArray", "openminds.ephys.Pipette"], - ["^vocab:insulatorMaterial", "^vocab:material"], + [ + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + ], + ["insulatorMaterial", "material"], reverse=["insulator_material", "material"], multiple=True, - doc="reverse of insulator_material, material", + description="reverse of insulator_material, material", ), Property( "labels", - "openminds.ephys.PipetteUsage", - "^vocab:labelingCompound", + "openminds.latest.ephys.PipetteUsage", + "labelingCompound", reverse="labeling_compound", multiple=True, - doc="reverse of 'labeling_compound'", + description="reverse of 'labeling_compound'", ), ] existence_query_properties = ("lookup_label",) @@ -77,7 +55,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/chemicals/product_source.py b/fairgraph/openminds/chemicals/product_source.py index 74f728a6..e52b5844 100644 --- a/fairgraph/openminds/chemicals/product_source.py +++ b/fairgraph/openminds/chemicals/product_source.py @@ -4,48 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.chemicals import ProductSource +from fairgraph import KGObject -class ProductSource(KGObject): +class ProductSource(KGObject, ProductSource): """ Structured information about the source of a chemical substance or mixture. """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/chemicals/ProductSource" - properties = [ - Property( - "digital_identifier", - "openminds.core.RRID", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("identifier", str, "vocab:identifier", doc="Term or code used to identify the product source."), - Property("product_name", str, "vocab:productName", required=True, doc="no description available"), - Property( - "provider", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:provider", - required=True, - doc="no description available", - ), - Property( - "purity", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:purity", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_source_of", - ["openminds.chemicals.ChemicalMixture", "openminds.chemicals.ChemicalSubstance"], - "^vocab:productSource", + ["openminds.latest.chemicals.ChemicalMixture", "openminds.latest.chemicals.ChemicalSubstance"], + "productSource", reverse="product_source", multiple=True, - doc="reverse of 'product_source'", + description="reverse of 'product_source'", ), ] existence_query_properties = ("product_name", "provider") @@ -63,7 +42,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/data_analysis.py b/fairgraph/openminds/computation/data_analysis.py index 2e3f21ae..80cba153 100644 --- a/fairgraph/openminds/computation/data_analysis.py +++ b/fairgraph/openminds/computation/data_analysis.py @@ -4,187 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import DataAnalysis +from fairgraph import KGObject from datetime import datetime, time -class DataAnalysis(KGObject): +class DataAnalysis(KGObject, DataAnalysis): """ Structured information on inspecting, cleansing, transforming, and modelling data. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/DataAnalysis" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the data analysis.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "environment", - ["openminds.computation.Environment", "openminds.core.WebServiceVersion"], - "vocab:environment", - required=True, - doc="no description available", - ), - Property( - "inputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.SoftwareVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "launch_configuration", - "openminds.computation.LaunchConfiguration", - "vocab:launchConfiguration", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileArchive", - "openminds.core.FileBundle", - ], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "resource_usages", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:resourceUsage", - multiple=True, - doc="no description available", - ), - Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - Property( - "status", "openminds.controlled_terms.ActionStatusType", "vocab:status", doc="no description available" - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property("tags", str, "vocab:tag", multiple=True, doc="no description available"), - Property( - "techniques", - "openminds.controlled_terms.AnalysisTechnique", - "vocab:technique", - multiple=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "was_informed_by", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:wasInformedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "informed", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:wasInformedBy", + "wasInformedBy", reverse="was_informed_by", multiple=True, - doc="reverse of 'was_informed_by'", + description="reverse of 'was_informed_by'", ), Property( "is_part_of", - "openminds.computation.WorkflowExecution", - "^vocab:stage", + "openminds.latest.computation.WorkflowExecution", + "stage", reverse="stages", multiple=True, - doc="reverse of 'stages'", + description="reverse of 'stages'", ), ] existence_query_properties = ("lookup_label",) @@ -216,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/data_copy.py b/fairgraph/openminds/computation/data_copy.py index 3a049b44..5363fc22 100644 --- a/fairgraph/openminds/computation/data_copy.py +++ b/fairgraph/openminds/computation/data_copy.py @@ -4,183 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import DataCopy +from fairgraph import KGObject from datetime import datetime, time -class DataCopy(KGObject): +class DataCopy(KGObject, DataCopy): """ """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/DataCopy" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the data copy.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "environment", - ["openminds.computation.Environment", "openminds.core.WebServiceVersion"], - "vocab:environment", - required=True, - doc="no description available", - ), - Property( - "inputs", - [ - "openminds.computation.LocalFile", - "openminds.computation.ValidationTestVersion", - "openminds.core.DatasetVersion", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "launch_configuration", - "openminds.computation.LaunchConfiguration", - "vocab:launchConfiguration", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - ["openminds.computation.LocalFile", "openminds.core.File", "openminds.core.FileBundle"], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "resource_usages", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:resourceUsage", - multiple=True, - doc="no description available", - ), - Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - Property( - "status", "openminds.controlled_terms.ActionStatusType", "vocab:status", doc="no description available" - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property("tags", str, "vocab:tag", multiple=True, doc="no description available"), - Property( - "techniques", - "openminds.controlled_terms.AnalysisTechnique", - "vocab:technique", - multiple=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "was_informed_by", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:wasInformedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "informed", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:wasInformedBy", + "wasInformedBy", reverse="was_informed_by", multiple=True, - doc="reverse of 'was_informed_by'", + description="reverse of 'was_informed_by'", ), Property( "is_part_of", - "openminds.computation.WorkflowExecution", - "^vocab:stage", + "openminds.latest.computation.WorkflowExecution", + "stage", reverse="stages", multiple=True, - doc="reverse of 'stages'", + description="reverse of 'stages'", ), ] existence_query_properties = ("lookup_label",) @@ -212,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/environment.py b/fairgraph/openminds/computation/environment.py index 416b4a27..61c90995 100644 --- a/fairgraph/openminds/computation/environment.py +++ b/fairgraph/openminds/computation/environment.py @@ -4,66 +4,36 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import Environment +from fairgraph import KGObject -class Environment(KGObject): +class Environment(KGObject, Environment): """ Structured information on the computer system or set of systems in which a computation is deployed and executed. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/Environment" - properties = [ - Property( - "configuration", "openminds.core.Configuration", "vocab:configuration", doc="no description available" - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the environment.", - ), - Property( - "hardware", - "openminds.computation.HardwareSystem", - "vocab:hardware", - required=True, - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the environment.", - ), - Property( - "software", - "openminds.core.SoftwareVersion", - "vocab:software", - multiple=True, - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "used_for", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.SoftwareAgent", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.SoftwareAgent", + "openminds.latest.computation.Visualization", ], - "^vocab:environment", + "environment", reverse="environment", multiple=True, - doc="reverse of 'environment'", + description="reverse of 'environment'", ), ] existence_query_properties = ("hardware", "name") @@ -81,7 +51,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/generic_computation.py b/fairgraph/openminds/computation/generic_computation.py index 038d5419..73129754 100644 --- a/fairgraph/openminds/computation/generic_computation.py +++ b/fairgraph/openminds/computation/generic_computation.py @@ -4,185 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import GenericComputation +from fairgraph import KGObject from datetime import datetime, time -class GenericComputation(KGObject): +class GenericComputation(KGObject, GenericComputation): """ Structured information about a computation whose type is unknown or unspecified. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/GenericComputation" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the generic computation.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "environment", - ["openminds.computation.Environment", "openminds.core.WebServiceVersion"], - "vocab:environment", - required=True, - doc="no description available", - ), - Property( - "inputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.SoftwareVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "launch_configuration", - "openminds.computation.LaunchConfiguration", - "vocab:launchConfiguration", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileArchive", - "openminds.core.FileBundle", - ], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "resource_usages", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:resourceUsage", - multiple=True, - doc="no description available", - ), - Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - Property( - "status", "openminds.controlled_terms.ActionStatusType", "vocab:status", doc="no description available" - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property("tags", str, "vocab:tag", multiple=True, doc="no description available"), - Property( - "techniques", - "openminds.controlled_terms.AnalysisTechnique", - "vocab:technique", - multiple=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "was_informed_by", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:wasInformedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "informed", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:wasInformedBy", + "wasInformedBy", reverse="was_informed_by", multiple=True, - doc="reverse of 'was_informed_by'", + description="reverse of 'was_informed_by'", ), Property( "is_part_of", - "openminds.computation.WorkflowExecution", - "^vocab:stage", + "openminds.latest.computation.WorkflowExecution", + "stage", reverse="stages", multiple=True, - doc="reverse of 'stages'", + description="reverse of 'stages'", ), ] existence_query_properties = ("lookup_label",) @@ -214,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/hardware_system.py b/fairgraph/openminds/computation/hardware_system.py index 8c3f2cba..1c43dcef 100644 --- a/fairgraph/openminds/computation/hardware_system.py +++ b/fairgraph/openminds/computation/hardware_system.py @@ -4,46 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import HardwareSystem +from fairgraph import KGObject -class HardwareSystem(KGObject): +class HardwareSystem(KGObject, HardwareSystem): """ Structured information about computing hardware. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/HardwareSystem" - properties = [ - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the hardware system.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the hardware system.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - doc="Term or code used to identify the version of something.", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "used_by", - "openminds.computation.Environment", - "^vocab:hardware", + "openminds.latest.computation.Environment", + "hardware", reverse="hardware", multiple=True, - doc="reverse of 'hardware'", + description="reverse of 'hardware'", ), ] existence_query_properties = ("name",) @@ -59,7 +40,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/launch_configuration.py b/fairgraph/openminds/computation/launch_configuration.py index c0f528ac..49dd446e 100644 --- a/fairgraph/openminds/computation/launch_configuration.py +++ b/fairgraph/openminds/computation/launch_configuration.py @@ -4,55 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import LaunchConfiguration +from fairgraph import KGObject -class LaunchConfiguration(KGObject): +class LaunchConfiguration(KGObject, LaunchConfiguration): """ Structured information about the launch of a computational process. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/LaunchConfiguration" - properties = [ - Property("arguments", str, "vocab:argument", multiple=True, doc="no description available"), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the launch configuration.", - ), - Property( - "environment_variables", - "openminds.core.PropertyValueList", - "vocab:environmentVariable", - doc="no description available", - ), - Property("executable", str, "vocab:executable", required=True, doc="no description available"), - Property( - "name", - str, - "vocab:name", - doc="Word or phrase that constitutes the distinctive designation of the launch configuration.", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_launch_configuration_of", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:launchConfiguration", + "launchConfiguration", reverse="launch_configuration", multiple=True, - doc="reverse of 'launch_configuration'", + description="reverse of 'launch_configuration'", ), ] existence_query_properties = ("executable", "name") @@ -70,7 +50,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/local_file.py b/fairgraph/openminds/computation/local_file.py index c569983c..ac53962a 100644 --- a/fairgraph/openminds/computation/local_file.py +++ b/fairgraph/openminds/computation/local_file.py @@ -4,84 +4,43 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import LocalFile +from fairgraph import KGObject -class LocalFile(KGObject): +class LocalFile(KGObject, LocalFile): """ Structured information about a file that is not accessible via a URL. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/LocalFile" - properties = [ - Property("content_description", str, "vocab:contentDescription", doc="no description available"), - Property("copy_of", "openminds.core.File", "vocab:copyOf", doc="no description available"), - Property( - "data_types", - "openminds.controlled_terms.DataType", - "vocab:dataType", - multiple=True, - doc="no description available", - ), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "hash", - "openminds.core.Hash", - "vocab:hash", - doc="Term used for the process of converting any data into a single value. Often also directly refers to the resulting single value.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the local file.", - ), - Property("path", str, "vocab:path", required=True, doc="no description available"), - Property( - "special_usage_role", - "openminds.controlled_terms.FileUsageRole", - "vocab:specialUsageRole", - doc="Particular function of something when it is used.", - ), - Property( - "storage_size", - "openminds.core.QuantitativeValue", - "vocab:storageSize", - doc="Quantitative value defining how much disk space is used by an object on a computer system.", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_output_of", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:output", + "output", reverse="outputs", multiple=True, - doc="reverse of 'outputs'", + description="reverse of 'outputs'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), ] existence_query_properties = ("name", "path") @@ -104,7 +63,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/model_validation.py b/fairgraph/openminds/computation/model_validation.py index 9300c453..cd606e93 100644 --- a/fairgraph/openminds/computation/model_validation.py +++ b/fairgraph/openminds/computation/model_validation.py @@ -4,184 +4,47 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import ModelValidation +from fairgraph import KGObject from datetime import datetime, time from numbers import Real -class ModelValidation(KGObject): +class ModelValidation(KGObject, ModelValidation): """ Structured information about a process of validating a computational model. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/ModelValidation" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the model validation.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "environment", - ["openminds.computation.Environment", "openminds.core.WebServiceVersion"], - "vocab:environment", - required=True, - doc="no description available", - ), - Property( - "inputs", - [ - "openminds.computation.LocalFile", - "openminds.computation.ValidationTestVersion", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "launch_configuration", - "openminds.computation.LaunchConfiguration", - "vocab:launchConfiguration", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - ["openminds.computation.LocalFile", "openminds.core.File", "openminds.core.FileBundle"], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "resource_usages", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:resourceUsage", - multiple=True, - doc="no description available", - ), - Property("score", Real, "vocab:score", doc="no description available"), - Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - Property( - "status", "openminds.controlled_terms.ActionStatusType", "vocab:status", doc="no description available" - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property("tags", str, "vocab:tag", multiple=True, doc="no description available"), - Property( - "techniques", - "openminds.controlled_terms.AnalysisTechnique", - "vocab:technique", - multiple=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "was_informed_by", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:wasInformedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "informed", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:wasInformedBy", + "wasInformedBy", reverse="was_informed_by", multiple=True, - doc="reverse of 'was_informed_by'", + description="reverse of 'was_informed_by'", ), Property( "is_part_of", - "openminds.computation.WorkflowExecution", - "^vocab:stage", + "openminds.latest.computation.WorkflowExecution", + "stage", reverse="stages", multiple=True, - doc="reverse of 'stages'", + description="reverse of 'stages'", ), ] existence_query_properties = ("lookup_label",) @@ -214,7 +77,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/optimization.py b/fairgraph/openminds/computation/optimization.py index 698f14a6..8f739724 100644 --- a/fairgraph/openminds/computation/optimization.py +++ b/fairgraph/openminds/computation/optimization.py @@ -4,186 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import Optimization +from fairgraph import KGObject from datetime import datetime, time -class Optimization(KGObject): +class Optimization(KGObject, Optimization): """ Structured information about a process of optimizing a model or a piece of code. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/Optimization" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the optimization.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "environment", - ["openminds.computation.Environment", "openminds.core.WebServiceVersion"], - "vocab:environment", - required=True, - doc="no description available", - ), - Property( - "inputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "launch_configuration", - "openminds.computation.LaunchConfiguration", - "vocab:launchConfiguration", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.ModelVersion", - ], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "resource_usages", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:resourceUsage", - multiple=True, - doc="no description available", - ), - Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - Property( - "status", "openminds.controlled_terms.ActionStatusType", "vocab:status", doc="no description available" - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property("tags", str, "vocab:tag", multiple=True, doc="no description available"), - Property( - "techniques", - "openminds.controlled_terms.AnalysisTechnique", - "vocab:technique", - multiple=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "was_informed_by", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:wasInformedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "informed", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:wasInformedBy", + "wasInformedBy", reverse="was_informed_by", multiple=True, - doc="reverse of 'was_informed_by'", + description="reverse of 'was_informed_by'", ), Property( "is_part_of", - "openminds.computation.WorkflowExecution", - "^vocab:stage", + "openminds.latest.computation.WorkflowExecution", + "stage", reverse="stages", multiple=True, - doc="reverse of 'stages'", + description="reverse of 'stages'", ), ] existence_query_properties = ("lookup_label",) @@ -215,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/simulation.py b/fairgraph/openminds/computation/simulation.py index 564c820c..ca469918 100644 --- a/fairgraph/openminds/computation/simulation.py +++ b/fairgraph/openminds/computation/simulation.py @@ -4,186 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import Simulation +from fairgraph import KGObject from datetime import datetime, time -class Simulation(KGObject): +class Simulation(KGObject, Simulation): """ Structured information about a process of running simulations of a computational model. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/Simulation" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the simulation.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "environment", - ["openminds.computation.Environment", "openminds.core.WebServiceVersion"], - "vocab:environment", - required=True, - doc="no description available", - ), - Property( - "inputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "launch_configuration", - "openminds.computation.LaunchConfiguration", - "vocab:launchConfiguration", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileArchive", - "openminds.core.FileBundle", - ], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "resource_usages", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:resourceUsage", - multiple=True, - doc="no description available", - ), - Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - Property( - "status", "openminds.controlled_terms.ActionStatusType", "vocab:status", doc="no description available" - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property("tags", str, "vocab:tag", multiple=True, doc="no description available"), - Property( - "techniques", - "openminds.controlled_terms.AnalysisTechnique", - "vocab:technique", - multiple=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "was_informed_by", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:wasInformedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "informed", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:wasInformedBy", + "wasInformedBy", reverse="was_informed_by", multiple=True, - doc="reverse of 'was_informed_by'", + description="reverse of 'was_informed_by'", ), Property( "is_part_of", - "openminds.computation.WorkflowExecution", - "^vocab:stage", + "openminds.latest.computation.WorkflowExecution", + "stage", reverse="stages", multiple=True, - doc="reverse of 'stages'", + description="reverse of 'stages'", ), ] existence_query_properties = ("lookup_label",) @@ -215,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/software_agent.py b/fairgraph/openminds/computation/software_agent.py index f1dc559a..1c78eaaa 100644 --- a/fairgraph/openminds/computation/software_agent.py +++ b/fairgraph/openminds/computation/software_agent.py @@ -4,70 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import SoftwareAgent +from fairgraph import KGObject -class SoftwareAgent(KGObject): +class SoftwareAgent(KGObject, SoftwareAgent): """ Structured information about a piece of software or web service that can perform a task autonomously. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/SoftwareAgent" - properties = [ - Property( - "environment", "openminds.computation.Environment", "vocab:environment", doc="no description available" - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the software agent.", - ), - Property( - "software", - "openminds.core.SoftwareVersion", - "vocab:software", - required=True, - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "activities", [ - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:performedBy", + "performedBy", reverse="performed_by", multiple=True, - doc="reverse of 'performed_by'", + description="reverse of 'performed_by'", ), Property( "started", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - "openminds.computation.WorkflowExecution", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", + "openminds.latest.computation.WorkflowExecution", ], - "^vocab:startedBy", + "startedBy", reverse="started_by", multiple=True, - doc="reverse of 'started_by'", + description="reverse of 'started_by'", ), ] existence_query_properties = ("name", "software") @@ -84,7 +67,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/validation_test.py b/fairgraph/openminds/computation/validation_test.py index 784e9643..9c2a485e 100644 --- a/fairgraph/openminds/computation/validation_test.py +++ b/fairgraph/openminds/computation/validation_test.py @@ -4,153 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import ValidationTest +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ValidationTest(KGObject): +class ValidationTest(KGObject, ValidationTest): """ Structured information about the definition of a process for validating a computational model. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/ValidationTest" - properties = [ - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the validation test.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - required=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", - str, - "vocab:fullName", - required=True, - doc="Whole, non-abbreviated name of the validation test.", - ), - Property( - "has_versions", - "openminds.computation.ValidationTestVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the validation test."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property("model_scope", "openminds.controlled_terms.ModelScope", "vocab:scope", doc="Extent of something."), - Property( - "reference_data_acquisitions", - "openminds.controlled_terms.Technique", - "vocab:referenceDataAcquisition", - multiple=True, - doc="no description available", - ), - Property( - "score_type", - "openminds.controlled_terms.DifferenceMeasure", - "vocab:scoreType", - doc="no description available", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the validation test.", - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -182,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/validation_test_version.py b/fairgraph/openminds/computation/validation_test_version.py index 9303dbb6..1b2c57aa 100644 --- a/fairgraph/openminds/computation/validation_test_version.py +++ b/fairgraph/openminds/computation/validation_test_version.py @@ -4,333 +4,72 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import ValidationTestVersion +from fairgraph import KGObject from fairgraph.errors import ResolutionFailure from .validation_test import ValidationTest from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class ValidationTestVersion(KGObject): +class ValidationTestVersion(KGObject, ValidationTestVersion): """ Structured information about a specific implementation of a validation test. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/ValidationTestVersion" - properties = [ - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the validation test version.", - ), - Property( - "configuration", - [ - "openminds.core.Configuration", - "openminds.core.File", - "openminds.core.PropertyValueList", - "openminds.core.WebResource", - ], - "vocab:configuration", - doc="no description available", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the validation test version.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("entry_point", str, "vocab:entryPoint", doc="no description available"), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - required=True, - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property( - "full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the validation test version." - ), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the validation test version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "is_alternative_version_of", - "openminds.computation.ValidationTestVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.computation.ValidationTestVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the validation test version.", - ), - Property( - "licenses", - "openminds.core.License", - "vocab:license", - multiple=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "reference_data", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.FileBundle", "openminds.core.WebResource"], - "vocab:referenceData", - multiple=True, - doc="no description available", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the validation test version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_input_to", - ["openminds.computation.DataCopy", "openminds.computation.ModelValidation"], - "^vocab:input", + ["openminds.latest.computation.DataCopy", "openminds.latest.computation.ModelValidation"], + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_old_version_of", - "openminds.computation.ValidationTestVersion", - "^vocab:isNewVersionOf", + "openminds.latest.computation.ValidationTestVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.computation.ValidationTest", - "^vocab:hasVersion", + "openminds.latest.computation.ValidationTest", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -378,7 +117,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/visualization.py b/fairgraph/openminds/computation/visualization.py index 8762ac6d..d406f313 100644 --- a/fairgraph/openminds/computation/visualization.py +++ b/fairgraph/openminds/computation/visualization.py @@ -4,185 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import Visualization +from fairgraph import KGObject from datetime import datetime, time -class Visualization(KGObject): +class Visualization(KGObject, Visualization): """ Structured information about a process of visualizing a computational model, a computational process, or a dataset. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/Visualization" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the visualization.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "environment", - ["openminds.computation.Environment", "openminds.core.WebServiceVersion"], - "vocab:environment", - required=True, - doc="no description available", - ), - Property( - "inputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.SoftwareVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "launch_configuration", - "openminds.computation.LaunchConfiguration", - "vocab:launchConfiguration", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - [ - "openminds.computation.LocalFile", - "openminds.core.File", - "openminds.core.FileArchive", - "openminds.core.FileBundle", - ], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "resource_usages", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:resourceUsage", - multiple=True, - doc="no description available", - ), - Property("start_time", [datetime, time], "vocab:startTime", required=True, doc="no description available"), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - Property( - "status", "openminds.controlled_terms.ActionStatusType", "vocab:status", doc="no description available" - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property("tags", str, "vocab:tag", multiple=True, doc="no description available"), - Property( - "techniques", - "openminds.controlled_terms.AnalysisTechnique", - "vocab:technique", - multiple=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "was_informed_by", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:wasInformedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "informed", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:wasInformedBy", + "wasInformedBy", reverse="was_informed_by", multiple=True, - doc="reverse of 'was_informed_by'", + description="reverse of 'was_informed_by'", ), Property( "is_part_of", - "openminds.computation.WorkflowExecution", - "^vocab:stage", + "openminds.latest.computation.WorkflowExecution", + "stage", reverse="stages", multiple=True, - doc="reverse of 'stages'", + description="reverse of 'stages'", ), ] existence_query_properties = ("lookup_label",) @@ -214,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/workflow_execution.py b/fairgraph/openminds/computation/workflow_execution.py index 5bb24608..b37c1ee4 100644 --- a/fairgraph/openminds/computation/workflow_execution.py +++ b/fairgraph/openminds/computation/workflow_execution.py @@ -4,57 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import WorkflowExecution +from fairgraph import KGObject -class WorkflowExecution(KGObject): +class WorkflowExecution(KGObject, WorkflowExecution): """ Structured information about an execution of a computational workflow. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/WorkflowExecution" - properties = [ - Property( - "configuration", - ["openminds.core.Configuration", "openminds.core.File"], - "vocab:configuration", - doc="no description available", - ), - Property( - "recipe", "openminds.computation.WorkflowRecipeVersion", "vocab:recipe", doc="no description available" - ), - Property( - "stages", - [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - ], - "vocab:stage", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "started_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:startedBy", - doc="no description available", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("stages",) def __init__( self, configuration=None, recipe=None, stages=None, started_by=None, id=None, data=None, space=None, scope=None ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/workflow_recipe.py b/fairgraph/openminds/computation/workflow_recipe.py index e73a3a1d..882e8448 100644 --- a/fairgraph/openminds/computation/workflow_recipe.py +++ b/fairgraph/openminds/computation/workflow_recipe.py @@ -4,103 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import WorkflowRecipe +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class WorkflowRecipe(KGObject): +class WorkflowRecipe(KGObject, WorkflowRecipe): """ Structured information about the description of a prospective workflow. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/WorkflowRecipe" - properties = [ - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the workflow recipe.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - required=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", - str, - "vocab:fullName", - required=True, - doc="Whole, non-abbreviated name of the workflow recipe.", - ), - Property( - "has_versions", - "openminds.computation.WorkflowRecipeVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the workflow recipe."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the workflow recipe.", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -128,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/computation/workflow_recipe_version.py b/fairgraph/openminds/computation/workflow_recipe_version.py index a40ca40f..206b2a44 100644 --- a/fairgraph/openminds/computation/workflow_recipe_version.py +++ b/fairgraph/openminds/computation/workflow_recipe_version.py @@ -4,334 +4,80 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.computation import WorkflowRecipeVersion +from fairgraph import KGObject from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class WorkflowRecipeVersion(KGObject): +class WorkflowRecipeVersion(KGObject, WorkflowRecipeVersion): """ Structured information about a specific implemented version of a workflow recipe. """ - default_space = "computation" type_ = "https://openminds.ebrains.eu/computation/WorkflowRecipeVersion" - properties = [ - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the workflow recipe version.", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the workflow recipe version.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - required=True, - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property( - "full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the workflow recipe version." - ), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "has_parts", - [ - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.SoftwareVersion", - ], - "vocab:hasPart", - multiple=True, - doc="no description available", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the workflow recipe version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "is_alternative_version_of", - "openminds.computation.WorkflowRecipeVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.computation.WorkflowRecipeVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the workflow recipe version.", - ), - Property( - "licenses", - "openminds.core.License", - "vocab:license", - multiple=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the workflow recipe version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "computation" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "defined", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - "openminds.computation.WorkflowExecution", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", + "openminds.latest.computation.WorkflowExecution", ], - "^vocab:recipe", + "recipe", reverse="recipe", multiple=True, - doc="reverse of 'recipe'", + description="reverse of 'recipe'", ), Property( "is_old_version_of", - "openminds.computation.WorkflowRecipeVersion", - "^vocab:isNewVersionOf", + "openminds.latest.computation.WorkflowRecipeVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.computation.WorkflowRecipe", - "^vocab:hasVersion", + "openminds.latest.computation.WorkflowRecipe", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -377,7 +123,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/action_status_type.py b/fairgraph/openminds/controlled_terms/action_status_type.py index 3b96544e..41a6c472 100644 --- a/fairgraph/openminds/controlled_terms/action_status_type.py +++ b/fairgraph/openminds/controlled_terms/action_status_type.py @@ -4,105 +4,61 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ActionStatusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ActionStatusType(KGObject): +class ActionStatusType(KGObject, ActionStatusType): """ Structured information about the status of an action. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ActionStatusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the action status type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the action status type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_status_of", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:status", + "status", reverse="status", multiple=True, - doc="reverse of 'status'", + description="reverse of 'status'", ), ] existence_query_properties = ("name",) @@ -123,7 +79,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/age_category.py b/fairgraph/openminds/controlled_terms/age_category.py index 982d872c..9a5778a9 100644 --- a/fairgraph/openminds/controlled_terms/age_category.py +++ b/fairgraph/openminds/controlled_terms/age_category.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AgeCategory +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AgeCategory(KGObject): +class AgeCategory(KGObject, AgeCategory): """ Structured information on the life cycle (semantic term) of a specific age group. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AgeCategory" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the age category.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the age category.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_age_category_of", - ["openminds.core.SubjectGroupState", "openminds.core.SubjectState"], - "^vocab:ageCategory", + ["openminds.latest.core.SubjectGroupState", "openminds.latest.core.SubjectState"], + "ageCategory", reverse="age_categories", multiple=True, - doc="reverse of 'age_categories'", + description="reverse of 'age_categories'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/analysis_technique.py b/fairgraph/openminds/controlled_terms/analysis_technique.py index b13b1084..cbbc07e5 100644 --- a/fairgraph/openminds/controlled_terms/analysis_technique.py +++ b/fairgraph/openminds/controlled_terms/analysis_technique.py @@ -4,114 +4,70 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AnalysisTechnique +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AnalysisTechnique(KGObject): +class AnalysisTechnique(KGObject, AnalysisTechnique): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AnalysisTechnique" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the analysis technique.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the analysis technique.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Protocol", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Protocol", ], - "^vocab:technique", + "technique", reverse="techniques", multiple=True, - doc="reverse of 'techniques'", + description="reverse of 'techniques'", ), ] existence_query_properties = ("name",) @@ -133,7 +89,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py index d146f7ea..d041b7a6 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py +++ b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AnatomicalAxesOrientation +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AnatomicalAxesOrientation(KGObject): +class AnatomicalAxesOrientation(KGObject, AnatomicalAxesOrientation): """ Structured information on the anatomical directions of the X, Y, and Z axis. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AnatomicalAxesOrientation" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the anatomical axes orientation.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the anatomical axes orientation.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_orientation_of", - "openminds.sands.CustomCoordinateSpace", - "^vocab:anatomicalAxesOrientation", + "openminds.latest.sands.CustomCoordinateSpace", + "anatomicalAxesOrientation", reverse="anatomical_axes_orientation", multiple=True, - doc="reverse of 'anatomical_axes_orientation'", + description="reverse of 'anatomical_axes_orientation'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py index 9d3f164e..d990e0c0 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py +++ b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AnatomicalIdentificationType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AnatomicalIdentificationType(KGObject): +class AnatomicalIdentificationType(KGObject, AnatomicalIdentificationType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AnatomicalIdentificationType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the anatomical identification type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the anatomical identification type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:targetIdentificationType", + "openminds.latest.sands.AnatomicalTargetPosition", + "targetIdentificationType", reverse="target_identification_type", multiple=True, - doc="reverse of 'target_identification_type'", + description="reverse of 'target_identification_type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/anatomical_plane.py b/fairgraph/openminds/controlled_terms/anatomical_plane.py index 6881cf3e..68067b65 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_plane.py +++ b/fairgraph/openminds/controlled_terms/anatomical_plane.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AnatomicalPlane +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AnatomicalPlane(KGObject): +class AnatomicalPlane(KGObject, AnatomicalPlane): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AnatomicalPlane" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the anatomical plane.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the anatomical plane.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_in", - "openminds.specimen_prep.SlicingDeviceUsage", - "^vocab:slicingPlane", + "openminds.latest.specimen_prep.SlicingDeviceUsage", + "slicingPlane", reverse="slicing_plane", multiple=True, - doc="reverse of 'slicing_plane'", + description="reverse of 'slicing_plane'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py index e13f5648..f4ff3ad8 100644 --- a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AnnotationCriteriaType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AnnotationCriteriaType(KGObject): +class AnnotationCriteriaType(KGObject, AnnotationCriteriaType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AnnotationCriteriaType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the annotation criteria type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the annotation criteria type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_by_annotation", - ["openminds.sands.AtlasAnnotation", "openminds.sands.CustomAnnotation"], - "^vocab:criteriaType", + ["openminds.latest.sands.AtlasAnnotation", "openminds.latest.sands.CustomAnnotation"], + "criteriaType", reverse="criteria_type", multiple=True, - doc="reverse of 'criteria_type'", + description="reverse of 'criteria_type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/annotation_type.py b/fairgraph/openminds/controlled_terms/annotation_type.py index e7d75766..3d328654 100644 --- a/fairgraph/openminds/controlled_terms/annotation_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AnnotationType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AnnotationType(KGObject): +class AnnotationType(KGObject, AnnotationType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AnnotationType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the annotation type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the annotation type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - ["openminds.sands.AtlasAnnotation", "openminds.sands.CustomAnnotation"], - "^vocab:type", + ["openminds.latest.sands.AtlasAnnotation", "openminds.latest.sands.CustomAnnotation"], + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/atlas_type.py b/fairgraph/openminds/controlled_terms/atlas_type.py index 6dc99afc..6a6e60e2 100644 --- a/fairgraph/openminds/controlled_terms/atlas_type.py +++ b/fairgraph/openminds/controlled_terms/atlas_type.py @@ -4,96 +4,52 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AtlasType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AtlasType(KGObject): +class AtlasType(KGObject, AtlasType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AtlasType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the atlas type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the atlas type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.sands.BrainAtlasVersion", - "^vocab:type", + "openminds.latest.sands.BrainAtlasVersion", + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), ] existence_query_properties = ("name",) @@ -114,7 +70,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py index 20aac91c..e1b89383 100644 --- a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import AuditoryStimulusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class AuditoryStimulusType(KGObject): +class AuditoryStimulusType(KGObject, AuditoryStimulusType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/AuditoryStimulusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the auditory stimulus type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the auditory stimulus type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:stimulusType", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "stimulusType", reverse="stimulus_types", multiple=True, - doc="reverse of 'stimulus_types'", + description="reverse of 'stimulus_types'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/biological_order.py b/fairgraph/openminds/controlled_terms/biological_order.py index fae48c3a..7a30e341 100644 --- a/fairgraph/openminds/controlled_terms/biological_order.py +++ b/fairgraph/openminds/controlled_terms/biological_order.py @@ -4,123 +4,79 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import BiologicalOrder +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class BiologicalOrder(KGObject): +class BiologicalOrder(KGObject, BiologicalOrder): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/BiologicalOrder" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the biological order.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the biological order.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -142,7 +98,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/biological_process.py b/fairgraph/openminds/controlled_terms/biological_process.py index 59f0dea7..0f2d9993 100644 --- a/fairgraph/openminds/controlled_terms/biological_process.py +++ b/fairgraph/openminds/controlled_terms/biological_process.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import BiologicalProcess +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class BiologicalProcess(KGObject): +class BiologicalProcess(KGObject, BiologicalProcess): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/BiologicalProcess" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the biological process.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the biological process.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/biological_sex.py b/fairgraph/openminds/controlled_terms/biological_sex.py index 3732794f..5c5459a1 100644 --- a/fairgraph/openminds/controlled_terms/biological_sex.py +++ b/fairgraph/openminds/controlled_terms/biological_sex.py @@ -4,136 +4,92 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import BiologicalSex +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class BiologicalSex(KGObject): +class BiologicalSex(KGObject, BiologicalSex): """ Structured information on the biological sex of a subject. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/BiologicalSex" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the biological sex.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the biological sex.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_biological_sex_of", [ - "openminds.core.Subject", - "openminds.core.SubjectGroup", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", + "openminds.latest.core.Subject", + "openminds.latest.core.SubjectGroup", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", ], - "^vocab:biologicalSex", + "biologicalSex", reverse="biological_sex", multiple=True, - doc="reverse of 'biological_sex'", + description="reverse of 'biological_sex'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -156,7 +112,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/breeding_type.py b/fairgraph/openminds/controlled_terms/breeding_type.py index 44b39c40..c556857a 100644 --- a/fairgraph/openminds/controlled_terms/breeding_type.py +++ b/fairgraph/openminds/controlled_terms/breeding_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import BreedingType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class BreedingType(KGObject): +class BreedingType(KGObject, BreedingType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/BreedingType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the breeding type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the breeding type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_breeding_type_of", - "openminds.core.Strain", - "^vocab:breedingType", + "openminds.latest.core.Strain", + "breedingType", reverse="breeding_type", multiple=True, - doc="reverse of 'breeding_type'", + description="reverse of 'breeding_type'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/cell_culture_type.py b/fairgraph/openminds/controlled_terms/cell_culture_type.py index dc8a83e4..1a86e70f 100644 --- a/fairgraph/openminds/controlled_terms/cell_culture_type.py +++ b/fairgraph/openminds/controlled_terms/cell_culture_type.py @@ -4,123 +4,79 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import CellCultureType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class CellCultureType(KGObject): +class CellCultureType(KGObject, CellCultureType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/CellCultureType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the cell culture type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the cell culture type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -142,7 +98,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/cell_type.py b/fairgraph/openminds/controlled_terms/cell_type.py index a8d1f0a5..6eac3954 100644 --- a/fairgraph/openminds/controlled_terms/cell_type.py +++ b/fairgraph/openminds/controlled_terms/cell_type.py @@ -4,147 +4,107 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import CellType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class CellType(KGObject): +class CellType(KGObject, CellType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/CellType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the cell type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the cell type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_location_of", - ["openminds.ephys.ElectrodeArrayUsage", "openminds.ephys.ElectrodeUsage", "openminds.ephys.PipetteUsage"], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes"], + [ + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", + ], + ["anatomicalLocation", "anatomicalLocationOfElectrodes"], reverse=["anatomical_location", "anatomical_locations_of_electrodes"], multiple=True, - doc="reverse of anatomical_location, anatomical_locations_of_electrodes", + description="reverse of anatomical_location, anatomical_locations_of_electrodes", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "sample", - ["openminds.core.TissueSample", "openminds.core.TissueSampleCollection"], - "^vocab:origin", + ["openminds.latest.core.TissueSample", "openminds.latest.core.TissueSampleCollection"], + "origin", reverse="origin", multiple=True, - doc="reverse of 'origin'", + description="reverse of 'origin'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -169,7 +129,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py index 0780ee8a..bbab89ba 100644 --- a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py +++ b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ChemicalMixtureType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ChemicalMixtureType(KGObject): +class ChemicalMixtureType(KGObject, ChemicalMixtureType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ChemicalMixtureType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the chemical mixture type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the chemical mixture type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.chemicals.ChemicalMixture", - "^vocab:type", + "openminds.latest.chemicals.ChemicalMixture", + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/colormap.py b/fairgraph/openminds/controlled_terms/colormap.py index 5dc6dc4d..072a8a65 100644 --- a/fairgraph/openminds/controlled_terms/colormap.py +++ b/fairgraph/openminds/controlled_terms/colormap.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Colormap +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Colormap(KGObject): +class Colormap(KGObject, Colormap): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Colormap" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the colormap.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the colormap.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/contribution_type.py b/fairgraph/openminds/controlled_terms/contribution_type.py index 312c2e63..b162fd6b 100644 --- a/fairgraph/openminds/controlled_terms/contribution_type.py +++ b/fairgraph/openminds/controlled_terms/contribution_type.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ContributionType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ContributionType(KGObject): +class ContributionType(KGObject, ContributionType): """ Structured information on the type of contribution a person or organization performed. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ContributionType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the contribution type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the contribution type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py index 83a98268..0f6ac9a1 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import CranialWindowConstructionType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class CranialWindowConstructionType(KGObject): +class CranialWindowConstructionType(KGObject, CranialWindowConstructionType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/CranialWindowConstructionType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the cranial window construction type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the cranial window construction type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_for", - "openminds.specimen_prep.CranialWindowPreparation", - "^vocab:constructionType", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "constructionType", reverse="construction_type", multiple=True, - doc="reverse of 'construction_type'", + description="reverse of 'construction_type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py index b6fd9b2d..658def24 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import CranialWindowReinforcementType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class CranialWindowReinforcementType(KGObject): +class CranialWindowReinforcementType(KGObject, CranialWindowReinforcementType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/CranialWindowReinforcementType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the cranial window reinforcement type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the cranial window reinforcement type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_for", - "openminds.specimen_prep.CranialWindowPreparation", - "^vocab:reinforcementType", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "reinforcementType", reverse="reinforcement_type", multiple=True, - doc="reverse of 'reinforcement_type'", + description="reverse of 'reinforcement_type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/criteria_quality_type.py b/fairgraph/openminds/controlled_terms/criteria_quality_type.py index ce338274..d3bf9916 100644 --- a/fairgraph/openminds/controlled_terms/criteria_quality_type.py +++ b/fairgraph/openminds/controlled_terms/criteria_quality_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import CriteriaQualityType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class CriteriaQualityType(KGObject): +class CriteriaQualityType(KGObject, CriteriaQualityType): """ Structured information on the quality type of the defined criteria for a measurement. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/CriteriaQualityType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the criteria quality type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the criteria quality type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_by_annotation", - ["openminds.sands.AtlasAnnotation", "openminds.sands.CustomAnnotation"], - "^vocab:criteriaQualityType", + ["openminds.latest.sands.AtlasAnnotation", "openminds.latest.sands.CustomAnnotation"], + "criteriaQualityType", reverse="criteria_quality_type", multiple=True, - doc="reverse of 'criteria_quality_type'", + description="reverse of 'criteria_quality_type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/data_type.py b/fairgraph/openminds/controlled_terms/data_type.py index 71632ff2..50fc701e 100644 --- a/fairgraph/openminds/controlled_terms/data_type.py +++ b/fairgraph/openminds/controlled_terms/data_type.py @@ -4,97 +4,57 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import DataType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class DataType(KGObject): +class DataType(KGObject, DataType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/DataType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the data type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the data type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_data_type_of", - ["openminds.computation.LocalFile", "openminds.core.ContentType", "openminds.core.File"], - "^vocab:dataType", + [ + "openminds.latest.computation.LocalFile", + "openminds.latest.core.ContentType", + "openminds.latest.core.File", + ], + "dataType", reverse="data_types", multiple=True, - doc="reverse of 'data_types'", + description="reverse of 'data_types'", ), ] existence_query_properties = ("name",) @@ -115,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/device_type.py b/fairgraph/openminds/controlled_terms/device_type.py index 970c531d..9e20c6d7 100644 --- a/fairgraph/openminds/controlled_terms/device_type.py +++ b/fairgraph/openminds/controlled_terms/device_type.py @@ -4,102 +4,58 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import DeviceType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class DeviceType(KGObject): +class DeviceType(KGObject, DeviceType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/DeviceType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the device type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the device type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", [ - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", - "openminds.specimen_prep.SlicingDevice", + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + "openminds.latest.specimen_prep.SlicingDevice", ], - "^vocab:deviceType", + "deviceType", reverse="device_type", multiple=True, - doc="reverse of 'device_type'", + description="reverse of 'device_type'", ), ] existence_query_properties = ("name",) @@ -120,7 +76,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/difference_measure.py b/fairgraph/openminds/controlled_terms/difference_measure.py index 92ada1ac..af9d2a7b 100644 --- a/fairgraph/openminds/controlled_terms/difference_measure.py +++ b/fairgraph/openminds/controlled_terms/difference_measure.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import DifferenceMeasure +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class DifferenceMeasure(KGObject): +class DifferenceMeasure(KGObject, DifferenceMeasure): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/DifferenceMeasure" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the difference measure.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the difference measure.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_score_type_of", - "openminds.computation.ValidationTest", - "^vocab:scoreType", + "openminds.latest.computation.ValidationTest", + "scoreType", reverse="score_type", multiple=True, - doc="reverse of 'score_type'", + description="reverse of 'score_type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/disease.py b/fairgraph/openminds/controlled_terms/disease.py index df12a39a..85b12775 100644 --- a/fairgraph/openminds/controlled_terms/disease.py +++ b/fairgraph/openminds/controlled_terms/disease.py @@ -4,144 +4,100 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Disease +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Disease(KGObject): +class Disease(KGObject, Disease): """ Structured information on a disease. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Disease" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the disease.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the disease.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_modeled_by", - "openminds.core.Strain", - "^vocab:diseaseModel", + "openminds.latest.core.Strain", + "diseaseModel", reverse="disease_models", multiple=True, - doc="reverse of 'disease_models'", + description="reverse of 'disease_models'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "specimen_state", [ - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", + "openminds.latest.core.SubjectGroupState", + "openminds.latest.core.SubjectState", + "openminds.latest.core.TissueSampleCollectionState", + "openminds.latest.core.TissueSampleState", ], - "^vocab:pathology", + "pathology", reverse="pathologies", multiple=True, - doc="reverse of 'pathologies'", + description="reverse of 'pathologies'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -165,7 +121,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/disease_model.py b/fairgraph/openminds/controlled_terms/disease_model.py index 0fdf8874..18ec52ac 100644 --- a/fairgraph/openminds/controlled_terms/disease_model.py +++ b/fairgraph/openminds/controlled_terms/disease_model.py @@ -4,144 +4,100 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import DiseaseModel +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class DiseaseModel(KGObject): +class DiseaseModel(KGObject, DiseaseModel): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/DiseaseModel" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the disease model.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the disease model.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_modeled_by", - "openminds.core.Strain", - "^vocab:diseaseModel", + "openminds.latest.core.Strain", + "diseaseModel", reverse="disease_models", multiple=True, - doc="reverse of 'disease_models'", + description="reverse of 'disease_models'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "specimen_state", [ - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", + "openminds.latest.core.SubjectGroupState", + "openminds.latest.core.SubjectState", + "openminds.latest.core.TissueSampleCollectionState", + "openminds.latest.core.TissueSampleState", ], - "^vocab:pathology", + "pathology", reverse="pathologies", multiple=True, - doc="reverse of 'pathologies'", + description="reverse of 'pathologies'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -165,7 +121,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/educational_level.py b/fairgraph/openminds/controlled_terms/educational_level.py index 092c4cfd..d4890290 100644 --- a/fairgraph/openminds/controlled_terms/educational_level.py +++ b/fairgraph/openminds/controlled_terms/educational_level.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import EducationalLevel +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class EducationalLevel(KGObject): +class EducationalLevel(KGObject, EducationalLevel): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/EducationalLevel" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the educational level.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the educational level.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py index 4ea48e00..03f6230d 100644 --- a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py @@ -4,139 +4,95 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ElectricalStimulusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ElectricalStimulusType(KGObject): +class ElectricalStimulusType(KGObject, ElectricalStimulusType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ElectricalStimulusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the electrical stimulus type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the electrical stimulus type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.stimulation.EphysStimulus", - "^vocab:type", + "openminds.latest.stimulation.EphysStimulus", + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:stimulusType", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "stimulusType", reverse="stimulus_types", multiple=True, - doc="reverse of 'stimulus_types'", + description="reverse of 'stimulus_types'", ), ] existence_query_properties = ("name",) @@ -160,7 +116,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/ethics_assessment.py b/fairgraph/openminds/controlled_terms/ethics_assessment.py index 22fc3457..cbda236d 100644 --- a/fairgraph/openminds/controlled_terms/ethics_assessment.py +++ b/fairgraph/openminds/controlled_terms/ethics_assessment.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import EthicsAssessment +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class EthicsAssessment(KGObject): +class EthicsAssessment(KGObject, EthicsAssessment): """ Structured information on the ethics assessment of a dataset. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/EthicsAssessment" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the ethics assessment.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the ethics assessment.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/experimental_approach.py b/fairgraph/openminds/controlled_terms/experimental_approach.py index 21d5d159..33b8841f 100644 --- a/fairgraph/openminds/controlled_terms/experimental_approach.py +++ b/fairgraph/openminds/controlled_terms/experimental_approach.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ExperimentalApproach +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ExperimentalApproach(KGObject): +class ExperimentalApproach(KGObject, ExperimentalApproach): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ExperimentalApproach" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the experimental approach.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the experimental approach.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py index e9f80170..8a5b9ba4 100644 --- a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py +++ b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py @@ -4,105 +4,61 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import FileBundleGrouping +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class FileBundleGrouping(KGObject): +class FileBundleGrouping(KGObject, FileBundleGrouping): """ Structured information on the grouping mechanism of a file bundle. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/FileBundleGrouping" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the file bundle grouping.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the file bundle grouping.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_defined_by", - "openminds.core.FilePathPattern", - "^vocab:groupingType", + "openminds.latest.core.FilePathPattern", + "groupingType", reverse="grouping_types", multiple=True, - doc="reverse of 'grouping_types'", + description="reverse of 'grouping_types'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupingType", + "openminds.latest.core.FileBundle", + "groupingType", reverse="grouping_types", multiple=True, - doc="reverse of 'grouping_types'", + description="reverse of 'grouping_types'", ), ] existence_query_properties = ("name",) @@ -124,7 +80,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/file_repository_type.py b/fairgraph/openminds/controlled_terms/file_repository_type.py index 6c670523..1562a09f 100644 --- a/fairgraph/openminds/controlled_terms/file_repository_type.py +++ b/fairgraph/openminds/controlled_terms/file_repository_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import FileRepositoryType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class FileRepositoryType(KGObject): +class FileRepositoryType(KGObject, FileRepositoryType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/FileRepositoryType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the file repository type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the file repository type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.core.FileRepository", - "^vocab:type", + "openminds.latest.core.FileRepository", + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/file_usage_role.py b/fairgraph/openminds/controlled_terms/file_usage_role.py index 5aaddb0b..3a180fb5 100644 --- a/fairgraph/openminds/controlled_terms/file_usage_role.py +++ b/fairgraph/openminds/controlled_terms/file_usage_role.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import FileUsageRole +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class FileUsageRole(KGObject): +class FileUsageRole(KGObject, FileUsageRole): """ Structured information on the usage role of a file instance or bundle. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/FileUsageRole" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the file usage role.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the file usage role.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "file", - ["openminds.computation.LocalFile", "openminds.core.File"], - "^vocab:specialUsageRole", + ["openminds.latest.computation.LocalFile", "openminds.latest.core.File"], + "specialUsageRole", reverse="special_usage_role", multiple=True, - doc="reverse of 'special_usage_role'", + description="reverse of 'special_usage_role'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/genetic_strain_type.py b/fairgraph/openminds/controlled_terms/genetic_strain_type.py index 3207800a..da9a90c2 100644 --- a/fairgraph/openminds/controlled_terms/genetic_strain_type.py +++ b/fairgraph/openminds/controlled_terms/genetic_strain_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import GeneticStrainType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class GeneticStrainType(KGObject): +class GeneticStrainType(KGObject, GeneticStrainType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/GeneticStrainType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the genetic strain type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the genetic strain type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_genetic_strain_type_of", - "openminds.core.Strain", - "^vocab:geneticStrainType", + "openminds.latest.core.Strain", + "geneticStrainType", reverse="genetic_strain_type", multiple=True, - doc="reverse of 'genetic_strain_type'", + description="reverse of 'genetic_strain_type'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py index f553da38..4bbd2edc 100644 --- a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import GustatoryStimulusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class GustatoryStimulusType(KGObject): +class GustatoryStimulusType(KGObject, GustatoryStimulusType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/GustatoryStimulusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the gustatory stimulus type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the gustatory stimulus type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:stimulusType", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "stimulusType", reverse="stimulus_types", multiple=True, - doc="reverse of 'stimulus_types'", + description="reverse of 'stimulus_types'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/handedness.py b/fairgraph/openminds/controlled_terms/handedness.py index 238575db..715d1faa 100644 --- a/fairgraph/openminds/controlled_terms/handedness.py +++ b/fairgraph/openminds/controlled_terms/handedness.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Handedness +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Handedness(KGObject): +class Handedness(KGObject, Handedness): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Handedness" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the handedness.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the handedness.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "subject_states", - ["openminds.core.SubjectGroupState", "openminds.core.SubjectState"], - "^vocab:handedness", + ["openminds.latest.core.SubjectGroupState", "openminds.latest.core.SubjectState"], + "handedness", reverse="handedness", multiple=True, - doc="reverse of 'handedness'", + description="reverse of 'handedness'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/language.py b/fairgraph/openminds/controlled_terms/language.py index b6448c91..147555e9 100644 --- a/fairgraph/openminds/controlled_terms/language.py +++ b/fairgraph/openminds/controlled_terms/language.py @@ -4,96 +4,52 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Language +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Language(KGObject): +class Language(KGObject, Language): """ Structured information on the available language setting. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Language" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the language.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the language.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_in", - "openminds.core.SoftwareVersion", - "^vocab:language", + "openminds.latest.core.SoftwareVersion", + "language", reverse="languages", multiple=True, - doc="reverse of 'languages'", + description="reverse of 'languages'", ), ] existence_query_properties = ("name",) @@ -114,7 +70,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/laterality.py b/fairgraph/openminds/controlled_terms/laterality.py index a64caf31..8ef37a3a 100644 --- a/fairgraph/openminds/controlled_terms/laterality.py +++ b/fairgraph/openminds/controlled_terms/laterality.py @@ -4,102 +4,58 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Laterality +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Laterality(KGObject): +class Laterality(KGObject, Laterality): """ Structured information on the lateral direction. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Laterality" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the laterality.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the laterality.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_laterality_of", [ - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - "openminds.sands.AtlasAnnotation", - "openminds.sands.CustomAnnotation", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", + "openminds.latest.sands.AtlasAnnotation", + "openminds.latest.sands.CustomAnnotation", ], - "^vocab:laterality", + "laterality", reverse="lateralities", multiple=True, - doc="reverse of 'lateralities'", + description="reverse of 'lateralities'", ), ] existence_query_properties = ("name",) @@ -120,7 +76,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/learning_resource_type.py b/fairgraph/openminds/controlled_terms/learning_resource_type.py index 035ca2dd..e5a9b0eb 100644 --- a/fairgraph/openminds/controlled_terms/learning_resource_type.py +++ b/fairgraph/openminds/controlled_terms/learning_resource_type.py @@ -4,96 +4,52 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import LearningResourceType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class LearningResourceType(KGObject): +class LearningResourceType(KGObject, LearningResourceType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/LearningResourceType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the learning resource type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the learning resource type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.publications.LearningResource", - "^vocab:type", + "openminds.latest.publications.LearningResource", + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), ] existence_query_properties = ("name",) @@ -114,7 +70,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/measured_quantity.py b/fairgraph/openminds/controlled_terms/measured_quantity.py index dbd2669b..47920bf3 100644 --- a/fairgraph/openminds/controlled_terms/measured_quantity.py +++ b/fairgraph/openminds/controlled_terms/measured_quantity.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import MeasuredQuantity +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MeasuredQuantity(KGObject): +class MeasuredQuantity(KGObject, MeasuredQuantity): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/MeasuredQuantity" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the measured quantity.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the measured quantity.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "measurement", - "openminds.core.Measurement", - "^vocab:measuredQuantity", + "openminds.latest.core.Measurement", + "measuredQuantity", reverse="measured_quantity", multiple=True, - doc="reverse of 'measured_quantity'", + description="reverse of 'measured_quantity'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/measured_signal_type.py b/fairgraph/openminds/controlled_terms/measured_signal_type.py index bb4454d4..6b217ee3 100644 --- a/fairgraph/openminds/controlled_terms/measured_signal_type.py +++ b/fairgraph/openminds/controlled_terms/measured_signal_type.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import MeasuredSignalType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MeasuredSignalType(KGObject): +class MeasuredSignalType(KGObject, MeasuredSignalType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/MeasuredSignalType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the measured signal type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the measured signal type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/meta_data_model_type.py b/fairgraph/openminds/controlled_terms/meta_data_model_type.py index f3d03745..c522b8c9 100644 --- a/fairgraph/openminds/controlled_terms/meta_data_model_type.py +++ b/fairgraph/openminds/controlled_terms/meta_data_model_type.py @@ -4,96 +4,52 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import MetaDataModelType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MetaDataModelType(KGObject): +class MetaDataModelType(KGObject, MetaDataModelType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/MetaDataModelType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the meta data model type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the meta data model type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.core.MetaDataModelVersion", - "^vocab:type", + "openminds.latest.core.MetaDataModelVersion", + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), ] existence_query_properties = ("name",) @@ -114,7 +70,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/model_abstraction_level.py b/fairgraph/openminds/controlled_terms/model_abstraction_level.py index 16fe7715..0f93ab53 100644 --- a/fairgraph/openminds/controlled_terms/model_abstraction_level.py +++ b/fairgraph/openminds/controlled_terms/model_abstraction_level.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ModelAbstractionLevel +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ModelAbstractionLevel(KGObject): +class ModelAbstractionLevel(KGObject, ModelAbstractionLevel): """ Structured information on abstraction level of the computational model. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ModelAbstractionLevel" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the model abstraction level.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the model abstraction level.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_abstraction_level_of", - "openminds.core.Model", - "^vocab:abstractionLevel", + "openminds.latest.core.Model", + "abstractionLevel", reverse="abstraction_level", multiple=True, - doc="reverse of 'abstraction_level'", + description="reverse of 'abstraction_level'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/model_scope.py b/fairgraph/openminds/controlled_terms/model_scope.py index 7a6d7065..5356c59c 100644 --- a/fairgraph/openminds/controlled_terms/model_scope.py +++ b/fairgraph/openminds/controlled_terms/model_scope.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ModelScope +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ModelScope(KGObject): +class ModelScope(KGObject, ModelScope): """ Structured information on the scope of the computational model. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ModelScope" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the model scope.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the model scope.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_scope_of", - ["openminds.computation.ValidationTest", "openminds.core.Model"], - "^vocab:scope", + ["openminds.latest.computation.ValidationTest", "openminds.latest.core.Model"], + "scope", reverse="model_scope", multiple=True, - doc="reverse of 'model_scope'", + description="reverse of 'model_scope'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/molecular_entity.py b/fairgraph/openminds/controlled_terms/molecular_entity.py index 2d002633..51e1096c 100644 --- a/fairgraph/openminds/controlled_terms/molecular_entity.py +++ b/fairgraph/openminds/controlled_terms/molecular_entity.py @@ -4,144 +4,100 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import MolecularEntity +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MolecularEntity(KGObject): +class MolecularEntity(KGObject, MolecularEntity): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/MolecularEntity" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the molecular entity.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the molecular entity.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "composes", [ - "openminds.chemicals.ChemicalSubstance", - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", + "openminds.latest.chemicals.ChemicalSubstance", + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", ], - ["^vocab:insulatorMaterial", "^vocab:material", "^vocab:molecularEntity"], + ["insulatorMaterial", "material", "molecularEntity"], reverse=["insulator_material", "material", "molecular_entity"], multiple=True, - doc="reverse of insulator_material, material, molecular_entity", + description="reverse of insulator_material, material, molecular_entity", ), Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "labels", - "openminds.ephys.PipetteUsage", - "^vocab:labelingCompound", + "openminds.latest.ephys.PipetteUsage", + "labelingCompound", reverse="labeling_compound", multiple=True, - doc="reverse of 'labeling_compound'", + description="reverse of 'labeling_compound'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -165,7 +121,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py b/fairgraph/openminds/controlled_terms/mr_acquisition_type.py index 96de3cea..94992b75 100644 --- a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py +++ b/fairgraph/openminds/controlled_terms/mr_acquisition_type.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import MRAcquisitionType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MRAcquisitionType(KGObject): +class MRAcquisitionType(KGObject, MRAcquisitionType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/MRAcquisitionType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the m r acquisition type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the m r acquisition type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py index 663d6553..76ed421a 100644 --- a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py +++ b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py @@ -4,104 +4,60 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import MRIPulseSequence +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MRIPulseSequence(KGObject): +class MRIPulseSequence(KGObject, MRIPulseSequence): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/MRIPulseSequence" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the m r i pulse sequence.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the m r i pulse sequence.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.core.DatasetVersion", "openminds.core.Protocol"], - "^vocab:technique", + ["openminds.latest.core.DatasetVersion", "openminds.latest.core.Protocol"], + "technique", reverse="techniques", multiple=True, - doc="reverse of 'techniques'", + description="reverse of 'techniques'", ), ] existence_query_properties = ("name",) @@ -123,7 +79,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/mri_weighting.py b/fairgraph/openminds/controlled_terms/mri_weighting.py index a18a3c7c..3645eebc 100644 --- a/fairgraph/openminds/controlled_terms/mri_weighting.py +++ b/fairgraph/openminds/controlled_terms/mri_weighting.py @@ -4,104 +4,60 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import MRIWeighting +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MRIWeighting(KGObject): +class MRIWeighting(KGObject, MRIWeighting): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/MRIWeighting" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the m r i weighting.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the m r i weighting.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.core.DatasetVersion", "openminds.core.Protocol"], - "^vocab:technique", + ["openminds.latest.core.DatasetVersion", "openminds.latest.core.Protocol"], + "technique", reverse="techniques", multiple=True, - doc="reverse of 'techniques'", + description="reverse of 'techniques'", ), ] existence_query_properties = ("name",) @@ -123,7 +79,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py index 3ad24e59..bf724109 100644 --- a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import OlfactoryStimulusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class OlfactoryStimulusType(KGObject): +class OlfactoryStimulusType(KGObject, OlfactoryStimulusType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/OlfactoryStimulusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the olfactory stimulus type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the olfactory stimulus type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:stimulusType", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "stimulusType", reverse="stimulus_types", multiple=True, - doc="reverse of 'stimulus_types'", + description="reverse of 'stimulus_types'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/operating_device.py b/fairgraph/openminds/controlled_terms/operating_device.py index 19e328fc..07a9047d 100644 --- a/fairgraph/openminds/controlled_terms/operating_device.py +++ b/fairgraph/openminds/controlled_terms/operating_device.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import OperatingDevice +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class OperatingDevice(KGObject): +class OperatingDevice(KGObject, OperatingDevice): """ Structured information on the operating device. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/OperatingDevice" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the operating device.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the operating device.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/operating_system.py b/fairgraph/openminds/controlled_terms/operating_system.py index bbc7b6d9..a680dcd2 100644 --- a/fairgraph/openminds/controlled_terms/operating_system.py +++ b/fairgraph/openminds/controlled_terms/operating_system.py @@ -4,96 +4,52 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import OperatingSystem +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class OperatingSystem(KGObject): +class OperatingSystem(KGObject, OperatingSystem): """ Structured information on the operating system. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/OperatingSystem" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the operating system.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the operating system.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_by", - "openminds.core.SoftwareVersion", - "^vocab:operatingSystem", + "openminds.latest.core.SoftwareVersion", + "operatingSystem", reverse="operating_systems", multiple=True, - doc="reverse of 'operating_systems'", + description="reverse of 'operating_systems'", ), ] existence_query_properties = ("name",) @@ -114,7 +70,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py index cc43eaab..d8807e2f 100644 --- a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import OpticalStimulusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class OpticalStimulusType(KGObject): +class OpticalStimulusType(KGObject, OpticalStimulusType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/OpticalStimulusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the optical stimulus type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the optical stimulus type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:stimulusType", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "stimulusType", reverse="stimulus_types", multiple=True, - doc="reverse of 'stimulus_types'", + description="reverse of 'stimulus_types'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/organ.py b/fairgraph/openminds/controlled_terms/organ.py index 051ae0ee..ee3630d1 100644 --- a/fairgraph/openminds/controlled_terms/organ.py +++ b/fairgraph/openminds/controlled_terms/organ.py @@ -4,155 +4,115 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Organ +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Organ(KGObject): +class Organ(KGObject, Organ): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Organ" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the organ.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the organ.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "defines", - ["openminds.sands.CustomAnatomicalEntity", "openminds.sands.ParcellationEntity"], - "^vocab:relatedUBERONTerm", + ["openminds.latest.sands.CustomAnatomicalEntity", "openminds.latest.sands.ParcellationEntity"], + "relatedUBERONTerm", reverse="related_uberon_term", multiple=True, - doc="reverse of 'related_uberon_term'", + description="reverse of 'related_uberon_term'", ), Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_location_of", - ["openminds.ephys.ElectrodeArrayUsage", "openminds.ephys.ElectrodeUsage", "openminds.ephys.PipetteUsage"], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes"], + [ + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", + ], + ["anatomicalLocation", "anatomicalLocationOfElectrodes"], reverse=["anatomical_location", "anatomical_locations_of_electrodes"], multiple=True, - doc="reverse of anatomical_location, anatomical_locations_of_electrodes", + description="reverse of anatomical_location, anatomical_locations_of_electrodes", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "sample", - ["openminds.core.TissueSample", "openminds.core.TissueSampleCollection"], - "^vocab:origin", + ["openminds.latest.core.TissueSample", "openminds.latest.core.TissueSampleCollection"], + "origin", reverse="origin", multiple=True, - doc="reverse of 'origin'", + description="reverse of 'origin'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -178,7 +138,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/organism_substance.py b/fairgraph/openminds/controlled_terms/organism_substance.py index e4a34256..ca807fab 100644 --- a/fairgraph/openminds/controlled_terms/organism_substance.py +++ b/fairgraph/openminds/controlled_terms/organism_substance.py @@ -4,147 +4,107 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import OrganismSubstance +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class OrganismSubstance(KGObject): +class OrganismSubstance(KGObject, OrganismSubstance): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/OrganismSubstance" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the organism substance.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the organism substance.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_location_of", - ["openminds.ephys.ElectrodeArrayUsage", "openminds.ephys.ElectrodeUsage", "openminds.ephys.PipetteUsage"], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes"], + [ + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", + ], + ["anatomicalLocation", "anatomicalLocationOfElectrodes"], reverse=["anatomical_location", "anatomical_locations_of_electrodes"], multiple=True, - doc="reverse of anatomical_location, anatomical_locations_of_electrodes", + description="reverse of anatomical_location, anatomical_locations_of_electrodes", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "sample", - ["openminds.core.TissueSample", "openminds.core.TissueSampleCollection"], - "^vocab:origin", + ["openminds.latest.core.TissueSample", "openminds.latest.core.TissueSampleCollection"], + "origin", reverse="origin", multiple=True, - doc="reverse of 'origin'", + description="reverse of 'origin'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -169,7 +129,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/organism_system.py b/fairgraph/openminds/controlled_terms/organism_system.py index 79ebf207..f31ac6e4 100644 --- a/fairgraph/openminds/controlled_terms/organism_system.py +++ b/fairgraph/openminds/controlled_terms/organism_system.py @@ -4,123 +4,79 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import OrganismSystem +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class OrganismSystem(KGObject): +class OrganismSystem(KGObject, OrganismSystem): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/OrganismSystem" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the organism system.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the organism system.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -142,7 +98,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py index 055d5058..8669a3ee 100644 --- a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py +++ b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import PatchClampVariation +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class PatchClampVariation(KGObject): +class PatchClampVariation(KGObject, PatchClampVariation): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/PatchClampVariation" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the patch clamp variation.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the patch clamp variation.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_in", - "openminds.ephys.CellPatching", - "^vocab:variation", + "openminds.latest.ephys.CellPatching", + "variation", reverse="variation", multiple=True, - doc="reverse of 'variation'", + description="reverse of 'variation'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/preparation_type.py b/fairgraph/openminds/controlled_terms/preparation_type.py index 31c4fa74..90c2e9ff 100644 --- a/fairgraph/openminds/controlled_terms/preparation_type.py +++ b/fairgraph/openminds/controlled_terms/preparation_type.py @@ -4,106 +4,62 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import PreparationType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class PreparationType(KGObject): +class PreparationType(KGObject, PreparationType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/PreparationType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the preparation type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the preparation type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_for", [ - "openminds.core.DatasetVersion", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:preparationDesign", + "preparationDesign", reverse="preparation_design", multiple=True, - doc="reverse of 'preparation_design'", + description="reverse of 'preparation_design'", ), ] existence_query_properties = ("name",) @@ -124,7 +80,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/product_accessibility.py b/fairgraph/openminds/controlled_terms/product_accessibility.py index 283b7a34..92b9b362 100644 --- a/fairgraph/openminds/controlled_terms/product_accessibility.py +++ b/fairgraph/openminds/controlled_terms/product_accessibility.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ProductAccessibility +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ProductAccessibility(KGObject): +class ProductAccessibility(KGObject, ProductAccessibility): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ProductAccessibility" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the product accessibility.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the product accessibility.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/programming_language.py b/fairgraph/openminds/controlled_terms/programming_language.py index 2434d713..f0f54328 100644 --- a/fairgraph/openminds/controlled_terms/programming_language.py +++ b/fairgraph/openminds/controlled_terms/programming_language.py @@ -4,96 +4,52 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import ProgrammingLanguage +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ProgrammingLanguage(KGObject): +class ProgrammingLanguage(KGObject, ProgrammingLanguage): """ Structured information on the programming language. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/ProgrammingLanguage" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the programming language.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the programming language.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_in", - "openminds.core.SoftwareVersion", - "^vocab:programmingLanguage", + "openminds.latest.core.SoftwareVersion", + "programmingLanguage", reverse="programming_languages", multiple=True, - doc="reverse of 'programming_languages'", + description="reverse of 'programming_languages'", ), ] existence_query_properties = ("name",) @@ -114,7 +70,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/qualitative_overlap.py b/fairgraph/openminds/controlled_terms/qualitative_overlap.py index 1874e9ce..5ebe8eb9 100644 --- a/fairgraph/openminds/controlled_terms/qualitative_overlap.py +++ b/fairgraph/openminds/controlled_terms/qualitative_overlap.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import QualitativeOverlap +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class QualitativeOverlap(KGObject): +class QualitativeOverlap(KGObject, QualitativeOverlap): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/QualitativeOverlap" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the qualitative overlap.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the qualitative overlap.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/semantic_data_type.py b/fairgraph/openminds/controlled_terms/semantic_data_type.py index bbb169d8..128abf55 100644 --- a/fairgraph/openminds/controlled_terms/semantic_data_type.py +++ b/fairgraph/openminds/controlled_terms/semantic_data_type.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import SemanticDataType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class SemanticDataType(KGObject): +class SemanticDataType(KGObject, SemanticDataType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/SemanticDataType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the semantic data type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the semantic data type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/service.py b/fairgraph/openminds/controlled_terms/service.py index 02eb4425..530a5bf6 100644 --- a/fairgraph/openminds/controlled_terms/service.py +++ b/fairgraph/openminds/controlled_terms/service.py @@ -4,105 +4,61 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Service +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Service(KGObject): +class Service(KGObject, Service): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Service" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the service.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the service.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "hosts", - "openminds.publications.LivePaperResourceItem", - "^vocab:hostedBy", + "openminds.latest.publications.LivePaperResourceItem", + "hostedBy", reverse="hosted_by", multiple=True, - doc="reverse of 'hosted_by'", + description="reverse of 'hosted_by'", ), Property( "linked_from", - "openminds.core.ServiceLink", - "^vocab:service", + "openminds.latest.core.ServiceLink", + "service", reverse="service", multiple=True, - doc="reverse of 'service'", + description="reverse of 'service'", ), ] existence_query_properties = ("name",) @@ -124,7 +80,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/setup_type.py b/fairgraph/openminds/controlled_terms/setup_type.py index b1d84104..75cecfe7 100644 --- a/fairgraph/openminds/controlled_terms/setup_type.py +++ b/fairgraph/openminds/controlled_terms/setup_type.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import SetupType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class SetupType(KGObject): +class SetupType(KGObject, SetupType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/SetupType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the setup type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the setup type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - "openminds.core.Setup", - "^vocab:type", + "openminds.latest.core.Setup", + "type", reverse="types", multiple=True, - doc="reverse of 'types'", + description="reverse of 'types'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/software_application_category.py b/fairgraph/openminds/controlled_terms/software_application_category.py index e4ebcc11..cab159b4 100644 --- a/fairgraph/openminds/controlled_terms/software_application_category.py +++ b/fairgraph/openminds/controlled_terms/software_application_category.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import SoftwareApplicationCategory +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class SoftwareApplicationCategory(KGObject): +class SoftwareApplicationCategory(KGObject, SoftwareApplicationCategory): """ Structured information on the category of the software application. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/SoftwareApplicationCategory" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the software application category.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the software application category.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/software_feature.py b/fairgraph/openminds/controlled_terms/software_feature.py index d7f62bb3..eb01b166 100644 --- a/fairgraph/openminds/controlled_terms/software_feature.py +++ b/fairgraph/openminds/controlled_terms/software_feature.py @@ -4,89 +4,45 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import SoftwareFeature +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class SoftwareFeature(KGObject): +class SoftwareFeature(KGObject, SoftwareFeature): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/SoftwareFeature" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the software feature.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the software feature.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), ] existence_query_properties = ("name",) @@ -106,7 +62,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/species.py b/fairgraph/openminds/controlled_terms/species.py index 40a3f754..c818aa89 100644 --- a/fairgraph/openminds/controlled_terms/species.py +++ b/fairgraph/openminds/controlled_terms/species.py @@ -4,145 +4,101 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Species +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Species(KGObject): +class Species(KGObject, Species): """ Structured information on the species. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Species" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the species.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the species.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "common_coordinate_space", - ["openminds.sands.BrainAtlas", "openminds.sands.CommonCoordinateSpace"], - "^vocab:usedSpecies", + ["openminds.latest.sands.BrainAtlas", "openminds.latest.sands.CommonCoordinateSpace"], + "usedSpecies", reverse="used_species", multiple=True, - doc="reverse of 'used_species'", + description="reverse of 'used_species'", ), Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_species_of", [ - "openminds.core.Strain", - "openminds.core.Subject", - "openminds.core.SubjectGroup", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", + "openminds.latest.core.Strain", + "openminds.latest.core.Subject", + "openminds.latest.core.SubjectGroup", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", ], - "^vocab:species", + "species", reverse="species", multiple=True, - doc="reverse of 'species'", + description="reverse of 'species'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -166,7 +122,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/stimulation_approach.py b/fairgraph/openminds/controlled_terms/stimulation_approach.py index 072983fe..211e1834 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_approach.py +++ b/fairgraph/openminds/controlled_terms/stimulation_approach.py @@ -4,104 +4,64 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import StimulationApproach +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class StimulationApproach(KGObject): +class StimulationApproach(KGObject, StimulationApproach): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/StimulationApproach" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the stimulation approach.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the stimulation approach.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.DatasetVersion", "openminds.core.Protocol"], - ["^vocab:stimulation", "^vocab:technique"], + [ + "openminds.latest.core.BehavioralProtocol", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Protocol", + ], + ["stimulation", "technique"], reverse=["stimulations", "techniques"], multiple=True, - doc="reverse of stimulations, techniques", + description="reverse of stimulations, techniques", ), ] existence_query_properties = ("name",) @@ -123,7 +83,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/stimulation_technique.py b/fairgraph/openminds/controlled_terms/stimulation_technique.py index d406b741..e6b3fc4f 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_technique.py +++ b/fairgraph/openminds/controlled_terms/stimulation_technique.py @@ -4,104 +4,64 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import StimulationTechnique +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class StimulationTechnique(KGObject): +class StimulationTechnique(KGObject, StimulationTechnique): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/StimulationTechnique" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the stimulation technique.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the stimulation technique.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.DatasetVersion", "openminds.core.Protocol"], - ["^vocab:stimulation", "^vocab:technique"], + [ + "openminds.latest.core.BehavioralProtocol", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Protocol", + ], + ["stimulation", "technique"], reverse=["stimulations", "techniques"], multiple=True, - doc="reverse of stimulations, techniques", + description="reverse of stimulations, techniques", ), ] existence_query_properties = ("name",) @@ -123,7 +83,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/subcellular_entity.py b/fairgraph/openminds/controlled_terms/subcellular_entity.py index a4de2b36..af12f813 100644 --- a/fairgraph/openminds/controlled_terms/subcellular_entity.py +++ b/fairgraph/openminds/controlled_terms/subcellular_entity.py @@ -4,145 +4,101 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import SubcellularEntity +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class SubcellularEntity(KGObject): +class SubcellularEntity(KGObject, SubcellularEntity): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/SubcellularEntity" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the subcellular entity.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the subcellular entity.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_location_of", [ - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", ], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes"], + ["anatomicalLocation", "anatomicalLocationOfElectrodes"], reverse=["anatomical_location", "anatomical_locations", "anatomical_locations_of_electrodes"], multiple=True, - doc="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", + description="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -166,7 +122,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/subject_attribute.py b/fairgraph/openminds/controlled_terms/subject_attribute.py index e47f1630..3f4796ab 100644 --- a/fairgraph/openminds/controlled_terms/subject_attribute.py +++ b/fairgraph/openminds/controlled_terms/subject_attribute.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import SubjectAttribute +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class SubjectAttribute(KGObject): +class SubjectAttribute(KGObject, SubjectAttribute): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/SubjectAttribute" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the subject attribute.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the subject attribute.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_attribute_of", - ["openminds.core.SubjectGroupState", "openminds.core.SubjectState"], - "^vocab:attribute", + ["openminds.latest.core.SubjectGroupState", "openminds.latest.core.SubjectState"], + "attribute", reverse="attributes", multiple=True, - doc="reverse of 'attributes'", + description="reverse of 'attributes'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py index 25f21e96..3ea67da4 100644 --- a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import TactileStimulusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class TactileStimulusType(KGObject): +class TactileStimulusType(KGObject, TactileStimulusType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/TactileStimulusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the tactile stimulus type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the tactile stimulus type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:stimulusType", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "stimulusType", reverse="stimulus_types", multiple=True, - doc="reverse of 'stimulus_types'", + description="reverse of 'stimulus_types'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/technique.py b/fairgraph/openminds/controlled_terms/technique.py index c63e8053..2d070fd7 100644 --- a/fairgraph/openminds/controlled_terms/technique.py +++ b/fairgraph/openminds/controlled_terms/technique.py @@ -4,112 +4,68 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Technique +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Technique(KGObject): +class Technique(KGObject, Technique): """ Structured information on the technique. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Technique" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the technique.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the technique.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_reference_for", - "openminds.computation.ValidationTest", - "^vocab:referenceDataAcquisition", + "openminds.latest.computation.ValidationTest", + "referenceDataAcquisition", reverse="reference_data_acquisitions", multiple=True, - doc="reverse of 'reference_data_acquisitions'", + description="reverse of 'reference_data_acquisitions'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.core.DatasetVersion", "openminds.core.Protocol"], - "^vocab:technique", + ["openminds.latest.core.DatasetVersion", "openminds.latest.core.Protocol"], + "technique", reverse="techniques", multiple=True, - doc="reverse of 'techniques'", + description="reverse of 'techniques'", ), ] existence_query_properties = ("name",) @@ -132,7 +88,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/term_suggestion.py b/fairgraph/openminds/controlled_terms/term_suggestion.py index 16452090..39aa8364 100644 --- a/fairgraph/openminds/controlled_terms/term_suggestion.py +++ b/fairgraph/openminds/controlled_terms/term_suggestion.py @@ -4,135 +4,79 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import TermSuggestion +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class TermSuggestion(KGObject): +class TermSuggestion(KGObject, TermSuggestion): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/TermSuggestion" - properties = [ - Property( - "add_existing_terminology", - "openminds.controlled_terms.Terminology", - "vocab:addExistingTerminology", - doc="Reference to an existing terminology (distinct class to group related terms).", - ), - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the term suggestion.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the term suggestion.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "suggest_new_terminology", - str, - "vocab:suggestNewTerminology", - doc="Proposal of a new distinct class to group related terms.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -156,7 +100,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/terminology.py b/fairgraph/openminds/controlled_terms/terminology.py index 2d5c2c1e..f253e5a5 100644 --- a/fairgraph/openminds/controlled_terms/terminology.py +++ b/fairgraph/openminds/controlled_terms/terminology.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import Terminology +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Terminology(KGObject): +class Terminology(KGObject, Terminology): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/Terminology" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the terminology.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the terminology.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "suggested_in", - "openminds.controlled_terms.TermSuggestion", - "^vocab:addExistingTerminology", + "openminds.latest.controlled_terms.TermSuggestion", + "addExistingTerminology", reverse="add_existing_terminology", multiple=True, - doc="reverse of 'add_existing_terminology'", + description="reverse of 'add_existing_terminology'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py index 6fa096af..37f3575c 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import TissueSampleAttribute +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class TissueSampleAttribute(KGObject): +class TissueSampleAttribute(KGObject, TissueSampleAttribute): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/TissueSampleAttribute" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the tissue sample attribute.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the tissue sample attribute.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_attribute_of", - ["openminds.core.TissueSampleCollectionState", "openminds.core.TissueSampleState"], - "^vocab:attribute", + ["openminds.latest.core.TissueSampleCollectionState", "openminds.latest.core.TissueSampleState"], + "attribute", reverse="attributes", multiple=True, - doc="reverse of 'attributes'", + description="reverse of 'attributes'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_type.py b/fairgraph/openminds/controlled_terms/tissue_sample_type.py index f8f2ecad..eb294c5d 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_type.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import TissueSampleType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class TissueSampleType(KGObject): +class TissueSampleType(KGObject, TissueSampleType): """ Structured information on the general type of the tissue sample. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/TissueSampleType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the tissue sample type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the tissue sample type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_type_of", - ["openminds.core.TissueSample", "openminds.core.TissueSampleCollection"], - "^vocab:type", + ["openminds.latest.core.TissueSample", "openminds.latest.core.TissueSampleCollection"], + "type", reverse="type", multiple=True, - doc="reverse of 'type'", + description="reverse of 'type'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py index 56548d86..d1e4b9ce 100644 --- a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py +++ b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py @@ -4,97 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import TypeOfUncertainty +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class TypeOfUncertainty(KGObject): +class TypeOfUncertainty(KGObject, TypeOfUncertainty): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/TypeOfUncertainty" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the type of uncertainty.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the type of uncertainty.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "value", - "openminds.core.QuantitativeValueArray", - "^vocab:typeOfUncertainty", + "openminds.latest.core.QuantitativeValueArray", + "typeOfUncertainty", reverse="type_of_uncertainty", multiple=True, - doc="reverse of 'type_of_uncertainty'", + description="reverse of 'type_of_uncertainty'", ), ] existence_query_properties = ("name",) @@ -115,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/uberon_parcellation.py b/fairgraph/openminds/controlled_terms/uberon_parcellation.py index 0a119258..8eda9f78 100644 --- a/fairgraph/openminds/controlled_terms/uberon_parcellation.py +++ b/fairgraph/openminds/controlled_terms/uberon_parcellation.py @@ -4,153 +4,109 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import UBERONParcellation +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class UBERONParcellation(KGObject): +class UBERONParcellation(KGObject, UBERONParcellation): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the UBERONParcellation.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the UBERONParcellation.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "defines", - ["openminds.sands.CustomAnatomicalEntity", "openminds.sands.ParcellationEntity"], - "^vocab:relatedUBERONTerm", + ["openminds.latest.sands.CustomAnatomicalEntity", "openminds.latest.sands.ParcellationEntity"], + "relatedUBERONTerm", reverse="related_uberon_term", multiple=True, - doc="reverse of 'related_uberon_term'", + description="reverse of 'related_uberon_term'", ), Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_location_of", [ - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", ], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes"], + ["anatomicalLocation", "anatomicalLocationOfElectrodes"], reverse=["anatomical_location", "anatomical_locations", "anatomical_locations_of_electrodes"], multiple=True, - doc="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", + description="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -175,7 +131,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/unit_of_measurement.py b/fairgraph/openminds/controlled_terms/unit_of_measurement.py index 54011f16..76ffe150 100644 --- a/fairgraph/openminds/controlled_terms/unit_of_measurement.py +++ b/fairgraph/openminds/controlled_terms/unit_of_measurement.py @@ -4,107 +4,68 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import UnitOfMeasurement +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class UnitOfMeasurement(KGObject): +class UnitOfMeasurement(KGObject, UnitOfMeasurement): """ Structured information on the unit of measurement. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the unit of measurement.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the unit of measurement.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "used_by", - ["openminds.sands.CommonCoordinateSpaceVersion", "openminds.sands.CustomCoordinateSpace"], - "^vocab:nativeUnit", + ["openminds.latest.sands.CommonCoordinateSpaceVersion", "openminds.latest.sands.CustomCoordinateSpace"], + "nativeUnit", reverse="native_unit", multiple=True, - doc="reverse of 'native_unit'", + description="reverse of 'native_unit'", ), Property( - "used_in", "openminds.ephys.Channel", "^vocab:unit", reverse="unit", multiple=True, doc="reverse of 'unit'" + "used_in", + "openminds.latest.ephys.Channel", + "unit", + reverse="unit", + multiple=True, + description="reverse of 'unit'", ), Property( "value", - "openminds.core.QuantitativeValueArray", - "^vocab:unit", + "openminds.latest.core.QuantitativeValueArray", + "unit", reverse="unit", multiple=True, - doc="reverse of 'unit'", + description="reverse of 'unit'", ), ] existence_query_properties = ("name",) @@ -127,7 +88,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py index 60494841..67b096ab 100644 --- a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py @@ -4,131 +4,87 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.controlled_terms import VisualStimulusType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class VisualStimulusType(KGObject): +class VisualStimulusType(KGObject, VisualStimulusType): """ """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/controlledTerms/VisualStimulusType" - properties = [ - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the visual stimulus type.", - ), - Property( - "interlex_identifier", - IRI, - "vocab:interlexIdentifier", - doc="Persistent identifier for a term registered in the InterLex project.", - ), - Property( - "knowledge_space_link", - IRI, - "vocab:knowledgeSpaceLink", - doc="Persistent link to an encyclopedia entry in the Knowledge Space project.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the visual stimulus type.", - ), - Property( - "preferred_ontology_identifier", - IRI, - "vocab:preferredOntologyIdentifier", - doc="Persistent identifier of a preferred ontological term.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:keyword", + "keyword", reverse="keywords", multiple=True, - doc="reverse of 'keywords'", + description="reverse of 'keywords'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), Property( "used_in", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:stimulusType", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "stimulusType", reverse="stimulus_types", multiple=True, - doc="reverse of 'stimulus_types'", + description="reverse of 'stimulus_types'", ), ] existence_query_properties = ("name",) @@ -151,7 +107,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/actors/account_information.py b/fairgraph/openminds/core/actors/account_information.py index 318281f3..7fc1ba78 100644 --- a/fairgraph/openminds/core/actors/account_information.py +++ b/fairgraph/openminds/core/actors/account_information.py @@ -4,36 +4,39 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import AccountInformation +from fairgraph import KGObject -class AccountInformation(KGObject): +class AccountInformation(KGObject, AccountInformation): """ Structured information about a user account for a web service. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/AccountInformation" - properties = [ - Property( - "service", "openminds.core.WebService", "vocab:service", required=True, doc="no description available" - ), - Property("user_name", str, "vocab:userName", required=True, doc="no description available"), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "belongs_to", - "openminds.core.Person", - "^vocab:associatedAccount", + "openminds.latest.core.Person", + "associatedAccount", reverse="associated_accounts", multiple=True, - doc="reverse of 'associated_accounts'", + description="reverse of 'associated_accounts'", ), ] existence_query_properties = ("service", "user_name") def __init__(self, belongs_to=None, service=None, user_name=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, belongs_to=belongs_to, service=service, user_name=user_name + return KGObject.__init__( + self, + id=id, + space=space, + scope=scope, + data=data, + belongs_to=belongs_to, + service=service, + user_name=user_name, ) diff --git a/fairgraph/openminds/core/actors/affiliation.py b/fairgraph/openminds/core/actors/affiliation.py index 253c5f9f..0327791e 100644 --- a/fairgraph/openminds/core/actors/affiliation.py +++ b/fairgraph/openminds/core/actors/affiliation.py @@ -4,41 +4,24 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Affiliation +from fairgraph import EmbeddedMetadata from datetime import date -class Affiliation(EmbeddedMetadata): +class Affiliation(EmbeddedMetadata, Affiliation): """ Structured information about a relationship between two entities, such as a person and their employer. """ type_ = "https://openminds.ebrains.eu/core/Affiliation" - properties = [ - Property( - "end_date", - date, - "vocab:endDate", - doc="Date in the Gregorian calendar at which something terminates in time.", - ), - Property( - "member_of", - ["openminds.core.Consortium", "openminds.core.Organization"], - "vocab:memberOf", - required=True, - doc="no description available", - ), - Property( - "start_date", - date, - "vocab:startDate", - doc="Date in the Gregorian calendar at which something begins in time", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, end_date=None, member_of=None, start_date=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, end_date=end_date, member_of=member_of, start_date=start_date) + return EmbeddedMetadata.__init__( + self, data=data, end_date=end_date, member_of=member_of, start_date=start_date + ) diff --git a/fairgraph/openminds/core/actors/consortium.py b/fairgraph/openminds/core/actors/consortium.py index ab004406..763aac3c 100644 --- a/fairgraph/openminds/core/actors/consortium.py +++ b/fairgraph/openminds/core/actors/consortium.py @@ -4,137 +4,126 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Consortium +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Consortium(KGObject): +class Consortium(KGObject, Consortium): """ Structured information about an association of two or more persons or organizations, with the objective of participating in a common activity. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/Consortium" - properties = [ - Property( - "contact_information", - "openminds.core.ContactInformation", - "vocab:contactInformation", - doc="Any available way used to contact a person or business (e.g., address, phone number, email address, etc.).", - ), - Property( - "full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the consortium." - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the consortium."), - Property("short_name", str, "vocab:shortName", doc="Shortened or fully abbreviated name of the consortium."), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "coordinated_projects", - "openminds.core.Project", - "^vocab:coordinator", + "openminds.latest.core.Project", + "coordinator", reverse="coordinators", multiple=True, - doc="reverse of 'coordinators'", + description="reverse of 'coordinators'", ), Property( "developed", [ - "openminds.computation.ValidationTest", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipe", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.WebService", - "openminds.core.WebServiceVersion", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipe", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModel", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.Software", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebService", + "openminds.latest.core.WebServiceVersion", ], - "^vocab:developer", + "developer", reverse="developers", multiple=True, - doc="reverse of 'developers'", + description="reverse of 'developers'", ), Property( "funded", - "openminds.core.Funding", - "^vocab:funder", + "openminds.latest.core.Funding", + "funder", reverse="funder", multiple=True, - doc="reverse of 'funder'", + description="reverse of 'funder'", ), Property( "has_members", - "openminds.core.Affiliation", - "^vocab:memberOf", + "openminds.latest.core.Affiliation", + "memberOf", reverse="member_of", multiple=True, - doc="reverse of 'member_of'", + description="reverse of 'member_of'", ), Property( "is_custodian_of", [ - "openminds.core.Dataset", - "openminds.core.DatasetVersion", - "openminds.publications.LivePaper", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.core.Dataset", + "openminds.latest.core.DatasetVersion", + "openminds.latest.publications.LivePaper", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlas", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpace", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:custodian", + "custodian", reverse="custodians", multiple=True, - doc="reverse of 'custodians'", + description="reverse of 'custodians'", ), Property( "is_owner_of", [ - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", - "openminds.specimen_prep.SlicingDevice", + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + "openminds.latest.specimen_prep.SlicingDevice", ], - "^vocab:owner", + "owner", reverse="owners", multiple=True, - doc="reverse of 'owners'", + description="reverse of 'owners'", ), Property( "is_provider_of", - "openminds.chemicals.ProductSource", - "^vocab:provider", + "openminds.latest.chemicals.ProductSource", + "provider", reverse="provider", multiple=True, - doc="reverse of 'provider'", + description="reverse of 'provider'", ), Property( "manufactured", - "openminds.core.Setup", - "^vocab:manufacturer", + "openminds.latest.core.Setup", + "manufacturer", reverse="manufacturers", multiple=True, - doc="reverse of 'manufacturers'", + description="reverse of 'manufacturers'", ), Property( "published", [ - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.ScholarlyArticle", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.ScholarlyArticle", ], - "^vocab:publisher", + "publisher", reverse="publisher", multiple=True, - doc="reverse of 'publisher'", + description="reverse of 'publisher'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -162,7 +151,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/actors/contact_information.py b/fairgraph/openminds/core/actors/contact_information.py index 576c29ec..942f3912 100644 --- a/fairgraph/openminds/core/actors/contact_information.py +++ b/fairgraph/openminds/core/actors/contact_information.py @@ -4,40 +4,34 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ContactInformation +from fairgraph import KGObject -class ContactInformation(KGObject): +class ContactInformation(KGObject, ContactInformation): """ Structured information about how to contact a given person or consortium. """ - default_space = "restricted" type_ = "https://openminds.ebrains.eu/core/ContactInformation" - properties = [ - Property( - "email", - str, - "vocab:email", - required=True, - doc="Address to which or from which an electronic mail can be sent.", - ), - ] + default_space = "restricted" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_contact_information_of", - ["openminds.core.Consortium", "openminds.core.Person"], - "^vocab:contactInformation", + ["openminds.latest.core.Consortium", "openminds.latest.core.Person"], + "contactInformation", reverse="contact_information", multiple=True, - doc="reverse of 'contact_information'", + description="reverse of 'contact_information'", ), ] existence_query_properties = ("email",) def __init__(self, email=None, is_contact_information_of=None, id=None, data=None, space=None, scope=None): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/actors/contribution.py b/fairgraph/openminds/core/actors/contribution.py index 754dbc98..ee48e7be 100644 --- a/fairgraph/openminds/core/actors/contribution.py +++ b/fairgraph/openminds/core/actors/contribution.py @@ -4,34 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Contribution +from fairgraph import EmbeddedMetadata -class Contribution(EmbeddedMetadata): +class Contribution(EmbeddedMetadata, Contribution): """ Structured information on the contribution made to a research product. """ type_ = "https://openminds.ebrains.eu/core/Contribution" - properties = [ - Property( - "contributor", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:contributor", - required=True, - doc="Legal person that gave or supplied something as a part or share.", - ), - Property( - "types", - "openminds.controlled_terms.ContributionType", - "vocab:type", - multiple=True, - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, contributor=None, types=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, contributor=contributor, types=types) + return EmbeddedMetadata.__init__(self, data=data, contributor=contributor, types=types) diff --git a/fairgraph/openminds/core/actors/organization.py b/fairgraph/openminds/core/actors/organization.py index a898ed0f..68060d72 100644 --- a/fairgraph/openminds/core/actors/organization.py +++ b/fairgraph/openminds/core/actors/organization.py @@ -4,168 +4,142 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Organization +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Organization(KGObject): +class Organization(KGObject, Organization): """ An entity comprised of one or more natural persons with a particular purpose. [adapted from Wikipedia](https://en.wikipedia.org/wiki/Organization) """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/Organization" - properties = [ - Property( - "affiliations", - "openminds.core.Affiliation", - "vocab:affiliation", - multiple=True, - doc="Declaration of a person being closely associated to an organization.", - ), - Property( - "digital_identifiers", - ["openminds.core.GRIDID", "openminds.core.RORID", "openminds.core.RRID"], - "vocab:digitalIdentifier", - multiple=True, - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the organization." - ), - Property( - "has_parents", - "openminds.core.Organization", - "vocab:hasParent", - multiple=True, - doc="Reference to a parent object or legal person.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the organization."), - Property("short_name", str, "vocab:shortName", doc="Shortened or fully abbreviated name of the organization."), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "coordinated_projects", - "openminds.core.Project", - "^vocab:coordinator", + "openminds.latest.core.Project", + "coordinator", reverse="coordinators", multiple=True, - doc="reverse of 'coordinators'", + description="reverse of 'coordinators'", ), Property( "developed", [ - "openminds.computation.ValidationTest", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipe", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.WebService", - "openminds.core.WebServiceVersion", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipe", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModel", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.Software", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebService", + "openminds.latest.core.WebServiceVersion", ], - "^vocab:developer", + "developer", reverse="developers", multiple=True, - doc="reverse of 'developers'", + description="reverse of 'developers'", ), Property( "funded", - "openminds.core.Funding", - "^vocab:funder", + "openminds.latest.core.Funding", + "funder", reverse="funder", multiple=True, - doc="reverse of 'funder'", + description="reverse of 'funder'", ), Property( "has_children", - "openminds.core.Organization", - "^vocab:hasParent", + "openminds.latest.core.Organization", + "hasParent", reverse="has_parents", multiple=True, - doc="reverse of 'has_parents'", + description="reverse of 'has_parents'", ), Property( "has_members", - "openminds.core.Affiliation", - "^vocab:memberOf", + "openminds.latest.core.Affiliation", + "memberOf", reverse="member_of", multiple=True, - doc="reverse of 'member_of'", + description="reverse of 'member_of'", ), Property( "hosts", - ["openminds.core.FileRepository", "openminds.publications.LivePaperResourceItem"], - "^vocab:hostedBy", + ["openminds.latest.core.FileRepository", "openminds.latest.publications.LivePaperResourceItem"], + "hostedBy", reverse="hosted_by", multiple=True, - doc="reverse of 'hosted_by'", + description="reverse of 'hosted_by'", ), Property( "is_custodian_of", [ - "openminds.core.Dataset", - "openminds.core.DatasetVersion", - "openminds.publications.LivePaper", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.core.Dataset", + "openminds.latest.core.DatasetVersion", + "openminds.latest.publications.LivePaper", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlas", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpace", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:custodian", + "custodian", reverse="custodians", multiple=True, - doc="reverse of 'custodians'", + description="reverse of 'custodians'", ), Property( "is_owner_of", [ - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", - "openminds.specimen_prep.SlicingDevice", + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + "openminds.latest.specimen_prep.SlicingDevice", ], - "^vocab:owner", + "owner", reverse="owners", multiple=True, - doc="reverse of 'owners'", + description="reverse of 'owners'", ), Property( "is_provider_of", - "openminds.chemicals.ProductSource", - "^vocab:provider", + "openminds.latest.chemicals.ProductSource", + "provider", reverse="provider", multiple=True, - doc="reverse of 'provider'", + description="reverse of 'provider'", ), Property( "manufactured", - "openminds.core.Setup", - "^vocab:manufacturer", + "openminds.latest.core.Setup", + "manufacturer", reverse="manufacturers", multiple=True, - doc="reverse of 'manufacturers'", + description="reverse of 'manufacturers'", ), Property( "published", [ - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.ScholarlyArticle", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.ScholarlyArticle", ], - "^vocab:publisher", + "publisher", reverse="publisher", multiple=True, - doc="reverse of 'publisher'", + description="reverse of 'publisher'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -197,7 +171,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/actors/person.py b/fairgraph/openminds/core/actors/person.py index e77a5f51..81726364 100644 --- a/fairgraph/openminds/core/actors/person.py +++ b/fairgraph/openminds/core/actors/person.py @@ -4,193 +4,157 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Person +from fairgraph import KGObject -class Person(KGObject): +class Person(KGObject, Person): """ Structured information on a person. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/Person" - properties = [ - Property( - "affiliations", - "openminds.core.Affiliation", - "vocab:affiliation", - multiple=True, - doc="Declaration of a person being closely associated to an organization.", - ), - Property("alternate_names", str, "vocab:alternateName", multiple=True, doc="no description available"), - Property( - "associated_accounts", - "openminds.core.AccountInformation", - "vocab:associatedAccount", - multiple=True, - doc="no description available", - ), - Property( - "contact_information", - "openminds.core.ContactInformation", - "vocab:contactInformation", - doc="Any available way used to contact a person or business (e.g., address, phone number, email address, etc.).", - ), - Property( - "digital_identifiers", - "openminds.core.ORCID", - "vocab:digitalIdentifier", - multiple=True, - doc="Digital handle to identify objects or legal persons.", - ), - Property("family_name", str, "vocab:familyName", doc="Name borne in common by members of a family."), - Property( - "given_name", - str, - "vocab:givenName", - required=True, - doc="Name given to a person, including all potential middle names, but excluding the family name.", - ), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "activities", [ - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:performedBy", + "performedBy", reverse="performed_by", multiple=True, - doc="reverse of 'performed_by'", + description="reverse of 'performed_by'", ), Property( "comments", - "openminds.core.Comment", - "^vocab:commenter", + "openminds.latest.core.Comment", + "commenter", reverse="commenter", multiple=True, - doc="reverse of 'commenter'", + description="reverse of 'commenter'", ), Property( "coordinated_projects", - "openminds.core.Project", - "^vocab:coordinator", + "openminds.latest.core.Project", + "coordinator", reverse="coordinators", multiple=True, - doc="reverse of 'coordinators'", + description="reverse of 'coordinators'", ), Property( "developed", [ - "openminds.computation.ValidationTest", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipe", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.WebService", - "openminds.core.WebServiceVersion", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipe", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModel", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.Software", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebService", + "openminds.latest.core.WebServiceVersion", ], - "^vocab:developer", + "developer", reverse="developers", multiple=True, - doc="reverse of 'developers'", + description="reverse of 'developers'", ), Property( "funded", - "openminds.core.Funding", - "^vocab:funder", + "openminds.latest.core.Funding", + "funder", reverse="funder", multiple=True, - doc="reverse of 'funder'", + description="reverse of 'funder'", ), Property( "is_custodian_of", [ - "openminds.core.Dataset", - "openminds.core.DatasetVersion", - "openminds.publications.LivePaper", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.core.Dataset", + "openminds.latest.core.DatasetVersion", + "openminds.latest.publications.LivePaper", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlas", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpace", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:custodian", + "custodian", reverse="custodians", multiple=True, - doc="reverse of 'custodians'", + description="reverse of 'custodians'", ), Property( "is_owner_of", [ - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", - "openminds.specimen_prep.SlicingDevice", + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + "openminds.latest.specimen_prep.SlicingDevice", ], - "^vocab:owner", + "owner", reverse="owners", multiple=True, - doc="reverse of 'owners'", + description="reverse of 'owners'", ), Property( "is_provider_of", - "openminds.chemicals.ProductSource", - "^vocab:provider", + "openminds.latest.chemicals.ProductSource", + "provider", reverse="provider", multiple=True, - doc="reverse of 'provider'", + description="reverse of 'provider'", ), Property( "manufactured", - "openminds.core.Setup", - "^vocab:manufacturer", + "openminds.latest.core.Setup", + "manufacturer", reverse="manufacturers", multiple=True, - doc="reverse of 'manufacturers'", + description="reverse of 'manufacturers'", ), Property( "published", [ - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.ScholarlyArticle", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.ScholarlyArticle", ], - "^vocab:publisher", + "publisher", reverse="publisher", multiple=True, - doc="reverse of 'publisher'", + description="reverse of 'publisher'", ), Property( "started", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - "openminds.computation.WorkflowExecution", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", + "openminds.latest.computation.WorkflowExecution", ], - "^vocab:startedBy", + "startedBy", reverse="started_by", multiple=True, - doc="reverse of 'started_by'", + description="reverse of 'started_by'", ), ] existence_query_properties = ("given_name", "family_name") @@ -220,7 +184,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/content_type.py b/fairgraph/openminds/core/data/content_type.py index d1ddcbaf..204f5d00 100644 --- a/fairgraph/openminds/core/data/content_type.py +++ b/fairgraph/openminds/core/data/content_type.py @@ -4,112 +4,65 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ContentType +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ContentType(KGObject): +class ContentType(KGObject, ContentType): """ Structured information on the content type of a file instance, bundle or repository. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/core/ContentType" - properties = [ - Property( - "data_types", - "openminds.controlled_terms.DataType", - "vocab:dataType", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the content type.", - ), - Property("display_label", str, "vocab:displayLabel", doc="no description available"), - Property( - "file_extensions", - str, - "vocab:fileExtension", - multiple=True, - doc="String of characters attached as suffix to the names of files of a particular format.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the content type.", - ), - Property( - "related_media_type", - IRI, - "vocab:relatedMediaType", - doc="Reference to an official two-part identifier for file formats and format contents.", - ), - Property( - "specification", - IRI, - "vocab:specification", - doc="Detailed and precise presentation of, or proposal for something.", - ), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_defined_by", - "openminds.core.ContentTypePattern", - "^vocab:contentType", + "openminds.latest.core.ContentTypePattern", + "contentType", reverse="content_type", multiple=True, - doc="reverse of 'content_type'", + description="reverse of 'content_type'", ), Property( "is_format_of", [ - "openminds.computation.LocalFile", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.Configuration", - "openminds.core.File", - "openminds.core.FileArchive", - "openminds.core.FileBundle", - "openminds.core.FileRepository", - "openminds.core.ModelVersion", - "openminds.core.WebResource", + "openminds.latest.computation.LocalFile", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.Configuration", + "openminds.latest.core.File", + "openminds.latest.core.FileArchive", + "openminds.latest.core.FileBundle", + "openminds.latest.core.FileRepository", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.WebResource", ], - "^vocab:format", + "format", reverse="format", multiple=True, - doc="reverse of 'format'", + description="reverse of 'format'", ), Property( "is_output_format_of", - ["openminds.core.SoftwareVersion", "openminds.core.WebServiceVersion"], - "^vocab:outputFormat", + ["openminds.latest.core.SoftwareVersion", "openminds.latest.core.WebServiceVersion"], + "outputFormat", reverse="output_formats", multiple=True, - doc="reverse of 'output_formats'", + description="reverse of 'output_formats'", ), Property( "is_specification_format_of", - "openminds.core.MetaDataModelVersion", - "^vocab:specificationFormat", + "openminds.latest.core.MetaDataModelVersion", + "specificationFormat", reverse="specification_formats", multiple=True, - doc="reverse of 'specification_formats'", + description="reverse of 'specification_formats'", ), ] existence_query_properties = ("name",) @@ -133,7 +86,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/content_type_pattern.py b/fairgraph/openminds/core/data/content_type_pattern.py index d963e091..bcf5d11f 100644 --- a/fairgraph/openminds/core/data/content_type_pattern.py +++ b/fairgraph/openminds/core/data/content_type_pattern.py @@ -4,36 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ContentTypePattern +from fairgraph import KGObject -class ContentTypePattern(KGObject): +class ContentTypePattern(KGObject, ContentTypePattern): """ """ - default_space = "files" type_ = "https://openminds.ebrains.eu/core/ContentTypePattern" - properties = [ - Property( - "content_type", - "openminds.core.ContentType", - "vocab:contentType", - required=True, - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property("regex", str, "vocab:regex", required=True, doc="no description available"), - ] + default_space = "files" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies_content_of", - "openminds.core.FileRepository", - "^vocab:contentTypePattern", + "openminds.latest.core.FileRepository", + "contentTypePattern", reverse="content_type_patterns", multiple=True, - doc="reverse of 'content_type_patterns'", + description="reverse of 'content_type_patterns'", ), ] existence_query_properties = ("lookup_label",) @@ -49,7 +40,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/copyright.py b/fairgraph/openminds/core/data/copyright.py index 4c687865..e26dfa98 100644 --- a/fairgraph/openminds/core/data/copyright.py +++ b/fairgraph/openminds/core/data/copyright.py @@ -4,35 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Copyright +from fairgraph import EmbeddedMetadata -class Copyright(EmbeddedMetadata): +class Copyright(EmbeddedMetadata, Copyright): """ Structured information on the copyright. """ type_ = "https://openminds.ebrains.eu/core/Copyright" - properties = [ - Property( - "holders", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:holder", - multiple=True, - required=True, - doc="Legal person in possession of something.", - ), - Property( - "years", - str, - "vocab:year", - multiple=True, - required=True, - doc="Cycle in the Gregorian calendar specified by a number and comprised of 365 or 366 days divided into 12 months beginning with January and ending with December.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, holders=None, years=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, holders=holders, years=years) + return EmbeddedMetadata.__init__(self, data=data, holders=holders, years=years) diff --git a/fairgraph/openminds/core/data/file.py b/fairgraph/openminds/core/data/file.py index b58cde23..fc8aade2 100644 --- a/fairgraph/openminds/core/data/file.py +++ b/fairgraph/openminds/core/data/file.py @@ -4,8 +4,9 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import File +from fairgraph import KGObject import os import mimetypes @@ -19,217 +20,159 @@ from fairgraph.utility import accepted_terms_of_use, sha1sum mimetypes.init() -from fairgraph.base import IRI +from openminds import IRI -class File(KGObject): +class File(KGObject, File): """ Structured information on a file instance that is accessible via a URL. """ - default_space = "files" type_ = "https://openminds.ebrains.eu/core/File" - properties = [ - Property("content_description", str, "vocab:contentDescription", doc="no description available"), - Property( - "data_types", - "openminds.controlled_terms.DataType", - "vocab:dataType", - multiple=True, - doc="no description available", - ), - Property( - "file_repository", "openminds.core.FileRepository", "vocab:fileRepository", doc="no description available" - ), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "hashes", - "openminds.core.Hash", - "vocab:hash", - multiple=True, - doc="Term used for the process of converting any data into a single value. Often also directly refers to the resulting single value.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - required=True, - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "is_part_of", - "openminds.core.FileBundle", - "vocab:isPartOf", - multiple=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the file.", - ), - Property( - "special_usage_role", - "openminds.controlled_terms.FileUsageRole", - "vocab:specialUsageRole", - doc="Particular function of something when it is used.", - ), - Property( - "storage_size", - "openminds.core.QuantitativeValue", - "vocab:storageSize", - doc="Quantitative value defining how much disk space is used by an object on a computer system.", - ), - ] + default_space = "files" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.core.BehavioralProtocol", - "openminds.core.Protocol", - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", + "openminds.latest.core.BehavioralProtocol", + "openminds.latest.core.Protocol", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", + "openminds.latest.specimen_prep.SlicingDeviceUsage", ], - ["^vocab:describedIn", "^vocab:metadataLocation"], + ["describedIn", "metadataLocation"], reverse=["described_in", "metadata_locations"], multiple=True, - doc="reverse of described_in, metadata_locations", + description="reverse of described_in, metadata_locations", ), Property( "fully_documents", [ - "openminds.core.MetaDataModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:fullDocumentation", + "fullDocumentation", reverse="full_documentation", multiple=True, - doc="reverse of 'full_documentation'", + description="reverse of 'full_documentation'", ), Property( "has_copies", - "openminds.computation.LocalFile", - "^vocab:copyOf", + "openminds.latest.computation.LocalFile", + "copyOf", reverse="copy_of", multiple=True, - doc="reverse of 'copy_of'", + description="reverse of 'copy_of'", ), Property( "is_also_part_of", - "openminds.computation.WorkflowRecipeVersion", - "^vocab:hasPart", + "openminds.latest.computation.WorkflowRecipeVersion", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_configuration_of", - "openminds.computation.WorkflowExecution", - "^vocab:configuration", + "openminds.latest.computation.WorkflowExecution", + "configuration", reverse="configuration", multiple=True, - doc="reverse of 'configuration'", + description="reverse of 'configuration'", ), Property( "is_default_image_for", - "openminds.sands.CustomCoordinateSpace", - "^vocab:defaultImage", + "openminds.latest.sands.CustomCoordinateSpace", + "defaultImage", reverse="default_images", multiple=True, - doc="reverse of 'default_images'", + description="reverse of 'default_images'", ), Property( "is_input_to", - "openminds.core.DatasetVersion", - "^vocab:inputData", + "openminds.latest.core.DatasetVersion", + "inputData", reverse="input_data", multiple=True, - doc="reverse of 'input_data'", + description="reverse of 'input_data'", ), Property( "is_location_of", - ["openminds.ephys.Recording", "openminds.sands.ParcellationTerminologyVersion"], - "^vocab:dataLocation", + ["openminds.latest.ephys.Recording", "openminds.latest.sands.ParcellationTerminologyVersion"], + "dataLocation", reverse="data_location", multiple=True, - doc="reverse of 'data_location'", + description="reverse of 'data_location'", ), Property( "is_output_of", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - "openminds.core.ModelVersion", - "openminds.core.ProtocolExecution", - "openminds.ephys.RecordingActivity", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.stimulation.StimulationActivity", ], - ["^vocab:output", "^vocab:outputData"], + ["output", "outputData"], reverse=["output_data", "outputs"], multiple=True, - doc="reverse of output_data, outputs", + description="reverse of output_data, outputs", ), Property( "is_preview_of", - "openminds.core.ServiceLink", - "^vocab:previewImage", + "openminds.latest.core.ServiceLink", + "previewImage", reverse="preview_image", multiple=True, - doc="reverse of 'preview_image'", + description="reverse of 'preview_image'", ), Property( "is_reference_for", - "openminds.computation.ValidationTestVersion", - "^vocab:referenceData", + "openminds.latest.computation.ValidationTestVersion", + "referenceData", reverse="reference_data", multiple=True, - doc="reverse of 'reference_data'", + description="reverse of 'reference_data'", ), Property( "is_source_data_of", - "openminds.core.FileArchive", - "^vocab:sourceData", + "openminds.latest.core.FileArchive", + "sourceData", reverse="source_data", multiple=True, - doc="reverse of 'source_data'", + description="reverse of 'source_data'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "specifies", [ - "openminds.sands.AtlasAnnotation", - "openminds.sands.CustomAnnotation", - "openminds.stimulation.EphysStimulus", + "openminds.latest.sands.AtlasAnnotation", + "openminds.latest.sands.CustomAnnotation", + "openminds.latest.stimulation.EphysStimulus", ], - "^vocab:specification", + "specification", reverse="specification", multiple=True, - doc="reverse of 'specification'", + description="reverse of 'specification'", ), ] aliases = {"hash": "hashes"} @@ -267,7 +210,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/file_archive.py b/fairgraph/openminds/core/data/file_archive.py index 6bc9ea61..c1072eda 100644 --- a/fairgraph/openminds/core/data/file_archive.py +++ b/fairgraph/openminds/core/data/file_archive.py @@ -4,60 +4,43 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import FileArchive +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class FileArchive(KGObject): +class FileArchive(KGObject, FileArchive): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/FileArchive" - properties = [ - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - required=True, - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - required=True, - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "source_data", "openminds.core.File", "vocab:sourceData", multiple=True, doc="no description available" - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_location_of", - "openminds.core.ServiceLink", - "^vocab:dataLocation", + "openminds.latest.core.ServiceLink", + "dataLocation", reverse="data_location", multiple=True, - doc="reverse of 'data_location'", + description="reverse of 'data_location'", ), Property( "is_output_of", [ - "openminds.computation.DataAnalysis", - "openminds.computation.GenericComputation", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:output", + "output", reverse="outputs", multiple=True, - doc="reverse of 'outputs'", + description="reverse of 'outputs'", ), ] existence_query_properties = ("iri", "format") @@ -74,7 +57,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/file_bundle.py b/fairgraph/openminds/core/data/file_bundle.py index 4eaddcba..5ffff406 100644 --- a/fairgraph/openminds/core/data/file_bundle.py +++ b/fairgraph/openminds/core/data/file_bundle.py @@ -4,197 +4,100 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import FileBundle +from fairgraph import KGObject -class FileBundle(KGObject): +class FileBundle(KGObject, FileBundle): """ Structured information on a bundle of file instances. """ - default_space = "files" type_ = "https://openminds.ebrains.eu/core/FileBundle" - properties = [ - Property("content_description", str, "vocab:contentDescription", doc="no description available"), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "grouped_by", - [ - "openminds.computation.LocalFile", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.core.BehavioralProtocol", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.Subject", - "openminds.core.SubjectGroup", - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.CustomCoordinateSpace", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:groupedBy", - multiple=True, - doc="Reference to the aspect used to group something.", - ), - Property( - "grouping_types", - "openminds.controlled_terms.FileBundleGrouping", - "vocab:groupingType", - multiple=True, - doc="no description available", - ), - Property( - "hash", - "openminds.core.Hash", - "vocab:hash", - doc="Term used for the process of converting any data into a single value. Often also directly refers to the resulting single value.", - ), - Property( - "is_part_of", - ["openminds.core.FileBundle", "openminds.core.FileRepository"], - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the file bundle.", - ), - Property( - "storage_size", - "openminds.core.QuantitativeValue", - "vocab:storageSize", - doc="Quantitative value defining how much disk space is used by an object on a computer system.", - ), - ] + default_space = "files" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", + "openminds.latest.specimen_prep.SlicingDeviceUsage", ], - "^vocab:metadataLocation", + "metadataLocation", reverse="metadata_locations", multiple=True, - doc="reverse of 'metadata_locations'", + description="reverse of 'metadata_locations'", ), Property( "has_parts", - ["openminds.core.File", "openminds.core.FileBundle"], - "^vocab:isPartOf", + ["openminds.latest.core.File", "openminds.latest.core.FileBundle"], + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), Property( "is_also_part_of", - "openminds.computation.WorkflowRecipeVersion", - "^vocab:hasPart", + "openminds.latest.computation.WorkflowRecipeVersion", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_input_to", - "openminds.core.DatasetVersion", - "^vocab:inputData", + "openminds.latest.core.DatasetVersion", + "inputData", reverse="input_data", multiple=True, - doc="reverse of 'input_data'", + description="reverse of 'input_data'", ), Property( "is_location_of", - ["openminds.core.ServiceLink", "openminds.ephys.Recording"], - "^vocab:dataLocation", + ["openminds.latest.core.ServiceLink", "openminds.latest.ephys.Recording"], + "dataLocation", reverse="data_location", multiple=True, - doc="reverse of 'data_location'", + description="reverse of 'data_location'", ), Property( "is_output_of", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", - "openminds.core.ModelVersion", - "openminds.core.ProtocolExecution", - "openminds.ephys.RecordingActivity", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.stimulation.StimulationActivity", ], - ["^vocab:output", "^vocab:outputData"], + ["output", "outputData"], reverse=["output_data", "outputs"], multiple=True, - doc="reverse of output_data, outputs", + description="reverse of output_data, outputs", ), Property( "is_reference_for", - "openminds.computation.ValidationTestVersion", - "^vocab:referenceData", + "openminds.latest.computation.ValidationTestVersion", + "referenceData", reverse="reference_data", multiple=True, - doc="reverse of 'reference_data'", + description="reverse of 'reference_data'", ), Property( "specifies", - "openminds.stimulation.EphysStimulus", - "^vocab:specification", + "openminds.latest.stimulation.EphysStimulus", + "specification", reverse="specifications", multiple=True, - doc="reverse of 'specifications'", + description="reverse of 'specifications'", ), ] existence_query_properties = ("is_part_of", "name") @@ -222,7 +125,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/file_path_pattern.py b/fairgraph/openminds/core/data/file_path_pattern.py index 72fce080..5389ed8f 100644 --- a/fairgraph/openminds/core/data/file_path_pattern.py +++ b/fairgraph/openminds/core/data/file_path_pattern.py @@ -4,28 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import FilePathPattern +from fairgraph import EmbeddedMetadata -class FilePathPattern(EmbeddedMetadata): +class FilePathPattern(EmbeddedMetadata, FilePathPattern): """ """ type_ = "https://openminds.ebrains.eu/core/FilePathPattern" - properties = [ - Property( - "grouping_types", - "openminds.controlled_terms.FileBundleGrouping", - "vocab:groupingType", - multiple=True, - required=True, - doc="no description available", - ), - Property("regex", str, "vocab:regex", required=True, doc="no description available"), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, grouping_types=None, regex=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, grouping_types=grouping_types, regex=regex) + return EmbeddedMetadata.__init__(self, data=data, grouping_types=grouping_types, regex=regex) diff --git a/fairgraph/openminds/core/data/file_repository.py b/fairgraph/openminds/core/data/file_repository.py index 1dd0d60c..65e5a2b4 100644 --- a/fairgraph/openminds/core/data/file_repository.py +++ b/fairgraph/openminds/core/data/file_repository.py @@ -4,115 +4,57 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import FileRepository +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class FileRepository(KGObject): +class FileRepository(KGObject, FileRepository): """ Structured information on a file repository. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/FileRepository" - properties = [ - Property( - "content_type_patterns", - "openminds.core.ContentTypePattern", - "vocab:contentTypePattern", - multiple=True, - doc="no description available", - ), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "hash", - "openminds.core.Hash", - "vocab:hash", - doc="Term used for the process of converting any data into a single value. Often also directly refers to the resulting single value.", - ), - Property( - "hosted_by", - "openminds.core.Organization", - "vocab:hostedBy", - required=True, - doc="Reference to an organization that provides facilities and services for something.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - required=True, - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the file repository.", - ), - Property( - "storage_size", - "openminds.core.QuantitativeValue", - "vocab:storageSize", - doc="Quantitative value defining how much disk space is used by an object on a computer system.", - ), - Property( - "structure_pattern", - "openminds.core.FileRepositoryStructure", - "vocab:structurePattern", - doc="no description available", - ), - Property( - "type", - "openminds.controlled_terms.FileRepositoryType", - "vocab:type", - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "contains_content_of", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:repository", + "repository", reverse="repository", multiple=True, - doc="reverse of 'repository'", + description="reverse of 'repository'", ), Property( "files", - "openminds.core.File", - "^vocab:fileRepository", + "openminds.latest.core.File", + "fileRepository", reverse="file_repository", multiple=True, - doc="reverse of 'file_repository'", + description="reverse of 'file_repository'", ), Property( "has_parts", - "openminds.core.FileBundle", - "^vocab:isPartOf", + "openminds.latest.core.FileBundle", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), ] existence_query_properties = ("iri",) @@ -136,7 +78,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/file_repository_structure.py b/fairgraph/openminds/core/data/file_repository_structure.py index 52543d33..d647caad 100644 --- a/fairgraph/openminds/core/data/file_repository_structure.py +++ b/fairgraph/openminds/core/data/file_repository_structure.py @@ -4,36 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import FileRepositoryStructure +from fairgraph import KGObject -class FileRepositoryStructure(KGObject): +class FileRepositoryStructure(KGObject, FileRepositoryStructure): """ """ - default_space = "files" type_ = "https://openminds.ebrains.eu/core/FileRepositoryStructure" - properties = [ - Property( - "file_path_patterns", - "openminds.core.FilePathPattern", - "vocab:filePathPattern", - multiple=True, - required=True, - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - ] + default_space = "files" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "structures", - "openminds.core.FileRepository", - "^vocab:structurePattern", + "openminds.latest.core.FileRepository", + "structurePattern", reverse="structure_pattern", multiple=True, - doc="reverse of 'structure_pattern'", + description="reverse of 'structure_pattern'", ), ] existence_query_properties = ("lookup_label",) @@ -41,7 +32,8 @@ class FileRepositoryStructure(KGObject): def __init__( self, lookup_label=None, file_path_patterns=None, structures=None, id=None, data=None, space=None, scope=None ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/hash.py b/fairgraph/openminds/core/data/hash.py index 1f2614bc..8d8b2973 100644 --- a/fairgraph/openminds/core/data/hash.py +++ b/fairgraph/openminds/core/data/hash.py @@ -4,29 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Hash +from fairgraph import EmbeddedMetadata -class Hash(EmbeddedMetadata): +class Hash(EmbeddedMetadata, Hash): """ Structured information on a hash. """ type_ = "https://openminds.ebrains.eu/core/Hash" - properties = [ - Property( - "algorithm", - str, - "vocab:algorithm", - required=True, - doc="Procedure for solving a mathematical problem in a finite number of steps. Can involve repetition of an operation.", - ), - Property( - "digest", str, "vocab:digest", required=True, doc="Summation or condensation of a body of information." - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, algorithm=None, digest=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, algorithm=algorithm, digest=digest) + return EmbeddedMetadata.__init__(self, data=data, algorithm=algorithm, digest=digest) diff --git a/fairgraph/openminds/core/data/license.py b/fairgraph/openminds/core/data/license.py index 9666d7d0..c4510c6e 100644 --- a/fairgraph/openminds/core/data/license.py +++ b/fairgraph/openminds/core/data/license.py @@ -4,66 +4,44 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import License +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class License(KGObject): +class License(KGObject, License): """ Structured information on a used license. """ - default_space = "controlled" type_ = "https://openminds.ebrains.eu/core/License" - properties = [ - Property("full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the license."), - Property( - "legal_code", - IRI, - "vocab:legalCode", - required=True, - doc="Type of legislation that claims to cover the law system (complete or parts) as it existed at the time the code was enacted.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the license.", - ), - Property( - "webpages", - str, - "vocab:webpage", - multiple=True, - doc="Hypertext document (block of information) found on the World Wide Web.", - ), - ] + default_space = "controlled" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_applied_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:license", + "license", reverse="license", multiple=True, - doc="reverse of 'license'", + description="reverse of 'license'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -83,7 +61,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/data/measurement.py b/fairgraph/openminds/core/data/measurement.py index ce74df08..e92e4496 100644 --- a/fairgraph/openminds/core/data/measurement.py +++ b/fairgraph/openminds/core/data/measurement.py @@ -4,54 +4,21 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Measurement +from fairgraph import EmbeddedMetadata from datetime import datetime -class Measurement(EmbeddedMetadata): +class Measurement(EmbeddedMetadata, Measurement): """ Structured information about a measurement performed during a scientific experiment. """ type_ = "https://openminds.ebrains.eu/core/Measurement" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "measured_quantity", - "openminds.controlled_terms.MeasuredQuantity", - "vocab:measuredQuantity", - required=True, - doc="no description available", - ), - Property( - "measured_with", - [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", - ], - "vocab:measuredWith", - doc="no description available", - ), - Property("timestamp", datetime, "vocab:timestamp", doc="no description available"), - Property( - "values", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:value", - multiple=True, - required=True, - doc="Entry for a property.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -66,7 +33,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, additional_remarks=additional_remarks, measured_quantity=measured_quantity, diff --git a/fairgraph/openminds/core/data/service_link.py b/fairgraph/openminds/core/data/service_link.py index 35db548f..f05caa5e 100644 --- a/fairgraph/openminds/core/data/service_link.py +++ b/fairgraph/openminds/core/data/service_link.py @@ -4,46 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ServiceLink +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class ServiceLink(KGObject): +class ServiceLink(KGObject, ServiceLink): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/ServiceLink" - properties = [ - Property( - "data_location", - [ - "openminds.core.File", - "openminds.core.FileArchive", - "openminds.core.FileBundle", - "openminds.core.ModelVersion", - "openminds.publications.LivePaperResourceItem", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:dataLocation", - required=True, - doc="no description available", - ), - Property("display_label", str, "vocab:displayLabel", doc="no description available"), - Property("open_data_in", IRI, "vocab:openDataIn", required=True, doc="no description available"), - Property("preview_image", "openminds.core.File", "vocab:previewImage", doc="no description available"), - Property( - "service", - "openminds.controlled_terms.Service", - "vocab:service", - required=True, - doc="no description available", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("data_location", "open_data_in", "service") @@ -59,7 +35,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/digital_identifier/doi.py b/fairgraph/openminds/core/digital_identifier/doi.py index ca0e6eda..cf909e64 100644 --- a/fairgraph/openminds/core/digital_identifier/doi.py +++ b/fairgraph/openminds/core/digital_identifier/doi.py @@ -4,73 +4,72 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import DOI +from fairgraph import KGObject -class DOI(KGObject): +class DOI(KGObject, DOI): """ Structured information about a digital object identifier, as standardized by the International Organization for Standardization. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/DOI" - properties = [ - Property("identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the DOI."), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:describedIn", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "describedIn", reverse="described_in", multiple=True, - doc="reverse of 'described_in'", + description="reverse of 'described_in'", ), Property( "identifies", [ - "openminds.computation.ValidationTest", - "openminds.computation.WorkflowRecipe", - "openminds.core.Dataset", - "openminds.core.MetaDataModel", - "openminds.core.Model", - "openminds.core.Software", - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaper", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlas", - "openminds.sands.CommonCoordinateSpace", - "openminds.specimen_prep.SlicingDevice", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.WorkflowRecipe", + "openminds.latest.core.Dataset", + "openminds.latest.core.MetaDataModel", + "openminds.latest.core.Model", + "openminds.latest.core.Software", + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaper", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlas", + "openminds.latest.sands.CommonCoordinateSpace", + "openminds.latest.specimen_prep.SlicingDevice", ], - "^vocab:digitalIdentifier", + "digitalIdentifier", reverse="digital_identifier", multiple=True, - doc="reverse of 'digital_identifier'", + description="reverse of 'digital_identifier'", ), Property( "related_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:relatedPublication", + "relatedPublication", reverse="related_publications", multiple=True, - doc="reverse of 'related_publications'", + description="reverse of 'related_publications'", ), ] existence_query_properties = ("identifier",) @@ -86,7 +85,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/digital_identifier/gridid.py b/fairgraph/openminds/core/digital_identifier/gridid.py index cb4661fa..0608acbe 100644 --- a/fairgraph/openminds/core/digital_identifier/gridid.py +++ b/fairgraph/openminds/core/digital_identifier/gridid.py @@ -4,35 +4,32 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import GRIDID +from fairgraph import KGObject -class GRIDID(KGObject): +class GRIDID(KGObject, GRIDID): """ A GRID (Global Research Identifier Database) identifier. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/GRIDID" - properties = [ - Property( - "identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the GRIDID." - ), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies", - "openminds.core.Organization", - "^vocab:digitalIdentifier", + "openminds.latest.core.Organization", + "digitalIdentifier", reverse="digital_identifiers", multiple=True, - doc="reverse of 'digital_identifiers'", + description="reverse of 'digital_identifiers'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) diff --git a/fairgraph/openminds/core/digital_identifier/handle.py b/fairgraph/openminds/core/digital_identifier/handle.py index 5c20cb48..d2da68eb 100644 --- a/fairgraph/openminds/core/digital_identifier/handle.py +++ b/fairgraph/openminds/core/digital_identifier/handle.py @@ -4,46 +4,43 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import HANDLE +from fairgraph import KGObject -class HANDLE(KGObject): +class HANDLE(KGObject, HANDLE): """ A persistent identifier for an information resource provided by the Handle System of the Corporation for National Research Initiatives. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/HANDLE" - properties = [ - Property( - "identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the HANDLE." - ), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "related_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:relatedPublication", + "relatedPublication", reverse="related_publications", multiple=True, - doc="reverse of 'related_publications'", + description="reverse of 'related_publications'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, related_to=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, identifier=identifier, related_to=related_to + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, identifier=identifier, related_to=related_to ) diff --git a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py index 39caf439..be6ad3e8 100644 --- a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py +++ b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py @@ -4,39 +4,32 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import IdentifiersDotOrgID +from fairgraph import KGObject -class IdentifiersDotOrgID(KGObject): +class IdentifiersDotOrgID(KGObject, IdentifiersDotOrgID): """ """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/IdentifiersDotOrgID" - properties = [ - Property( - "identifier", - str, - "vocab:identifier", - required=True, - doc="Term or code used to identify the identifiers dot org i d.", - ), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies", - ["openminds.core.Dataset", "openminds.core.DatasetVersion"], - "^vocab:digitalIdentifier", + ["openminds.latest.core.Dataset", "openminds.latest.core.DatasetVersion"], + "digitalIdentifier", reverse="digital_identifier", multiple=True, - doc="reverse of 'digital_identifier'", + description="reverse of 'digital_identifier'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) diff --git a/fairgraph/openminds/core/digital_identifier/isbn.py b/fairgraph/openminds/core/digital_identifier/isbn.py index a5c8c234..3ef08149 100644 --- a/fairgraph/openminds/core/digital_identifier/isbn.py +++ b/fairgraph/openminds/core/digital_identifier/isbn.py @@ -4,59 +4,62 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ISBN +from fairgraph import KGObject -class ISBN(KGObject): +class ISBN(KGObject, ISBN): """ An International Standard Book Number of the International ISBN Agency. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/ISBN" - properties = [ - Property("identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the ISBN."), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "cited_in", [ - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.ScholarlyArticle", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.ScholarlyArticle", ], - "^vocab:citedPublication", + "citedPublication", reverse="cited_publications", multiple=True, - doc="reverse of 'cited_publications'", + description="reverse of 'cited_publications'", ), Property( "identifies", - ["openminds.publications.Book", "openminds.sands.BrainAtlas", "openminds.sands.CommonCoordinateSpace"], - "^vocab:digitalIdentifier", + [ + "openminds.latest.publications.Book", + "openminds.latest.sands.BrainAtlas", + "openminds.latest.sands.CommonCoordinateSpace", + ], + "digitalIdentifier", reverse="digital_identifier", multiple=True, - doc="reverse of 'digital_identifier'", + description="reverse of 'digital_identifier'", ), Property( "related_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:relatedPublication", + "relatedPublication", reverse="related_publications", multiple=True, - doc="reverse of 'related_publications'", + description="reverse of 'related_publications'", ), ] existence_query_properties = ("identifier",) @@ -72,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/digital_identifier/issn.py b/fairgraph/openminds/core/digital_identifier/issn.py index 98bcaf5e..2f999e5e 100644 --- a/fairgraph/openminds/core/digital_identifier/issn.py +++ b/fairgraph/openminds/core/digital_identifier/issn.py @@ -4,53 +4,53 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ISSN +from fairgraph import KGObject -class ISSN(KGObject): +class ISSN(KGObject, ISSN): """ An International Standard Serial Number of the ISSN International Centre. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/ISSN" - properties = [ - Property("identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the ISSN."), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies", - "openminds.publications.Periodical", - "^vocab:digitalIdentifier", + "openminds.latest.publications.Periodical", + "digitalIdentifier", reverse="digital_identifier", multiple=True, - doc="reverse of 'digital_identifier'", + description="reverse of 'digital_identifier'", ), Property( "related_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:relatedPublication", + "relatedPublication", reverse="related_publications", multiple=True, - doc="reverse of 'related_publications'", + description="reverse of 'related_publications'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, identifies=None, related_to=None, id=None, data=None, space=None, scope=None): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/digital_identifier/orcid.py b/fairgraph/openminds/core/digital_identifier/orcid.py index 8757f3f9..86154b3c 100644 --- a/fairgraph/openminds/core/digital_identifier/orcid.py +++ b/fairgraph/openminds/core/digital_identifier/orcid.py @@ -4,33 +4,32 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ORCID +from fairgraph import KGObject -class ORCID(KGObject): +class ORCID(KGObject, ORCID): """ A persistent identifier for a researcher provided by Open Researcher and Contributor ID, Inc. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/ORCID" - properties = [ - Property("identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the ORCID."), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies", - "openminds.core.Person", - "^vocab:digitalIdentifier", + "openminds.latest.core.Person", + "digitalIdentifier", reverse="digital_identifiers", multiple=True, - doc="reverse of 'digital_identifiers'", + description="reverse of 'digital_identifiers'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) diff --git a/fairgraph/openminds/core/digital_identifier/rorid.py b/fairgraph/openminds/core/digital_identifier/rorid.py index 55d78681..b80aa922 100644 --- a/fairgraph/openminds/core/digital_identifier/rorid.py +++ b/fairgraph/openminds/core/digital_identifier/rorid.py @@ -4,33 +4,32 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import RORID +from fairgraph import KGObject -class RORID(KGObject): +class RORID(KGObject, RORID): """ A persistent identifier for a research organization, provided by the Research Organization Registry. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/RORID" - properties = [ - Property("identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the RORID."), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies", - "openminds.core.Organization", - "^vocab:digitalIdentifier", + "openminds.latest.core.Organization", + "digitalIdentifier", reverse="digital_identifiers", multiple=True, - doc="reverse of 'digital_identifiers'", + description="reverse of 'digital_identifiers'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) diff --git a/fairgraph/openminds/core/digital_identifier/rrid.py b/fairgraph/openminds/core/digital_identifier/rrid.py index 42519f76..f8933074 100644 --- a/fairgraph/openminds/core/digital_identifier/rrid.py +++ b/fairgraph/openminds/core/digital_identifier/rrid.py @@ -4,47 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import RRID +from fairgraph import KGObject -class RRID(KGObject): +class RRID(KGObject, RRID): """ A persistent identifier for a research resource provided by the Resource Identification Initiative. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/RRID" - properties = [ - Property("identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the RRID."), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies", [ - "openminds.chemicals.ProductSource", - "openminds.core.Organization", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.Strain", - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", - "openminds.specimen_prep.SlicingDevice", + "openminds.latest.chemicals.ProductSource", + "openminds.latest.core.Organization", + "openminds.latest.core.Software", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.Strain", + "openminds.latest.ephys.Electrode", + "openminds.latest.ephys.ElectrodeArray", + "openminds.latest.ephys.Pipette", + "openminds.latest.sands.BrainAtlas", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpace", + "openminds.latest.sands.CommonCoordinateSpaceVersion", + "openminds.latest.specimen_prep.SlicingDevice", ], - "^vocab:digitalIdentifier", + "digitalIdentifier", reverse="digital_identifier", multiple=True, - doc="reverse of 'digital_identifier'", + description="reverse of 'digital_identifier'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) diff --git a/fairgraph/openminds/core/digital_identifier/stock_number.py b/fairgraph/openminds/core/digital_identifier/stock_number.py index 683c8734..ebb443d1 100644 --- a/fairgraph/openminds/core/digital_identifier/stock_number.py +++ b/fairgraph/openminds/core/digital_identifier/stock_number.py @@ -4,25 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import StockNumber +from fairgraph import EmbeddedMetadata -class StockNumber(EmbeddedMetadata): +class StockNumber(EmbeddedMetadata, StockNumber): """ """ type_ = "https://openminds.ebrains.eu/core/StockNumber" - properties = [ - Property( - "identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the stock number." - ), - Property( - "vendor", "openminds.core.Organization", "vocab:vendor", required=True, doc="no description available" - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, identifier=None, vendor=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, identifier=identifier, vendor=vendor) + return EmbeddedMetadata.__init__(self, data=data, identifier=identifier, vendor=vendor) diff --git a/fairgraph/openminds/core/digital_identifier/swhid.py b/fairgraph/openminds/core/digital_identifier/swhid.py index 3af5cc89..290e6fac 100644 --- a/fairgraph/openminds/core/digital_identifier/swhid.py +++ b/fairgraph/openminds/core/digital_identifier/swhid.py @@ -4,40 +4,39 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import SWHID +from fairgraph import KGObject -class SWHID(KGObject): +class SWHID(KGObject, SWHID): """ """ - default_space = "software" type_ = "https://openminds.ebrains.eu/core/SWHID" - properties = [ - Property("identifier", str, "vocab:identifier", required=True, doc="Term or code used to identify the SWHID."), - ] + default_space = "software" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "identifies", [ - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", + "openminds.latest.core.MetaDataModel", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.Software", + "openminds.latest.core.SoftwareVersion", ], - "^vocab:digitalIdentifier", + "digitalIdentifier", reverse="digital_identifier", multiple=True, - doc="reverse of 'digital_identifier'", + description="reverse of 'digital_identifier'", ), ] existence_query_properties = ("identifier",) def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): - return super().__init__( - id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) diff --git a/fairgraph/openminds/core/miscellaneous/comment.py b/fairgraph/openminds/core/miscellaneous/comment.py index d0fbebcd..f3f8d39b 100644 --- a/fairgraph/openminds/core/miscellaneous/comment.py +++ b/fairgraph/openminds/core/miscellaneous/comment.py @@ -4,62 +4,30 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Comment +from fairgraph import KGObject from datetime import datetime -class Comment(KGObject): +class Comment(KGObject, Comment): """ Structured information about a short text expressing an opinion on, or giving information about some entity. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/Comment" - properties = [ - Property( - "about", - [ - "openminds.computation.ValidationTest", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipe", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.Dataset", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.WebService", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaper", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:about", - required=True, - doc="no description available", - ), - Property("comment", str, "vocab:comment", required=True, doc="no description available"), - Property( - "commenter", "openminds.core.Person", "vocab:commenter", required=True, doc="no description available" - ), - Property("timestamp", datetime, "vocab:timestamp", required=True, doc="no description available"), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("about", "comment", "commenter", "timestamp") def __init__( self, about=None, comment=None, commenter=None, timestamp=None, id=None, data=None, space=None, scope=None ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/miscellaneous/funding.py b/fairgraph/openminds/core/miscellaneous/funding.py index 6cab27d1..bbad5283 100644 --- a/fairgraph/openminds/core/miscellaneous/funding.py +++ b/fairgraph/openminds/core/miscellaneous/funding.py @@ -4,67 +4,42 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Funding +from fairgraph import KGObject -class Funding(KGObject): +class Funding(KGObject, Funding): """ Structured information on used funding. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/Funding" - properties = [ - Property( - "acknowledgement", - str, - "vocab:acknowledgement", - doc="Official declaration or avowal of appreciation of an act or achievement.", - ), - Property( - "award_number", - str, - "vocab:awardNumber", - doc="Machine-readable identifier for a benefit that is conferred or bestowed on the basis of merit or need.", - ), - Property( - "award_title", - str, - "vocab:awardTitle", - doc="Human-readable identifier for a benefit that is conferred or bestowed on the basis of merit or need.", - ), - Property( - "funder", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:funder", - required=True, - doc="Legal person that provides money for a particular purpose.", - ), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "funded", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.LearningResource", - "openminds.publications.LivePaperVersion", - "openminds.publications.ScholarlyArticle", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.Book", + "openminds.latest.publications.Chapter", + "openminds.latest.publications.LearningResource", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.publications.ScholarlyArticle", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:funding", + "funding", reverse="funding", multiple=True, - doc="reverse of 'funding'", + description="reverse of 'funding'", ), ] existence_query_properties = ("funder",) @@ -81,7 +56,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value.py b/fairgraph/openminds/core/miscellaneous/quantitative_value.py index c113644c..22eceaf5 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value.py @@ -4,41 +4,21 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import QuantitativeValue +from fairgraph import EmbeddedMetadata from numbers import Real -class QuantitativeValue(EmbeddedMetadata): +class QuantitativeValue(EmbeddedMetadata, QuantitativeValue): """ Structured information on a quantitative value. """ type_ = "https://openminds.ebrains.eu/core/QuantitativeValue" - properties = [ - Property( - "type_of_uncertainty", - "openminds.controlled_terms.TypeOfUncertainty", - "vocab:typeOfUncertainty", - doc="Distinct technique used to quantify the uncertainty of a measurement.", - ), - Property( - "uncertainties", - Real, - "vocab:uncertainty", - multiple=True, - doc="Quantitative value range defining the uncertainty of a measurement.", - ), - Property( - "unit", - "openminds.controlled_terms.UnitOfMeasurement", - "vocab:unit", - doc="Determinate quantity adopted as a standard of measurement.", - ), - Property("value", Real, "vocab:value", required=True, doc="Entry for a property."), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -52,6 +32,11 @@ def __init__( space=None, scope=None, ): - return super().__init__( - data=data, type_of_uncertainty=type_of_uncertainty, uncertainties=uncertainties, unit=unit, value=value + return EmbeddedMetadata.__init__( + self, + data=data, + type_of_uncertainty=type_of_uncertainty, + uncertainties=uncertainties, + unit=unit, + value=value, ) diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py index 456c2a0f..56784116 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py @@ -4,49 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import QuantitativeValueArray +from fairgraph import KGObject from numbers import Real -class QuantitativeValueArray(KGObject): +class QuantitativeValueArray(KGObject, QuantitativeValueArray): """ A representation of an array of quantitative values, optionally with uncertainties. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/QuantitativeValueArray" - properties = [ - Property( - "negative_uncertainties", - Real, - "vocab:negativeUncertainties", - multiple=True, - doc="no description available", - ), - Property( - "positive_uncertainties", - Real, - "vocab:positiveUncertainties", - multiple=True, - doc="no description available", - ), - Property( - "type_of_uncertainty", - "openminds.controlled_terms.TypeOfUncertainty", - "vocab:typeOfUncertainty", - doc="Distinct technique used to quantify the uncertainty of a measurement.", - ), - Property( - "unit", - "openminds.controlled_terms.UnitOfMeasurement", - "vocab:unit", - doc="Determinate quantity adopted as a standard of measurement.", - ), - Property("values", Real, "vocab:values", multiple=True, required=True, doc="no description available"), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("values",) @@ -62,7 +35,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py index 2b27bf2c..d11fa7b2 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py @@ -4,35 +4,21 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import QuantitativeValueRange +from fairgraph import EmbeddedMetadata from numbers import Real -class QuantitativeValueRange(EmbeddedMetadata): +class QuantitativeValueRange(EmbeddedMetadata, QuantitativeValueRange): """ A representation of a range of quantitative values. """ type_ = "https://openminds.ebrains.eu/core/QuantitativeValueRange" - properties = [ - Property("max_value", Real, "vocab:maxValue", required=True, doc="Greatest quantity attained or allowed."), - Property( - "max_value_unit", - "openminds.controlled_terms.UnitOfMeasurement", - "vocab:maxValueUnit", - doc="no description available", - ), - Property("min_value", Real, "vocab:minValue", required=True, doc="Smallest quantity attained or allowed."), - Property( - "min_value_unit", - "openminds.controlled_terms.UnitOfMeasurement", - "vocab:minValueUnit", - doc="no description available", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -46,7 +32,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, max_value=max_value, max_value_unit=max_value_unit, diff --git a/fairgraph/openminds/core/miscellaneous/research_product_group.py b/fairgraph/openminds/core/miscellaneous/research_product_group.py index 0f629f30..2a90a565 100644 --- a/fairgraph/openminds/core/miscellaneous/research_product_group.py +++ b/fairgraph/openminds/core/miscellaneous/research_product_group.py @@ -4,51 +4,23 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ResearchProductGroup +from fairgraph import KGObject -class ResearchProductGroup(KGObject): +class ResearchProductGroup(KGObject, ResearchProductGroup): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/ResearchProductGroup" - properties = [ - Property("context", str, "vocab:context", required=True, doc="no description available"), - Property( - "has_parts", - [ - "openminds.computation.ValidationTest", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipe", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.Dataset", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.WebService", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaper", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:hasPart", - multiple=True, - required=True, - doc="no description available", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("context", "has_parts") def __init__(self, context=None, has_parts=None, id=None, data=None, space=None, scope=None): - return super().__init__(id=id, space=space, scope=scope, data=data, context=context, has_parts=has_parts) + return KGObject.__init__( + self, id=id, space=space, scope=scope, data=data, context=context, has_parts=has_parts + ) diff --git a/fairgraph/openminds/core/miscellaneous/web_resource.py b/fairgraph/openminds/core/miscellaneous/web_resource.py index 7e55fcfc..a126ffc9 100644 --- a/fairgraph/openminds/core/miscellaneous/web_resource.py +++ b/fairgraph/openminds/core/miscellaneous/web_resource.py @@ -4,84 +4,70 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import WebResource +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class WebResource(KGObject): +class WebResource(KGObject, WebResource): """ """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/WebResource" - properties = [ - Property("content_description", str, "vocab:contentDescription", doc="no description available"), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - required=True, - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "describes", - ["openminds.core.BehavioralProtocol", "openminds.core.Protocol"], - "^vocab:describedIn", + ["openminds.latest.core.BehavioralProtocol", "openminds.latest.core.Protocol"], + "describedIn", reverse="described_in", multiple=True, - doc="reverse of 'described_in'", + description="reverse of 'described_in'", ), Property( "fully_documents", [ - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:fullDocumentation", + "fullDocumentation", reverse="full_documentation", multiple=True, - doc="reverse of 'full_documentation'", + description="reverse of 'full_documentation'", ), Property( "is_applied_to", - "openminds.core.DatasetVersion", - "^vocab:license", + "openminds.latest.core.DatasetVersion", + "license", reverse="license", multiple=True, - doc="reverse of 'license'", + description="reverse of 'license'", ), Property( "is_output_of", - "openminds.core.ModelVersion", - "^vocab:outputData", + "openminds.latest.core.ModelVersion", + "outputData", reverse="output_data", multiple=True, - doc="reverse of 'output_data'", + description="reverse of 'output_data'", ), Property( "is_reference_for", - "openminds.computation.ValidationTestVersion", - "^vocab:referenceData", + "openminds.latest.computation.ValidationTestVersion", + "referenceData", reverse="reference_data", multiple=True, - doc="reverse of 'reference_data'", + description="reverse of 'reference_data'", ), ] existence_query_properties = ("iri",) @@ -101,7 +87,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/dataset.py b/fairgraph/openminds/core/products/dataset.py index 6ce54819..50f8bd7c 100644 --- a/fairgraph/openminds/core/products/dataset.py +++ b/fairgraph/openminds/core/products/dataset.py @@ -4,97 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Dataset +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Dataset(KGObject): +class Dataset(KGObject, Dataset): """ Structured information on data originating from human/animal studies or simulations (concept level). """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/Dataset" - properties = [ - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - required=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the dataset.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.IdentifiersDotOrgID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the dataset."), - Property( - "has_versions", - "openminds.core.DatasetVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the dataset."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the dataset.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -122,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/dataset_version.py b/fairgraph/openminds/core/products/dataset_version.py index b49dcfe0..774f9af1 100644 --- a/fairgraph/openminds/core/products/dataset_version.py +++ b/fairgraph/openminds/core/products/dataset_version.py @@ -4,455 +4,98 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import DatasetVersion +from fairgraph import KGObject from urllib.request import urlretrieve from pathlib import Path from ....utility import accepted_terms_of_use from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class DatasetVersion(KGObject): +class DatasetVersion(KGObject, DatasetVersion): """ Structured information on data originating from human/animal studies or simulations (version level). """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/DatasetVersion" - properties = [ - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the dataset version.", - ), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "behavioral_protocols", - "openminds.core.BehavioralProtocol", - "vocab:behavioralProtocol", - multiple=True, - doc="no description available", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "data_types", - "openminds.controlled_terms.SemanticDataType", - "vocab:dataType", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the dataset version.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.IdentifiersDotOrgID"], - "vocab:digitalIdentifier", - required=True, - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "ethics_assessment", - "openminds.controlled_terms.EthicsAssessment", - "vocab:ethicsAssessment", - required=True, - doc="Judgment about the applied principles of conduct governing an individual or a group.", - ), - Property( - "experimental_approaches", - "openminds.controlled_terms.ExperimentalApproach", - "vocab:experimentalApproach", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property("full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the dataset version."), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the dataset version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "input_data", - [ - "openminds.core.DOI", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.WebResource", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:inputData", - multiple=True, - doc="Data that is put into a process or machine.", - ), - Property( - "is_alternative_version_of", - "openminds.core.DatasetVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.core.DatasetVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the dataset version.", - ), - Property( - "license", - ["openminds.core.License", "openminds.core.WebResource"], - "vocab:license", - required=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "preparation_designs", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - multiple=True, - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the dataset version.", - ), - Property( - "studied_specimens", - [ - "openminds.core.Subject", - "openminds.core.SubjectGroup", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - ], - "vocab:studiedSpecimen", - multiple=True, - doc="no description available", - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "techniques", - [ - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.Technique", - ], - "vocab:technique", - multiple=True, - required=True, - doc="Method of accomplishing a desired aim.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "has_parts", [ - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:isPartOf", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), Property( "is_input_to", - "openminds.computation.DataCopy", - "^vocab:input", + "openminds.latest.computation.DataCopy", + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_old_version_of", - "openminds.core.DatasetVersion", - "^vocab:isNewVersionOf", + "openminds.latest.core.DatasetVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.core.Dataset", - "^vocab:hasVersion", + "openminds.latest.core.Dataset", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "publication", - "openminds.publications.LivePaperVersion", - "^vocab:about", + "openminds.latest.publications.LivePaperVersion", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -508,7 +151,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/meta_data_model.py b/fairgraph/openminds/core/products/meta_data_model.py index 359e7f37..515c9ebd 100644 --- a/fairgraph/openminds/core/products/meta_data_model.py +++ b/fairgraph/openminds/core/products/meta_data_model.py @@ -4,103 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import MetaDataModel +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class MetaDataModel(KGObject): +class MetaDataModel(KGObject, MetaDataModel): """ """ - default_space = "metadatamodel" type_ = "https://openminds.ebrains.eu/core/MetaDataModel" - properties = [ - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the meta data model.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - required=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.SWHID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", - str, - "vocab:fullName", - required=True, - doc="Whole, non-abbreviated name of the meta data model.", - ), - Property( - "has_versions", - "openminds.core.MetaDataModelVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the meta data model."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the meta data model.", - ), - ] + default_space = "metadatamodel" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -128,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/meta_data_model_version.py b/fairgraph/openminds/core/products/meta_data_model_version.py index 2dd0064b..bc550551 100644 --- a/fairgraph/openminds/core/products/meta_data_model_version.py +++ b/fairgraph/openminds/core/products/meta_data_model_version.py @@ -4,319 +4,63 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import MetaDataModelVersion +from fairgraph import KGObject from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class MetaDataModelVersion(KGObject): +class MetaDataModelVersion(KGObject, MetaDataModelVersion): """ """ - default_space = "metadatamodel" type_ = "https://openminds.ebrains.eu/core/MetaDataModelVersion" - properties = [ - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the meta data model version.", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the meta data model version.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.SWHID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property( - "full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the meta data model version." - ), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the meta data model version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "is_alternative_version_of", - "openminds.core.MetaDataModelVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.core.MetaDataModelVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the meta data model version.", - ), - Property( - "license", - "openminds.core.License", - "vocab:license", - required=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "serialization_formats", - "openminds.core.ContentType", - "vocab:serializationFormat", - multiple=True, - doc="Form in which a particular data structure or object state is translated to for storage.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the meta data model version.", - ), - Property( - "specification_formats", - "openminds.core.ContentType", - "vocab:specificationFormat", - multiple=True, - doc="Form in which a particular data structure or object state is specified in.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "type", - "openminds.controlled_terms.MetaDataModelType", - "vocab:type", - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "metadatamodel" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_old_version_of", - "openminds.core.MetaDataModelVersion", - "^vocab:isNewVersionOf", + "openminds.latest.core.MetaDataModelVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.core.MetaDataModel", - "^vocab:hasVersion", + "openminds.latest.core.MetaDataModel", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -362,7 +106,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/model.py b/fairgraph/openminds/core/products/model.py index 73e0aadf..87894af4 100644 --- a/fairgraph/openminds/core/products/model.py +++ b/fairgraph/openminds/core/products/model.py @@ -4,148 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Model +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Model(KGObject): +class Model(KGObject, Model): """ Structured information on a computational model (concept level). """ - default_space = "model" type_ = "https://openminds.ebrains.eu/core/Model" - properties = [ - Property( - "abstraction_level", - "openminds.controlled_terms.ModelAbstractionLevel", - "vocab:abstractionLevel", - required=True, - doc="Extent of simplification of physical, spatial, or temporal details or attributes in the study of objects or systems.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the model.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - required=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.SWHID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the model."), - Property( - "has_versions", - "openminds.core.ModelVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the model."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "model_scope", - "openminds.controlled_terms.ModelScope", - "vocab:scope", - required=True, - doc="Extent of something.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the model.", - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - required=True, - doc="Structure or function that was targeted within a study.", - ), - ] + default_space = "model" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -176,7 +74,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/model_version.py b/fairgraph/openminds/core/products/model_version.py index 57eecc25..a03d3c39 100644 --- a/fairgraph/openminds/core/products/model_version.py +++ b/fairgraph/openminds/core/products/model_version.py @@ -4,368 +4,104 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ModelVersion +from fairgraph import KGObject from fairgraph.errors import ResolutionFailure from .model import Model from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class ModelVersion(KGObject): +class ModelVersion(KGObject, ModelVersion): """ Structured information on a computational model (version level). """ - default_space = "model" type_ = "https://openminds.ebrains.eu/core/ModelVersion" - properties = [ - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the model version.", - ), - Property( - "configuration", - [ - "openminds.core.Configuration", - "openminds.core.File", - "openminds.core.PropertyValueList", - "openminds.core.WebResource", - ], - "vocab:configuration", - doc="no description available", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the model version.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.SWHID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("entry_point", str, "vocab:entryPoint", doc="no description available"), - Property( - "formats", - "openminds.core.ContentType", - "vocab:format", - multiple=True, - required=True, - doc="Method of digitally organizing and structuring data or information.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property("full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the model version."), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the model version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "input_data", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.FileBundle", "openminds.core.WebResource"], - "vocab:inputData", - multiple=True, - doc="Data that is put into a process or machine.", - ), - Property( - "is_alternative_version_of", - "openminds.core.ModelVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.core.ModelVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the model version.", - ), - Property( - "licenses", - "openminds.core.License", - "vocab:license", - multiple=True, - required=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "output_data", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.FileBundle", "openminds.core.WebResource"], - "vocab:outputData", - multiple=True, - doc="Data that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the model version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "model" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_input_to", [ - "openminds.computation.DataCopy", - "openminds.computation.ModelValidation", - "openminds.computation.Simulation", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Simulation", ], - "^vocab:input", + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_location_of", - "openminds.core.ServiceLink", - "^vocab:dataLocation", + "openminds.latest.core.ServiceLink", + "dataLocation", reverse="data_location", multiple=True, - doc="reverse of 'data_location'", + description="reverse of 'data_location'", ), Property( "is_old_version_of", - "openminds.core.ModelVersion", - "^vocab:isNewVersionOf", + "openminds.latest.core.ModelVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_output_of", - "openminds.computation.Optimization", - "^vocab:output", + "openminds.latest.computation.Optimization", + "output", reverse="outputs", multiple=True, - doc="reverse of 'outputs'", + description="reverse of 'outputs'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup", "openminds.core.SoftwareVersion"], - "^vocab:hasPart", + [ + "openminds.latest.core.Project", + "openminds.latest.core.ResearchProductGroup", + "openminds.latest.core.SoftwareVersion", + ], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.core.Model", - "^vocab:hasVersion", + "openminds.latest.core.Model", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "publication", - "openminds.publications.LivePaperVersion", - "^vocab:about", + "openminds.latest.publications.LivePaperVersion", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -417,7 +153,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/project.py b/fairgraph/openminds/core/products/project.py index 172c2b07..97e86c6e 100644 --- a/fairgraph/openminds/core/products/project.py +++ b/fairgraph/openminds/core/products/project.py @@ -4,74 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Project +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Project(KGObject): +class Project(KGObject, Project): """ Structured information on a research project. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/Project" - properties = [ - Property( - "coordinators", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:coordinator", - multiple=True, - doc="Legal person who organizes the collaborative work of people or groups.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the project.", - ), - Property("full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the project."), - Property( - "has_parts", - [ - "openminds.computation.ValidationTest", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipe", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.Dataset", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.WebService", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaper", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:hasPart", - multiple=True, - required=True, - doc="no description available", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the project."), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the project.", - ), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] aliases = {"name": "full_name", "alias": "short_name"} existence_query_properties = ("short_name",) @@ -91,7 +39,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/setup.py b/fairgraph/openminds/core/products/setup.py index 405b0a42..c235b526 100644 --- a/fairgraph/openminds/core/products/setup.py +++ b/fairgraph/openminds/core/products/setup.py @@ -4,79 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Setup +from fairgraph import KGObject -class Setup(KGObject): +class Setup(KGObject, Setup): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/Setup" - properties = [ - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the setup.", - ), - Property( - "has_parts", - [ - "openminds.core.Setup", - "openminds.core.SoftwareVersion", - "openminds.ephys.Electrode", - "openminds.ephys.ElectrodeArray", - "openminds.ephys.Pipette", - "openminds.specimen_prep.SlicingDevice", - ], - "vocab:hasPart", - multiple=True, - required=True, - doc="no description available", - ), - Property("location", str, "vocab:location", doc="no description available"), - Property( - "manufacturers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:manufacturer", - multiple=True, - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the setup.", - ), - Property( - "types", - "openminds.controlled_terms.SetupType", - "vocab:type", - multiple=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_part_of", - "openminds.core.Setup", - "^vocab:hasPart", + "openminds.latest.core.Setup", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "used_in", - "openminds.stimulation.StimulationActivity", - "^vocab:setup", + "openminds.latest.stimulation.StimulationActivity", + "setup", reverse="setup", multiple=True, - doc="reverse of 'setup'", + description="reverse of 'setup'", ), ] existence_query_properties = ("description", "has_parts", "name") @@ -96,7 +52,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/software.py b/fairgraph/openminds/core/products/software.py index 72dfaa79..72ece2dd 100644 --- a/fairgraph/openminds/core/products/software.py +++ b/fairgraph/openminds/core/products/software.py @@ -4,99 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Software +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class Software(KGObject): +class Software(KGObject, Software): """ Structured information on a software tool (concept level). """ - default_space = "software" type_ = "https://openminds.ebrains.eu/core/Software" - properties = [ - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the software.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - required=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.RRID", "openminds.core.SWHID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the software." - ), - Property( - "has_versions", - "openminds.core.SoftwareVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the software."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the software.", - ), - ] + default_space = "software" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -124,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/software_version.py b/fairgraph/openminds/core/products/software_version.py index 4d297189..2939b5a6 100644 --- a/fairgraph/openminds/core/products/software_version.py +++ b/fairgraph/openminds/core/products/software_version.py @@ -4,417 +4,102 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import SoftwareVersion +from fairgraph import KGObject from fairgraph.errors import ResolutionFailure from .software import Software from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class SoftwareVersion(KGObject): +class SoftwareVersion(KGObject, SoftwareVersion): """ """ - default_space = "software" type_ = "https://openminds.ebrains.eu/core/SoftwareVersion" - properties = [ - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the software version.", - ), - Property( - "application_categories", - "openminds.controlled_terms.SoftwareApplicationCategory", - "vocab:applicationCategory", - multiple=True, - required=True, - doc="Distinct class that groups software programs which perform a similar task or set of tasks.", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the software version.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "devices", - "openminds.controlled_terms.OperatingDevice", - "vocab:device", - multiple=True, - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.SWHID", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "features", - "openminds.controlled_terms.SoftwareFeature", - "vocab:feature", - multiple=True, - required=True, - doc="Structure, form, or appearance that characterizes the software version.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property("full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the software version."), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "has_parts", - [ - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:hasPart", - multiple=True, - doc="no description available", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the software version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "input_formats", - "openminds.core.ContentType", - "vocab:inputFormat", - multiple=True, - doc="Format of data that is put into a process or machine.", - ), - Property( - "is_alternative_version_of", - "openminds.core.SoftwareVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.core.SoftwareVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the software version.", - ), - Property( - "languages", - "openminds.controlled_terms.Language", - "vocab:language", - multiple=True, - required=True, - doc="System of communication (words, their pronunciation, and the methods of combining them) used and understood by a particular community.", - ), - Property( - "licenses", - "openminds.core.License", - "vocab:license", - multiple=True, - required=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property( - "operating_systems", - "openminds.controlled_terms.OperatingSystem", - "vocab:operatingSystem", - multiple=True, - required=True, - doc="Software that controls the operation of a computer and directs the processing of programs.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "output_formats", - "openminds.core.ContentType", - "vocab:outputFormat", - multiple=True, - doc="Format of data that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "programming_languages", - "openminds.controlled_terms.ProgrammingLanguage", - "vocab:programmingLanguage", - multiple=True, - required=True, - doc="Distinct set of instructions for computer programs in order to produce various kinds of output.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "requirements", - str, - "vocab:requirement", - multiple=True, - doc="Something essential to the existence, occurrence or function of something else.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the software version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "software" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_input_to", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:input", + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_old_version_of", - "openminds.core.SoftwareVersion", - "^vocab:isNewVersionOf", + "openminds.latest.core.SoftwareVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", [ - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.Project", - "openminds.core.ResearchProductGroup", - "openminds.core.Setup", - "openminds.core.WebServiceVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.Project", + "openminds.latest.core.ResearchProductGroup", + "openminds.latest.core.Setup", + "openminds.latest.core.WebServiceVersion", ], - "^vocab:hasPart", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.core.Software", - "^vocab:hasVersion", + "openminds.latest.core.Software", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "publication", - "openminds.publications.LivePaperVersion", - "^vocab:about", + "openminds.latest.publications.LivePaperVersion", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "used_in", - ["openminds.computation.Environment", "openminds.computation.SoftwareAgent"], - "^vocab:software", + ["openminds.latest.computation.Environment", "openminds.latest.computation.SoftwareAgent"], + "software", reverse="software", multiple=True, - doc="reverse of 'software'", + description="reverse of 'software'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -470,7 +155,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/web_service.py b/fairgraph/openminds/core/products/web_service.py index 2fc717d3..9707989f 100644 --- a/fairgraph/openminds/core/products/web_service.py +++ b/fairgraph/openminds/core/products/web_service.py @@ -4,109 +4,62 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import WebService +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class WebService(KGObject): +class WebService(KGObject, WebService): """ """ - default_space = "webservice" type_ = "https://openminds.ebrains.eu/core/WebService" - properties = [ - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the web service.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - required=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the web service." - ), - Property( - "has_versions", - "openminds.core.WebServiceVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the web service."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the web service.", - ), - ] + default_space = "webservice" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "has_accounts", - "openminds.core.AccountInformation", - "^vocab:service", + "openminds.latest.core.AccountInformation", + "service", reverse="service", multiple=True, - doc="reverse of 'service'", + description="reverse of 'service'", ), Property( "hosts", - "openminds.publications.LivePaperResourceItem", - "^vocab:hostedBy", + "openminds.latest.publications.LivePaperResourceItem", + "hostedBy", reverse="hosted_by", multiple=True, - doc="reverse of 'hosted_by'", + description="reverse of 'hosted_by'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -135,7 +88,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/products/web_service_version.py b/fairgraph/openminds/core/products/web_service_version.py index c271e516..23ea4f8e 100644 --- a/fairgraph/openminds/core/products/web_service_version.py +++ b/fairgraph/openminds/core/products/web_service_version.py @@ -4,321 +4,80 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import WebServiceVersion +from fairgraph import KGObject from fairgraph.errors import ResolutionFailure from .web_service import WebService from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class WebServiceVersion(KGObject): +class WebServiceVersion(KGObject, WebServiceVersion): """ """ - default_space = "webservice" type_ = "https://openminds.ebrains.eu/core/WebServiceVersion" - properties = [ - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the web service version.", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the web service version.", - ), - Property( - "developers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:developer", - multiple=True, - doc="Legal person that creates or improves products or services (e.g., software, applications, etc.).", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property("full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the web service version."), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "has_parts", - "openminds.core.SoftwareVersion", - "vocab:hasPart", - multiple=True, - doc="no description available", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the web service version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "input_formats", - "openminds.core.ContentType", - "vocab:inputFormat", - multiple=True, - doc="Format of data that is put into a process or machine.", - ), - Property( - "is_alternative_version_of", - "openminds.core.WebServiceVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.core.WebServiceVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the web service version.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "output_formats", - "openminds.core.ContentType", - "vocab:outputFormat", - multiple=True, - doc="Format of data that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the web service version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "webservice" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_old_version_of", - "openminds.core.WebServiceVersion", - "^vocab:isNewVersionOf", + "openminds.latest.core.WebServiceVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.core.WebService", - "^vocab:hasVersion", + "openminds.latest.core.WebService", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "used_for", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.Visualization", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.Visualization", ], - "^vocab:environment", + "environment", reverse="environment", multiple=True, - doc="reverse of 'environment'", + description="reverse of 'environment'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -363,7 +122,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/behavioral_protocol.py b/fairgraph/openminds/core/research/behavioral_protocol.py index 5da37173..215915d5 100644 --- a/fairgraph/openminds/core/research/behavioral_protocol.py +++ b/fairgraph/openminds/core/research/behavioral_protocol.py @@ -4,84 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import BehavioralProtocol +from fairgraph import KGObject -class BehavioralProtocol(KGObject): +class BehavioralProtocol(KGObject, BehavioralProtocol): """ Structured information about a protocol used in an experiment studying human or animal behavior. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/BehavioralProtocol" - properties = [ - Property( - "described_in", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.WebResource"], - "vocab:describedIn", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the behavioral protocol.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the behavioral protocol within a particular product.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the behavioral protocol.", - ), - Property( - "stimulations", - ["openminds.controlled_terms.StimulationApproach", "openminds.controlled_terms.StimulationTechnique"], - "vocab:stimulation", - multiple=True, - doc="no description available", - ), - Property( - "stimulus_types", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:stimulusType", - multiple=True, - doc="no description available", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.core.DatasetVersion", "openminds.core.ProtocolExecution"], - "^vocab:behavioralProtocol", + ["openminds.latest.core.DatasetVersion", "openminds.latest.core.ProtocolExecution"], + "behavioralProtocol", reverse="behavioral_protocols", multiple=True, - doc="reverse of 'behavioral_protocols'", + description="reverse of 'behavioral_protocols'", ), ] existence_query_properties = ("description", "name") @@ -101,7 +52,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/configuration.py b/fairgraph/openminds/core/research/configuration.py index 18fbb94e..865195c3 100644 --- a/fairgraph/openminds/core/research/configuration.py +++ b/fairgraph/openminds/core/research/configuration.py @@ -4,49 +4,40 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Configuration +from fairgraph import KGObject -class Configuration(KGObject): +class Configuration(KGObject, Configuration): """ Structured information about the properties or parameters of an entity or process. """ - default_space = "common" type_ = "https://openminds.ebrains.eu/core/Configuration" - properties = [ - Property("configuration", str, "vocab:configuration", required=True, doc="no description available"), - Property( - "format", - "openminds.core.ContentType", - "vocab:format", - required=True, - doc="Method of digitally organizing and structuring data or information.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - ] + default_space = "common" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_configuration_of", [ - "openminds.computation.Environment", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowExecution", - "openminds.core.ModelVersion", + "openminds.latest.computation.Environment", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowExecution", + "openminds.latest.core.ModelVersion", ], - "^vocab:configuration", + "configuration", reverse="configuration", multiple=True, - doc="reverse of 'configuration'", + description="reverse of 'configuration'", ), Property( "specifies", - "openminds.stimulation.EphysStimulus", - "^vocab:specification", + "openminds.latest.stimulation.EphysStimulus", + "specification", reverse="specifications", multiple=True, - doc="reverse of 'specifications'", + description="reverse of 'specifications'", ), ] existence_query_properties = ("configuration",) @@ -63,7 +54,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/custom_property_set.py b/fairgraph/openminds/core/research/custom_property_set.py index c7ce4b9d..cb4b551c 100644 --- a/fairgraph/openminds/core/research/custom_property_set.py +++ b/fairgraph/openminds/core/research/custom_property_set.py @@ -4,43 +4,23 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import CustomPropertySet +from fairgraph import EmbeddedMetadata -class CustomPropertySet(EmbeddedMetadata): +class CustomPropertySet(EmbeddedMetadata, CustomPropertySet): """ Structured information about properties of an entity that are not represented in an openMINDS schema. """ type_ = "https://openminds.ebrains.eu/core/CustomPropertySet" - properties = [ - Property("context", str, "vocab:context", required=True, doc="no description available"), - Property( - "data_location", - ["openminds.core.Configuration", "openminds.core.File", "openminds.core.PropertyValueList"], - "vocab:dataLocation", - required=True, - doc="no description available", - ), - Property( - "relevant_for", - [ - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.Technique", - ], - "vocab:relevantFor", - required=True, - doc="Reference to what or whom the custom property set bears significance.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( self, context=None, data_location=None, relevant_for=None, id=None, data=None, space=None, scope=None ): - return super().__init__(data=data, context=context, data_location=data_location, relevant_for=relevant_for) + return EmbeddedMetadata.__init__( + self, data=data, context=context, data_location=data_location, relevant_for=relevant_for + ) diff --git a/fairgraph/openminds/core/research/numerical_property.py b/fairgraph/openminds/core/research/numerical_property.py index fe79e254..77397f81 100644 --- a/fairgraph/openminds/core/research/numerical_property.py +++ b/fairgraph/openminds/core/research/numerical_property.py @@ -4,34 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import NumericalProperty +from fairgraph import EmbeddedMetadata -class NumericalProperty(EmbeddedMetadata): +class NumericalProperty(EmbeddedMetadata, NumericalProperty): """ Structured information about a property of some entity or process whose value is a number. """ type_ = "https://openminds.ebrains.eu/core/NumericalProperty" - properties = [ - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the numerical property.", - ), - Property( - "values", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:value", - multiple=True, - required=True, - doc="Entry for a property.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, name=None, values=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, name=name, values=values) + return EmbeddedMetadata.__init__(self, data=data, name=name, values=values) diff --git a/fairgraph/openminds/core/research/property_value_list.py b/fairgraph/openminds/core/research/property_value_list.py index bd741dff..112b499c 100644 --- a/fairgraph/openminds/core/research/property_value_list.py +++ b/fairgraph/openminds/core/research/property_value_list.py @@ -4,52 +4,43 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import PropertyValueList +from fairgraph import KGObject -class PropertyValueList(KGObject): +class PropertyValueList(KGObject, PropertyValueList): """ An identifiable list of property-value pairs. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/PropertyValueList" - properties = [ - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "property_value_pairs", - ["openminds.core.NumericalProperty", "openminds.core.StringProperty"], - "vocab:propertyValuePair", - multiple=True, - required=True, - doc="no description available", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "defines_environment_of", - "openminds.computation.LaunchConfiguration", - "^vocab:environmentVariable", + "openminds.latest.computation.LaunchConfiguration", + "environmentVariable", reverse="environment_variable", multiple=True, - doc="reverse of 'environment_variable'", + description="reverse of 'environment_variable'", ), Property( "is_configuration_of", - ["openminds.computation.ValidationTestVersion", "openminds.core.ModelVersion"], - "^vocab:configuration", + ["openminds.latest.computation.ValidationTestVersion", "openminds.latest.core.ModelVersion"], + "configuration", reverse="configuration", multiple=True, - doc="reverse of 'configuration'", + description="reverse of 'configuration'", ), Property( "specifies", - ["openminds.sands.CustomAnnotation", "openminds.stimulation.EphysStimulus"], - "^vocab:specification", + ["openminds.latest.sands.CustomAnnotation", "openminds.latest.stimulation.EphysStimulus"], + "specification", reverse="specification", multiple=True, - doc="reverse of 'specification'", + description="reverse of 'specification'", ), ] existence_query_properties = ("lookup_label",) @@ -66,7 +57,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/protocol.py b/fairgraph/openminds/core/research/protocol.py index 2b547b83..3b762f63 100644 --- a/fairgraph/openminds/core/research/protocol.py +++ b/fairgraph/openminds/core/research/protocol.py @@ -4,87 +4,37 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Protocol +from fairgraph import KGObject -class Protocol(KGObject): +class Protocol(KGObject, Protocol): """ Structured information on a research project. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/Protocol" - properties = [ - Property( - "described_in", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.WebResource"], - "vocab:describedIn", - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the protocol.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the protocol.", - ), - Property( - "stimulus_types", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:stimulusType", - multiple=True, - doc="no description available", - ), - Property( - "techniques", - [ - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.Technique", - ], - "vocab:technique", - multiple=True, - required=True, - doc="Method of accomplishing a desired aim.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "used_in", [ - "openminds.core.DatasetVersion", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:protocol", + "protocol", reverse="protocols", multiple=True, - doc="reverse of 'protocols'", + description="reverse of 'protocols'", ), ] existence_query_properties = ("name",) @@ -102,7 +52,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/protocol_execution.py b/fairgraph/openminds/core/research/protocol_execution.py index e4fd443f..2703d666 100644 --- a/fairgraph/openminds/core/research/protocol_execution.py +++ b/fairgraph/openminds/core/research/protocol_execution.py @@ -4,149 +4,30 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import ProtocolExecution +from fairgraph import KGObject from datetime import datetime, time -class ProtocolExecution(KGObject): +class ProtocolExecution(KGObject, ProtocolExecution): """ Structured information on a protocol execution. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/ProtocolExecution" - properties = [ - Property( - "behavioral_protocols", - "openminds.core.BehavioralProtocol", - "vocab:behavioralProtocol", - multiple=True, - doc="no description available", - ), - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the protocol execution.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - [ - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - [ - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - ], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "based_on_protocol_execution", - ["openminds.sands.AtlasAnnotation", "openminds.sands.CustomAnnotation"], - "^vocab:criteria", + ["openminds.latest.sands.AtlasAnnotation", "openminds.latest.sands.CustomAnnotation"], + "criteria", reverse="criteria", multiple=True, - doc="reverse of 'criteria'", + description="reverse of 'criteria'", ), ] existence_query_properties = ("lookup_label",) @@ -172,7 +53,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/strain.py b/fairgraph/openminds/core/research/strain.py index fa6277a7..bc461696 100644 --- a/fairgraph/openminds/core/research/strain.py +++ b/fairgraph/openminds/core/research/strain.py @@ -4,113 +4,40 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Strain +from fairgraph import KGObject -class Strain(KGObject): +class Strain(KGObject, Strain): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/Strain" - properties = [ - Property( - "alternate_identifiers", str, "vocab:alternateIdentifier", multiple=True, doc="no description available" - ), - Property( - "background_strains", - "openminds.core.Strain", - "vocab:backgroundStrain", - multiple=True, - doc="no description available", - ), - Property( - "breeding_type", - "openminds.controlled_terms.BreedingType", - "vocab:breedingType", - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the strain.", - ), - Property( - "digital_identifier", - "openminds.core.RRID", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "disease_models", - ["openminds.controlled_terms.Disease", "openminds.controlled_terms.DiseaseModel"], - "vocab:diseaseModel", - multiple=True, - doc="no description available", - ), - Property( - "genetic_strain_type", - "openminds.controlled_terms.GeneticStrainType", - "vocab:geneticStrainType", - required=True, - doc="no description available", - ), - Property("laboratory_code", str, "vocab:laboratoryCode", doc="no description available"), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the strain.", - ), - Property( - "ontology_identifiers", - str, - "vocab:ontologyIdentifier", - multiple=True, - doc="Term or code used to identify the strain registered within a particular ontology.", - ), - Property("phenotype", str, "vocab:phenotype", doc="Physical expression of one or more genes of an organism."), - Property( - "species", - "openminds.controlled_terms.Species", - "vocab:species", - required=True, - doc="Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.", - ), - Property("stock_number", "openminds.core.StockNumber", "vocab:stockNumber", doc="no description available"), - Property( - "synonyms", - str, - "vocab:synonym", - multiple=True, - doc="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_background_strain_of", - "openminds.core.Strain", - "^vocab:backgroundStrain", + "openminds.latest.core.Strain", + "backgroundStrain", reverse="background_strains", multiple=True, - doc="reverse of 'background_strains'", + description="reverse of 'background_strains'", ), Property( "is_species_of", [ - "openminds.core.Subject", - "openminds.core.SubjectGroup", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", + "openminds.latest.core.Subject", + "openminds.latest.core.SubjectGroup", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", ], - "^vocab:species", + "species", reverse="species", multiple=True, - doc="reverse of 'species'", + description="reverse of 'species'", ), ] existence_query_properties = ("genetic_strain_type", "name", "species") @@ -138,7 +65,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/string_property.py b/fairgraph/openminds/core/research/string_property.py index 81238ad9..e74fd0a2 100644 --- a/fairgraph/openminds/core/research/string_property.py +++ b/fairgraph/openminds/core/research/string_property.py @@ -4,27 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import StringProperty +from fairgraph import EmbeddedMetadata -class StringProperty(EmbeddedMetadata): +class StringProperty(EmbeddedMetadata, StringProperty): """ """ type_ = "https://openminds.ebrains.eu/core/StringProperty" - properties = [ - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the string property.", - ), - Property("value", str, "vocab:value", required=True, doc="Entry for a property."), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, name=None, value=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, name=name, value=value) + return EmbeddedMetadata.__init__(self, data=data, name=name, value=value) diff --git a/fairgraph/openminds/core/research/subject.py b/fairgraph/openminds/core/research/subject.py index 769ecdf6..03ddd875 100644 --- a/fairgraph/openminds/core/research/subject.py +++ b/fairgraph/openminds/core/research/subject.py @@ -4,78 +4,43 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import Subject +from fairgraph import KGObject -class Subject(KGObject): +class Subject(KGObject, Subject): """ Structured information on a subject. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/Subject" - properties = [ - Property( - "biological_sex", - "openminds.controlled_terms.BiologicalSex", - "vocab:biologicalSex", - doc="Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the subject within a particular product.", - ), - Property( - "is_part_of", - "openminds.core.SubjectGroup", - "vocab:isPartOf", - multiple=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "species", - ["openminds.controlled_terms.Species", "openminds.core.Strain"], - "vocab:species", - required=True, - doc="Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.", - ), - Property( - "studied_states", - "openminds.core.SubjectState", - "vocab:studiedState", - multiple=True, - required=True, - doc="Reference to a point in time at which the subject was studied in a particular mode or condition.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_study_results_in", - "openminds.core.DatasetVersion", - "^vocab:studiedSpecimen", + "openminds.latest.core.DatasetVersion", + "studiedSpecimen", reverse="studied_specimens", multiple=True, - doc="reverse of 'studied_specimens'", + description="reverse of 'studied_specimens'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.sands.BrainAtlasVersion", "openminds.sands.CommonCoordinateSpaceVersion"], - "^vocab:usedSpecimen", + ["openminds.latest.sands.BrainAtlasVersion", "openminds.latest.sands.CommonCoordinateSpaceVersion"], + "usedSpecimen", reverse="used_specimens", multiple=True, - doc="reverse of 'used_specimens'", + description="reverse of 'used_specimens'", ), ] existence_query_properties = ("lookup_label",) @@ -96,7 +61,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/subject_group.py b/fairgraph/openminds/core/research/subject_group.py index 44350603..810aebc5 100644 --- a/fairgraph/openminds/core/research/subject_group.py +++ b/fairgraph/openminds/core/research/subject_group.py @@ -4,88 +4,51 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import SubjectGroup +from fairgraph import KGObject -class SubjectGroup(KGObject): +class SubjectGroup(KGObject, SubjectGroup): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/SubjectGroup" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "biological_sexes", - "openminds.controlled_terms.BiologicalSex", - "vocab:biologicalSex", - multiple=True, - doc="Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the subject group within a particular product.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property("number_of_subjects", int, "vocab:numberOfSubjects", doc="no description available"), - Property( - "species", - ["openminds.controlled_terms.Species", "openminds.core.Strain"], - "vocab:species", - multiple=True, - required=True, - doc="Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.", - ), - Property( - "studied_states", - "openminds.core.SubjectGroupState", - "vocab:studiedState", - multiple=True, - required=True, - doc="Reference to a point in time at which the subject group was studied in a particular mode or condition.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_parts", - "openminds.core.Subject", - "^vocab:isPartOf", + "openminds.latest.core.Subject", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), Property( "has_study_results_in", - "openminds.core.DatasetVersion", - "^vocab:studiedSpecimen", + "openminds.latest.core.DatasetVersion", + "studiedSpecimen", reverse="studied_specimens", multiple=True, - doc="reverse of 'studied_specimens'", + description="reverse of 'studied_specimens'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.sands.BrainAtlasVersion", "openminds.sands.CommonCoordinateSpaceVersion"], - "^vocab:usedSpecimen", + ["openminds.latest.sands.BrainAtlasVersion", "openminds.latest.sands.CommonCoordinateSpaceVersion"], + "usedSpecimen", reverse="used_specimens", multiple=True, - doc="reverse of 'used_specimens'", + description="reverse of 'used_specimens'", ), ] existence_query_properties = ("lookup_label",) @@ -108,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/subject_group_state.py b/fairgraph/openminds/core/research/subject_group_state.py index 1b92e2e9..9885fd11 100644 --- a/fairgraph/openminds/core/research/subject_group_state.py +++ b/fairgraph/openminds/core/research/subject_group_state.py @@ -4,126 +4,63 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import SubjectGroupState +from fairgraph import KGObject -class SubjectGroupState(KGObject): +class SubjectGroupState(KGObject, SubjectGroupState): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/SubjectGroupState" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "age", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:age", - doc="Time of life or existence at which some particular qualification, capacity or event arises.", - ), - Property( - "age_categories", - "openminds.controlled_terms.AgeCategory", - "vocab:ageCategory", - multiple=True, - required=True, - doc="Distinct life cycle class that is defined by a similar age or age range (developmental stage) within a group of individual beings.", - ), - Property( - "attributes", - "openminds.controlled_terms.SubjectAttribute", - "vocab:attribute", - multiple=True, - doc="no description available", - ), - Property( - "descended_from", "openminds.core.SubjectGroupState", "vocab:descendedFrom", doc="no description available" - ), - Property( - "handedness", - "openminds.controlled_terms.Handedness", - "vocab:handedness", - multiple=True, - doc="Degree to which an organism prefers one hand or foot over the other hand or foot during the performance of a task.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the subject group state within a particular product.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "pathologies", - ["openminds.controlled_terms.Disease", "openminds.controlled_terms.DiseaseModel"], - "vocab:pathology", - multiple=True, - doc="Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.", - ), - Property( - "relative_time_indication", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:relativeTimeIndication", - doc="no description available", - ), - Property( - "weight", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:weight", - doc="Amount that a thing or being weighs.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_children", [ - "openminds.core.SubjectGroupState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", + "openminds.latest.core.SubjectGroupState", + "openminds.latest.core.TissueSampleCollectionState", + "openminds.latest.core.TissueSampleState", ], - "^vocab:descendedFrom", + "descendedFrom", reverse="descended_from", multiple=True, - doc="reverse of 'descended_from'", + description="reverse of 'descended_from'", ), Property( "is_input_to", - ["openminds.ephys.RecordingActivity", "openminds.specimen_prep.TissueCulturePreparation"], - "^vocab:input", + ["openminds.latest.ephys.RecordingActivity", "openminds.latest.specimen_prep.TissueCulturePreparation"], + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_output_of", - ["openminds.core.ProtocolExecution", "openminds.stimulation.StimulationActivity"], - "^vocab:output", + ["openminds.latest.core.ProtocolExecution", "openminds.latest.stimulation.StimulationActivity"], + "output", reverse="outputs", multiple=True, - doc="reverse of 'outputs'", + description="reverse of 'outputs'", ), Property( "is_state_of", - "openminds.core.SubjectGroup", - "^vocab:studiedState", + "openminds.latest.core.SubjectGroup", + "studiedState", reverse="studied_states", multiple=True, - doc="reverse of 'studied_states'", + description="reverse of 'studied_states'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), ] existence_query_properties = ("lookup_label",) @@ -151,7 +88,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/subject_state.py b/fairgraph/openminds/core/research/subject_state.py index fde4baa1..4133ad89 100644 --- a/fairgraph/openminds/core/research/subject_state.py +++ b/fairgraph/openminds/core/research/subject_state.py @@ -4,147 +4,86 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import SubjectState +from fairgraph import KGObject -class SubjectState(KGObject): +class SubjectState(KGObject, SubjectState): """ Structured information on a temporary state of a subject. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/SubjectState" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "age", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:age", - doc="Time of life or existence at which some particular qualification, capacity or event arises.", - ), - Property( - "age_category", - "openminds.controlled_terms.AgeCategory", - "vocab:ageCategory", - required=True, - doc="Distinct life cycle class that is defined by a similar age or age range (developmental stage) within a group of individual beings.", - ), - Property( - "attributes", - "openminds.controlled_terms.SubjectAttribute", - "vocab:attribute", - multiple=True, - doc="no description available", - ), - Property( - "descended_from", "openminds.core.SubjectState", "vocab:descendedFrom", doc="no description available" - ), - Property( - "handedness", - "openminds.controlled_terms.Handedness", - "vocab:handedness", - doc="Degree to which an organism prefers one hand or foot over the other hand or foot during the performance of a task.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the subject state within a particular product.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "pathologies", - ["openminds.controlled_terms.Disease", "openminds.controlled_terms.DiseaseModel"], - "vocab:pathology", - multiple=True, - doc="Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.", - ), - Property( - "relative_time_indication", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:relativeTimeIndication", - doc="no description available", - ), - Property( - "weight", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:weight", - doc="Amount that a thing or being weighs.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_children", [ - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", + "openminds.latest.core.SubjectState", + "openminds.latest.core.TissueSampleCollectionState", + "openminds.latest.core.TissueSampleState", ], - "^vocab:descendedFrom", + "descendedFrom", reverse="descended_from", multiple=True, - doc="reverse of 'descended_from'", + description="reverse of 'descended_from'", ), Property( "is_input_to", [ - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", ], - "^vocab:input", + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_output_of", [ - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:output", + "output", reverse="outputs", multiple=True, - doc="reverse of 'outputs'", + description="reverse of 'outputs'", ), Property( "is_state_of", - "openminds.core.Subject", - "^vocab:studiedState", + "openminds.latest.core.Subject", + "studiedState", reverse="studied_states", multiple=True, - doc="reverse of 'studied_states'", + description="reverse of 'studied_states'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", + "openminds.latest.specimen_prep.SlicingDeviceUsage", ], - "^vocab:usedSpecimen", + "usedSpecimen", reverse="used_specimen", multiple=True, - doc="reverse of 'used_specimen'", + description="reverse of 'used_specimen'", ), ] existence_query_properties = ("lookup_label",) @@ -173,7 +112,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/tissue_sample.py b/fairgraph/openminds/core/research/tissue_sample.py index a414f98e..09cbd11a 100644 --- a/fairgraph/openminds/core/research/tissue_sample.py +++ b/fairgraph/openminds/core/research/tissue_sample.py @@ -4,119 +4,43 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import TissueSample +from fairgraph import KGObject -class TissueSample(KGObject): +class TissueSample(KGObject, TissueSample): """ Structured information on a tissue sample. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/TissueSample" - properties = [ - Property( - "anatomical_locations", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.UBERONParcellation", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:anatomicalLocation", - multiple=True, - doc="no description available", - ), - Property( - "biological_sex", - "openminds.controlled_terms.BiologicalSex", - "vocab:biologicalSex", - doc="Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the tissue sample within a particular product.", - ), - Property( - "is_part_of", - "openminds.core.TissueSampleCollection", - "vocab:isPartOf", - multiple=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property( - "lateralities", - "openminds.controlled_terms.Laterality", - "vocab:laterality", - multiple=True, - doc="Differentiation between a pair of lateral homologous parts of the body.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "origin", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - ], - "vocab:origin", - required=True, - doc="Source at which something begins or rises, or from which something derives.", - ), - Property( - "species", - ["openminds.controlled_terms.Species", "openminds.core.Strain"], - "vocab:species", - required=True, - doc="Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.", - ), - Property( - "studied_states", - "openminds.core.TissueSampleState", - "vocab:studiedState", - multiple=True, - required=True, - doc="Reference to a point in time at which the tissue sample was studied in a particular mode or condition.", - ), - Property( - "type", - "openminds.controlled_terms.TissueSampleType", - "vocab:type", - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_study_results_in", - "openminds.core.DatasetVersion", - "^vocab:studiedSpecimen", + "openminds.latest.core.DatasetVersion", + "studiedSpecimen", reverse="studied_specimens", multiple=True, - doc="reverse of 'studied_specimens'", + description="reverse of 'studied_specimens'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.sands.BrainAtlasVersion", "openminds.sands.CommonCoordinateSpaceVersion"], - "^vocab:usedSpecimen", + ["openminds.latest.sands.BrainAtlasVersion", "openminds.latest.sands.CommonCoordinateSpaceVersion"], + "usedSpecimen", reverse="used_specimens", multiple=True, - doc="reverse of 'used_specimens'", + description="reverse of 'used_specimens'", ), ] existence_query_properties = ("lookup_label",) @@ -141,7 +65,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/tissue_sample_collection.py b/fairgraph/openminds/core/research/tissue_sample_collection.py index 70c60c71..8194557f 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection.py @@ -4,131 +4,51 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import TissueSampleCollection +from fairgraph import KGObject -class TissueSampleCollection(KGObject): +class TissueSampleCollection(KGObject, TissueSampleCollection): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/TissueSampleCollection" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "anatomical_locations", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.UBERONParcellation", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:anatomicalLocation", - multiple=True, - doc="no description available", - ), - Property( - "biological_sexes", - "openminds.controlled_terms.BiologicalSex", - "vocab:biologicalSex", - multiple=True, - doc="Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the tissue sample collection within a particular product.", - ), - Property( - "lateralities", - "openminds.controlled_terms.Laterality", - "vocab:laterality", - multiple=True, - doc="Differentiation between a pair of lateral homologous parts of the body.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property("number_of_tissue_samples", int, "vocab:numberOfTissueSamples", doc="no description available"), - Property( - "origins", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - ], - "vocab:origin", - multiple=True, - required=True, - doc="Source at which something begins or rises, or from which something derives.", - ), - Property( - "species", - ["openminds.controlled_terms.Species", "openminds.core.Strain"], - "vocab:species", - multiple=True, - required=True, - doc="Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.", - ), - Property( - "studied_states", - "openminds.core.TissueSampleCollectionState", - "vocab:studiedState", - multiple=True, - required=True, - doc="Reference to a point in time at which the tissue sample collection was studied in a particular mode or condition.", - ), - Property( - "types", - "openminds.controlled_terms.TissueSampleType", - "vocab:type", - multiple=True, - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_parts", - "openminds.core.TissueSample", - "^vocab:isPartOf", + "openminds.latest.core.TissueSample", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), Property( "has_study_results_in", - "openminds.core.DatasetVersion", - "^vocab:studiedSpecimen", + "openminds.latest.core.DatasetVersion", + "studiedSpecimen", reverse="studied_specimens", multiple=True, - doc="reverse of 'studied_specimens'", + description="reverse of 'studied_specimens'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", - ["openminds.sands.BrainAtlasVersion", "openminds.sands.CommonCoordinateSpaceVersion"], - "^vocab:usedSpecimen", + ["openminds.latest.sands.BrainAtlasVersion", "openminds.latest.sands.CommonCoordinateSpaceVersion"], + "usedSpecimen", reverse="used_specimens", multiple=True, - doc="reverse of 'used_specimens'", + description="reverse of 'used_specimens'", ), ] existence_query_properties = ("lookup_label",) @@ -155,7 +75,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/tissue_sample_collection_state.py b/fairgraph/openminds/core/research/tissue_sample_collection_state.py index 07497820..9bcf13d2 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection_state.py @@ -4,120 +4,63 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import TissueSampleCollectionState +from fairgraph import KGObject -class TissueSampleCollectionState(KGObject): +class TissueSampleCollectionState(KGObject, TissueSampleCollectionState): """ """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/TissueSampleCollectionState" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "age", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:age", - doc="Time of life or existence at which some particular qualification, capacity or event arises.", - ), - Property( - "attributes", - "openminds.controlled_terms.TissueSampleAttribute", - "vocab:attribute", - multiple=True, - doc="no description available", - ), - Property( - "descended_from", - [ - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - ], - "vocab:descendedFrom", - multiple=True, - doc="no description available", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the tissue sample collection state within a particular product.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "pathologies", - ["openminds.controlled_terms.Disease", "openminds.controlled_terms.DiseaseModel"], - "vocab:pathology", - multiple=True, - doc="Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.", - ), - Property( - "relative_time_indication", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:relativeTimeIndication", - doc="no description available", - ), - Property( - "weight", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:weight", - doc="Amount that a thing or being weighs.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_children", - ["openminds.core.TissueSampleCollectionState", "openminds.core.TissueSampleState"], - "^vocab:descendedFrom", + ["openminds.latest.core.TissueSampleCollectionState", "openminds.latest.core.TissueSampleState"], + "descendedFrom", reverse="descended_from", multiple=True, - doc="reverse of 'descended_from'", + description="reverse of 'descended_from'", ), Property( "is_input_to", - ["openminds.ephys.RecordingActivity", "openminds.specimen_prep.TissueCulturePreparation"], - "^vocab:input", + ["openminds.latest.ephys.RecordingActivity", "openminds.latest.specimen_prep.TissueCulturePreparation"], + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_output_of", [ - "openminds.core.ProtocolExecution", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:output", + "output", reverse="outputs", multiple=True, - doc="reverse of 'outputs'", + description="reverse of 'outputs'", ), Property( "is_state_of", - "openminds.core.TissueSampleCollection", - "^vocab:studiedState", + "openminds.latest.core.TissueSampleCollection", + "studiedState", reverse="studied_states", multiple=True, - doc="reverse of 'studied_states'", + description="reverse of 'studied_states'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), ] existence_query_properties = ("lookup_label",) @@ -143,7 +86,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/core/research/tissue_sample_state.py b/fairgraph/openminds/core/research/tissue_sample_state.py index ba728a7f..6cdff63d 100644 --- a/fairgraph/openminds/core/research/tissue_sample_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_state.py @@ -4,136 +4,79 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.core import TissueSampleState +from fairgraph import KGObject -class TissueSampleState(KGObject): +class TissueSampleState(KGObject, TissueSampleState): """ Structured information on a temporary state of a tissue sample. """ - default_space = "dataset" type_ = "https://openminds.ebrains.eu/core/TissueSampleState" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "age", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:age", - doc="Time of life or existence at which some particular qualification, capacity or event arises.", - ), - Property( - "attributes", - "openminds.controlled_terms.TissueSampleAttribute", - "vocab:attribute", - multiple=True, - doc="no description available", - ), - Property( - "descended_from", - [ - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - ], - "vocab:descendedFrom", - multiple=True, - doc="no description available", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the tissue sample state within a particular product.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "pathologies", - ["openminds.controlled_terms.Disease", "openminds.controlled_terms.DiseaseModel"], - "vocab:pathology", - multiple=True, - doc="Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.", - ), - Property( - "relative_time_indication", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:relativeTimeIndication", - doc="no description available", - ), - Property( - "weight", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:weight", - doc="Amount that a thing or being weighs.", - ), - ] + default_space = "dataset" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_children", - ["openminds.core.TissueSampleCollectionState", "openminds.core.TissueSampleState"], - "^vocab:descendedFrom", + ["openminds.latest.core.TissueSampleCollectionState", "openminds.latest.core.TissueSampleState"], + "descendedFrom", reverse="descended_from", multiple=True, - doc="reverse of 'descended_from'", + description="reverse of 'descended_from'", ), Property( "is_input_to", - "openminds.ephys.RecordingActivity", - "^vocab:input", + "openminds.latest.ephys.RecordingActivity", + "input", reverse="inputs", multiple=True, - doc="reverse of 'inputs'", + description="reverse of 'inputs'", ), Property( "is_output_of", [ - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:output", + "output", reverse="outputs", multiple=True, - doc="reverse of 'outputs'", + description="reverse of 'outputs'", ), Property( "is_state_of", - "openminds.core.TissueSample", - "^vocab:studiedState", + "openminds.latest.core.TissueSample", + "studiedState", reverse="studied_states", multiple=True, - doc="reverse of 'studied_states'", + description="reverse of 'studied_states'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "used_in", [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", + "openminds.latest.specimen_prep.SlicingDeviceUsage", ], - "^vocab:usedSpecimen", + "usedSpecimen", reverse="used_specimen", multiple=True, - doc="reverse of 'used_specimen'", + description="reverse of 'used_specimen'", ), ] existence_query_properties = ("lookup_label",) @@ -160,7 +103,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/activity/cell_patching.py b/fairgraph/openminds/ephys/activity/cell_patching.py index a2355f0c..af1f7702 100644 --- a/fairgraph/openminds/ephys/activity/cell_patching.py +++ b/fairgraph/openminds/ephys/activity/cell_patching.py @@ -4,155 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import CellPatching +from fairgraph import KGObject from datetime import datetime, time -class CellPatching(KGObject): +class CellPatching(KGObject, CellPatching): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/CellPatching" - properties = [ - Property( - "bath_temperature", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:bathTemperature", - doc="no description available", - ), - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the cell patching.", - ), - Property( - "devices", - [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", - ], - "vocab:device", - multiple=True, - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - ["openminds.core.TissueSampleState", "openminds.core.SubjectState"], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - ["openminds.core.TissueSampleState", "openminds.core.SubjectState"], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property( - "target_position", - "openminds.sands.AnatomicalTargetPosition", - "vocab:targetPosition", - doc="no description available", - ), - Property( - "tissue_bath_solution", - "openminds.chemicals.ChemicalMixture", - "vocab:tissueBathSolution", - doc="no description available", - ), - Property( - "variation", - "openminds.controlled_terms.PatchClampVariation", - "vocab:variation", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("lookup_label",) @@ -180,7 +47,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/activity/electrode_placement.py b/fairgraph/openminds/ephys/activity/electrode_placement.py index fab90a0e..8410c417 100644 --- a/fairgraph/openminds/ephys/activity/electrode_placement.py +++ b/fairgraph/openminds/ephys/activity/electrode_placement.py @@ -4,137 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import ElectrodePlacement +from fairgraph import KGObject from datetime import datetime, time -class ElectrodePlacement(KGObject): +class ElectrodePlacement(KGObject, ElectrodePlacement): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/ElectrodePlacement" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the electrode placement.", - ), - Property( - "devices", - [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", - ], - "vocab:device", - multiple=True, - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - ["openminds.core.TissueSampleState", "openminds.core.SubjectState"], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - ["openminds.core.TissueSampleState", "openminds.core.SubjectState"], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property( - "target_position", - "openminds.sands.AnatomicalTargetPosition", - "vocab:targetPosition", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("lookup_label",) @@ -159,7 +44,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/activity/recording_activity.py b/fairgraph/openminds/ephys/activity/recording_activity.py index 6019d76f..e2050dd3 100644 --- a/fairgraph/openminds/ephys/activity/recording_activity.py +++ b/fairgraph/openminds/ephys/activity/recording_activity.py @@ -4,136 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import RecordingActivity +from fairgraph import KGObject from datetime import datetime, time -class RecordingActivity(KGObject): +class RecordingActivity(KGObject, RecordingActivity): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/RecordingActivity" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the recording activity.", - ), - Property( - "devices", - ["openminds.ephys.ElectrodeArrayUsage", "openminds.ephys.ElectrodeUsage", "openminds.ephys.PipetteUsage"], - "vocab:device", - multiple=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - [ - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the recording activity within a particular product.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - ["openminds.core.File", "openminds.core.FileBundle"], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("lookup_label",) @@ -158,7 +44,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/device/electrode.py b/fairgraph/openminds/ephys/device/electrode.py index 88b91c08..4bb59465 100644 --- a/fairgraph/openminds/ephys/device/electrode.py +++ b/fairgraph/openminds/ephys/device/electrode.py @@ -4,109 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import Electrode +from fairgraph import KGObject -class Electrode(KGObject): +class Electrode(KGObject, Electrode): """ Structured information on an electrode. """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/Electrode" - properties = [ - Property( - "conductor_material", - [ - "openminds.chemicals.ChemicalMixture", - "openminds.chemicals.ChemicalSubstance", - "openminds.controlled_terms.MolecularEntity", - ], - "vocab:conductorMaterial", - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the electrode.", - ), - Property( - "device_type", - "openminds.controlled_terms.DeviceType", - "vocab:deviceType", - required=True, - doc="no description available", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "insulator_material", - [ - "openminds.chemicals.ChemicalMixture", - "openminds.chemicals.ChemicalSubstance", - "openminds.controlled_terms.MolecularEntity", - ], - "vocab:insulatorMaterial", - doc="no description available", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the electrode within a particular product.", - ), - Property( - "intrinsic_resistance", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:intrinsicResistance", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "manufacturers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:manufacturer", - multiple=True, - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the electrode.", - ), - Property( - "owners", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:owner", - multiple=True, - doc="no description available", - ), - Property("serial_number", str, "vocab:serialNumber", doc="no description available"), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_part_of", - "openminds.core.Setup", - "^vocab:hasPart", + "openminds.latest.core.Setup", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "usage", - "openminds.ephys.ElectrodeUsage", - "^vocab:device", + "openminds.latest.ephys.ElectrodeUsage", + "device", reverse="device", multiple=True, - doc="reverse of 'device'", + description="reverse of 'device'", ), ] existence_query_properties = ("lookup_label",) @@ -132,7 +58,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/device/electrode_array.py b/fairgraph/openminds/ephys/device/electrode_array.py index 0c9041ae..2382ffac 100644 --- a/fairgraph/openminds/ephys/device/electrode_array.py +++ b/fairgraph/openminds/ephys/device/electrode_array.py @@ -4,120 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import ElectrodeArray +from fairgraph import KGObject -class ElectrodeArray(KGObject): +class ElectrodeArray(KGObject, ElectrodeArray): """ Structured information on an electrode array. """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/ElectrodeArray" - properties = [ - Property( - "conductor_material", - [ - "openminds.chemicals.ChemicalMixture", - "openminds.chemicals.ChemicalSubstance", - "openminds.controlled_terms.MolecularEntity", - ], - "vocab:conductorMaterial", - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the electrode array.", - ), - Property( - "device_type", - "openminds.controlled_terms.DeviceType", - "vocab:deviceType", - required=True, - doc="no description available", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "electrode_identifiers", - str, - "vocab:electrodeIdentifier", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "insulator_material", - [ - "openminds.chemicals.ChemicalMixture", - "openminds.chemicals.ChemicalSubstance", - "openminds.controlled_terms.MolecularEntity", - ], - "vocab:insulatorMaterial", - doc="no description available", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the electrode array within a particular product.", - ), - Property( - "intrinsic_resistance", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:intrinsicResistance", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "manufacturers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:manufacturer", - multiple=True, - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the electrode array.", - ), - Property( - "number_of_electrodes", int, "vocab:numberOfElectrodes", required=True, doc="no description available" - ), - Property( - "owners", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:owner", - multiple=True, - doc="no description available", - ), - Property("serial_number", str, "vocab:serialNumber", doc="no description available"), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_part_of", - "openminds.core.Setup", - "^vocab:hasPart", + "openminds.latest.core.Setup", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "usage", - "openminds.ephys.ElectrodeArrayUsage", - "^vocab:device", + "openminds.latest.ephys.ElectrodeArrayUsage", + "device", reverse="device", multiple=True, - doc="reverse of 'device'", + description="reverse of 'device'", ), ] existence_query_properties = ("lookup_label",) @@ -145,7 +60,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/device/electrode_array_usage.py b/fairgraph/openminds/ephys/device/electrode_array_usage.py index e59f0e4c..eb137225 100644 --- a/fairgraph/openminds/ephys/device/electrode_array_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_array_usage.py @@ -4,127 +4,59 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import ElectrodeArrayUsage +from fairgraph import KGObject -class ElectrodeArrayUsage(KGObject): +class ElectrodeArrayUsage(KGObject, ElectrodeArrayUsage): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/ElectrodeArrayUsage" - properties = [ - Property( - "anatomical_locations_of_arrays", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.UBERONParcellation", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:anatomicalLocationOfArray", - multiple=True, - doc="no description available", - ), - Property( - "anatomical_locations_of_electrodes", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.UBERONParcellation", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:anatomicalLocationOfElectrodes", - multiple=True, - doc="no description available", - ), - Property( - "contact_resistances", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:contactResistances", - multiple=True, - doc="no description available", - ), - Property( - "device", - "openminds.ephys.ElectrodeArray", - "vocab:device", - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "metadata_locations", - ["openminds.core.File", "openminds.core.FileBundle"], - "vocab:metadataLocation", - multiple=True, - doc="no description available", - ), - Property( - "spatial_locations_of_electrodes", - "openminds.sands.CoordinatePoint", - "vocab:spatialLocationOfElectrodes", - multiple=True, - doc="no description available", - ), - Property("used_electrodes", str, "vocab:usedElectrode", multiple=True, doc="no description available"), - Property( - "used_specimen", - ["openminds.core.SubjectState", "openminds.core.TissueSampleState"], - "vocab:usedSpecimen", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "generation_device", - "openminds.stimulation.EphysStimulus", - "^vocab:generatedBy", + "openminds.latest.stimulation.EphysStimulus", + "generatedBy", reverse="generated_by", multiple=True, - doc="reverse of 'generated_by'", + description="reverse of 'generated_by'", ), Property( "placed_by", - "openminds.ephys.ElectrodePlacement", - "^vocab:device", + "openminds.latest.ephys.ElectrodePlacement", + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_in", - ["openminds.ephys.CellPatching", "openminds.ephys.RecordingActivity"], - "^vocab:device", + ["openminds.latest.ephys.CellPatching", "openminds.latest.ephys.RecordingActivity"], + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_to_measure", - "openminds.core.Measurement", - "^vocab:measuredWith", + "openminds.latest.core.Measurement", + "measuredWith", reverse="measured_with", multiple=True, - doc="reverse of 'measured_with'", + description="reverse of 'measured_with'", ), Property( "used_to_record", - "openminds.ephys.Recording", - "^vocab:recordedWith", + "openminds.latest.ephys.Recording", + "recordedWith", reverse="recorded_with", multiple=True, - doc="reverse of 'recorded_with'", + description="reverse of 'recorded_with'", ), ] existence_query_properties = ("lookup_label",) @@ -150,7 +82,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/device/electrode_usage.py b/fairgraph/openminds/ephys/device/electrode_usage.py index 42636f5c..71d46cee 100644 --- a/fairgraph/openminds/ephys/device/electrode_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_usage.py @@ -4,107 +4,59 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import ElectrodeUsage +from fairgraph import KGObject -class ElectrodeUsage(KGObject): +class ElectrodeUsage(KGObject, ElectrodeUsage): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/ElectrodeUsage" - properties = [ - Property( - "anatomical_location", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.UBERONParcellation", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:anatomicalLocation", - doc="no description available", - ), - Property( - "contact_resistance", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:contactResistance", - doc="no description available", - ), - Property( - "device", - "openminds.ephys.Electrode", - "vocab:device", - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "metadata_locations", - ["openminds.core.File", "openminds.core.FileBundle"], - "vocab:metadataLocation", - multiple=True, - doc="no description available", - ), - Property( - "spatial_location", - "openminds.sands.CoordinatePoint", - "vocab:spatialLocation", - doc="no description available", - ), - Property( - "used_specimen", - ["openminds.core.SubjectState", "openminds.core.TissueSampleState"], - "vocab:usedSpecimen", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "generation_device", - "openminds.stimulation.EphysStimulus", - "^vocab:generatedBy", + "openminds.latest.stimulation.EphysStimulus", + "generatedBy", reverse="generated_by", multiple=True, - doc="reverse of 'generated_by'", + description="reverse of 'generated_by'", ), Property( "placed_by", - "openminds.ephys.ElectrodePlacement", - "^vocab:device", + "openminds.latest.ephys.ElectrodePlacement", + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_in", - ["openminds.ephys.CellPatching", "openminds.ephys.RecordingActivity"], - "^vocab:device", + ["openminds.latest.ephys.CellPatching", "openminds.latest.ephys.RecordingActivity"], + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_to_measure", - "openminds.core.Measurement", - "^vocab:measuredWith", + "openminds.latest.core.Measurement", + "measuredWith", reverse="measured_with", multiple=True, - doc="reverse of 'measured_with'", + description="reverse of 'measured_with'", ), Property( "used_to_record", - "openminds.ephys.Recording", - "^vocab:recordedWith", + "openminds.latest.ephys.Recording", + "recordedWith", reverse="recorded_with", multiple=True, - doc="reverse of 'recorded_with'", + description="reverse of 'recorded_with'", ), ] existence_query_properties = ("lookup_label",) @@ -128,7 +80,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/device/pipette.py b/fairgraph/openminds/ephys/device/pipette.py index 81037768..52be90db 100644 --- a/fairgraph/openminds/ephys/device/pipette.py +++ b/fairgraph/openminds/ephys/device/pipette.py @@ -4,105 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import Pipette +from fairgraph import KGObject -class Pipette(KGObject): +class Pipette(KGObject, Pipette): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/Pipette" - properties = [ - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the pipette.", - ), - Property( - "device_type", - "openminds.controlled_terms.DeviceType", - "vocab:deviceType", - required=True, - doc="no description available", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "external_diameter", - "openminds.core.QuantitativeValue", - "vocab:externalDiameter", - doc="no description available", - ), - Property( - "internal_diameter", - "openminds.core.QuantitativeValue", - "vocab:internalDiameter", - doc="no description available", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the pipette within a particular product.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "manufacturers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:manufacturer", - multiple=True, - doc="no description available", - ), - Property( - "material", - [ - "openminds.chemicals.ChemicalMixture", - "openminds.chemicals.ChemicalSubstance", - "openminds.controlled_terms.MolecularEntity", - ], - "vocab:material", - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the pipette.", - ), - Property( - "owners", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:owner", - multiple=True, - doc="no description available", - ), - Property("serial_number", str, "vocab:serialNumber", doc="no description available"), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_part_of", - "openminds.core.Setup", - "^vocab:hasPart", + "openminds.latest.core.Setup", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "usage", - "openminds.ephys.PipetteUsage", - "^vocab:device", + "openminds.latest.ephys.PipetteUsage", + "device", reverse="device", multiple=True, - doc="reverse of 'device'", + description="reverse of 'device'", ), ] existence_query_properties = ("lookup_label",) @@ -128,7 +58,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/device/pipette_usage.py b/fairgraph/openminds/ephys/device/pipette_usage.py index 7ec02172..c7ec325e 100644 --- a/fairgraph/openminds/ephys/device/pipette_usage.py +++ b/fairgraph/openminds/ephys/device/pipette_usage.py @@ -4,167 +4,59 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import PipetteUsage +from fairgraph import KGObject -class PipetteUsage(KGObject): +class PipetteUsage(KGObject, PipetteUsage): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/PipetteUsage" - properties = [ - Property( - "anatomical_location", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.UBERONParcellation", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:anatomicalLocation", - doc="no description available", - ), - Property( - "chloride_reversal_potentials", - "openminds.core.Measurement", - "vocab:chlorideReversalPotential", - multiple=True, - doc="no description available", - ), - Property( - "compensation_current", - "openminds.core.Measurement", - "vocab:compensationCurrent", - doc="no description available", - ), - Property( - "device", - "openminds.ephys.Pipette", - "vocab:device", - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property( - "end_membrane_potential", - "openminds.core.Measurement", - "vocab:endMembranePotential", - doc="no description available", - ), - Property( - "holding_potential", "openminds.core.Measurement", "vocab:holdingPotential", doc="no description available" - ), - Property( - "input_resistance", "openminds.core.Measurement", "vocab:inputResistance", doc="no description available" - ), - Property( - "labeling_compound", - [ - "openminds.chemicals.ChemicalMixture", - "openminds.chemicals.ChemicalSubstance", - "openminds.controlled_terms.MolecularEntity", - ], - "vocab:labelingCompound", - doc="no description available", - ), - Property( - "liquid_junction_potential", - "openminds.core.Measurement", - "vocab:liquidJunctionPotential", - doc="no description available", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "metadata_locations", - ["openminds.core.File", "openminds.core.FileBundle"], - "vocab:metadataLocation", - multiple=True, - doc="no description available", - ), - Property( - "pipette_resistance", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:pipetteResistance", - doc="no description available", - ), - Property( - "pipette_solution", - "openminds.chemicals.ChemicalMixture", - "vocab:pipetteSolution", - required=True, - doc="no description available", - ), - Property( - "seal_resistance", "openminds.core.Measurement", "vocab:sealResistance", doc="no description available" - ), - Property( - "series_resistance", "openminds.core.Measurement", "vocab:seriesResistance", doc="no description available" - ), - Property( - "spatial_location", - "openminds.sands.CoordinatePoint", - "vocab:spatialLocation", - doc="no description available", - ), - Property( - "start_membrane_potential", - "openminds.core.Measurement", - "vocab:startMembranePotential", - doc="no description available", - ), - Property( - "used_specimen", - ["openminds.core.SubjectState", "openminds.core.TissueSampleState"], - "vocab:usedSpecimen", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "generation_device", - "openminds.stimulation.EphysStimulus", - "^vocab:generatedBy", + "openminds.latest.stimulation.EphysStimulus", + "generatedBy", reverse="generated_by", multiple=True, - doc="reverse of 'generated_by'", + description="reverse of 'generated_by'", ), Property( "placed_by", - "openminds.ephys.ElectrodePlacement", - "^vocab:device", + "openminds.latest.ephys.ElectrodePlacement", + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_in", - ["openminds.ephys.CellPatching", "openminds.ephys.RecordingActivity"], - "^vocab:device", + ["openminds.latest.ephys.CellPatching", "openminds.latest.ephys.RecordingActivity"], + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_to_measure", - "openminds.core.Measurement", - "^vocab:measuredWith", + "openminds.latest.core.Measurement", + "measuredWith", reverse="measured_with", multiple=True, - doc="reverse of 'measured_with'", + description="reverse of 'measured_with'", ), Property( "used_to_record", - "openminds.ephys.Recording", - "^vocab:recordedWith", + "openminds.latest.ephys.Recording", + "recordedWith", reverse="recorded_with", multiple=True, - doc="reverse of 'recorded_with'", + description="reverse of 'recorded_with'", ), ] existence_query_properties = ("lookup_label",) @@ -199,7 +91,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/ephys/entity/channel.py b/fairgraph/openminds/ephys/entity/channel.py index 101c617a..0dfca3b1 100644 --- a/fairgraph/openminds/ephys/entity/channel.py +++ b/fairgraph/openminds/ephys/entity/channel.py @@ -4,33 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import Channel +from fairgraph import EmbeddedMetadata -class Channel(EmbeddedMetadata): +class Channel(EmbeddedMetadata, Channel): """ """ type_ = "https://openminds.ebrains.eu/ephys/Channel" - properties = [ - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - required=True, - doc="Term or code that identifies the channel within a particular product.", - ), - Property( - "unit", - "openminds.controlled_terms.UnitOfMeasurement", - "vocab:unit", - required=True, - doc="Determinate quantity adopted as a standard of measurement.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, internal_identifier=None, unit=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, internal_identifier=internal_identifier, unit=unit) + return EmbeddedMetadata.__init__(self, data=data, internal_identifier=internal_identifier, unit=unit) diff --git a/fairgraph/openminds/ephys/entity/recording.py b/fairgraph/openminds/ephys/entity/recording.py index 40ff0c81..2ce01c45 100644 --- a/fairgraph/openminds/ephys/entity/recording.py +++ b/fairgraph/openminds/ephys/entity/recording.py @@ -4,85 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.ephys import Recording +from fairgraph import KGObject -class Recording(KGObject): +class Recording(KGObject, Recording): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/ephys/Recording" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "channels", - "openminds.ephys.Channel", - "vocab:channel", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "data_location", - ["openminds.core.File", "openminds.core.FileBundle"], - "vocab:dataLocation", - required=True, - doc="no description available", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the recording within a particular product.", - ), - Property( - "name", - str, - "vocab:name", - doc="Word or phrase that constitutes the distinctive designation of the recording.", - ), - Property( - "previous_recording", - "openminds.ephys.Recording", - "vocab:previousRecording", - doc="no description available", - ), - Property( - "recorded_with", - [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", - ], - "vocab:recordedWith", - required=True, - doc="no description available", - ), - Property( - "sampling_frequency", - "openminds.core.QuantitativeValue", - "vocab:samplingFrequency", - required=True, - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "next_recording", - "openminds.ephys.Recording", - "^vocab:previousRecording", + "openminds.latest.ephys.Recording", + "previousRecording", reverse="previous_recording", multiple=True, - doc="reverse of 'previous_recording'", + description="reverse of 'previous_recording'", ), ] existence_query_properties = ("channels", "data_location", "recorded_with", "sampling_frequency") @@ -103,7 +45,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/book.py b/fairgraph/openminds/publications/book.py index 8d69a52d..99a36892 100644 --- a/fairgraph/openminds/publications/book.py +++ b/fairgraph/openminds/publications/book.py @@ -4,215 +4,50 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import Book +from fairgraph import KGObject from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class Book(KGObject): +class Book(KGObject, Book): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/Book" - properties = [ - Property("abstract", str, "vocab:abstract", doc="no description available"), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "cited_publications", - ["openminds.core.DOI", "openminds.core.ISBN"], - "vocab:citedPublication", - multiple=True, - doc="no description available", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property("creation_date", date, "vocab:creationDate", doc="no description available"), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.ISBN"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("editors", "openminds.core.Person", "vocab:editor", multiple=True, doc="no description available"), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the book.", - ), - Property( - "license", - "openminds.core.License", - "vocab:license", - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property("modification_date", date, "vocab:modificationDate", doc="no description available"), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the book.", - ), - Property("publication_date", date, "vocab:publicationDate", required=True, doc="no description available"), - Property( - "publisher", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:publisher", - doc="no description available", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - doc="Term or code used to identify the version of something.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_parts", - "openminds.publications.Chapter", - "^vocab:isPartOf", + "openminds.latest.publications.Chapter", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), Property( "related_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:relatedPublication", + "relatedPublication", reverse="related_publications", multiple=True, - doc="reverse of 'related_publications'", + description="reverse of 'related_publications'", ), ] existence_query_properties = ("name", "publication_date") @@ -243,7 +78,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/chapter.py b/fairgraph/openminds/publications/chapter.py index fdcc416c..1cc1f737 100644 --- a/fairgraph/openminds/publications/chapter.py +++ b/fairgraph/openminds/publications/chapter.py @@ -4,216 +4,42 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import Chapter +from fairgraph import KGObject from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class Chapter(KGObject): +class Chapter(KGObject, Chapter): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/Chapter" - properties = [ - Property("abstract", str, "vocab:abstract", doc="no description available"), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - required=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "cited_publications", - ["openminds.core.DOI", "openminds.core.ISBN"], - "vocab:citedPublication", - multiple=True, - doc="no description available", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property("creation_date", date, "vocab:creationDate", doc="no description available"), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("editors", "openminds.core.Person", "vocab:editor", multiple=True, doc="no description available"), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "is_part_of", - "openminds.publications.Book", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the chapter.", - ), - Property( - "license", - "openminds.core.License", - "vocab:license", - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property("modification_date", date, "vocab:modificationDate", doc="no description available"), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the chapter.", - ), - Property("pagination", str, "vocab:pagination", doc="no description available"), - Property("publication_date", date, "vocab:publicationDate", required=True, doc="no description available"), - Property( - "publisher", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:publisher", - doc="no description available", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - doc="Term or code used to identify the version of something.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "related_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:relatedPublication", + "relatedPublication", reverse="related_publications", multiple=True, - doc="reverse of 'related_publications'", + description="reverse of 'related_publications'", ), ] existence_query_properties = ("authors", "is_part_of", "name", "publication_date") @@ -245,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/learning_resource.py b/fairgraph/openminds/publications/learning_resource.py index 3dc91195..ee3aeb0a 100644 --- a/fairgraph/openminds/publications/learning_resource.py +++ b/fairgraph/openminds/publications/learning_resource.py @@ -4,239 +4,23 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import LearningResource +from fairgraph import KGObject from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class LearningResource(KGObject): +class LearningResource(KGObject, LearningResource): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/LearningResource" - properties = [ - Property( - "about", - [ - "openminds.computation.ValidationTest", - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipe", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.Dataset", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModel", - "openminds.core.MetaDataModelVersion", - "openminds.core.Model", - "openminds.core.ModelVersion", - "openminds.core.Software", - "openminds.core.SoftwareVersion", - "openminds.core.WebService", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaper", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlas", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpace", - "openminds.sands.CommonCoordinateSpaceVersion", - ], - "vocab:about", - multiple=True, - required=True, - doc="no description available", - ), - Property("abstract", str, "vocab:abstract", doc="no description available"), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "cited_publications", - ["openminds.core.DOI", "openminds.core.ISBN"], - "vocab:citedPublication", - multiple=True, - doc="no description available", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property("creation_date", date, "vocab:creationDate", doc="no description available"), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("editors", "openminds.core.Person", "vocab:editor", multiple=True, doc="no description available"), - Property( - "educational_level", - "openminds.controlled_terms.EducationalLevel", - "vocab:educationalLevel", - doc="no description available", - ), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the learning resource.", - ), - Property("learning_outcome", str, "vocab:learningOutcome", doc="no description available"), - Property( - "license", - "openminds.core.License", - "vocab:license", - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property("modification_date", date, "vocab:modificationDate", doc="no description available"), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the learning resource.", - ), - Property("order", int, "vocab:order", doc="no description available"), - Property("prerequisite", str, "vocab:prerequisite", doc="no description available"), - Property("publication_date", date, "vocab:publicationDate", required=True, doc="no description available"), - Property( - "publisher", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:publisher", - doc="no description available", - ), - Property( - "required_time", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:requiredTime", - doc="no description available", - ), - Property("topic", str, "vocab:topic", doc="no description available"), - Property( - "type", - "openminds.controlled_terms.LearningResourceType", - "vocab:type", - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - doc="Term or code used to identify the version of something.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("about", "name", "publication_date") @@ -272,7 +56,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/live_paper.py b/fairgraph/openminds/publications/live_paper.py index c1a2b331..acb327de 100644 --- a/fairgraph/openminds/publications/live_paper.py +++ b/fairgraph/openminds/publications/live_paper.py @@ -4,99 +4,46 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import LivePaper +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class LivePaper(KGObject): +class LivePaper(KGObject, LivePaper): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/LivePaper" - properties = [ - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - required=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the live paper.", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the live paper." - ), - Property( - "has_versions", - "openminds.publications.LivePaperVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the live paper."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the live paper.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -124,7 +71,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/live_paper_resource_item.py b/fairgraph/openminds/publications/live_paper_resource_item.py index 39a1a937..e6f9f413 100644 --- a/fairgraph/openminds/publications/live_paper_resource_item.py +++ b/fairgraph/openminds/publications/live_paper_resource_item.py @@ -4,58 +4,30 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import LivePaperResourceItem +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class LivePaperResourceItem(KGObject): +class LivePaperResourceItem(KGObject, LivePaperResourceItem): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/LivePaperResourceItem" - properties = [ - Property( - "hosted_by", - ["openminds.core.Organization", "openminds.core.WebService", "openminds.controlled_terms.Service"], - "vocab:hostedBy", - required=True, - doc="Reference to an organization that provides facilities and services for something.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - required=True, - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "is_part_of", - "openminds.publications.LivePaperSection", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the live paper resource item.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_location_of", - "openminds.core.ServiceLink", - "^vocab:dataLocation", + "openminds.latest.core.ServiceLink", + "dataLocation", reverse="data_location", multiple=True, - doc="reverse of 'data_location'", + description="reverse of 'data_location'", ), ] existence_query_properties = ("name", "iri", "is_part_of") @@ -72,7 +44,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/live_paper_section.py b/fairgraph/openminds/publications/live_paper_section.py index aa3556a8..062b60f0 100644 --- a/fairgraph/openminds/publications/live_paper_section.py +++ b/fairgraph/openminds/publications/live_paper_section.py @@ -4,55 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import LivePaperSection +from fairgraph import KGObject -class LivePaperSection(KGObject): +class LivePaperSection(KGObject, LivePaperSection): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/LivePaperSection" - properties = [ - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the live paper section.", - ), - Property( - "is_part_of", - "openminds.publications.LivePaperVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the live paper section.", - ), - Property("order", int, "vocab:order", required=True, doc="no description available"), - Property( - "type", - str, - "vocab:type", - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_parts", - "openminds.publications.LivePaperResourceItem", - "^vocab:isPartOf", + "openminds.latest.publications.LivePaperResourceItem", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), ] existence_query_properties = ("is_part_of", "name", "order", "type") @@ -70,7 +42,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/live_paper_version.py b/fairgraph/openminds/publications/live_paper_version.py index 9123f1da..19da490a 100644 --- a/fairgraph/openminds/publications/live_paper_version.py +++ b/fairgraph/openminds/publications/live_paper_version.py @@ -4,315 +4,73 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import LivePaperVersion +from fairgraph import KGObject from fairgraph.errors import ResolutionFailure from .live_paper import LivePaper from datetime import date from datetime import datetime -from fairgraph.base import IRI +from openminds import IRI -class LivePaperVersion(KGObject): +class LivePaperVersion(KGObject, LivePaperVersion): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/LivePaperVersion" - properties = [ - Property( - "about", - ["openminds.core.DatasetVersion", "openminds.core.ModelVersion", "openminds.core.SoftwareVersion"], - "vocab:about", - multiple=True, - doc="no description available", - ), - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the live paper version.", - ), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the live paper version.", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - required=True, - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property("full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the live paper version."), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the live paper version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "is_alternative_version_of", - "openminds.publications.LivePaperVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.publications.LivePaperVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the live paper version.", - ), - Property( - "license", - "openminds.core.License", - "vocab:license", - required=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property("modification_date", datetime, "vocab:modificationDate", doc="no description available"), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the live paper version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "has_parts", - "openminds.publications.LivePaperSection", - "^vocab:isPartOf", + "openminds.latest.publications.LivePaperSection", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), Property( "is_old_version_of", - "openminds.publications.LivePaperVersion", - "^vocab:isNewVersionOf", + "openminds.latest.publications.LivePaperVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.publications.LivePaper", - "^vocab:hasVersion", + "openminds.latest.publications.LivePaper", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -358,7 +116,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/periodical.py b/fairgraph/openminds/publications/periodical.py index 00301997..a57769c1 100644 --- a/fairgraph/openminds/publications/periodical.py +++ b/fairgraph/openminds/publications/periodical.py @@ -4,41 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import Periodical +from fairgraph import KGObject -class Periodical(KGObject): +class Periodical(KGObject, Periodical): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/Periodical" - properties = [ - Property("abbreviation", str, "vocab:abbreviation", doc="no description available"), - Property( - "digital_identifier", - "openminds.core.ISSN", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the periodical.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_parts", - "openminds.publications.PublicationVolume", - "^vocab:isPartOf", + "openminds.latest.publications.PublicationVolume", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), ] existence_query_properties = ("abbreviation",) @@ -54,7 +40,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/publication_issue.py b/fairgraph/openminds/publications/publication_issue.py index 3db06256..62eb40b7 100644 --- a/fairgraph/openminds/publications/publication_issue.py +++ b/fairgraph/openminds/publications/publication_issue.py @@ -4,41 +4,34 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import PublicationIssue +from fairgraph import KGObject -class PublicationIssue(KGObject): +class PublicationIssue(KGObject, PublicationIssue): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/PublicationIssue" - properties = [ - Property( - "is_part_of", - "openminds.publications.PublicationVolume", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("issue_number", str, "vocab:issueNumber", required=True, doc="no description available"), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_parts", - "openminds.publications.ScholarlyArticle", - "^vocab:isPartOf", + "openminds.latest.publications.ScholarlyArticle", + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), ] existence_query_properties = ("is_part_of", "issue_number") def __init__(self, has_parts=None, is_part_of=None, issue_number=None, id=None, data=None, space=None, scope=None): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/publication_volume.py b/fairgraph/openminds/publications/publication_volume.py index 607ad6d4..529ac5af 100644 --- a/fairgraph/openminds/publications/publication_volume.py +++ b/fairgraph/openminds/publications/publication_volume.py @@ -4,35 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import PublicationVolume +from fairgraph import KGObject -class PublicationVolume(KGObject): +class PublicationVolume(KGObject, PublicationVolume): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/PublicationVolume" - properties = [ - Property( - "is_part_of", - "openminds.publications.Periodical", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("volume_number", str, "vocab:volumeNumber", required=True, doc="no description available"), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_parts", - ["openminds.publications.PublicationIssue", "openminds.publications.ScholarlyArticle"], - "^vocab:isPartOf", + ["openminds.latest.publications.PublicationIssue", "openminds.latest.publications.ScholarlyArticle"], + "isPartOf", reverse="is_part_of", multiple=True, - doc="reverse of 'is_part_of'", + description="reverse of 'is_part_of'", ), ] existence_query_properties = ("is_part_of", "volume_number") @@ -40,7 +32,8 @@ class PublicationVolume(KGObject): def __init__( self, has_parts=None, is_part_of=None, volume_number=None, id=None, data=None, space=None, scope=None ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/publications/scholarly_article.py b/fairgraph/openminds/publications/scholarly_article.py index dfc5e7b7..38236b19 100644 --- a/fairgraph/openminds/publications/scholarly_article.py +++ b/fairgraph/openminds/publications/scholarly_article.py @@ -4,218 +4,44 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.publications import ScholarlyArticle +from fairgraph import KGObject from fairgraph.utility import as_list from .publication_issue import PublicationIssue from .periodical import Periodical from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class ScholarlyArticle(KGObject): +class ScholarlyArticle(KGObject, ScholarlyArticle): """ """ - default_space = "livepapers" type_ = "https://openminds.ebrains.eu/publications/ScholarlyArticle" - properties = [ - Property("abstract", str, "vocab:abstract", doc="no description available"), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - required=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "cited_publications", - ["openminds.core.DOI", "openminds.core.ISBN"], - "vocab:citedPublication", - multiple=True, - doc="no description available", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property("creation_date", date, "vocab:creationDate", doc="no description available"), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "digital_identifier", - "openminds.core.DOI", - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("editors", "openminds.core.Person", "vocab:editor", multiple=True, doc="no description available"), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "iri", - IRI, - "vocab:IRI", - doc="Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.", - ), - Property( - "is_part_of", - ["openminds.publications.PublicationIssue", "openminds.publications.PublicationVolume"], - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the scholarly article.", - ), - Property( - "license", - "openminds.core.License", - "vocab:license", - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property("modification_date", date, "vocab:modificationDate", doc="no description available"), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the scholarly article.", - ), - Property("pagination", str, "vocab:pagination", doc="no description available"), - Property("publication_date", date, "vocab:publicationDate", required=True, doc="no description available"), - Property( - "publisher", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:publisher", - doc="no description available", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - doc="Term or code used to identify the version of something.", - ), - ] + default_space = "livepapers" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "related_to", [ - "openminds.computation.ValidationTestVersion", - "openminds.computation.WorkflowRecipeVersion", - "openminds.core.DatasetVersion", - "openminds.core.MetaDataModelVersion", - "openminds.core.ModelVersion", - "openminds.core.SoftwareVersion", - "openminds.core.WebServiceVersion", - "openminds.publications.LivePaperVersion", - "openminds.sands.BrainAtlasVersion", - "openminds.sands.CommonCoordinateSpaceVersion", + "openminds.latest.computation.ValidationTestVersion", + "openminds.latest.computation.WorkflowRecipeVersion", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.MetaDataModelVersion", + "openminds.latest.core.ModelVersion", + "openminds.latest.core.SoftwareVersion", + "openminds.latest.core.WebServiceVersion", + "openminds.latest.publications.LivePaperVersion", + "openminds.latest.sands.BrainAtlasVersion", + "openminds.latest.sands.CommonCoordinateSpaceVersion", ], - "^vocab:relatedPublication", + "relatedPublication", reverse="related_publications", multiple=True, - doc="reverse of 'related_publications'", + description="reverse of 'related_publications'", ), ] existence_query_properties = ("name",) @@ -247,7 +73,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/atlas/atlas_annotation.py b/fairgraph/openminds/sands/atlas/atlas_annotation.py index c44018f8..e78a6787 100644 --- a/fairgraph/openminds/sands/atlas/atlas_annotation.py +++ b/fairgraph/openminds/sands/atlas/atlas_annotation.py @@ -4,84 +4,18 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import AtlasAnnotation +from fairgraph import EmbeddedMetadata -class AtlasAnnotation(EmbeddedMetadata): +class AtlasAnnotation(EmbeddedMetadata, AtlasAnnotation): """ """ type_ = "https://openminds.ebrains.eu/sands/AtlasAnnotation" - properties = [ - Property( - "anchor_points", - "openminds.core.QuantitativeValue", - "vocab:anchorPoint", - multiple=True, - doc="no description available", - ), - Property( - "criteria", - "openminds.core.ProtocolExecution", - "vocab:criteria", - doc="Aspects or standards on which a judgement or decision is based.", - ), - Property( - "criteria_quality_type", - "openminds.controlled_terms.CriteriaQualityType", - "vocab:criteriaQualityType", - required=True, - doc="Distinct class that defines how the judgement or decision was made for a particular criteria.", - ), - Property( - "criteria_type", - "openminds.controlled_terms.AnnotationCriteriaType", - "vocab:criteriaType", - required=True, - doc="no description available", - ), - Property( - "inspired_by", - "openminds.core.File", - "vocab:inspiredBy", - multiple=True, - doc="Reference to an inspiring element.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the atlas annotation within a particular product.", - ), - Property( - "lateralities", - "openminds.controlled_terms.Laterality", - "vocab:laterality", - multiple=True, - doc="Differentiation between a pair of lateral homologous parts of the body.", - ), - Property( - "preferred_visualization", - "openminds.sands.ViewerSpecification", - "vocab:preferredVisualization", - doc="no description available", - ), - Property( - "specification", - "openminds.core.File", - "vocab:specification", - doc="Detailed and precise presentation of, or proposal for something.", - ), - Property( - "type", - "openminds.controlled_terms.AnnotationType", - "vocab:type", - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -101,7 +35,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, anchor_points=anchor_points, criteria=criteria, diff --git a/fairgraph/openminds/sands/atlas/brain_atlas.py b/fairgraph/openminds/sands/atlas/brain_atlas.py index 7e722978..982815e0 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas.py @@ -4,124 +4,54 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import BrainAtlas +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class BrainAtlas(KGObject): +class BrainAtlas(KGObject, BrainAtlas): """ """ - default_space = "atlas" type_ = "https://openminds.ebrains.eu/sands/BrainAtlas" - properties = [ - Property("abbreviation", str, "vocab:abbreviation", doc="no description available"), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - required=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the brain atlas.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.ISBN", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", str, "vocab:fullName", required=True, doc="Whole, non-abbreviated name of the brain atlas." - ), - Property( - "has_terminology", - "openminds.sands.ParcellationTerminology", - "vocab:hasTerminology", - required=True, - doc="no description available", - ), - Property( - "has_versions", - "openminds.sands.BrainAtlasVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the brain atlas."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "ontology_identifier", - IRI, - "vocab:ontologyIdentifier", - doc="Term or code used to identify the brain atlas registered within a particular ontology.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the brain atlas.", - ), - Property( - "used_species", "openminds.controlled_terms.Species", "vocab:usedSpecies", doc="no description available" - ), - ] + default_space = "atlas" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_input_to", - "openminds.core.DatasetVersion", - "^vocab:inputData", + "openminds.latest.core.DatasetVersion", + "inputData", reverse="input_data", multiple=True, - doc="reverse of 'input_data'", + description="reverse of 'input_data'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -154,7 +84,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/atlas/brain_atlas_version.py b/fairgraph/openminds/sands/atlas/brain_atlas_version.py index 84019085..7ba7488b 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas_version.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas_version.py @@ -4,348 +4,79 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import BrainAtlasVersion +from fairgraph import KGObject from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class BrainAtlasVersion(KGObject): +class BrainAtlasVersion(KGObject, BrainAtlasVersion): """ """ - default_space = "atlas" type_ = "https://openminds.ebrains.eu/sands/BrainAtlasVersion" - properties = [ - Property("abbreviation", str, "vocab:abbreviation", doc="no description available"), - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the brain atlas version.", - ), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "coordinate_space", - "openminds.sands.CommonCoordinateSpaceVersion", - "vocab:coordinateSpace", - required=True, - doc="Two or three dimensional geometric setting.", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the brain atlas version.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.ISBN", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property("full_name", str, "vocab:fullName", doc="Whole, non-abbreviated name of the brain atlas version."), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property( - "has_terminology", - "openminds.sands.ParcellationTerminologyVersion", - "vocab:hasTerminology", - required=True, - doc="no description available", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the brain atlas version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "is_alternative_version_of", - "openminds.sands.BrainAtlasVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.sands.BrainAtlasVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the brain atlas version.", - ), - Property( - "license", - "openminds.core.License", - "vocab:license", - required=True, - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property("major_version_identifier", str, "vocab:majorVersionIdentifier", doc="no description available"), - Property( - "ontology_identifier", - IRI, - "vocab:ontologyIdentifier", - doc="Term or code used to identify the brain atlas version registered within a particular ontology.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the brain atlas version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "type", - "openminds.controlled_terms.AtlasType", - "vocab:type", - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - Property( - "used_specimens", - [ - "openminds.core.Subject", - "openminds.core.SubjectGroup", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - ], - "vocab:usedSpecimen", - multiple=True, - doc="no description available", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "atlas" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_input_to", [ - "openminds.computation.DataAnalysis", - "openminds.core.DatasetVersion", - "openminds.core.ProtocolExecution", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.ProtocolExecution", ], - ["^vocab:input", "^vocab:inputData"], + ["input", "inputData"], reverse=["input_data", "inputs"], multiple=True, - doc="reverse of input_data, inputs", + description="reverse of input_data, inputs", ), Property( "is_old_version_of", - "openminds.sands.BrainAtlasVersion", - "^vocab:isNewVersionOf", + "openminds.latest.sands.BrainAtlasVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup", "openminds.core.SoftwareVersion"], - "^vocab:hasPart", + [ + "openminds.latest.core.Project", + "openminds.latest.core.ResearchProductGroup", + "openminds.latest.core.SoftwareVersion", + ], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_version_of", - "openminds.sands.BrainAtlas", - "^vocab:hasVersion", + "openminds.latest.sands.BrainAtlas", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -396,7 +127,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space.py b/fairgraph/openminds/sands/atlas/common_coordinate_space.py index a1e85f6f..519fdeae 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space.py @@ -4,133 +4,62 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import CommonCoordinateSpace +from fairgraph import KGObject -from fairgraph.base import IRI +from openminds import IRI -class CommonCoordinateSpace(KGObject): +class CommonCoordinateSpace(KGObject, CommonCoordinateSpace): """ """ - default_space = "atlas" type_ = "https://openminds.ebrains.eu/sands/CommonCoordinateSpace" - properties = [ - Property("abbreviation", str, "vocab:abbreviation", doc="no description available"), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "description", - str, - "vocab:description", - required=True, - doc="Longer statement or account giving the characteristics of the common coordinate space.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.ISBN", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_name", - str, - "vocab:fullName", - required=True, - doc="Whole, non-abbreviated name of the common coordinate space.", - ), - Property( - "has_versions", - "openminds.sands.CommonCoordinateSpaceVersion", - "vocab:hasVersion", - multiple=True, - required=True, - doc="Reference to variants of an original.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the common coordinate space."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "ontology_identifiers", - str, - "vocab:ontologyIdentifier", - multiple=True, - doc="Term or code used to identify the common coordinate space registered within a particular ontology.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the common coordinate space.", - ), - Property( - "used_species", - "openminds.controlled_terms.Species", - "vocab:usedSpecies", - required=True, - doc="no description available", - ), - ] + default_space = "atlas" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_input_to", - "openminds.core.DatasetVersion", - "^vocab:inputData", + "openminds.latest.core.DatasetVersion", + "inputData", reverse="input_data", multiple=True, - doc="reverse of 'input_data'", + description="reverse of 'input_data'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup"], - "^vocab:hasPart", + ["openminds.latest.core.Project", "openminds.latest.core.ResearchProductGroup"], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} @@ -163,7 +92,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py index 2cdbf49d..3bdcef11 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py @@ -4,377 +4,95 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import CommonCoordinateSpaceVersion +from fairgraph import KGObject from datetime import date -from fairgraph.base import IRI +from openminds import IRI -class CommonCoordinateSpaceVersion(KGObject): +class CommonCoordinateSpaceVersion(KGObject, CommonCoordinateSpaceVersion): """ """ - default_space = "atlas" type_ = "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion" - properties = [ - Property("abbreviation", str, "vocab:abbreviation", doc="no description available"), - Property( - "accessibility", - "openminds.controlled_terms.ProductAccessibility", - "vocab:accessibility", - required=True, - doc="Level to which something is accessible to the common coordinate space version.", - ), - Property( - "anatomical_axes_orientation", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "vocab:anatomicalAxesOrientation", - required=True, - doc="Relation between reference planes used in anatomy and mathematics.", - ), - Property( - "authors", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:author", - multiple=True, - doc="Creator of a literary or creative work, as well as a dataset publication.", - ), - Property( - "axes_origins", - "openminds.core.QuantitativeValue", - "vocab:axesOrigin", - multiple=True, - required=True, - doc="Special point in a coordinate system used as a fixed point of reference for the geometry of the surrounding space.", - ), - Property( - "copyright", - "openminds.core.Copyright", - "vocab:copyright", - doc="Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.", - ), - Property( - "custodians", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:custodian", - multiple=True, - doc="The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.", - ), - Property( - "default_images", - "openminds.core.File", - "vocab:defaultImage", - multiple=True, - doc="Two or three dimensional image that particluarly represents a specific coordinate space.", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the common coordinate space version.", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.ISBN", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property( - "full_documentation", - ["openminds.core.DOI", "openminds.core.File", "openminds.core.ISBN", "openminds.core.WebResource"], - "vocab:fullDocumentation", - required=True, - doc="Non-abridged instructions, comments, and information for using a particular product.", - ), - Property( - "full_name", - str, - "vocab:fullName", - doc="Whole, non-abbreviated name of the common coordinate space version.", - ), - Property( - "funding", - "openminds.core.Funding", - "vocab:funding", - multiple=True, - doc="Money provided by a legal person for a particular purpose.", - ), - Property("homepage", IRI, "vocab:homepage", doc="Main website of the common coordinate space version."), - Property( - "how_to_cite", - str, - "vocab:howToCite", - doc="Preferred format for citing a particular object or legal person.", - ), - Property( - "is_alternative_version_of", - "openminds.sands.CommonCoordinateSpaceVersion", - "vocab:isAlternativeVersionOf", - multiple=True, - doc="Reference to an original form where the essence was preserved, but presented in an alternative form.", - ), - Property( - "is_new_version_of", - "openminds.sands.CommonCoordinateSpaceVersion", - "vocab:isNewVersionOf", - doc="Reference to a previous (potentially outdated) particular form of something.", - ), - Property( - "keywords", - [ - "openminds.controlled_terms.ActionStatusType", - "openminds.controlled_terms.AgeCategory", - "openminds.controlled_terms.AnalysisTechnique", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "openminds.controlled_terms.AnatomicalIdentificationType", - "openminds.controlled_terms.AnatomicalPlane", - "openminds.controlled_terms.AnnotationCriteriaType", - "openminds.controlled_terms.AnnotationType", - "openminds.controlled_terms.AtlasType", - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalProcess", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.ChemicalMixtureType", - "openminds.controlled_terms.Colormap", - "openminds.controlled_terms.ContributionType", - "openminds.controlled_terms.CranialWindowConstructionType", - "openminds.controlled_terms.CranialWindowReinforcementType", - "openminds.controlled_terms.CriteriaQualityType", - "openminds.controlled_terms.DataType", - "openminds.controlled_terms.DeviceType", - "openminds.controlled_terms.DifferenceMeasure", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.EducationalLevel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.EthicsAssessment", - "openminds.controlled_terms.ExperimentalApproach", - "openminds.controlled_terms.FileBundleGrouping", - "openminds.controlled_terms.FileRepositoryType", - "openminds.controlled_terms.FileUsageRole", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.Language", - "openminds.controlled_terms.Laterality", - "openminds.controlled_terms.LearningResourceType", - "openminds.controlled_terms.MRAcquisitionType", - "openminds.controlled_terms.MRIPulseSequence", - "openminds.controlled_terms.MRIWeighting", - "openminds.controlled_terms.MeasuredQuantity", - "openminds.controlled_terms.MeasuredSignalType", - "openminds.controlled_terms.MetaDataModelType", - "openminds.controlled_terms.ModelAbstractionLevel", - "openminds.controlled_terms.ModelScope", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OperatingDevice", - "openminds.controlled_terms.OperatingSystem", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.PatchClampVariation", - "openminds.controlled_terms.PreparationType", - "openminds.controlled_terms.ProductAccessibility", - "openminds.controlled_terms.ProgrammingLanguage", - "openminds.controlled_terms.QualitativeOverlap", - "openminds.controlled_terms.SemanticDataType", - "openminds.controlled_terms.Service", - "openminds.controlled_terms.SetupType", - "openminds.controlled_terms.SoftwareApplicationCategory", - "openminds.controlled_terms.SoftwareFeature", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.StimulationApproach", - "openminds.controlled_terms.StimulationTechnique", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.SubjectAttribute", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.Technique", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.Terminology", - "openminds.controlled_terms.TissueSampleAttribute", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.TypeOfUncertainty", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.UnitOfMeasurement", - "openminds.controlled_terms.VisualStimulusType", - ], - "vocab:keyword", - multiple=True, - doc="Significant word or concept that are representative of the common coordinate space version.", - ), - Property( - "license", - "openminds.core.License", - "vocab:license", - doc="Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.", - ), - Property( - "native_unit", - "openminds.controlled_terms.UnitOfMeasurement", - "vocab:nativeUnit", - required=True, - doc="Determinate quantity used in the original measurement.", - ), - Property( - "ontology_identifiers", - str, - "vocab:ontologyIdentifier", - multiple=True, - doc="Term or code used to identify the common coordinate space version registered within a particular ontology.", - ), - Property( - "other_contributions", - "openminds.core.Contribution", - "vocab:otherContribution", - multiple=True, - doc="Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.", - ), - Property( - "related_publications", - [ - "openminds.core.DOI", - "openminds.core.HANDLE", - "openminds.core.ISBN", - "openminds.core.ISSN", - "openminds.publications.Book", - "openminds.publications.Chapter", - "openminds.publications.ScholarlyArticle", - ], - "vocab:relatedPublication", - multiple=True, - doc="Reference to something that was made available for the general public to see or buy.", - ), - Property( - "release_date", - date, - "vocab:releaseDate", - required=True, - doc="Fixed date on which a product is due to become or was made available for the general public to see or buy", - ), - Property( - "repository", - "openminds.core.FileRepository", - "vocab:repository", - doc="Place, room, or container where something is deposited or stored.", - ), - Property( - "short_name", - str, - "vocab:shortName", - required=True, - doc="Shortened or fully abbreviated name of the common coordinate space version.", - ), - Property( - "support_channels", - str, - "vocab:supportChannel", - multiple=True, - doc="Way of communication used to interact with users or customers.", - ), - Property( - "used_specimens", - [ - "openminds.core.Subject", - "openminds.core.SubjectGroup", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - ], - "vocab:usedSpecimen", - multiple=True, - doc="no description available", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - required=True, - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "atlas" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "comments", - "openminds.core.Comment", - "^vocab:about", + "openminds.latest.core.Comment", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), Property( "is_coordinate_space_of", - ["openminds.sands.BrainAtlasVersion", "openminds.sands.CustomAnnotation"], - "^vocab:coordinateSpace", + ["openminds.latest.sands.BrainAtlasVersion", "openminds.latest.sands.CustomAnnotation"], + "coordinateSpace", reverse="coordinate_space", multiple=True, - doc="reverse of 'coordinate_space'", + description="reverse of 'coordinate_space'", ), Property( "is_input_to", [ - "openminds.computation.DataAnalysis", - "openminds.core.DatasetVersion", - "openminds.core.ProtocolExecution", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.ProtocolExecution", ], - ["^vocab:input", "^vocab:inputData"], + ["input", "inputData"], reverse=["input_data", "inputs"], multiple=True, - doc="reverse of input_data, inputs", + description="reverse of input_data, inputs", ), Property( "is_old_version_of", - "openminds.sands.CommonCoordinateSpaceVersion", - "^vocab:isNewVersionOf", + "openminds.latest.sands.CommonCoordinateSpaceVersion", + "isNewVersionOf", reverse="is_new_version_of", multiple=True, - doc="reverse of 'is_new_version_of'", + description="reverse of 'is_new_version_of'", ), Property( "is_part_of", - ["openminds.core.Project", "openminds.core.ResearchProductGroup", "openminds.core.SoftwareVersion"], - "^vocab:hasPart", + [ + "openminds.latest.core.Project", + "openminds.latest.core.ResearchProductGroup", + "openminds.latest.core.SoftwareVersion", + ], + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "is_version_of", - "openminds.sands.CommonCoordinateSpace", - "^vocab:hasVersion", + "openminds.latest.sands.CommonCoordinateSpace", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "learning_resources", - "openminds.publications.LearningResource", - "^vocab:about", + "openminds.latest.publications.LearningResource", + "about", reverse="about", multiple=True, - doc="reverse of 'about'", + description="reverse of 'about'", ), ] aliases = {"name": "full_name", "alias": "short_name"} @@ -437,7 +155,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity.py b/fairgraph/openminds/sands/atlas/parcellation_entity.py index d3279917..6a0664d1 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity.py @@ -4,127 +4,84 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import ParcellationEntity +from fairgraph import KGObject -class ParcellationEntity(KGObject): +class ParcellationEntity(KGObject, ParcellationEntity): """ """ - default_space = "atlas" type_ = "https://openminds.ebrains.eu/sands/ParcellationEntity" - properties = [ - Property("abbreviation", str, "vocab:abbreviation", doc="no description available"), - Property("alternate_names", str, "vocab:alternateName", multiple=True, doc="no description available"), - Property( - "definition", - str, - "vocab:definition", - doc="Short, but precise statement of the meaning of a word, word group, sign or a symbol.", - ), - Property( - "has_parents", - "openminds.sands.ParcellationEntity", - "vocab:hasParent", - multiple=True, - doc="Reference to a parent object or legal person.", - ), - Property( - "has_versions", - "openminds.sands.ParcellationEntityVersion", - "vocab:hasVersion", - multiple=True, - doc="Reference to variants of an original.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the parcellation entity.", - ), - Property( - "ontology_identifiers", - str, - "vocab:ontologyIdentifier", - multiple=True, - doc="Term or code used to identify the parcellation entity registered within a particular ontology.", - ), - Property( - "related_uberon_term", - ["openminds.controlled_terms.Organ", "openminds.controlled_terms.UBERONParcellation"], - "vocab:relatedUBERONTerm", - doc="no description available", - ), - ] + default_space = "atlas" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_children", - ["openminds.sands.ParcellationEntity", "openminds.sands.ParcellationEntityVersion"], - "^vocab:hasParent", + ["openminds.latest.sands.ParcellationEntity", "openminds.latest.sands.ParcellationEntityVersion"], + "hasParent", reverse="has_parents", multiple=True, - doc="reverse of 'has_parents'", + description="reverse of 'has_parents'", ), Property( "is_location_of", [ - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", ], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes"], + ["anatomicalLocation", "anatomicalLocationOfElectrodes"], reverse=["anatomical_location", "anatomical_locations", "anatomical_locations_of_electrodes"], multiple=True, - doc="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", + description="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] aliases = {"versions": "has_versions"} @@ -152,7 +109,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py index 8616a577..225dcd31 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py @@ -4,97 +4,39 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import ParcellationEntityVersion +from fairgraph import KGObject -class ParcellationEntityVersion(KGObject): +class ParcellationEntityVersion(KGObject, ParcellationEntityVersion): """ """ - default_space = "atlas" type_ = "https://openminds.ebrains.eu/sands/ParcellationEntityVersion" - properties = [ - Property("abbreviation", str, "vocab:abbreviation", doc="no description available"), - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property("alternate_names", str, "vocab:alternateName", multiple=True, doc="no description available"), - Property("corrected_name", str, "vocab:correctedName", doc="no description available"), - Property( - "has_annotations", - "openminds.sands.AtlasAnnotation", - "vocab:hasAnnotation", - multiple=True, - doc="no description available", - ), - Property( - "has_parents", - ["openminds.sands.ParcellationEntity", "openminds.sands.ParcellationEntityVersion"], - "vocab:hasParent", - multiple=True, - doc="Reference to a parent object or legal person.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the parcellation entity version.", - ), - Property( - "ontology_identifiers", - str, - "vocab:ontologyIdentifier", - multiple=True, - doc="Term or code used to identify the parcellation entity version registered within a particular ontology.", - ), - Property( - "relation_assessments", - ["openminds.sands.QualitativeRelationAssessment", "openminds.sands.QuantitativeRelationAssessment"], - "vocab:relationAssessment", - multiple=True, - doc="no description available", - ), - Property( - "version_identifier", - str, - "vocab:versionIdentifier", - required=True, - doc="Term or code used to identify the version of something.", - ), - Property( - "version_innovation", - str, - "vocab:versionInnovation", - doc="Documentation on what changed in comparison to a previously published form of something.", - ), - ] + default_space = "atlas" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "has_children", - "openminds.sands.ParcellationEntityVersion", - "^vocab:hasParent", + "openminds.latest.sands.ParcellationEntityVersion", + "hasParent", reverse="has_parents", multiple=True, - doc="reverse of 'has_parents'", + description="reverse of 'has_parents'", ), Property( "is_location_of", [ - "openminds.core.ServiceLink", - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", + "openminds.latest.core.ServiceLink", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", ], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes", "^vocab:dataLocation"], + ["anatomicalLocation", "anatomicalLocationOfElectrodes", "dataLocation"], reverse=[ "anatomical_location", "anatomical_locations", @@ -102,66 +44,66 @@ class ParcellationEntityVersion(KGObject): "data_location", ], multiple=True, - doc="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes, data_location", + description="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes, data_location", ), Property( "is_part_of", - "openminds.sands.ParcellationTerminologyVersion", - "^vocab:hasEntity", + "openminds.latest.sands.ParcellationTerminologyVersion", + "hasEntity", reverse="has_entities", multiple=True, - doc="reverse of 'has_entities'", + description="reverse of 'has_entities'", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "is_version_of", - "openminds.sands.ParcellationEntity", - "^vocab:hasVersion", + "openminds.latest.sands.ParcellationEntity", + "hasVersion", reverse="has_versions", multiple=True, - doc="reverse of 'has_versions'", + description="reverse of 'has_versions'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name", "version_identifier") @@ -192,7 +134,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology.py b/fairgraph/openminds/sands/atlas/parcellation_terminology.py index b853aec2..9326ef05 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology.py @@ -4,40 +4,18 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import ParcellationTerminology +from fairgraph import EmbeddedMetadata -class ParcellationTerminology(EmbeddedMetadata): +class ParcellationTerminology(EmbeddedMetadata, ParcellationTerminology): """ """ type_ = "https://openminds.ebrains.eu/sands/ParcellationTerminology" - properties = [ - Property( - "data_locations", - "openminds.core.File", - "vocab:dataLocation", - multiple=True, - doc="no description available", - ), - Property( - "has_entities", - "openminds.sands.ParcellationEntity", - "vocab:hasEntity", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "ontology_identifiers", - str, - "vocab:ontologyIdentifier", - multiple=True, - doc="Term or code used to identify the parcellation terminology registered within a particular ontology.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -50,7 +28,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, data_locations=data_locations, has_entities=has_entities, diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py index d9d98398..3cd4719a 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py @@ -4,40 +4,18 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import ParcellationTerminologyVersion +from fairgraph import EmbeddedMetadata -class ParcellationTerminologyVersion(EmbeddedMetadata): +class ParcellationTerminologyVersion(EmbeddedMetadata, ParcellationTerminologyVersion): """ """ type_ = "https://openminds.ebrains.eu/sands/ParcellationTerminologyVersion" - properties = [ - Property( - "data_locations", - "openminds.core.File", - "vocab:dataLocation", - multiple=True, - doc="no description available", - ), - Property( - "has_entities", - "openminds.sands.ParcellationEntityVersion", - "vocab:hasEntity", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "ontology_identifiers", - str, - "vocab:ontologyIdentifier", - multiple=True, - doc="Term or code used to identify the parcellation terminology version registered within a particular ontology.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -50,7 +28,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, data_locations=data_locations, has_entities=has_entities, diff --git a/fairgraph/openminds/sands/mathematical_shapes/circle.py b/fairgraph/openminds/sands/mathematical_shapes/circle.py index cdf8c833..750435de 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/circle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/circle.py @@ -4,22 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import Circle +from fairgraph import EmbeddedMetadata -class Circle(EmbeddedMetadata): +class Circle(EmbeddedMetadata, Circle): """ """ type_ = "https://openminds.ebrains.eu/sands/Circle" - properties = [ - Property( - "radius", "openminds.core.QuantitativeValue", "vocab:radius", required=True, doc="no description available" - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, radius=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, radius=radius) + return EmbeddedMetadata.__init__(self, data=data, radius=radius) diff --git a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py index cbd9358f..8756c81a 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py +++ b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py @@ -4,33 +4,21 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import Ellipse +from fairgraph import EmbeddedMetadata -class Ellipse(EmbeddedMetadata): +class Ellipse(EmbeddedMetadata, Ellipse): """ """ type_ = "https://openminds.ebrains.eu/sands/Ellipse" - properties = [ - Property( - "semi_major_axis", - "openminds.core.QuantitativeValue", - "vocab:semiMajorAxis", - required=True, - doc="no description available", - ), - Property( - "semi_minor_axis", - "openminds.core.QuantitativeValue", - "vocab:semiMinorAxis", - required=True, - doc="no description available", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, semi_major_axis=None, semi_minor_axis=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, semi_major_axis=semi_major_axis, semi_minor_axis=semi_minor_axis) + return EmbeddedMetadata.__init__( + self, data=data, semi_major_axis=semi_major_axis, semi_minor_axis=semi_minor_axis + ) diff --git a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py index 24a2d619..126b404c 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py @@ -4,25 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import Rectangle +from fairgraph import EmbeddedMetadata -class Rectangle(EmbeddedMetadata): +class Rectangle(EmbeddedMetadata, Rectangle): """ """ type_ = "https://openminds.ebrains.eu/sands/Rectangle" - properties = [ - Property( - "length", "openminds.core.QuantitativeValue", "vocab:length", required=True, doc="no description available" - ), - Property( - "width", "openminds.core.QuantitativeValue", "vocab:width", required=True, doc="no description available" - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, length=None, width=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, length=length, width=width) + return EmbeddedMetadata.__init__(self, data=data, length=length, width=width) diff --git a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py index 3f283067..fd288d6f 100644 --- a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py +++ b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py @@ -4,55 +4,18 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import AnatomicalTargetPosition +from fairgraph import EmbeddedMetadata -class AnatomicalTargetPosition(EmbeddedMetadata): +class AnatomicalTargetPosition(EmbeddedMetadata, AnatomicalTargetPosition): """ """ type_ = "https://openminds.ebrains.eu/sands/AnatomicalTargetPosition" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "anatomical_targets", - [ - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.UBERONParcellation", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:anatomicalTarget", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "spatial_locations", - "openminds.sands.CoordinatePoint", - "vocab:spatialLocation", - multiple=True, - doc="no description available", - ), - Property( - "target_identification_type", - "openminds.controlled_terms.AnatomicalIdentificationType", - "vocab:targetIdentificationType", - required=True, - doc="no description available", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -66,7 +29,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, additional_remarks=additional_remarks, anatomical_targets=anatomical_targets, diff --git a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py index dc57ee06..99a98a77 100644 --- a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py +++ b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py @@ -4,34 +4,19 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import CoordinatePoint +from fairgraph import EmbeddedMetadata -class CoordinatePoint(EmbeddedMetadata): +class CoordinatePoint(EmbeddedMetadata, CoordinatePoint): """ """ type_ = "https://openminds.ebrains.eu/sands/CoordinatePoint" - properties = [ - Property( - "coordinate_space", - ["openminds.sands.CommonCoordinateSpaceVersion", "openminds.sands.CustomCoordinateSpace"], - "vocab:coordinateSpace", - required=True, - doc="Two or three dimensional geometric setting.", - ), - Property( - "coordinates", - "openminds.core.QuantitativeValue", - "vocab:coordinates", - multiple=True, - required=True, - doc="Pair or triplet of numbers defining a location in a given coordinate space.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__(self, coordinate_space=None, coordinates=None, id=None, data=None, space=None, scope=None): - return super().__init__(data=data, coordinate_space=coordinate_space, coordinates=coordinates) + return EmbeddedMetadata.__init__(self, data=data, coordinate_space=coordinate_space, coordinates=coordinates) diff --git a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py index 299a355e..85e7d6bc 100644 --- a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py @@ -4,47 +4,23 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import QualitativeRelationAssessment +from fairgraph import EmbeddedMetadata -class QualitativeRelationAssessment(EmbeddedMetadata): +class QualitativeRelationAssessment(EmbeddedMetadata, QualitativeRelationAssessment): """ """ type_ = "https://openminds.ebrains.eu/sands/QualitativeRelationAssessment" - properties = [ - Property( - "criteria", - "openminds.core.ProtocolExecution", - "vocab:criteria", - doc="Aspects or standards on which a judgement or decision is based.", - ), - Property( - "in_relation_to", - [ - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:inRelationTo", - required=True, - doc="Reference to a related element.", - ), - Property( - "qualitative_overlap", - "openminds.controlled_terms.QualitativeOverlap", - "vocab:qualitativeOverlap", - required=True, - doc="Semantic characterization of how much two things occupy the same space.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( self, criteria=None, in_relation_to=None, qualitative_overlap=None, id=None, data=None, space=None, scope=None ): - return super().__init__( - data=data, criteria=criteria, in_relation_to=in_relation_to, qualitative_overlap=qualitative_overlap + return EmbeddedMetadata.__init__( + self, data=data, criteria=criteria, in_relation_to=in_relation_to, qualitative_overlap=qualitative_overlap ) diff --git a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py index 2f0b0221..238b6967 100644 --- a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py @@ -4,43 +4,27 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import QuantitativeRelationAssessment +from fairgraph import EmbeddedMetadata -class QuantitativeRelationAssessment(EmbeddedMetadata): +class QuantitativeRelationAssessment(EmbeddedMetadata, QuantitativeRelationAssessment): """ """ type_ = "https://openminds.ebrains.eu/sands/QuantitativeRelationAssessment" - properties = [ - Property( - "criteria", - "openminds.core.ProtocolExecution", - "vocab:criteria", - doc="Aspects or standards on which a judgement or decision is based.", - ), - Property( - "in_relation_to", - "openminds.sands.ParcellationEntityVersion", - "vocab:inRelationTo", - required=True, - doc="Reference to a related element.", - ), - Property( - "quantitative_overlap", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:quantitativeOverlap", - required=True, - doc="Numerical characterization of how much two things occupy the same space.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( self, criteria=None, in_relation_to=None, quantitative_overlap=None, id=None, data=None, space=None, scope=None ): - return super().__init__( - data=data, criteria=criteria, in_relation_to=in_relation_to, quantitative_overlap=quantitative_overlap + return EmbeddedMetadata.__init__( + self, + data=data, + criteria=criteria, + in_relation_to=in_relation_to, + quantitative_overlap=quantitative_overlap, ) diff --git a/fairgraph/openminds/sands/miscellaneous/single_color.py b/fairgraph/openminds/sands/miscellaneous/single_color.py index fcee185e..e79f5b21 100644 --- a/fairgraph/openminds/sands/miscellaneous/single_color.py +++ b/fairgraph/openminds/sands/miscellaneous/single_color.py @@ -4,22 +4,21 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import SingleColor +from fairgraph import KGObject -class SingleColor(KGObject): +class SingleColor(KGObject, SingleColor): """ """ - default_space = "atlas" type_ = "https://openminds.ebrains.eu/sands/SingleColor" - properties = [ - Property("value", str, "vocab:value", required=True, doc="Entry for a property."), - ] + default_space = "atlas" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("value",) def __init__(self, value=None, id=None, data=None, space=None, scope=None): - return super().__init__(id=id, space=space, scope=scope, data=data, value=value) + return KGObject.__init__(self, id=id, space=space, scope=scope, data=data, value=value) diff --git a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py index fa9fdb56..e54844ea 100644 --- a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py +++ b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py @@ -4,44 +4,18 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import ViewerSpecification +from fairgraph import EmbeddedMetadata -class ViewerSpecification(EmbeddedMetadata): +class ViewerSpecification(EmbeddedMetadata, ViewerSpecification): """ """ type_ = "https://openminds.ebrains.eu/sands/ViewerSpecification" - properties = [ - Property( - "additional_remarks", - str, - "vocab:additionalRemarks", - doc="Mention of what deserves additional attention or notice.", - ), - Property( - "anchor_points", - "openminds.core.QuantitativeValue", - "vocab:anchorPoint", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "camera_position", - "openminds.sands.CoordinatePoint", - "vocab:cameraPosition", - doc="no description available", - ), - Property( - "preferred_display_color", - ["openminds.controlled_terms.Colormap", "openminds.sands.SingleColor"], - "vocab:preferredDisplayColor", - doc="no description available", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -55,7 +29,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, additional_remarks=additional_remarks, anchor_points=anchor_points, diff --git a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py index 4fb7e9ae..352933d4 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py +++ b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py @@ -4,103 +4,76 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import CustomAnatomicalEntity +from fairgraph import KGObject -class CustomAnatomicalEntity(KGObject): +class CustomAnatomicalEntity(KGObject, CustomAnatomicalEntity): """ """ - default_space = "spatial" type_ = "https://openminds.ebrains.eu/sands/CustomAnatomicalEntity" - properties = [ - Property( - "has_annotations", - "openminds.sands.CustomAnnotation", - "vocab:hasAnnotation", - multiple=True, - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the custom anatomical entity.", - ), - Property( - "related_uberon_term", - ["openminds.controlled_terms.Organ", "openminds.controlled_terms.UBERONParcellation"], - "vocab:relatedUBERONTerm", - doc="no description available", - ), - Property( - "relation_assessments", - ["openminds.sands.QualitativeRelationAssessment", "openminds.sands.QuantitativeRelationAssessment"], - "vocab:relationAssessment", - multiple=True, - doc="no description available", - ), - ] + default_space = "spatial" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_location_of", [ - "openminds.core.TissueSample", - "openminds.core.TissueSampleCollection", - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", + "openminds.latest.core.TissueSample", + "openminds.latest.core.TissueSampleCollection", + "openminds.latest.ephys.ElectrodeArrayUsage", + "openminds.latest.ephys.ElectrodeUsage", + "openminds.latest.ephys.PipetteUsage", ], - ["^vocab:anatomicalLocation", "^vocab:anatomicalLocationOfElectrodes"], + ["anatomicalLocation", "anatomicalLocationOfElectrodes"], reverse=["anatomical_location", "anatomical_locations", "anatomical_locations_of_electrodes"], multiple=True, - doc="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", + description="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes", ), Property( "is_target_of", - "openminds.sands.AnatomicalTargetPosition", - "^vocab:anatomicalTarget", + "openminds.latest.sands.AnatomicalTargetPosition", + "anatomicalTarget", reverse="anatomical_targets", multiple=True, - doc="reverse of 'anatomical_targets'", + description="reverse of 'anatomical_targets'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), Property( "studied_in", [ - "openminds.computation.DataAnalysis", - "openminds.computation.DataCopy", - "openminds.computation.GenericComputation", - "openminds.computation.ModelValidation", - "openminds.computation.Optimization", - "openminds.computation.Simulation", - "openminds.computation.ValidationTest", - "openminds.computation.Visualization", - "openminds.core.DatasetVersion", - "openminds.core.Model", - "openminds.core.ProtocolExecution", - "openminds.ephys.CellPatching", - "openminds.ephys.ElectrodePlacement", - "openminds.ephys.RecordingActivity", - "openminds.specimen_prep.CranialWindowPreparation", - "openminds.specimen_prep.TissueCulturePreparation", - "openminds.specimen_prep.TissueSampleSlicing", - "openminds.stimulation.StimulationActivity", + "openminds.latest.computation.DataAnalysis", + "openminds.latest.computation.DataCopy", + "openminds.latest.computation.GenericComputation", + "openminds.latest.computation.ModelValidation", + "openminds.latest.computation.Optimization", + "openminds.latest.computation.Simulation", + "openminds.latest.computation.ValidationTest", + "openminds.latest.computation.Visualization", + "openminds.latest.core.DatasetVersion", + "openminds.latest.core.Model", + "openminds.latest.core.ProtocolExecution", + "openminds.latest.ephys.CellPatching", + "openminds.latest.ephys.ElectrodePlacement", + "openminds.latest.ephys.RecordingActivity", + "openminds.latest.specimen_prep.CranialWindowPreparation", + "openminds.latest.specimen_prep.TissueCulturePreparation", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "openminds.latest.stimulation.StimulationActivity", ], - "^vocab:studyTarget", + "studyTarget", reverse="study_targets", multiple=True, - doc="reverse of 'study_targets'", + description="reverse of 'study_targets'", ), ] existence_query_properties = ("name",) @@ -120,7 +93,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/sands/non_atlas/custom_annotation.py b/fairgraph/openminds/sands/non_atlas/custom_annotation.py index 7b7d46b4..d166caca 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_annotation.py +++ b/fairgraph/openminds/sands/non_atlas/custom_annotation.py @@ -4,91 +4,18 @@ # this file was auto-generated -from fairgraph import EmbeddedMetadata, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import CustomAnnotation +from fairgraph import EmbeddedMetadata -class CustomAnnotation(EmbeddedMetadata): +class CustomAnnotation(EmbeddedMetadata, CustomAnnotation): """ """ type_ = "https://openminds.ebrains.eu/sands/CustomAnnotation" - properties = [ - Property( - "anchor_points", - "openminds.core.QuantitativeValue", - "vocab:anchorPoint", - multiple=True, - doc="no description available", - ), - Property( - "coordinate_space", - ["openminds.sands.CommonCoordinateSpaceVersion", "openminds.sands.CustomCoordinateSpace"], - "vocab:coordinateSpace", - required=True, - doc="Two or three dimensional geometric setting.", - ), - Property( - "criteria", - "openminds.core.ProtocolExecution", - "vocab:criteria", - doc="Aspects or standards on which a judgement or decision is based.", - ), - Property( - "criteria_quality_type", - "openminds.controlled_terms.CriteriaQualityType", - "vocab:criteriaQualityType", - required=True, - doc="Distinct class that defines how the judgement or decision was made for a particular criteria.", - ), - Property( - "criteria_type", - "openminds.controlled_terms.AnnotationCriteriaType", - "vocab:criteriaType", - required=True, - doc="no description available", - ), - Property( - "inspired_by", - "openminds.core.File", - "vocab:inspiredBy", - multiple=True, - doc="Reference to an inspiring element.", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - doc="Term or code that identifies the custom annotation within a particular product.", - ), - Property( - "lateralities", - "openminds.controlled_terms.Laterality", - "vocab:laterality", - multiple=True, - doc="Differentiation between a pair of lateral homologous parts of the body.", - ), - Property( - "preferred_visualization", - "openminds.sands.ViewerSpecification", - "vocab:preferredVisualization", - doc="no description available", - ), - Property( - "specification", - ["openminds.core.File", "openminds.core.PropertyValueList"], - "vocab:specification", - doc="Detailed and precise presentation of, or proposal for something.", - ), - Property( - "type", - "openminds.controlled_terms.AnnotationType", - "vocab:type", - required=True, - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] def __init__( @@ -109,7 +36,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return EmbeddedMetadata.__init__( + self, data=data, anchor_points=anchor_points, coordinate_space=coordinate_space, diff --git a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py index 6fafdda0..1f4f0bd8 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py +++ b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py @@ -4,71 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.sands import CustomCoordinateSpace +from fairgraph import KGObject -class CustomCoordinateSpace(KGObject): +class CustomCoordinateSpace(KGObject, CustomCoordinateSpace): """ """ - default_space = "spatial" type_ = "https://openminds.ebrains.eu/sands/CustomCoordinateSpace" - properties = [ - Property( - "anatomical_axes_orientation", - "openminds.controlled_terms.AnatomicalAxesOrientation", - "vocab:anatomicalAxesOrientation", - required=True, - doc="Relation between reference planes used in anatomy and mathematics.", - ), - Property( - "axes_origins", - "openminds.core.QuantitativeValue", - "vocab:axesOrigin", - multiple=True, - required=True, - doc="Special point in a coordinate system used as a fixed point of reference for the geometry of the surrounding space.", - ), - Property( - "default_images", - "openminds.core.File", - "vocab:defaultImage", - multiple=True, - doc="Two or three dimensional image that particluarly represents a specific coordinate space.", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the custom coordinate space.", - ), - Property( - "native_unit", - "openminds.controlled_terms.UnitOfMeasurement", - "vocab:nativeUnit", - required=True, - doc="Determinate quantity used in the original measurement.", - ), - ] + default_space = "spatial" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_coordinate_space_of", - "openminds.sands.CustomAnnotation", - "^vocab:coordinateSpace", + "openminds.latest.sands.CustomAnnotation", + "coordinateSpace", reverse="coordinate_space", multiple=True, - doc="reverse of 'coordinate_space'", + description="reverse of 'coordinate_space'", ), Property( "is_used_to_group", - "openminds.core.FileBundle", - "^vocab:groupedBy", + "openminds.latest.core.FileBundle", + "groupedBy", reverse="grouped_by", multiple=True, - doc="reverse of 'grouped_by'", + description="reverse of 'grouped_by'", ), ] existence_query_properties = ("name",) @@ -87,7 +51,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py index 72d47acb..f5052ba7 100644 --- a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py @@ -4,137 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.specimen_prep import CranialWindowPreparation +from fairgraph import KGObject from datetime import datetime, time -class CranialWindowPreparation(KGObject): +class CranialWindowPreparation(KGObject, CranialWindowPreparation): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/specimenPrep/CranialWindowPreparation" - properties = [ - Property( - "construction_type", - "openminds.controlled_terms.CranialWindowConstructionType", - "vocab:constructionType", - required=True, - doc="no description available", - ), - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the cranial window preparation.", - ), - Property( - "dimension", - ["openminds.sands.Circle", "openminds.sands.Ellipse", "openminds.sands.Rectangle"], - "vocab:dimension", - doc="no description available", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - "openminds.core.SubjectState", - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - "openminds.core.SubjectState", - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property( - "reinforcement_type", - "openminds.controlled_terms.CranialWindowReinforcementType", - "vocab:reinforcementType", - doc="no description available", - ), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("lookup_label",) @@ -160,7 +45,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py index 532c5887..80434849 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py @@ -4,137 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.specimen_prep import TissueCulturePreparation +from fairgraph import KGObject from datetime import datetime, time -class TissueCulturePreparation(KGObject): +class TissueCulturePreparation(KGObject, TissueCulturePreparation): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/specimenPrep/TissueCulturePreparation" - properties = [ - Property( - "culture_medium", - "openminds.chemicals.ChemicalMixture", - "vocab:cultureMedium", - required=True, - doc="no description available", - ), - Property( - "culture_type", - "openminds.controlled_terms.CellCultureType", - "vocab:cultureType", - required=True, - doc="no description available", - ), - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the tissue culture preparation.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - [ - "openminds.core.TissueSampleState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - "openminds.core.TissueSampleState", - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("lookup_label",) @@ -159,7 +44,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py index ba374a8a..6b490ac2 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py @@ -4,141 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.specimen_prep import TissueSampleSlicing +from fairgraph import KGObject from datetime import datetime, time -class TissueSampleSlicing(KGObject): +class TissueSampleSlicing(KGObject, TissueSampleSlicing): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/specimenPrep/TissueSampleSlicing" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the tissue sample slicing.", - ), - Property( - "device", - "openminds.specimen_prep.SlicingDeviceUsage", - "vocab:device", - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - [ - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - ["openminds.core.TissueSampleCollectionState", "openminds.core.TissueSampleState"], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - Property( - "temperature", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:temperature", - doc="no description available", - ), - Property( - "tissue_bath_solution", - "openminds.chemicals.ChemicalMixture", - "vocab:tissueBathSolution", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("lookup_label",) @@ -164,7 +45,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device.py b/fairgraph/openminds/specimen_prep/device/slicing_device.py index b9507e10..32392863 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device.py @@ -4,77 +4,35 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.specimen_prep import SlicingDevice +from fairgraph import KGObject -class SlicingDevice(KGObject): +class SlicingDevice(KGObject, SlicingDevice): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/specimenPrep/SlicingDevice" - properties = [ - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the slicing device.", - ), - Property( - "device_type", - "openminds.controlled_terms.DeviceType", - "vocab:deviceType", - required=True, - doc="no description available", - ), - Property( - "digital_identifier", - ["openminds.core.DOI", "openminds.core.RRID"], - "vocab:digitalIdentifier", - doc="Digital handle to identify objects or legal persons.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "manufacturers", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:manufacturer", - multiple=True, - doc="no description available", - ), - Property( - "name", - str, - "vocab:name", - required=True, - doc="Word or phrase that constitutes the distinctive designation of the slicing device.", - ), - Property( - "owners", - ["openminds.core.Consortium", "openminds.core.Organization", "openminds.core.Person"], - "vocab:owner", - multiple=True, - doc="no description available", - ), - Property("serial_number", str, "vocab:serialNumber", doc="no description available"), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_part_of", - "openminds.core.Setup", - "^vocab:hasPart", + "openminds.latest.core.Setup", + "hasPart", reverse="has_parts", multiple=True, - doc="reverse of 'has_parts'", + description="reverse of 'has_parts'", ), Property( "usage", - "openminds.specimen_prep.SlicingDeviceUsage", - "^vocab:device", + "openminds.latest.specimen_prep.SlicingDeviceUsage", + "device", reverse="device", multiple=True, - doc="reverse of 'device'", + description="reverse of 'device'", ), ] existence_query_properties = ("lookup_label",) @@ -96,7 +54,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py index f833b719..84cc2eda 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py @@ -4,124 +4,67 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.specimen_prep import SlicingDeviceUsage +from fairgraph import KGObject -class SlicingDeviceUsage(KGObject): +class SlicingDeviceUsage(KGObject, SlicingDeviceUsage): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/specimenPrep/SlicingDeviceUsage" - properties = [ - Property( - "device", - "openminds.specimen_prep.SlicingDevice", - "vocab:device", - required=True, - doc="Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "metadata_locations", - ["openminds.core.File", "openminds.core.FileBundle"], - "vocab:metadataLocation", - multiple=True, - doc="no description available", - ), - Property( - "oscillation_amplitude", - "openminds.core.QuantitativeValue", - "vocab:oscillationAmplitude", - doc="no description available", - ), - Property( - "slice_thickness", - ["openminds.core.QuantitativeValue", "openminds.core.QuantitativeValueRange"], - "vocab:sliceThickness", - required=True, - doc="no description available", - ), - Property( - "slicing_angles", - ["openminds.core.QuantitativeValue", "openminds.core.NumericalProperty"], - "vocab:slicingAngle", - multiple=True, - doc="no description available", - ), - Property( - "slicing_plane", - "openminds.controlled_terms.AnatomicalPlane", - "vocab:slicingPlane", - required=True, - doc="no description available", - ), - Property( - "slicing_speed", "openminds.core.QuantitativeValue", "vocab:slicingSpeed", doc="no description available" - ), - Property( - "used_specimen", - ["openminds.core.SubjectState", "openminds.core.TissueSampleState"], - "vocab:usedSpecimen", - doc="no description available", - ), - Property( - "vibration_frequency", - "openminds.core.QuantitativeValue", - "vocab:vibrationFrequency", - doc="no description available", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "generation_device", - "openminds.stimulation.EphysStimulus", - "^vocab:generatedBy", + "openminds.latest.stimulation.EphysStimulus", + "generatedBy", reverse="generated_by", multiple=True, - doc="reverse of 'generated_by'", + description="reverse of 'generated_by'", ), Property( "placed_by", - "openminds.ephys.ElectrodePlacement", - "^vocab:device", + "openminds.latest.ephys.ElectrodePlacement", + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_for", - "openminds.specimen_prep.TissueSampleSlicing", - "^vocab:device", + "openminds.latest.specimen_prep.TissueSampleSlicing", + "device", reverse="device", multiple=True, - doc="reverse of 'device'", + description="reverse of 'device'", ), Property( "used_in", - "openminds.ephys.CellPatching", - "^vocab:device", + "openminds.latest.ephys.CellPatching", + "device", reverse="devices", multiple=True, - doc="reverse of 'devices'", + description="reverse of 'devices'", ), Property( "used_to_measure", - "openminds.core.Measurement", - "^vocab:measuredWith", + "openminds.latest.core.Measurement", + "measuredWith", reverse="measured_with", multiple=True, - doc="reverse of 'measured_with'", + description="reverse of 'measured_with'", ), Property( "used_to_record", - "openminds.ephys.Recording", - "^vocab:recordedWith", + "openminds.latest.ephys.Recording", + "recordedWith", reverse="recorded_with", multiple=True, - doc="reverse of 'recorded_with'", + description="reverse of 'recorded_with'", ), ] existence_query_properties = ("lookup_label",) @@ -149,7 +92,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/stimulation/activity/stimulation_activity.py b/fairgraph/openminds/stimulation/activity/stimulation_activity.py index 3665b6ee..77463544 100644 --- a/fairgraph/openminds/stimulation/activity/stimulation_activity.py +++ b/fairgraph/openminds/stimulation/activity/stimulation_activity.py @@ -4,139 +4,22 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.stimulation import StimulationActivity +from fairgraph import KGObject from datetime import datetime, time -class StimulationActivity(KGObject): +class StimulationActivity(KGObject, StimulationActivity): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/stimulation/StimulationActivity" - properties = [ - Property( - "custom_property_sets", - "openminds.core.CustomPropertySet", - "vocab:customPropertySet", - multiple=True, - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the stimulation activity.", - ), - Property("end_time", [datetime, time], "vocab:endTime", doc="no description available"), - Property( - "inputs", - [ - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - ], - "vocab:input", - multiple=True, - required=True, - doc="Something or someone that is put into or participates in a process or machine.", - ), - Property( - "is_part_of", - "openminds.core.DatasetVersion", - "vocab:isPartOf", - required=True, - doc="Reference to the ensemble of multiple things or beings.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "outputs", - [ - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.SubjectGroupState", - "openminds.core.SubjectState", - "openminds.core.TissueSampleCollectionState", - "openminds.core.TissueSampleState", - ], - "vocab:output", - multiple=True, - required=True, - doc="Something or someone that comes out of, is delivered or produced by a process or machine.", - ), - Property( - "performed_by", - ["openminds.computation.SoftwareAgent", "openminds.core.Person"], - "vocab:performedBy", - multiple=True, - doc="no description available", - ), - Property( - "preparation_design", - "openminds.controlled_terms.PreparationType", - "vocab:preparationDesign", - doc="no description available", - ), - Property( - "protocols", - "openminds.core.Protocol", - "vocab:protocol", - multiple=True, - required=True, - doc="Plan that describes the process of a scientific or medical experiment, treatment, or procedure.", - ), - Property("setup", "openminds.core.Setup", "vocab:setup", doc="no description available"), - Property("start_time", [datetime, time], "vocab:startTime", doc="no description available"), - Property( - "stimuli", - "openminds.stimulation.EphysStimulus", - "vocab:stimulus", - multiple=True, - required=True, - doc="no description available", - ), - Property( - "study_targets", - [ - "openminds.controlled_terms.AuditoryStimulusType", - "openminds.controlled_terms.BiologicalOrder", - "openminds.controlled_terms.BiologicalSex", - "openminds.controlled_terms.BreedingType", - "openminds.controlled_terms.CellCultureType", - "openminds.controlled_terms.CellType", - "openminds.controlled_terms.Disease", - "openminds.controlled_terms.DiseaseModel", - "openminds.controlled_terms.ElectricalStimulusType", - "openminds.controlled_terms.GeneticStrainType", - "openminds.controlled_terms.GustatoryStimulusType", - "openminds.controlled_terms.Handedness", - "openminds.controlled_terms.MolecularEntity", - "openminds.controlled_terms.OlfactoryStimulusType", - "openminds.controlled_terms.OpticalStimulusType", - "openminds.controlled_terms.Organ", - "openminds.controlled_terms.OrganismSubstance", - "openminds.controlled_terms.OrganismSystem", - "openminds.controlled_terms.Species", - "openminds.controlled_terms.SubcellularEntity", - "openminds.controlled_terms.TactileStimulusType", - "openminds.controlled_terms.TermSuggestion", - "openminds.controlled_terms.TissueSampleType", - "openminds.controlled_terms.UBERONParcellation", - "openminds.controlled_terms.VisualStimulusType", - "openminds.sands.CustomAnatomicalEntity", - "openminds.sands.ParcellationEntity", - "openminds.sands.ParcellationEntityVersion", - ], - "vocab:studyTarget", - multiple=True, - doc="Structure or function that was targeted within a study.", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] existence_query_properties = ("lookup_label",) @@ -161,7 +44,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, diff --git a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py index 70574f12..f891d921 100644 --- a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py +++ b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py @@ -4,82 +4,27 @@ # this file was auto-generated -from fairgraph import KGObject, IRI -from fairgraph.properties import Property +from openminds.properties import Property +from openminds.latest.stimulation import EphysStimulus +from fairgraph import KGObject -class EphysStimulus(KGObject): +class EphysStimulus(KGObject, EphysStimulus): """ """ - default_space = "in-depth" type_ = "https://openminds.ebrains.eu/stimulation/EphysStimulus" - properties = [ - Property( - "delivered_by", - [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", - ], - "vocab:deliveredBy", - doc="no description available", - ), - Property( - "description", - str, - "vocab:description", - doc="Longer statement or account giving the characteristics of the ephys stimulus.", - ), - Property("epoch", "openminds.core.QuantitativeValue", "vocab:epoch", doc="no description available"), - Property( - "generated_by", - [ - "openminds.ephys.ElectrodeArrayUsage", - "openminds.ephys.ElectrodeUsage", - "openminds.ephys.PipetteUsage", - "openminds.specimen_prep.SlicingDeviceUsage", - ], - "vocab:generatedBy", - doc="no description available", - ), - Property( - "internal_identifier", - str, - "vocab:internalIdentifier", - required=True, - doc="Term or code that identifies the ephys stimulus within a particular product.", - ), - Property("lookup_label", str, "vocab:lookupLabel", doc="no description available"), - Property( - "specifications", - [ - "openminds.core.Configuration", - "openminds.core.File", - "openminds.core.FileBundle", - "openminds.core.PropertyValueList", - ], - "vocab:specification", - multiple=True, - doc="Detailed and precise presentation of, or proposal for something.", - ), - Property( - "type", - "openminds.controlled_terms.ElectricalStimulusType", - "vocab:type", - doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.", - ), - ] + default_space = "in-depth" + # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ Property( "is_stimulus_for", - "openminds.stimulation.StimulationActivity", - "^vocab:stimulus", + "openminds.latest.stimulation.StimulationActivity", + "stimulus", reverse="stimuli", multiple=True, - doc="reverse of 'stimuli'", + description="reverse of 'stimuli'", ), ] existence_query_properties = ("lookup_label",) @@ -100,7 +45,8 @@ def __init__( space=None, scope=None, ): - return super().__init__( + return KGObject.__init__( + self, id=id, space=space, scope=scope, From 04712199159e24ec4c6732f747439720cdac6653 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Thu, 31 Jul 2025 15:35:31 +0200 Subject: [PATCH 08/25] Use new namespace (openMINDS v4+) everywhere internally; all namespace conversions (needed until KG is migrated to v4) happen inside KGClient --- builder/update_openminds.py | 13 +- fairgraph/client.py | 52 +++-- fairgraph/embedded.py | 1 - fairgraph/kgobject.py | 12 +- fairgraph/kgproxy.py | 4 +- fairgraph/node.py | 35 ++-- .../openminds/chemicals/amount_of_chemical.py | 2 +- .../openminds/chemicals/chemical_mixture.py | 2 +- .../openminds/chemicals/chemical_substance.py | 2 +- .../openminds/chemicals/product_source.py | 2 +- .../openminds/computation/data_analysis.py | 2 +- fairgraph/openminds/computation/data_copy.py | 2 +- .../openminds/computation/environment.py | 2 +- .../computation/generic_computation.py | 2 +- .../openminds/computation/hardware_system.py | 2 +- .../computation/launch_configuration.py | 2 +- fairgraph/openminds/computation/local_file.py | 2 +- .../openminds/computation/model_validation.py | 2 +- .../openminds/computation/optimization.py | 2 +- fairgraph/openminds/computation/simulation.py | 2 +- .../openminds/computation/software_agent.py | 2 +- .../openminds/computation/validation_test.py | 2 +- .../computation/validation_test_version.py | 2 +- .../openminds/computation/visualization.py | 2 +- .../computation/workflow_execution.py | 2 +- .../openminds/computation/workflow_recipe.py | 2 +- .../computation/workflow_recipe_version.py | 2 +- .../controlled_terms/action_status_type.py | 2 +- .../controlled_terms/age_category.py | 2 +- .../controlled_terms/analysis_technique.py | 2 +- .../anatomical_axes_orientation.py | 2 +- .../anatomical_identification_type.py | 2 +- .../controlled_terms/anatomical_plane.py | 2 +- .../annotation_criteria_type.py | 2 +- .../controlled_terms/annotation_type.py | 2 +- .../openminds/controlled_terms/atlas_type.py | 2 +- .../auditory_stimulus_type.py | 2 +- .../controlled_terms/biological_order.py | 2 +- .../controlled_terms/biological_process.py | 2 +- .../controlled_terms/biological_sex.py | 2 +- .../controlled_terms/breeding_type.py | 2 +- .../controlled_terms/cell_culture_type.py | 2 +- .../openminds/controlled_terms/cell_type.py | 2 +- .../controlled_terms/chemical_mixture_type.py | 2 +- .../openminds/controlled_terms/colormap.py | 2 +- .../controlled_terms/contribution_type.py | 2 +- .../cranial_window_construction_type.py | 2 +- .../cranial_window_reinforcement_type.py | 2 +- .../controlled_terms/criteria_quality_type.py | 2 +- .../openminds/controlled_terms/data_type.py | 2 +- .../openminds/controlled_terms/device_type.py | 2 +- .../controlled_terms/difference_measure.py | 2 +- .../openminds/controlled_terms/disease.py | 2 +- .../controlled_terms/disease_model.py | 2 +- .../controlled_terms/educational_level.py | 2 +- .../electrical_stimulus_type.py | 2 +- .../controlled_terms/ethics_assessment.py | 2 +- .../controlled_terms/experimental_approach.py | 2 +- .../controlled_terms/file_bundle_grouping.py | 2 +- .../controlled_terms/file_repository_type.py | 2 +- .../controlled_terms/file_usage_role.py | 2 +- .../controlled_terms/genetic_strain_type.py | 2 +- .../gustatory_stimulus_type.py | 2 +- .../openminds/controlled_terms/handedness.py | 2 +- .../openminds/controlled_terms/language.py | 2 +- .../openminds/controlled_terms/laterality.py | 2 +- .../learning_resource_type.py | 2 +- .../controlled_terms/measured_quantity.py | 2 +- .../controlled_terms/measured_signal_type.py | 2 +- .../controlled_terms/meta_data_model_type.py | 2 +- .../model_abstraction_level.py | 2 +- .../openminds/controlled_terms/model_scope.py | 2 +- .../controlled_terms/molecular_entity.py | 2 +- .../controlled_terms/mr_acquisition_type.py | 2 +- .../controlled_terms/mri_pulse_sequence.py | 2 +- .../controlled_terms/mri_weighting.py | 2 +- .../olfactory_stimulus_type.py | 2 +- .../controlled_terms/operating_device.py | 2 +- .../controlled_terms/operating_system.py | 2 +- .../controlled_terms/optical_stimulus_type.py | 2 +- fairgraph/openminds/controlled_terms/organ.py | 2 +- .../controlled_terms/organism_substance.py | 2 +- .../controlled_terms/organism_system.py | 2 +- .../controlled_terms/patch_clamp_variation.py | 2 +- .../controlled_terms/preparation_type.py | 2 +- .../controlled_terms/product_accessibility.py | 2 +- .../controlled_terms/programming_language.py | 2 +- .../controlled_terms/qualitative_overlap.py | 2 +- .../controlled_terms/semantic_data_type.py | 2 +- .../openminds/controlled_terms/service.py | 2 +- .../openminds/controlled_terms/setup_type.py | 2 +- .../software_application_category.py | 2 +- .../controlled_terms/software_feature.py | 2 +- .../openminds/controlled_terms/species.py | 2 +- .../controlled_terms/stimulation_approach.py | 2 +- .../controlled_terms/stimulation_technique.py | 2 +- .../controlled_terms/subcellular_entity.py | 2 +- .../controlled_terms/subject_attribute.py | 2 +- .../controlled_terms/tactile_stimulus_type.py | 2 +- .../openminds/controlled_terms/technique.py | 2 +- .../controlled_terms/term_suggestion.py | 2 +- .../openminds/controlled_terms/terminology.py | 2 +- .../tissue_sample_attribute.py | 2 +- .../controlled_terms/tissue_sample_type.py | 2 +- .../controlled_terms/type_of_uncertainty.py | 2 +- .../controlled_terms/uberon_parcellation.py | 2 +- .../controlled_terms/unit_of_measurement.py | 2 +- .../controlled_terms/visual_stimulus_type.py | 2 +- .../core/actors/account_information.py | 2 +- .../openminds/core/actors/affiliation.py | 2 +- fairgraph/openminds/core/actors/consortium.py | 2 +- .../core/actors/contact_information.py | 2 +- .../openminds/core/actors/contribution.py | 2 +- .../openminds/core/actors/organization.py | 2 +- fairgraph/openminds/core/actors/person.py | 2 +- fairgraph/openminds/core/data/content_type.py | 2 +- .../core/data/content_type_pattern.py | 2 +- fairgraph/openminds/core/data/copyright.py | 2 +- fairgraph/openminds/core/data/file.py | 2 +- fairgraph/openminds/core/data/file_archive.py | 2 +- fairgraph/openminds/core/data/file_bundle.py | 2 +- .../openminds/core/data/file_path_pattern.py | 2 +- .../openminds/core/data/file_repository.py | 2 +- .../core/data/file_repository_structure.py | 2 +- fairgraph/openminds/core/data/hash.py | 2 +- fairgraph/openminds/core/data/license.py | 2 +- fairgraph/openminds/core/data/measurement.py | 2 +- fairgraph/openminds/core/data/service_link.py | 2 +- .../openminds/core/digital_identifier/doi.py | 2 +- .../core/digital_identifier/gridid.py | 2 +- .../core/digital_identifier/handle.py | 2 +- .../identifiers_dot_org_id.py | 2 +- .../openminds/core/digital_identifier/isbn.py | 2 +- .../openminds/core/digital_identifier/issn.py | 2 +- .../core/digital_identifier/orcid.py | 2 +- .../core/digital_identifier/rorid.py | 2 +- .../openminds/core/digital_identifier/rrid.py | 2 +- .../core/digital_identifier/stock_number.py | 2 +- .../core/digital_identifier/swhid.py | 2 +- .../openminds/core/miscellaneous/comment.py | 2 +- .../openminds/core/miscellaneous/funding.py | 2 +- .../core/miscellaneous/quantitative_value.py | 2 +- .../miscellaneous/quantitative_value_array.py | 2 +- .../miscellaneous/quantitative_value_range.py | 2 +- .../miscellaneous/research_product_group.py | 2 +- .../core/miscellaneous/web_resource.py | 2 +- fairgraph/openminds/core/products/dataset.py | 2 +- .../core/products/dataset_version.py | 2 +- .../core/products/meta_data_model.py | 2 +- .../core/products/meta_data_model_version.py | 2 +- fairgraph/openminds/core/products/model.py | 2 +- .../openminds/core/products/model_version.py | 2 +- fairgraph/openminds/core/products/project.py | 2 +- fairgraph/openminds/core/products/setup.py | 2 +- fairgraph/openminds/core/products/software.py | 2 +- .../core/products/software_version.py | 2 +- .../openminds/core/products/web_service.py | 2 +- .../core/products/web_service_version.py | 2 +- .../core/research/behavioral_protocol.py | 2 +- .../openminds/core/research/configuration.py | 2 +- .../core/research/custom_property_set.py | 2 +- .../core/research/numerical_property.py | 2 +- .../core/research/property_value_list.py | 2 +- fairgraph/openminds/core/research/protocol.py | 2 +- .../core/research/protocol_execution.py | 2 +- fairgraph/openminds/core/research/strain.py | 2 +- .../core/research/string_property.py | 2 +- fairgraph/openminds/core/research/subject.py | 2 +- .../openminds/core/research/subject_group.py | 2 +- .../core/research/subject_group_state.py | 2 +- .../openminds/core/research/subject_state.py | 2 +- .../openminds/core/research/tissue_sample.py | 2 +- .../core/research/tissue_sample_collection.py | 2 +- .../tissue_sample_collection_state.py | 2 +- .../core/research/tissue_sample_state.py | 2 +- .../openminds/ephys/activity/cell_patching.py | 2 +- .../ephys/activity/electrode_placement.py | 2 +- .../ephys/activity/recording_activity.py | 2 +- fairgraph/openminds/ephys/device/electrode.py | 2 +- .../openminds/ephys/device/electrode_array.py | 2 +- .../ephys/device/electrode_array_usage.py | 2 +- .../openminds/ephys/device/electrode_usage.py | 2 +- fairgraph/openminds/ephys/device/pipette.py | 2 +- .../openminds/ephys/device/pipette_usage.py | 2 +- fairgraph/openminds/ephys/entity/channel.py | 2 +- fairgraph/openminds/ephys/entity/recording.py | 2 +- fairgraph/openminds/publications/book.py | 2 +- fairgraph/openminds/publications/chapter.py | 2 +- .../publications/learning_resource.py | 2 +- .../openminds/publications/live_paper.py | 2 +- .../publications/live_paper_resource_item.py | 2 +- .../publications/live_paper_section.py | 2 +- .../publications/live_paper_version.py | 2 +- .../openminds/publications/periodical.py | 2 +- .../publications/publication_issue.py | 2 +- .../publications/publication_volume.py | 2 +- .../publications/scholarly_article.py | 2 +- .../openminds/sands/atlas/atlas_annotation.py | 2 +- .../openminds/sands/atlas/brain_atlas.py | 2 +- .../sands/atlas/brain_atlas_version.py | 2 +- .../sands/atlas/common_coordinate_space.py | 2 +- .../atlas/common_coordinate_space_version.py | 2 +- .../sands/atlas/parcellation_entity.py | 2 +- .../atlas/parcellation_entity_version.py | 2 +- .../sands/atlas/parcellation_terminology.py | 2 +- .../atlas/parcellation_terminology_version.py | 2 +- .../sands/mathematical_shapes/circle.py | 2 +- .../sands/mathematical_shapes/ellipse.py | 2 +- .../sands/mathematical_shapes/rectangle.py | 2 +- .../anatomical_target_position.py | 2 +- .../sands/miscellaneous/coordinate_point.py | 2 +- .../qualitative_relation_assessment.py | 2 +- .../quantitative_relation_assessment.py | 2 +- .../sands/miscellaneous/single_color.py | 2 +- .../miscellaneous/viewer_specification.py | 2 +- .../non_atlas/custom_anatomical_entity.py | 2 +- .../sands/non_atlas/custom_annotation.py | 2 +- .../non_atlas/custom_coordinate_space.py | 2 +- .../activity/cranial_window_preparation.py | 2 +- .../activity/tissue_culture_preparation.py | 2 +- .../activity/tissue_sample_slicing.py | 2 +- .../specimen_prep/device/slicing_device.py | 2 +- .../device/slicing_device_usage.py | 2 +- .../activity/stimulation_activity.py | 2 +- .../stimulation/stimulus/ephys_stimulus.py | 2 +- fairgraph/queries.py | 23 +-- fairgraph/registry.py | 1 - fairgraph/utility.py | 97 ++++++++- test/test_base.py | 38 ++-- test/test_client.py | 16 +- .../core/accountinformation_simple_query.json | 8 +- .../core/behavioralprotocol_simple_query.json | 18 +- .../openminds/core/comment_simple_query.json | 10 +- .../core/configuration_simple_query.json | 12 +- .../core/consortium_simple_query.json | 34 ++-- .../core/contactinformation_simple_query.json | 6 +- .../core/contenttype_simple_query.json | 26 +-- .../core/contenttypepattern_simple_query.json | 10 +- .../openminds/core/dataset_simple_query.json | 26 +-- .../core/dataset_simple_query_v4.json | 163 --------------- .../core/datasetversion_simple_query.json | 92 ++++----- .../openminds/core/doi_simple_query.json | 10 +- .../openminds/core/file_simple_query.json | 54 ++--- .../core/filearchive_simple_query.json | 12 +- .../core/filebundle_simple_query.json | 44 ++--- .../core/filerepository_simple_query.json | 38 ++-- .../filerepositorystructure_simple_query.json | 12 +- .../openminds/core/funding_simple_query.json | 12 +- .../openminds/core/gridid_simple_query.json | 6 +- .../openminds/core/handle_simple_query.json | 6 +- .../identifiersdotorgid_simple_query.json | 6 +- .../openminds/core/isbn_simple_query.json | 10 +- .../openminds/core/issn_simple_query.json | 8 +- .../openminds/core/license_simple_query.json | 12 +- .../core/metadatamodel_simple_query.json | 26 +-- .../metadatamodelversion_simple_query.json | 72 +++---- .../openminds/core/model_simple_query.json | 32 +-- .../core/modelversion_simple_query.json | 84 ++++---- .../openminds/core/orcid_simple_query.json | 6 +- .../core/organization_simple_query.json | 48 ++--- .../openminds/core/person_newstyle_query.json | 186 +++++++++--------- .../core/person_resolved-1_query.json | 142 ++++++------- .../openminds/core/person_simple_query.json | 44 ++--- .../openminds/core/project_simple_query.json | 14 +- .../core/propertyvaluelist_simple_query.json | 46 ++--- .../openminds/core/protocol_simple_query.json | 14 +- .../core/protocolexecution_simple_query.json | 156 +++++++-------- .../quantitativevaluearray_simple_query.json | 12 +- .../researchproductgroup_simple_query.json | 6 +- .../openminds/core/rorid_simple_query.json | 6 +- .../openminds/core/rrid_simple_query.json | 6 +- .../core/servicelink_simple_query.json | 12 +- .../openminds/core/setup_simple_query.json | 18 +- .../openminds/core/software_simple_query.json | 26 +-- .../core/softwareversion_simple_query.json | 92 ++++----- .../openminds/core/strain_simple_query.json | 38 ++-- .../openminds/core/subject_simple_query.json | 20 +- .../core/subjectgroup_simple_query.json | 24 +-- .../core/subjectgroupstate_simple_query.json | 100 +++++----- .../core/subjectstate_simple_query.json | 102 +++++----- .../openminds/core/swhid_simple_query.json | 6 +- .../core/tissuesample_simple_query.json | 28 +-- .../tissuesamplecollection_simple_query.json | 32 +-- ...suesamplecollectionstate_simple_query.json | 96 ++++----- .../core/tissuesamplestate_simple_query.json | 98 ++++----- .../core/webresource_simple_query.json | 18 +- .../core/webservice_simple_query.json | 28 +-- .../core/webserviceversion_simple_query.json | 70 +++---- test/test_openminds_computation.py | 22 +-- test/test_openminds_core.py | 70 +++---- test/test_queries.py | 175 ++++++++-------- test/test_utility.py | 64 +++++- test/utils.py | 26 +-- 293 files changed, 1687 insertions(+), 1743 deletions(-) delete mode 100644 test/test_data/queries/openminds/core/dataset_simple_query_v4.json diff --git a/builder/update_openminds.py b/builder/update_openminds.py index dc8045ff..b8f0b990 100644 --- a/builder/update_openminds.py +++ b/builder/update_openminds.py @@ -586,17 +586,6 @@ def get_controlled_terms_table(type_): } -def get_type_from_schema(schema_payload, override=True): - if override: # temporarily use the old namespaces, until the KG is updated - cls_name = schema_payload["_type"].split("/")[-1] - module_name = schema_payload['_module'] - if module_name == "SANDS": - module_name = "sands" - return f"https://openminds.ebrains.eu/{module_name}/{cls_name}" - else: - return schema_payload["_type"] - - class FairgraphClassBuilder: """docstring""" @@ -783,7 +772,7 @@ def get_type(prop): "module_name": module_name, "class_name": class_name, "default_space": default_space, - "openminds_type": get_type_from_schema(self._schema_payload, override=True), + "openminds_type": self._schema_payload["_type"], "properties": sorted(properties, key=lambda p: p["name"]), "reverse_properties": sorted(reverse_properties, key=lambda p: p["name"]), "additional_methods": "", diff --git a/fairgraph/client.py b/fairgraph/client.py index b680be09..5f0fd410 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -19,6 +19,7 @@ # limitations under the License. from __future__ import annotations +from copy import deepcopy import os import logging from typing import Any, Dict, Iterable, List, Optional, Union, TYPE_CHECKING @@ -36,7 +37,7 @@ from openminds.registry import lookup_type from .errors import AuthenticationError, AuthorizationError, ResourceExistsError -from .queries import migrate_query +from .utility import adapt_namespaces_for_query, adapt_namespaces_3to4, adapt_namespaces_4to3, adapt_type_4to3 if TYPE_CHECKING: from .kgobject import KGObject @@ -134,7 +135,7 @@ def __init__( self.cache: Dict[str, JsonLdDocument] = {} self._query_cache: Dict[str, str] = {} self.accepted_terms_of_use = False - self.migrated = None + self._migrated = None @property def _kg_admin_client(self): @@ -183,8 +184,25 @@ def _check_response( else: raise Exception(f"Error: {response.error} {error_context}") else: + if self.migrated is False: + adapt_namespaces_3to4(response.data) return response + @property + def migrated(self): + # This is a temporary work-around for use during the transitional period + # from openMINDS v3 to v4 (change of namespace) + if self._migrated is None: + self._migrated = True # to stop the call to _check_response() in instance_from_full_uri from recurring + + # This is the released controlled term for "left handedness", which should be accessible to everyone + result = self.instance_from_full_uri("https://kg.ebrains.eu/api/instances/92631f2e-fc6e-4122-8015-a0731c67f66c", scope="released") + if "om-i.org" in result["@type"]: + self._migrated = True + else: + self._migrated = False + return self._migrated + def query( self, query: Dict[str, Any], @@ -216,18 +234,8 @@ def query( along with metadata about the query results such as total number of instances, and pagination information. """ - # the following section is a temporary work-around for use during the transitional period - # from openMINDS v3 to v4 (change of namespace) - if self.migrated is None: - # this is the released controlled term for "left handedness", which should be accessible to everyone - result = self.instance_from_full_uri("https://kg.ebrains.eu/api/instances/92631f2e-fc6e-4122-8015-a0731c67f66c", scope="released") - if "om-i.org" in result["@type"]: - self.migrated = True - else: - self.migrated = False - - if self.migrated: - query = migrate_query(query) + if self.migrated is False: + query = adapt_namespaces_for_query(query) query_id = query.get("@id", None) @@ -282,9 +290,9 @@ def _query(scope, from_index, size): response.data = list(instances.values())[from_index : from_index + size] response.size = len(response.data) response.total = len(instances) - return response else: - return _query(scope, from_index, size) + response = _query(scope, from_index, size) + return response def list( self, @@ -311,6 +319,9 @@ def list( along with metadata about the query results such as total number of instances, and pagination information. """ + if self.migrated is False: + target_type = adapt_type_4to3(target_type) + def _list(scope, from_index, size): response = self._kg_client.instances.list( stage=STAGE_MAP[scope], @@ -414,6 +425,9 @@ def create_new_instance( """ if "'@id': None" in str(data): raise ValueError("payload contains undefined ids") + if self.migrated is False: + data = deepcopy(data) + adapt_namespaces_4to3(data) if instance_id: response = self._kg_client.instances.create_new_with_id( space=space, @@ -438,6 +452,9 @@ def update_instance(self, instance_id: str, data: JsonLdDocument) -> JsonLdDocum instance_id (UUID): the instance's persistent identifier. data (dict): a JSON-LD document that modifies some or all of the data of the existing instance. """ + if self.migrated is False: + data = deepcopy(data) + adapt_namespaces_4to3(data) response = self._kg_client.instances.contribute_to_partial_replacement( instance_id=instance_id, payload=data, @@ -454,6 +471,9 @@ def replace_instance(self, instance_id: str, data: JsonLdDocument) -> JsonLdDocu instance_id (UUID): the instance's persistent identifier. data (dict): a JSON-LD document that will replace the existing instance. """ + if self.migrated is False: + data = deepcopy(data) + adapt_namespaces_4to3(data) response = self._kg_client.instances.contribute_to_full_replacement( instance_id=instance_id, payload=data, diff --git a/fairgraph/embedded.py b/fairgraph/embedded.py index b35c6bf3..8d1951c4 100644 --- a/fairgraph/embedded.py +++ b/fairgraph/embedded.py @@ -90,7 +90,6 @@ def save( Save to the KG any sub-components of the metadata object that are KGObjects. """ for prop in self.properties: - assert prop.intrinsic # embedded metadata should not contain any reverse properties values = getattr(self, prop.name) for value in as_list(values): if isinstance(value, ContainsMetadata): diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index 092e1028..c06b6e5d 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -156,7 +156,6 @@ def from_uri( results = client.query(query, instance_id=client.uuid_from_uri(uri), size=1, scope=scope).data if results: data = results[0] - data["@context"] = cls.context else: data = None else: @@ -236,7 +235,11 @@ def from_id( if follow_links is not None: raise NotImplementedError data = client.instance_from_full_uri(uri, use_cache=use_cache, scope=scope) - cls_from_data = lookup_type(data["@type"][0]) + type_ = data["@type"] + if isinstance(type_, list): + assert len(type_) == 1 + type_ = type_[0] + cls_from_data = lookup_type(type_) return cls_from_data.from_jsonld(data, scope=scope) @classmethod @@ -365,8 +368,6 @@ def list( size=size, scope=scope, ).data - for instance in instances: - instance["@context"] = cls.context elif api == "core": if filters: raise ValueError("Cannot use filters with api='core'") @@ -438,7 +439,7 @@ def _update_empty_properties(self, data: JSONdict): setattr(self, prop.name, value) assert self.remote_data is not None for key, value in data.items(): - if not key.startswith("Q"): + if not (key.startswith("Q") or key == "@context"): expanded_path = expand_uri(key, cls.context) assert isinstance(expanded_path, str) self.remote_data[expanded_path] = data[key] @@ -913,7 +914,6 @@ def children( self.resolve(client, follow_links=follow_links) all_children = [] for prop in self.properties: - assert prop.intrinsic if prop.is_link: children = as_list(getattr(self, prop.name)) all_children.extend(children) diff --git a/fairgraph/kgproxy.py b/fairgraph/kgproxy.py index 6d96c7b3..d7a711bd 100644 --- a/fairgraph/kgproxy.py +++ b/fairgraph/kgproxy.py @@ -22,6 +22,7 @@ import logging from typing import List, Optional, Tuple, Union, Dict, Any, TYPE_CHECKING +from openminds.base import Link from openminds.registry import lookup from .errors import ResolutionFailure @@ -36,7 +37,7 @@ logger = logging.getLogger("fairgraph") -class KGProxy(RepresentsSingleObject): +class KGProxy(RepresentsSingleObject, Link): """ Representation of an KGObject whose identifier, and possibly type, are known but whose other metadata have not been retrieved from the KG. @@ -81,6 +82,7 @@ def __init__( self.id = uri self.preferred_scope = preferred_scope self.remote_data = None + Link.__init__(self, self.id, allowed_types=self.classes) @property def type(self) -> List[str]: diff --git a/fairgraph/node.py b/fairgraph/node.py index f7cf6331..a3bbc01b 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -34,19 +34,11 @@ JSONdict = Dict[str, Any] # see https://github.com/python/typing/issues/182 for some possible improvements -default_context = { - "v3": { - "@vocab": "https://openminds.ebrains.eu/vocab/", - }, - "v4": { - "@vocab": "https://openminds.om-i.org/props/" - } -} - class ContainsMetadata(Resolvable, metaclass=Node): # KGObject and EmbeddedMetadata + properties: List[Property] reverse_properties: List[Property] = [] - context: Dict[str, str] = default_context["v3"] + context: Dict[str, str] type_: str scope: Optional[str] space: Union[str, None] @@ -216,13 +208,13 @@ def generate_query_properties(cls, follow_links: Optional[Dict[str, Any]] = None for prop in cls.all_properties: if prop.is_link and follow_links: if prop.name in follow_links: - properties.extend(get_query_properties(prop, follow_links[prop.name])) + properties.extend(get_query_properties(prop, cls.context, follow_links[prop.name])) elif reverse_aliases.get(prop.name, None) in follow_links: - properties.extend(get_query_properties(prop, follow_links[reverse_aliases[prop.name]])) + properties.extend(get_query_properties(prop, cls.context, follow_links[reverse_aliases[prop.name]])) else: - properties.extend(get_query_properties(prop)) + properties.extend(get_query_properties(prop, cls.context)) else: - properties.extend(get_query_properties(prop)) + properties.extend(get_query_properties(prop, cls.context)) return properties @classmethod @@ -240,7 +232,7 @@ def generate_query_filter_properties( properties = [] for prop in cls.all_properties: if prop.name in filters: - properties.append(get_query_filter_property(prop, filters[prop.name])) + properties.append(get_query_filter_property(prop, cls.context, filters[prop.name])) return properties @classmethod @@ -249,7 +241,7 @@ def _deserialize_data(cls, data: JSONdict, include_id: bool = False): def _get_type_from_data(data_item): # KG returns a list of types, openMINDS expects only a single string if isinstance(data_item, dict) and "@type" in data_item: - if isinstance(data_item["@type"], list): + if isinstance(data_item["@type"], (list, tuple)): assert len(data_item["@type"]) == 1 return data_item["@type"][0] else: @@ -274,18 +266,13 @@ def _normalize_type(data_item): raise TypeError("type mismatch {} - {}".format(cls.type_, type_from_data)) # normalize data by expanding keys - if "om-i.org" in type_from_data: - context = default_context["v4"] - else: - context = default_context["v3"] - D = {"@type": type_from_data} if include_id: D["@id"] = data["@id"] for key, value in data.items(): if "__" in key: key, type_filter = key.split("__") - normalised_key = expand_uri(key, context) + normalised_key = expand_uri(key, cls.context) value = [item for item in as_list(value) if _get_type_from_data(item).endswith(type_filter)] if normalised_key in D: D[normalised_key].extend(value) @@ -294,12 +281,12 @@ def _normalize_type(data_item): elif key.startswith("Q"): # for 'Q' properties in data from queries D[key] = value elif key[0] != "@": - normalised_key = expand_uri(key, context) + normalised_key = expand_uri(key, cls.context) D[normalised_key] = value deserialized_data = {} for prop in cls.all_properties: - expanded_path = expand_uri(prop.path, context) + expanded_path = expand_uri(prop.path, cls.context) data_item = _normalize_type(D.get(expanded_path)) if data_item is not None and prop.reverse: diff --git a/fairgraph/openminds/chemicals/amount_of_chemical.py b/fairgraph/openminds/chemicals/amount_of_chemical.py index f4e11536..f9c516f1 100644 --- a/fairgraph/openminds/chemicals/amount_of_chemical.py +++ b/fairgraph/openminds/chemicals/amount_of_chemical.py @@ -14,7 +14,7 @@ class AmountOfChemical(EmbeddedMetadata, AmountOfChemical): Structured information about the amount of a given chemical that was used. """ - type_ = "https://openminds.ebrains.eu/chemicals/AmountOfChemical" + type_ = "https://openminds.om-i.org/types/AmountOfChemical" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/chemicals/chemical_mixture.py b/fairgraph/openminds/chemicals/chemical_mixture.py index 7435385f..1ec85633 100644 --- a/fairgraph/openminds/chemicals/chemical_mixture.py +++ b/fairgraph/openminds/chemicals/chemical_mixture.py @@ -14,7 +14,7 @@ class ChemicalMixture(KGObject, ChemicalMixture): Structured information about a mixture of chemical substances. """ - type_ = "https://openminds.ebrains.eu/chemicals/ChemicalMixture" + type_ = "https://openminds.om-i.org/types/ChemicalMixture" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/chemicals/chemical_substance.py b/fairgraph/openminds/chemicals/chemical_substance.py index 8c9fdabd..36bac286 100644 --- a/fairgraph/openminds/chemicals/chemical_substance.py +++ b/fairgraph/openminds/chemicals/chemical_substance.py @@ -14,7 +14,7 @@ class ChemicalSubstance(KGObject, ChemicalSubstance): Structured information about a chemical substance. """ - type_ = "https://openminds.ebrains.eu/chemicals/ChemicalSubstance" + type_ = "https://openminds.om-i.org/types/ChemicalSubstance" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/chemicals/product_source.py b/fairgraph/openminds/chemicals/product_source.py index e52b5844..5e61acba 100644 --- a/fairgraph/openminds/chemicals/product_source.py +++ b/fairgraph/openminds/chemicals/product_source.py @@ -14,7 +14,7 @@ class ProductSource(KGObject, ProductSource): Structured information about the source of a chemical substance or mixture. """ - type_ = "https://openminds.ebrains.eu/chemicals/ProductSource" + type_ = "https://openminds.om-i.org/types/ProductSource" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/data_analysis.py b/fairgraph/openminds/computation/data_analysis.py index 80cba153..cf7d4957 100644 --- a/fairgraph/openminds/computation/data_analysis.py +++ b/fairgraph/openminds/computation/data_analysis.py @@ -17,7 +17,7 @@ class DataAnalysis(KGObject, DataAnalysis): Structured information on inspecting, cleansing, transforming, and modelling data. """ - type_ = "https://openminds.ebrains.eu/computation/DataAnalysis" + type_ = "https://openminds.om-i.org/types/DataAnalysis" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/data_copy.py b/fairgraph/openminds/computation/data_copy.py index 5363fc22..655e339b 100644 --- a/fairgraph/openminds/computation/data_copy.py +++ b/fairgraph/openminds/computation/data_copy.py @@ -17,7 +17,7 @@ class DataCopy(KGObject, DataCopy): """ - type_ = "https://openminds.ebrains.eu/computation/DataCopy" + type_ = "https://openminds.om-i.org/types/DataCopy" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/environment.py b/fairgraph/openminds/computation/environment.py index 61c90995..6777da3d 100644 --- a/fairgraph/openminds/computation/environment.py +++ b/fairgraph/openminds/computation/environment.py @@ -14,7 +14,7 @@ class Environment(KGObject, Environment): Structured information on the computer system or set of systems in which a computation is deployed and executed. """ - type_ = "https://openminds.ebrains.eu/computation/Environment" + type_ = "https://openminds.om-i.org/types/Environment" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/generic_computation.py b/fairgraph/openminds/computation/generic_computation.py index 73129754..e4d461a9 100644 --- a/fairgraph/openminds/computation/generic_computation.py +++ b/fairgraph/openminds/computation/generic_computation.py @@ -17,7 +17,7 @@ class GenericComputation(KGObject, GenericComputation): Structured information about a computation whose type is unknown or unspecified. """ - type_ = "https://openminds.ebrains.eu/computation/GenericComputation" + type_ = "https://openminds.om-i.org/types/GenericComputation" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/hardware_system.py b/fairgraph/openminds/computation/hardware_system.py index 1c43dcef..cf5f5f51 100644 --- a/fairgraph/openminds/computation/hardware_system.py +++ b/fairgraph/openminds/computation/hardware_system.py @@ -14,7 +14,7 @@ class HardwareSystem(KGObject, HardwareSystem): Structured information about computing hardware. """ - type_ = "https://openminds.ebrains.eu/computation/HardwareSystem" + type_ = "https://openminds.om-i.org/types/HardwareSystem" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/launch_configuration.py b/fairgraph/openminds/computation/launch_configuration.py index 49dd446e..d0d378c3 100644 --- a/fairgraph/openminds/computation/launch_configuration.py +++ b/fairgraph/openminds/computation/launch_configuration.py @@ -14,7 +14,7 @@ class LaunchConfiguration(KGObject, LaunchConfiguration): Structured information about the launch of a computational process. """ - type_ = "https://openminds.ebrains.eu/computation/LaunchConfiguration" + type_ = "https://openminds.om-i.org/types/LaunchConfiguration" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/local_file.py b/fairgraph/openminds/computation/local_file.py index ac53962a..0f988746 100644 --- a/fairgraph/openminds/computation/local_file.py +++ b/fairgraph/openminds/computation/local_file.py @@ -14,7 +14,7 @@ class LocalFile(KGObject, LocalFile): Structured information about a file that is not accessible via a URL. """ - type_ = "https://openminds.ebrains.eu/computation/LocalFile" + type_ = "https://openminds.om-i.org/types/LocalFile" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/model_validation.py b/fairgraph/openminds/computation/model_validation.py index cd606e93..8487f3df 100644 --- a/fairgraph/openminds/computation/model_validation.py +++ b/fairgraph/openminds/computation/model_validation.py @@ -18,7 +18,7 @@ class ModelValidation(KGObject, ModelValidation): Structured information about a process of validating a computational model. """ - type_ = "https://openminds.ebrains.eu/computation/ModelValidation" + type_ = "https://openminds.om-i.org/types/ModelValidation" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/optimization.py b/fairgraph/openminds/computation/optimization.py index 8f739724..7c8a2fc1 100644 --- a/fairgraph/openminds/computation/optimization.py +++ b/fairgraph/openminds/computation/optimization.py @@ -17,7 +17,7 @@ class Optimization(KGObject, Optimization): Structured information about a process of optimizing a model or a piece of code. """ - type_ = "https://openminds.ebrains.eu/computation/Optimization" + type_ = "https://openminds.om-i.org/types/Optimization" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/simulation.py b/fairgraph/openminds/computation/simulation.py index ca469918..b974fd37 100644 --- a/fairgraph/openminds/computation/simulation.py +++ b/fairgraph/openminds/computation/simulation.py @@ -17,7 +17,7 @@ class Simulation(KGObject, Simulation): Structured information about a process of running simulations of a computational model. """ - type_ = "https://openminds.ebrains.eu/computation/Simulation" + type_ = "https://openminds.om-i.org/types/Simulation" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/software_agent.py b/fairgraph/openminds/computation/software_agent.py index 1c78eaaa..61e782bb 100644 --- a/fairgraph/openminds/computation/software_agent.py +++ b/fairgraph/openminds/computation/software_agent.py @@ -14,7 +14,7 @@ class SoftwareAgent(KGObject, SoftwareAgent): Structured information about a piece of software or web service that can perform a task autonomously. """ - type_ = "https://openminds.ebrains.eu/computation/SoftwareAgent" + type_ = "https://openminds.om-i.org/types/SoftwareAgent" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/validation_test.py b/fairgraph/openminds/computation/validation_test.py index 9c2a485e..48606dbf 100644 --- a/fairgraph/openminds/computation/validation_test.py +++ b/fairgraph/openminds/computation/validation_test.py @@ -17,7 +17,7 @@ class ValidationTest(KGObject, ValidationTest): Structured information about the definition of a process for validating a computational model. """ - type_ = "https://openminds.ebrains.eu/computation/ValidationTest" + type_ = "https://openminds.om-i.org/types/ValidationTest" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/validation_test_version.py b/fairgraph/openminds/computation/validation_test_version.py index 1b2c57aa..05ba3683 100644 --- a/fairgraph/openminds/computation/validation_test_version.py +++ b/fairgraph/openminds/computation/validation_test_version.py @@ -19,7 +19,7 @@ class ValidationTestVersion(KGObject, ValidationTestVersion): Structured information about a specific implementation of a validation test. """ - type_ = "https://openminds.ebrains.eu/computation/ValidationTestVersion" + type_ = "https://openminds.om-i.org/types/ValidationTestVersion" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/visualization.py b/fairgraph/openminds/computation/visualization.py index d406f313..3be6aa9d 100644 --- a/fairgraph/openminds/computation/visualization.py +++ b/fairgraph/openminds/computation/visualization.py @@ -17,7 +17,7 @@ class Visualization(KGObject, Visualization): Structured information about a process of visualizing a computational model, a computational process, or a dataset. """ - type_ = "https://openminds.ebrains.eu/computation/Visualization" + type_ = "https://openminds.om-i.org/types/Visualization" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/workflow_execution.py b/fairgraph/openminds/computation/workflow_execution.py index b37c1ee4..5488a431 100644 --- a/fairgraph/openminds/computation/workflow_execution.py +++ b/fairgraph/openminds/computation/workflow_execution.py @@ -14,7 +14,7 @@ class WorkflowExecution(KGObject, WorkflowExecution): Structured information about an execution of a computational workflow. """ - type_ = "https://openminds.ebrains.eu/computation/WorkflowExecution" + type_ = "https://openminds.om-i.org/types/WorkflowExecution" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/computation/workflow_recipe.py b/fairgraph/openminds/computation/workflow_recipe.py index 882e8448..937780e1 100644 --- a/fairgraph/openminds/computation/workflow_recipe.py +++ b/fairgraph/openminds/computation/workflow_recipe.py @@ -17,7 +17,7 @@ class WorkflowRecipe(KGObject, WorkflowRecipe): Structured information about the description of a prospective workflow. """ - type_ = "https://openminds.ebrains.eu/computation/WorkflowRecipe" + type_ = "https://openminds.om-i.org/types/WorkflowRecipe" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/computation/workflow_recipe_version.py b/fairgraph/openminds/computation/workflow_recipe_version.py index 206b2a44..6d2fbed4 100644 --- a/fairgraph/openminds/computation/workflow_recipe_version.py +++ b/fairgraph/openminds/computation/workflow_recipe_version.py @@ -18,7 +18,7 @@ class WorkflowRecipeVersion(KGObject, WorkflowRecipeVersion): Structured information about a specific implemented version of a workflow recipe. """ - type_ = "https://openminds.ebrains.eu/computation/WorkflowRecipeVersion" + type_ = "https://openminds.om-i.org/types/WorkflowRecipeVersion" default_space = "computation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/action_status_type.py b/fairgraph/openminds/controlled_terms/action_status_type.py index 41a6c472..74341b88 100644 --- a/fairgraph/openminds/controlled_terms/action_status_type.py +++ b/fairgraph/openminds/controlled_terms/action_status_type.py @@ -17,7 +17,7 @@ class ActionStatusType(KGObject, ActionStatusType): Structured information about the status of an action. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ActionStatusType" + type_ = "https://openminds.om-i.org/types/ActionStatusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/age_category.py b/fairgraph/openminds/controlled_terms/age_category.py index 9a5778a9..2003c2d4 100644 --- a/fairgraph/openminds/controlled_terms/age_category.py +++ b/fairgraph/openminds/controlled_terms/age_category.py @@ -17,7 +17,7 @@ class AgeCategory(KGObject, AgeCategory): Structured information on the life cycle (semantic term) of a specific age group. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AgeCategory" + type_ = "https://openminds.om-i.org/types/AgeCategory" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/analysis_technique.py b/fairgraph/openminds/controlled_terms/analysis_technique.py index cbbc07e5..8b2d3c57 100644 --- a/fairgraph/openminds/controlled_terms/analysis_technique.py +++ b/fairgraph/openminds/controlled_terms/analysis_technique.py @@ -17,7 +17,7 @@ class AnalysisTechnique(KGObject, AnalysisTechnique): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AnalysisTechnique" + type_ = "https://openminds.om-i.org/types/AnalysisTechnique" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py index d041b7a6..e94c1ab1 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py +++ b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py @@ -17,7 +17,7 @@ class AnatomicalAxesOrientation(KGObject, AnatomicalAxesOrientation): Structured information on the anatomical directions of the X, Y, and Z axis. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AnatomicalAxesOrientation" + type_ = "https://openminds.om-i.org/types/AnatomicalAxesOrientation" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py index d990e0c0..63ad5b28 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py +++ b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py @@ -17,7 +17,7 @@ class AnatomicalIdentificationType(KGObject, AnatomicalIdentificationType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AnatomicalIdentificationType" + type_ = "https://openminds.om-i.org/types/AnatomicalIdentificationType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/anatomical_plane.py b/fairgraph/openminds/controlled_terms/anatomical_plane.py index 68067b65..6e323dc5 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_plane.py +++ b/fairgraph/openminds/controlled_terms/anatomical_plane.py @@ -17,7 +17,7 @@ class AnatomicalPlane(KGObject, AnatomicalPlane): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AnatomicalPlane" + type_ = "https://openminds.om-i.org/types/AnatomicalPlane" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py index f4ff3ad8..ab51999d 100644 --- a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py @@ -17,7 +17,7 @@ class AnnotationCriteriaType(KGObject, AnnotationCriteriaType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AnnotationCriteriaType" + type_ = "https://openminds.om-i.org/types/AnnotationCriteriaType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/annotation_type.py b/fairgraph/openminds/controlled_terms/annotation_type.py index 3d328654..bba5d5a5 100644 --- a/fairgraph/openminds/controlled_terms/annotation_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_type.py @@ -17,7 +17,7 @@ class AnnotationType(KGObject, AnnotationType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AnnotationType" + type_ = "https://openminds.om-i.org/types/AnnotationType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/atlas_type.py b/fairgraph/openminds/controlled_terms/atlas_type.py index 6a6e60e2..050db47a 100644 --- a/fairgraph/openminds/controlled_terms/atlas_type.py +++ b/fairgraph/openminds/controlled_terms/atlas_type.py @@ -17,7 +17,7 @@ class AtlasType(KGObject, AtlasType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AtlasType" + type_ = "https://openminds.om-i.org/types/AtlasType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py index e1b89383..03600ecc 100644 --- a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py @@ -17,7 +17,7 @@ class AuditoryStimulusType(KGObject, AuditoryStimulusType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/AuditoryStimulusType" + type_ = "https://openminds.om-i.org/types/AuditoryStimulusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/biological_order.py b/fairgraph/openminds/controlled_terms/biological_order.py index 7a30e341..4449b14c 100644 --- a/fairgraph/openminds/controlled_terms/biological_order.py +++ b/fairgraph/openminds/controlled_terms/biological_order.py @@ -17,7 +17,7 @@ class BiologicalOrder(KGObject, BiologicalOrder): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/BiologicalOrder" + type_ = "https://openminds.om-i.org/types/BiologicalOrder" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/biological_process.py b/fairgraph/openminds/controlled_terms/biological_process.py index 0f2d9993..e529723b 100644 --- a/fairgraph/openminds/controlled_terms/biological_process.py +++ b/fairgraph/openminds/controlled_terms/biological_process.py @@ -17,7 +17,7 @@ class BiologicalProcess(KGObject, BiologicalProcess): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/BiologicalProcess" + type_ = "https://openminds.om-i.org/types/BiologicalProcess" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/biological_sex.py b/fairgraph/openminds/controlled_terms/biological_sex.py index 5c5459a1..0bce5b3d 100644 --- a/fairgraph/openminds/controlled_terms/biological_sex.py +++ b/fairgraph/openminds/controlled_terms/biological_sex.py @@ -17,7 +17,7 @@ class BiologicalSex(KGObject, BiologicalSex): Structured information on the biological sex of a subject. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/BiologicalSex" + type_ = "https://openminds.om-i.org/types/BiologicalSex" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/breeding_type.py b/fairgraph/openminds/controlled_terms/breeding_type.py index c556857a..6885631a 100644 --- a/fairgraph/openminds/controlled_terms/breeding_type.py +++ b/fairgraph/openminds/controlled_terms/breeding_type.py @@ -17,7 +17,7 @@ class BreedingType(KGObject, BreedingType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/BreedingType" + type_ = "https://openminds.om-i.org/types/BreedingType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/cell_culture_type.py b/fairgraph/openminds/controlled_terms/cell_culture_type.py index 1a86e70f..9e471178 100644 --- a/fairgraph/openminds/controlled_terms/cell_culture_type.py +++ b/fairgraph/openminds/controlled_terms/cell_culture_type.py @@ -17,7 +17,7 @@ class CellCultureType(KGObject, CellCultureType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/CellCultureType" + type_ = "https://openminds.om-i.org/types/CellCultureType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/cell_type.py b/fairgraph/openminds/controlled_terms/cell_type.py index 6eac3954..d7448477 100644 --- a/fairgraph/openminds/controlled_terms/cell_type.py +++ b/fairgraph/openminds/controlled_terms/cell_type.py @@ -17,7 +17,7 @@ class CellType(KGObject, CellType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/CellType" + type_ = "https://openminds.om-i.org/types/CellType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py index bbab89ba..a3f0b0f3 100644 --- a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py +++ b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py @@ -17,7 +17,7 @@ class ChemicalMixtureType(KGObject, ChemicalMixtureType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ChemicalMixtureType" + type_ = "https://openminds.om-i.org/types/ChemicalMixtureType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/colormap.py b/fairgraph/openminds/controlled_terms/colormap.py index 072a8a65..e48f5ed3 100644 --- a/fairgraph/openminds/controlled_terms/colormap.py +++ b/fairgraph/openminds/controlled_terms/colormap.py @@ -17,7 +17,7 @@ class Colormap(KGObject, Colormap): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Colormap" + type_ = "https://openminds.om-i.org/types/Colormap" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/contribution_type.py b/fairgraph/openminds/controlled_terms/contribution_type.py index b162fd6b..7a39edaf 100644 --- a/fairgraph/openminds/controlled_terms/contribution_type.py +++ b/fairgraph/openminds/controlled_terms/contribution_type.py @@ -17,7 +17,7 @@ class ContributionType(KGObject, ContributionType): Structured information on the type of contribution a person or organization performed. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ContributionType" + type_ = "https://openminds.om-i.org/types/ContributionType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py index 0f6ac9a1..73a16e8c 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py @@ -17,7 +17,7 @@ class CranialWindowConstructionType(KGObject, CranialWindowConstructionType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/CranialWindowConstructionType" + type_ = "https://openminds.om-i.org/types/CranialWindowConstructionType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py index 658def24..f32c26d7 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py @@ -17,7 +17,7 @@ class CranialWindowReinforcementType(KGObject, CranialWindowReinforcementType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/CranialWindowReinforcementType" + type_ = "https://openminds.om-i.org/types/CranialWindowReinforcementType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/criteria_quality_type.py b/fairgraph/openminds/controlled_terms/criteria_quality_type.py index d3bf9916..a751d594 100644 --- a/fairgraph/openminds/controlled_terms/criteria_quality_type.py +++ b/fairgraph/openminds/controlled_terms/criteria_quality_type.py @@ -17,7 +17,7 @@ class CriteriaQualityType(KGObject, CriteriaQualityType): Structured information on the quality type of the defined criteria for a measurement. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/CriteriaQualityType" + type_ = "https://openminds.om-i.org/types/CriteriaQualityType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/data_type.py b/fairgraph/openminds/controlled_terms/data_type.py index 50fc701e..1497fbdf 100644 --- a/fairgraph/openminds/controlled_terms/data_type.py +++ b/fairgraph/openminds/controlled_terms/data_type.py @@ -17,7 +17,7 @@ class DataType(KGObject, DataType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/DataType" + type_ = "https://openminds.om-i.org/types/DataType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/device_type.py b/fairgraph/openminds/controlled_terms/device_type.py index 9e20c6d7..6f88a66c 100644 --- a/fairgraph/openminds/controlled_terms/device_type.py +++ b/fairgraph/openminds/controlled_terms/device_type.py @@ -17,7 +17,7 @@ class DeviceType(KGObject, DeviceType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/DeviceType" + type_ = "https://openminds.om-i.org/types/DeviceType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/difference_measure.py b/fairgraph/openminds/controlled_terms/difference_measure.py index af9d2a7b..971832e8 100644 --- a/fairgraph/openminds/controlled_terms/difference_measure.py +++ b/fairgraph/openminds/controlled_terms/difference_measure.py @@ -17,7 +17,7 @@ class DifferenceMeasure(KGObject, DifferenceMeasure): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/DifferenceMeasure" + type_ = "https://openminds.om-i.org/types/DifferenceMeasure" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/disease.py b/fairgraph/openminds/controlled_terms/disease.py index 85b12775..2cd5e17c 100644 --- a/fairgraph/openminds/controlled_terms/disease.py +++ b/fairgraph/openminds/controlled_terms/disease.py @@ -17,7 +17,7 @@ class Disease(KGObject, Disease): Structured information on a disease. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Disease" + type_ = "https://openminds.om-i.org/types/Disease" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/disease_model.py b/fairgraph/openminds/controlled_terms/disease_model.py index 18ec52ac..c0c193c8 100644 --- a/fairgraph/openminds/controlled_terms/disease_model.py +++ b/fairgraph/openminds/controlled_terms/disease_model.py @@ -17,7 +17,7 @@ class DiseaseModel(KGObject, DiseaseModel): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/DiseaseModel" + type_ = "https://openminds.om-i.org/types/DiseaseModel" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/educational_level.py b/fairgraph/openminds/controlled_terms/educational_level.py index d4890290..a2039468 100644 --- a/fairgraph/openminds/controlled_terms/educational_level.py +++ b/fairgraph/openminds/controlled_terms/educational_level.py @@ -17,7 +17,7 @@ class EducationalLevel(KGObject, EducationalLevel): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/EducationalLevel" + type_ = "https://openminds.om-i.org/types/EducationalLevel" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py index 03f6230d..1fd15f66 100644 --- a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py @@ -17,7 +17,7 @@ class ElectricalStimulusType(KGObject, ElectricalStimulusType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ElectricalStimulusType" + type_ = "https://openminds.om-i.org/types/ElectricalStimulusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/ethics_assessment.py b/fairgraph/openminds/controlled_terms/ethics_assessment.py index cbda236d..fff63db3 100644 --- a/fairgraph/openminds/controlled_terms/ethics_assessment.py +++ b/fairgraph/openminds/controlled_terms/ethics_assessment.py @@ -17,7 +17,7 @@ class EthicsAssessment(KGObject, EthicsAssessment): Structured information on the ethics assessment of a dataset. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/EthicsAssessment" + type_ = "https://openminds.om-i.org/types/EthicsAssessment" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/experimental_approach.py b/fairgraph/openminds/controlled_terms/experimental_approach.py index 33b8841f..6e270c97 100644 --- a/fairgraph/openminds/controlled_terms/experimental_approach.py +++ b/fairgraph/openminds/controlled_terms/experimental_approach.py @@ -17,7 +17,7 @@ class ExperimentalApproach(KGObject, ExperimentalApproach): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ExperimentalApproach" + type_ = "https://openminds.om-i.org/types/ExperimentalApproach" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py index 8a5b9ba4..ae7da719 100644 --- a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py +++ b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py @@ -17,7 +17,7 @@ class FileBundleGrouping(KGObject, FileBundleGrouping): Structured information on the grouping mechanism of a file bundle. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/FileBundleGrouping" + type_ = "https://openminds.om-i.org/types/FileBundleGrouping" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/file_repository_type.py b/fairgraph/openminds/controlled_terms/file_repository_type.py index 1562a09f..6d28d8bf 100644 --- a/fairgraph/openminds/controlled_terms/file_repository_type.py +++ b/fairgraph/openminds/controlled_terms/file_repository_type.py @@ -17,7 +17,7 @@ class FileRepositoryType(KGObject, FileRepositoryType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/FileRepositoryType" + type_ = "https://openminds.om-i.org/types/FileRepositoryType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/file_usage_role.py b/fairgraph/openminds/controlled_terms/file_usage_role.py index 3a180fb5..7748435c 100644 --- a/fairgraph/openminds/controlled_terms/file_usage_role.py +++ b/fairgraph/openminds/controlled_terms/file_usage_role.py @@ -17,7 +17,7 @@ class FileUsageRole(KGObject, FileUsageRole): Structured information on the usage role of a file instance or bundle. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/FileUsageRole" + type_ = "https://openminds.om-i.org/types/FileUsageRole" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/genetic_strain_type.py b/fairgraph/openminds/controlled_terms/genetic_strain_type.py index da9a90c2..e86732c2 100644 --- a/fairgraph/openminds/controlled_terms/genetic_strain_type.py +++ b/fairgraph/openminds/controlled_terms/genetic_strain_type.py @@ -17,7 +17,7 @@ class GeneticStrainType(KGObject, GeneticStrainType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/GeneticStrainType" + type_ = "https://openminds.om-i.org/types/GeneticStrainType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py index 4bbd2edc..538abf18 100644 --- a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py @@ -17,7 +17,7 @@ class GustatoryStimulusType(KGObject, GustatoryStimulusType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/GustatoryStimulusType" + type_ = "https://openminds.om-i.org/types/GustatoryStimulusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/handedness.py b/fairgraph/openminds/controlled_terms/handedness.py index 715d1faa..87553ca3 100644 --- a/fairgraph/openminds/controlled_terms/handedness.py +++ b/fairgraph/openminds/controlled_terms/handedness.py @@ -17,7 +17,7 @@ class Handedness(KGObject, Handedness): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Handedness" + type_ = "https://openminds.om-i.org/types/Handedness" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/language.py b/fairgraph/openminds/controlled_terms/language.py index 147555e9..0a8250ec 100644 --- a/fairgraph/openminds/controlled_terms/language.py +++ b/fairgraph/openminds/controlled_terms/language.py @@ -17,7 +17,7 @@ class Language(KGObject, Language): Structured information on the available language setting. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Language" + type_ = "https://openminds.om-i.org/types/Language" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/laterality.py b/fairgraph/openminds/controlled_terms/laterality.py index 8ef37a3a..8d3915f4 100644 --- a/fairgraph/openminds/controlled_terms/laterality.py +++ b/fairgraph/openminds/controlled_terms/laterality.py @@ -17,7 +17,7 @@ class Laterality(KGObject, Laterality): Structured information on the lateral direction. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Laterality" + type_ = "https://openminds.om-i.org/types/Laterality" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/learning_resource_type.py b/fairgraph/openminds/controlled_terms/learning_resource_type.py index e5a9b0eb..7356980c 100644 --- a/fairgraph/openminds/controlled_terms/learning_resource_type.py +++ b/fairgraph/openminds/controlled_terms/learning_resource_type.py @@ -17,7 +17,7 @@ class LearningResourceType(KGObject, LearningResourceType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/LearningResourceType" + type_ = "https://openminds.om-i.org/types/LearningResourceType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/measured_quantity.py b/fairgraph/openminds/controlled_terms/measured_quantity.py index 47920bf3..7875a106 100644 --- a/fairgraph/openminds/controlled_terms/measured_quantity.py +++ b/fairgraph/openminds/controlled_terms/measured_quantity.py @@ -17,7 +17,7 @@ class MeasuredQuantity(KGObject, MeasuredQuantity): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/MeasuredQuantity" + type_ = "https://openminds.om-i.org/types/MeasuredQuantity" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/measured_signal_type.py b/fairgraph/openminds/controlled_terms/measured_signal_type.py index 6b217ee3..848be7a4 100644 --- a/fairgraph/openminds/controlled_terms/measured_signal_type.py +++ b/fairgraph/openminds/controlled_terms/measured_signal_type.py @@ -17,7 +17,7 @@ class MeasuredSignalType(KGObject, MeasuredSignalType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/MeasuredSignalType" + type_ = "https://openminds.om-i.org/types/MeasuredSignalType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/meta_data_model_type.py b/fairgraph/openminds/controlled_terms/meta_data_model_type.py index c522b8c9..5bf0d7f2 100644 --- a/fairgraph/openminds/controlled_terms/meta_data_model_type.py +++ b/fairgraph/openminds/controlled_terms/meta_data_model_type.py @@ -17,7 +17,7 @@ class MetaDataModelType(KGObject, MetaDataModelType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/MetaDataModelType" + type_ = "https://openminds.om-i.org/types/MetaDataModelType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/model_abstraction_level.py b/fairgraph/openminds/controlled_terms/model_abstraction_level.py index 0f93ab53..8e8d05e9 100644 --- a/fairgraph/openminds/controlled_terms/model_abstraction_level.py +++ b/fairgraph/openminds/controlled_terms/model_abstraction_level.py @@ -17,7 +17,7 @@ class ModelAbstractionLevel(KGObject, ModelAbstractionLevel): Structured information on abstraction level of the computational model. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ModelAbstractionLevel" + type_ = "https://openminds.om-i.org/types/ModelAbstractionLevel" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/model_scope.py b/fairgraph/openminds/controlled_terms/model_scope.py index 5356c59c..5eda8e48 100644 --- a/fairgraph/openminds/controlled_terms/model_scope.py +++ b/fairgraph/openminds/controlled_terms/model_scope.py @@ -17,7 +17,7 @@ class ModelScope(KGObject, ModelScope): Structured information on the scope of the computational model. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ModelScope" + type_ = "https://openminds.om-i.org/types/ModelScope" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/molecular_entity.py b/fairgraph/openminds/controlled_terms/molecular_entity.py index 51e1096c..6e8b62e3 100644 --- a/fairgraph/openminds/controlled_terms/molecular_entity.py +++ b/fairgraph/openminds/controlled_terms/molecular_entity.py @@ -17,7 +17,7 @@ class MolecularEntity(KGObject, MolecularEntity): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/MolecularEntity" + type_ = "https://openminds.om-i.org/types/MolecularEntity" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py b/fairgraph/openminds/controlled_terms/mr_acquisition_type.py index 94992b75..b73e3190 100644 --- a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py +++ b/fairgraph/openminds/controlled_terms/mr_acquisition_type.py @@ -17,7 +17,7 @@ class MRAcquisitionType(KGObject, MRAcquisitionType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/MRAcquisitionType" + type_ = "https://openminds.om-i.org/types/MRAcquisitionType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py index 76ed421a..3ec02593 100644 --- a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py +++ b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py @@ -17,7 +17,7 @@ class MRIPulseSequence(KGObject, MRIPulseSequence): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/MRIPulseSequence" + type_ = "https://openminds.om-i.org/types/MRIPulseSequence" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/mri_weighting.py b/fairgraph/openminds/controlled_terms/mri_weighting.py index 3645eebc..a8c3f091 100644 --- a/fairgraph/openminds/controlled_terms/mri_weighting.py +++ b/fairgraph/openminds/controlled_terms/mri_weighting.py @@ -17,7 +17,7 @@ class MRIWeighting(KGObject, MRIWeighting): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/MRIWeighting" + type_ = "https://openminds.om-i.org/types/MRIWeighting" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py index bf724109..2ab5d3b3 100644 --- a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py @@ -17,7 +17,7 @@ class OlfactoryStimulusType(KGObject, OlfactoryStimulusType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/OlfactoryStimulusType" + type_ = "https://openminds.om-i.org/types/OlfactoryStimulusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/operating_device.py b/fairgraph/openminds/controlled_terms/operating_device.py index 07a9047d..c28b9337 100644 --- a/fairgraph/openminds/controlled_terms/operating_device.py +++ b/fairgraph/openminds/controlled_terms/operating_device.py @@ -17,7 +17,7 @@ class OperatingDevice(KGObject, OperatingDevice): Structured information on the operating device. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/OperatingDevice" + type_ = "https://openminds.om-i.org/types/OperatingDevice" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/operating_system.py b/fairgraph/openminds/controlled_terms/operating_system.py index a680dcd2..519c09ee 100644 --- a/fairgraph/openminds/controlled_terms/operating_system.py +++ b/fairgraph/openminds/controlled_terms/operating_system.py @@ -17,7 +17,7 @@ class OperatingSystem(KGObject, OperatingSystem): Structured information on the operating system. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/OperatingSystem" + type_ = "https://openminds.om-i.org/types/OperatingSystem" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py index d8807e2f..c4b59d58 100644 --- a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py @@ -17,7 +17,7 @@ class OpticalStimulusType(KGObject, OpticalStimulusType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/OpticalStimulusType" + type_ = "https://openminds.om-i.org/types/OpticalStimulusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/organ.py b/fairgraph/openminds/controlled_terms/organ.py index ee3630d1..9e5ee421 100644 --- a/fairgraph/openminds/controlled_terms/organ.py +++ b/fairgraph/openminds/controlled_terms/organ.py @@ -17,7 +17,7 @@ class Organ(KGObject, Organ): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Organ" + type_ = "https://openminds.om-i.org/types/Organ" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/organism_substance.py b/fairgraph/openminds/controlled_terms/organism_substance.py index ca807fab..b1f094ef 100644 --- a/fairgraph/openminds/controlled_terms/organism_substance.py +++ b/fairgraph/openminds/controlled_terms/organism_substance.py @@ -17,7 +17,7 @@ class OrganismSubstance(KGObject, OrganismSubstance): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/OrganismSubstance" + type_ = "https://openminds.om-i.org/types/OrganismSubstance" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/organism_system.py b/fairgraph/openminds/controlled_terms/organism_system.py index f31ac6e4..4c08b6d2 100644 --- a/fairgraph/openminds/controlled_terms/organism_system.py +++ b/fairgraph/openminds/controlled_terms/organism_system.py @@ -17,7 +17,7 @@ class OrganismSystem(KGObject, OrganismSystem): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/OrganismSystem" + type_ = "https://openminds.om-i.org/types/OrganismSystem" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py index 8669a3ee..ffa3ba39 100644 --- a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py +++ b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py @@ -17,7 +17,7 @@ class PatchClampVariation(KGObject, PatchClampVariation): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/PatchClampVariation" + type_ = "https://openminds.om-i.org/types/PatchClampVariation" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/preparation_type.py b/fairgraph/openminds/controlled_terms/preparation_type.py index 90c2e9ff..0998e0f0 100644 --- a/fairgraph/openminds/controlled_terms/preparation_type.py +++ b/fairgraph/openminds/controlled_terms/preparation_type.py @@ -17,7 +17,7 @@ class PreparationType(KGObject, PreparationType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/PreparationType" + type_ = "https://openminds.om-i.org/types/PreparationType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/product_accessibility.py b/fairgraph/openminds/controlled_terms/product_accessibility.py index 92b9b362..d55b6738 100644 --- a/fairgraph/openminds/controlled_terms/product_accessibility.py +++ b/fairgraph/openminds/controlled_terms/product_accessibility.py @@ -17,7 +17,7 @@ class ProductAccessibility(KGObject, ProductAccessibility): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ProductAccessibility" + type_ = "https://openminds.om-i.org/types/ProductAccessibility" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/programming_language.py b/fairgraph/openminds/controlled_terms/programming_language.py index f0f54328..f4f3f7e8 100644 --- a/fairgraph/openminds/controlled_terms/programming_language.py +++ b/fairgraph/openminds/controlled_terms/programming_language.py @@ -17,7 +17,7 @@ class ProgrammingLanguage(KGObject, ProgrammingLanguage): Structured information on the programming language. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/ProgrammingLanguage" + type_ = "https://openminds.om-i.org/types/ProgrammingLanguage" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/qualitative_overlap.py b/fairgraph/openminds/controlled_terms/qualitative_overlap.py index 5ebe8eb9..6fd1f6a3 100644 --- a/fairgraph/openminds/controlled_terms/qualitative_overlap.py +++ b/fairgraph/openminds/controlled_terms/qualitative_overlap.py @@ -17,7 +17,7 @@ class QualitativeOverlap(KGObject, QualitativeOverlap): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/QualitativeOverlap" + type_ = "https://openminds.om-i.org/types/QualitativeOverlap" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/semantic_data_type.py b/fairgraph/openminds/controlled_terms/semantic_data_type.py index 128abf55..a2bca312 100644 --- a/fairgraph/openminds/controlled_terms/semantic_data_type.py +++ b/fairgraph/openminds/controlled_terms/semantic_data_type.py @@ -17,7 +17,7 @@ class SemanticDataType(KGObject, SemanticDataType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/SemanticDataType" + type_ = "https://openminds.om-i.org/types/SemanticDataType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/service.py b/fairgraph/openminds/controlled_terms/service.py index 530a5bf6..9cfa1666 100644 --- a/fairgraph/openminds/controlled_terms/service.py +++ b/fairgraph/openminds/controlled_terms/service.py @@ -17,7 +17,7 @@ class Service(KGObject, Service): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Service" + type_ = "https://openminds.om-i.org/types/Service" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/setup_type.py b/fairgraph/openminds/controlled_terms/setup_type.py index 75cecfe7..8efbed91 100644 --- a/fairgraph/openminds/controlled_terms/setup_type.py +++ b/fairgraph/openminds/controlled_terms/setup_type.py @@ -17,7 +17,7 @@ class SetupType(KGObject, SetupType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/SetupType" + type_ = "https://openminds.om-i.org/types/SetupType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/software_application_category.py b/fairgraph/openminds/controlled_terms/software_application_category.py index cab159b4..dd804f36 100644 --- a/fairgraph/openminds/controlled_terms/software_application_category.py +++ b/fairgraph/openminds/controlled_terms/software_application_category.py @@ -17,7 +17,7 @@ class SoftwareApplicationCategory(KGObject, SoftwareApplicationCategory): Structured information on the category of the software application. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/SoftwareApplicationCategory" + type_ = "https://openminds.om-i.org/types/SoftwareApplicationCategory" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/software_feature.py b/fairgraph/openminds/controlled_terms/software_feature.py index eb01b166..5126e779 100644 --- a/fairgraph/openminds/controlled_terms/software_feature.py +++ b/fairgraph/openminds/controlled_terms/software_feature.py @@ -17,7 +17,7 @@ class SoftwareFeature(KGObject, SoftwareFeature): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/SoftwareFeature" + type_ = "https://openminds.om-i.org/types/SoftwareFeature" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/species.py b/fairgraph/openminds/controlled_terms/species.py index c818aa89..ec201aa6 100644 --- a/fairgraph/openminds/controlled_terms/species.py +++ b/fairgraph/openminds/controlled_terms/species.py @@ -17,7 +17,7 @@ class Species(KGObject, Species): Structured information on the species. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Species" + type_ = "https://openminds.om-i.org/types/Species" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/stimulation_approach.py b/fairgraph/openminds/controlled_terms/stimulation_approach.py index 211e1834..ba530e75 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_approach.py +++ b/fairgraph/openminds/controlled_terms/stimulation_approach.py @@ -17,7 +17,7 @@ class StimulationApproach(KGObject, StimulationApproach): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/StimulationApproach" + type_ = "https://openminds.om-i.org/types/StimulationApproach" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/stimulation_technique.py b/fairgraph/openminds/controlled_terms/stimulation_technique.py index e6b3fc4f..0241b5fe 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_technique.py +++ b/fairgraph/openminds/controlled_terms/stimulation_technique.py @@ -17,7 +17,7 @@ class StimulationTechnique(KGObject, StimulationTechnique): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/StimulationTechnique" + type_ = "https://openminds.om-i.org/types/StimulationTechnique" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/subcellular_entity.py b/fairgraph/openminds/controlled_terms/subcellular_entity.py index af12f813..406f9cdf 100644 --- a/fairgraph/openminds/controlled_terms/subcellular_entity.py +++ b/fairgraph/openminds/controlled_terms/subcellular_entity.py @@ -17,7 +17,7 @@ class SubcellularEntity(KGObject, SubcellularEntity): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/SubcellularEntity" + type_ = "https://openminds.om-i.org/types/SubcellularEntity" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/subject_attribute.py b/fairgraph/openminds/controlled_terms/subject_attribute.py index 3f4796ab..e498acaa 100644 --- a/fairgraph/openminds/controlled_terms/subject_attribute.py +++ b/fairgraph/openminds/controlled_terms/subject_attribute.py @@ -17,7 +17,7 @@ class SubjectAttribute(KGObject, SubjectAttribute): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/SubjectAttribute" + type_ = "https://openminds.om-i.org/types/SubjectAttribute" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py index 3ea67da4..899ceed2 100644 --- a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py @@ -17,7 +17,7 @@ class TactileStimulusType(KGObject, TactileStimulusType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/TactileStimulusType" + type_ = "https://openminds.om-i.org/types/TactileStimulusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/technique.py b/fairgraph/openminds/controlled_terms/technique.py index 2d070fd7..792534db 100644 --- a/fairgraph/openminds/controlled_terms/technique.py +++ b/fairgraph/openminds/controlled_terms/technique.py @@ -17,7 +17,7 @@ class Technique(KGObject, Technique): Structured information on the technique. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Technique" + type_ = "https://openminds.om-i.org/types/Technique" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/term_suggestion.py b/fairgraph/openminds/controlled_terms/term_suggestion.py index 39aa8364..bc85815f 100644 --- a/fairgraph/openminds/controlled_terms/term_suggestion.py +++ b/fairgraph/openminds/controlled_terms/term_suggestion.py @@ -17,7 +17,7 @@ class TermSuggestion(KGObject, TermSuggestion): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/TermSuggestion" + type_ = "https://openminds.om-i.org/types/TermSuggestion" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/terminology.py b/fairgraph/openminds/controlled_terms/terminology.py index f253e5a5..7bf24ad8 100644 --- a/fairgraph/openminds/controlled_terms/terminology.py +++ b/fairgraph/openminds/controlled_terms/terminology.py @@ -17,7 +17,7 @@ class Terminology(KGObject, Terminology): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/Terminology" + type_ = "https://openminds.om-i.org/types/Terminology" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py index 37f3575c..883c881a 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py @@ -17,7 +17,7 @@ class TissueSampleAttribute(KGObject, TissueSampleAttribute): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/TissueSampleAttribute" + type_ = "https://openminds.om-i.org/types/TissueSampleAttribute" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_type.py b/fairgraph/openminds/controlled_terms/tissue_sample_type.py index eb294c5d..26ad9190 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_type.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_type.py @@ -17,7 +17,7 @@ class TissueSampleType(KGObject, TissueSampleType): Structured information on the general type of the tissue sample. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/TissueSampleType" + type_ = "https://openminds.om-i.org/types/TissueSampleType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py index d1e4b9ce..868b31be 100644 --- a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py +++ b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py @@ -17,7 +17,7 @@ class TypeOfUncertainty(KGObject, TypeOfUncertainty): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/TypeOfUncertainty" + type_ = "https://openminds.om-i.org/types/TypeOfUncertainty" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/uberon_parcellation.py b/fairgraph/openminds/controlled_terms/uberon_parcellation.py index 8eda9f78..674597d2 100644 --- a/fairgraph/openminds/controlled_terms/uberon_parcellation.py +++ b/fairgraph/openminds/controlled_terms/uberon_parcellation.py @@ -17,7 +17,7 @@ class UBERONParcellation(KGObject, UBERONParcellation): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation" + type_ = "https://openminds.om-i.org/types/UBERONParcellation" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/unit_of_measurement.py b/fairgraph/openminds/controlled_terms/unit_of_measurement.py index 76ffe150..32204a79 100644 --- a/fairgraph/openminds/controlled_terms/unit_of_measurement.py +++ b/fairgraph/openminds/controlled_terms/unit_of_measurement.py @@ -17,7 +17,7 @@ class UnitOfMeasurement(KGObject, UnitOfMeasurement): Structured information on the unit of measurement. """ - type_ = "https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement" + type_ = "https://openminds.om-i.org/types/UnitOfMeasurement" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py index 67b096ab..91f69160 100644 --- a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py @@ -17,7 +17,7 @@ class VisualStimulusType(KGObject, VisualStimulusType): """ - type_ = "https://openminds.ebrains.eu/controlledTerms/VisualStimulusType" + type_ = "https://openminds.om-i.org/types/VisualStimulusType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/actors/account_information.py b/fairgraph/openminds/core/actors/account_information.py index 7fc1ba78..60c640af 100644 --- a/fairgraph/openminds/core/actors/account_information.py +++ b/fairgraph/openminds/core/actors/account_information.py @@ -14,7 +14,7 @@ class AccountInformation(KGObject, AccountInformation): Structured information about a user account for a web service. """ - type_ = "https://openminds.ebrains.eu/core/AccountInformation" + type_ = "https://openminds.om-i.org/types/AccountInformation" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/actors/affiliation.py b/fairgraph/openminds/core/actors/affiliation.py index 0327791e..8e314fe3 100644 --- a/fairgraph/openminds/core/actors/affiliation.py +++ b/fairgraph/openminds/core/actors/affiliation.py @@ -17,7 +17,7 @@ class Affiliation(EmbeddedMetadata, Affiliation): Structured information about a relationship between two entities, such as a person and their employer. """ - type_ = "https://openminds.ebrains.eu/core/Affiliation" + type_ = "https://openminds.om-i.org/types/Affiliation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/actors/consortium.py b/fairgraph/openminds/core/actors/consortium.py index 763aac3c..d3ca8fae 100644 --- a/fairgraph/openminds/core/actors/consortium.py +++ b/fairgraph/openminds/core/actors/consortium.py @@ -17,7 +17,7 @@ class Consortium(KGObject, Consortium): Structured information about an association of two or more persons or organizations, with the objective of participating in a common activity. """ - type_ = "https://openminds.ebrains.eu/core/Consortium" + type_ = "https://openminds.om-i.org/types/Consortium" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/actors/contact_information.py b/fairgraph/openminds/core/actors/contact_information.py index 942f3912..26c18f89 100644 --- a/fairgraph/openminds/core/actors/contact_information.py +++ b/fairgraph/openminds/core/actors/contact_information.py @@ -14,7 +14,7 @@ class ContactInformation(KGObject, ContactInformation): Structured information about how to contact a given person or consortium. """ - type_ = "https://openminds.ebrains.eu/core/ContactInformation" + type_ = "https://openminds.om-i.org/types/ContactInformation" default_space = "restricted" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/actors/contribution.py b/fairgraph/openminds/core/actors/contribution.py index ee48e7be..a4530369 100644 --- a/fairgraph/openminds/core/actors/contribution.py +++ b/fairgraph/openminds/core/actors/contribution.py @@ -14,7 +14,7 @@ class Contribution(EmbeddedMetadata, Contribution): Structured information on the contribution made to a research product. """ - type_ = "https://openminds.ebrains.eu/core/Contribution" + type_ = "https://openminds.om-i.org/types/Contribution" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/actors/organization.py b/fairgraph/openminds/core/actors/organization.py index 68060d72..c145c45f 100644 --- a/fairgraph/openminds/core/actors/organization.py +++ b/fairgraph/openminds/core/actors/organization.py @@ -17,7 +17,7 @@ class Organization(KGObject, Organization): An entity comprised of one or more natural persons with a particular purpose. [adapted from Wikipedia](https://en.wikipedia.org/wiki/Organization) """ - type_ = "https://openminds.ebrains.eu/core/Organization" + type_ = "https://openminds.om-i.org/types/Organization" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/actors/person.py b/fairgraph/openminds/core/actors/person.py index 81726364..54163e33 100644 --- a/fairgraph/openminds/core/actors/person.py +++ b/fairgraph/openminds/core/actors/person.py @@ -14,7 +14,7 @@ class Person(KGObject, Person): Structured information on a person. """ - type_ = "https://openminds.ebrains.eu/core/Person" + type_ = "https://openminds.om-i.org/types/Person" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/content_type.py b/fairgraph/openminds/core/data/content_type.py index 204f5d00..c25e30b1 100644 --- a/fairgraph/openminds/core/data/content_type.py +++ b/fairgraph/openminds/core/data/content_type.py @@ -17,7 +17,7 @@ class ContentType(KGObject, ContentType): Structured information on the content type of a file instance, bundle or repository. """ - type_ = "https://openminds.ebrains.eu/core/ContentType" + type_ = "https://openminds.om-i.org/types/ContentType" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/content_type_pattern.py b/fairgraph/openminds/core/data/content_type_pattern.py index bcf5d11f..5297fc20 100644 --- a/fairgraph/openminds/core/data/content_type_pattern.py +++ b/fairgraph/openminds/core/data/content_type_pattern.py @@ -14,7 +14,7 @@ class ContentTypePattern(KGObject, ContentTypePattern): """ - type_ = "https://openminds.ebrains.eu/core/ContentTypePattern" + type_ = "https://openminds.om-i.org/types/ContentTypePattern" default_space = "files" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/copyright.py b/fairgraph/openminds/core/data/copyright.py index e26dfa98..5350dab6 100644 --- a/fairgraph/openminds/core/data/copyright.py +++ b/fairgraph/openminds/core/data/copyright.py @@ -14,7 +14,7 @@ class Copyright(EmbeddedMetadata, Copyright): Structured information on the copyright. """ - type_ = "https://openminds.ebrains.eu/core/Copyright" + type_ = "https://openminds.om-i.org/types/Copyright" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/data/file.py b/fairgraph/openminds/core/data/file.py index fc8aade2..adc5ffee 100644 --- a/fairgraph/openminds/core/data/file.py +++ b/fairgraph/openminds/core/data/file.py @@ -28,7 +28,7 @@ class File(KGObject, File): Structured information on a file instance that is accessible via a URL. """ - type_ = "https://openminds.ebrains.eu/core/File" + type_ = "https://openminds.om-i.org/types/File" default_space = "files" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/file_archive.py b/fairgraph/openminds/core/data/file_archive.py index c1072eda..9c91b29b 100644 --- a/fairgraph/openminds/core/data/file_archive.py +++ b/fairgraph/openminds/core/data/file_archive.py @@ -17,7 +17,7 @@ class FileArchive(KGObject, FileArchive): """ - type_ = "https://openminds.ebrains.eu/core/FileArchive" + type_ = "https://openminds.om-i.org/types/FileArchive" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/file_bundle.py b/fairgraph/openminds/core/data/file_bundle.py index 5ffff406..91616fe1 100644 --- a/fairgraph/openminds/core/data/file_bundle.py +++ b/fairgraph/openminds/core/data/file_bundle.py @@ -14,7 +14,7 @@ class FileBundle(KGObject, FileBundle): Structured information on a bundle of file instances. """ - type_ = "https://openminds.ebrains.eu/core/FileBundle" + type_ = "https://openminds.om-i.org/types/FileBundle" default_space = "files" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/file_path_pattern.py b/fairgraph/openminds/core/data/file_path_pattern.py index 5389ed8f..c3c9a9dc 100644 --- a/fairgraph/openminds/core/data/file_path_pattern.py +++ b/fairgraph/openminds/core/data/file_path_pattern.py @@ -14,7 +14,7 @@ class FilePathPattern(EmbeddedMetadata, FilePathPattern): """ - type_ = "https://openminds.ebrains.eu/core/FilePathPattern" + type_ = "https://openminds.om-i.org/types/FilePathPattern" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/data/file_repository.py b/fairgraph/openminds/core/data/file_repository.py index 65e5a2b4..0b31d283 100644 --- a/fairgraph/openminds/core/data/file_repository.py +++ b/fairgraph/openminds/core/data/file_repository.py @@ -17,7 +17,7 @@ class FileRepository(KGObject, FileRepository): Structured information on a file repository. """ - type_ = "https://openminds.ebrains.eu/core/FileRepository" + type_ = "https://openminds.om-i.org/types/FileRepository" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/file_repository_structure.py b/fairgraph/openminds/core/data/file_repository_structure.py index d647caad..4b289f42 100644 --- a/fairgraph/openminds/core/data/file_repository_structure.py +++ b/fairgraph/openminds/core/data/file_repository_structure.py @@ -14,7 +14,7 @@ class FileRepositoryStructure(KGObject, FileRepositoryStructure): """ - type_ = "https://openminds.ebrains.eu/core/FileRepositoryStructure" + type_ = "https://openminds.om-i.org/types/FileRepositoryStructure" default_space = "files" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/hash.py b/fairgraph/openminds/core/data/hash.py index 8d8b2973..45f4eb8d 100644 --- a/fairgraph/openminds/core/data/hash.py +++ b/fairgraph/openminds/core/data/hash.py @@ -14,7 +14,7 @@ class Hash(EmbeddedMetadata, Hash): Structured information on a hash. """ - type_ = "https://openminds.ebrains.eu/core/Hash" + type_ = "https://openminds.om-i.org/types/Hash" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/data/license.py b/fairgraph/openminds/core/data/license.py index c4510c6e..9e957c41 100644 --- a/fairgraph/openminds/core/data/license.py +++ b/fairgraph/openminds/core/data/license.py @@ -17,7 +17,7 @@ class License(KGObject, License): Structured information on a used license. """ - type_ = "https://openminds.ebrains.eu/core/License" + type_ = "https://openminds.om-i.org/types/License" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/data/measurement.py b/fairgraph/openminds/core/data/measurement.py index e92e4496..afab14d7 100644 --- a/fairgraph/openminds/core/data/measurement.py +++ b/fairgraph/openminds/core/data/measurement.py @@ -17,7 +17,7 @@ class Measurement(EmbeddedMetadata, Measurement): Structured information about a measurement performed during a scientific experiment. """ - type_ = "https://openminds.ebrains.eu/core/Measurement" + type_ = "https://openminds.om-i.org/types/Measurement" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/data/service_link.py b/fairgraph/openminds/core/data/service_link.py index f05caa5e..57a12eaf 100644 --- a/fairgraph/openminds/core/data/service_link.py +++ b/fairgraph/openminds/core/data/service_link.py @@ -17,7 +17,7 @@ class ServiceLink(KGObject, ServiceLink): """ - type_ = "https://openminds.ebrains.eu/core/ServiceLink" + type_ = "https://openminds.om-i.org/types/ServiceLink" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/digital_identifier/doi.py b/fairgraph/openminds/core/digital_identifier/doi.py index cf909e64..a7fd5f8a 100644 --- a/fairgraph/openminds/core/digital_identifier/doi.py +++ b/fairgraph/openminds/core/digital_identifier/doi.py @@ -14,7 +14,7 @@ class DOI(KGObject, DOI): Structured information about a digital object identifier, as standardized by the International Organization for Standardization. """ - type_ = "https://openminds.ebrains.eu/core/DOI" + type_ = "https://openminds.om-i.org/types/DOI" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/gridid.py b/fairgraph/openminds/core/digital_identifier/gridid.py index 0608acbe..2596321d 100644 --- a/fairgraph/openminds/core/digital_identifier/gridid.py +++ b/fairgraph/openminds/core/digital_identifier/gridid.py @@ -14,7 +14,7 @@ class GRIDID(KGObject, GRIDID): A GRID (Global Research Identifier Database) identifier. """ - type_ = "https://openminds.ebrains.eu/core/GRIDID" + type_ = "https://openminds.om-i.org/types/GRIDID" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/handle.py b/fairgraph/openminds/core/digital_identifier/handle.py index d2da68eb..d9530dfc 100644 --- a/fairgraph/openminds/core/digital_identifier/handle.py +++ b/fairgraph/openminds/core/digital_identifier/handle.py @@ -14,7 +14,7 @@ class HANDLE(KGObject, HANDLE): A persistent identifier for an information resource provided by the Handle System of the Corporation for National Research Initiatives. """ - type_ = "https://openminds.ebrains.eu/core/HANDLE" + type_ = "https://openminds.om-i.org/types/HANDLE" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py index be6ad3e8..29724ceb 100644 --- a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py +++ b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py @@ -14,7 +14,7 @@ class IdentifiersDotOrgID(KGObject, IdentifiersDotOrgID): """ - type_ = "https://openminds.ebrains.eu/core/IdentifiersDotOrgID" + type_ = "https://openminds.om-i.org/types/IdentifiersDotOrgID" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/isbn.py b/fairgraph/openminds/core/digital_identifier/isbn.py index 3ef08149..dcd1aa46 100644 --- a/fairgraph/openminds/core/digital_identifier/isbn.py +++ b/fairgraph/openminds/core/digital_identifier/isbn.py @@ -14,7 +14,7 @@ class ISBN(KGObject, ISBN): An International Standard Book Number of the International ISBN Agency. """ - type_ = "https://openminds.ebrains.eu/core/ISBN" + type_ = "https://openminds.om-i.org/types/ISBN" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/issn.py b/fairgraph/openminds/core/digital_identifier/issn.py index 2f999e5e..b2d4d380 100644 --- a/fairgraph/openminds/core/digital_identifier/issn.py +++ b/fairgraph/openminds/core/digital_identifier/issn.py @@ -14,7 +14,7 @@ class ISSN(KGObject, ISSN): An International Standard Serial Number of the ISSN International Centre. """ - type_ = "https://openminds.ebrains.eu/core/ISSN" + type_ = "https://openminds.om-i.org/types/ISSN" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/orcid.py b/fairgraph/openminds/core/digital_identifier/orcid.py index 86154b3c..cf1a103d 100644 --- a/fairgraph/openminds/core/digital_identifier/orcid.py +++ b/fairgraph/openminds/core/digital_identifier/orcid.py @@ -14,7 +14,7 @@ class ORCID(KGObject, ORCID): A persistent identifier for a researcher provided by Open Researcher and Contributor ID, Inc. """ - type_ = "https://openminds.ebrains.eu/core/ORCID" + type_ = "https://openminds.om-i.org/types/ORCID" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/rorid.py b/fairgraph/openminds/core/digital_identifier/rorid.py index b80aa922..1be099ce 100644 --- a/fairgraph/openminds/core/digital_identifier/rorid.py +++ b/fairgraph/openminds/core/digital_identifier/rorid.py @@ -14,7 +14,7 @@ class RORID(KGObject, RORID): A persistent identifier for a research organization, provided by the Research Organization Registry. """ - type_ = "https://openminds.ebrains.eu/core/RORID" + type_ = "https://openminds.om-i.org/types/RORID" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/rrid.py b/fairgraph/openminds/core/digital_identifier/rrid.py index f8933074..9a9164c9 100644 --- a/fairgraph/openminds/core/digital_identifier/rrid.py +++ b/fairgraph/openminds/core/digital_identifier/rrid.py @@ -14,7 +14,7 @@ class RRID(KGObject, RRID): A persistent identifier for a research resource provided by the Resource Identification Initiative. """ - type_ = "https://openminds.ebrains.eu/core/RRID" + type_ = "https://openminds.om-i.org/types/RRID" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/digital_identifier/stock_number.py b/fairgraph/openminds/core/digital_identifier/stock_number.py index ebb443d1..bc62b583 100644 --- a/fairgraph/openminds/core/digital_identifier/stock_number.py +++ b/fairgraph/openminds/core/digital_identifier/stock_number.py @@ -14,7 +14,7 @@ class StockNumber(EmbeddedMetadata, StockNumber): """ - type_ = "https://openminds.ebrains.eu/core/StockNumber" + type_ = "https://openminds.om-i.org/types/StockNumber" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/digital_identifier/swhid.py b/fairgraph/openminds/core/digital_identifier/swhid.py index 290e6fac..5eb9b473 100644 --- a/fairgraph/openminds/core/digital_identifier/swhid.py +++ b/fairgraph/openminds/core/digital_identifier/swhid.py @@ -14,7 +14,7 @@ class SWHID(KGObject, SWHID): """ - type_ = "https://openminds.ebrains.eu/core/SWHID" + type_ = "https://openminds.om-i.org/types/SWHID" default_space = "software" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/miscellaneous/comment.py b/fairgraph/openminds/core/miscellaneous/comment.py index f3f8d39b..f0f63086 100644 --- a/fairgraph/openminds/core/miscellaneous/comment.py +++ b/fairgraph/openminds/core/miscellaneous/comment.py @@ -17,7 +17,7 @@ class Comment(KGObject, Comment): Structured information about a short text expressing an opinion on, or giving information about some entity. """ - type_ = "https://openminds.ebrains.eu/core/Comment" + type_ = "https://openminds.om-i.org/types/Comment" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/miscellaneous/funding.py b/fairgraph/openminds/core/miscellaneous/funding.py index bbad5283..af678517 100644 --- a/fairgraph/openminds/core/miscellaneous/funding.py +++ b/fairgraph/openminds/core/miscellaneous/funding.py @@ -14,7 +14,7 @@ class Funding(KGObject, Funding): Structured information on used funding. """ - type_ = "https://openminds.ebrains.eu/core/Funding" + type_ = "https://openminds.om-i.org/types/Funding" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value.py b/fairgraph/openminds/core/miscellaneous/quantitative_value.py index 22eceaf5..ae10032c 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value.py @@ -17,7 +17,7 @@ class QuantitativeValue(EmbeddedMetadata, QuantitativeValue): Structured information on a quantitative value. """ - type_ = "https://openminds.ebrains.eu/core/QuantitativeValue" + type_ = "https://openminds.om-i.org/types/QuantitativeValue" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py index 56784116..90fb8456 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py @@ -17,7 +17,7 @@ class QuantitativeValueArray(KGObject, QuantitativeValueArray): A representation of an array of quantitative values, optionally with uncertainties. """ - type_ = "https://openminds.ebrains.eu/core/QuantitativeValueArray" + type_ = "https://openminds.om-i.org/types/QuantitativeValueArray" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py index d11fa7b2..d9327ebd 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py @@ -17,7 +17,7 @@ class QuantitativeValueRange(EmbeddedMetadata, QuantitativeValueRange): A representation of a range of quantitative values. """ - type_ = "https://openminds.ebrains.eu/core/QuantitativeValueRange" + type_ = "https://openminds.om-i.org/types/QuantitativeValueRange" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/miscellaneous/research_product_group.py b/fairgraph/openminds/core/miscellaneous/research_product_group.py index 2a90a565..2a6cfb03 100644 --- a/fairgraph/openminds/core/miscellaneous/research_product_group.py +++ b/fairgraph/openminds/core/miscellaneous/research_product_group.py @@ -14,7 +14,7 @@ class ResearchProductGroup(KGObject, ResearchProductGroup): """ - type_ = "https://openminds.ebrains.eu/core/ResearchProductGroup" + type_ = "https://openminds.om-i.org/types/ResearchProductGroup" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/miscellaneous/web_resource.py b/fairgraph/openminds/core/miscellaneous/web_resource.py index a126ffc9..ff57a6d4 100644 --- a/fairgraph/openminds/core/miscellaneous/web_resource.py +++ b/fairgraph/openminds/core/miscellaneous/web_resource.py @@ -17,7 +17,7 @@ class WebResource(KGObject, WebResource): """ - type_ = "https://openminds.ebrains.eu/core/WebResource" + type_ = "https://openminds.om-i.org/types/WebResource" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/dataset.py b/fairgraph/openminds/core/products/dataset.py index 50f8bd7c..639b597d 100644 --- a/fairgraph/openminds/core/products/dataset.py +++ b/fairgraph/openminds/core/products/dataset.py @@ -17,7 +17,7 @@ class Dataset(KGObject, Dataset): Structured information on data originating from human/animal studies or simulations (concept level). """ - type_ = "https://openminds.ebrains.eu/core/Dataset" + type_ = "https://openminds.om-i.org/types/Dataset" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/dataset_version.py b/fairgraph/openminds/core/products/dataset_version.py index 774f9af1..b5c82abf 100644 --- a/fairgraph/openminds/core/products/dataset_version.py +++ b/fairgraph/openminds/core/products/dataset_version.py @@ -20,7 +20,7 @@ class DatasetVersion(KGObject, DatasetVersion): Structured information on data originating from human/animal studies or simulations (version level). """ - type_ = "https://openminds.ebrains.eu/core/DatasetVersion" + type_ = "https://openminds.om-i.org/types/DatasetVersion" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/meta_data_model.py b/fairgraph/openminds/core/products/meta_data_model.py index 515c9ebd..efb943d9 100644 --- a/fairgraph/openminds/core/products/meta_data_model.py +++ b/fairgraph/openminds/core/products/meta_data_model.py @@ -17,7 +17,7 @@ class MetaDataModel(KGObject, MetaDataModel): """ - type_ = "https://openminds.ebrains.eu/core/MetaDataModel" + type_ = "https://openminds.om-i.org/types/MetaDataModel" default_space = "metadatamodel" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/meta_data_model_version.py b/fairgraph/openminds/core/products/meta_data_model_version.py index bc550551..4a5866e8 100644 --- a/fairgraph/openminds/core/products/meta_data_model_version.py +++ b/fairgraph/openminds/core/products/meta_data_model_version.py @@ -18,7 +18,7 @@ class MetaDataModelVersion(KGObject, MetaDataModelVersion): """ - type_ = "https://openminds.ebrains.eu/core/MetaDataModelVersion" + type_ = "https://openminds.om-i.org/types/MetaDataModelVersion" default_space = "metadatamodel" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/model.py b/fairgraph/openminds/core/products/model.py index 87894af4..a65a327f 100644 --- a/fairgraph/openminds/core/products/model.py +++ b/fairgraph/openminds/core/products/model.py @@ -17,7 +17,7 @@ class Model(KGObject, Model): Structured information on a computational model (concept level). """ - type_ = "https://openminds.ebrains.eu/core/Model" + type_ = "https://openminds.om-i.org/types/Model" default_space = "model" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/model_version.py b/fairgraph/openminds/core/products/model_version.py index a03d3c39..7a3ac7a3 100644 --- a/fairgraph/openminds/core/products/model_version.py +++ b/fairgraph/openminds/core/products/model_version.py @@ -19,7 +19,7 @@ class ModelVersion(KGObject, ModelVersion): Structured information on a computational model (version level). """ - type_ = "https://openminds.ebrains.eu/core/ModelVersion" + type_ = "https://openminds.om-i.org/types/ModelVersion" default_space = "model" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/project.py b/fairgraph/openminds/core/products/project.py index 97e86c6e..2d6e00a3 100644 --- a/fairgraph/openminds/core/products/project.py +++ b/fairgraph/openminds/core/products/project.py @@ -17,7 +17,7 @@ class Project(KGObject, Project): Structured information on a research project. """ - type_ = "https://openminds.ebrains.eu/core/Project" + type_ = "https://openminds.om-i.org/types/Project" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/products/setup.py b/fairgraph/openminds/core/products/setup.py index c235b526..f08884b3 100644 --- a/fairgraph/openminds/core/products/setup.py +++ b/fairgraph/openminds/core/products/setup.py @@ -14,7 +14,7 @@ class Setup(KGObject, Setup): """ - type_ = "https://openminds.ebrains.eu/core/Setup" + type_ = "https://openminds.om-i.org/types/Setup" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/software.py b/fairgraph/openminds/core/products/software.py index 72ece2dd..53aea868 100644 --- a/fairgraph/openminds/core/products/software.py +++ b/fairgraph/openminds/core/products/software.py @@ -17,7 +17,7 @@ class Software(KGObject, Software): Structured information on a software tool (concept level). """ - type_ = "https://openminds.ebrains.eu/core/Software" + type_ = "https://openminds.om-i.org/types/Software" default_space = "software" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/software_version.py b/fairgraph/openminds/core/products/software_version.py index 2939b5a6..8228a957 100644 --- a/fairgraph/openminds/core/products/software_version.py +++ b/fairgraph/openminds/core/products/software_version.py @@ -19,7 +19,7 @@ class SoftwareVersion(KGObject, SoftwareVersion): """ - type_ = "https://openminds.ebrains.eu/core/SoftwareVersion" + type_ = "https://openminds.om-i.org/types/SoftwareVersion" default_space = "software" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/web_service.py b/fairgraph/openminds/core/products/web_service.py index 9707989f..2105b61e 100644 --- a/fairgraph/openminds/core/products/web_service.py +++ b/fairgraph/openminds/core/products/web_service.py @@ -17,7 +17,7 @@ class WebService(KGObject, WebService): """ - type_ = "https://openminds.ebrains.eu/core/WebService" + type_ = "https://openminds.om-i.org/types/WebService" default_space = "webservice" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/products/web_service_version.py b/fairgraph/openminds/core/products/web_service_version.py index 23ea4f8e..1b1b9c1e 100644 --- a/fairgraph/openminds/core/products/web_service_version.py +++ b/fairgraph/openminds/core/products/web_service_version.py @@ -19,7 +19,7 @@ class WebServiceVersion(KGObject, WebServiceVersion): """ - type_ = "https://openminds.ebrains.eu/core/WebServiceVersion" + type_ = "https://openminds.om-i.org/types/WebServiceVersion" default_space = "webservice" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/behavioral_protocol.py b/fairgraph/openminds/core/research/behavioral_protocol.py index 215915d5..986474a1 100644 --- a/fairgraph/openminds/core/research/behavioral_protocol.py +++ b/fairgraph/openminds/core/research/behavioral_protocol.py @@ -14,7 +14,7 @@ class BehavioralProtocol(KGObject, BehavioralProtocol): Structured information about a protocol used in an experiment studying human or animal behavior. """ - type_ = "https://openminds.ebrains.eu/core/BehavioralProtocol" + type_ = "https://openminds.om-i.org/types/BehavioralProtocol" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/configuration.py b/fairgraph/openminds/core/research/configuration.py index 865195c3..98c1eb7d 100644 --- a/fairgraph/openminds/core/research/configuration.py +++ b/fairgraph/openminds/core/research/configuration.py @@ -14,7 +14,7 @@ class Configuration(KGObject, Configuration): Structured information about the properties or parameters of an entity or process. """ - type_ = "https://openminds.ebrains.eu/core/Configuration" + type_ = "https://openminds.om-i.org/types/Configuration" default_space = "common" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/custom_property_set.py b/fairgraph/openminds/core/research/custom_property_set.py index cb4b551c..58e18aca 100644 --- a/fairgraph/openminds/core/research/custom_property_set.py +++ b/fairgraph/openminds/core/research/custom_property_set.py @@ -14,7 +14,7 @@ class CustomPropertySet(EmbeddedMetadata, CustomPropertySet): Structured information about properties of an entity that are not represented in an openMINDS schema. """ - type_ = "https://openminds.ebrains.eu/core/CustomPropertySet" + type_ = "https://openminds.om-i.org/types/CustomPropertySet" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/research/numerical_property.py b/fairgraph/openminds/core/research/numerical_property.py index 77397f81..5d4abe86 100644 --- a/fairgraph/openminds/core/research/numerical_property.py +++ b/fairgraph/openminds/core/research/numerical_property.py @@ -14,7 +14,7 @@ class NumericalProperty(EmbeddedMetadata, NumericalProperty): Structured information about a property of some entity or process whose value is a number. """ - type_ = "https://openminds.ebrains.eu/core/NumericalProperty" + type_ = "https://openminds.om-i.org/types/NumericalProperty" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/research/property_value_list.py b/fairgraph/openminds/core/research/property_value_list.py index 112b499c..27f81b92 100644 --- a/fairgraph/openminds/core/research/property_value_list.py +++ b/fairgraph/openminds/core/research/property_value_list.py @@ -14,7 +14,7 @@ class PropertyValueList(KGObject, PropertyValueList): An identifiable list of property-value pairs. """ - type_ = "https://openminds.ebrains.eu/core/PropertyValueList" + type_ = "https://openminds.om-i.org/types/PropertyValueList" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/protocol.py b/fairgraph/openminds/core/research/protocol.py index 3b762f63..16af0ad7 100644 --- a/fairgraph/openminds/core/research/protocol.py +++ b/fairgraph/openminds/core/research/protocol.py @@ -14,7 +14,7 @@ class Protocol(KGObject, Protocol): Structured information on a research project. """ - type_ = "https://openminds.ebrains.eu/core/Protocol" + type_ = "https://openminds.om-i.org/types/Protocol" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/protocol_execution.py b/fairgraph/openminds/core/research/protocol_execution.py index 2703d666..1b6bfddd 100644 --- a/fairgraph/openminds/core/research/protocol_execution.py +++ b/fairgraph/openminds/core/research/protocol_execution.py @@ -17,7 +17,7 @@ class ProtocolExecution(KGObject, ProtocolExecution): Structured information on a protocol execution. """ - type_ = "https://openminds.ebrains.eu/core/ProtocolExecution" + type_ = "https://openminds.om-i.org/types/ProtocolExecution" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/strain.py b/fairgraph/openminds/core/research/strain.py index bc461696..b57b3086 100644 --- a/fairgraph/openminds/core/research/strain.py +++ b/fairgraph/openminds/core/research/strain.py @@ -14,7 +14,7 @@ class Strain(KGObject, Strain): """ - type_ = "https://openminds.ebrains.eu/core/Strain" + type_ = "https://openminds.om-i.org/types/Strain" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/string_property.py b/fairgraph/openminds/core/research/string_property.py index e74fd0a2..9f69c4b8 100644 --- a/fairgraph/openminds/core/research/string_property.py +++ b/fairgraph/openminds/core/research/string_property.py @@ -14,7 +14,7 @@ class StringProperty(EmbeddedMetadata, StringProperty): """ - type_ = "https://openminds.ebrains.eu/core/StringProperty" + type_ = "https://openminds.om-i.org/types/StringProperty" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/core/research/subject.py b/fairgraph/openminds/core/research/subject.py index 03ddd875..ff15c1ba 100644 --- a/fairgraph/openminds/core/research/subject.py +++ b/fairgraph/openminds/core/research/subject.py @@ -14,7 +14,7 @@ class Subject(KGObject, Subject): Structured information on a subject. """ - type_ = "https://openminds.ebrains.eu/core/Subject" + type_ = "https://openminds.om-i.org/types/Subject" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/subject_group.py b/fairgraph/openminds/core/research/subject_group.py index 810aebc5..06dec4d0 100644 --- a/fairgraph/openminds/core/research/subject_group.py +++ b/fairgraph/openminds/core/research/subject_group.py @@ -14,7 +14,7 @@ class SubjectGroup(KGObject, SubjectGroup): """ - type_ = "https://openminds.ebrains.eu/core/SubjectGroup" + type_ = "https://openminds.om-i.org/types/SubjectGroup" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/subject_group_state.py b/fairgraph/openminds/core/research/subject_group_state.py index 9885fd11..a416d31c 100644 --- a/fairgraph/openminds/core/research/subject_group_state.py +++ b/fairgraph/openminds/core/research/subject_group_state.py @@ -14,7 +14,7 @@ class SubjectGroupState(KGObject, SubjectGroupState): """ - type_ = "https://openminds.ebrains.eu/core/SubjectGroupState" + type_ = "https://openminds.om-i.org/types/SubjectGroupState" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/subject_state.py b/fairgraph/openminds/core/research/subject_state.py index 4133ad89..2322c444 100644 --- a/fairgraph/openminds/core/research/subject_state.py +++ b/fairgraph/openminds/core/research/subject_state.py @@ -14,7 +14,7 @@ class SubjectState(KGObject, SubjectState): Structured information on a temporary state of a subject. """ - type_ = "https://openminds.ebrains.eu/core/SubjectState" + type_ = "https://openminds.om-i.org/types/SubjectState" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/tissue_sample.py b/fairgraph/openminds/core/research/tissue_sample.py index 09cbd11a..d045e94d 100644 --- a/fairgraph/openminds/core/research/tissue_sample.py +++ b/fairgraph/openminds/core/research/tissue_sample.py @@ -14,7 +14,7 @@ class TissueSample(KGObject, TissueSample): Structured information on a tissue sample. """ - type_ = "https://openminds.ebrains.eu/core/TissueSample" + type_ = "https://openminds.om-i.org/types/TissueSample" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/tissue_sample_collection.py b/fairgraph/openminds/core/research/tissue_sample_collection.py index 8194557f..743cf91f 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection.py @@ -14,7 +14,7 @@ class TissueSampleCollection(KGObject, TissueSampleCollection): """ - type_ = "https://openminds.ebrains.eu/core/TissueSampleCollection" + type_ = "https://openminds.om-i.org/types/TissueSampleCollection" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/tissue_sample_collection_state.py b/fairgraph/openminds/core/research/tissue_sample_collection_state.py index 9bcf13d2..44232354 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection_state.py @@ -14,7 +14,7 @@ class TissueSampleCollectionState(KGObject, TissueSampleCollectionState): """ - type_ = "https://openminds.ebrains.eu/core/TissueSampleCollectionState" + type_ = "https://openminds.om-i.org/types/TissueSampleCollectionState" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/core/research/tissue_sample_state.py b/fairgraph/openminds/core/research/tissue_sample_state.py index 6cdff63d..950343ab 100644 --- a/fairgraph/openminds/core/research/tissue_sample_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_state.py @@ -14,7 +14,7 @@ class TissueSampleState(KGObject, TissueSampleState): Structured information on a temporary state of a tissue sample. """ - type_ = "https://openminds.ebrains.eu/core/TissueSampleState" + type_ = "https://openminds.om-i.org/types/TissueSampleState" default_space = "dataset" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/ephys/activity/cell_patching.py b/fairgraph/openminds/ephys/activity/cell_patching.py index af1f7702..5a13c81b 100644 --- a/fairgraph/openminds/ephys/activity/cell_patching.py +++ b/fairgraph/openminds/ephys/activity/cell_patching.py @@ -17,7 +17,7 @@ class CellPatching(KGObject, CellPatching): """ - type_ = "https://openminds.ebrains.eu/ephys/CellPatching" + type_ = "https://openminds.om-i.org/types/CellPatching" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/ephys/activity/electrode_placement.py b/fairgraph/openminds/ephys/activity/electrode_placement.py index 8410c417..33307898 100644 --- a/fairgraph/openminds/ephys/activity/electrode_placement.py +++ b/fairgraph/openminds/ephys/activity/electrode_placement.py @@ -17,7 +17,7 @@ class ElectrodePlacement(KGObject, ElectrodePlacement): """ - type_ = "https://openminds.ebrains.eu/ephys/ElectrodePlacement" + type_ = "https://openminds.om-i.org/types/ElectrodePlacement" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/ephys/activity/recording_activity.py b/fairgraph/openminds/ephys/activity/recording_activity.py index e2050dd3..e7e09d7e 100644 --- a/fairgraph/openminds/ephys/activity/recording_activity.py +++ b/fairgraph/openminds/ephys/activity/recording_activity.py @@ -17,7 +17,7 @@ class RecordingActivity(KGObject, RecordingActivity): """ - type_ = "https://openminds.ebrains.eu/ephys/RecordingActivity" + type_ = "https://openminds.om-i.org/types/RecordingActivity" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/ephys/device/electrode.py b/fairgraph/openminds/ephys/device/electrode.py index 4bb59465..cdb2c892 100644 --- a/fairgraph/openminds/ephys/device/electrode.py +++ b/fairgraph/openminds/ephys/device/electrode.py @@ -14,7 +14,7 @@ class Electrode(KGObject, Electrode): Structured information on an electrode. """ - type_ = "https://openminds.ebrains.eu/ephys/Electrode" + type_ = "https://openminds.om-i.org/types/Electrode" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/ephys/device/electrode_array.py b/fairgraph/openminds/ephys/device/electrode_array.py index 2382ffac..896362d1 100644 --- a/fairgraph/openminds/ephys/device/electrode_array.py +++ b/fairgraph/openminds/ephys/device/electrode_array.py @@ -14,7 +14,7 @@ class ElectrodeArray(KGObject, ElectrodeArray): Structured information on an electrode array. """ - type_ = "https://openminds.ebrains.eu/ephys/ElectrodeArray" + type_ = "https://openminds.om-i.org/types/ElectrodeArray" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/ephys/device/electrode_array_usage.py b/fairgraph/openminds/ephys/device/electrode_array_usage.py index eb137225..b0c528c5 100644 --- a/fairgraph/openminds/ephys/device/electrode_array_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_array_usage.py @@ -14,7 +14,7 @@ class ElectrodeArrayUsage(KGObject, ElectrodeArrayUsage): """ - type_ = "https://openminds.ebrains.eu/ephys/ElectrodeArrayUsage" + type_ = "https://openminds.om-i.org/types/ElectrodeArrayUsage" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/ephys/device/electrode_usage.py b/fairgraph/openminds/ephys/device/electrode_usage.py index 71d46cee..8eddce21 100644 --- a/fairgraph/openminds/ephys/device/electrode_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_usage.py @@ -14,7 +14,7 @@ class ElectrodeUsage(KGObject, ElectrodeUsage): """ - type_ = "https://openminds.ebrains.eu/ephys/ElectrodeUsage" + type_ = "https://openminds.om-i.org/types/ElectrodeUsage" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/ephys/device/pipette.py b/fairgraph/openminds/ephys/device/pipette.py index 52be90db..5a6febc5 100644 --- a/fairgraph/openminds/ephys/device/pipette.py +++ b/fairgraph/openminds/ephys/device/pipette.py @@ -14,7 +14,7 @@ class Pipette(KGObject, Pipette): """ - type_ = "https://openminds.ebrains.eu/ephys/Pipette" + type_ = "https://openminds.om-i.org/types/Pipette" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/ephys/device/pipette_usage.py b/fairgraph/openminds/ephys/device/pipette_usage.py index c7ec325e..fd2fa196 100644 --- a/fairgraph/openminds/ephys/device/pipette_usage.py +++ b/fairgraph/openminds/ephys/device/pipette_usage.py @@ -14,7 +14,7 @@ class PipetteUsage(KGObject, PipetteUsage): """ - type_ = "https://openminds.ebrains.eu/ephys/PipetteUsage" + type_ = "https://openminds.om-i.org/types/PipetteUsage" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/ephys/entity/channel.py b/fairgraph/openminds/ephys/entity/channel.py index 0dfca3b1..ee1f0109 100644 --- a/fairgraph/openminds/ephys/entity/channel.py +++ b/fairgraph/openminds/ephys/entity/channel.py @@ -14,7 +14,7 @@ class Channel(EmbeddedMetadata, Channel): """ - type_ = "https://openminds.ebrains.eu/ephys/Channel" + type_ = "https://openminds.om-i.org/types/Channel" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/ephys/entity/recording.py b/fairgraph/openminds/ephys/entity/recording.py index 2ce01c45..621d2ffe 100644 --- a/fairgraph/openminds/ephys/entity/recording.py +++ b/fairgraph/openminds/ephys/entity/recording.py @@ -14,7 +14,7 @@ class Recording(KGObject, Recording): """ - type_ = "https://openminds.ebrains.eu/ephys/Recording" + type_ = "https://openminds.om-i.org/types/Recording" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/book.py b/fairgraph/openminds/publications/book.py index 99a36892..3fe1fdd6 100644 --- a/fairgraph/openminds/publications/book.py +++ b/fairgraph/openminds/publications/book.py @@ -18,7 +18,7 @@ class Book(KGObject, Book): """ - type_ = "https://openminds.ebrains.eu/publications/Book" + type_ = "https://openminds.om-i.org/types/Book" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/chapter.py b/fairgraph/openminds/publications/chapter.py index 1cc1f737..65b97c5a 100644 --- a/fairgraph/openminds/publications/chapter.py +++ b/fairgraph/openminds/publications/chapter.py @@ -18,7 +18,7 @@ class Chapter(KGObject, Chapter): """ - type_ = "https://openminds.ebrains.eu/publications/Chapter" + type_ = "https://openminds.om-i.org/types/Chapter" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/learning_resource.py b/fairgraph/openminds/publications/learning_resource.py index ee3aeb0a..fdbf4e87 100644 --- a/fairgraph/openminds/publications/learning_resource.py +++ b/fairgraph/openminds/publications/learning_resource.py @@ -18,7 +18,7 @@ class LearningResource(KGObject, LearningResource): """ - type_ = "https://openminds.ebrains.eu/publications/LearningResource" + type_ = "https://openminds.om-i.org/types/LearningResource" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/publications/live_paper.py b/fairgraph/openminds/publications/live_paper.py index acb327de..ffbf5c8f 100644 --- a/fairgraph/openminds/publications/live_paper.py +++ b/fairgraph/openminds/publications/live_paper.py @@ -17,7 +17,7 @@ class LivePaper(KGObject, LivePaper): """ - type_ = "https://openminds.ebrains.eu/publications/LivePaper" + type_ = "https://openminds.om-i.org/types/LivePaper" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/live_paper_resource_item.py b/fairgraph/openminds/publications/live_paper_resource_item.py index e6f9f413..cb009609 100644 --- a/fairgraph/openminds/publications/live_paper_resource_item.py +++ b/fairgraph/openminds/publications/live_paper_resource_item.py @@ -17,7 +17,7 @@ class LivePaperResourceItem(KGObject, LivePaperResourceItem): """ - type_ = "https://openminds.ebrains.eu/publications/LivePaperResourceItem" + type_ = "https://openminds.om-i.org/types/LivePaperResourceItem" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/live_paper_section.py b/fairgraph/openminds/publications/live_paper_section.py index 062b60f0..b7a10943 100644 --- a/fairgraph/openminds/publications/live_paper_section.py +++ b/fairgraph/openminds/publications/live_paper_section.py @@ -14,7 +14,7 @@ class LivePaperSection(KGObject, LivePaperSection): """ - type_ = "https://openminds.ebrains.eu/publications/LivePaperSection" + type_ = "https://openminds.om-i.org/types/LivePaperSection" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/live_paper_version.py b/fairgraph/openminds/publications/live_paper_version.py index 19da490a..5878a162 100644 --- a/fairgraph/openminds/publications/live_paper_version.py +++ b/fairgraph/openminds/publications/live_paper_version.py @@ -20,7 +20,7 @@ class LivePaperVersion(KGObject, LivePaperVersion): """ - type_ = "https://openminds.ebrains.eu/publications/LivePaperVersion" + type_ = "https://openminds.om-i.org/types/LivePaperVersion" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/periodical.py b/fairgraph/openminds/publications/periodical.py index a57769c1..b3f6e956 100644 --- a/fairgraph/openminds/publications/periodical.py +++ b/fairgraph/openminds/publications/periodical.py @@ -14,7 +14,7 @@ class Periodical(KGObject, Periodical): """ - type_ = "https://openminds.ebrains.eu/publications/Periodical" + type_ = "https://openminds.om-i.org/types/Periodical" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/publication_issue.py b/fairgraph/openminds/publications/publication_issue.py index 62eb40b7..a5bf707a 100644 --- a/fairgraph/openminds/publications/publication_issue.py +++ b/fairgraph/openminds/publications/publication_issue.py @@ -14,7 +14,7 @@ class PublicationIssue(KGObject, PublicationIssue): """ - type_ = "https://openminds.ebrains.eu/publications/PublicationIssue" + type_ = "https://openminds.om-i.org/types/PublicationIssue" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/publication_volume.py b/fairgraph/openminds/publications/publication_volume.py index 529ac5af..98e0aa4c 100644 --- a/fairgraph/openminds/publications/publication_volume.py +++ b/fairgraph/openminds/publications/publication_volume.py @@ -14,7 +14,7 @@ class PublicationVolume(KGObject, PublicationVolume): """ - type_ = "https://openminds.ebrains.eu/publications/PublicationVolume" + type_ = "https://openminds.om-i.org/types/PublicationVolume" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/publications/scholarly_article.py b/fairgraph/openminds/publications/scholarly_article.py index 38236b19..0b04b8a9 100644 --- a/fairgraph/openminds/publications/scholarly_article.py +++ b/fairgraph/openminds/publications/scholarly_article.py @@ -20,7 +20,7 @@ class ScholarlyArticle(KGObject, ScholarlyArticle): """ - type_ = "https://openminds.ebrains.eu/publications/ScholarlyArticle" + type_ = "https://openminds.om-i.org/types/ScholarlyArticle" default_space = "livepapers" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/atlas/atlas_annotation.py b/fairgraph/openminds/sands/atlas/atlas_annotation.py index e78a6787..e955671b 100644 --- a/fairgraph/openminds/sands/atlas/atlas_annotation.py +++ b/fairgraph/openminds/sands/atlas/atlas_annotation.py @@ -14,7 +14,7 @@ class AtlasAnnotation(EmbeddedMetadata, AtlasAnnotation): """ - type_ = "https://openminds.ebrains.eu/sands/AtlasAnnotation" + type_ = "https://openminds.om-i.org/types/AtlasAnnotation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/atlas/brain_atlas.py b/fairgraph/openminds/sands/atlas/brain_atlas.py index 982815e0..24ca08d8 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas.py @@ -17,7 +17,7 @@ class BrainAtlas(KGObject, BrainAtlas): """ - type_ = "https://openminds.ebrains.eu/sands/BrainAtlas" + type_ = "https://openminds.om-i.org/types/BrainAtlas" default_space = "atlas" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/atlas/brain_atlas_version.py b/fairgraph/openminds/sands/atlas/brain_atlas_version.py index 7ba7488b..b8ebb8af 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas_version.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas_version.py @@ -18,7 +18,7 @@ class BrainAtlasVersion(KGObject, BrainAtlasVersion): """ - type_ = "https://openminds.ebrains.eu/sands/BrainAtlasVersion" + type_ = "https://openminds.om-i.org/types/BrainAtlasVersion" default_space = "atlas" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space.py b/fairgraph/openminds/sands/atlas/common_coordinate_space.py index 519fdeae..2577c88a 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space.py @@ -17,7 +17,7 @@ class CommonCoordinateSpace(KGObject, CommonCoordinateSpace): """ - type_ = "https://openminds.ebrains.eu/sands/CommonCoordinateSpace" + type_ = "https://openminds.om-i.org/types/CommonCoordinateSpace" default_space = "atlas" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py index 3bdcef11..dbd1786e 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py @@ -18,7 +18,7 @@ class CommonCoordinateSpaceVersion(KGObject, CommonCoordinateSpaceVersion): """ - type_ = "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion" + type_ = "https://openminds.om-i.org/types/CommonCoordinateSpaceVersion" default_space = "atlas" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity.py b/fairgraph/openminds/sands/atlas/parcellation_entity.py index 6a0664d1..804e6fc0 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity.py @@ -14,7 +14,7 @@ class ParcellationEntity(KGObject, ParcellationEntity): """ - type_ = "https://openminds.ebrains.eu/sands/ParcellationEntity" + type_ = "https://openminds.om-i.org/types/ParcellationEntity" default_space = "atlas" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py index 225dcd31..a7b8eb72 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py @@ -14,7 +14,7 @@ class ParcellationEntityVersion(KGObject, ParcellationEntityVersion): """ - type_ = "https://openminds.ebrains.eu/sands/ParcellationEntityVersion" + type_ = "https://openminds.om-i.org/types/ParcellationEntityVersion" default_space = "atlas" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology.py b/fairgraph/openminds/sands/atlas/parcellation_terminology.py index 9326ef05..d174142e 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology.py @@ -14,7 +14,7 @@ class ParcellationTerminology(EmbeddedMetadata, ParcellationTerminology): """ - type_ = "https://openminds.ebrains.eu/sands/ParcellationTerminology" + type_ = "https://openminds.om-i.org/types/ParcellationTerminology" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py index 3cd4719a..3cfa19d6 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py @@ -14,7 +14,7 @@ class ParcellationTerminologyVersion(EmbeddedMetadata, ParcellationTerminologyVe """ - type_ = "https://openminds.ebrains.eu/sands/ParcellationTerminologyVersion" + type_ = "https://openminds.om-i.org/types/ParcellationTerminologyVersion" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/mathematical_shapes/circle.py b/fairgraph/openminds/sands/mathematical_shapes/circle.py index 750435de..67a42260 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/circle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/circle.py @@ -14,7 +14,7 @@ class Circle(EmbeddedMetadata, Circle): """ - type_ = "https://openminds.ebrains.eu/sands/Circle" + type_ = "https://openminds.om-i.org/types/Circle" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py index 8756c81a..9baeb5b0 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py +++ b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py @@ -14,7 +14,7 @@ class Ellipse(EmbeddedMetadata, Ellipse): """ - type_ = "https://openminds.ebrains.eu/sands/Ellipse" + type_ = "https://openminds.om-i.org/types/Ellipse" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py index 126b404c..157c227c 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py @@ -14,7 +14,7 @@ class Rectangle(EmbeddedMetadata, Rectangle): """ - type_ = "https://openminds.ebrains.eu/sands/Rectangle" + type_ = "https://openminds.om-i.org/types/Rectangle" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py index fd288d6f..0a8ede02 100644 --- a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py +++ b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py @@ -14,7 +14,7 @@ class AnatomicalTargetPosition(EmbeddedMetadata, AnatomicalTargetPosition): """ - type_ = "https://openminds.ebrains.eu/sands/AnatomicalTargetPosition" + type_ = "https://openminds.om-i.org/types/AnatomicalTargetPosition" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py index 99a98a77..f2414511 100644 --- a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py +++ b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py @@ -14,7 +14,7 @@ class CoordinatePoint(EmbeddedMetadata, CoordinatePoint): """ - type_ = "https://openminds.ebrains.eu/sands/CoordinatePoint" + type_ = "https://openminds.om-i.org/types/CoordinatePoint" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py index 85e7d6bc..4926d1c3 100644 --- a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py @@ -14,7 +14,7 @@ class QualitativeRelationAssessment(EmbeddedMetadata, QualitativeRelationAssessm """ - type_ = "https://openminds.ebrains.eu/sands/QualitativeRelationAssessment" + type_ = "https://openminds.om-i.org/types/QualitativeRelationAssessment" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py index 238b6967..dcf99412 100644 --- a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py @@ -14,7 +14,7 @@ class QuantitativeRelationAssessment(EmbeddedMetadata, QuantitativeRelationAsses """ - type_ = "https://openminds.ebrains.eu/sands/QuantitativeRelationAssessment" + type_ = "https://openminds.om-i.org/types/QuantitativeRelationAssessment" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/miscellaneous/single_color.py b/fairgraph/openminds/sands/miscellaneous/single_color.py index e79f5b21..19067931 100644 --- a/fairgraph/openminds/sands/miscellaneous/single_color.py +++ b/fairgraph/openminds/sands/miscellaneous/single_color.py @@ -14,7 +14,7 @@ class SingleColor(KGObject, SingleColor): """ - type_ = "https://openminds.ebrains.eu/sands/SingleColor" + type_ = "https://openminds.om-i.org/types/SingleColor" default_space = "atlas" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py index e54844ea..802986f6 100644 --- a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py +++ b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py @@ -14,7 +14,7 @@ class ViewerSpecification(EmbeddedMetadata, ViewerSpecification): """ - type_ = "https://openminds.ebrains.eu/sands/ViewerSpecification" + type_ = "https://openminds.om-i.org/types/ViewerSpecification" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py index 352933d4..139f005b 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py +++ b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py @@ -14,7 +14,7 @@ class CustomAnatomicalEntity(KGObject, CustomAnatomicalEntity): """ - type_ = "https://openminds.ebrains.eu/sands/CustomAnatomicalEntity" + type_ = "https://openminds.om-i.org/types/CustomAnatomicalEntity" default_space = "spatial" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/sands/non_atlas/custom_annotation.py b/fairgraph/openminds/sands/non_atlas/custom_annotation.py index d166caca..ce0e4c5e 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_annotation.py +++ b/fairgraph/openminds/sands/non_atlas/custom_annotation.py @@ -14,7 +14,7 @@ class CustomAnnotation(EmbeddedMetadata, CustomAnnotation): """ - type_ = "https://openminds.ebrains.eu/sands/CustomAnnotation" + type_ = "https://openminds.om-i.org/types/CustomAnnotation" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py index 1f4f0bd8..6b463fb8 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py +++ b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py @@ -14,7 +14,7 @@ class CustomCoordinateSpace(KGObject, CustomCoordinateSpace): """ - type_ = "https://openminds.ebrains.eu/sands/CustomCoordinateSpace" + type_ = "https://openminds.om-i.org/types/CustomCoordinateSpace" default_space = "spatial" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py index f5052ba7..a777469a 100644 --- a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py @@ -17,7 +17,7 @@ class CranialWindowPreparation(KGObject, CranialWindowPreparation): """ - type_ = "https://openminds.ebrains.eu/specimenPrep/CranialWindowPreparation" + type_ = "https://openminds.om-i.org/types/CranialWindowPreparation" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py index 80434849..20f64fa1 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py @@ -17,7 +17,7 @@ class TissueCulturePreparation(KGObject, TissueCulturePreparation): """ - type_ = "https://openminds.ebrains.eu/specimenPrep/TissueCulturePreparation" + type_ = "https://openminds.om-i.org/types/TissueCulturePreparation" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py index 6b490ac2..5665be21 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py @@ -17,7 +17,7 @@ class TissueSampleSlicing(KGObject, TissueSampleSlicing): """ - type_ = "https://openminds.ebrains.eu/specimenPrep/TissueSampleSlicing" + type_ = "https://openminds.om-i.org/types/TissueSampleSlicing" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device.py b/fairgraph/openminds/specimen_prep/device/slicing_device.py index 32392863..ce094a77 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device.py @@ -14,7 +14,7 @@ class SlicingDevice(KGObject, SlicingDevice): """ - type_ = "https://openminds.ebrains.eu/specimenPrep/SlicingDevice" + type_ = "https://openminds.om-i.org/types/SlicingDevice" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py index 84cc2eda..ace49eb3 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py @@ -14,7 +14,7 @@ class SlicingDeviceUsage(KGObject, SlicingDeviceUsage): """ - type_ = "https://openminds.ebrains.eu/specimenPrep/SlicingDeviceUsage" + type_ = "https://openminds.om-i.org/types/SlicingDeviceUsage" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/openminds/stimulation/activity/stimulation_activity.py b/fairgraph/openminds/stimulation/activity/stimulation_activity.py index 77463544..c178c7f2 100644 --- a/fairgraph/openminds/stimulation/activity/stimulation_activity.py +++ b/fairgraph/openminds/stimulation/activity/stimulation_activity.py @@ -17,7 +17,7 @@ class StimulationActivity(KGObject, StimulationActivity): """ - type_ = "https://openminds.ebrains.eu/stimulation/StimulationActivity" + type_ = "https://openminds.om-i.org/types/StimulationActivity" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [] diff --git a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py index f891d921..4b9cef7d 100644 --- a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py +++ b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py @@ -14,7 +14,7 @@ class EphysStimulus(KGObject, EphysStimulus): """ - type_ = "https://openminds.ebrains.eu/stimulation/EphysStimulus" + type_ = "https://openminds.om-i.org/types/EphysStimulus" default_space = "in-depth" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ diff --git a/fairgraph/queries.py b/fairgraph/queries.py index 1c9be049..d1f5c25c 100644 --- a/fairgraph/queries.py +++ b/fairgraph/queries.py @@ -17,7 +17,6 @@ # limitations under the License. from __future__ import annotations -from copy import deepcopy from typing import Optional, List, Any, Dict, Union from uuid import UUID from datetime import date, datetime @@ -296,12 +295,12 @@ def _get_query_property_name(property, possible_classes): return property_name -def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None) -> List[QueryProperty]: +def get_query_properties(property, context, follow_links: Optional[Dict[str, Any]] = None) -> List[QueryProperty]: """ Generate one or more QueryProperty instances for this property, for use in constructing a KG query definition. """ - expanded_path = expand_uri(property.path, {"@vocab": "https://openminds.ebrains.eu/vocab/"}) + expanded_path = expand_uri(property.path, context) properties = [] if any(issubclass(_type, EmbeddedMetadata) for _type in property.types): @@ -384,7 +383,7 @@ def get_query_properties(property, follow_links: Optional[Dict[str, Any]] = None return properties -def get_query_filter_property(property, filter: Any) -> QueryProperty: +def get_query_filter_property(property, context, filter: Any) -> QueryProperty: """ Generate a QueryProperty instance containing a filter, for use in constructing a KG query definition. @@ -401,7 +400,7 @@ def get_query_filter_property(property, filter: Any) -> QueryProperty: op = "CONTAINS" filter_obj = Filter(op, value=filter) - expanded_path = expand_uri(property.path, {"@vocab": "https://openminds.ebrains.eu/vocab/"}) + expanded_path = expand_uri(property.path, context) if any(issubclass(_type, Node) for _type in property.types): assert all(issubclass(_type, Node) for _type in property.types) @@ -484,17 +483,3 @@ def is_valid(val): return filter_items else: return filter_items[0] - - -def migrate_query(query): - """Map from v3 to v4+ openMINDS namespace""" - migrated_query = deepcopy(query) - type_ = migrated_query["meta"]["type"] - migrated_query["meta"]["type"] = f'https://openminds.om-i.org/types/{type_.split("/")[-1]}' - replacement = ("openminds.ebrains.eu/vocab", "openminds.om-i.org/props") - for item in migrated_query["structure"]: - if isinstance(item["path"], str): - item["path"] = item["path"].replace(*replacement) - else: - item["path"]["@id"] = item["path"]["@id"].replace(*replacement) - return migrated_query diff --git a/fairgraph/registry.py b/fairgraph/registry.py index 5e323065..95349c3b 100644 --- a/fairgraph/registry.py +++ b/fairgraph/registry.py @@ -6,7 +6,6 @@ from __future__ import annotations from itertools import chain -import logging from typing import TYPE_CHECKING, Union, List, Dict from warnings import warn diff --git a/fairgraph/utility.py b/fairgraph/utility.py index f2311975..520323a7 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -18,11 +18,14 @@ # limitations under the License. from __future__ import annotations +from copy import deepcopy import hashlib import logging from typing import Any, Dict, Iterable, List, Optional, Tuple, Union, TYPE_CHECKING import warnings +from openminds.registry import lookup_type + if TYPE_CHECKING: from .client import KGClient from .kgobject import KGObject @@ -145,7 +148,10 @@ def compact_uri( if uri.startswith(base_url): start = len(base_url) identifier = uri[start:].strip("/") - compacted_uris.append(f"{prefix}:{identifier}") + if prefix == "@vocab": + compacted_uris.append(identifier) + else: + compacted_uris.append(f"{prefix}:{identifier}") found = True break if not found: @@ -213,9 +219,6 @@ def normalize_data(data: Union[None, JSONdict], context: Dict[str, Any]) -> Unio elif value is None: pass elif expanded_key == "@type": - if isinstance(value, str): - # KG makes @type a list - value = [value] normalized[expanded_key] = value elif isinstance(value, (list, tuple)): normalized[expanded_key] = [] @@ -224,8 +227,6 @@ def normalize_data(data: Union[None, JSONdict], context: Dict[str, Any]) -> Unio normalized[expanded_key].append(normalize_data(item, context)) else: normalized[expanded_key].append(item) - if len(value) == 1: - normalized[expanded_key] = normalized[expanded_key][0] elif isinstance(value, dict): normalized[expanded_key] = normalize_data(value, context) else: @@ -439,7 +440,89 @@ def types_match(a, b): if a == b: return True elif a.split("/")[-1] == b.split("/")[-1]: - logger.warning(f"Replacing {a} with {b}") + logger.warning(f"Assuming {a} matches {b} in types_match()") return True else: return False + + +def _adapt_namespaces(data, adapt_keys, adapt_type): + if isinstance(data, list): + for item in data: + _adapt_namespaces(item, adapt_keys, adapt_type) + elif isinstance(data, dict): + # adapt property URIs + old_keys = tuple(data.keys()) + new_keys = adapt_keys(old_keys) + for old_key, new_key in zip(old_keys, new_keys): + data[new_key] = data.pop(old_key) + for value in data.values(): + if isinstance(value, (list, dict)): + _adapt_namespaces(value, adapt_keys, adapt_type) + # adapt @type URIs + if "@type" in data: + data["@type"] = adapt_type(data["@type"]) + else: + pass + + +def adapt_namespaces_3to4(data): + + def adapt_keys_3to4(uri_list): + replacement = ("openminds.ebrains.eu/vocab", "openminds.om-i.org/props") + return (uri.replace(*replacement) for uri in uri_list) + + def adapt_type_3to4(uri): + if isinstance(uri, list): + assert len(uri) == 1 + uri = uri[0] + return f"https://openminds.om-i.org/types/{uri.split('/')[-1]}" + + return _adapt_namespaces(data, adapt_keys_3to4, adapt_type_3to4) + + +def adapt_type_4to3(uri): + if isinstance(uri, list): + assert len(uri) == 1 + uri = uri[0] + cls = lookup_type(uri) + module_name = cls.__module__.split(".")[2] # e.g., 'fairgraph.openminds.core.actors.person' -> "core" + module_name = { + "controlled_terms": "controlledTerms", + "specimen_prep": "specimenPrep" + }.get(module_name, module_name) + return f"https://openminds.ebrains.eu/{module_name}/{cls.__name__}" + + +def adapt_namespaces_4to3(data): + + def adapt_keys_4to3(uri_list): + replacement = ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab") + return (uri.replace(*replacement) for uri in uri_list) + + return _adapt_namespaces(data, adapt_keys_4to3, adapt_type_4to3) + + +def adapt_namespaces_for_query(query): + """Map from v4+ to v3 openMINDS namespace""" + + def adapt_structure(structure, replacement): + for item in structure: + if isinstance(item["path"], str): + item["path"] = item["path"].replace(*replacement) + elif isinstance(item["path"], list): + item["path"] = [part.replace(*replacement) for part in item["path"]] + # todo: individual parts could be dicts with "@id", "typeFilter" + else: + assert isinstance(item["path"], dict) + item["path"]["@id"] = item["path"]["@id"].replace(*replacement) + if "typeFilter" in item["path"]: + item["path"]["typeFilter"]["@id"] = adapt_type_4to3(item["path"]["typeFilter"]["@id"]) + if "structure" in item: + adapt_structure(item["structure"], replacement) + + migrated_query = deepcopy(query) + migrated_query["meta"]["type"] = adapt_type_4to3(migrated_query["meta"]["type"]) + replacement = ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab") + adapt_structure(migrated_query["structure"], replacement) + return migrated_query diff --git a/test/test_base.py b/test/test_base.py index 119825ef..86774205 100644 --- a/test/test_base.py +++ b/test/test_base.py @@ -216,7 +216,7 @@ def _construct_object_required_properties(self): data = { "https://openminds.ebrains.eu/vocab/aRequiredDateTime": "1789-07-14T00:00:00", "https://openminds.ebrains.eu/vocab/aRequiredEmbeddedObject": { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": -1.0, }, "https://openminds.ebrains.eu/vocab/aRequiredLinkedObject": { @@ -228,11 +228,11 @@ def _construct_object_required_properties(self): ], "https://openminds.ebrains.eu/vocab/aRequiredListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 100.0, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 200.0, }, ], @@ -275,7 +275,7 @@ def _construct_object_all_properties(self): data = { "https://openminds.ebrains.eu/vocab/aRequiredDateTime": "1789-07-14T00:00:00", "https://openminds.ebrains.eu/vocab/aRequiredEmbeddedObject": { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": -1.0, }, "https://openminds.ebrains.eu/vocab/aRequiredLinkedObject": { @@ -287,11 +287,11 @@ def _construct_object_all_properties(self): ], "https://openminds.ebrains.eu/vocab/aRequiredListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 100.0, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 200.0, }, ], @@ -303,7 +303,7 @@ def _construct_object_all_properties(self): "https://openminds.ebrains.eu/vocab/aRequiredString": "apple", "https://openminds.ebrains.eu/vocab/anOptionalDateTime": "1605-11-05T00:00:00", "https://openminds.ebrains.eu/vocab/anOptionalEmbeddedObject": { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 17.0, }, "https://openminds.ebrains.eu/vocab/anOptionalLinkedObject": { @@ -315,11 +315,11 @@ def _construct_object_all_properties(self): ], "https://openminds.ebrains.eu/vocab/anOptionalListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 18.0, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 19.0, }, ], @@ -417,7 +417,7 @@ def test_build_data_all_properties(self): "https://openminds.ebrains.eu/vocab/aRequiredDateTime": "1789-07-14T00:00:00", "https://openminds.ebrains.eu/vocab/aRequiredEmbeddedObject": { "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aNumber": -1.0, + "https://openminds.ebrains.eu/vocab/aNumber": -1, }, "https://openminds.ebrains.eu/vocab/aRequiredLinkedObject": { "@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000000002", @@ -429,11 +429,11 @@ def test_build_data_all_properties(self): "https://openminds.ebrains.eu/vocab/aRequiredListOfEmbeddedObjects": [ { "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aNumber": 100.0, + "https://openminds.ebrains.eu/vocab/aNumber": 100, }, { "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aNumber": 200.0, + "https://openminds.ebrains.eu/vocab/aNumber": 200, }, ], "https://openminds.ebrains.eu/vocab/aRequiredListOfLinkedObjects": [ @@ -445,7 +445,7 @@ def test_build_data_all_properties(self): "https://openminds.ebrains.eu/vocab/anOptionalDateTime": "1605-11-05T00:00:00", "https://openminds.ebrains.eu/vocab/anOptionalEmbeddedObject": { "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aNumber": 17.0, + "https://openminds.ebrains.eu/vocab/aNumber": 17, }, "https://openminds.ebrains.eu/vocab/anOptionalLinkedObject": { "@id": "https://kg.ebrains.eu/api/instances/00000000-0000-0000-0000-000000000123" @@ -457,11 +457,11 @@ def test_build_data_all_properties(self): "https://openminds.ebrains.eu/vocab/anOptionalListOfEmbeddedObjects": [ { "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aNumber": 18.0, + "https://openminds.ebrains.eu/vocab/aNumber": 18, }, { "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", - "https://openminds.ebrains.eu/vocab/aNumber": 19.0, + "https://openminds.ebrains.eu/vocab/aNumber": 19, }, ], "https://openminds.ebrains.eu/vocab/anOptionalListOfLinkedObjects": [ @@ -487,11 +487,11 @@ def test_modified_data(self): "https://openminds.ebrains.eu/vocab/aRequiredString": "pomme", "https://openminds.ebrains.eu/vocab/anOptionalListOfEmbeddedObjects": [ { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": -18, }, { - "@type": ["https://openminds.ebrains.eu/mock/MockEmbeddedObject"], + "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject", "https://openminds.ebrains.eu/vocab/aNumber": 19, }, ], @@ -522,7 +522,6 @@ def instance_from_full_uri(self, id, use_cache=True, scope="in progress", requir data = orig_object.to_jsonld(include_empty_properties=False, embed_linked_nodes=False) data["https://core.kg.ebrains.eu/vocab/meta/space"] = "collab-foobar" data["@id"] = orig_object.id - data["@context"] = orig_object.context data["@type"] = orig_object.type_ return data @@ -544,7 +543,6 @@ def instance_from_full_uri(self, id, use_cache=True, scope="in progress", requir # check that all the metadata for the existing instance have been retrieved expected = { - "@context": MockKGObject.context, "@id": orig_object.id, "@type": MockKGObject.type_, "https://core.kg.ebrains.eu/vocab/meta/space": "collab-foobar", @@ -594,7 +592,7 @@ def instance_from_full_uri(self, id, use_cache=True, scope="in progress", requir # not just those that have changed "https://openminds.ebrains.eu/vocab/aNumber": 41, "https://openminds.ebrains.eu/vocab/aString": "forty one", - "https://openminds.ebrains.eu/vocab/aDate": None, + #"https://openminds.ebrains.eu/vocab/aDate": None, }, } assert new_obj.modified_data() == expected diff --git a/test/test_client.py b/test/test_client.py index 8515933b..bed42958 100644 --- a/test/test_client.py +++ b/test/test_client.py @@ -42,8 +42,10 @@ def test_spaces_names_only(kg_client): @skip_if_no_connection def test_query_filter_by_space(kg_client): + import fairgraph.openminds.core # needed to populate registry + query = Query( - node_type="https://openminds.ebrains.eu/core/Model", + node_type="https://openminds.om-i.org/types/Model", label="fg-testing-model", properties=[ QueryProperty("@type"), @@ -53,19 +55,19 @@ def test_query_filter_by_space(kg_client): filter=Filter("EQUALS", value="model"), ), QueryProperty( - "https://openminds.ebrains.eu/vocab/fullName", + "https://openminds.om-i.org/props/fullName", name="fullName", filter=Filter("CONTAINS", parameter="name"), sorted=True, required=True, ), QueryProperty( - "https://openminds.ebrains.eu/vocab/custodian", + "https://openminds.om-i.org/props/custodian", name="custodian", - type_filter="https://openminds.ebrains.eu/core/Person", + type_filter="https://openminds.om-i.org/types/Person", properties=[ QueryProperty( - "https://openminds.ebrains.eu/vocab/familyName", + "https://openminds.om-i.org/props/familyName", name="familyName", ), ], @@ -94,9 +96,11 @@ def test_get_admin_client(kg_client): @skip_if_no_connection def test_list_scopes(kg_client): + import fairgraph.openminds.core + def _get_models(scope): return kg_client.list( - target_type="https://openminds.ebrains.eu/core/Model", + target_type="https://openminds.om-i.org/types/Model", space="model", from_index=0, size=10000, diff --git a/test/test_data/queries/openminds/core/accountinformation_simple_query.json b/test/test_data/queries/openminds/core/accountinformation_simple_query.json index fdef1e90..5d740115 100644 --- a/test/test_data/queries/openminds/core/accountinformation_simple_query.json +++ b/test/test_data/queries/openminds/core/accountinformation_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/AccountInformation", + "type": "https://openminds.om-i.org/types/AccountInformation", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/service", + "path": "https://openminds.om-i.org/props/service", "propertyName": "service", "structure": [ { @@ -52,12 +52,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/userName", + "path": "https://openminds.om-i.org/props/userName", "propertyName": "userName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/associatedAccount", + "@id": "https://openminds.om-i.org/props/associatedAccount", "reverse": true }, "propertyName": "associatedAccount", diff --git a/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json b/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json index 048c90ad..427642ae 100644 --- a/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json +++ b/test/test_data/queries/openminds/core/behavioralprotocol_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/BehavioralProtocol", + "type": "https://openminds.om-i.org/types/BehavioralProtocol", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/describedIn", + "path": "https://openminds.om-i.org/props/describedIn", "propertyName": "describedIn", "ensureOrder": true, "structure": [ @@ -52,20 +52,20 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/stimulation", + "path": "https://openminds.om-i.org/props/stimulation", "propertyName": "stimulation", "ensureOrder": true, "structure": [ @@ -78,7 +78,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/stimulusType", + "path": "https://openminds.om-i.org/props/stimulusType", "propertyName": "stimulusType", "ensureOrder": true, "structure": [ @@ -92,7 +92,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", @@ -108,7 +108,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/behavioralProtocol", + "@id": "https://openminds.om-i.org/props/behavioralProtocol", "reverse": true }, "propertyName": "behavioralProtocol", diff --git a/test/test_data/queries/openminds/core/comment_simple_query.json b/test/test_data/queries/openminds/core/comment_simple_query.json index 31faf675..07595bd5 100644 --- a/test/test_data/queries/openminds/core/comment_simple_query.json +++ b/test/test_data/queries/openminds/core/comment_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Comment", + "type": "https://openminds.om-i.org/types/Comment", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/about", + "path": "https://openminds.om-i.org/props/about", "propertyName": "about", "structure": [ { @@ -52,11 +52,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/comment", + "path": "https://openminds.om-i.org/props/comment", "propertyName": "comment" }, { - "path": "https://openminds.ebrains.eu/vocab/commenter", + "path": "https://openminds.om-i.org/props/commenter", "propertyName": "commenter", "structure": [ { @@ -69,7 +69,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/timestamp", + "path": "https://openminds.om-i.org/props/timestamp", "propertyName": "timestamp" } ] diff --git a/test/test_data/queries/openminds/core/configuration_simple_query.json b/test/test_data/queries/openminds/core/configuration_simple_query.json index 92e453d7..5a44fb46 100644 --- a/test/test_data/queries/openminds/core/configuration_simple_query.json +++ b/test/test_data/queries/openminds/core/configuration_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Configuration", + "type": "https://openminds.om-i.org/types/Configuration", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/configuration", + "path": "https://openminds.om-i.org/props/configuration", "propertyName": "configuration" }, { - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "structure": [ { @@ -56,13 +56,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/configuration", + "@id": "https://openminds.om-i.org/props/configuration", "reverse": true }, "propertyName": "configuration", @@ -78,7 +78,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/specification", + "@id": "https://openminds.om-i.org/props/specification", "reverse": true }, "propertyName": "specification", diff --git a/test/test_data/queries/openminds/core/consortium_simple_query.json b/test/test_data/queries/openminds/core/consortium_simple_query.json index ec5fab28..ead5dfd2 100644 --- a/test/test_data/queries/openminds/core/consortium_simple_query.json +++ b/test/test_data/queries/openminds/core/consortium_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Consortium", + "type": "https://openminds.om-i.org/types/Consortium", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contactInformation", + "path": "https://openminds.om-i.org/props/contactInformation", "propertyName": "contactInformation", "structure": [ { @@ -52,21 +52,21 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -82,7 +82,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -98,7 +98,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -114,7 +114,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "reverse": true }, "propertyName": "memberOf", @@ -124,11 +124,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -141,14 +141,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -164,7 +164,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -180,7 +180,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -196,7 +196,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -212,7 +212,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", diff --git a/test/test_data/queries/openminds/core/contactinformation_simple_query.json b/test/test_data/queries/openminds/core/contactinformation_simple_query.json index 6c96b297..fc7141c9 100644 --- a/test/test_data/queries/openminds/core/contactinformation_simple_query.json +++ b/test/test_data/queries/openminds/core/contactinformation_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ContactInformation", + "type": "https://openminds.om-i.org/types/ContactInformation", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/email", + "path": "https://openminds.om-i.org/props/email", "propertyName": "email" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/contactInformation", + "@id": "https://openminds.om-i.org/props/contactInformation", "reverse": true }, "propertyName": "contactInformation", diff --git a/test/test_data/queries/openminds/core/contenttype_simple_query.json b/test/test_data/queries/openminds/core/contenttype_simple_query.json index cc7ba6a1..9651e773 100644 --- a/test/test_data/queries/openminds/core/contenttype_simple_query.json +++ b/test/test_data/queries/openminds/core/contenttype_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ContentType", + "type": "https://openminds.om-i.org/types/ContentType", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/dataType", + "path": "https://openminds.om-i.org/props/dataType", "propertyName": "dataType", "ensureOrder": true, "structure": [ @@ -52,39 +52,39 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/displayLabel", + "path": "https://openminds.om-i.org/props/displayLabel", "propertyName": "displayLabel" }, { - "path": "https://openminds.ebrains.eu/vocab/fileExtension", + "path": "https://openminds.om-i.org/props/fileExtension", "propertyName": "fileExtension", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/relatedMediaType", + "path": "https://openminds.om-i.org/props/relatedMediaType", "propertyName": "relatedMediaType" }, { - "path": "https://openminds.ebrains.eu/vocab/specification", + "path": "https://openminds.om-i.org/props/specification", "propertyName": "specification" }, { - "path": "https://openminds.ebrains.eu/vocab/synonym", + "path": "https://openminds.om-i.org/props/synonym", "propertyName": "synonym", "ensureOrder": true }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/contentType", + "@id": "https://openminds.om-i.org/props/contentType", "reverse": true }, "propertyName": "contentType", @@ -100,7 +100,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/format", + "@id": "https://openminds.om-i.org/props/format", "reverse": true }, "propertyName": "format", @@ -116,7 +116,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/outputFormat", + "@id": "https://openminds.om-i.org/props/outputFormat", "reverse": true }, "propertyName": "outputFormat", @@ -132,7 +132,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/specificationFormat", + "@id": "https://openminds.om-i.org/props/specificationFormat", "reverse": true }, "propertyName": "specificationFormat", diff --git a/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json b/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json index 60cf2e8d..c4ef9edb 100644 --- a/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json +++ b/test/test_data/queries/openminds/core/contenttypepattern_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ContentTypePattern", + "type": "https://openminds.om-i.org/types/ContentTypePattern", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contentType", + "path": "https://openminds.om-i.org/props/contentType", "propertyName": "contentType", "structure": [ { @@ -52,17 +52,17 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/regex", + "path": "https://openminds.om-i.org/props/regex", "propertyName": "regex" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/contentTypePattern", + "@id": "https://openminds.om-i.org/props/contentTypePattern", "reverse": true }, "propertyName": "contentTypePattern", diff --git a/test/test_data/queries/openminds/core/dataset_simple_query.json b/test/test_data/queries/openminds/core/dataset_simple_query.json index 08f5a4be..26c8c211 100644 --- a/test/test_data/queries/openminds/core/dataset_simple_query.json +++ b/test/test_data/queries/openminds/core/dataset_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Dataset", + "type": "https://openminds.om-i.org/types/Dataset", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/author", + "path": "https://openminds.om-i.org/props/author", "propertyName": "author", "ensureOrder": true, "structure": [ @@ -52,7 +52,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -65,11 +65,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -82,12 +82,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/hasVersion", + "path": "https://openminds.om-i.org/props/hasVersion", "propertyName": "hasVersion", "ensureOrder": true, "structure": [ @@ -100,20 +100,20 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -129,7 +129,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -145,7 +145,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/dataset_simple_query_v4.json b/test/test_data/queries/openminds/core/dataset_simple_query_v4.json deleted file mode 100644 index 2174c2b5..00000000 --- a/test/test_data/queries/openminds/core/dataset_simple_query_v4.json +++ /dev/null @@ -1,163 +0,0 @@ -{ - "@context": { - "@vocab": "https://core.kg.ebrains.eu/vocab/query/", - "query": "https://schema.hbp.eu/myQuery/", - "propertyName": { - "@id": "propertyName", - "@type": "@id" - }, - "merge": { - "@type": "@id", - "@id": "merge" - }, - "path": { - "@id": "path", - "@type": "@id" - } - }, - "meta": { - "type": "https://openminds.om-i.org/types/Dataset", - "description": "Automatically generated by fairgraph" - }, - "structure": [ - { - "path": "@id", - "filter": { - "op": "EQUALS", - "parameter": "id" - } - }, - { - "path": "https://core.kg.ebrains.eu/vocab/meta/space", - "propertyName": "query:space", - "filter": { - "op": "EQUALS", - "value": "collab-foobar" - } - }, - { - "path": "@type" - }, - { - "path": "https://openminds.om-i.org/props/author", - "propertyName": "author", - "ensureOrder": true, - "structure": [ - { - "path": "@id" - }, - { - "path": "@type" - } - ] - }, - { - "path": "https://openminds.om-i.org/props/custodian", - "propertyName": "custodian", - "ensureOrder": true, - "structure": [ - { - "path": "@id" - }, - { - "path": "@type" - } - ] - }, - { - "path": "https://openminds.om-i.org/props/description", - "propertyName": "description" - }, - { - "path": "https://openminds.om-i.org/props/digitalIdentifier", - "propertyName": "digitalIdentifier", - "singleValue": "FIRST", - "structure": [ - { - "path": "@id" - }, - { - "path": "@type" - } - ] - }, - { - "path": "https://openminds.om-i.org/props/fullName", - "propertyName": "fullName", - "sort": true - }, - { - "path": "https://openminds.om-i.org/props/hasVersion", - "propertyName": "hasVersion", - "ensureOrder": true, - "structure": [ - { - "path": "@id" - }, - { - "path": "@type" - } - ] - }, - { - "path": "https://openminds.om-i.org/props/homepage", - "propertyName": "homepage" - }, - { - "path": "https://openminds.om-i.org/props/howToCite", - "propertyName": "howToCite" - }, - { - "path": "https://openminds.om-i.org/props/shortName", - "propertyName": "shortName" - }, - { - "path": { - "@id": "https://openminds.om-i.org/props/about", - "reverse": true - }, - "propertyName": "about", - "ensureOrder": true, - "structure": [ - { - "path": "@id" - }, - { - "path": "@type" - } - ] - }, - { - "path": { - "@id": "https://openminds.om-i.org/props/hasPart", - "reverse": true - }, - "propertyName": "hasPart", - "ensureOrder": true, - "structure": [ - { - "path": "@id" - }, - { - "path": "@type" - } - ] - }, - { - "path": { - "@id": "https://openminds.om-i.org/props/about", - "reverse": true - }, - "propertyName": "about", - "ensureOrder": true, - "structure": [ - { - "path": "@id" - }, - { - "path": "@type" - } - ] - } - ] -} \ No newline at end of file diff --git a/test/test_data/queries/openminds/core/datasetversion_simple_query.json b/test/test_data/queries/openminds/core/datasetversion_simple_query.json index 17e55b11..91674699 100644 --- a/test/test_data/queries/openminds/core/datasetversion_simple_query.json +++ b/test/test_data/queries/openminds/core/datasetversion_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/DatasetVersion", + "type": "https://openminds.om-i.org/types/DatasetVersion", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/accessibility", + "path": "https://openminds.om-i.org/props/accessibility", "propertyName": "accessibility", "structure": [ { @@ -52,7 +52,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/author", + "path": "https://openminds.om-i.org/props/author", "propertyName": "author", "ensureOrder": true, "structure": [ @@ -65,7 +65,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/behavioralProtocol", + "path": "https://openminds.om-i.org/props/behavioralProtocol", "propertyName": "behavioralProtocol", "ensureOrder": true, "structure": [ @@ -78,14 +78,14 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/copyright", + "path": "https://openminds.om-i.org/props/copyright", "propertyName": "copyright", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/holder", + "path": "https://openminds.om-i.org/props/holder", "propertyName": "holder", "ensureOrder": true, "structure": [ @@ -98,7 +98,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/year", + "path": "https://openminds.om-i.org/props/year", "propertyName": "year", "ensureOrder": true } @@ -106,7 +106,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -119,7 +119,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/dataType", + "path": "https://openminds.om-i.org/props/dataType", "propertyName": "dataType", "ensureOrder": true, "structure": [ @@ -132,11 +132,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -149,7 +149,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/ethicsAssessment", + "path": "https://openminds.om-i.org/props/ethicsAssessment", "propertyName": "ethicsAssessment", "structure": [ { @@ -162,7 +162,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/experimentalApproach", + "path": "https://openminds.om-i.org/props/experimentalApproach", "propertyName": "experimentalApproach", "ensureOrder": true, "structure": [ @@ -175,7 +175,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", + "path": "https://openminds.om-i.org/props/fullDocumentation", "propertyName": "fullDocumentation", "structure": [ { @@ -188,12 +188,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/funding", + "path": "https://openminds.om-i.org/props/funding", "propertyName": "funding", "ensureOrder": true, "structure": [ @@ -206,15 +206,15 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/inputData", + "path": "https://openminds.om-i.org/props/inputData", "propertyName": "inputData", "ensureOrder": true, "structure": [ @@ -227,7 +227,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", + "path": "https://openminds.om-i.org/props/isAlternativeVersionOf", "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ @@ -240,7 +240,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "path": "https://openminds.om-i.org/props/isNewVersionOf", "propertyName": "isNewVersionOf", "structure": [ { @@ -253,7 +253,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/keyword", + "path": "https://openminds.om-i.org/props/keyword", "propertyName": "keyword", "ensureOrder": true, "structure": [ @@ -266,7 +266,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/license", + "path": "https://openminds.om-i.org/props/license", "propertyName": "license", "structure": [ { @@ -279,7 +279,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/otherContribution", + "path": "https://openminds.om-i.org/props/otherContribution", "propertyName": "otherContribution", "ensureOrder": true, "structure": [ @@ -287,7 +287,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contributor", + "path": "https://openminds.om-i.org/props/contributor", "propertyName": "contributor", "structure": [ { @@ -300,7 +300,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "ensureOrder": true, "structure": [ @@ -315,7 +315,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/preparationDesign", + "path": "https://openminds.om-i.org/props/preparationDesign", "propertyName": "preparationDesign", "ensureOrder": true, "structure": [ @@ -328,7 +328,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/protocol", + "path": "https://openminds.om-i.org/props/protocol", "propertyName": "protocol", "ensureOrder": true, "structure": [ @@ -341,7 +341,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/relatedPublication", + "path": "https://openminds.om-i.org/props/relatedPublication", "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ @@ -354,11 +354,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/releaseDate", + "path": "https://openminds.om-i.org/props/releaseDate", "propertyName": "releaseDate" }, { - "path": "https://openminds.ebrains.eu/vocab/repository", + "path": "https://openminds.om-i.org/props/repository", "propertyName": "repository", "structure": [ { @@ -371,11 +371,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { - "path": "https://openminds.ebrains.eu/vocab/studiedSpecimen", + "path": "https://openminds.om-i.org/props/studiedSpecimen", "propertyName": "studiedSpecimen", "ensureOrder": true, "structure": [ @@ -388,7 +388,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/studyTarget", + "path": "https://openminds.om-i.org/props/studyTarget", "propertyName": "studyTarget", "ensureOrder": true, "structure": [ @@ -401,12 +401,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/supportChannel", + "path": "https://openminds.om-i.org/props/supportChannel", "propertyName": "supportChannel", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/technique", + "path": "https://openminds.om-i.org/props/technique", "propertyName": "technique", "ensureOrder": true, "structure": [ @@ -419,16 +419,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", + "path": "https://openminds.om-i.org/props/versionIdentifier", "propertyName": "versionIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/versionInnovation", + "path": "https://openminds.om-i.org/props/versionInnovation", "propertyName": "versionInnovation" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -444,7 +444,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isPartOf", + "@id": "https://openminds.om-i.org/props/isPartOf", "reverse": true }, "propertyName": "isPartOf", @@ -460,7 +460,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/input", + "@id": "https://openminds.om-i.org/props/input", "reverse": true }, "propertyName": "input", @@ -476,7 +476,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "@id": "https://openminds.om-i.org/props/isNewVersionOf", "reverse": true }, "propertyName": "isNewVersionOf", @@ -492,7 +492,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -508,7 +508,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasVersion", + "@id": "https://openminds.om-i.org/props/hasVersion", "reverse": true }, "propertyName": "hasVersion", @@ -524,7 +524,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -540,7 +540,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/doi_simple_query.json b/test/test_data/queries/openminds/core/doi_simple_query.json index fca0fc36..8c15499b 100644 --- a/test/test_data/queries/openminds/core/doi_simple_query.json +++ b/test/test_data/queries/openminds/core/doi_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/DOI", + "type": "https://openminds.om-i.org/types/DOI", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/describedIn", + "@id": "https://openminds.om-i.org/props/describedIn", "reverse": true }, "propertyName": "describedIn", @@ -60,7 +60,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", @@ -76,7 +76,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", + "@id": "https://openminds.om-i.org/props/relatedPublication", "reverse": true }, "propertyName": "relatedPublication", diff --git a/test/test_data/queries/openminds/core/file_simple_query.json b/test/test_data/queries/openminds/core/file_simple_query.json index 39ce1045..b2073a8f 100644 --- a/test/test_data/queries/openminds/core/file_simple_query.json +++ b/test/test_data/queries/openminds/core/file_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/File", + "type": "https://openminds.om-i.org/types/File", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contentDescription", + "path": "https://openminds.om-i.org/props/contentDescription", "propertyName": "contentDescription" }, { - "path": "https://openminds.ebrains.eu/vocab/dataType", + "path": "https://openminds.om-i.org/props/dataType", "propertyName": "dataType", "ensureOrder": true, "structure": [ @@ -56,7 +56,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fileRepository", + "path": "https://openminds.om-i.org/props/fileRepository", "propertyName": "fileRepository", "structure": [ { @@ -69,7 +69,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "structure": [ { @@ -82,7 +82,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/hash", + "path": "https://openminds.om-i.org/props/hash", "propertyName": "hash", "ensureOrder": true, "structure": [ @@ -90,21 +90,21 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/algorithm", + "path": "https://openminds.om-i.org/props/algorithm", "propertyName": "algorithm" }, { - "path": "https://openminds.ebrains.eu/vocab/digest", + "path": "https://openminds.om-i.org/props/digest", "propertyName": "digest" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/IRI", + "path": "https://openminds.om-i.org/props/IRI", "propertyName": "IRI" }, { - "path": "https://openminds.ebrains.eu/vocab/isPartOf", + "path": "https://openminds.om-i.org/props/isPartOf", "propertyName": "isPartOf", "ensureOrder": true, "structure": [ @@ -117,12 +117,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/specialUsageRole", + "path": "https://openminds.om-i.org/props/specialUsageRole", "propertyName": "specialUsageRole", "structure": [ { @@ -135,14 +135,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/storageSize", + "path": "https://openminds.om-i.org/props/storageSize", "propertyName": "storageSize", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -155,12 +155,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -173,7 +173,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -181,7 +181,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/fullDocumentation", + "@id": "https://openminds.om-i.org/props/fullDocumentation", "reverse": true }, "propertyName": "fullDocumentation", @@ -197,7 +197,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/copyOf", + "@id": "https://openminds.om-i.org/props/copyOf", "reverse": true }, "propertyName": "copyOf", @@ -213,7 +213,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -229,7 +229,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/configuration", + "@id": "https://openminds.om-i.org/props/configuration", "reverse": true }, "propertyName": "configuration", @@ -245,7 +245,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/defaultImage", + "@id": "https://openminds.om-i.org/props/defaultImage", "reverse": true }, "propertyName": "defaultImage", @@ -261,7 +261,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/inputData", + "@id": "https://openminds.om-i.org/props/inputData", "reverse": true }, "propertyName": "inputData", @@ -277,7 +277,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/previewImage", + "@id": "https://openminds.om-i.org/props/previewImage", "reverse": true }, "propertyName": "previewImage", @@ -293,7 +293,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/referenceData", + "@id": "https://openminds.om-i.org/props/referenceData", "reverse": true }, "propertyName": "referenceData", @@ -309,7 +309,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/sourceData", + "@id": "https://openminds.om-i.org/props/sourceData", "reverse": true }, "propertyName": "sourceData", @@ -325,7 +325,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", diff --git a/test/test_data/queries/openminds/core/filearchive_simple_query.json b/test/test_data/queries/openminds/core/filearchive_simple_query.json index aa16ef7f..9db348a4 100644 --- a/test/test_data/queries/openminds/core/filearchive_simple_query.json +++ b/test/test_data/queries/openminds/core/filearchive_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/FileArchive", + "type": "https://openminds.om-i.org/types/FileArchive", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "structure": [ { @@ -52,11 +52,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/IRI", + "path": "https://openminds.om-i.org/props/IRI", "propertyName": "IRI" }, { - "path": "https://openminds.ebrains.eu/vocab/sourceData", + "path": "https://openminds.om-i.org/props/sourceData", "propertyName": "sourceData", "ensureOrder": true, "structure": [ @@ -70,7 +70,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/dataLocation", + "@id": "https://openminds.om-i.org/props/dataLocation", "reverse": true }, "propertyName": "dataLocation", @@ -86,7 +86,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/output", + "@id": "https://openminds.om-i.org/props/output", "reverse": true }, "propertyName": "output", diff --git a/test/test_data/queries/openminds/core/filebundle_simple_query.json b/test/test_data/queries/openminds/core/filebundle_simple_query.json index d902c0c3..8ac3f637 100644 --- a/test/test_data/queries/openminds/core/filebundle_simple_query.json +++ b/test/test_data/queries/openminds/core/filebundle_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/FileBundle", + "type": "https://openminds.om-i.org/types/FileBundle", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contentDescription", + "path": "https://openminds.om-i.org/props/contentDescription", "propertyName": "contentDescription" }, { - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "structure": [ { @@ -56,7 +56,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/groupedBy", + "path": "https://openminds.om-i.org/props/groupedBy", "propertyName": "groupedBy", "ensureOrder": true, "structure": [ @@ -69,7 +69,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/groupingType", + "path": "https://openminds.om-i.org/props/groupingType", "propertyName": "groupingType", "ensureOrder": true, "structure": [ @@ -82,25 +82,25 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/hash", + "path": "https://openminds.om-i.org/props/hash", "propertyName": "hash", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/algorithm", + "path": "https://openminds.om-i.org/props/algorithm", "propertyName": "algorithm" }, { - "path": "https://openminds.ebrains.eu/vocab/digest", + "path": "https://openminds.om-i.org/props/digest", "propertyName": "digest" } ], "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/isPartOf", + "path": "https://openminds.om-i.org/props/isPartOf", "propertyName": "isPartOf", "structure": [ { @@ -113,19 +113,19 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/storageSize", + "path": "https://openminds.om-i.org/props/storageSize", "propertyName": "storageSize", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -138,12 +138,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -156,7 +156,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -164,7 +164,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/metadataLocation", + "@id": "https://openminds.om-i.org/props/metadataLocation", "reverse": true }, "propertyName": "metadataLocation", @@ -180,7 +180,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isPartOf", + "@id": "https://openminds.om-i.org/props/isPartOf", "reverse": true }, "propertyName": "isPartOf", @@ -196,7 +196,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -212,7 +212,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/inputData", + "@id": "https://openminds.om-i.org/props/inputData", "reverse": true }, "propertyName": "inputData", @@ -228,7 +228,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/dataLocation", + "@id": "https://openminds.om-i.org/props/dataLocation", "reverse": true }, "propertyName": "dataLocation", @@ -244,7 +244,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/referenceData", + "@id": "https://openminds.om-i.org/props/referenceData", "reverse": true }, "propertyName": "referenceData", @@ -260,7 +260,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/specification", + "@id": "https://openminds.om-i.org/props/specification", "reverse": true }, "propertyName": "specification", diff --git a/test/test_data/queries/openminds/core/filerepository_simple_query.json b/test/test_data/queries/openminds/core/filerepository_simple_query.json index 44f5d7ff..0f3a5cf0 100644 --- a/test/test_data/queries/openminds/core/filerepository_simple_query.json +++ b/test/test_data/queries/openminds/core/filerepository_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/FileRepository", + "type": "https://openminds.om-i.org/types/FileRepository", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contentTypePattern", + "path": "https://openminds.om-i.org/props/contentTypePattern", "propertyName": "contentTypePattern", "ensureOrder": true, "structure": [ @@ -52,7 +52,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "structure": [ { @@ -65,25 +65,25 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/hash", + "path": "https://openminds.om-i.org/props/hash", "propertyName": "hash", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/algorithm", + "path": "https://openminds.om-i.org/props/algorithm", "propertyName": "algorithm" }, { - "path": "https://openminds.ebrains.eu/vocab/digest", + "path": "https://openminds.om-i.org/props/digest", "propertyName": "digest" } ], "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/hostedBy", + "path": "https://openminds.om-i.org/props/hostedBy", "propertyName": "hostedBy", "structure": [ { @@ -96,23 +96,23 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/IRI", + "path": "https://openminds.om-i.org/props/IRI", "propertyName": "IRI" }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/storageSize", + "path": "https://openminds.om-i.org/props/storageSize", "propertyName": "storageSize", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -125,12 +125,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -143,14 +143,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/structurePattern", + "path": "https://openminds.om-i.org/props/structurePattern", "propertyName": "structurePattern", "structure": [ { @@ -163,7 +163,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "structure": [ { @@ -177,7 +177,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/repository", + "@id": "https://openminds.om-i.org/props/repository", "reverse": true }, "propertyName": "repository", @@ -193,7 +193,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/fileRepository", + "@id": "https://openminds.om-i.org/props/fileRepository", "reverse": true }, "propertyName": "fileRepository", @@ -209,7 +209,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isPartOf", + "@id": "https://openminds.om-i.org/props/isPartOf", "reverse": true }, "propertyName": "isPartOf", diff --git a/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json b/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json index 59b619e3..b606b81e 100644 --- a/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json +++ b/test/test_data/queries/openminds/core/filerepositorystructure_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/FileRepositoryStructure", + "type": "https://openminds.om-i.org/types/FileRepositoryStructure", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/filePathPattern", + "path": "https://openminds.om-i.org/props/filePathPattern", "propertyName": "filePathPattern", "ensureOrder": true, "structure": [ @@ -47,7 +47,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/groupingType", + "path": "https://openminds.om-i.org/props/groupingType", "propertyName": "groupingType", "ensureOrder": true, "structure": [ @@ -60,19 +60,19 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/regex", + "path": "https://openminds.om-i.org/props/regex", "propertyName": "regex" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/structurePattern", + "@id": "https://openminds.om-i.org/props/structurePattern", "reverse": true }, "propertyName": "structurePattern", diff --git a/test/test_data/queries/openminds/core/funding_simple_query.json b/test/test_data/queries/openminds/core/funding_simple_query.json index 035671df..0189ac84 100644 --- a/test/test_data/queries/openminds/core/funding_simple_query.json +++ b/test/test_data/queries/openminds/core/funding_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Funding", + "type": "https://openminds.om-i.org/types/Funding", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,19 +39,19 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/acknowledgement", + "path": "https://openminds.om-i.org/props/acknowledgement", "propertyName": "acknowledgement" }, { - "path": "https://openminds.ebrains.eu/vocab/awardNumber", + "path": "https://openminds.om-i.org/props/awardNumber", "propertyName": "awardNumber" }, { - "path": "https://openminds.ebrains.eu/vocab/awardTitle", + "path": "https://openminds.om-i.org/props/awardTitle", "propertyName": "awardTitle" }, { - "path": "https://openminds.ebrains.eu/vocab/funder", + "path": "https://openminds.om-i.org/props/funder", "propertyName": "funder", "structure": [ { @@ -65,7 +65,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funding", + "@id": "https://openminds.om-i.org/props/funding", "reverse": true }, "propertyName": "funding", diff --git a/test/test_data/queries/openminds/core/gridid_simple_query.json b/test/test_data/queries/openminds/core/gridid_simple_query.json index 42919def..9c2ef223 100644 --- a/test/test_data/queries/openminds/core/gridid_simple_query.json +++ b/test/test_data/queries/openminds/core/gridid_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/GRIDID", + "type": "https://openminds.om-i.org/types/GRIDID", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", diff --git a/test/test_data/queries/openminds/core/handle_simple_query.json b/test/test_data/queries/openminds/core/handle_simple_query.json index 82aa4d13..bffcbd6e 100644 --- a/test/test_data/queries/openminds/core/handle_simple_query.json +++ b/test/test_data/queries/openminds/core/handle_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/HANDLE", + "type": "https://openminds.om-i.org/types/HANDLE", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", + "@id": "https://openminds.om-i.org/props/relatedPublication", "reverse": true }, "propertyName": "relatedPublication", diff --git a/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json b/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json index bac1a184..fba2c76a 100644 --- a/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json +++ b/test/test_data/queries/openminds/core/identifiersdotorgid_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/IdentifiersDotOrgID", + "type": "https://openminds.om-i.org/types/IdentifiersDotOrgID", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", diff --git a/test/test_data/queries/openminds/core/isbn_simple_query.json b/test/test_data/queries/openminds/core/isbn_simple_query.json index d56b3024..33925758 100644 --- a/test/test_data/queries/openminds/core/isbn_simple_query.json +++ b/test/test_data/queries/openminds/core/isbn_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ISBN", + "type": "https://openminds.om-i.org/types/ISBN", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/citedPublication", + "@id": "https://openminds.om-i.org/props/citedPublication", "reverse": true }, "propertyName": "citedPublication", @@ -60,7 +60,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", @@ -76,7 +76,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", + "@id": "https://openminds.om-i.org/props/relatedPublication", "reverse": true }, "propertyName": "relatedPublication", diff --git a/test/test_data/queries/openminds/core/issn_simple_query.json b/test/test_data/queries/openminds/core/issn_simple_query.json index 43922e23..db0e3179 100644 --- a/test/test_data/queries/openminds/core/issn_simple_query.json +++ b/test/test_data/queries/openminds/core/issn_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ISSN", + "type": "https://openminds.om-i.org/types/ISSN", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", @@ -60,7 +60,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", + "@id": "https://openminds.om-i.org/props/relatedPublication", "reverse": true }, "propertyName": "relatedPublication", diff --git a/test/test_data/queries/openminds/core/license_simple_query.json b/test/test_data/queries/openminds/core/license_simple_query.json index 1bb1fd0a..0bdbfd2c 100644 --- a/test/test_data/queries/openminds/core/license_simple_query.json +++ b/test/test_data/queries/openminds/core/license_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/License", + "type": "https://openminds.om-i.org/types/License", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,26 +39,26 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/legalCode", + "path": "https://openminds.om-i.org/props/legalCode", "propertyName": "legalCode" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { - "path": "https://openminds.ebrains.eu/vocab/webpage", + "path": "https://openminds.om-i.org/props/webpage", "propertyName": "webpage", "ensureOrder": true }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/license", + "@id": "https://openminds.om-i.org/props/license", "reverse": true }, "propertyName": "license", diff --git a/test/test_data/queries/openminds/core/metadatamodel_simple_query.json b/test/test_data/queries/openminds/core/metadatamodel_simple_query.json index 73276d87..c1148c9a 100644 --- a/test/test_data/queries/openminds/core/metadatamodel_simple_query.json +++ b/test/test_data/queries/openminds/core/metadatamodel_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/MetaDataModel", + "type": "https://openminds.om-i.org/types/MetaDataModel", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -52,11 +52,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -69,7 +69,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -82,12 +82,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/hasVersion", + "path": "https://openminds.om-i.org/props/hasVersion", "propertyName": "hasVersion", "ensureOrder": true, "structure": [ @@ -100,20 +100,20 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -129,7 +129,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -145,7 +145,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json b/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json index ba4c03ad..48b24fe4 100644 --- a/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json +++ b/test/test_data/queries/openminds/core/metadatamodelversion_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/MetaDataModelVersion", + "type": "https://openminds.om-i.org/types/MetaDataModelVersion", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/accessibility", + "path": "https://openminds.om-i.org/props/accessibility", "propertyName": "accessibility", "structure": [ { @@ -52,14 +52,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/copyright", + "path": "https://openminds.om-i.org/props/copyright", "propertyName": "copyright", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/holder", + "path": "https://openminds.om-i.org/props/holder", "propertyName": "holder", "ensureOrder": true, "structure": [ @@ -72,7 +72,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/year", + "path": "https://openminds.om-i.org/props/year", "propertyName": "year", "ensureOrder": true } @@ -80,7 +80,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -93,11 +93,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -110,7 +110,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -123,7 +123,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", + "path": "https://openminds.om-i.org/props/fullDocumentation", "propertyName": "fullDocumentation", "structure": [ { @@ -136,12 +136,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/funding", + "path": "https://openminds.om-i.org/props/funding", "propertyName": "funding", "ensureOrder": true, "structure": [ @@ -154,15 +154,15 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", + "path": "https://openminds.om-i.org/props/isAlternativeVersionOf", "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ @@ -175,7 +175,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "path": "https://openminds.om-i.org/props/isNewVersionOf", "propertyName": "isNewVersionOf", "structure": [ { @@ -188,7 +188,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/keyword", + "path": "https://openminds.om-i.org/props/keyword", "propertyName": "keyword", "ensureOrder": true, "structure": [ @@ -201,7 +201,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/license", + "path": "https://openminds.om-i.org/props/license", "propertyName": "license", "structure": [ { @@ -214,7 +214,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/otherContribution", + "path": "https://openminds.om-i.org/props/otherContribution", "propertyName": "otherContribution", "ensureOrder": true, "structure": [ @@ -222,7 +222,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contributor", + "path": "https://openminds.om-i.org/props/contributor", "propertyName": "contributor", "structure": [ { @@ -235,7 +235,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "ensureOrder": true, "structure": [ @@ -250,7 +250,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/relatedPublication", + "path": "https://openminds.om-i.org/props/relatedPublication", "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ @@ -263,11 +263,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/releaseDate", + "path": "https://openminds.om-i.org/props/releaseDate", "propertyName": "releaseDate" }, { - "path": "https://openminds.ebrains.eu/vocab/repository", + "path": "https://openminds.om-i.org/props/repository", "propertyName": "repository", "structure": [ { @@ -280,7 +280,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/serializationFormat", + "path": "https://openminds.om-i.org/props/serializationFormat", "propertyName": "serializationFormat", "ensureOrder": true, "structure": [ @@ -293,11 +293,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { - "path": "https://openminds.ebrains.eu/vocab/specificationFormat", + "path": "https://openminds.om-i.org/props/specificationFormat", "propertyName": "specificationFormat", "ensureOrder": true, "structure": [ @@ -310,12 +310,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/supportChannel", + "path": "https://openminds.om-i.org/props/supportChannel", "propertyName": "supportChannel", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "structure": [ { @@ -328,16 +328,16 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", + "path": "https://openminds.om-i.org/props/versionIdentifier", "propertyName": "versionIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/versionInnovation", + "path": "https://openminds.om-i.org/props/versionInnovation", "propertyName": "versionInnovation" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -353,7 +353,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "@id": "https://openminds.om-i.org/props/isNewVersionOf", "reverse": true }, "propertyName": "isNewVersionOf", @@ -369,7 +369,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -385,7 +385,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasVersion", + "@id": "https://openminds.om-i.org/props/hasVersion", "reverse": true }, "propertyName": "hasVersion", @@ -401,7 +401,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/model_simple_query.json b/test/test_data/queries/openminds/core/model_simple_query.json index 6dad9d6a..eeb65908 100644 --- a/test/test_data/queries/openminds/core/model_simple_query.json +++ b/test/test_data/queries/openminds/core/model_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Model", + "type": "https://openminds.om-i.org/types/Model", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/abstractionLevel", + "path": "https://openminds.om-i.org/props/abstractionLevel", "propertyName": "abstractionLevel", "structure": [ { @@ -52,7 +52,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -65,11 +65,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -82,7 +82,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -95,12 +95,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/hasVersion", + "path": "https://openminds.om-i.org/props/hasVersion", "propertyName": "hasVersion", "ensureOrder": true, "structure": [ @@ -113,15 +113,15 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/scope", + "path": "https://openminds.om-i.org/props/scope", "propertyName": "scope", "structure": [ { @@ -134,11 +134,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { - "path": "https://openminds.ebrains.eu/vocab/studyTarget", + "path": "https://openminds.om-i.org/props/studyTarget", "propertyName": "studyTarget", "ensureOrder": true, "structure": [ @@ -152,7 +152,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -168,7 +168,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -184,7 +184,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/modelversion_simple_query.json b/test/test_data/queries/openminds/core/modelversion_simple_query.json index 63380f4b..383fc8e0 100644 --- a/test/test_data/queries/openminds/core/modelversion_simple_query.json +++ b/test/test_data/queries/openminds/core/modelversion_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ModelVersion", + "type": "https://openminds.om-i.org/types/ModelVersion", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/accessibility", + "path": "https://openminds.om-i.org/props/accessibility", "propertyName": "accessibility", "structure": [ { @@ -52,7 +52,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/configuration", + "path": "https://openminds.om-i.org/props/configuration", "propertyName": "configuration", "structure": [ { @@ -65,14 +65,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/copyright", + "path": "https://openminds.om-i.org/props/copyright", "propertyName": "copyright", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/holder", + "path": "https://openminds.om-i.org/props/holder", "propertyName": "holder", "ensureOrder": true, "structure": [ @@ -85,7 +85,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/year", + "path": "https://openminds.om-i.org/props/year", "propertyName": "year", "ensureOrder": true } @@ -93,7 +93,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -106,11 +106,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -123,7 +123,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -136,11 +136,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/entryPoint", + "path": "https://openminds.om-i.org/props/entryPoint", "propertyName": "entryPoint" }, { - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "ensureOrder": true, "structure": [ @@ -153,7 +153,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", + "path": "https://openminds.om-i.org/props/fullDocumentation", "propertyName": "fullDocumentation", "structure": [ { @@ -166,12 +166,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/funding", + "path": "https://openminds.om-i.org/props/funding", "propertyName": "funding", "ensureOrder": true, "structure": [ @@ -184,15 +184,15 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/inputData", + "path": "https://openminds.om-i.org/props/inputData", "propertyName": "inputData", "ensureOrder": true, "structure": [ @@ -205,7 +205,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", + "path": "https://openminds.om-i.org/props/isAlternativeVersionOf", "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ @@ -218,7 +218,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "path": "https://openminds.om-i.org/props/isNewVersionOf", "propertyName": "isNewVersionOf", "structure": [ { @@ -231,7 +231,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/keyword", + "path": "https://openminds.om-i.org/props/keyword", "propertyName": "keyword", "ensureOrder": true, "structure": [ @@ -244,7 +244,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/license", + "path": "https://openminds.om-i.org/props/license", "propertyName": "license", "ensureOrder": true, "structure": [ @@ -257,7 +257,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/otherContribution", + "path": "https://openminds.om-i.org/props/otherContribution", "propertyName": "otherContribution", "ensureOrder": true, "structure": [ @@ -265,7 +265,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contributor", + "path": "https://openminds.om-i.org/props/contributor", "propertyName": "contributor", "structure": [ { @@ -278,7 +278,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "ensureOrder": true, "structure": [ @@ -293,7 +293,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/outputData", + "path": "https://openminds.om-i.org/props/outputData", "propertyName": "outputData", "ensureOrder": true, "structure": [ @@ -306,7 +306,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/relatedPublication", + "path": "https://openminds.om-i.org/props/relatedPublication", "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ @@ -319,11 +319,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/releaseDate", + "path": "https://openminds.om-i.org/props/releaseDate", "propertyName": "releaseDate" }, { - "path": "https://openminds.ebrains.eu/vocab/repository", + "path": "https://openminds.om-i.org/props/repository", "propertyName": "repository", "structure": [ { @@ -336,25 +336,25 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { - "path": "https://openminds.ebrains.eu/vocab/supportChannel", + "path": "https://openminds.om-i.org/props/supportChannel", "propertyName": "supportChannel", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", + "path": "https://openminds.om-i.org/props/versionIdentifier", "propertyName": "versionIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/versionInnovation", + "path": "https://openminds.om-i.org/props/versionInnovation", "propertyName": "versionInnovation" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -370,7 +370,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/input", + "@id": "https://openminds.om-i.org/props/input", "reverse": true }, "propertyName": "input", @@ -386,7 +386,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/dataLocation", + "@id": "https://openminds.om-i.org/props/dataLocation", "reverse": true }, "propertyName": "dataLocation", @@ -402,7 +402,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "@id": "https://openminds.om-i.org/props/isNewVersionOf", "reverse": true }, "propertyName": "isNewVersionOf", @@ -418,7 +418,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/output", + "@id": "https://openminds.om-i.org/props/output", "reverse": true }, "propertyName": "output", @@ -434,7 +434,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -450,7 +450,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasVersion", + "@id": "https://openminds.om-i.org/props/hasVersion", "reverse": true }, "propertyName": "hasVersion", @@ -466,7 +466,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -482,7 +482,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/orcid_simple_query.json b/test/test_data/queries/openminds/core/orcid_simple_query.json index 42159fb8..d9e92ca4 100644 --- a/test/test_data/queries/openminds/core/orcid_simple_query.json +++ b/test/test_data/queries/openminds/core/orcid_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ORCID", + "type": "https://openminds.om-i.org/types/ORCID", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", diff --git a/test/test_data/queries/openminds/core/organization_simple_query.json b/test/test_data/queries/openminds/core/organization_simple_query.json index e0b33697..d045e237 100644 --- a/test/test_data/queries/openminds/core/organization_simple_query.json +++ b/test/test_data/queries/openminds/core/organization_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Organization", + "type": "https://openminds.om-i.org/types/Organization", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "ensureOrder": true, "structure": [ @@ -47,11 +47,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -64,13 +64,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ @@ -83,12 +83,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/hasParent", + "path": "https://openminds.om-i.org/props/hasParent", "propertyName": "hasParent", "ensureOrder": true, "structure": [ @@ -101,16 +101,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -126,7 +126,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -142,7 +142,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -158,7 +158,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasParent", + "@id": "https://openminds.om-i.org/props/hasParent", "reverse": true }, "propertyName": "hasParent", @@ -174,7 +174,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "reverse": true }, "propertyName": "memberOf", @@ -184,11 +184,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -201,14 +201,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hostedBy", + "@id": "https://openminds.om-i.org/props/hostedBy", "reverse": true }, "propertyName": "hostedBy", @@ -224,7 +224,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -240,7 +240,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -256,7 +256,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -272,7 +272,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -288,7 +288,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", diff --git a/test/test_data/queries/openminds/core/person_newstyle_query.json b/test/test_data/queries/openminds/core/person_newstyle_query.json index afd6dc62..529fb424 100644 --- a/test/test_data/queries/openminds/core/person_newstyle_query.json +++ b/test/test_data/queries/openminds/core/person_newstyle_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Person", + "type": "https://openminds.om-i.org/types/Person", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -35,7 +35,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "ensureOrder": true, "structure": [ @@ -43,14 +43,14 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/Consortium" + "@id": "https://openminds.om-i.org/types/Consortium" } }, "propertyName": "memberOf__Consortium", @@ -66,7 +66,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contactInformation", + "path": "https://openminds.om-i.org/props/contactInformation", "propertyName": "contactInformation", "structure": [ { @@ -79,20 +79,20 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName" }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -108,7 +108,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -124,7 +124,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -140,7 +140,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "reverse": true }, "propertyName": "memberOf", @@ -150,11 +150,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -167,14 +167,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -190,7 +190,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -206,7 +206,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -222,7 +222,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -238,7 +238,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -257,9 +257,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/Organization" + "@id": "https://openminds.om-i.org/types/Organization" } }, "propertyName": "memberOf__Organization", @@ -275,7 +275,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "ensureOrder": true, "structure": [ @@ -283,11 +283,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -300,13 +300,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ @@ -319,11 +319,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName" }, { - "path": "https://openminds.ebrains.eu/vocab/hasParent", + "path": "https://openminds.om-i.org/props/hasParent", "propertyName": "hasParent", "ensureOrder": true, "structure": [ @@ -338,7 +338,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "ensureOrder": true, "structure": [ @@ -346,11 +346,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -363,13 +363,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ @@ -382,11 +382,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName" }, { - "path": "https://openminds.ebrains.eu/vocab/hasParent", + "path": "https://openminds.om-i.org/props/hasParent", "propertyName": "hasParent", "ensureOrder": true, "structure": [ @@ -399,16 +399,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -424,7 +424,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -440,7 +440,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -456,7 +456,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasParent", + "@id": "https://openminds.om-i.org/props/hasParent", "reverse": true }, "propertyName": "hasParent", @@ -472,7 +472,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "reverse": true }, "propertyName": "memberOf", @@ -482,11 +482,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -499,14 +499,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hostedBy", + "@id": "https://openminds.om-i.org/props/hostedBy", "reverse": true }, "propertyName": "hostedBy", @@ -522,7 +522,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -538,7 +538,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -554,7 +554,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -570,7 +570,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -586,7 +586,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -603,16 +603,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -628,7 +628,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -644,7 +644,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -660,7 +660,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasParent", + "@id": "https://openminds.om-i.org/props/hasParent", "reverse": true }, "propertyName": "hasParent", @@ -676,7 +676,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "reverse": true }, "propertyName": "memberOf", @@ -686,11 +686,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -703,14 +703,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hostedBy", + "@id": "https://openminds.om-i.org/props/hostedBy", "reverse": true }, "propertyName": "hostedBy", @@ -726,7 +726,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -742,7 +742,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -758,7 +758,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -774,7 +774,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -790,7 +790,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -808,18 +808,18 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/alternateName", + "path": "https://openminds.om-i.org/props/alternateName", "propertyName": "alternateName", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/associatedAccount", + "path": "https://openminds.om-i.org/props/associatedAccount", "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ @@ -832,7 +832,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/contactInformation", + "path": "https://openminds.om-i.org/props/contactInformation", "propertyName": "contactInformation", "structure": [ { @@ -846,12 +846,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/email", + "path": "https://openminds.om-i.org/props/email", "propertyName": "email" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/contactInformation", + "@id": "https://openminds.om-i.org/props/contactInformation", "reverse": true }, "propertyName": "contactInformation", @@ -869,7 +869,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ @@ -882,16 +882,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/familyName", + "path": "https://openminds.om-i.org/props/familyName", "propertyName": "familyName" }, { - "path": "https://openminds.ebrains.eu/vocab/givenName", + "path": "https://openminds.om-i.org/props/givenName", "propertyName": "givenName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/performedBy", + "@id": "https://openminds.om-i.org/props/performedBy", "reverse": true }, "propertyName": "performedBy", @@ -907,7 +907,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/commenter", + "@id": "https://openminds.om-i.org/props/commenter", "reverse": true }, "propertyName": "commenter", @@ -923,7 +923,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -939,7 +939,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -955,7 +955,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -971,7 +971,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -987,7 +987,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -1003,7 +1003,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -1019,7 +1019,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -1035,7 +1035,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -1051,7 +1051,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/startedBy", + "@id": "https://openminds.om-i.org/props/startedBy", "reverse": true }, "propertyName": "startedBy", @@ -1066,22 +1066,22 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "Qaffiliations", "required": true, "structure": [ { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "Qmember_of", "required": true, "structure": [ { - "path": "https://openminds.ebrains.eu/vocab/hasParent", + "path": "https://openminds.om-i.org/props/hasParent", "propertyName": "Qhas_parents", "required": true, "structure": [ { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "Qshort_name", "filter": { "op": "CONTAINS", diff --git a/test/test_data/queries/openminds/core/person_resolved-1_query.json b/test/test_data/queries/openminds/core/person_resolved-1_query.json index 916eafd7..c31f15ed 100644 --- a/test/test_data/queries/openminds/core/person_resolved-1_query.json +++ b/test/test_data/queries/openminds/core/person_resolved-1_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Person", + "type": "https://openminds.om-i.org/types/Person", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -35,7 +35,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "ensureOrder": true, "structure": [ @@ -43,14 +43,14 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/Consortium" + "@id": "https://openminds.om-i.org/types/Consortium" } }, "propertyName": "memberOf__Consortium", @@ -66,7 +66,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contactInformation", + "path": "https://openminds.om-i.org/props/contactInformation", "propertyName": "contactInformation", "structure": [ { @@ -79,20 +79,20 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName" }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -108,7 +108,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -124,7 +124,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -140,7 +140,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "reverse": true }, "propertyName": "memberOf", @@ -150,11 +150,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -167,14 +167,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -190,7 +190,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -206,7 +206,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -222,7 +222,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -238,7 +238,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -257,9 +257,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/Organization" + "@id": "https://openminds.om-i.org/types/Organization" } }, "propertyName": "memberOf__Organization", @@ -275,7 +275,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "ensureOrder": true, "structure": [ @@ -283,11 +283,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -300,13 +300,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ @@ -319,11 +319,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName" }, { - "path": "https://openminds.ebrains.eu/vocab/hasParent", + "path": "https://openminds.om-i.org/props/hasParent", "propertyName": "hasParent", "ensureOrder": true, "structure": [ @@ -336,16 +336,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -361,7 +361,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -377,7 +377,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -393,7 +393,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasParent", + "@id": "https://openminds.om-i.org/props/hasParent", "reverse": true }, "propertyName": "hasParent", @@ -409,7 +409,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/memberOf", + "@id": "https://openminds.om-i.org/props/memberOf", "reverse": true }, "propertyName": "memberOf", @@ -419,11 +419,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -436,14 +436,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hostedBy", + "@id": "https://openminds.om-i.org/props/hostedBy", "reverse": true }, "propertyName": "hostedBy", @@ -459,7 +459,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -475,7 +475,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -491,7 +491,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -507,7 +507,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -523,7 +523,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -541,18 +541,18 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/alternateName", + "path": "https://openminds.om-i.org/props/alternateName", "propertyName": "alternateName", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/associatedAccount", + "path": "https://openminds.om-i.org/props/associatedAccount", "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ @@ -567,7 +567,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/service", + "path": "https://openminds.om-i.org/props/service", "propertyName": "service", "structure": [ { @@ -580,12 +580,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/userName", + "path": "https://openminds.om-i.org/props/userName", "propertyName": "userName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/associatedAccount", + "@id": "https://openminds.om-i.org/props/associatedAccount", "reverse": true }, "propertyName": "associatedAccount", @@ -602,7 +602,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/contactInformation", + "path": "https://openminds.om-i.org/props/contactInformation", "propertyName": "contactInformation", "structure": [ { @@ -616,12 +616,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/email", + "path": "https://openminds.om-i.org/props/email", "propertyName": "email" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/contactInformation", + "@id": "https://openminds.om-i.org/props/contactInformation", "reverse": true }, "propertyName": "contactInformation", @@ -639,7 +639,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ @@ -654,12 +654,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", @@ -676,16 +676,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/familyName", + "path": "https://openminds.om-i.org/props/familyName", "propertyName": "familyName" }, { - "path": "https://openminds.ebrains.eu/vocab/givenName", + "path": "https://openminds.om-i.org/props/givenName", "propertyName": "givenName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/performedBy", + "@id": "https://openminds.om-i.org/props/performedBy", "reverse": true }, "propertyName": "performedBy", @@ -701,7 +701,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/commenter", + "@id": "https://openminds.om-i.org/props/commenter", "reverse": true }, "propertyName": "commenter", @@ -717,7 +717,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -733,7 +733,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -749,7 +749,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -765,7 +765,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -781,7 +781,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -797,7 +797,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -813,7 +813,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -829,7 +829,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -845,7 +845,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/startedBy", + "@id": "https://openminds.om-i.org/props/startedBy", "reverse": true }, "propertyName": "startedBy", diff --git a/test/test_data/queries/openminds/core/person_simple_query.json b/test/test_data/queries/openminds/core/person_simple_query.json index 53e9b929..af8ffa17 100644 --- a/test/test_data/queries/openminds/core/person_simple_query.json +++ b/test/test_data/queries/openminds/core/person_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Person", + "type": "https://openminds.om-i.org/types/Person", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "ensureOrder": true, "structure": [ @@ -47,11 +47,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/endDate", + "path": "https://openminds.om-i.org/props/endDate", "propertyName": "endDate" }, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [ { @@ -64,18 +64,18 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/alternateName", + "path": "https://openminds.om-i.org/props/alternateName", "propertyName": "alternateName", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/associatedAccount", + "path": "https://openminds.om-i.org/props/associatedAccount", "propertyName": "associatedAccount", "ensureOrder": true, "structure": [ @@ -88,7 +88,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/contactInformation", + "path": "https://openminds.om-i.org/props/contactInformation", "propertyName": "contactInformation", "structure": [ { @@ -101,7 +101,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "ensureOrder": true, "structure": [ @@ -114,16 +114,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/familyName", + "path": "https://openminds.om-i.org/props/familyName", "propertyName": "familyName" }, { - "path": "https://openminds.ebrains.eu/vocab/givenName", + "path": "https://openminds.om-i.org/props/givenName", "propertyName": "givenName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/performedBy", + "@id": "https://openminds.om-i.org/props/performedBy", "reverse": true }, "propertyName": "performedBy", @@ -139,7 +139,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/commenter", + "@id": "https://openminds.om-i.org/props/commenter", "reverse": true }, "propertyName": "commenter", @@ -155,7 +155,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/coordinator", + "@id": "https://openminds.om-i.org/props/coordinator", "reverse": true }, "propertyName": "coordinator", @@ -171,7 +171,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/developer", + "@id": "https://openminds.om-i.org/props/developer", "reverse": true }, "propertyName": "developer", @@ -187,7 +187,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/funder", + "@id": "https://openminds.om-i.org/props/funder", "reverse": true }, "propertyName": "funder", @@ -203,7 +203,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", + "@id": "https://openminds.om-i.org/props/custodian", "reverse": true }, "propertyName": "custodian", @@ -219,7 +219,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/owner", + "@id": "https://openminds.om-i.org/props/owner", "reverse": true }, "propertyName": "owner", @@ -235,7 +235,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/provider", + "@id": "https://openminds.om-i.org/props/provider", "reverse": true }, "propertyName": "provider", @@ -251,7 +251,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/manufacturer", + "@id": "https://openminds.om-i.org/props/manufacturer", "reverse": true }, "propertyName": "manufacturer", @@ -267,7 +267,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/publisher", + "@id": "https://openminds.om-i.org/props/publisher", "reverse": true }, "propertyName": "publisher", @@ -283,7 +283,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/startedBy", + "@id": "https://openminds.om-i.org/props/startedBy", "reverse": true }, "propertyName": "startedBy", diff --git a/test/test_data/queries/openminds/core/project_simple_query.json b/test/test_data/queries/openminds/core/project_simple_query.json index bc21b1bd..3aa3d385 100644 --- a/test/test_data/queries/openminds/core/project_simple_query.json +++ b/test/test_data/queries/openminds/core/project_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Project", + "type": "https://openminds.om-i.org/types/Project", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/coordinator", + "path": "https://openminds.om-i.org/props/coordinator", "propertyName": "coordinator", "ensureOrder": true, "structure": [ @@ -52,16 +52,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/hasPart", + "path": "https://openminds.om-i.org/props/hasPart", "propertyName": "hasPart", "ensureOrder": true, "structure": [ @@ -74,11 +74,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" } ] diff --git a/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json b/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json index 8157ff31..58868bc7 100644 --- a/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json +++ b/test/test_data/queries/openminds/core/propertyvaluelist_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/PropertyValueList", + "type": "https://openminds.om-i.org/types/PropertyValueList", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,15 +39,15 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/propertyValuePair", + "@id": "https://openminds.om-i.org/props/propertyValuePair", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/NumericalProperty" + "@id": "https://openminds.om-i.org/types/NumericalProperty" } }, "propertyName": "propertyValuePair__NumericalProperty", @@ -57,14 +57,14 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/value", + "@id": "https://openminds.om-i.org/props/value", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "value__QuantitativeValue", @@ -74,7 +74,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -87,12 +87,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -105,16 +105,16 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/value", + "@id": "https://openminds.om-i.org/props/value", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "value__QuantitativeValueRange", @@ -124,11 +124,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -141,11 +141,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -163,9 +163,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/propertyValuePair", + "@id": "https://openminds.om-i.org/props/propertyValuePair", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/StringProperty" + "@id": "https://openminds.om-i.org/types/StringProperty" } }, "propertyName": "propertyValuePair__StringProperty", @@ -175,18 +175,18 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/environmentVariable", + "@id": "https://openminds.om-i.org/props/environmentVariable", "reverse": true }, "propertyName": "environmentVariable", @@ -202,7 +202,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/configuration", + "@id": "https://openminds.om-i.org/props/configuration", "reverse": true }, "propertyName": "configuration", diff --git a/test/test_data/queries/openminds/core/protocol_simple_query.json b/test/test_data/queries/openminds/core/protocol_simple_query.json index 5ac62482..5fdcc914 100644 --- a/test/test_data/queries/openminds/core/protocol_simple_query.json +++ b/test/test_data/queries/openminds/core/protocol_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Protocol", + "type": "https://openminds.om-i.org/types/Protocol", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/describedIn", + "path": "https://openminds.om-i.org/props/describedIn", "propertyName": "describedIn", "structure": [ { @@ -52,16 +52,16 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/stimulusType", + "path": "https://openminds.om-i.org/props/stimulusType", "propertyName": "stimulusType", "ensureOrder": true, "structure": [ @@ -74,7 +74,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/technique", + "path": "https://openminds.om-i.org/props/technique", "propertyName": "technique", "ensureOrder": true, "structure": [ @@ -88,7 +88,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/protocol", + "@id": "https://openminds.om-i.org/props/protocol", "reverse": true }, "propertyName": "protocol", diff --git a/test/test_data/queries/openminds/core/protocolexecution_simple_query.json b/test/test_data/queries/openminds/core/protocolexecution_simple_query.json index 623fc446..dc47184b 100644 --- a/test/test_data/queries/openminds/core/protocolexecution_simple_query.json +++ b/test/test_data/queries/openminds/core/protocolexecution_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ProtocolExecution", + "type": "https://openminds.om-i.org/types/ProtocolExecution", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/behavioralProtocol", + "path": "https://openminds.om-i.org/props/behavioralProtocol", "propertyName": "behavioralProtocol", "ensureOrder": true, "structure": [ @@ -52,7 +52,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/customPropertySet", + "path": "https://openminds.om-i.org/props/customPropertySet", "propertyName": "customPropertySet", "ensureOrder": true, "structure": [ @@ -60,11 +60,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/context", + "path": "https://openminds.om-i.org/props/context", "propertyName": "context" }, { - "path": "https://openminds.ebrains.eu/vocab/dataLocation", + "path": "https://openminds.om-i.org/props/dataLocation", "propertyName": "dataLocation", "structure": [ { @@ -77,7 +77,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/relevantFor", + "path": "https://openminds.om-i.org/props/relevantFor", "propertyName": "relevantFor", "structure": [ { @@ -92,15 +92,15 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/endTime", + "path": "https://openminds.om-i.org/props/endTime", "propertyName": "endTime" }, { - "path": "https://openminds.ebrains.eu/vocab/input", + "path": "https://openminds.om-i.org/props/input", "propertyName": "input", "ensureOrder": true, "structure": [ @@ -113,7 +113,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isPartOf", + "path": "https://openminds.om-i.org/props/isPartOf", "propertyName": "isPartOf", "structure": [ { @@ -126,12 +126,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/output", + "path": "https://openminds.om-i.org/props/output", "propertyName": "output", "ensureOrder": true, "structure": [ @@ -144,7 +144,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/performedBy", + "path": "https://openminds.om-i.org/props/performedBy", "propertyName": "performedBy", "ensureOrder": true, "structure": [ @@ -157,7 +157,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/preparationDesign", + "path": "https://openminds.om-i.org/props/preparationDesign", "propertyName": "preparationDesign", "structure": [ { @@ -170,7 +170,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/protocol", + "path": "https://openminds.om-i.org/props/protocol", "propertyName": "protocol", "ensureOrder": true, "structure": [ @@ -183,11 +183,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/startTime", + "path": "https://openminds.om-i.org/props/startTime", "propertyName": "startTime" }, { - "path": "https://openminds.ebrains.eu/vocab/studyTarget", + "path": "https://openminds.om-i.org/props/studyTarget", "propertyName": "studyTarget", "ensureOrder": true, "structure": [ @@ -201,9 +201,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/criteria", + "@id": "https://openminds.om-i.org/props/criteria", "typeFilter": { - "@id": "https://openminds.ebrains.eu/sands/AtlasAnnotation" + "@id": "https://openminds.om-i.org/types/AtlasAnnotation" }, "reverse": true }, @@ -214,7 +214,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/anchorPoint", + "path": "https://openminds.om-i.org/props/anchorPoint", "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ @@ -222,7 +222,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -235,12 +235,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -253,13 +253,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/criteria", + "path": "https://openminds.om-i.org/props/criteria", "propertyName": "criteria", "structure": [ { @@ -272,7 +272,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/criteriaQualityType", + "path": "https://openminds.om-i.org/props/criteriaQualityType", "propertyName": "criteriaQualityType", "structure": [ { @@ -285,7 +285,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/criteriaType", + "path": "https://openminds.om-i.org/props/criteriaType", "propertyName": "criteriaType", "structure": [ { @@ -298,7 +298,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/inspiredBy", + "path": "https://openminds.om-i.org/props/inspiredBy", "propertyName": "inspiredBy", "ensureOrder": true, "structure": [ @@ -311,11 +311,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/laterality", + "path": "https://openminds.om-i.org/props/laterality", "propertyName": "laterality", "ensureOrder": true, "structure": [ @@ -328,18 +328,18 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/preferredVisualization", + "path": "https://openminds.om-i.org/props/preferredVisualization", "propertyName": "preferredVisualization", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { - "path": "https://openminds.ebrains.eu/vocab/anchorPoint", + "path": "https://openminds.om-i.org/props/anchorPoint", "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ @@ -347,7 +347,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -360,12 +360,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -378,20 +378,20 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/cameraPosition", + "path": "https://openminds.om-i.org/props/cameraPosition", "propertyName": "cameraPosition", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/coordinateSpace", + "path": "https://openminds.om-i.org/props/coordinateSpace", "propertyName": "coordinateSpace", "structure": [ { @@ -404,7 +404,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/coordinates", + "path": "https://openminds.om-i.org/props/coordinates", "propertyName": "coordinates", "ensureOrder": true, "structure": [ @@ -412,7 +412,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -425,12 +425,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -443,7 +443,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] @@ -452,7 +452,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/preferredDisplayColor", + "path": "https://openminds.om-i.org/props/preferredDisplayColor", "propertyName": "preferredDisplayColor", "structure": [ { @@ -468,7 +468,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/specification", + "path": "https://openminds.om-i.org/props/specification", "propertyName": "specification", "structure": [ { @@ -481,7 +481,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "structure": [ { @@ -497,9 +497,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/criteria", + "@id": "https://openminds.om-i.org/props/criteria", "typeFilter": { - "@id": "https://openminds.ebrains.eu/sands/CustomAnnotation" + "@id": "https://openminds.om-i.org/types/CustomAnnotation" }, "reverse": true }, @@ -510,7 +510,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/anchorPoint", + "path": "https://openminds.om-i.org/props/anchorPoint", "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ @@ -518,7 +518,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -531,12 +531,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -549,13 +549,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/coordinateSpace", + "path": "https://openminds.om-i.org/props/coordinateSpace", "propertyName": "coordinateSpace", "structure": [ { @@ -568,7 +568,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/criteria", + "path": "https://openminds.om-i.org/props/criteria", "propertyName": "criteria", "structure": [ { @@ -581,7 +581,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/criteriaQualityType", + "path": "https://openminds.om-i.org/props/criteriaQualityType", "propertyName": "criteriaQualityType", "structure": [ { @@ -594,7 +594,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/criteriaType", + "path": "https://openminds.om-i.org/props/criteriaType", "propertyName": "criteriaType", "structure": [ { @@ -607,7 +607,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/inspiredBy", + "path": "https://openminds.om-i.org/props/inspiredBy", "propertyName": "inspiredBy", "ensureOrder": true, "structure": [ @@ -620,11 +620,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/laterality", + "path": "https://openminds.om-i.org/props/laterality", "propertyName": "laterality", "ensureOrder": true, "structure": [ @@ -637,18 +637,18 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/preferredVisualization", + "path": "https://openminds.om-i.org/props/preferredVisualization", "propertyName": "preferredVisualization", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { - "path": "https://openminds.ebrains.eu/vocab/anchorPoint", + "path": "https://openminds.om-i.org/props/anchorPoint", "propertyName": "anchorPoint", "ensureOrder": true, "structure": [ @@ -656,7 +656,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -669,12 +669,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -687,20 +687,20 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] }, { - "path": "https://openminds.ebrains.eu/vocab/cameraPosition", + "path": "https://openminds.om-i.org/props/cameraPosition", "propertyName": "cameraPosition", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/coordinateSpace", + "path": "https://openminds.om-i.org/props/coordinateSpace", "propertyName": "coordinateSpace", "structure": [ { @@ -713,7 +713,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/coordinates", + "path": "https://openminds.om-i.org/props/coordinates", "propertyName": "coordinates", "ensureOrder": true, "structure": [ @@ -721,7 +721,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -734,12 +734,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -752,7 +752,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ] @@ -761,7 +761,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/preferredDisplayColor", + "path": "https://openminds.om-i.org/props/preferredDisplayColor", "propertyName": "preferredDisplayColor", "structure": [ { @@ -777,7 +777,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/specification", + "path": "https://openminds.om-i.org/props/specification", "propertyName": "specification", "structure": [ { @@ -790,7 +790,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "structure": [ { diff --git a/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json b/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json index 153db241..e26b08e1 100644 --- a/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json +++ b/test/test_data/queries/openminds/core/quantitativevaluearray_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/QuantitativeValueArray", + "type": "https://openminds.om-i.org/types/QuantitativeValueArray", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,17 +39,17 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/negativeUncertainties", + "path": "https://openminds.om-i.org/props/negativeUncertainties", "propertyName": "negativeUncertainties", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/positiveUncertainties", + "path": "https://openminds.om-i.org/props/positiveUncertainties", "propertyName": "positiveUncertainties", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -62,7 +62,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -75,7 +75,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/values", + "path": "https://openminds.om-i.org/props/values", "propertyName": "values", "ensureOrder": true } diff --git a/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json b/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json index c2521385..31f2ed3c 100644 --- a/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json +++ b/test/test_data/queries/openminds/core/researchproductgroup_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ResearchProductGroup", + "type": "https://openminds.om-i.org/types/ResearchProductGroup", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/context", + "path": "https://openminds.om-i.org/props/context", "propertyName": "context" }, { - "path": "https://openminds.ebrains.eu/vocab/hasPart", + "path": "https://openminds.om-i.org/props/hasPart", "propertyName": "hasPart", "ensureOrder": true, "structure": [ diff --git a/test/test_data/queries/openminds/core/rorid_simple_query.json b/test/test_data/queries/openminds/core/rorid_simple_query.json index 023053d0..bc2e0171 100644 --- a/test/test_data/queries/openminds/core/rorid_simple_query.json +++ b/test/test_data/queries/openminds/core/rorid_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/RORID", + "type": "https://openminds.om-i.org/types/RORID", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", diff --git a/test/test_data/queries/openminds/core/rrid_simple_query.json b/test/test_data/queries/openminds/core/rrid_simple_query.json index fe3073ac..9ddf5749 100644 --- a/test/test_data/queries/openminds/core/rrid_simple_query.json +++ b/test/test_data/queries/openminds/core/rrid_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/RRID", + "type": "https://openminds.om-i.org/types/RRID", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", diff --git a/test/test_data/queries/openminds/core/servicelink_simple_query.json b/test/test_data/queries/openminds/core/servicelink_simple_query.json index 6fd03f4b..aea47af3 100644 --- a/test/test_data/queries/openminds/core/servicelink_simple_query.json +++ b/test/test_data/queries/openminds/core/servicelink_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/ServiceLink", + "type": "https://openminds.om-i.org/types/ServiceLink", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/dataLocation", + "path": "https://openminds.om-i.org/props/dataLocation", "propertyName": "dataLocation", "structure": [ { @@ -52,15 +52,15 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/displayLabel", + "path": "https://openminds.om-i.org/props/displayLabel", "propertyName": "displayLabel" }, { - "path": "https://openminds.ebrains.eu/vocab/openDataIn", + "path": "https://openminds.om-i.org/props/openDataIn", "propertyName": "openDataIn" }, { - "path": "https://openminds.ebrains.eu/vocab/previewImage", + "path": "https://openminds.om-i.org/props/previewImage", "propertyName": "previewImage", "structure": [ { @@ -73,7 +73,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/service", + "path": "https://openminds.om-i.org/props/service", "propertyName": "service", "structure": [ { diff --git a/test/test_data/queries/openminds/core/setup_simple_query.json b/test/test_data/queries/openminds/core/setup_simple_query.json index 08549beb..2a2fb326 100644 --- a/test/test_data/queries/openminds/core/setup_simple_query.json +++ b/test/test_data/queries/openminds/core/setup_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Setup", + "type": "https://openminds.om-i.org/types/Setup", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/hasPart", + "path": "https://openminds.om-i.org/props/hasPart", "propertyName": "hasPart", "ensureOrder": true, "structure": [ @@ -56,11 +56,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/location", + "path": "https://openminds.om-i.org/props/location", "propertyName": "location" }, { - "path": "https://openminds.ebrains.eu/vocab/manufacturer", + "path": "https://openminds.om-i.org/props/manufacturer", "propertyName": "manufacturer", "ensureOrder": true, "structure": [ @@ -73,12 +73,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "ensureOrder": true, "structure": [ @@ -92,7 +92,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -108,7 +108,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/setup", + "@id": "https://openminds.om-i.org/props/setup", "reverse": true }, "propertyName": "setup", diff --git a/test/test_data/queries/openminds/core/software_simple_query.json b/test/test_data/queries/openminds/core/software_simple_query.json index add69c5b..f045b6a4 100644 --- a/test/test_data/queries/openminds/core/software_simple_query.json +++ b/test/test_data/queries/openminds/core/software_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Software", + "type": "https://openminds.om-i.org/types/Software", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -52,11 +52,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -69,7 +69,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -82,12 +82,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/hasVersion", + "path": "https://openminds.om-i.org/props/hasVersion", "propertyName": "hasVersion", "ensureOrder": true, "structure": [ @@ -100,20 +100,20 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -129,7 +129,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -145,7 +145,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/softwareversion_simple_query.json b/test/test_data/queries/openminds/core/softwareversion_simple_query.json index 20410699..bdcfd18b 100644 --- a/test/test_data/queries/openminds/core/softwareversion_simple_query.json +++ b/test/test_data/queries/openminds/core/softwareversion_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/SoftwareVersion", + "type": "https://openminds.om-i.org/types/SoftwareVersion", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/accessibility", + "path": "https://openminds.om-i.org/props/accessibility", "propertyName": "accessibility", "structure": [ { @@ -52,7 +52,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/applicationCategory", + "path": "https://openminds.om-i.org/props/applicationCategory", "propertyName": "applicationCategory", "ensureOrder": true, "structure": [ @@ -65,14 +65,14 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/copyright", + "path": "https://openminds.om-i.org/props/copyright", "propertyName": "copyright", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/holder", + "path": "https://openminds.om-i.org/props/holder", "propertyName": "holder", "ensureOrder": true, "structure": [ @@ -85,7 +85,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/year", + "path": "https://openminds.om-i.org/props/year", "propertyName": "year", "ensureOrder": true } @@ -93,7 +93,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -106,11 +106,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -123,7 +123,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/device", + "path": "https://openminds.om-i.org/props/device", "propertyName": "device", "ensureOrder": true, "structure": [ @@ -136,7 +136,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -149,7 +149,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/feature", + "path": "https://openminds.om-i.org/props/feature", "propertyName": "feature", "ensureOrder": true, "structure": [ @@ -162,7 +162,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", + "path": "https://openminds.om-i.org/props/fullDocumentation", "propertyName": "fullDocumentation", "structure": [ { @@ -175,12 +175,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/funding", + "path": "https://openminds.om-i.org/props/funding", "propertyName": "funding", "ensureOrder": true, "structure": [ @@ -193,7 +193,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/hasPart", + "path": "https://openminds.om-i.org/props/hasPart", "propertyName": "hasPart", "ensureOrder": true, "structure": [ @@ -206,15 +206,15 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/inputFormat", + "path": "https://openminds.om-i.org/props/inputFormat", "propertyName": "inputFormat", "ensureOrder": true, "structure": [ @@ -227,7 +227,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", + "path": "https://openminds.om-i.org/props/isAlternativeVersionOf", "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ @@ -240,7 +240,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "path": "https://openminds.om-i.org/props/isNewVersionOf", "propertyName": "isNewVersionOf", "structure": [ { @@ -253,7 +253,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/keyword", + "path": "https://openminds.om-i.org/props/keyword", "propertyName": "keyword", "ensureOrder": true, "structure": [ @@ -266,7 +266,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/language", + "path": "https://openminds.om-i.org/props/language", "propertyName": "language", "ensureOrder": true, "structure": [ @@ -279,7 +279,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/license", + "path": "https://openminds.om-i.org/props/license", "propertyName": "license", "ensureOrder": true, "structure": [ @@ -292,7 +292,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/operatingSystem", + "path": "https://openminds.om-i.org/props/operatingSystem", "propertyName": "operatingSystem", "ensureOrder": true, "structure": [ @@ -305,7 +305,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/otherContribution", + "path": "https://openminds.om-i.org/props/otherContribution", "propertyName": "otherContribution", "ensureOrder": true, "structure": [ @@ -313,7 +313,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contributor", + "path": "https://openminds.om-i.org/props/contributor", "propertyName": "contributor", "structure": [ { @@ -326,7 +326,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "ensureOrder": true, "structure": [ @@ -341,7 +341,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/outputFormat", + "path": "https://openminds.om-i.org/props/outputFormat", "propertyName": "outputFormat", "ensureOrder": true, "structure": [ @@ -354,7 +354,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/programmingLanguage", + "path": "https://openminds.om-i.org/props/programmingLanguage", "propertyName": "programmingLanguage", "ensureOrder": true, "structure": [ @@ -367,7 +367,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/relatedPublication", + "path": "https://openminds.om-i.org/props/relatedPublication", "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ @@ -380,11 +380,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/releaseDate", + "path": "https://openminds.om-i.org/props/releaseDate", "propertyName": "releaseDate" }, { - "path": "https://openminds.ebrains.eu/vocab/repository", + "path": "https://openminds.om-i.org/props/repository", "propertyName": "repository", "structure": [ { @@ -397,30 +397,30 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/requirement", + "path": "https://openminds.om-i.org/props/requirement", "propertyName": "requirement", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { - "path": "https://openminds.ebrains.eu/vocab/supportChannel", + "path": "https://openminds.om-i.org/props/supportChannel", "propertyName": "supportChannel", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", + "path": "https://openminds.om-i.org/props/versionIdentifier", "propertyName": "versionIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/versionInnovation", + "path": "https://openminds.om-i.org/props/versionInnovation", "propertyName": "versionInnovation" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -436,7 +436,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/input", + "@id": "https://openminds.om-i.org/props/input", "reverse": true }, "propertyName": "input", @@ -452,7 +452,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "@id": "https://openminds.om-i.org/props/isNewVersionOf", "reverse": true }, "propertyName": "isNewVersionOf", @@ -468,7 +468,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -484,7 +484,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasVersion", + "@id": "https://openminds.om-i.org/props/hasVersion", "reverse": true }, "propertyName": "hasVersion", @@ -500,7 +500,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -516,7 +516,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -532,7 +532,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/software", + "@id": "https://openminds.om-i.org/props/software", "reverse": true }, "propertyName": "software", diff --git a/test/test_data/queries/openminds/core/strain_simple_query.json b/test/test_data/queries/openminds/core/strain_simple_query.json index 0886db65..08fe371a 100644 --- a/test/test_data/queries/openminds/core/strain_simple_query.json +++ b/test/test_data/queries/openminds/core/strain_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Strain", + "type": "https://openminds.om-i.org/types/Strain", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/alternateIdentifier", + "path": "https://openminds.om-i.org/props/alternateIdentifier", "propertyName": "alternateIdentifier", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/backgroundStrain", + "path": "https://openminds.om-i.org/props/backgroundStrain", "propertyName": "backgroundStrain", "ensureOrder": true, "structure": [ @@ -57,7 +57,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/breedingType", + "path": "https://openminds.om-i.org/props/breedingType", "propertyName": "breedingType", "structure": [ { @@ -70,11 +70,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "path": "https://openminds.om-i.org/props/digitalIdentifier", "propertyName": "digitalIdentifier", "structure": [ { @@ -87,7 +87,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/diseaseModel", + "path": "https://openminds.om-i.org/props/diseaseModel", "propertyName": "diseaseModel", "ensureOrder": true, "structure": [ @@ -100,7 +100,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/geneticStrainType", + "path": "https://openminds.om-i.org/props/geneticStrainType", "propertyName": "geneticStrainType", "structure": [ { @@ -113,25 +113,25 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/laboratoryCode", + "path": "https://openminds.om-i.org/props/laboratoryCode", "propertyName": "laboratoryCode" }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/ontologyIdentifier", + "path": "https://openminds.om-i.org/props/ontologyIdentifier", "propertyName": "ontologyIdentifier", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/phenotype", + "path": "https://openminds.om-i.org/props/phenotype", "propertyName": "phenotype" }, { - "path": "https://openminds.ebrains.eu/vocab/species", + "path": "https://openminds.om-i.org/props/species", "propertyName": "species", "structure": [ { @@ -144,18 +144,18 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/stockNumber", + "path": "https://openminds.om-i.org/props/stockNumber", "propertyName": "stockNumber", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { - "path": "https://openminds.ebrains.eu/vocab/vendor", + "path": "https://openminds.om-i.org/props/vendor", "propertyName": "vendor", "structure": [ { @@ -171,13 +171,13 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/synonym", + "path": "https://openminds.om-i.org/props/synonym", "propertyName": "synonym", "ensureOrder": true }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/backgroundStrain", + "@id": "https://openminds.om-i.org/props/backgroundStrain", "reverse": true }, "propertyName": "backgroundStrain", @@ -193,7 +193,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/species", + "@id": "https://openminds.om-i.org/props/species", "reverse": true }, "propertyName": "species", diff --git a/test/test_data/queries/openminds/core/subject_simple_query.json b/test/test_data/queries/openminds/core/subject_simple_query.json index ee5e1eac..3b7c982d 100644 --- a/test/test_data/queries/openminds/core/subject_simple_query.json +++ b/test/test_data/queries/openminds/core/subject_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/Subject", + "type": "https://openminds.om-i.org/types/Subject", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/biologicalSex", + "path": "https://openminds.om-i.org/props/biologicalSex", "propertyName": "biologicalSex", "structure": [ { @@ -52,11 +52,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/isPartOf", + "path": "https://openminds.om-i.org/props/isPartOf", "propertyName": "isPartOf", "ensureOrder": true, "structure": [ @@ -69,12 +69,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/species", + "path": "https://openminds.om-i.org/props/species", "propertyName": "species", "structure": [ { @@ -87,7 +87,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/studiedState", + "path": "https://openminds.om-i.org/props/studiedState", "propertyName": "studiedState", "ensureOrder": true, "structure": [ @@ -101,7 +101,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", + "@id": "https://openminds.om-i.org/props/studiedSpecimen", "reverse": true }, "propertyName": "studiedSpecimen", @@ -117,7 +117,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", @@ -133,7 +133,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", + "@id": "https://openminds.om-i.org/props/usedSpecimen", "reverse": true }, "propertyName": "usedSpecimen", diff --git a/test/test_data/queries/openminds/core/subjectgroup_simple_query.json b/test/test_data/queries/openminds/core/subjectgroup_simple_query.json index c44ec337..13b7b187 100644 --- a/test/test_data/queries/openminds/core/subjectgroup_simple_query.json +++ b/test/test_data/queries/openminds/core/subjectgroup_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/SubjectGroup", + "type": "https://openminds.om-i.org/types/SubjectGroup", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { - "path": "https://openminds.ebrains.eu/vocab/biologicalSex", + "path": "https://openminds.om-i.org/props/biologicalSex", "propertyName": "biologicalSex", "ensureOrder": true, "structure": [ @@ -56,20 +56,20 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/numberOfSubjects", + "path": "https://openminds.om-i.org/props/numberOfSubjects", "propertyName": "numberOfSubjects" }, { - "path": "https://openminds.ebrains.eu/vocab/species", + "path": "https://openminds.om-i.org/props/species", "propertyName": "species", "ensureOrder": true, "structure": [ @@ -82,7 +82,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/studiedState", + "path": "https://openminds.om-i.org/props/studiedState", "propertyName": "studiedState", "ensureOrder": true, "structure": [ @@ -96,7 +96,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isPartOf", + "@id": "https://openminds.om-i.org/props/isPartOf", "reverse": true }, "propertyName": "isPartOf", @@ -112,7 +112,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", + "@id": "https://openminds.om-i.org/props/studiedSpecimen", "reverse": true }, "propertyName": "studiedSpecimen", @@ -128,7 +128,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", @@ -144,7 +144,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", + "@id": "https://openminds.om-i.org/props/usedSpecimen", "reverse": true }, "propertyName": "usedSpecimen", diff --git a/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json b/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json index 5b842d7e..c8f09fd0 100644 --- a/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json +++ b/test/test_data/queries/openminds/core/subjectgroupstate_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/SubjectGroupState", + "type": "https://openminds.om-i.org/types/SubjectGroupState", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,14 +39,14 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "age__QuantitativeValue", @@ -55,7 +55,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -68,12 +68,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -86,7 +86,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -94,9 +94,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "age__QuantitativeValueRange", @@ -105,11 +105,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -122,11 +122,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -142,7 +142,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/ageCategory", + "path": "https://openminds.om-i.org/props/ageCategory", "propertyName": "ageCategory", "ensureOrder": true, "structure": [ @@ -155,7 +155,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/attribute", + "path": "https://openminds.om-i.org/props/attribute", "propertyName": "attribute", "ensureOrder": true, "structure": [ @@ -168,7 +168,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/descendedFrom", + "path": "https://openminds.om-i.org/props/descendedFrom", "propertyName": "descendedFrom", "structure": [ { @@ -181,7 +181,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/handedness", + "path": "https://openminds.om-i.org/props/handedness", "propertyName": "handedness", "ensureOrder": true, "structure": [ @@ -194,16 +194,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/pathology", + "path": "https://openminds.om-i.org/props/pathology", "propertyName": "pathology", "ensureOrder": true, "structure": [ @@ -217,9 +217,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "relativeTimeIndication__QuantitativeValue", @@ -228,7 +228,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -241,12 +241,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -259,7 +259,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -267,9 +267,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "relativeTimeIndication__QuantitativeValueRange", @@ -278,11 +278,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -295,11 +295,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -316,9 +316,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "weight__QuantitativeValue", @@ -327,7 +327,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -340,12 +340,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -358,7 +358,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -366,9 +366,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "weight__QuantitativeValueRange", @@ -377,11 +377,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -394,11 +394,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -415,7 +415,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", + "@id": "https://openminds.om-i.org/props/descendedFrom", "reverse": true }, "propertyName": "descendedFrom", @@ -431,7 +431,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/input", + "@id": "https://openminds.om-i.org/props/input", "reverse": true }, "propertyName": "input", @@ -447,7 +447,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/output", + "@id": "https://openminds.om-i.org/props/output", "reverse": true }, "propertyName": "output", @@ -463,7 +463,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedState", + "@id": "https://openminds.om-i.org/props/studiedState", "reverse": true }, "propertyName": "studiedState", @@ -479,7 +479,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", diff --git a/test/test_data/queries/openminds/core/subjectstate_simple_query.json b/test/test_data/queries/openminds/core/subjectstate_simple_query.json index e2b6d7f0..aab6f1d0 100644 --- a/test/test_data/queries/openminds/core/subjectstate_simple_query.json +++ b/test/test_data/queries/openminds/core/subjectstate_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/SubjectState", + "type": "https://openminds.om-i.org/types/SubjectState", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,14 +39,14 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "age__QuantitativeValue", @@ -55,7 +55,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -68,12 +68,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -86,7 +86,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -94,9 +94,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "age__QuantitativeValueRange", @@ -105,11 +105,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -122,11 +122,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -142,7 +142,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/ageCategory", + "path": "https://openminds.om-i.org/props/ageCategory", "propertyName": "ageCategory", "structure": [ { @@ -155,7 +155,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/attribute", + "path": "https://openminds.om-i.org/props/attribute", "propertyName": "attribute", "ensureOrder": true, "structure": [ @@ -168,7 +168,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/descendedFrom", + "path": "https://openminds.om-i.org/props/descendedFrom", "propertyName": "descendedFrom", "structure": [ { @@ -181,7 +181,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/handedness", + "path": "https://openminds.om-i.org/props/handedness", "propertyName": "handedness", "structure": [ { @@ -194,16 +194,16 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/pathology", + "path": "https://openminds.om-i.org/props/pathology", "propertyName": "pathology", "ensureOrder": true, "structure": [ @@ -217,9 +217,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "relativeTimeIndication__QuantitativeValue", @@ -228,7 +228,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -241,12 +241,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -259,7 +259,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -267,9 +267,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "relativeTimeIndication__QuantitativeValueRange", @@ -278,11 +278,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -295,11 +295,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -316,9 +316,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "weight__QuantitativeValue", @@ -327,7 +327,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -340,12 +340,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -358,7 +358,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -366,9 +366,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "weight__QuantitativeValueRange", @@ -377,11 +377,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -394,11 +394,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -415,7 +415,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", + "@id": "https://openminds.om-i.org/props/descendedFrom", "reverse": true }, "propertyName": "descendedFrom", @@ -431,7 +431,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/input", + "@id": "https://openminds.om-i.org/props/input", "reverse": true }, "propertyName": "input", @@ -447,7 +447,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/output", + "@id": "https://openminds.om-i.org/props/output", "reverse": true }, "propertyName": "output", @@ -463,7 +463,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedState", + "@id": "https://openminds.om-i.org/props/studiedState", "reverse": true }, "propertyName": "studiedState", @@ -479,7 +479,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", @@ -495,7 +495,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", + "@id": "https://openminds.om-i.org/props/usedSpecimen", "reverse": true }, "propertyName": "usedSpecimen", diff --git a/test/test_data/queries/openminds/core/swhid_simple_query.json b/test/test_data/queries/openminds/core/swhid_simple_query.json index 00d78bb5..2bf90150 100644 --- a/test/test_data/queries/openminds/core/swhid_simple_query.json +++ b/test/test_data/queries/openminds/core/swhid_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/SWHID", + "type": "https://openminds.om-i.org/types/SWHID", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,12 +39,12 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/identifier", + "path": "https://openminds.om-i.org/props/identifier", "propertyName": "identifier" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/digitalIdentifier", + "@id": "https://openminds.om-i.org/props/digitalIdentifier", "reverse": true }, "propertyName": "digitalIdentifier", diff --git a/test/test_data/queries/openminds/core/tissuesample_simple_query.json b/test/test_data/queries/openminds/core/tissuesample_simple_query.json index 1612e22f..0978d25d 100644 --- a/test/test_data/queries/openminds/core/tissuesample_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesample_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/TissueSample", + "type": "https://openminds.om-i.org/types/TissueSample", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/anatomicalLocation", + "path": "https://openminds.om-i.org/props/anatomicalLocation", "propertyName": "anatomicalLocation", "ensureOrder": true, "structure": [ @@ -52,7 +52,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/biologicalSex", + "path": "https://openminds.om-i.org/props/biologicalSex", "propertyName": "biologicalSex", "structure": [ { @@ -65,11 +65,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/isPartOf", + "path": "https://openminds.om-i.org/props/isPartOf", "propertyName": "isPartOf", "ensureOrder": true, "structure": [ @@ -82,7 +82,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/laterality", + "path": "https://openminds.om-i.org/props/laterality", "propertyName": "laterality", "ensureOrder": true, "structure": [ @@ -95,12 +95,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/origin", + "path": "https://openminds.om-i.org/props/origin", "propertyName": "origin", "structure": [ { @@ -113,7 +113,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/species", + "path": "https://openminds.om-i.org/props/species", "propertyName": "species", "structure": [ { @@ -126,7 +126,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/studiedState", + "path": "https://openminds.om-i.org/props/studiedState", "propertyName": "studiedState", "ensureOrder": true, "structure": [ @@ -139,7 +139,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "structure": [ { @@ -153,7 +153,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", + "@id": "https://openminds.om-i.org/props/studiedSpecimen", "reverse": true }, "propertyName": "studiedSpecimen", @@ -169,7 +169,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", @@ -185,7 +185,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", + "@id": "https://openminds.om-i.org/props/usedSpecimen", "reverse": true }, "propertyName": "usedSpecimen", diff --git a/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json b/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json index 9360af19..2fdd4ffa 100644 --- a/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesamplecollection_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/TissueSampleCollection", + "type": "https://openminds.om-i.org/types/TissueSampleCollection", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { - "path": "https://openminds.ebrains.eu/vocab/anatomicalLocation", + "path": "https://openminds.om-i.org/props/anatomicalLocation", "propertyName": "anatomicalLocation", "ensureOrder": true, "structure": [ @@ -56,7 +56,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/biologicalSex", + "path": "https://openminds.om-i.org/props/biologicalSex", "propertyName": "biologicalSex", "ensureOrder": true, "structure": [ @@ -69,11 +69,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/laterality", + "path": "https://openminds.om-i.org/props/laterality", "propertyName": "laterality", "ensureOrder": true, "structure": [ @@ -86,16 +86,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/numberOfTissueSamples", + "path": "https://openminds.om-i.org/props/numberOfTissueSamples", "propertyName": "numberOfTissueSamples" }, { - "path": "https://openminds.ebrains.eu/vocab/origin", + "path": "https://openminds.om-i.org/props/origin", "propertyName": "origin", "ensureOrder": true, "structure": [ @@ -108,7 +108,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/species", + "path": "https://openminds.om-i.org/props/species", "propertyName": "species", "ensureOrder": true, "structure": [ @@ -121,7 +121,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/studiedState", + "path": "https://openminds.om-i.org/props/studiedState", "propertyName": "studiedState", "ensureOrder": true, "structure": [ @@ -134,7 +134,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "ensureOrder": true, "structure": [ @@ -148,7 +148,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isPartOf", + "@id": "https://openminds.om-i.org/props/isPartOf", "reverse": true }, "propertyName": "isPartOf", @@ -164,7 +164,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedSpecimen", + "@id": "https://openminds.om-i.org/props/studiedSpecimen", "reverse": true }, "propertyName": "studiedSpecimen", @@ -180,7 +180,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", @@ -196,7 +196,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", + "@id": "https://openminds.om-i.org/props/usedSpecimen", "reverse": true }, "propertyName": "usedSpecimen", diff --git a/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json b/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json index 5a0308e4..e026008d 100644 --- a/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesamplecollectionstate_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/TissueSampleCollectionState", + "type": "https://openminds.om-i.org/types/TissueSampleCollectionState", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,14 +39,14 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "age__QuantitativeValue", @@ -55,7 +55,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -68,12 +68,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -86,7 +86,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -94,9 +94,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "age__QuantitativeValueRange", @@ -105,11 +105,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -122,11 +122,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -142,7 +142,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/attribute", + "path": "https://openminds.om-i.org/props/attribute", "propertyName": "attribute", "ensureOrder": true, "structure": [ @@ -155,7 +155,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/descendedFrom", + "path": "https://openminds.om-i.org/props/descendedFrom", "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ @@ -168,16 +168,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/pathology", + "path": "https://openminds.om-i.org/props/pathology", "propertyName": "pathology", "ensureOrder": true, "structure": [ @@ -191,9 +191,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "relativeTimeIndication__QuantitativeValue", @@ -202,7 +202,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -215,12 +215,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -233,7 +233,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -241,9 +241,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "relativeTimeIndication__QuantitativeValueRange", @@ -252,11 +252,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -269,11 +269,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -290,9 +290,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "weight__QuantitativeValue", @@ -301,7 +301,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -314,12 +314,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -332,7 +332,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -340,9 +340,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "weight__QuantitativeValueRange", @@ -351,11 +351,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -368,11 +368,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -389,7 +389,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", + "@id": "https://openminds.om-i.org/props/descendedFrom", "reverse": true }, "propertyName": "descendedFrom", @@ -405,7 +405,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/input", + "@id": "https://openminds.om-i.org/props/input", "reverse": true }, "propertyName": "input", @@ -421,7 +421,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/output", + "@id": "https://openminds.om-i.org/props/output", "reverse": true }, "propertyName": "output", @@ -437,7 +437,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedState", + "@id": "https://openminds.om-i.org/props/studiedState", "reverse": true }, "propertyName": "studiedState", @@ -453,7 +453,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", diff --git a/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json b/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json index 674cd480..cca6d633 100644 --- a/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json +++ b/test/test_data/queries/openminds/core/tissuesamplestate_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/TissueSampleState", + "type": "https://openminds.om-i.org/types/TissueSampleState", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,14 +39,14 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/additionalRemarks", + "path": "https://openminds.om-i.org/props/additionalRemarks", "propertyName": "additionalRemarks" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "age__QuantitativeValue", @@ -55,7 +55,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -68,12 +68,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -86,7 +86,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -94,9 +94,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/age", + "@id": "https://openminds.om-i.org/props/age", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "age__QuantitativeValueRange", @@ -105,11 +105,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -122,11 +122,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -142,7 +142,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/attribute", + "path": "https://openminds.om-i.org/props/attribute", "propertyName": "attribute", "ensureOrder": true, "structure": [ @@ -155,7 +155,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/descendedFrom", + "path": "https://openminds.om-i.org/props/descendedFrom", "propertyName": "descendedFrom", "ensureOrder": true, "structure": [ @@ -168,16 +168,16 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/internalIdentifier", + "path": "https://openminds.om-i.org/props/internalIdentifier", "propertyName": "internalIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/lookupLabel", + "path": "https://openminds.om-i.org/props/lookupLabel", "propertyName": "lookupLabel", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/pathology", + "path": "https://openminds.om-i.org/props/pathology", "propertyName": "pathology", "ensureOrder": true, "structure": [ @@ -191,9 +191,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "relativeTimeIndication__QuantitativeValue", @@ -202,7 +202,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -215,12 +215,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -233,7 +233,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -241,9 +241,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/relativeTimeIndication", + "@id": "https://openminds.om-i.org/props/relativeTimeIndication", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "relativeTimeIndication__QuantitativeValueRange", @@ -252,11 +252,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -269,11 +269,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -290,9 +290,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValue" + "@id": "https://openminds.om-i.org/types/QuantitativeValue" } }, "propertyName": "weight__QuantitativeValue", @@ -301,7 +301,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/typeOfUncertainty", + "path": "https://openminds.om-i.org/props/typeOfUncertainty", "propertyName": "typeOfUncertainty", "structure": [ { @@ -314,12 +314,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/uncertainty", + "path": "https://openminds.om-i.org/props/uncertainty", "propertyName": "uncertainty", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/unit", + "path": "https://openminds.om-i.org/props/unit", "propertyName": "unit", "structure": [ { @@ -332,7 +332,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", "propertyName": "value" } ], @@ -340,9 +340,9 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/weight", + "@id": "https://openminds.om-i.org/props/weight", "typeFilter": { - "@id": "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "@id": "https://openminds.om-i.org/types/QuantitativeValueRange" } }, "propertyName": "weight__QuantitativeValueRange", @@ -351,11 +351,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValue", + "path": "https://openminds.om-i.org/props/maxValue", "propertyName": "maxValue" }, { - "path": "https://openminds.ebrains.eu/vocab/maxValueUnit", + "path": "https://openminds.om-i.org/props/maxValueUnit", "propertyName": "maxValueUnit", "structure": [ { @@ -368,11 +368,11 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/minValue", + "path": "https://openminds.om-i.org/props/minValue", "propertyName": "minValue" }, { - "path": "https://openminds.ebrains.eu/vocab/minValueUnit", + "path": "https://openminds.om-i.org/props/minValueUnit", "propertyName": "minValueUnit", "structure": [ { @@ -389,7 +389,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/descendedFrom", + "@id": "https://openminds.om-i.org/props/descendedFrom", "reverse": true }, "propertyName": "descendedFrom", @@ -405,7 +405,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/input", + "@id": "https://openminds.om-i.org/props/input", "reverse": true }, "propertyName": "input", @@ -421,7 +421,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/output", + "@id": "https://openminds.om-i.org/props/output", "reverse": true }, "propertyName": "output", @@ -437,7 +437,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/studiedState", + "@id": "https://openminds.om-i.org/props/studiedState", "reverse": true }, "propertyName": "studiedState", @@ -453,7 +453,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/groupedBy", + "@id": "https://openminds.om-i.org/props/groupedBy", "reverse": true }, "propertyName": "groupedBy", @@ -469,7 +469,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/usedSpecimen", + "@id": "https://openminds.om-i.org/props/usedSpecimen", "reverse": true }, "propertyName": "usedSpecimen", diff --git a/test/test_data/queries/openminds/core/webresource_simple_query.json b/test/test_data/queries/openminds/core/webresource_simple_query.json index 06196a4c..9f046d60 100644 --- a/test/test_data/queries/openminds/core/webresource_simple_query.json +++ b/test/test_data/queries/openminds/core/webresource_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/WebResource", + "type": "https://openminds.om-i.org/types/WebResource", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,11 +39,11 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contentDescription", + "path": "https://openminds.om-i.org/props/contentDescription", "propertyName": "contentDescription" }, { - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "structure": [ { @@ -56,12 +56,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/IRI", + "path": "https://openminds.om-i.org/props/IRI", "propertyName": "IRI" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/describedIn", + "@id": "https://openminds.om-i.org/props/describedIn", "reverse": true }, "propertyName": "describedIn", @@ -77,7 +77,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/fullDocumentation", + "@id": "https://openminds.om-i.org/props/fullDocumentation", "reverse": true }, "propertyName": "fullDocumentation", @@ -93,7 +93,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/license", + "@id": "https://openminds.om-i.org/props/license", "reverse": true }, "propertyName": "license", @@ -109,7 +109,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/outputData", + "@id": "https://openminds.om-i.org/props/outputData", "reverse": true }, "propertyName": "outputData", @@ -125,7 +125,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/referenceData", + "@id": "https://openminds.om-i.org/props/referenceData", "reverse": true }, "propertyName": "referenceData", diff --git a/test/test_data/queries/openminds/core/webservice_simple_query.json b/test/test_data/queries/openminds/core/webservice_simple_query.json index d4999f43..ac1292e8 100644 --- a/test/test_data/queries/openminds/core/webservice_simple_query.json +++ b/test/test_data/queries/openminds/core/webservice_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/WebService", + "type": "https://openminds.om-i.org/types/WebService", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -52,11 +52,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -69,12 +69,12 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/hasVersion", + "path": "https://openminds.om-i.org/props/hasVersion", "propertyName": "hasVersion", "ensureOrder": true, "structure": [ @@ -87,20 +87,20 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -116,7 +116,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/service", + "@id": "https://openminds.om-i.org/props/service", "reverse": true }, "propertyName": "service", @@ -132,7 +132,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hostedBy", + "@id": "https://openminds.om-i.org/props/hostedBy", "reverse": true }, "propertyName": "hostedBy", @@ -148,7 +148,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -164,7 +164,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", diff --git a/test/test_data/queries/openminds/core/webserviceversion_simple_query.json b/test/test_data/queries/openminds/core/webserviceversion_simple_query.json index f1d7473b..afca5d11 100644 --- a/test/test_data/queries/openminds/core/webserviceversion_simple_query.json +++ b/test/test_data/queries/openminds/core/webserviceversion_simple_query.json @@ -16,7 +16,7 @@ } }, "meta": { - "type": "https://openminds.ebrains.eu/core/WebServiceVersion", + "type": "https://openminds.om-i.org/types/WebServiceVersion", "description": "Automatically generated by fairgraph" }, "structure": [ @@ -39,7 +39,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/accessibility", + "path": "https://openminds.om-i.org/props/accessibility", "propertyName": "accessibility", "structure": [ { @@ -52,14 +52,14 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/copyright", + "path": "https://openminds.om-i.org/props/copyright", "propertyName": "copyright", "structure": [ { "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/holder", + "path": "https://openminds.om-i.org/props/holder", "propertyName": "holder", "ensureOrder": true, "structure": [ @@ -72,7 +72,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/year", + "path": "https://openminds.om-i.org/props/year", "propertyName": "year", "ensureOrder": true } @@ -80,7 +80,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/custodian", + "path": "https://openminds.om-i.org/props/custodian", "propertyName": "custodian", "ensureOrder": true, "structure": [ @@ -93,11 +93,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "description" }, { - "path": "https://openminds.ebrains.eu/vocab/developer", + "path": "https://openminds.om-i.org/props/developer", "propertyName": "developer", "ensureOrder": true, "structure": [ @@ -110,7 +110,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/fullDocumentation", + "path": "https://openminds.om-i.org/props/fullDocumentation", "propertyName": "fullDocumentation", "structure": [ { @@ -123,12 +123,12 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "sort": true }, { - "path": "https://openminds.ebrains.eu/vocab/funding", + "path": "https://openminds.om-i.org/props/funding", "propertyName": "funding", "ensureOrder": true, "structure": [ @@ -141,7 +141,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/hasPart", + "path": "https://openminds.om-i.org/props/hasPart", "propertyName": "hasPart", "ensureOrder": true, "structure": [ @@ -154,15 +154,15 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/homepage", + "path": "https://openminds.om-i.org/props/homepage", "propertyName": "homepage" }, { - "path": "https://openminds.ebrains.eu/vocab/howToCite", + "path": "https://openminds.om-i.org/props/howToCite", "propertyName": "howToCite" }, { - "path": "https://openminds.ebrains.eu/vocab/inputFormat", + "path": "https://openminds.om-i.org/props/inputFormat", "propertyName": "inputFormat", "ensureOrder": true, "structure": [ @@ -175,7 +175,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf", + "path": "https://openminds.om-i.org/props/isAlternativeVersionOf", "propertyName": "isAlternativeVersionOf", "ensureOrder": true, "structure": [ @@ -188,7 +188,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "path": "https://openminds.om-i.org/props/isNewVersionOf", "propertyName": "isNewVersionOf", "structure": [ { @@ -201,7 +201,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/keyword", + "path": "https://openminds.om-i.org/props/keyword", "propertyName": "keyword", "ensureOrder": true, "structure": [ @@ -214,7 +214,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/otherContribution", + "path": "https://openminds.om-i.org/props/otherContribution", "propertyName": "otherContribution", "ensureOrder": true, "structure": [ @@ -222,7 +222,7 @@ "path": "@type" }, { - "path": "https://openminds.ebrains.eu/vocab/contributor", + "path": "https://openminds.om-i.org/props/contributor", "propertyName": "contributor", "structure": [ { @@ -235,7 +235,7 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/type", + "path": "https://openminds.om-i.org/props/type", "propertyName": "type", "ensureOrder": true, "structure": [ @@ -250,7 +250,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/outputFormat", + "path": "https://openminds.om-i.org/props/outputFormat", "propertyName": "outputFormat", "ensureOrder": true, "structure": [ @@ -263,7 +263,7 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/relatedPublication", + "path": "https://openminds.om-i.org/props/relatedPublication", "propertyName": "relatedPublication", "ensureOrder": true, "structure": [ @@ -276,11 +276,11 @@ ] }, { - "path": "https://openminds.ebrains.eu/vocab/releaseDate", + "path": "https://openminds.om-i.org/props/releaseDate", "propertyName": "releaseDate" }, { - "path": "https://openminds.ebrains.eu/vocab/repository", + "path": "https://openminds.om-i.org/props/repository", "propertyName": "repository", "structure": [ { @@ -293,25 +293,25 @@ "singleValue": "FIRST" }, { - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "shortName" }, { - "path": "https://openminds.ebrains.eu/vocab/supportChannel", + "path": "https://openminds.om-i.org/props/supportChannel", "propertyName": "supportChannel", "ensureOrder": true }, { - "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", + "path": "https://openminds.om-i.org/props/versionIdentifier", "propertyName": "versionIdentifier" }, { - "path": "https://openminds.ebrains.eu/vocab/versionInnovation", + "path": "https://openminds.om-i.org/props/versionInnovation", "propertyName": "versionInnovation" }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -327,7 +327,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/isNewVersionOf", + "@id": "https://openminds.om-i.org/props/isNewVersionOf", "reverse": true }, "propertyName": "isNewVersionOf", @@ -343,7 +343,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasPart", + "@id": "https://openminds.om-i.org/props/hasPart", "reverse": true }, "propertyName": "hasPart", @@ -359,7 +359,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/hasVersion", + "@id": "https://openminds.om-i.org/props/hasVersion", "reverse": true }, "propertyName": "hasVersion", @@ -375,7 +375,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/about", + "@id": "https://openminds.om-i.org/props/about", "reverse": true }, "propertyName": "about", @@ -391,7 +391,7 @@ }, { "path": { - "@id": "https://openminds.ebrains.eu/vocab/environment", + "@id": "https://openminds.om-i.org/props/environment", "reverse": true }, "propertyName": "environment", diff --git a/test/test_openminds_computation.py b/test/test_openminds_computation.py index c3cb0519..5a2e7f22 100644 --- a/test/test_openminds_computation.py +++ b/test/test_openminds_computation.py @@ -25,7 +25,7 @@ def test_generate_query(self, mock_client): "path": {"@id": "path", "@type": "@id"}, }, "meta": { - "type": "https://openminds.ebrains.eu/computation/Environment", + "type": "https://openminds.om-i.org/types/Environment", "description": "Automatically generated by fairgraph", }, "structure": [ @@ -37,51 +37,51 @@ def test_generate_query(self, mock_client): }, {"path": "@type"}, { - "path": "https://openminds.ebrains.eu/vocab/configuration", + "path": "https://openminds.om-i.org/props/configuration", "propertyName": "configuration", "singleValue": "FIRST", "structure": [{"path": "@id"}, {"path": "@type"}], }, - {"path": "https://openminds.ebrains.eu/vocab/description", "propertyName": "description"}, + {"path": "https://openminds.om-i.org/props/description", "propertyName": "description"}, { - "path": "https://openminds.ebrains.eu/vocab/hardware", + "path": "https://openminds.om-i.org/props/hardware", "propertyName": "hardware", "singleValue": "FIRST", "structure": [{"path": "@id"}, {"path": "@type"}], }, - {"path": "https://openminds.ebrains.eu/vocab/name", "propertyName": "name", "sort": True}, + {"path": "https://openminds.om-i.org/props/name", "propertyName": "name", "sort": True}, { - "path": "https://openminds.ebrains.eu/vocab/software", + "path": "https://openminds.om-i.org/props/software", "propertyName": "software", "ensureOrder": True, "structure": [{"path": "@id"}, {"path": "@type"}], }, { - "path": {"@id": "https://openminds.ebrains.eu/vocab/environment", "reverse": True}, + "path": {"@id": "https://openminds.om-i.org/props/environment", "reverse": True}, "propertyName": "environment", "ensureOrder": True, "structure": [{"path": "@id"}, {"path": "@type"}], }, { - "path": "https://openminds.ebrains.eu/vocab/description", + "path": "https://openminds.om-i.org/props/description", "propertyName": "Qdescription", "filter": {"op": "CONTAINS", "value": "bar"}, "required": True, }, { - "path": "https://openminds.ebrains.eu/vocab/hardware", + "path": "https://openminds.om-i.org/props/hardware", "propertyName": "Qhardware", "required": True, "structure": [{"path": "@id", "filter": {"op": "CONTAINS", "value": "some_id"}}], }, { - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", "propertyName": "Qname", "filter": {"op": "CONTAINS", "value": "foo"}, "required": True, }, { - "path": "https://openminds.ebrains.eu/vocab/software", + "path": "https://openminds.om-i.org/props/software", "propertyName": "Qsoftware", "required": True, "structure": [{"path": "@id", "filter": {"op": "CONTAINS", "value": "another_id"}}], diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index 28ab19e3..d0eb5163 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -410,7 +410,7 @@ def test_exists_method_without_id(kg_client): def test__update(): example_data = { "@id": "https://kg.ebrains.eu/api/instances/e90fc25a-fc35-4066-9ff2-ca3583a2d008", - "@type": ["https://openminds.ebrains.eu/core/Person"], + "@type": "https://openminds.om-i.org/types/Person", "http://schema.org/identifier": [ "ba78ffe138e3a79a7514f26441fba6ff", "https://nexus.humanbrainproject.org/v0/data/uniminds/core/person/v1.0.0/e90fc25a-fc35-4066-9ff2-ca3583a2d008", @@ -418,18 +418,18 @@ def test__update(): ], "https://core.kg.ebrains.eu/vocab/meta/revision": "_fCLxIMC---", "https://core.kg.ebrains.eu/vocab/meta/space": "common", - "https://openminds.ebrains.eu/vocab/affiliation": { - "@type": ["https://openminds.ebrains.eu/core/Affiliation"], - "https://openminds.ebrains.eu/vocab/memberOf": { + "https://openminds.om-i.org/props/affiliation": [{ + "@type": "https://openminds.om-i.org/types/Affiliation", + "https://openminds.om-i.org/props/memberOf": { "@id": "https://kg.ebrains.eu/api/instances/05c23d56-b27e-4cf2-8c47-ed12c1a441e7" }, - }, - "https://openminds.ebrains.eu/vocab/contactInformation": [ + }], + "https://openminds.om-i.org/props/contactInformation": [ {"@id": "https://kg.ebrains.eu/api/instances/4b88cd1e-e222-47e9-9b4a-32b648bddbca"}, {"@id": "https://kg.ebrains.eu/api/instances/bc036c71-084b-4ffa-8430-4543095660f2"}, ], - "https://openminds.ebrains.eu/vocab/familyName": "Bianchi", - "https://openminds.ebrains.eu/vocab/givenName": "Daniela", + "https://openminds.om-i.org/props/familyName": "Bianchi", + "https://openminds.om-i.org/props/givenName": "Daniela", } person = omcore.Person.from_jsonld(example_data, scope="in progress") for key in ( @@ -476,14 +476,14 @@ def test_to_jsonld(): ) expected1 = { "@context": { - "@vocab": "https://openminds.ebrains.eu/vocab/" + "@vocab": "https://openminds.om-i.org/props/" }, "@id": "0000", - "@type": "https://openminds.ebrains.eu/core/Person", + "@type": "https://openminds.om-i.org/types/Person", "affiliation": [{ - "@type": "https://openminds.ebrains.eu/core/Affiliation", + "@type": "https://openminds.om-i.org/types/Affiliation", "memberOf": { - "@type": "https://openminds.ebrains.eu/core/Organization", + "@type": "https://openminds.om-i.org/types/Organization", "fullName": "The Lonely Mountain", }, }], @@ -503,15 +503,15 @@ def test_to_jsonld(): ) expected2a = { "@context": { - "@vocab": "https://openminds.ebrains.eu/vocab/" + "@vocab": "https://openminds.om-i.org/props/" }, "@id": "0000", - "@type": "https://openminds.ebrains.eu/core/Person", + "@type": "https://openminds.om-i.org/types/Person", "affiliation": [{ - "@type": "https://openminds.ebrains.eu/core/Affiliation", + "@type": "https://openminds.om-i.org/types/Affiliation", "memberOf": { "@id": "1111", - "@type": "https://openminds.ebrains.eu/core/Organization", + "@type": "https://openminds.om-i.org/types/Organization", "fullName": "The Lonely Mountain", }, }], @@ -520,12 +520,12 @@ def test_to_jsonld(): } expected2b = { "@context": { - "@vocab": "https://openminds.ebrains.eu/vocab/" + "@vocab": "https://openminds.om-i.org/props/" }, "@id": "0000", - "@type": "https://openminds.ebrains.eu/core/Person", + "@type": "https://openminds.om-i.org/types/Person", "affiliation": [{ - "@type": "https://openminds.ebrains.eu/core/Affiliation", + "@type": "https://openminds.om-i.org/types/Affiliation", "memberOf": {"@id": "1111"}, }], "familyName": "Oakenshield", @@ -826,7 +826,7 @@ def test_with_new_namespace_from_core(): "https://openminds.om-i.org/props/hasVersion": { "@id": "https://kg.ebrains.eu/api/instances/7035d53f-1597-4a45-9f72-23c2c933ec66" }, - "@type": ["https://openminds.om-i.org/types/Model"], + "@type": "https://openminds.om-i.org/types/Model", "https://openminds.om-i.org/props/description": "The scaffolding procedure has been enhanced compared to version 1.0. It's able to generate a scalable cerebellar structure, embedding specific 3D positions for each neuron and specific pair connections. Customized placement strategies allow to match layered density and encumbrance for each neuron type. Customized connection strategies allow to match anisotropic geometrical fields of intersection, and statistical convergence and divergence ratios.\nThe scaffold can host different neuron models. Several input stimulation patterns can be used to investigate network complex dynamics, revealing the relationships between structural constraints and underlying neuron mechanisms with the cerebellar circuit functioning, over space and time.\n\nMain link to Sonata conversion can be found here:\nhttps://github.com/SelezioneCasuale/scaffold/tree/sonata-version/scaffold", "https://openminds.om-i.org/props/studyTarget": [ {"@id": "https://kg.ebrains.eu/api/instances/ab532423-1fd7-4255-8c6f-f99dc6df814f"}, @@ -871,51 +871,51 @@ def test_with_new_namespace_from_query(): data = { "@id": "https://kg.ebrains.eu/api/instances/708024f7-9dd7-4c92-ae95-936db23c6d99", "https://schema.hbp.eu/myQuery/space": "model", - "@type": ["https://openminds.om-i.org/types/Model"], + "@type": "https://openminds.om-i.org/types/Model", "abstractionLevel": {"@id": "https://kg.ebrains.eu/api/instances/57becc19-f0a1-4d23-99bb-eb3b7d3cdb9a"}, "custodian": [ { "@id": "https://kg.ebrains.eu/api/instances/2905ce6c-bc89-4c99-b8b0-0fa9a17d1897", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/3477f916-5494-42ae-8b07-d2cb48231657", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/a594cfe2-f53a-470f-b52e-697b8d5a8958", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/5dcb9bd9-f93f-48c4-88e0-ff0ed4221ac8", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/5ad4749a-6e5a-4512-86ff-b89834c1b87c", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, ], "description": "The scaffolding procedure has been enhanced compared to version 1.0. It's able to generate a scalable cerebellar structure, embedding specific 3D positions for each neuron and specific pair connections. Customized placement strategies allow to match layered density and encumbrance for each neuron type. Customized connection strategies allow to match anisotropic geometrical fields of intersection, and statistical convergence and divergence ratios.\nThe scaffold can host different neuron models. Several input stimulation patterns can be used to investigate network complex dynamics, revealing the relationships between structural constraints and underlying neuron mechanisms with the cerebellar circuit functioning, over space and time.\n\nMain link to Sonata conversion can be found here:\nhttps://github.com/SelezioneCasuale/scaffold/tree/sonata-version/scaffold", "developer": [ { "@id": "https://kg.ebrains.eu/api/instances/2905ce6c-bc89-4c99-b8b0-0fa9a17d1897", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/3477f916-5494-42ae-8b07-d2cb48231657", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/a594cfe2-f53a-470f-b52e-697b8d5a8958", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/5dcb9bd9-f93f-48c4-88e0-ff0ed4221ac8", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, { "@id": "https://kg.ebrains.eu/api/instances/5ad4749a-6e5a-4512-86ff-b89834c1b87c", - "@type": ["https://openminds.om-i.org/types/Person"], + "@type": "https://openminds.om-i.org/types/Person", }, ], "digitalIdentifier": [], @@ -923,7 +923,7 @@ def test_with_new_namespace_from_query(): "hasVersion": [ { "@id": "https://kg.ebrains.eu/api/instances/7035d53f-1597-4a45-9f72-23c2c933ec66", - "@type": ["https://openminds.om-i.org/types/ModelVersion"], + "@type": "https://openminds.om-i.org/types/ModelVersion", } ], "homepage": None, @@ -931,18 +931,18 @@ def test_with_new_namespace_from_query(): "scope": [ { "@id": "https://kg.ebrains.eu/api/instances/6c678004-b8e0-4339-90c5-824e66503eb9", - "@type": ["https://openminds.om-i.org/types/ModelScope"], + "@type": "https://openminds.om-i.org/types/ModelScope", } ], "shortName": None, "studyTarget": [ { "@id": "https://kg.ebrains.eu/api/instances/ab532423-1fd7-4255-8c6f-f99dc6df814f", - "@type": ["https://openminds.om-i.org/types/Species"], + "@type": "https://openminds.om-i.org/types/Species", }, { "@id": "https://kg.ebrains.eu/api/instances/a70b0307-22fc-4730-a61f-fd279f43a3cf", - "@type": ["https://openminds.om-i.org/types/UBERONParcellation"], + "@type": "https://openminds.om-i.org/types/UBERONParcellation", }, ], "about": [], diff --git a/test/test_queries.py b/test/test_queries.py index 1630abd2..0e283e40 100644 --- a/test/test_queries.py +++ b/test/test_queries.py @@ -2,7 +2,8 @@ import json import pytest from kg_core.request import Stage, Pagination -from fairgraph.queries import Query, QueryProperty, Filter, migrate_query +from fairgraph.queries import Query, QueryProperty, Filter +from fairgraph.utility import adapt_namespaces_for_query import fairgraph.openminds.core as omcore from .utils import kg_client, mock_client, skip_if_no_connection @@ -10,7 +11,7 @@ @pytest.fixture() def example_query_model_version(): return Query( - node_type="https://openminds.ebrains.eu/core/ModelVersion", + node_type="https://openminds.om-i.org/types/ModelVersion", label="fg-testing-modelversion", space="model", properties=[ @@ -20,20 +21,20 @@ def example_query_model_version(): ), QueryProperty("@type"), QueryProperty( - "https://openminds.ebrains.eu/vocab/fullName", + "https://openminds.om-i.org/props/fullName", name="fullName", filter=Filter("CONTAINS", parameter="name"), sorted=True, required=True, ), QueryProperty( - "https://openminds.ebrains.eu/vocab/versionIdentifier", + "https://openminds.om-i.org/props/versionIdentifier", name="versionIdentifier", filter=Filter("EQUALS", parameter="version"), required=True, ), QueryProperty( - "https://openminds.ebrains.eu/vocab/format", + "https://openminds.om-i.org/props/format", name="format", ensure_order=True, properties=[ @@ -42,24 +43,24 @@ def example_query_model_version(): ], ), QueryProperty( - "https://openminds.ebrains.eu/vocab/custodian", + "https://openminds.om-i.org/props/custodian", name="custodian", ensure_order=True, - type_filter="https://openminds.ebrains.eu/core/Person", + type_filter="https://openminds.om-i.org/types/Person", properties=[ QueryProperty("@id", filter=Filter("EQUALS", parameter="custodian")), QueryProperty( - "https://openminds.ebrains.eu/vocab/affiliation", + "https://openminds.om-i.org/props/affiliation", name="affiliation", properties=[ QueryProperty("@type"), QueryProperty( - "https://openminds.ebrains.eu/vocab/memberOf", + "https://openminds.om-i.org/props/memberOf", name="memberOf", properties=[QueryProperty("@id")], ), QueryProperty( - "https://openminds.ebrains.eu/vocab/startDate", + "https://openminds.om-i.org/props/startDate", name="startDate", ), ], @@ -73,7 +74,7 @@ def example_query_model_version(): @pytest.fixture() def example_query_model(): return Query( - node_type="https://openminds.ebrains.eu/core/Model", + node_type="https://openminds.om-i.org/types/Model", label="fg-testing-model", space="model", properties=[ @@ -83,32 +84,32 @@ def example_query_model(): ), QueryProperty("@type"), QueryProperty( - "https://openminds.ebrains.eu/vocab/fullName", + "https://openminds.om-i.org/props/fullName", name="fullName", filter=Filter("CONTAINS", parameter="name"), sorted=True, required=True, ), QueryProperty( - "https://openminds.ebrains.eu/vocab/custodian", + "https://openminds.om-i.org/props/custodian", name="custodian", - type_filter="https://openminds.ebrains.eu/core/Person", + type_filter="https://openminds.om-i.org/types/Person", properties=[ # QueryProperty("@type"), QueryProperty( - "https://openminds.ebrains.eu/vocab/familyName", + "https://openminds.om-i.org/props/familyName", name="familyName", ), ], ), QueryProperty( - "https://openminds.ebrains.eu/vocab/custodian", + "https://openminds.om-i.org/props/custodian", name="organization", - type_filter="https://openminds.ebrains.eu/core/Organization", + type_filter="https://openminds.om-i.org/types/Organization", properties=[ # QueryProperty("@type"), QueryProperty( - "https://openminds.ebrains.eu/vocab/shortName", + "https://openminds.om-i.org/props/shortName", name="shortName", ), ], @@ -120,50 +121,50 @@ def example_query_model(): @pytest.fixture() def example_query_repository_with_reverse(): return Query( - node_type="https://openminds.ebrains.eu/core/FileRepository", + node_type="https://openminds.om-i.org/types/FileRepository", properties=[ QueryProperty( "https://core.kg.ebrains.eu/vocab/meta/space", name="query:space" ), - QueryProperty("https://openminds.ebrains.eu/vocab/IRI", name="location"), + QueryProperty("https://openminds.om-i.org/props/IRI", name="location"), QueryProperty( - "https://openminds.ebrains.eu/vocab/fileRepository", + "https://openminds.om-i.org/props/fileRepository", reverse=True, name="files", properties=[ - QueryProperty("https://openminds.ebrains.eu/vocab/name", name="filename"), + QueryProperty("https://openminds.om-i.org/props/name", name="filename"), QueryProperty( [ - "https://openminds.ebrains.eu/vocab/format", - "https://openminds.ebrains.eu/vocab/name", + "https://openminds.om-i.org/props/format", + "https://openminds.om-i.org/props/name", ], name="format", ), QueryProperty( - "https://openminds.ebrains.eu/vocab/hash", + "https://openminds.om-i.org/props/hash", name="hash", properties=[ QueryProperty( - "https://openminds.ebrains.eu/vocab/digest", + "https://openminds.om-i.org/props/digest", name="digest", ), QueryProperty( - "https://openminds.ebrains.eu/vocab/algorithm", + "https://openminds.om-i.org/props/algorithm", name="algorithm", ), ], ), QueryProperty( - "https://openminds.ebrains.eu/vocab/storageSize", + "https://openminds.om-i.org/props/storageSize", name="size", expect_single=True, properties=[ - QueryProperty("https://openminds.ebrains.eu/vocab/value", name="value"), + QueryProperty("https://openminds.om-i.org/props/value", name="value"), QueryProperty( [ - "https://openminds.ebrains.eu/vocab/unit", - "https://openminds.ebrains.eu/vocab/name", + "https://openminds.om-i.org/props/unit", + "https://openminds.om-i.org/props/name", ], name="units", expect_single=True, @@ -173,14 +174,14 @@ def example_query_repository_with_reverse(): ], ), QueryProperty( - "https://openminds.ebrains.eu/vocab/repository", + "https://openminds.om-i.org/props/repository", reverse=True, required=True, name="contains_dataset_version", properties=[ QueryProperty("@id"), QueryProperty( - "https://openminds.ebrains.eu/vocab/shortName", + "https://openminds.om-i.org/props/shortName", name="alias", filter=Filter("EQUALS", parameter="dataset_alias"), ), @@ -203,7 +204,7 @@ def test_query_builder(example_query_model_version): "meta": { "description": "Automatically generated by fairgraph", "name": "fg-testing-modelversion", - "type": "https://openminds.ebrains.eu/core/ModelVersion", + "type": "https://openminds.om-i.org/types/ModelVersion", }, "structure": [ { @@ -218,20 +219,20 @@ def test_query_builder(example_query_model_version): {"path": "@type"}, { "filter": {"op": "CONTAINS", "parameter": "name"}, - "path": "https://openminds.ebrains.eu/vocab/fullName", + "path": "https://openminds.om-i.org/props/fullName", "propertyName": "fullName", "required": True, "sort": True, }, { "filter": {"op": "EQUALS", "parameter": "version"}, - "path": "https://openminds.ebrains.eu/vocab/versionIdentifier", + "path": "https://openminds.om-i.org/props/versionIdentifier", "propertyName": "versionIdentifier", "required": True, }, { "ensureOrder": True, - "path": "https://openminds.ebrains.eu/vocab/format", + "path": "https://openminds.om-i.org/props/format", "propertyName": "format", "structure": [ {"filter": {"op": "EQUALS", "parameter": "format"}, "path": "@id"}, @@ -241,8 +242,8 @@ def test_query_builder(example_query_model_version): { "ensureOrder": True, "path": { - "@id": "https://openminds.ebrains.eu/vocab/custodian", - "typeFilter": {"@id": "https://openminds.ebrains.eu/core/Person"}, + "@id": "https://openminds.om-i.org/props/custodian", + "typeFilter": {"@id": "https://openminds.om-i.org/types/Person"}, }, "propertyName": "custodian", "structure": [ @@ -251,17 +252,17 @@ def test_query_builder(example_query_model_version): "path": "@id", }, { - "path": "https://openminds.ebrains.eu/vocab/affiliation", + "path": "https://openminds.om-i.org/props/affiliation", "propertyName": "affiliation", "structure": [ {"path": "@type"}, { - "path": "https://openminds.ebrains.eu/vocab/memberOf", + "path": "https://openminds.om-i.org/props/memberOf", "propertyName": "memberOf", "structure": [{"path": "@id"}], }, { - "path": "https://openminds.ebrains.eu/vocab/startDate", + "path": "https://openminds.om-i.org/props/startDate", "propertyName": "startDate", }, ], @@ -284,7 +285,7 @@ def test_query_with_reverse_properties(example_query_repository_with_reverse): "path": {"@id": "path", "@type": "@id"}, }, "meta": { - "type": "https://openminds.ebrains.eu/core/FileRepository", + "type": "https://openminds.om-i.org/types/FileRepository", "description": "Automatically generated by fairgraph", }, "structure": [ @@ -295,55 +296,55 @@ def test_query_with_reverse_properties(example_query_repository_with_reverse): }, { "propertyName": "location", - "path": "https://openminds.ebrains.eu/vocab/IRI", + "path": "https://openminds.om-i.org/props/IRI", }, { "propertyName": "files", "path": { - "@id": "https://openminds.ebrains.eu/vocab/fileRepository", + "@id": "https://openminds.om-i.org/props/fileRepository", "reverse": True, }, "structure": [ { "propertyName": "filename", - "path": "https://openminds.ebrains.eu/vocab/name", + "path": "https://openminds.om-i.org/props/name", }, { "propertyName": "format", "path": [ - "https://openminds.ebrains.eu/vocab/format", - "https://openminds.ebrains.eu/vocab/name", + "https://openminds.om-i.org/props/format", + "https://openminds.om-i.org/props/name", ], }, { "propertyName": "hash", - "path": "https://openminds.ebrains.eu/vocab/hash", + "path": "https://openminds.om-i.org/props/hash", "structure": [ { "propertyName": "digest", - "path": "https://openminds.ebrains.eu/vocab/digest", + "path": "https://openminds.om-i.org/props/digest", }, { "propertyName": "algorithm", - "path": "https://openminds.ebrains.eu/vocab/algorithm", + "path": "https://openminds.om-i.org/props/algorithm", }, ], }, { "propertyName": "size", - "path": "https://openminds.ebrains.eu/vocab/storageSize", + "path": "https://openminds.om-i.org/props/storageSize", "singleValue": "FIRST", "structure": [ { "propertyName": "value", - "path": "https://openminds.ebrains.eu/vocab/value", + "path": "https://openminds.om-i.org/props/value", }, { "propertyName": "units", "singleValue": "FIRST", "path": [ - "https://openminds.ebrains.eu/vocab/unit", - "https://openminds.ebrains.eu/vocab/name", + "https://openminds.om-i.org/props/unit", + "https://openminds.om-i.org/props/name", ], }, ], @@ -351,14 +352,14 @@ def test_query_with_reverse_properties(example_query_repository_with_reverse): ], }, { - "path": {"@id": "https://openminds.ebrains.eu/vocab/repository", "reverse": True}, + "path": {"@id": "https://openminds.om-i.org/props/repository", "reverse": True}, "propertyName": "contains_dataset_version", "required": True, "structure": [ {"path": "@id"}, { "filter": {"op": "EQUALS", "parameter": "dataset_alias"}, - "path": "https://openminds.ebrains.eu/vocab/shortName", + "path": "https://openminds.om-i.org/props/shortName", "propertyName": "alias", }, ], @@ -370,8 +371,11 @@ def test_query_with_reverse_properties(example_query_repository_with_reverse): @skip_if_no_connection def test_execute_query(kg_client, example_query_model_version): + query = example_query_model_version.serialize() + if kg_client.migrated is False: + query = adapt_namespaces_for_query(query) response = kg_client._kg_client.queries.test_query( - payload=example_query_model_version.serialize(), + payload=query, stage=Stage.IN_PROGRESS, pagination=Pagination(start=0, size=3), ) @@ -402,8 +406,11 @@ def test_execute_query(kg_client, example_query_model_version): @skip_if_no_connection def test_execute_query_with_id_filter(kg_client, example_query_model): target_id = "https://kg.ebrains.eu/api/instances/3ca9ae35-c9df-451f-ac76-4925bd2c7dc6" + query = example_query_model.serialize() + if kg_client.migrated is False: + query = adapt_namespaces_for_query(query) response = kg_client._kg_client.queries.test_query( - payload=example_query_model.serialize(), + payload=query, instance_id=kg_client.uuid_from_uri(target_id), stage=Stage.IN_PROGRESS, pagination=Pagination(start=0, size=10), @@ -418,8 +425,11 @@ def test_execute_query_with_id_filter(kg_client, example_query_model): @skip_if_no_connection def test_execute_query_with_reverse_properties_and_instance_id(kg_client, example_query_repository_with_reverse): target_id = "https://kg.ebrains.eu/api/instances/2f8d64f3-d848-49bd-baa6-a2c7080c98da" + query = example_query_repository_with_reverse.serialize() + if kg_client.migrated is False: + query = adapt_namespaces_for_query(query) response = kg_client._kg_client.queries.test_query( - payload=example_query_repository_with_reverse.serialize(), + payload=query, instance_id=kg_client.uuid_from_uri(target_id), stage=Stage.IN_PROGRESS, pagination=Pagination(start=0, size=10), @@ -436,8 +446,11 @@ def test_execute_query_with_reverse_properties_and_instance_id(kg_client, exampl @skip_if_no_connection def test_execute_query_with_reverse_properties_and_filter(kg_client, example_query_repository_with_reverse): + query = example_query_repository_with_reverse.serialize() + if kg_client.migrated is False: + query = adapt_namespaces_for_query(query) response = kg_client._kg_client.queries.test_query( - payload=example_query_repository_with_reverse.serialize(), + payload=query, additional_request_params={"dataset_alias": "data-brette-etal-2007-benchmark2-v1"}, stage=Stage.IN_PROGRESS, pagination=Pagination(start=0, size=10), @@ -520,39 +533,19 @@ def test_generate_query_with_follow_named_links(mock_client): assert generated == expected -def test_migrate_query(): - path_orig = os.path.join( - os.path.dirname(__file__), - "test_data", - "queries", - "openminds", - "core", - "dataset_simple_query.json", - ) - with open(path_orig) as fp: - orig_query = json.load(fp) - migrated_query = migrate_query(orig_query) - - path_expected = path_orig.replace(".json", "_v4.json") - with open(path_expected) as fp: - expected = json.load(fp) - - assert migrated_query == expected - - def test_generate_query_type_filter_flattened(): query = Query( - node_type="https://openminds.ebrains.eu/publications/LivePaperVersion", + node_type="https://openminds.om-i.org/types/LivePaperVersion", label="fg-testing-livepaperversion", space="livepapers", properties=[ - QueryProperty("https://openminds.ebrains.eu/vocab/shortName", name="short_name"), + QueryProperty("https://openminds.om-i.org/props/shortName", name="short_name"), QueryProperty( [ - "https://openminds.ebrains.eu/vocab/relatedPublication", - "https://openminds.ebrains.eu/vocab/identifier", + "https://openminds.om-i.org/props/relatedPublication", + "https://openminds.om-i.org/props/identifier", ], - type_filter="https://openminds.ebrains.eu/core/DOI", + type_filter="https://openminds.om-i.org/types/DOI", name="related_publications", ), ], @@ -566,7 +559,7 @@ def test_generate_query_type_filter_flattened(): "path": {"@id": "path", "@type": "@id"} }, "meta": { - "type": "https://openminds.ebrains.eu/publications/LivePaperVersion", + "type": "https://openminds.om-i.org/types/LivePaperVersion", "description": "Automatically generated by fairgraph", "name": "fg-testing-livepaperversion" }, @@ -578,15 +571,15 @@ def test_generate_query_type_filter_flattened(): "parameter": "id" } }, - {"propertyName": "short_name", "path": "https://openminds.ebrains.eu/vocab/shortName"}, + {"propertyName": "short_name", "path": "https://openminds.om-i.org/props/shortName"}, { "propertyName": "related_publications", "path": [ { - "@id": "https://openminds.ebrains.eu/vocab/relatedPublication", - "typeFilter": {"@id": "https://openminds.ebrains.eu/core/DOI"} + "@id": "https://openminds.om-i.org/props/relatedPublication", + "typeFilter": {"@id": "https://openminds.om-i.org/types/DOI"} }, - "https://openminds.ebrains.eu/vocab/identifier" + "https://openminds.om-i.org/props/identifier" ] }, { diff --git a/test/test_utility.py b/test/test_utility.py index 2a3a237e..c2cd18c6 100644 --- a/test/test_utility.py +++ b/test/test_utility.py @@ -1,7 +1,17 @@ +from copy import deepcopy import os import tempfile import pytest -from fairgraph.utility import (expand_filter, compact_uri, in_notebook, accepted_terms_of_use, sha1sum, normalize_data) +from fairgraph.utility import ( + expand_filter, + compact_uri, + in_notebook, + accepted_terms_of_use, + sha1sum, + normalize_data, + adapt_namespaces_3to4, + adapt_namespaces_4to3 +) from .utils import kg_client, skip_if_no_connection @@ -61,9 +71,6 @@ def test_sha1sum(): def test_normalize_data(): data = { - "@context": { - "@vocab": "https://openminds.ebrains.eu/vocab/" - }, "@id": "0000", "@type": "https://openminds.ebrains.eu/core/Person", "affiliation": { @@ -76,14 +83,14 @@ def test_normalize_data(): "familyName": "Oakenshield", "givenName": "Thorin", } - context = data.pop("@context") + context = {"@vocab": "https://openminds.ebrains.eu/vocab/"} expected = { "@id": "0000", - "@type": ["https://openminds.ebrains.eu/core/Person"], + "@type": "https://openminds.ebrains.eu/core/Person", "https://openminds.ebrains.eu/vocab/affiliation": { - "@type": ["https://openminds.ebrains.eu/core/Affiliation"], + "@type": "https://openminds.ebrains.eu/core/Affiliation", "https://openminds.ebrains.eu/vocab/memberOf": { - "@type": ["https://openminds.ebrains.eu/core/Organization"], + "@type": "https://openminds.ebrains.eu/core/Organization", "https://openminds.ebrains.eu/vocab/fullName": "The Lonely Mountain", }, }, @@ -91,3 +98,44 @@ def test_normalize_data(): "https://openminds.ebrains.eu/vocab/givenName": "Thorin", } assert normalize_data(data, context) == expected + + +def test_adapt_namespaces(): + import fairgraph.openminds.core # needed to populate the registry for lookup + + data_v3 = [{ + "@id": "0000", + "@type": "https://openminds.ebrains.eu/core/Person", + "https://openminds.ebrains.eu/vocab/affiliation": { + "@type": "https://openminds.ebrains.eu/core/Affiliation", + "https://openminds.ebrains.eu/vocab/memberOf": { + "@type": "https://openminds.ebrains.eu/core/Organization", + "https://openminds.ebrains.eu/vocab/fullName": "The Lonely Mountain", + }, + }, + "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield", + "https://openminds.ebrains.eu/vocab/givenName": "Thorin", + }] + data_v4 = [{ + "@id": "0000", + "@type": "https://openminds.om-i.org/types/Person", + "https://openminds.om-i.org/props/affiliation": { + "@type": "https://openminds.om-i.org/types/Affiliation", + "https://openminds.om-i.org/props/memberOf": { + "@type": "https://openminds.om-i.org/types/Organization", + "https://openminds.om-i.org/props/fullName": "The Lonely Mountain", + }, + }, + "https://openminds.om-i.org/props/familyName": "Oakenshield", + "https://openminds.om-i.org/props/givenName": "Thorin", + }] + + data = deepcopy(data_v3) + adapt_namespaces_3to4(data) + assert data == data_v4 + + data = deepcopy(data_v4) + adapt_namespaces_4to3(data) + assert data == data_v3 + + assert data_v3 != data_v4 diff --git a/test/utils.py b/test/utils.py index bc858214..21dc6c29 100644 --- a/test/utils.py +++ b/test/utils.py @@ -6,8 +6,8 @@ import pytest -#kg_host = "core.kg-ppd.ebrains.eu" # don't use production for testing -kg_host = "core.kg.ebrains.eu" # don't use production for testing +kg_host = "core.kg-ppd.ebrains.eu" # don't use production for testing +#kg_host = "core.kg.ebrains.eu" # don't use production for testing have_kg_connection = False no_kg_err_msg = "No KG connection - have you set the environment variable KG_AUTH_TOKEN?" @@ -64,7 +64,7 @@ def instance_from_full_uri( require_full_data: bool = True, ): if uri == "0000": - return {"@id": "0000", "@type": ["https://openminds.ebrains.eu/core/Model"]} + return {"@id": "0000", "@type": ["https://openminds.om-i.org/types/Model"]} else: raise NotImplementedError @@ -78,10 +78,10 @@ def query(self, query, filter=None, space=None, size=100, from_index=0, scope="r return MockKGResponse( [ { - "vocab:name": filter_value, + "https://openminds.om-i.org/props/name": filter_value, "@id": "fake_uuid", "https://core.kg.ebrains.eu/vocab/meta/space": "controlled", - "@type": ["https://openminds.ebrains.eu/controlledTerms/ModelAbstractionLevel"], + "@type": ["https://openminds.om-i.org/types/ModelAbstractionLevel"], } ] ) @@ -89,10 +89,10 @@ def query(self, query, filter=None, space=None, size=100, from_index=0, scope="r return MockKGResponse( [ { - "vocab:name": filter_value, + "https://openminds.om-i.org/props/name": filter_value, "@id": "fake_uuid", "https://core.kg.ebrains.eu/vocab/meta/space": "controlled", - "@type": ["https://openminds.ebrains.eu/controlledTerms/ModelScope"], + "@type": ["https://openminds.om-i.org/types/ModelScope"], } ] ) @@ -100,10 +100,10 @@ def query(self, query, filter=None, space=None, size=100, from_index=0, scope="r return MockKGResponse( [ { - "vocab:name": filter_value, + "https://openminds.om-i.org/props/name": filter_value, "@id": "fake_uuid", "https://core.kg.ebrains.eu/vocab/meta/space": "controlled", - "@type": ["https://openminds.ebrains.eu/controlledTerms/Species"], + "@type": ["https://openminds.om-i.org/types/Species"], } ] ) @@ -111,10 +111,10 @@ def query(self, query, filter=None, space=None, size=100, from_index=0, scope="r return MockKGResponse( [ { - "vocab:name": filter_value, + "https://openminds.om-i.org/props/name": filter_value, "@id": "fake_uuid", "https://core.kg.ebrains.eu/vocab/meta/space": "controlled", - "@type": ["https://openminds.ebrains.eu/controlledTerms/CellType"], + "@type": ["https://openminds.om-i.org/types/CellType"], } ] ) @@ -122,10 +122,10 @@ def query(self, query, filter=None, space=None, size=100, from_index=0, scope="r return MockKGResponse( [ { - "vocab:name": filter_value, + "https://openminds.om-i.org/props/name": filter_value, "@id": "fake_uuid", "https://core.kg.ebrains.eu/vocab/meta/space": "controlled", - "@type": ["https://openminds.ebrains.eu/controlledTerms/UBERONParcellation"], + "@type": ["https://openminds.om-i.org/types/UBERONParcellation"], } ] ) From b25091a51dd481a169b45a07c01c7ca2381c55b1 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 8 Sep 2025 11:18:41 +0200 Subject: [PATCH 09/25] wip --- builder/fairgraph_module_template.py.txt | 12 ++++++++++-- fairgraph/node.py | 10 ++++++---- fairgraph/openminds/controlled_terms/species.py | 14 ++++++++++++-- 3 files changed, 28 insertions(+), 8 deletions(-) diff --git a/builder/fairgraph_module_template.py.txt b/builder/fairgraph_module_template.py.txt index c0c025ba..4b777141 100644 --- a/builder/fairgraph_module_template.py.txt +++ b/builder/fairgraph_module_template.py.txt @@ -5,13 +5,13 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.{{ module_name }} import {{ class_name }} +from openminds.latest.{{ module_name }} import {{ class_name }} as OM{{ class_name }} from fairgraph import {{ base_class }} {{preamble}} -class {{ class_name }}({{base_class}}, {{ class_name }}): +class {{ class_name }}({{base_class}}, OM{{ class_name }}): """ {{ docstring }} """ @@ -49,3 +49,11 @@ class {{ class_name }}({{base_class}}, {{ class_name }}): def __init__(self {%- for arg in constructor_arguments -%}, {{arg}}=None{%- endfor -%}, id=None, data=None, space=None, scope=None): return {{ base_class }}.__init__(self, {{ standard_init_properties }}data=data {%- for arg in constructor_arguments -%}, {{arg}}={{arg}}{%- endfor -%}) {{ additional_methods }} + + +# cast openMINDS instances to their fairgraph subclass +for key, value in OM{{ class_name }}.__dict__.items(): + if isinstance(value, OM{{ class_name }}): + fg_instance = {{ class_name }}.from_jsonld(value.to_jsonld()) + fg_instance._space = {{ class_name }}.default_space + setattr({{ class_name }}, key, fg_instance) diff --git a/fairgraph/node.py b/fairgraph/node.py index a3bbc01b..d90241ed 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -106,10 +106,12 @@ def __setattr__(self, name, value): else: super().__setattr__(name, value) else: - failures = prop.validate(value) - if failures: - errmsg = str(failures) # todo: create a nicer error message - ErrorHandling.handle_violation(self.error_handling, errmsg) + if not isinstance(value, KGQuery): + failures = prop.validate(value) + if failures: + errmsg = str(failures) # todo: create a nicer error message + breakpoint() + ErrorHandling.handle_violation(self.error_handling, errmsg) super().__setattr__(name, value) @classmethod diff --git a/fairgraph/openminds/controlled_terms/species.py b/fairgraph/openminds/controlled_terms/species.py index ec201aa6..890d9076 100644 --- a/fairgraph/openminds/controlled_terms/species.py +++ b/fairgraph/openminds/controlled_terms/species.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Species +from openminds.latest.controlled_terms import Species as OMSpecies from fairgraph import KGObject from openminds import IRI -class Species(KGObject, Species): +class Species(KGObject, OMSpecies): """ Structured information on the species. """ @@ -141,3 +141,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + # @classmethod + # def instances(cls): + # return [value for value in OMSpecies.__dict__.values() if isinstance(value, OMSpecies)] + +for key, value in OMSpecies.__dict__.items(): + if isinstance(value, OMSpecies): + fg_instance = Species.from_jsonld(value.to_jsonld()) + fg_instance._space = "controlled" + setattr(Species, key, fg_instance) From e4df6ff0ae6930c33b5ee5af60f865fc26f3607f Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Tue, 9 Sep 2025 10:54:06 +0200 Subject: [PATCH 10/25] Cast openMINDS terminology instances to their fairgraph subclasses --- builder/fairgraph_module_template.py.txt | 2 ++ .../openminds/chemicals/amount_of_chemical.py | 14 ++++++++++++-- fairgraph/openminds/chemicals/chemical_mixture.py | 14 ++++++++++++-- .../openminds/chemicals/chemical_substance.py | 14 ++++++++++++-- fairgraph/openminds/chemicals/product_source.py | 14 ++++++++++++-- fairgraph/openminds/computation/data_analysis.py | 14 ++++++++++++-- fairgraph/openminds/computation/data_copy.py | 14 ++++++++++++-- fairgraph/openminds/computation/environment.py | 14 ++++++++++++-- .../openminds/computation/generic_computation.py | 14 ++++++++++++-- fairgraph/openminds/computation/hardware_system.py | 14 ++++++++++++-- .../openminds/computation/launch_configuration.py | 14 ++++++++++++-- fairgraph/openminds/computation/local_file.py | 14 ++++++++++++-- .../openminds/computation/model_validation.py | 14 ++++++++++++-- fairgraph/openminds/computation/optimization.py | 14 ++++++++++++-- fairgraph/openminds/computation/simulation.py | 14 ++++++++++++-- fairgraph/openminds/computation/software_agent.py | 14 ++++++++++++-- fairgraph/openminds/computation/validation_test.py | 14 ++++++++++++-- .../computation/validation_test_version.py | 14 ++++++++++++-- fairgraph/openminds/computation/visualization.py | 14 ++++++++++++-- .../openminds/computation/workflow_execution.py | 14 ++++++++++++-- fairgraph/openminds/computation/workflow_recipe.py | 14 ++++++++++++-- .../computation/workflow_recipe_version.py | 14 ++++++++++++-- .../controlled_terms/action_status_type.py | 14 ++++++++++++-- .../openminds/controlled_terms/age_category.py | 14 ++++++++++++-- .../controlled_terms/analysis_technique.py | 14 ++++++++++++-- .../anatomical_axes_orientation.py | 14 ++++++++++++-- .../anatomical_identification_type.py | 14 ++++++++++++-- .../openminds/controlled_terms/anatomical_plane.py | 14 ++++++++++++-- .../controlled_terms/annotation_criteria_type.py | 14 ++++++++++++-- .../openminds/controlled_terms/annotation_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/atlas_type.py | 14 ++++++++++++-- .../controlled_terms/auditory_stimulus_type.py | 14 ++++++++++++-- .../openminds/controlled_terms/biological_order.py | 14 ++++++++++++-- .../controlled_terms/biological_process.py | 14 ++++++++++++-- .../openminds/controlled_terms/biological_sex.py | 14 ++++++++++++-- .../openminds/controlled_terms/breeding_type.py | 14 ++++++++++++-- .../controlled_terms/cell_culture_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/cell_type.py | 14 ++++++++++++-- .../controlled_terms/chemical_mixture_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/colormap.py | 14 ++++++++++++-- .../controlled_terms/contribution_type.py | 14 ++++++++++++-- .../cranial_window_construction_type.py | 14 ++++++++++++-- .../cranial_window_reinforcement_type.py | 14 ++++++++++++-- .../controlled_terms/criteria_quality_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/data_type.py | 14 ++++++++++++-- .../openminds/controlled_terms/device_type.py | 14 ++++++++++++-- .../controlled_terms/difference_measure.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/disease.py | 14 ++++++++++++-- .../openminds/controlled_terms/disease_model.py | 14 ++++++++++++-- .../controlled_terms/educational_level.py | 14 ++++++++++++-- .../controlled_terms/electrical_stimulus_type.py | 14 ++++++++++++-- .../controlled_terms/ethics_assessment.py | 14 ++++++++++++-- .../controlled_terms/experimental_approach.py | 14 ++++++++++++-- .../controlled_terms/file_bundle_grouping.py | 14 ++++++++++++-- .../controlled_terms/file_repository_type.py | 14 ++++++++++++-- .../openminds/controlled_terms/file_usage_role.py | 14 ++++++++++++-- .../controlled_terms/genetic_strain_type.py | 14 ++++++++++++-- .../controlled_terms/gustatory_stimulus_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/handedness.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/language.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/laterality.py | 14 ++++++++++++-- .../controlled_terms/learning_resource_type.py | 14 ++++++++++++-- .../controlled_terms/measured_quantity.py | 14 ++++++++++++-- .../controlled_terms/measured_signal_type.py | 14 ++++++++++++-- .../controlled_terms/meta_data_model_type.py | 14 ++++++++++++-- .../controlled_terms/model_abstraction_level.py | 14 ++++++++++++-- .../openminds/controlled_terms/model_scope.py | 14 ++++++++++++-- .../openminds/controlled_terms/molecular_entity.py | 14 ++++++++++++-- .../controlled_terms/mr_acquisition_type.py | 14 ++++++++++++-- .../controlled_terms/mri_pulse_sequence.py | 14 ++++++++++++-- .../openminds/controlled_terms/mri_weighting.py | 14 ++++++++++++-- .../controlled_terms/olfactory_stimulus_type.py | 14 ++++++++++++-- .../openminds/controlled_terms/operating_device.py | 14 ++++++++++++-- .../openminds/controlled_terms/operating_system.py | 14 ++++++++++++-- .../controlled_terms/optical_stimulus_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/organ.py | 14 ++++++++++++-- .../controlled_terms/organism_substance.py | 14 ++++++++++++-- .../openminds/controlled_terms/organism_system.py | 14 ++++++++++++-- .../controlled_terms/patch_clamp_variation.py | 14 ++++++++++++-- .../openminds/controlled_terms/preparation_type.py | 14 ++++++++++++-- .../controlled_terms/product_accessibility.py | 14 ++++++++++++-- .../controlled_terms/programming_language.py | 14 ++++++++++++-- .../controlled_terms/qualitative_overlap.py | 14 ++++++++++++-- .../controlled_terms/semantic_data_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/service.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/setup_type.py | 14 ++++++++++++-- .../software_application_category.py | 14 ++++++++++++-- .../openminds/controlled_terms/software_feature.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/species.py | 8 ++++---- .../controlled_terms/stimulation_approach.py | 14 ++++++++++++-- .../controlled_terms/stimulation_technique.py | 14 ++++++++++++-- .../controlled_terms/subcellular_entity.py | 14 ++++++++++++-- .../controlled_terms/subject_attribute.py | 14 ++++++++++++-- .../controlled_terms/tactile_stimulus_type.py | 14 ++++++++++++-- fairgraph/openminds/controlled_terms/technique.py | 14 ++++++++++++-- .../openminds/controlled_terms/term_suggestion.py | 14 ++++++++++++-- .../openminds/controlled_terms/terminology.py | 14 ++++++++++++-- .../controlled_terms/tissue_sample_attribute.py | 14 ++++++++++++-- .../controlled_terms/tissue_sample_type.py | 14 ++++++++++++-- .../controlled_terms/type_of_uncertainty.py | 14 ++++++++++++-- .../controlled_terms/uberon_parcellation.py | 14 ++++++++++++-- .../controlled_terms/unit_of_measurement.py | 14 ++++++++++++-- .../controlled_terms/visual_stimulus_type.py | 14 ++++++++++++-- .../openminds/core/actors/account_information.py | 14 ++++++++++++-- fairgraph/openminds/core/actors/affiliation.py | 14 ++++++++++++-- fairgraph/openminds/core/actors/consortium.py | 14 ++++++++++++-- .../openminds/core/actors/contact_information.py | 14 ++++++++++++-- fairgraph/openminds/core/actors/contribution.py | 14 ++++++++++++-- fairgraph/openminds/core/actors/organization.py | 14 ++++++++++++-- fairgraph/openminds/core/actors/person.py | 14 ++++++++++++-- fairgraph/openminds/core/data/content_type.py | 14 ++++++++++++-- .../openminds/core/data/content_type_pattern.py | 14 ++++++++++++-- fairgraph/openminds/core/data/copyright.py | 14 ++++++++++++-- fairgraph/openminds/core/data/file.py | 14 ++++++++++++-- fairgraph/openminds/core/data/file_archive.py | 14 ++++++++++++-- fairgraph/openminds/core/data/file_bundle.py | 14 ++++++++++++-- fairgraph/openminds/core/data/file_path_pattern.py | 14 ++++++++++++-- fairgraph/openminds/core/data/file_repository.py | 14 ++++++++++++-- .../core/data/file_repository_structure.py | 14 ++++++++++++-- fairgraph/openminds/core/data/hash.py | 14 ++++++++++++-- fairgraph/openminds/core/data/license.py | 14 ++++++++++++-- fairgraph/openminds/core/data/measurement.py | 14 ++++++++++++-- fairgraph/openminds/core/data/service_link.py | 14 ++++++++++++-- fairgraph/openminds/core/digital_identifier/doi.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/gridid.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/handle.py | 14 ++++++++++++-- .../digital_identifier/identifiers_dot_org_id.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/isbn.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/issn.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/orcid.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/rorid.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/rrid.py | 14 ++++++++++++-- .../core/digital_identifier/stock_number.py | 14 ++++++++++++-- .../openminds/core/digital_identifier/swhid.py | 14 ++++++++++++-- fairgraph/openminds/core/miscellaneous/comment.py | 14 ++++++++++++-- fairgraph/openminds/core/miscellaneous/funding.py | 14 ++++++++++++-- .../core/miscellaneous/quantitative_value.py | 14 ++++++++++++-- .../core/miscellaneous/quantitative_value_array.py | 14 ++++++++++++-- .../core/miscellaneous/quantitative_value_range.py | 14 ++++++++++++-- .../core/miscellaneous/research_product_group.py | 14 ++++++++++++-- .../openminds/core/miscellaneous/web_resource.py | 14 ++++++++++++-- fairgraph/openminds/core/products/dataset.py | 14 ++++++++++++-- .../openminds/core/products/dataset_version.py | 14 ++++++++++++-- .../openminds/core/products/meta_data_model.py | 14 ++++++++++++-- .../core/products/meta_data_model_version.py | 14 ++++++++++++-- fairgraph/openminds/core/products/model.py | 14 ++++++++++++-- fairgraph/openminds/core/products/model_version.py | 14 ++++++++++++-- fairgraph/openminds/core/products/project.py | 14 ++++++++++++-- fairgraph/openminds/core/products/setup.py | 14 ++++++++++++-- fairgraph/openminds/core/products/software.py | 14 ++++++++++++-- .../openminds/core/products/software_version.py | 14 ++++++++++++-- fairgraph/openminds/core/products/web_service.py | 14 ++++++++++++-- .../openminds/core/products/web_service_version.py | 14 ++++++++++++-- .../openminds/core/research/behavioral_protocol.py | 14 ++++++++++++-- fairgraph/openminds/core/research/configuration.py | 14 ++++++++++++-- .../openminds/core/research/custom_property_set.py | 14 ++++++++++++-- .../openminds/core/research/numerical_property.py | 14 ++++++++++++-- .../openminds/core/research/property_value_list.py | 14 ++++++++++++-- fairgraph/openminds/core/research/protocol.py | 14 ++++++++++++-- .../openminds/core/research/protocol_execution.py | 14 ++++++++++++-- fairgraph/openminds/core/research/strain.py | 14 ++++++++++++-- .../openminds/core/research/string_property.py | 14 ++++++++++++-- fairgraph/openminds/core/research/subject.py | 14 ++++++++++++-- fairgraph/openminds/core/research/subject_group.py | 14 ++++++++++++-- .../openminds/core/research/subject_group_state.py | 14 ++++++++++++-- fairgraph/openminds/core/research/subject_state.py | 14 ++++++++++++-- fairgraph/openminds/core/research/tissue_sample.py | 14 ++++++++++++-- .../core/research/tissue_sample_collection.py | 14 ++++++++++++-- .../research/tissue_sample_collection_state.py | 14 ++++++++++++-- .../openminds/core/research/tissue_sample_state.py | 14 ++++++++++++-- .../openminds/ephys/activity/cell_patching.py | 14 ++++++++++++-- .../ephys/activity/electrode_placement.py | 14 ++++++++++++-- .../openminds/ephys/activity/recording_activity.py | 14 ++++++++++++-- fairgraph/openminds/ephys/device/electrode.py | 14 ++++++++++++-- .../openminds/ephys/device/electrode_array.py | 14 ++++++++++++-- .../ephys/device/electrode_array_usage.py | 14 ++++++++++++-- .../openminds/ephys/device/electrode_usage.py | 14 ++++++++++++-- fairgraph/openminds/ephys/device/pipette.py | 14 ++++++++++++-- fairgraph/openminds/ephys/device/pipette_usage.py | 14 ++++++++++++-- fairgraph/openminds/ephys/entity/channel.py | 14 ++++++++++++-- fairgraph/openminds/ephys/entity/recording.py | 14 ++++++++++++-- fairgraph/openminds/publications/book.py | 14 ++++++++++++-- fairgraph/openminds/publications/chapter.py | 14 ++++++++++++-- .../openminds/publications/learning_resource.py | 14 ++++++++++++-- fairgraph/openminds/publications/live_paper.py | 14 ++++++++++++-- .../publications/live_paper_resource_item.py | 14 ++++++++++++-- .../openminds/publications/live_paper_section.py | 14 ++++++++++++-- .../openminds/publications/live_paper_version.py | 14 ++++++++++++-- fairgraph/openminds/publications/periodical.py | 14 ++++++++++++-- .../openminds/publications/publication_issue.py | 14 ++++++++++++-- .../openminds/publications/publication_volume.py | 14 ++++++++++++-- .../openminds/publications/scholarly_article.py | 14 ++++++++++++-- .../openminds/sands/atlas/atlas_annotation.py | 14 ++++++++++++-- fairgraph/openminds/sands/atlas/brain_atlas.py | 14 ++++++++++++-- .../openminds/sands/atlas/brain_atlas_version.py | 14 ++++++++++++-- .../sands/atlas/common_coordinate_space.py | 14 ++++++++++++-- .../sands/atlas/common_coordinate_space_version.py | 14 ++++++++++++-- .../openminds/sands/atlas/parcellation_entity.py | 14 ++++++++++++-- .../sands/atlas/parcellation_entity_version.py | 14 ++++++++++++-- .../sands/atlas/parcellation_terminology.py | 14 ++++++++++++-- .../atlas/parcellation_terminology_version.py | 14 ++++++++++++-- .../openminds/sands/mathematical_shapes/circle.py | 14 ++++++++++++-- .../openminds/sands/mathematical_shapes/ellipse.py | 14 ++++++++++++-- .../sands/mathematical_shapes/rectangle.py | 14 ++++++++++++-- .../miscellaneous/anatomical_target_position.py | 14 ++++++++++++-- .../sands/miscellaneous/coordinate_point.py | 14 ++++++++++++-- .../qualitative_relation_assessment.py | 14 ++++++++++++-- .../quantitative_relation_assessment.py | 14 ++++++++++++-- .../openminds/sands/miscellaneous/single_color.py | 14 ++++++++++++-- .../sands/miscellaneous/viewer_specification.py | 14 ++++++++++++-- .../sands/non_atlas/custom_anatomical_entity.py | 14 ++++++++++++-- .../openminds/sands/non_atlas/custom_annotation.py | 14 ++++++++++++-- .../sands/non_atlas/custom_coordinate_space.py | 14 ++++++++++++-- .../activity/cranial_window_preparation.py | 14 ++++++++++++-- .../activity/tissue_culture_preparation.py | 14 ++++++++++++-- .../activity/tissue_sample_slicing.py | 14 ++++++++++++-- .../specimen_prep/device/slicing_device.py | 14 ++++++++++++-- .../specimen_prep/device/slicing_device_usage.py | 14 ++++++++++++-- .../stimulation/activity/stimulation_activity.py | 14 ++++++++++++-- .../stimulation/stimulus/ephys_stimulus.py | 14 ++++++++++++-- 220 files changed, 2622 insertions(+), 440 deletions(-) diff --git a/builder/fairgraph_module_template.py.txt b/builder/fairgraph_module_template.py.txt index 4b777141..3717ea4f 100644 --- a/builder/fairgraph_module_template.py.txt +++ b/builder/fairgraph_module_template.py.txt @@ -52,8 +52,10 @@ class {{ class_name }}({{base_class}}, OM{{ class_name }}): # cast openMINDS instances to their fairgraph subclass +{{ class_name }}.set_error_handling(None) for key, value in OM{{ class_name }}.__dict__.items(): if isinstance(value, OM{{ class_name }}): fg_instance = {{ class_name }}.from_jsonld(value.to_jsonld()) fg_instance._space = {{ class_name }}.default_space setattr({{ class_name }}, key, fg_instance) +{{ class_name }}.set_error_handling("log") diff --git a/fairgraph/openminds/chemicals/amount_of_chemical.py b/fairgraph/openminds/chemicals/amount_of_chemical.py index f9c516f1..2b18efb5 100644 --- a/fairgraph/openminds/chemicals/amount_of_chemical.py +++ b/fairgraph/openminds/chemicals/amount_of_chemical.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.chemicals import AmountOfChemical +from openminds.latest.chemicals import AmountOfChemical as OMAmountOfChemical from fairgraph import EmbeddedMetadata -class AmountOfChemical(EmbeddedMetadata, AmountOfChemical): +class AmountOfChemical(EmbeddedMetadata, OMAmountOfChemical): """ Structured information about the amount of a given chemical that was used. """ @@ -20,3 +20,13 @@ class AmountOfChemical(EmbeddedMetadata, AmountOfChemical): def __init__(self, amount=None, chemical_product=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, amount=amount, chemical_product=chemical_product) + + +# cast openMINDS instances to their fairgraph subclass +AmountOfChemical.set_error_handling(None) +for key, value in OMAmountOfChemical.__dict__.items(): + if isinstance(value, OMAmountOfChemical): + fg_instance = AmountOfChemical.from_jsonld(value.to_jsonld()) + fg_instance._space = AmountOfChemical.default_space + setattr(AmountOfChemical, key, fg_instance) +AmountOfChemical.set_error_handling("log") diff --git a/fairgraph/openminds/chemicals/chemical_mixture.py b/fairgraph/openminds/chemicals/chemical_mixture.py index 1ec85633..1b51361c 100644 --- a/fairgraph/openminds/chemicals/chemical_mixture.py +++ b/fairgraph/openminds/chemicals/chemical_mixture.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.chemicals import ChemicalMixture +from openminds.latest.chemicals import ChemicalMixture as OMChemicalMixture from fairgraph import KGObject -class ChemicalMixture(KGObject, ChemicalMixture): +class ChemicalMixture(KGObject, OMChemicalMixture): """ Structured information about a mixture of chemical substances. """ @@ -74,3 +74,13 @@ def __init__( type=type, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +ChemicalMixture.set_error_handling(None) +for key, value in OMChemicalMixture.__dict__.items(): + if isinstance(value, OMChemicalMixture): + fg_instance = ChemicalMixture.from_jsonld(value.to_jsonld()) + fg_instance._space = ChemicalMixture.default_space + setattr(ChemicalMixture, key, fg_instance) +ChemicalMixture.set_error_handling("log") diff --git a/fairgraph/openminds/chemicals/chemical_substance.py b/fairgraph/openminds/chemicals/chemical_substance.py index 36bac286..f1a6d77c 100644 --- a/fairgraph/openminds/chemicals/chemical_substance.py +++ b/fairgraph/openminds/chemicals/chemical_substance.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.chemicals import ChemicalSubstance +from openminds.latest.chemicals import ChemicalSubstance as OMChemicalSubstance from fairgraph import KGObject -class ChemicalSubstance(KGObject, ChemicalSubstance): +class ChemicalSubstance(KGObject, OMChemicalSubstance): """ Structured information about a chemical substance. """ @@ -69,3 +69,13 @@ def __init__( product_source=product_source, purity=purity, ) + + +# cast openMINDS instances to their fairgraph subclass +ChemicalSubstance.set_error_handling(None) +for key, value in OMChemicalSubstance.__dict__.items(): + if isinstance(value, OMChemicalSubstance): + fg_instance = ChemicalSubstance.from_jsonld(value.to_jsonld()) + fg_instance._space = ChemicalSubstance.default_space + setattr(ChemicalSubstance, key, fg_instance) +ChemicalSubstance.set_error_handling("log") diff --git a/fairgraph/openminds/chemicals/product_source.py b/fairgraph/openminds/chemicals/product_source.py index 5e61acba..73f559cb 100644 --- a/fairgraph/openminds/chemicals/product_source.py +++ b/fairgraph/openminds/chemicals/product_source.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.chemicals import ProductSource +from openminds.latest.chemicals import ProductSource as OMProductSource from fairgraph import KGObject -class ProductSource(KGObject, ProductSource): +class ProductSource(KGObject, OMProductSource): """ Structured information about the source of a chemical substance or mixture. """ @@ -55,3 +55,13 @@ def __init__( provider=provider, purity=purity, ) + + +# cast openMINDS instances to their fairgraph subclass +ProductSource.set_error_handling(None) +for key, value in OMProductSource.__dict__.items(): + if isinstance(value, OMProductSource): + fg_instance = ProductSource.from_jsonld(value.to_jsonld()) + fg_instance._space = ProductSource.default_space + setattr(ProductSource, key, fg_instance) +ProductSource.set_error_handling("log") diff --git a/fairgraph/openminds/computation/data_analysis.py b/fairgraph/openminds/computation/data_analysis.py index cf7d4957..3ba130d6 100644 --- a/fairgraph/openminds/computation/data_analysis.py +++ b/fairgraph/openminds/computation/data_analysis.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import DataAnalysis +from openminds.latest.computation import DataAnalysis as OMDataAnalysis from fairgraph import KGObject from datetime import datetime, time -class DataAnalysis(KGObject, DataAnalysis): +class DataAnalysis(KGObject, OMDataAnalysis): """ Structured information on inspecting, cleansing, transforming, and modelling data. """ @@ -102,3 +102,13 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) + + +# cast openMINDS instances to their fairgraph subclass +DataAnalysis.set_error_handling(None) +for key, value in OMDataAnalysis.__dict__.items(): + if isinstance(value, OMDataAnalysis): + fg_instance = DataAnalysis.from_jsonld(value.to_jsonld()) + fg_instance._space = DataAnalysis.default_space + setattr(DataAnalysis, key, fg_instance) +DataAnalysis.set_error_handling("log") diff --git a/fairgraph/openminds/computation/data_copy.py b/fairgraph/openminds/computation/data_copy.py index 655e339b..13313ac0 100644 --- a/fairgraph/openminds/computation/data_copy.py +++ b/fairgraph/openminds/computation/data_copy.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import DataCopy +from openminds.latest.computation import DataCopy as OMDataCopy from fairgraph import KGObject from datetime import datetime, time -class DataCopy(KGObject, DataCopy): +class DataCopy(KGObject, OMDataCopy): """ """ @@ -102,3 +102,13 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) + + +# cast openMINDS instances to their fairgraph subclass +DataCopy.set_error_handling(None) +for key, value in OMDataCopy.__dict__.items(): + if isinstance(value, OMDataCopy): + fg_instance = DataCopy.from_jsonld(value.to_jsonld()) + fg_instance._space = DataCopy.default_space + setattr(DataCopy, key, fg_instance) +DataCopy.set_error_handling("log") diff --git a/fairgraph/openminds/computation/environment.py b/fairgraph/openminds/computation/environment.py index 6777da3d..bd043ae9 100644 --- a/fairgraph/openminds/computation/environment.py +++ b/fairgraph/openminds/computation/environment.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import Environment +from openminds.latest.computation import Environment as OMEnvironment from fairgraph import KGObject -class Environment(KGObject, Environment): +class Environment(KGObject, OMEnvironment): """ Structured information on the computer system or set of systems in which a computation is deployed and executed. """ @@ -64,3 +64,13 @@ def __init__( software=software, used_for=used_for, ) + + +# cast openMINDS instances to their fairgraph subclass +Environment.set_error_handling(None) +for key, value in OMEnvironment.__dict__.items(): + if isinstance(value, OMEnvironment): + fg_instance = Environment.from_jsonld(value.to_jsonld()) + fg_instance._space = Environment.default_space + setattr(Environment, key, fg_instance) +Environment.set_error_handling("log") diff --git a/fairgraph/openminds/computation/generic_computation.py b/fairgraph/openminds/computation/generic_computation.py index e4d461a9..048a442c 100644 --- a/fairgraph/openminds/computation/generic_computation.py +++ b/fairgraph/openminds/computation/generic_computation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import GenericComputation +from openminds.latest.computation import GenericComputation as OMGenericComputation from fairgraph import KGObject from datetime import datetime, time -class GenericComputation(KGObject, GenericComputation): +class GenericComputation(KGObject, OMGenericComputation): """ Structured information about a computation whose type is unknown or unspecified. """ @@ -102,3 +102,13 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) + + +# cast openMINDS instances to their fairgraph subclass +GenericComputation.set_error_handling(None) +for key, value in OMGenericComputation.__dict__.items(): + if isinstance(value, OMGenericComputation): + fg_instance = GenericComputation.from_jsonld(value.to_jsonld()) + fg_instance._space = GenericComputation.default_space + setattr(GenericComputation, key, fg_instance) +GenericComputation.set_error_handling("log") diff --git a/fairgraph/openminds/computation/hardware_system.py b/fairgraph/openminds/computation/hardware_system.py index cf5f5f51..e62f240a 100644 --- a/fairgraph/openminds/computation/hardware_system.py +++ b/fairgraph/openminds/computation/hardware_system.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import HardwareSystem +from openminds.latest.computation import HardwareSystem as OMHardwareSystem from fairgraph import KGObject -class HardwareSystem(KGObject, HardwareSystem): +class HardwareSystem(KGObject, OMHardwareSystem): """ Structured information about computing hardware. """ @@ -51,3 +51,13 @@ def __init__( used_by=used_by, version_identifier=version_identifier, ) + + +# cast openMINDS instances to their fairgraph subclass +HardwareSystem.set_error_handling(None) +for key, value in OMHardwareSystem.__dict__.items(): + if isinstance(value, OMHardwareSystem): + fg_instance = HardwareSystem.from_jsonld(value.to_jsonld()) + fg_instance._space = HardwareSystem.default_space + setattr(HardwareSystem, key, fg_instance) +HardwareSystem.set_error_handling("log") diff --git a/fairgraph/openminds/computation/launch_configuration.py b/fairgraph/openminds/computation/launch_configuration.py index d0d378c3..3e5f3ca4 100644 --- a/fairgraph/openminds/computation/launch_configuration.py +++ b/fairgraph/openminds/computation/launch_configuration.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import LaunchConfiguration +from openminds.latest.computation import LaunchConfiguration as OMLaunchConfiguration from fairgraph import KGObject -class LaunchConfiguration(KGObject, LaunchConfiguration): +class LaunchConfiguration(KGObject, OMLaunchConfiguration): """ Structured information about the launch of a computational process. """ @@ -63,3 +63,13 @@ def __init__( executable=executable, is_launch_configuration_of=is_launch_configuration_of, ) + + +# cast openMINDS instances to their fairgraph subclass +LaunchConfiguration.set_error_handling(None) +for key, value in OMLaunchConfiguration.__dict__.items(): + if isinstance(value, OMLaunchConfiguration): + fg_instance = LaunchConfiguration.from_jsonld(value.to_jsonld()) + fg_instance._space = LaunchConfiguration.default_space + setattr(LaunchConfiguration, key, fg_instance) +LaunchConfiguration.set_error_handling("log") diff --git a/fairgraph/openminds/computation/local_file.py b/fairgraph/openminds/computation/local_file.py index 0f988746..eefe436b 100644 --- a/fairgraph/openminds/computation/local_file.py +++ b/fairgraph/openminds/computation/local_file.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import LocalFile +from openminds.latest.computation import LocalFile as OMLocalFile from fairgraph import KGObject -class LocalFile(KGObject, LocalFile): +class LocalFile(KGObject, OMLocalFile): """ Structured information about a file that is not accessible via a URL. """ @@ -81,3 +81,13 @@ def __init__( special_usage_role=special_usage_role, storage_size=storage_size, ) + + +# cast openMINDS instances to their fairgraph subclass +LocalFile.set_error_handling(None) +for key, value in OMLocalFile.__dict__.items(): + if isinstance(value, OMLocalFile): + fg_instance = LocalFile.from_jsonld(value.to_jsonld()) + fg_instance._space = LocalFile.default_space + setattr(LocalFile, key, fg_instance) +LocalFile.set_error_handling("log") diff --git a/fairgraph/openminds/computation/model_validation.py b/fairgraph/openminds/computation/model_validation.py index 8487f3df..96dda549 100644 --- a/fairgraph/openminds/computation/model_validation.py +++ b/fairgraph/openminds/computation/model_validation.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import ModelValidation +from openminds.latest.computation import ModelValidation as OMModelValidation from fairgraph import KGObject @@ -13,7 +13,7 @@ from numbers import Real -class ModelValidation(KGObject, ModelValidation): +class ModelValidation(KGObject, OMModelValidation): """ Structured information about a process of validating a computational model. """ @@ -105,3 +105,13 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) + + +# cast openMINDS instances to their fairgraph subclass +ModelValidation.set_error_handling(None) +for key, value in OMModelValidation.__dict__.items(): + if isinstance(value, OMModelValidation): + fg_instance = ModelValidation.from_jsonld(value.to_jsonld()) + fg_instance._space = ModelValidation.default_space + setattr(ModelValidation, key, fg_instance) +ModelValidation.set_error_handling("log") diff --git a/fairgraph/openminds/computation/optimization.py b/fairgraph/openminds/computation/optimization.py index 7c8a2fc1..11cad8ad 100644 --- a/fairgraph/openminds/computation/optimization.py +++ b/fairgraph/openminds/computation/optimization.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import Optimization +from openminds.latest.computation import Optimization as OMOptimization from fairgraph import KGObject from datetime import datetime, time -class Optimization(KGObject, Optimization): +class Optimization(KGObject, OMOptimization): """ Structured information about a process of optimizing a model or a piece of code. """ @@ -102,3 +102,13 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) + + +# cast openMINDS instances to their fairgraph subclass +Optimization.set_error_handling(None) +for key, value in OMOptimization.__dict__.items(): + if isinstance(value, OMOptimization): + fg_instance = Optimization.from_jsonld(value.to_jsonld()) + fg_instance._space = Optimization.default_space + setattr(Optimization, key, fg_instance) +Optimization.set_error_handling("log") diff --git a/fairgraph/openminds/computation/simulation.py b/fairgraph/openminds/computation/simulation.py index b974fd37..a49f4dae 100644 --- a/fairgraph/openminds/computation/simulation.py +++ b/fairgraph/openminds/computation/simulation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import Simulation +from openminds.latest.computation import Simulation as OMSimulation from fairgraph import KGObject from datetime import datetime, time -class Simulation(KGObject, Simulation): +class Simulation(KGObject, OMSimulation): """ Structured information about a process of running simulations of a computational model. """ @@ -102,3 +102,13 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) + + +# cast openMINDS instances to their fairgraph subclass +Simulation.set_error_handling(None) +for key, value in OMSimulation.__dict__.items(): + if isinstance(value, OMSimulation): + fg_instance = Simulation.from_jsonld(value.to_jsonld()) + fg_instance._space = Simulation.default_space + setattr(Simulation, key, fg_instance) +Simulation.set_error_handling("log") diff --git a/fairgraph/openminds/computation/software_agent.py b/fairgraph/openminds/computation/software_agent.py index 61e782bb..4f980100 100644 --- a/fairgraph/openminds/computation/software_agent.py +++ b/fairgraph/openminds/computation/software_agent.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import SoftwareAgent +from openminds.latest.computation import SoftwareAgent as OMSoftwareAgent from fairgraph import KGObject -class SoftwareAgent(KGObject, SoftwareAgent): +class SoftwareAgent(KGObject, OMSoftwareAgent): """ Structured information about a piece of software or web service that can perform a task autonomously. """ @@ -79,3 +79,13 @@ def __init__( software=software, started=started, ) + + +# cast openMINDS instances to their fairgraph subclass +SoftwareAgent.set_error_handling(None) +for key, value in OMSoftwareAgent.__dict__.items(): + if isinstance(value, OMSoftwareAgent): + fg_instance = SoftwareAgent.from_jsonld(value.to_jsonld()) + fg_instance._space = SoftwareAgent.default_space + setattr(SoftwareAgent, key, fg_instance) +SoftwareAgent.set_error_handling("log") diff --git a/fairgraph/openminds/computation/validation_test.py b/fairgraph/openminds/computation/validation_test.py index 48606dbf..92afb712 100644 --- a/fairgraph/openminds/computation/validation_test.py +++ b/fairgraph/openminds/computation/validation_test.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import ValidationTest +from openminds.latest.computation import ValidationTest as OMValidationTest from fairgraph import KGObject from openminds import IRI -class ValidationTest(KGObject, ValidationTest): +class ValidationTest(KGObject, OMValidationTest): """ Structured information about the definition of a process for validating a computational model. """ @@ -101,3 +101,13 @@ def __init__( study_targets=study_targets, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +ValidationTest.set_error_handling(None) +for key, value in OMValidationTest.__dict__.items(): + if isinstance(value, OMValidationTest): + fg_instance = ValidationTest.from_jsonld(value.to_jsonld()) + fg_instance._space = ValidationTest.default_space + setattr(ValidationTest, key, fg_instance) +ValidationTest.set_error_handling("log") diff --git a/fairgraph/openminds/computation/validation_test_version.py b/fairgraph/openminds/computation/validation_test_version.py index 05ba3683..2219b059 100644 --- a/fairgraph/openminds/computation/validation_test_version.py +++ b/fairgraph/openminds/computation/validation_test_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import ValidationTestVersion +from openminds.latest.computation import ValidationTestVersion as OMValidationTestVersion from fairgraph import KGObject from fairgraph.errors import ResolutionFailure @@ -14,7 +14,7 @@ from openminds import IRI -class ValidationTestVersion(KGObject, ValidationTestVersion): +class ValidationTestVersion(KGObject, OMValidationTestVersion): """ Structured information about a specific implementation of a validation test. """ @@ -167,3 +167,13 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] + + +# cast openMINDS instances to their fairgraph subclass +ValidationTestVersion.set_error_handling(None) +for key, value in OMValidationTestVersion.__dict__.items(): + if isinstance(value, OMValidationTestVersion): + fg_instance = ValidationTestVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = ValidationTestVersion.default_space + setattr(ValidationTestVersion, key, fg_instance) +ValidationTestVersion.set_error_handling("log") diff --git a/fairgraph/openminds/computation/visualization.py b/fairgraph/openminds/computation/visualization.py index 3be6aa9d..7ab6565a 100644 --- a/fairgraph/openminds/computation/visualization.py +++ b/fairgraph/openminds/computation/visualization.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import Visualization +from openminds.latest.computation import Visualization as OMVisualization from fairgraph import KGObject from datetime import datetime, time -class Visualization(KGObject, Visualization): +class Visualization(KGObject, OMVisualization): """ Structured information about a process of visualizing a computational model, a computational process, or a dataset. """ @@ -102,3 +102,13 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) + + +# cast openMINDS instances to their fairgraph subclass +Visualization.set_error_handling(None) +for key, value in OMVisualization.__dict__.items(): + if isinstance(value, OMVisualization): + fg_instance = Visualization.from_jsonld(value.to_jsonld()) + fg_instance._space = Visualization.default_space + setattr(Visualization, key, fg_instance) +Visualization.set_error_handling("log") diff --git a/fairgraph/openminds/computation/workflow_execution.py b/fairgraph/openminds/computation/workflow_execution.py index 5488a431..74e53c66 100644 --- a/fairgraph/openminds/computation/workflow_execution.py +++ b/fairgraph/openminds/computation/workflow_execution.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import WorkflowExecution +from openminds.latest.computation import WorkflowExecution as OMWorkflowExecution from fairgraph import KGObject -class WorkflowExecution(KGObject, WorkflowExecution): +class WorkflowExecution(KGObject, OMWorkflowExecution): """ Structured information about an execution of a computational workflow. """ @@ -34,3 +34,13 @@ def __init__( stages=stages, started_by=started_by, ) + + +# cast openMINDS instances to their fairgraph subclass +WorkflowExecution.set_error_handling(None) +for key, value in OMWorkflowExecution.__dict__.items(): + if isinstance(value, OMWorkflowExecution): + fg_instance = WorkflowExecution.from_jsonld(value.to_jsonld()) + fg_instance._space = WorkflowExecution.default_space + setattr(WorkflowExecution, key, fg_instance) +WorkflowExecution.set_error_handling("log") diff --git a/fairgraph/openminds/computation/workflow_recipe.py b/fairgraph/openminds/computation/workflow_recipe.py index 937780e1..497b24e4 100644 --- a/fairgraph/openminds/computation/workflow_recipe.py +++ b/fairgraph/openminds/computation/workflow_recipe.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import WorkflowRecipe +from openminds.latest.computation import WorkflowRecipe as OMWorkflowRecipe from fairgraph import KGObject from openminds import IRI -class WorkflowRecipe(KGObject, WorkflowRecipe): +class WorkflowRecipe(KGObject, OMWorkflowRecipe): """ Structured information about the description of a prospective workflow. """ @@ -93,3 +93,13 @@ def __init__( short_name=short_name, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +WorkflowRecipe.set_error_handling(None) +for key, value in OMWorkflowRecipe.__dict__.items(): + if isinstance(value, OMWorkflowRecipe): + fg_instance = WorkflowRecipe.from_jsonld(value.to_jsonld()) + fg_instance._space = WorkflowRecipe.default_space + setattr(WorkflowRecipe, key, fg_instance) +WorkflowRecipe.set_error_handling("log") diff --git a/fairgraph/openminds/computation/workflow_recipe_version.py b/fairgraph/openminds/computation/workflow_recipe_version.py index 6d2fbed4..852f67e9 100644 --- a/fairgraph/openminds/computation/workflow_recipe_version.py +++ b/fairgraph/openminds/computation/workflow_recipe_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.computation import WorkflowRecipeVersion +from openminds.latest.computation import WorkflowRecipeVersion as OMWorkflowRecipeVersion from fairgraph import KGObject @@ -13,7 +13,7 @@ from openminds import IRI -class WorkflowRecipeVersion(KGObject, WorkflowRecipeVersion): +class WorkflowRecipeVersion(KGObject, OMWorkflowRecipeVersion): """ Structured information about a specific implemented version of a workflow recipe. """ @@ -163,3 +163,13 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) + + +# cast openMINDS instances to their fairgraph subclass +WorkflowRecipeVersion.set_error_handling(None) +for key, value in OMWorkflowRecipeVersion.__dict__.items(): + if isinstance(value, OMWorkflowRecipeVersion): + fg_instance = WorkflowRecipeVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = WorkflowRecipeVersion.default_space + setattr(WorkflowRecipeVersion, key, fg_instance) +WorkflowRecipeVersion.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/action_status_type.py b/fairgraph/openminds/controlled_terms/action_status_type.py index 74341b88..a010d55d 100644 --- a/fairgraph/openminds/controlled_terms/action_status_type.py +++ b/fairgraph/openminds/controlled_terms/action_status_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ActionStatusType +from openminds.latest.controlled_terms import ActionStatusType as OMActionStatusType from fairgraph import KGObject from openminds import IRI -class ActionStatusType(KGObject, ActionStatusType): +class ActionStatusType(KGObject, OMActionStatusType): """ Structured information about the status of an action. """ @@ -95,3 +95,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ActionStatusType.set_error_handling(None) +for key, value in OMActionStatusType.__dict__.items(): + if isinstance(value, OMActionStatusType): + fg_instance = ActionStatusType.from_jsonld(value.to_jsonld()) + fg_instance._space = ActionStatusType.default_space + setattr(ActionStatusType, key, fg_instance) +ActionStatusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/age_category.py b/fairgraph/openminds/controlled_terms/age_category.py index 2003c2d4..6d348775 100644 --- a/fairgraph/openminds/controlled_terms/age_category.py +++ b/fairgraph/openminds/controlled_terms/age_category.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AgeCategory +from openminds.latest.controlled_terms import AgeCategory as OMAgeCategory from fairgraph import KGObject from openminds import IRI -class AgeCategory(KGObject, AgeCategory): +class AgeCategory(KGObject, OMAgeCategory): """ Structured information on the life cycle (semantic term) of a specific age group. """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +AgeCategory.set_error_handling(None) +for key, value in OMAgeCategory.__dict__.items(): + if isinstance(value, OMAgeCategory): + fg_instance = AgeCategory.from_jsonld(value.to_jsonld()) + fg_instance._space = AgeCategory.default_space + setattr(AgeCategory, key, fg_instance) +AgeCategory.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/analysis_technique.py b/fairgraph/openminds/controlled_terms/analysis_technique.py index 8b2d3c57..3636e029 100644 --- a/fairgraph/openminds/controlled_terms/analysis_technique.py +++ b/fairgraph/openminds/controlled_terms/analysis_technique.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AnalysisTechnique +from openminds.latest.controlled_terms import AnalysisTechnique as OMAnalysisTechnique from fairgraph import KGObject from openminds import IRI -class AnalysisTechnique(KGObject, AnalysisTechnique): +class AnalysisTechnique(KGObject, OMAnalysisTechnique): """ """ @@ -106,3 +106,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +AnalysisTechnique.set_error_handling(None) +for key, value in OMAnalysisTechnique.__dict__.items(): + if isinstance(value, OMAnalysisTechnique): + fg_instance = AnalysisTechnique.from_jsonld(value.to_jsonld()) + fg_instance._space = AnalysisTechnique.default_space + setattr(AnalysisTechnique, key, fg_instance) +AnalysisTechnique.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py index e94c1ab1..7f813d19 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py +++ b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AnatomicalAxesOrientation +from openminds.latest.controlled_terms import AnatomicalAxesOrientation as OMAnatomicalAxesOrientation from fairgraph import KGObject from openminds import IRI -class AnatomicalAxesOrientation(KGObject, AnatomicalAxesOrientation): +class AnatomicalAxesOrientation(KGObject, OMAnatomicalAxesOrientation): """ Structured information on the anatomical directions of the X, Y, and Z axis. """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +AnatomicalAxesOrientation.set_error_handling(None) +for key, value in OMAnatomicalAxesOrientation.__dict__.items(): + if isinstance(value, OMAnatomicalAxesOrientation): + fg_instance = AnatomicalAxesOrientation.from_jsonld(value.to_jsonld()) + fg_instance._space = AnatomicalAxesOrientation.default_space + setattr(AnatomicalAxesOrientation, key, fg_instance) +AnatomicalAxesOrientation.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py index 63ad5b28..9e61fcd2 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py +++ b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AnatomicalIdentificationType +from openminds.latest.controlled_terms import AnatomicalIdentificationType as OMAnatomicalIdentificationType from fairgraph import KGObject from openminds import IRI -class AnatomicalIdentificationType(KGObject, AnatomicalIdentificationType): +class AnatomicalIdentificationType(KGObject, OMAnatomicalIdentificationType): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +AnatomicalIdentificationType.set_error_handling(None) +for key, value in OMAnatomicalIdentificationType.__dict__.items(): + if isinstance(value, OMAnatomicalIdentificationType): + fg_instance = AnatomicalIdentificationType.from_jsonld(value.to_jsonld()) + fg_instance._space = AnatomicalIdentificationType.default_space + setattr(AnatomicalIdentificationType, key, fg_instance) +AnatomicalIdentificationType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/anatomical_plane.py b/fairgraph/openminds/controlled_terms/anatomical_plane.py index 6e323dc5..ea5adad1 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_plane.py +++ b/fairgraph/openminds/controlled_terms/anatomical_plane.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AnatomicalPlane +from openminds.latest.controlled_terms import AnatomicalPlane as OMAnatomicalPlane from fairgraph import KGObject from openminds import IRI -class AnatomicalPlane(KGObject, AnatomicalPlane): +class AnatomicalPlane(KGObject, OMAnatomicalPlane): """ """ @@ -87,3 +87,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +AnatomicalPlane.set_error_handling(None) +for key, value in OMAnatomicalPlane.__dict__.items(): + if isinstance(value, OMAnatomicalPlane): + fg_instance = AnatomicalPlane.from_jsonld(value.to_jsonld()) + fg_instance._space = AnatomicalPlane.default_space + setattr(AnatomicalPlane, key, fg_instance) +AnatomicalPlane.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py index ab51999d..87bc8f20 100644 --- a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AnnotationCriteriaType +from openminds.latest.controlled_terms import AnnotationCriteriaType as OMAnnotationCriteriaType from fairgraph import KGObject from openminds import IRI -class AnnotationCriteriaType(KGObject, AnnotationCriteriaType): +class AnnotationCriteriaType(KGObject, OMAnnotationCriteriaType): """ """ @@ -87,3 +87,13 @@ def __init__( synonyms=synonyms, used_by_annotation=used_by_annotation, ) + + +# cast openMINDS instances to their fairgraph subclass +AnnotationCriteriaType.set_error_handling(None) +for key, value in OMAnnotationCriteriaType.__dict__.items(): + if isinstance(value, OMAnnotationCriteriaType): + fg_instance = AnnotationCriteriaType.from_jsonld(value.to_jsonld()) + fg_instance._space = AnnotationCriteriaType.default_space + setattr(AnnotationCriteriaType, key, fg_instance) +AnnotationCriteriaType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/annotation_type.py b/fairgraph/openminds/controlled_terms/annotation_type.py index bba5d5a5..aadcd822 100644 --- a/fairgraph/openminds/controlled_terms/annotation_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AnnotationType +from openminds.latest.controlled_terms import AnnotationType as OMAnnotationType from fairgraph import KGObject from openminds import IRI -class AnnotationType(KGObject, AnnotationType): +class AnnotationType(KGObject, OMAnnotationType): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +AnnotationType.set_error_handling(None) +for key, value in OMAnnotationType.__dict__.items(): + if isinstance(value, OMAnnotationType): + fg_instance = AnnotationType.from_jsonld(value.to_jsonld()) + fg_instance._space = AnnotationType.default_space + setattr(AnnotationType, key, fg_instance) +AnnotationType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/atlas_type.py b/fairgraph/openminds/controlled_terms/atlas_type.py index 050db47a..a1b8af57 100644 --- a/fairgraph/openminds/controlled_terms/atlas_type.py +++ b/fairgraph/openminds/controlled_terms/atlas_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AtlasType +from openminds.latest.controlled_terms import AtlasType as OMAtlasType from fairgraph import KGObject from openminds import IRI -class AtlasType(KGObject, AtlasType): +class AtlasType(KGObject, OMAtlasType): """ """ @@ -86,3 +86,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +AtlasType.set_error_handling(None) +for key, value in OMAtlasType.__dict__.items(): + if isinstance(value, OMAtlasType): + fg_instance = AtlasType.from_jsonld(value.to_jsonld()) + fg_instance._space = AtlasType.default_space + setattr(AtlasType, key, fg_instance) +AtlasType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py index 03600ecc..49cac42d 100644 --- a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import AuditoryStimulusType +from openminds.latest.controlled_terms import AuditoryStimulusType as OMAuditoryStimulusType from fairgraph import KGObject from openminds import IRI -class AuditoryStimulusType(KGObject, AuditoryStimulusType): +class AuditoryStimulusType(KGObject, OMAuditoryStimulusType): """ """ @@ -125,3 +125,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +AuditoryStimulusType.set_error_handling(None) +for key, value in OMAuditoryStimulusType.__dict__.items(): + if isinstance(value, OMAuditoryStimulusType): + fg_instance = AuditoryStimulusType.from_jsonld(value.to_jsonld()) + fg_instance._space = AuditoryStimulusType.default_space + setattr(AuditoryStimulusType, key, fg_instance) +AuditoryStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/biological_order.py b/fairgraph/openminds/controlled_terms/biological_order.py index 4449b14c..6d0c9298 100644 --- a/fairgraph/openminds/controlled_terms/biological_order.py +++ b/fairgraph/openminds/controlled_terms/biological_order.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import BiologicalOrder +from openminds.latest.controlled_terms import BiologicalOrder as OMBiologicalOrder from fairgraph import KGObject from openminds import IRI -class BiologicalOrder(KGObject, BiologicalOrder): +class BiologicalOrder(KGObject, OMBiologicalOrder): """ """ @@ -115,3 +115,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +BiologicalOrder.set_error_handling(None) +for key, value in OMBiologicalOrder.__dict__.items(): + if isinstance(value, OMBiologicalOrder): + fg_instance = BiologicalOrder.from_jsonld(value.to_jsonld()) + fg_instance._space = BiologicalOrder.default_space + setattr(BiologicalOrder, key, fg_instance) +BiologicalOrder.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/biological_process.py b/fairgraph/openminds/controlled_terms/biological_process.py index e529723b..b10b959c 100644 --- a/fairgraph/openminds/controlled_terms/biological_process.py +++ b/fairgraph/openminds/controlled_terms/biological_process.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import BiologicalProcess +from openminds.latest.controlled_terms import BiologicalProcess as OMBiologicalProcess from fairgraph import KGObject from openminds import IRI -class BiologicalProcess(KGObject, BiologicalProcess): +class BiologicalProcess(KGObject, OMBiologicalProcess): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +BiologicalProcess.set_error_handling(None) +for key, value in OMBiologicalProcess.__dict__.items(): + if isinstance(value, OMBiologicalProcess): + fg_instance = BiologicalProcess.from_jsonld(value.to_jsonld()) + fg_instance._space = BiologicalProcess.default_space + setattr(BiologicalProcess, key, fg_instance) +BiologicalProcess.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/biological_sex.py b/fairgraph/openminds/controlled_terms/biological_sex.py index 0bce5b3d..441cf625 100644 --- a/fairgraph/openminds/controlled_terms/biological_sex.py +++ b/fairgraph/openminds/controlled_terms/biological_sex.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import BiologicalSex +from openminds.latest.controlled_terms import BiologicalSex as OMBiologicalSex from fairgraph import KGObject from openminds import IRI -class BiologicalSex(KGObject, BiologicalSex): +class BiologicalSex(KGObject, OMBiologicalSex): """ Structured information on the biological sex of a subject. """ @@ -130,3 +130,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +BiologicalSex.set_error_handling(None) +for key, value in OMBiologicalSex.__dict__.items(): + if isinstance(value, OMBiologicalSex): + fg_instance = BiologicalSex.from_jsonld(value.to_jsonld()) + fg_instance._space = BiologicalSex.default_space + setattr(BiologicalSex, key, fg_instance) +BiologicalSex.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/breeding_type.py b/fairgraph/openminds/controlled_terms/breeding_type.py index 6885631a..09c1f674 100644 --- a/fairgraph/openminds/controlled_terms/breeding_type.py +++ b/fairgraph/openminds/controlled_terms/breeding_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import BreedingType +from openminds.latest.controlled_terms import BreedingType as OMBreedingType from fairgraph import KGObject from openminds import IRI -class BreedingType(KGObject, BreedingType): +class BreedingType(KGObject, OMBreedingType): """ """ @@ -125,3 +125,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +BreedingType.set_error_handling(None) +for key, value in OMBreedingType.__dict__.items(): + if isinstance(value, OMBreedingType): + fg_instance = BreedingType.from_jsonld(value.to_jsonld()) + fg_instance._space = BreedingType.default_space + setattr(BreedingType, key, fg_instance) +BreedingType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cell_culture_type.py b/fairgraph/openminds/controlled_terms/cell_culture_type.py index 9e471178..65439d30 100644 --- a/fairgraph/openminds/controlled_terms/cell_culture_type.py +++ b/fairgraph/openminds/controlled_terms/cell_culture_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import CellCultureType +from openminds.latest.controlled_terms import CellCultureType as OMCellCultureType from fairgraph import KGObject from openminds import IRI -class CellCultureType(KGObject, CellCultureType): +class CellCultureType(KGObject, OMCellCultureType): """ """ @@ -115,3 +115,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +CellCultureType.set_error_handling(None) +for key, value in OMCellCultureType.__dict__.items(): + if isinstance(value, OMCellCultureType): + fg_instance = CellCultureType.from_jsonld(value.to_jsonld()) + fg_instance._space = CellCultureType.default_space + setattr(CellCultureType, key, fg_instance) +CellCultureType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cell_type.py b/fairgraph/openminds/controlled_terms/cell_type.py index d7448477..5bc6b89c 100644 --- a/fairgraph/openminds/controlled_terms/cell_type.py +++ b/fairgraph/openminds/controlled_terms/cell_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import CellType +from openminds.latest.controlled_terms import CellType as OMCellType from fairgraph import KGObject from openminds import IRI -class CellType(KGObject, CellType): +class CellType(KGObject, OMCellType): """ """ @@ -149,3 +149,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +CellType.set_error_handling(None) +for key, value in OMCellType.__dict__.items(): + if isinstance(value, OMCellType): + fg_instance = CellType.from_jsonld(value.to_jsonld()) + fg_instance._space = CellType.default_space + setattr(CellType, key, fg_instance) +CellType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py index a3f0b0f3..b4c8544c 100644 --- a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py +++ b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ChemicalMixtureType +from openminds.latest.controlled_terms import ChemicalMixtureType as OMChemicalMixtureType from fairgraph import KGObject from openminds import IRI -class ChemicalMixtureType(KGObject, ChemicalMixtureType): +class ChemicalMixtureType(KGObject, OMChemicalMixtureType): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ChemicalMixtureType.set_error_handling(None) +for key, value in OMChemicalMixtureType.__dict__.items(): + if isinstance(value, OMChemicalMixtureType): + fg_instance = ChemicalMixtureType.from_jsonld(value.to_jsonld()) + fg_instance._space = ChemicalMixtureType.default_space + setattr(ChemicalMixtureType, key, fg_instance) +ChemicalMixtureType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/colormap.py b/fairgraph/openminds/controlled_terms/colormap.py index e48f5ed3..d2b016a8 100644 --- a/fairgraph/openminds/controlled_terms/colormap.py +++ b/fairgraph/openminds/controlled_terms/colormap.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Colormap +from openminds.latest.controlled_terms import Colormap as OMColormap from fairgraph import KGObject from openminds import IRI -class Colormap(KGObject, Colormap): +class Colormap(KGObject, OMColormap): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Colormap.set_error_handling(None) +for key, value in OMColormap.__dict__.items(): + if isinstance(value, OMColormap): + fg_instance = Colormap.from_jsonld(value.to_jsonld()) + fg_instance._space = Colormap.default_space + setattr(Colormap, key, fg_instance) +Colormap.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/contribution_type.py b/fairgraph/openminds/controlled_terms/contribution_type.py index 7a39edaf..0a86a1d7 100644 --- a/fairgraph/openminds/controlled_terms/contribution_type.py +++ b/fairgraph/openminds/controlled_terms/contribution_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ContributionType +from openminds.latest.controlled_terms import ContributionType as OMContributionType from fairgraph import KGObject from openminds import IRI -class ContributionType(KGObject, ContributionType): +class ContributionType(KGObject, OMContributionType): """ Structured information on the type of contribution a person or organization performed. """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ContributionType.set_error_handling(None) +for key, value in OMContributionType.__dict__.items(): + if isinstance(value, OMContributionType): + fg_instance = ContributionType.from_jsonld(value.to_jsonld()) + fg_instance._space = ContributionType.default_space + setattr(ContributionType, key, fg_instance) +ContributionType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py index 73a16e8c..8a49118c 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import CranialWindowConstructionType +from openminds.latest.controlled_terms import CranialWindowConstructionType as OMCranialWindowConstructionType from fairgraph import KGObject from openminds import IRI -class CranialWindowConstructionType(KGObject, CranialWindowConstructionType): +class CranialWindowConstructionType(KGObject, OMCranialWindowConstructionType): """ """ @@ -87,3 +87,13 @@ def __init__( synonyms=synonyms, used_for=used_for, ) + + +# cast openMINDS instances to their fairgraph subclass +CranialWindowConstructionType.set_error_handling(None) +for key, value in OMCranialWindowConstructionType.__dict__.items(): + if isinstance(value, OMCranialWindowConstructionType): + fg_instance = CranialWindowConstructionType.from_jsonld(value.to_jsonld()) + fg_instance._space = CranialWindowConstructionType.default_space + setattr(CranialWindowConstructionType, key, fg_instance) +CranialWindowConstructionType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py index f32c26d7..1d9a8bab 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import CranialWindowReinforcementType +from openminds.latest.controlled_terms import CranialWindowReinforcementType as OMCranialWindowReinforcementType from fairgraph import KGObject from openminds import IRI -class CranialWindowReinforcementType(KGObject, CranialWindowReinforcementType): +class CranialWindowReinforcementType(KGObject, OMCranialWindowReinforcementType): """ """ @@ -87,3 +87,13 @@ def __init__( synonyms=synonyms, used_for=used_for, ) + + +# cast openMINDS instances to their fairgraph subclass +CranialWindowReinforcementType.set_error_handling(None) +for key, value in OMCranialWindowReinforcementType.__dict__.items(): + if isinstance(value, OMCranialWindowReinforcementType): + fg_instance = CranialWindowReinforcementType.from_jsonld(value.to_jsonld()) + fg_instance._space = CranialWindowReinforcementType.default_space + setattr(CranialWindowReinforcementType, key, fg_instance) +CranialWindowReinforcementType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/criteria_quality_type.py b/fairgraph/openminds/controlled_terms/criteria_quality_type.py index a751d594..1ba335be 100644 --- a/fairgraph/openminds/controlled_terms/criteria_quality_type.py +++ b/fairgraph/openminds/controlled_terms/criteria_quality_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import CriteriaQualityType +from openminds.latest.controlled_terms import CriteriaQualityType as OMCriteriaQualityType from fairgraph import KGObject from openminds import IRI -class CriteriaQualityType(KGObject, CriteriaQualityType): +class CriteriaQualityType(KGObject, OMCriteriaQualityType): """ Structured information on the quality type of the defined criteria for a measurement. """ @@ -87,3 +87,13 @@ def __init__( synonyms=synonyms, used_by_annotation=used_by_annotation, ) + + +# cast openMINDS instances to their fairgraph subclass +CriteriaQualityType.set_error_handling(None) +for key, value in OMCriteriaQualityType.__dict__.items(): + if isinstance(value, OMCriteriaQualityType): + fg_instance = CriteriaQualityType.from_jsonld(value.to_jsonld()) + fg_instance._space = CriteriaQualityType.default_space + setattr(CriteriaQualityType, key, fg_instance) +CriteriaQualityType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/data_type.py b/fairgraph/openminds/controlled_terms/data_type.py index 1497fbdf..0aea9114 100644 --- a/fairgraph/openminds/controlled_terms/data_type.py +++ b/fairgraph/openminds/controlled_terms/data_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import DataType +from openminds.latest.controlled_terms import DataType as OMDataType from fairgraph import KGObject from openminds import IRI -class DataType(KGObject, DataType): +class DataType(KGObject, OMDataType): """ """ @@ -91,3 +91,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +DataType.set_error_handling(None) +for key, value in OMDataType.__dict__.items(): + if isinstance(value, OMDataType): + fg_instance = DataType.from_jsonld(value.to_jsonld()) + fg_instance._space = DataType.default_space + setattr(DataType, key, fg_instance) +DataType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/device_type.py b/fairgraph/openminds/controlled_terms/device_type.py index 6f88a66c..bc8ba967 100644 --- a/fairgraph/openminds/controlled_terms/device_type.py +++ b/fairgraph/openminds/controlled_terms/device_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import DeviceType +from openminds.latest.controlled_terms import DeviceType as OMDeviceType from fairgraph import KGObject from openminds import IRI -class DeviceType(KGObject, DeviceType): +class DeviceType(KGObject, OMDeviceType): """ """ @@ -92,3 +92,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +DeviceType.set_error_handling(None) +for key, value in OMDeviceType.__dict__.items(): + if isinstance(value, OMDeviceType): + fg_instance = DeviceType.from_jsonld(value.to_jsonld()) + fg_instance._space = DeviceType.default_space + setattr(DeviceType, key, fg_instance) +DeviceType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/difference_measure.py b/fairgraph/openminds/controlled_terms/difference_measure.py index 971832e8..93900878 100644 --- a/fairgraph/openminds/controlled_terms/difference_measure.py +++ b/fairgraph/openminds/controlled_terms/difference_measure.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import DifferenceMeasure +from openminds.latest.controlled_terms import DifferenceMeasure as OMDifferenceMeasure from fairgraph import KGObject from openminds import IRI -class DifferenceMeasure(KGObject, DifferenceMeasure): +class DifferenceMeasure(KGObject, OMDifferenceMeasure): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +DifferenceMeasure.set_error_handling(None) +for key, value in OMDifferenceMeasure.__dict__.items(): + if isinstance(value, OMDifferenceMeasure): + fg_instance = DifferenceMeasure.from_jsonld(value.to_jsonld()) + fg_instance._space = DifferenceMeasure.default_space + setattr(DifferenceMeasure, key, fg_instance) +DifferenceMeasure.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/disease.py b/fairgraph/openminds/controlled_terms/disease.py index 2cd5e17c..5c039783 100644 --- a/fairgraph/openminds/controlled_terms/disease.py +++ b/fairgraph/openminds/controlled_terms/disease.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Disease +from openminds.latest.controlled_terms import Disease as OMDisease from fairgraph import KGObject from openminds import IRI -class Disease(KGObject, Disease): +class Disease(KGObject, OMDisease): """ Structured information on a disease. """ @@ -140,3 +140,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Disease.set_error_handling(None) +for key, value in OMDisease.__dict__.items(): + if isinstance(value, OMDisease): + fg_instance = Disease.from_jsonld(value.to_jsonld()) + fg_instance._space = Disease.default_space + setattr(Disease, key, fg_instance) +Disease.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/disease_model.py b/fairgraph/openminds/controlled_terms/disease_model.py index c0c193c8..fa29baaa 100644 --- a/fairgraph/openminds/controlled_terms/disease_model.py +++ b/fairgraph/openminds/controlled_terms/disease_model.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import DiseaseModel +from openminds.latest.controlled_terms import DiseaseModel as OMDiseaseModel from fairgraph import KGObject from openminds import IRI -class DiseaseModel(KGObject, DiseaseModel): +class DiseaseModel(KGObject, OMDiseaseModel): """ """ @@ -140,3 +140,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +DiseaseModel.set_error_handling(None) +for key, value in OMDiseaseModel.__dict__.items(): + if isinstance(value, OMDiseaseModel): + fg_instance = DiseaseModel.from_jsonld(value.to_jsonld()) + fg_instance._space = DiseaseModel.default_space + setattr(DiseaseModel, key, fg_instance) +DiseaseModel.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/educational_level.py b/fairgraph/openminds/controlled_terms/educational_level.py index a2039468..96b3b024 100644 --- a/fairgraph/openminds/controlled_terms/educational_level.py +++ b/fairgraph/openminds/controlled_terms/educational_level.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import EducationalLevel +from openminds.latest.controlled_terms import EducationalLevel as OMEducationalLevel from fairgraph import KGObject from openminds import IRI -class EducationalLevel(KGObject, EducationalLevel): +class EducationalLevel(KGObject, OMEducationalLevel): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +EducationalLevel.set_error_handling(None) +for key, value in OMEducationalLevel.__dict__.items(): + if isinstance(value, OMEducationalLevel): + fg_instance = EducationalLevel.from_jsonld(value.to_jsonld()) + fg_instance._space = EducationalLevel.default_space + setattr(EducationalLevel, key, fg_instance) +EducationalLevel.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py index 1fd15f66..d13ac4e0 100644 --- a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ElectricalStimulusType +from openminds.latest.controlled_terms import ElectricalStimulusType as OMElectricalStimulusType from fairgraph import KGObject from openminds import IRI -class ElectricalStimulusType(KGObject, ElectricalStimulusType): +class ElectricalStimulusType(KGObject, OMElectricalStimulusType): """ """ @@ -135,3 +135,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +ElectricalStimulusType.set_error_handling(None) +for key, value in OMElectricalStimulusType.__dict__.items(): + if isinstance(value, OMElectricalStimulusType): + fg_instance = ElectricalStimulusType.from_jsonld(value.to_jsonld()) + fg_instance._space = ElectricalStimulusType.default_space + setattr(ElectricalStimulusType, key, fg_instance) +ElectricalStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/ethics_assessment.py b/fairgraph/openminds/controlled_terms/ethics_assessment.py index fff63db3..563d1f4a 100644 --- a/fairgraph/openminds/controlled_terms/ethics_assessment.py +++ b/fairgraph/openminds/controlled_terms/ethics_assessment.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import EthicsAssessment +from openminds.latest.controlled_terms import EthicsAssessment as OMEthicsAssessment from fairgraph import KGObject from openminds import IRI -class EthicsAssessment(KGObject, EthicsAssessment): +class EthicsAssessment(KGObject, OMEthicsAssessment): """ Structured information on the ethics assessment of a dataset. """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +EthicsAssessment.set_error_handling(None) +for key, value in OMEthicsAssessment.__dict__.items(): + if isinstance(value, OMEthicsAssessment): + fg_instance = EthicsAssessment.from_jsonld(value.to_jsonld()) + fg_instance._space = EthicsAssessment.default_space + setattr(EthicsAssessment, key, fg_instance) +EthicsAssessment.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/experimental_approach.py b/fairgraph/openminds/controlled_terms/experimental_approach.py index 6e270c97..62466140 100644 --- a/fairgraph/openminds/controlled_terms/experimental_approach.py +++ b/fairgraph/openminds/controlled_terms/experimental_approach.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ExperimentalApproach +from openminds.latest.controlled_terms import ExperimentalApproach as OMExperimentalApproach from fairgraph import KGObject from openminds import IRI -class ExperimentalApproach(KGObject, ExperimentalApproach): +class ExperimentalApproach(KGObject, OMExperimentalApproach): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ExperimentalApproach.set_error_handling(None) +for key, value in OMExperimentalApproach.__dict__.items(): + if isinstance(value, OMExperimentalApproach): + fg_instance = ExperimentalApproach.from_jsonld(value.to_jsonld()) + fg_instance._space = ExperimentalApproach.default_space + setattr(ExperimentalApproach, key, fg_instance) +ExperimentalApproach.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py index ae7da719..0b002bd5 100644 --- a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py +++ b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import FileBundleGrouping +from openminds.latest.controlled_terms import FileBundleGrouping as OMFileBundleGrouping from fairgraph import KGObject from openminds import IRI -class FileBundleGrouping(KGObject, FileBundleGrouping): +class FileBundleGrouping(KGObject, OMFileBundleGrouping): """ Structured information on the grouping mechanism of a file bundle. """ @@ -97,3 +97,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +FileBundleGrouping.set_error_handling(None) +for key, value in OMFileBundleGrouping.__dict__.items(): + if isinstance(value, OMFileBundleGrouping): + fg_instance = FileBundleGrouping.from_jsonld(value.to_jsonld()) + fg_instance._space = FileBundleGrouping.default_space + setattr(FileBundleGrouping, key, fg_instance) +FileBundleGrouping.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/file_repository_type.py b/fairgraph/openminds/controlled_terms/file_repository_type.py index 6d28d8bf..5f41dc63 100644 --- a/fairgraph/openminds/controlled_terms/file_repository_type.py +++ b/fairgraph/openminds/controlled_terms/file_repository_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import FileRepositoryType +from openminds.latest.controlled_terms import FileRepositoryType as OMFileRepositoryType from fairgraph import KGObject from openminds import IRI -class FileRepositoryType(KGObject, FileRepositoryType): +class FileRepositoryType(KGObject, OMFileRepositoryType): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +FileRepositoryType.set_error_handling(None) +for key, value in OMFileRepositoryType.__dict__.items(): + if isinstance(value, OMFileRepositoryType): + fg_instance = FileRepositoryType.from_jsonld(value.to_jsonld()) + fg_instance._space = FileRepositoryType.default_space + setattr(FileRepositoryType, key, fg_instance) +FileRepositoryType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/file_usage_role.py b/fairgraph/openminds/controlled_terms/file_usage_role.py index 7748435c..15bda2aa 100644 --- a/fairgraph/openminds/controlled_terms/file_usage_role.py +++ b/fairgraph/openminds/controlled_terms/file_usage_role.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import FileUsageRole +from openminds.latest.controlled_terms import FileUsageRole as OMFileUsageRole from fairgraph import KGObject from openminds import IRI -class FileUsageRole(KGObject, FileUsageRole): +class FileUsageRole(KGObject, OMFileUsageRole): """ Structured information on the usage role of a file instance or bundle. """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +FileUsageRole.set_error_handling(None) +for key, value in OMFileUsageRole.__dict__.items(): + if isinstance(value, OMFileUsageRole): + fg_instance = FileUsageRole.from_jsonld(value.to_jsonld()) + fg_instance._space = FileUsageRole.default_space + setattr(FileUsageRole, key, fg_instance) +FileUsageRole.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/genetic_strain_type.py b/fairgraph/openminds/controlled_terms/genetic_strain_type.py index e86732c2..256af37a 100644 --- a/fairgraph/openminds/controlled_terms/genetic_strain_type.py +++ b/fairgraph/openminds/controlled_terms/genetic_strain_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import GeneticStrainType +from openminds.latest.controlled_terms import GeneticStrainType as OMGeneticStrainType from fairgraph import KGObject from openminds import IRI -class GeneticStrainType(KGObject, GeneticStrainType): +class GeneticStrainType(KGObject, OMGeneticStrainType): """ """ @@ -125,3 +125,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +GeneticStrainType.set_error_handling(None) +for key, value in OMGeneticStrainType.__dict__.items(): + if isinstance(value, OMGeneticStrainType): + fg_instance = GeneticStrainType.from_jsonld(value.to_jsonld()) + fg_instance._space = GeneticStrainType.default_space + setattr(GeneticStrainType, key, fg_instance) +GeneticStrainType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py index 538abf18..88fc7159 100644 --- a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import GustatoryStimulusType +from openminds.latest.controlled_terms import GustatoryStimulusType as OMGustatoryStimulusType from fairgraph import KGObject from openminds import IRI -class GustatoryStimulusType(KGObject, GustatoryStimulusType): +class GustatoryStimulusType(KGObject, OMGustatoryStimulusType): """ """ @@ -125,3 +125,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +GustatoryStimulusType.set_error_handling(None) +for key, value in OMGustatoryStimulusType.__dict__.items(): + if isinstance(value, OMGustatoryStimulusType): + fg_instance = GustatoryStimulusType.from_jsonld(value.to_jsonld()) + fg_instance._space = GustatoryStimulusType.default_space + setattr(GustatoryStimulusType, key, fg_instance) +GustatoryStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/handedness.py b/fairgraph/openminds/controlled_terms/handedness.py index 87553ca3..52674ccb 100644 --- a/fairgraph/openminds/controlled_terms/handedness.py +++ b/fairgraph/openminds/controlled_terms/handedness.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Handedness +from openminds.latest.controlled_terms import Handedness as OMHandedness from fairgraph import KGObject from openminds import IRI -class Handedness(KGObject, Handedness): +class Handedness(KGObject, OMHandedness): """ """ @@ -125,3 +125,13 @@ def __init__( subject_states=subject_states, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Handedness.set_error_handling(None) +for key, value in OMHandedness.__dict__.items(): + if isinstance(value, OMHandedness): + fg_instance = Handedness.from_jsonld(value.to_jsonld()) + fg_instance._space = Handedness.default_space + setattr(Handedness, key, fg_instance) +Handedness.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/language.py b/fairgraph/openminds/controlled_terms/language.py index 0a8250ec..12d628a0 100644 --- a/fairgraph/openminds/controlled_terms/language.py +++ b/fairgraph/openminds/controlled_terms/language.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Language +from openminds.latest.controlled_terms import Language as OMLanguage from fairgraph import KGObject from openminds import IRI -class Language(KGObject, Language): +class Language(KGObject, OMLanguage): """ Structured information on the available language setting. """ @@ -86,3 +86,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +Language.set_error_handling(None) +for key, value in OMLanguage.__dict__.items(): + if isinstance(value, OMLanguage): + fg_instance = Language.from_jsonld(value.to_jsonld()) + fg_instance._space = Language.default_space + setattr(Language, key, fg_instance) +Language.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/laterality.py b/fairgraph/openminds/controlled_terms/laterality.py index 8d3915f4..6d208f61 100644 --- a/fairgraph/openminds/controlled_terms/laterality.py +++ b/fairgraph/openminds/controlled_terms/laterality.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Laterality +from openminds.latest.controlled_terms import Laterality as OMLaterality from fairgraph import KGObject from openminds import IRI -class Laterality(KGObject, Laterality): +class Laterality(KGObject, OMLaterality): """ Structured information on the lateral direction. """ @@ -92,3 +92,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Laterality.set_error_handling(None) +for key, value in OMLaterality.__dict__.items(): + if isinstance(value, OMLaterality): + fg_instance = Laterality.from_jsonld(value.to_jsonld()) + fg_instance._space = Laterality.default_space + setattr(Laterality, key, fg_instance) +Laterality.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/learning_resource_type.py b/fairgraph/openminds/controlled_terms/learning_resource_type.py index 7356980c..3cd55cba 100644 --- a/fairgraph/openminds/controlled_terms/learning_resource_type.py +++ b/fairgraph/openminds/controlled_terms/learning_resource_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import LearningResourceType +from openminds.latest.controlled_terms import LearningResourceType as OMLearningResourceType from fairgraph import KGObject from openminds import IRI -class LearningResourceType(KGObject, LearningResourceType): +class LearningResourceType(KGObject, OMLearningResourceType): """ """ @@ -86,3 +86,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +LearningResourceType.set_error_handling(None) +for key, value in OMLearningResourceType.__dict__.items(): + if isinstance(value, OMLearningResourceType): + fg_instance = LearningResourceType.from_jsonld(value.to_jsonld()) + fg_instance._space = LearningResourceType.default_space + setattr(LearningResourceType, key, fg_instance) +LearningResourceType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/measured_quantity.py b/fairgraph/openminds/controlled_terms/measured_quantity.py index 7875a106..6c355b6e 100644 --- a/fairgraph/openminds/controlled_terms/measured_quantity.py +++ b/fairgraph/openminds/controlled_terms/measured_quantity.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MeasuredQuantity +from openminds.latest.controlled_terms import MeasuredQuantity as OMMeasuredQuantity from fairgraph import KGObject from openminds import IRI -class MeasuredQuantity(KGObject, MeasuredQuantity): +class MeasuredQuantity(KGObject, OMMeasuredQuantity): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +MeasuredQuantity.set_error_handling(None) +for key, value in OMMeasuredQuantity.__dict__.items(): + if isinstance(value, OMMeasuredQuantity): + fg_instance = MeasuredQuantity.from_jsonld(value.to_jsonld()) + fg_instance._space = MeasuredQuantity.default_space + setattr(MeasuredQuantity, key, fg_instance) +MeasuredQuantity.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/measured_signal_type.py b/fairgraph/openminds/controlled_terms/measured_signal_type.py index 848be7a4..acf30a5a 100644 --- a/fairgraph/openminds/controlled_terms/measured_signal_type.py +++ b/fairgraph/openminds/controlled_terms/measured_signal_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MeasuredSignalType +from openminds.latest.controlled_terms import MeasuredSignalType as OMMeasuredSignalType from fairgraph import KGObject from openminds import IRI -class MeasuredSignalType(KGObject, MeasuredSignalType): +class MeasuredSignalType(KGObject, OMMeasuredSignalType): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +MeasuredSignalType.set_error_handling(None) +for key, value in OMMeasuredSignalType.__dict__.items(): + if isinstance(value, OMMeasuredSignalType): + fg_instance = MeasuredSignalType.from_jsonld(value.to_jsonld()) + fg_instance._space = MeasuredSignalType.default_space + setattr(MeasuredSignalType, key, fg_instance) +MeasuredSignalType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/meta_data_model_type.py b/fairgraph/openminds/controlled_terms/meta_data_model_type.py index 5bf0d7f2..2ff6aa67 100644 --- a/fairgraph/openminds/controlled_terms/meta_data_model_type.py +++ b/fairgraph/openminds/controlled_terms/meta_data_model_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MetaDataModelType +from openminds.latest.controlled_terms import MetaDataModelType as OMMetaDataModelType from fairgraph import KGObject from openminds import IRI -class MetaDataModelType(KGObject, MetaDataModelType): +class MetaDataModelType(KGObject, OMMetaDataModelType): """ """ @@ -86,3 +86,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +MetaDataModelType.set_error_handling(None) +for key, value in OMMetaDataModelType.__dict__.items(): + if isinstance(value, OMMetaDataModelType): + fg_instance = MetaDataModelType.from_jsonld(value.to_jsonld()) + fg_instance._space = MetaDataModelType.default_space + setattr(MetaDataModelType, key, fg_instance) +MetaDataModelType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/model_abstraction_level.py b/fairgraph/openminds/controlled_terms/model_abstraction_level.py index 8e8d05e9..134fdd04 100644 --- a/fairgraph/openminds/controlled_terms/model_abstraction_level.py +++ b/fairgraph/openminds/controlled_terms/model_abstraction_level.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ModelAbstractionLevel +from openminds.latest.controlled_terms import ModelAbstractionLevel as OMModelAbstractionLevel from fairgraph import KGObject from openminds import IRI -class ModelAbstractionLevel(KGObject, ModelAbstractionLevel): +class ModelAbstractionLevel(KGObject, OMModelAbstractionLevel): """ Structured information on abstraction level of the computational model. """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ModelAbstractionLevel.set_error_handling(None) +for key, value in OMModelAbstractionLevel.__dict__.items(): + if isinstance(value, OMModelAbstractionLevel): + fg_instance = ModelAbstractionLevel.from_jsonld(value.to_jsonld()) + fg_instance._space = ModelAbstractionLevel.default_space + setattr(ModelAbstractionLevel, key, fg_instance) +ModelAbstractionLevel.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/model_scope.py b/fairgraph/openminds/controlled_terms/model_scope.py index 5eda8e48..1af6c6e1 100644 --- a/fairgraph/openminds/controlled_terms/model_scope.py +++ b/fairgraph/openminds/controlled_terms/model_scope.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ModelScope +from openminds.latest.controlled_terms import ModelScope as OMModelScope from fairgraph import KGObject from openminds import IRI -class ModelScope(KGObject, ModelScope): +class ModelScope(KGObject, OMModelScope): """ Structured information on the scope of the computational model. """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ModelScope.set_error_handling(None) +for key, value in OMModelScope.__dict__.items(): + if isinstance(value, OMModelScope): + fg_instance = ModelScope.from_jsonld(value.to_jsonld()) + fg_instance._space = ModelScope.default_space + setattr(ModelScope, key, fg_instance) +ModelScope.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/molecular_entity.py b/fairgraph/openminds/controlled_terms/molecular_entity.py index 6e8b62e3..5f1ede72 100644 --- a/fairgraph/openminds/controlled_terms/molecular_entity.py +++ b/fairgraph/openminds/controlled_terms/molecular_entity.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MolecularEntity +from openminds.latest.controlled_terms import MolecularEntity as OMMolecularEntity from fairgraph import KGObject from openminds import IRI -class MolecularEntity(KGObject, MolecularEntity): +class MolecularEntity(KGObject, OMMolecularEntity): """ """ @@ -140,3 +140,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +MolecularEntity.set_error_handling(None) +for key, value in OMMolecularEntity.__dict__.items(): + if isinstance(value, OMMolecularEntity): + fg_instance = MolecularEntity.from_jsonld(value.to_jsonld()) + fg_instance._space = MolecularEntity.default_space + setattr(MolecularEntity, key, fg_instance) +MolecularEntity.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py b/fairgraph/openminds/controlled_terms/mr_acquisition_type.py index b73e3190..b91b1dde 100644 --- a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py +++ b/fairgraph/openminds/controlled_terms/mr_acquisition_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MRAcquisitionType +from openminds.latest.controlled_terms import MRAcquisitionType as OMMRAcquisitionType from fairgraph import KGObject from openminds import IRI -class MRAcquisitionType(KGObject, MRAcquisitionType): +class MRAcquisitionType(KGObject, OMMRAcquisitionType): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +MRAcquisitionType.set_error_handling(None) +for key, value in OMMRAcquisitionType.__dict__.items(): + if isinstance(value, OMMRAcquisitionType): + fg_instance = MRAcquisitionType.from_jsonld(value.to_jsonld()) + fg_instance._space = MRAcquisitionType.default_space + setattr(MRAcquisitionType, key, fg_instance) +MRAcquisitionType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py index 3ec02593..dff20b25 100644 --- a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py +++ b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MRIPulseSequence +from openminds.latest.controlled_terms import MRIPulseSequence as OMMRIPulseSequence from fairgraph import KGObject from openminds import IRI -class MRIPulseSequence(KGObject, MRIPulseSequence): +class MRIPulseSequence(KGObject, OMMRIPulseSequence): """ """ @@ -96,3 +96,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +MRIPulseSequence.set_error_handling(None) +for key, value in OMMRIPulseSequence.__dict__.items(): + if isinstance(value, OMMRIPulseSequence): + fg_instance = MRIPulseSequence.from_jsonld(value.to_jsonld()) + fg_instance._space = MRIPulseSequence.default_space + setattr(MRIPulseSequence, key, fg_instance) +MRIPulseSequence.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/mri_weighting.py b/fairgraph/openminds/controlled_terms/mri_weighting.py index a8c3f091..45fe4994 100644 --- a/fairgraph/openminds/controlled_terms/mri_weighting.py +++ b/fairgraph/openminds/controlled_terms/mri_weighting.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MRIWeighting +from openminds.latest.controlled_terms import MRIWeighting as OMMRIWeighting from fairgraph import KGObject from openminds import IRI -class MRIWeighting(KGObject, MRIWeighting): +class MRIWeighting(KGObject, OMMRIWeighting): """ """ @@ -96,3 +96,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +MRIWeighting.set_error_handling(None) +for key, value in OMMRIWeighting.__dict__.items(): + if isinstance(value, OMMRIWeighting): + fg_instance = MRIWeighting.from_jsonld(value.to_jsonld()) + fg_instance._space = MRIWeighting.default_space + setattr(MRIWeighting, key, fg_instance) +MRIWeighting.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py index 2ab5d3b3..6691b79c 100644 --- a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import OlfactoryStimulusType +from openminds.latest.controlled_terms import OlfactoryStimulusType as OMOlfactoryStimulusType from fairgraph import KGObject from openminds import IRI -class OlfactoryStimulusType(KGObject, OlfactoryStimulusType): +class OlfactoryStimulusType(KGObject, OMOlfactoryStimulusType): """ """ @@ -125,3 +125,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +OlfactoryStimulusType.set_error_handling(None) +for key, value in OMOlfactoryStimulusType.__dict__.items(): + if isinstance(value, OMOlfactoryStimulusType): + fg_instance = OlfactoryStimulusType.from_jsonld(value.to_jsonld()) + fg_instance._space = OlfactoryStimulusType.default_space + setattr(OlfactoryStimulusType, key, fg_instance) +OlfactoryStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/operating_device.py b/fairgraph/openminds/controlled_terms/operating_device.py index c28b9337..03f8a2c3 100644 --- a/fairgraph/openminds/controlled_terms/operating_device.py +++ b/fairgraph/openminds/controlled_terms/operating_device.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import OperatingDevice +from openminds.latest.controlled_terms import OperatingDevice as OMOperatingDevice from fairgraph import KGObject from openminds import IRI -class OperatingDevice(KGObject, OperatingDevice): +class OperatingDevice(KGObject, OMOperatingDevice): """ Structured information on the operating device. """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +OperatingDevice.set_error_handling(None) +for key, value in OMOperatingDevice.__dict__.items(): + if isinstance(value, OMOperatingDevice): + fg_instance = OperatingDevice.from_jsonld(value.to_jsonld()) + fg_instance._space = OperatingDevice.default_space + setattr(OperatingDevice, key, fg_instance) +OperatingDevice.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/operating_system.py b/fairgraph/openminds/controlled_terms/operating_system.py index 519c09ee..dde6d146 100644 --- a/fairgraph/openminds/controlled_terms/operating_system.py +++ b/fairgraph/openminds/controlled_terms/operating_system.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import OperatingSystem +from openminds.latest.controlled_terms import OperatingSystem as OMOperatingSystem from fairgraph import KGObject from openminds import IRI -class OperatingSystem(KGObject, OperatingSystem): +class OperatingSystem(KGObject, OMOperatingSystem): """ Structured information on the operating system. """ @@ -86,3 +86,13 @@ def __init__( synonyms=synonyms, used_by=used_by, ) + + +# cast openMINDS instances to their fairgraph subclass +OperatingSystem.set_error_handling(None) +for key, value in OMOperatingSystem.__dict__.items(): + if isinstance(value, OMOperatingSystem): + fg_instance = OperatingSystem.from_jsonld(value.to_jsonld()) + fg_instance._space = OperatingSystem.default_space + setattr(OperatingSystem, key, fg_instance) +OperatingSystem.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py index c4b59d58..2298d05f 100644 --- a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import OpticalStimulusType +from openminds.latest.controlled_terms import OpticalStimulusType as OMOpticalStimulusType from fairgraph import KGObject from openminds import IRI -class OpticalStimulusType(KGObject, OpticalStimulusType): +class OpticalStimulusType(KGObject, OMOpticalStimulusType): """ """ @@ -125,3 +125,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +OpticalStimulusType.set_error_handling(None) +for key, value in OMOpticalStimulusType.__dict__.items(): + if isinstance(value, OMOpticalStimulusType): + fg_instance = OpticalStimulusType.from_jsonld(value.to_jsonld()) + fg_instance._space = OpticalStimulusType.default_space + setattr(OpticalStimulusType, key, fg_instance) +OpticalStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/organ.py b/fairgraph/openminds/controlled_terms/organ.py index 9e5ee421..3ffc7576 100644 --- a/fairgraph/openminds/controlled_terms/organ.py +++ b/fairgraph/openminds/controlled_terms/organ.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Organ +from openminds.latest.controlled_terms import Organ as OMOrgan from fairgraph import KGObject from openminds import IRI -class Organ(KGObject, Organ): +class Organ(KGObject, OMOrgan): """ """ @@ -159,3 +159,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Organ.set_error_handling(None) +for key, value in OMOrgan.__dict__.items(): + if isinstance(value, OMOrgan): + fg_instance = Organ.from_jsonld(value.to_jsonld()) + fg_instance._space = Organ.default_space + setattr(Organ, key, fg_instance) +Organ.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/organism_substance.py b/fairgraph/openminds/controlled_terms/organism_substance.py index b1f094ef..bc586006 100644 --- a/fairgraph/openminds/controlled_terms/organism_substance.py +++ b/fairgraph/openminds/controlled_terms/organism_substance.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import OrganismSubstance +from openminds.latest.controlled_terms import OrganismSubstance as OMOrganismSubstance from fairgraph import KGObject from openminds import IRI -class OrganismSubstance(KGObject, OrganismSubstance): +class OrganismSubstance(KGObject, OMOrganismSubstance): """ """ @@ -149,3 +149,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +OrganismSubstance.set_error_handling(None) +for key, value in OMOrganismSubstance.__dict__.items(): + if isinstance(value, OMOrganismSubstance): + fg_instance = OrganismSubstance.from_jsonld(value.to_jsonld()) + fg_instance._space = OrganismSubstance.default_space + setattr(OrganismSubstance, key, fg_instance) +OrganismSubstance.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/organism_system.py b/fairgraph/openminds/controlled_terms/organism_system.py index 4c08b6d2..e9233611 100644 --- a/fairgraph/openminds/controlled_terms/organism_system.py +++ b/fairgraph/openminds/controlled_terms/organism_system.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import OrganismSystem +from openminds.latest.controlled_terms import OrganismSystem as OMOrganismSystem from fairgraph import KGObject from openminds import IRI -class OrganismSystem(KGObject, OrganismSystem): +class OrganismSystem(KGObject, OMOrganismSystem): """ """ @@ -115,3 +115,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +OrganismSystem.set_error_handling(None) +for key, value in OMOrganismSystem.__dict__.items(): + if isinstance(value, OMOrganismSystem): + fg_instance = OrganismSystem.from_jsonld(value.to_jsonld()) + fg_instance._space = OrganismSystem.default_space + setattr(OrganismSystem, key, fg_instance) +OrganismSystem.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py index ffa3ba39..74909adf 100644 --- a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py +++ b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import PatchClampVariation +from openminds.latest.controlled_terms import PatchClampVariation as OMPatchClampVariation from fairgraph import KGObject from openminds import IRI -class PatchClampVariation(KGObject, PatchClampVariation): +class PatchClampVariation(KGObject, OMPatchClampVariation): """ """ @@ -87,3 +87,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +PatchClampVariation.set_error_handling(None) +for key, value in OMPatchClampVariation.__dict__.items(): + if isinstance(value, OMPatchClampVariation): + fg_instance = PatchClampVariation.from_jsonld(value.to_jsonld()) + fg_instance._space = PatchClampVariation.default_space + setattr(PatchClampVariation, key, fg_instance) +PatchClampVariation.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/preparation_type.py b/fairgraph/openminds/controlled_terms/preparation_type.py index 0998e0f0..17c77f69 100644 --- a/fairgraph/openminds/controlled_terms/preparation_type.py +++ b/fairgraph/openminds/controlled_terms/preparation_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import PreparationType +from openminds.latest.controlled_terms import PreparationType as OMPreparationType from fairgraph import KGObject from openminds import IRI -class PreparationType(KGObject, PreparationType): +class PreparationType(KGObject, OMPreparationType): """ """ @@ -96,3 +96,13 @@ def __init__( synonyms=synonyms, used_for=used_for, ) + + +# cast openMINDS instances to their fairgraph subclass +PreparationType.set_error_handling(None) +for key, value in OMPreparationType.__dict__.items(): + if isinstance(value, OMPreparationType): + fg_instance = PreparationType.from_jsonld(value.to_jsonld()) + fg_instance._space = PreparationType.default_space + setattr(PreparationType, key, fg_instance) +PreparationType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/product_accessibility.py b/fairgraph/openminds/controlled_terms/product_accessibility.py index d55b6738..850d544b 100644 --- a/fairgraph/openminds/controlled_terms/product_accessibility.py +++ b/fairgraph/openminds/controlled_terms/product_accessibility.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ProductAccessibility +from openminds.latest.controlled_terms import ProductAccessibility as OMProductAccessibility from fairgraph import KGObject from openminds import IRI -class ProductAccessibility(KGObject, ProductAccessibility): +class ProductAccessibility(KGObject, OMProductAccessibility): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ProductAccessibility.set_error_handling(None) +for key, value in OMProductAccessibility.__dict__.items(): + if isinstance(value, OMProductAccessibility): + fg_instance = ProductAccessibility.from_jsonld(value.to_jsonld()) + fg_instance._space = ProductAccessibility.default_space + setattr(ProductAccessibility, key, fg_instance) +ProductAccessibility.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/programming_language.py b/fairgraph/openminds/controlled_terms/programming_language.py index f4f3f7e8..c28368a6 100644 --- a/fairgraph/openminds/controlled_terms/programming_language.py +++ b/fairgraph/openminds/controlled_terms/programming_language.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import ProgrammingLanguage +from openminds.latest.controlled_terms import ProgrammingLanguage as OMProgrammingLanguage from fairgraph import KGObject from openminds import IRI -class ProgrammingLanguage(KGObject, ProgrammingLanguage): +class ProgrammingLanguage(KGObject, OMProgrammingLanguage): """ Structured information on the programming language. """ @@ -86,3 +86,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +ProgrammingLanguage.set_error_handling(None) +for key, value in OMProgrammingLanguage.__dict__.items(): + if isinstance(value, OMProgrammingLanguage): + fg_instance = ProgrammingLanguage.from_jsonld(value.to_jsonld()) + fg_instance._space = ProgrammingLanguage.default_space + setattr(ProgrammingLanguage, key, fg_instance) +ProgrammingLanguage.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/qualitative_overlap.py b/fairgraph/openminds/controlled_terms/qualitative_overlap.py index 6fd1f6a3..bd760a5e 100644 --- a/fairgraph/openminds/controlled_terms/qualitative_overlap.py +++ b/fairgraph/openminds/controlled_terms/qualitative_overlap.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import QualitativeOverlap +from openminds.latest.controlled_terms import QualitativeOverlap as OMQualitativeOverlap from fairgraph import KGObject from openminds import IRI -class QualitativeOverlap(KGObject, QualitativeOverlap): +class QualitativeOverlap(KGObject, OMQualitativeOverlap): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +QualitativeOverlap.set_error_handling(None) +for key, value in OMQualitativeOverlap.__dict__.items(): + if isinstance(value, OMQualitativeOverlap): + fg_instance = QualitativeOverlap.from_jsonld(value.to_jsonld()) + fg_instance._space = QualitativeOverlap.default_space + setattr(QualitativeOverlap, key, fg_instance) +QualitativeOverlap.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/semantic_data_type.py b/fairgraph/openminds/controlled_terms/semantic_data_type.py index a2bca312..1efe5331 100644 --- a/fairgraph/openminds/controlled_terms/semantic_data_type.py +++ b/fairgraph/openminds/controlled_terms/semantic_data_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import SemanticDataType +from openminds.latest.controlled_terms import SemanticDataType as OMSemanticDataType from fairgraph import KGObject from openminds import IRI -class SemanticDataType(KGObject, SemanticDataType): +class SemanticDataType(KGObject, OMSemanticDataType): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +SemanticDataType.set_error_handling(None) +for key, value in OMSemanticDataType.__dict__.items(): + if isinstance(value, OMSemanticDataType): + fg_instance = SemanticDataType.from_jsonld(value.to_jsonld()) + fg_instance._space = SemanticDataType.default_space + setattr(SemanticDataType, key, fg_instance) +SemanticDataType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/service.py b/fairgraph/openminds/controlled_terms/service.py index 9cfa1666..1243a95f 100644 --- a/fairgraph/openminds/controlled_terms/service.py +++ b/fairgraph/openminds/controlled_terms/service.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Service +from openminds.latest.controlled_terms import Service as OMService from fairgraph import KGObject from openminds import IRI -class Service(KGObject, Service): +class Service(KGObject, OMService): """ """ @@ -97,3 +97,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Service.set_error_handling(None) +for key, value in OMService.__dict__.items(): + if isinstance(value, OMService): + fg_instance = Service.from_jsonld(value.to_jsonld()) + fg_instance._space = Service.default_space + setattr(Service, key, fg_instance) +Service.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/setup_type.py b/fairgraph/openminds/controlled_terms/setup_type.py index 8efbed91..05c1d73f 100644 --- a/fairgraph/openminds/controlled_terms/setup_type.py +++ b/fairgraph/openminds/controlled_terms/setup_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import SetupType +from openminds.latest.controlled_terms import SetupType as OMSetupType from fairgraph import KGObject from openminds import IRI -class SetupType(KGObject, SetupType): +class SetupType(KGObject, OMSetupType): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +SetupType.set_error_handling(None) +for key, value in OMSetupType.__dict__.items(): + if isinstance(value, OMSetupType): + fg_instance = SetupType.from_jsonld(value.to_jsonld()) + fg_instance._space = SetupType.default_space + setattr(SetupType, key, fg_instance) +SetupType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/software_application_category.py b/fairgraph/openminds/controlled_terms/software_application_category.py index dd804f36..2270e95c 100644 --- a/fairgraph/openminds/controlled_terms/software_application_category.py +++ b/fairgraph/openminds/controlled_terms/software_application_category.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import SoftwareApplicationCategory +from openminds.latest.controlled_terms import SoftwareApplicationCategory as OMSoftwareApplicationCategory from fairgraph import KGObject from openminds import IRI -class SoftwareApplicationCategory(KGObject, SoftwareApplicationCategory): +class SoftwareApplicationCategory(KGObject, OMSoftwareApplicationCategory): """ Structured information on the category of the software application. """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +SoftwareApplicationCategory.set_error_handling(None) +for key, value in OMSoftwareApplicationCategory.__dict__.items(): + if isinstance(value, OMSoftwareApplicationCategory): + fg_instance = SoftwareApplicationCategory.from_jsonld(value.to_jsonld()) + fg_instance._space = SoftwareApplicationCategory.default_space + setattr(SoftwareApplicationCategory, key, fg_instance) +SoftwareApplicationCategory.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/software_feature.py b/fairgraph/openminds/controlled_terms/software_feature.py index 5126e779..d5d47f19 100644 --- a/fairgraph/openminds/controlled_terms/software_feature.py +++ b/fairgraph/openminds/controlled_terms/software_feature.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import SoftwareFeature +from openminds.latest.controlled_terms import SoftwareFeature as OMSoftwareFeature from fairgraph import KGObject from openminds import IRI -class SoftwareFeature(KGObject, SoftwareFeature): +class SoftwareFeature(KGObject, OMSoftwareFeature): """ """ @@ -77,3 +77,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +SoftwareFeature.set_error_handling(None) +for key, value in OMSoftwareFeature.__dict__.items(): + if isinstance(value, OMSoftwareFeature): + fg_instance = SoftwareFeature.from_jsonld(value.to_jsonld()) + fg_instance._space = SoftwareFeature.default_space + setattr(SoftwareFeature, key, fg_instance) +SoftwareFeature.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/species.py b/fairgraph/openminds/controlled_terms/species.py index 890d9076..9b492c8d 100644 --- a/fairgraph/openminds/controlled_terms/species.py +++ b/fairgraph/openminds/controlled_terms/species.py @@ -142,12 +142,12 @@ def __init__( synonyms=synonyms, ) - # @classmethod - # def instances(cls): - # return [value for value in OMSpecies.__dict__.values() if isinstance(value, OMSpecies)] +# cast openMINDS instances to their fairgraph subclass +Species.set_error_handling(None) for key, value in OMSpecies.__dict__.items(): if isinstance(value, OMSpecies): fg_instance = Species.from_jsonld(value.to_jsonld()) - fg_instance._space = "controlled" + fg_instance._space = Species.default_space setattr(Species, key, fg_instance) +Species.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/stimulation_approach.py b/fairgraph/openminds/controlled_terms/stimulation_approach.py index ba530e75..b0a08927 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_approach.py +++ b/fairgraph/openminds/controlled_terms/stimulation_approach.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import StimulationApproach +from openminds.latest.controlled_terms import StimulationApproach as OMStimulationApproach from fairgraph import KGObject from openminds import IRI -class StimulationApproach(KGObject, StimulationApproach): +class StimulationApproach(KGObject, OMStimulationApproach): """ """ @@ -100,3 +100,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +StimulationApproach.set_error_handling(None) +for key, value in OMStimulationApproach.__dict__.items(): + if isinstance(value, OMStimulationApproach): + fg_instance = StimulationApproach.from_jsonld(value.to_jsonld()) + fg_instance._space = StimulationApproach.default_space + setattr(StimulationApproach, key, fg_instance) +StimulationApproach.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/stimulation_technique.py b/fairgraph/openminds/controlled_terms/stimulation_technique.py index 0241b5fe..339af597 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_technique.py +++ b/fairgraph/openminds/controlled_terms/stimulation_technique.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import StimulationTechnique +from openminds.latest.controlled_terms import StimulationTechnique as OMStimulationTechnique from fairgraph import KGObject from openminds import IRI -class StimulationTechnique(KGObject, StimulationTechnique): +class StimulationTechnique(KGObject, OMStimulationTechnique): """ """ @@ -100,3 +100,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +StimulationTechnique.set_error_handling(None) +for key, value in OMStimulationTechnique.__dict__.items(): + if isinstance(value, OMStimulationTechnique): + fg_instance = StimulationTechnique.from_jsonld(value.to_jsonld()) + fg_instance._space = StimulationTechnique.default_space + setattr(StimulationTechnique, key, fg_instance) +StimulationTechnique.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/subcellular_entity.py b/fairgraph/openminds/controlled_terms/subcellular_entity.py index 406f9cdf..35b0f5d4 100644 --- a/fairgraph/openminds/controlled_terms/subcellular_entity.py +++ b/fairgraph/openminds/controlled_terms/subcellular_entity.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import SubcellularEntity +from openminds.latest.controlled_terms import SubcellularEntity as OMSubcellularEntity from fairgraph import KGObject from openminds import IRI -class SubcellularEntity(KGObject, SubcellularEntity): +class SubcellularEntity(KGObject, OMSubcellularEntity): """ """ @@ -141,3 +141,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +SubcellularEntity.set_error_handling(None) +for key, value in OMSubcellularEntity.__dict__.items(): + if isinstance(value, OMSubcellularEntity): + fg_instance = SubcellularEntity.from_jsonld(value.to_jsonld()) + fg_instance._space = SubcellularEntity.default_space + setattr(SubcellularEntity, key, fg_instance) +SubcellularEntity.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/subject_attribute.py b/fairgraph/openminds/controlled_terms/subject_attribute.py index e498acaa..a89798d9 100644 --- a/fairgraph/openminds/controlled_terms/subject_attribute.py +++ b/fairgraph/openminds/controlled_terms/subject_attribute.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import SubjectAttribute +from openminds.latest.controlled_terms import SubjectAttribute as OMSubjectAttribute from fairgraph import KGObject from openminds import IRI -class SubjectAttribute(KGObject, SubjectAttribute): +class SubjectAttribute(KGObject, OMSubjectAttribute): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +SubjectAttribute.set_error_handling(None) +for key, value in OMSubjectAttribute.__dict__.items(): + if isinstance(value, OMSubjectAttribute): + fg_instance = SubjectAttribute.from_jsonld(value.to_jsonld()) + fg_instance._space = SubjectAttribute.default_space + setattr(SubjectAttribute, key, fg_instance) +SubjectAttribute.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py index 899ceed2..06ab6d8d 100644 --- a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import TactileStimulusType +from openminds.latest.controlled_terms import TactileStimulusType as OMTactileStimulusType from fairgraph import KGObject from openminds import IRI -class TactileStimulusType(KGObject, TactileStimulusType): +class TactileStimulusType(KGObject, OMTactileStimulusType): """ """ @@ -125,3 +125,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +TactileStimulusType.set_error_handling(None) +for key, value in OMTactileStimulusType.__dict__.items(): + if isinstance(value, OMTactileStimulusType): + fg_instance = TactileStimulusType.from_jsonld(value.to_jsonld()) + fg_instance._space = TactileStimulusType.default_space + setattr(TactileStimulusType, key, fg_instance) +TactileStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/technique.py b/fairgraph/openminds/controlled_terms/technique.py index 792534db..045abf5e 100644 --- a/fairgraph/openminds/controlled_terms/technique.py +++ b/fairgraph/openminds/controlled_terms/technique.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Technique +from openminds.latest.controlled_terms import Technique as OMTechnique from fairgraph import KGObject from openminds import IRI -class Technique(KGObject, Technique): +class Technique(KGObject, OMTechnique): """ Structured information on the technique. """ @@ -106,3 +106,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +Technique.set_error_handling(None) +for key, value in OMTechnique.__dict__.items(): + if isinstance(value, OMTechnique): + fg_instance = Technique.from_jsonld(value.to_jsonld()) + fg_instance._space = Technique.default_space + setattr(Technique, key, fg_instance) +Technique.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/term_suggestion.py b/fairgraph/openminds/controlled_terms/term_suggestion.py index bc85815f..43f23f79 100644 --- a/fairgraph/openminds/controlled_terms/term_suggestion.py +++ b/fairgraph/openminds/controlled_terms/term_suggestion.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import TermSuggestion +from openminds.latest.controlled_terms import TermSuggestion as OMTermSuggestion from fairgraph import KGObject from openminds import IRI -class TermSuggestion(KGObject, TermSuggestion): +class TermSuggestion(KGObject, OMTermSuggestion): """ """ @@ -119,3 +119,13 @@ def __init__( suggest_new_terminology=suggest_new_terminology, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +TermSuggestion.set_error_handling(None) +for key, value in OMTermSuggestion.__dict__.items(): + if isinstance(value, OMTermSuggestion): + fg_instance = TermSuggestion.from_jsonld(value.to_jsonld()) + fg_instance._space = TermSuggestion.default_space + setattr(TermSuggestion, key, fg_instance) +TermSuggestion.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/terminology.py b/fairgraph/openminds/controlled_terms/terminology.py index 7bf24ad8..fb0e542f 100644 --- a/fairgraph/openminds/controlled_terms/terminology.py +++ b/fairgraph/openminds/controlled_terms/terminology.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import Terminology +from openminds.latest.controlled_terms import Terminology as OMTerminology from fairgraph import KGObject from openminds import IRI -class Terminology(KGObject, Terminology): +class Terminology(KGObject, OMTerminology): """ """ @@ -87,3 +87,13 @@ def __init__( suggested_in=suggested_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Terminology.set_error_handling(None) +for key, value in OMTerminology.__dict__.items(): + if isinstance(value, OMTerminology): + fg_instance = Terminology.from_jsonld(value.to_jsonld()) + fg_instance._space = Terminology.default_space + setattr(Terminology, key, fg_instance) +Terminology.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py index 883c881a..603cea09 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import TissueSampleAttribute +from openminds.latest.controlled_terms import TissueSampleAttribute as OMTissueSampleAttribute from fairgraph import KGObject from openminds import IRI -class TissueSampleAttribute(KGObject, TissueSampleAttribute): +class TissueSampleAttribute(KGObject, OMTissueSampleAttribute): """ """ @@ -87,3 +87,13 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueSampleAttribute.set_error_handling(None) +for key, value in OMTissueSampleAttribute.__dict__.items(): + if isinstance(value, OMTissueSampleAttribute): + fg_instance = TissueSampleAttribute.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueSampleAttribute.default_space + setattr(TissueSampleAttribute, key, fg_instance) +TissueSampleAttribute.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_type.py b/fairgraph/openminds/controlled_terms/tissue_sample_type.py index 26ad9190..da33c8e7 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_type.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import TissueSampleType +from openminds.latest.controlled_terms import TissueSampleType as OMTissueSampleType from fairgraph import KGObject from openminds import IRI -class TissueSampleType(KGObject, TissueSampleType): +class TissueSampleType(KGObject, OMTissueSampleType): """ Structured information on the general type of the tissue sample. """ @@ -125,3 +125,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueSampleType.set_error_handling(None) +for key, value in OMTissueSampleType.__dict__.items(): + if isinstance(value, OMTissueSampleType): + fg_instance = TissueSampleType.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueSampleType.default_space + setattr(TissueSampleType, key, fg_instance) +TissueSampleType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py index 868b31be..c3defc8e 100644 --- a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py +++ b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import TypeOfUncertainty +from openminds.latest.controlled_terms import TypeOfUncertainty as OMTypeOfUncertainty from fairgraph import KGObject from openminds import IRI -class TypeOfUncertainty(KGObject, TypeOfUncertainty): +class TypeOfUncertainty(KGObject, OMTypeOfUncertainty): """ """ @@ -87,3 +87,13 @@ def __init__( synonyms=synonyms, value=value, ) + + +# cast openMINDS instances to their fairgraph subclass +TypeOfUncertainty.set_error_handling(None) +for key, value in OMTypeOfUncertainty.__dict__.items(): + if isinstance(value, OMTypeOfUncertainty): + fg_instance = TypeOfUncertainty.from_jsonld(value.to_jsonld()) + fg_instance._space = TypeOfUncertainty.default_space + setattr(TypeOfUncertainty, key, fg_instance) +TypeOfUncertainty.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/uberon_parcellation.py b/fairgraph/openminds/controlled_terms/uberon_parcellation.py index 674597d2..dd63ae70 100644 --- a/fairgraph/openminds/controlled_terms/uberon_parcellation.py +++ b/fairgraph/openminds/controlled_terms/uberon_parcellation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import UBERONParcellation +from openminds.latest.controlled_terms import UBERONParcellation as OMUBERONParcellation from fairgraph import KGObject from openminds import IRI -class UBERONParcellation(KGObject, UBERONParcellation): +class UBERONParcellation(KGObject, OMUBERONParcellation): """ """ @@ -151,3 +151,13 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +UBERONParcellation.set_error_handling(None) +for key, value in OMUBERONParcellation.__dict__.items(): + if isinstance(value, OMUBERONParcellation): + fg_instance = UBERONParcellation.from_jsonld(value.to_jsonld()) + fg_instance._space = UBERONParcellation.default_space + setattr(UBERONParcellation, key, fg_instance) +UBERONParcellation.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/unit_of_measurement.py b/fairgraph/openminds/controlled_terms/unit_of_measurement.py index 32204a79..e3253364 100644 --- a/fairgraph/openminds/controlled_terms/unit_of_measurement.py +++ b/fairgraph/openminds/controlled_terms/unit_of_measurement.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import UnitOfMeasurement +from openminds.latest.controlled_terms import UnitOfMeasurement as OMUnitOfMeasurement from fairgraph import KGObject from openminds import IRI -class UnitOfMeasurement(KGObject, UnitOfMeasurement): +class UnitOfMeasurement(KGObject, OMUnitOfMeasurement): """ Structured information on the unit of measurement. """ @@ -106,3 +106,13 @@ def __init__( used_in=used_in, value=value, ) + + +# cast openMINDS instances to their fairgraph subclass +UnitOfMeasurement.set_error_handling(None) +for key, value in OMUnitOfMeasurement.__dict__.items(): + if isinstance(value, OMUnitOfMeasurement): + fg_instance = UnitOfMeasurement.from_jsonld(value.to_jsonld()) + fg_instance._space = UnitOfMeasurement.default_space + setattr(UnitOfMeasurement, key, fg_instance) +UnitOfMeasurement.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py index 91f69160..daf03550 100644 --- a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import VisualStimulusType +from openminds.latest.controlled_terms import VisualStimulusType as OMVisualStimulusType from fairgraph import KGObject from openminds import IRI -class VisualStimulusType(KGObject, VisualStimulusType): +class VisualStimulusType(KGObject, OMVisualStimulusType): """ """ @@ -125,3 +125,13 @@ def __init__( synonyms=synonyms, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +VisualStimulusType.set_error_handling(None) +for key, value in OMVisualStimulusType.__dict__.items(): + if isinstance(value, OMVisualStimulusType): + fg_instance = VisualStimulusType.from_jsonld(value.to_jsonld()) + fg_instance._space = VisualStimulusType.default_space + setattr(VisualStimulusType, key, fg_instance) +VisualStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/account_information.py b/fairgraph/openminds/core/actors/account_information.py index 60c640af..f4a70c5c 100644 --- a/fairgraph/openminds/core/actors/account_information.py +++ b/fairgraph/openminds/core/actors/account_information.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import AccountInformation +from openminds.latest.core import AccountInformation as OMAccountInformation from fairgraph import KGObject -class AccountInformation(KGObject, AccountInformation): +class AccountInformation(KGObject, OMAccountInformation): """ Structured information about a user account for a web service. """ @@ -40,3 +40,13 @@ def __init__(self, belongs_to=None, service=None, user_name=None, id=None, data= service=service, user_name=user_name, ) + + +# cast openMINDS instances to their fairgraph subclass +AccountInformation.set_error_handling(None) +for key, value in OMAccountInformation.__dict__.items(): + if isinstance(value, OMAccountInformation): + fg_instance = AccountInformation.from_jsonld(value.to_jsonld()) + fg_instance._space = AccountInformation.default_space + setattr(AccountInformation, key, fg_instance) +AccountInformation.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/affiliation.py b/fairgraph/openminds/core/actors/affiliation.py index 8e314fe3..84a68910 100644 --- a/fairgraph/openminds/core/actors/affiliation.py +++ b/fairgraph/openminds/core/actors/affiliation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Affiliation +from openminds.latest.core import Affiliation as OMAffiliation from fairgraph import EmbeddedMetadata from datetime import date -class Affiliation(EmbeddedMetadata, Affiliation): +class Affiliation(EmbeddedMetadata, OMAffiliation): """ Structured information about a relationship between two entities, such as a person and their employer. """ @@ -25,3 +25,13 @@ def __init__(self, end_date=None, member_of=None, start_date=None, id=None, data return EmbeddedMetadata.__init__( self, data=data, end_date=end_date, member_of=member_of, start_date=start_date ) + + +# cast openMINDS instances to their fairgraph subclass +Affiliation.set_error_handling(None) +for key, value in OMAffiliation.__dict__.items(): + if isinstance(value, OMAffiliation): + fg_instance = Affiliation.from_jsonld(value.to_jsonld()) + fg_instance._space = Affiliation.default_space + setattr(Affiliation, key, fg_instance) +Affiliation.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/consortium.py b/fairgraph/openminds/core/actors/consortium.py index d3ca8fae..60be5b94 100644 --- a/fairgraph/openminds/core/actors/consortium.py +++ b/fairgraph/openminds/core/actors/consortium.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Consortium +from openminds.latest.core import Consortium as OMConsortium from fairgraph import KGObject from openminds import IRI -class Consortium(KGObject, Consortium): +class Consortium(KGObject, OMConsortium): """ Structured information about an association of two or more persons or organizations, with the objective of participating in a common activity. """ @@ -173,3 +173,13 @@ def __init__( published=published, short_name=short_name, ) + + +# cast openMINDS instances to their fairgraph subclass +Consortium.set_error_handling(None) +for key, value in OMConsortium.__dict__.items(): + if isinstance(value, OMConsortium): + fg_instance = Consortium.from_jsonld(value.to_jsonld()) + fg_instance._space = Consortium.default_space + setattr(Consortium, key, fg_instance) +Consortium.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/contact_information.py b/fairgraph/openminds/core/actors/contact_information.py index 26c18f89..70631b9c 100644 --- a/fairgraph/openminds/core/actors/contact_information.py +++ b/fairgraph/openminds/core/actors/contact_information.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ContactInformation +from openminds.latest.core import ContactInformation as OMContactInformation from fairgraph import KGObject -class ContactInformation(KGObject, ContactInformation): +class ContactInformation(KGObject, OMContactInformation): """ Structured information about how to contact a given person or consortium. """ @@ -39,3 +39,13 @@ def __init__(self, email=None, is_contact_information_of=None, id=None, data=Non email=email, is_contact_information_of=is_contact_information_of, ) + + +# cast openMINDS instances to their fairgraph subclass +ContactInformation.set_error_handling(None) +for key, value in OMContactInformation.__dict__.items(): + if isinstance(value, OMContactInformation): + fg_instance = ContactInformation.from_jsonld(value.to_jsonld()) + fg_instance._space = ContactInformation.default_space + setattr(ContactInformation, key, fg_instance) +ContactInformation.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/contribution.py b/fairgraph/openminds/core/actors/contribution.py index a4530369..4756ba13 100644 --- a/fairgraph/openminds/core/actors/contribution.py +++ b/fairgraph/openminds/core/actors/contribution.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Contribution +from openminds.latest.core import Contribution as OMContribution from fairgraph import EmbeddedMetadata -class Contribution(EmbeddedMetadata, Contribution): +class Contribution(EmbeddedMetadata, OMContribution): """ Structured information on the contribution made to a research product. """ @@ -20,3 +20,13 @@ class Contribution(EmbeddedMetadata, Contribution): def __init__(self, contributor=None, types=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, contributor=contributor, types=types) + + +# cast openMINDS instances to their fairgraph subclass +Contribution.set_error_handling(None) +for key, value in OMContribution.__dict__.items(): + if isinstance(value, OMContribution): + fg_instance = Contribution.from_jsonld(value.to_jsonld()) + fg_instance._space = Contribution.default_space + setattr(Contribution, key, fg_instance) +Contribution.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/organization.py b/fairgraph/openminds/core/actors/organization.py index c145c45f..6e312ca2 100644 --- a/fairgraph/openminds/core/actors/organization.py +++ b/fairgraph/openminds/core/actors/organization.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Organization +from openminds.latest.core import Organization as OMOrganization from fairgraph import KGObject from openminds import IRI -class Organization(KGObject, Organization): +class Organization(KGObject, OMOrganization): """ An entity comprised of one or more natural persons with a particular purpose. [adapted from Wikipedia](https://en.wikipedia.org/wiki/Organization) """ @@ -197,3 +197,13 @@ def __init__( published=published, short_name=short_name, ) + + +# cast openMINDS instances to their fairgraph subclass +Organization.set_error_handling(None) +for key, value in OMOrganization.__dict__.items(): + if isinstance(value, OMOrganization): + fg_instance = Organization.from_jsonld(value.to_jsonld()) + fg_instance._space = Organization.default_space + setattr(Organization, key, fg_instance) +Organization.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/person.py b/fairgraph/openminds/core/actors/person.py index 54163e33..d9206bb5 100644 --- a/fairgraph/openminds/core/actors/person.py +++ b/fairgraph/openminds/core/actors/person.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Person +from openminds.latest.core import Person as OMPerson from fairgraph import KGObject -class Person(KGObject, Person): +class Person(KGObject, OMPerson): """ Structured information on a person. """ @@ -234,3 +234,13 @@ def me(cls, client, allow_multiple=False, follow_links=None): else: raise Exception("Found multiple matches") return person + + +# cast openMINDS instances to their fairgraph subclass +Person.set_error_handling(None) +for key, value in OMPerson.__dict__.items(): + if isinstance(value, OMPerson): + fg_instance = Person.from_jsonld(value.to_jsonld()) + fg_instance._space = Person.default_space + setattr(Person, key, fg_instance) +Person.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/content_type.py b/fairgraph/openminds/core/data/content_type.py index c25e30b1..da36b408 100644 --- a/fairgraph/openminds/core/data/content_type.py +++ b/fairgraph/openminds/core/data/content_type.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ContentType +from openminds.latest.core import ContentType as OMContentType from fairgraph import KGObject from openminds import IRI -class ContentType(KGObject, ContentType): +class ContentType(KGObject, OMContentType): """ Structured information on the content type of a file instance, bundle or repository. """ @@ -105,3 +105,13 @@ def __init__( specification=specification, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +ContentType.set_error_handling(None) +for key, value in OMContentType.__dict__.items(): + if isinstance(value, OMContentType): + fg_instance = ContentType.from_jsonld(value.to_jsonld()) + fg_instance._space = ContentType.default_space + setattr(ContentType, key, fg_instance) +ContentType.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/content_type_pattern.py b/fairgraph/openminds/core/data/content_type_pattern.py index 5297fc20..854fb761 100644 --- a/fairgraph/openminds/core/data/content_type_pattern.py +++ b/fairgraph/openminds/core/data/content_type_pattern.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ContentTypePattern +from openminds.latest.core import ContentTypePattern as OMContentTypePattern from fairgraph import KGObject -class ContentTypePattern(KGObject, ContentTypePattern): +class ContentTypePattern(KGObject, OMContentTypePattern): """ """ @@ -51,3 +51,13 @@ def __init__( identifies_content_of=identifies_content_of, regex=regex, ) + + +# cast openMINDS instances to their fairgraph subclass +ContentTypePattern.set_error_handling(None) +for key, value in OMContentTypePattern.__dict__.items(): + if isinstance(value, OMContentTypePattern): + fg_instance = ContentTypePattern.from_jsonld(value.to_jsonld()) + fg_instance._space = ContentTypePattern.default_space + setattr(ContentTypePattern, key, fg_instance) +ContentTypePattern.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/copyright.py b/fairgraph/openminds/core/data/copyright.py index 5350dab6..6b77a5a2 100644 --- a/fairgraph/openminds/core/data/copyright.py +++ b/fairgraph/openminds/core/data/copyright.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Copyright +from openminds.latest.core import Copyright as OMCopyright from fairgraph import EmbeddedMetadata -class Copyright(EmbeddedMetadata, Copyright): +class Copyright(EmbeddedMetadata, OMCopyright): """ Structured information on the copyright. """ @@ -20,3 +20,13 @@ class Copyright(EmbeddedMetadata, Copyright): def __init__(self, holders=None, years=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, holders=holders, years=years) + + +# cast openMINDS instances to their fairgraph subclass +Copyright.set_error_handling(None) +for key, value in OMCopyright.__dict__.items(): + if isinstance(value, OMCopyright): + fg_instance = Copyright.from_jsonld(value.to_jsonld()) + fg_instance._space = Copyright.default_space + setattr(Copyright, key, fg_instance) +Copyright.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file.py b/fairgraph/openminds/core/data/file.py index adc5ffee..3d8254c4 100644 --- a/fairgraph/openminds/core/data/file.py +++ b/fairgraph/openminds/core/data/file.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import File +from openminds.latest.core import File as OMFile from fairgraph import KGObject import os @@ -23,7 +23,7 @@ from openminds import IRI -class File(KGObject, File): +class File(KGObject, OMFile): """ Structured information on a file instance that is accessible via a URL. """ @@ -273,3 +273,13 @@ def download(self, local_path, client, accept_terms_of_use=False): # rather than a filename, create that directory and save a file called self.name # within it return local_filename + + +# cast openMINDS instances to their fairgraph subclass +File.set_error_handling(None) +for key, value in OMFile.__dict__.items(): + if isinstance(value, OMFile): + fg_instance = File.from_jsonld(value.to_jsonld()) + fg_instance._space = File.default_space + setattr(File, key, fg_instance) +File.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_archive.py b/fairgraph/openminds/core/data/file_archive.py index 9c91b29b..e563a976 100644 --- a/fairgraph/openminds/core/data/file_archive.py +++ b/fairgraph/openminds/core/data/file_archive.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import FileArchive +from openminds.latest.core import FileArchive as OMFileArchive from fairgraph import KGObject from openminds import IRI -class FileArchive(KGObject, FileArchive): +class FileArchive(KGObject, OMFileArchive): """ """ @@ -69,3 +69,13 @@ def __init__( is_output_of=is_output_of, source_data=source_data, ) + + +# cast openMINDS instances to their fairgraph subclass +FileArchive.set_error_handling(None) +for key, value in OMFileArchive.__dict__.items(): + if isinstance(value, OMFileArchive): + fg_instance = FileArchive.from_jsonld(value.to_jsonld()) + fg_instance._space = FileArchive.default_space + setattr(FileArchive, key, fg_instance) +FileArchive.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_bundle.py b/fairgraph/openminds/core/data/file_bundle.py index 91616fe1..1c146327 100644 --- a/fairgraph/openminds/core/data/file_bundle.py +++ b/fairgraph/openminds/core/data/file_bundle.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import FileBundle +from openminds.latest.core import FileBundle as OMFileBundle from fairgraph import KGObject -class FileBundle(KGObject, FileBundle): +class FileBundle(KGObject, OMFileBundle): """ Structured information on a bundle of file instances. """ @@ -148,3 +148,13 @@ def __init__( specifies=specifies, storage_size=storage_size, ) + + +# cast openMINDS instances to their fairgraph subclass +FileBundle.set_error_handling(None) +for key, value in OMFileBundle.__dict__.items(): + if isinstance(value, OMFileBundle): + fg_instance = FileBundle.from_jsonld(value.to_jsonld()) + fg_instance._space = FileBundle.default_space + setattr(FileBundle, key, fg_instance) +FileBundle.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_path_pattern.py b/fairgraph/openminds/core/data/file_path_pattern.py index c3c9a9dc..f92d3d8b 100644 --- a/fairgraph/openminds/core/data/file_path_pattern.py +++ b/fairgraph/openminds/core/data/file_path_pattern.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import FilePathPattern +from openminds.latest.core import FilePathPattern as OMFilePathPattern from fairgraph import EmbeddedMetadata -class FilePathPattern(EmbeddedMetadata, FilePathPattern): +class FilePathPattern(EmbeddedMetadata, OMFilePathPattern): """ """ @@ -20,3 +20,13 @@ class FilePathPattern(EmbeddedMetadata, FilePathPattern): def __init__(self, grouping_types=None, regex=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, grouping_types=grouping_types, regex=regex) + + +# cast openMINDS instances to their fairgraph subclass +FilePathPattern.set_error_handling(None) +for key, value in OMFilePathPattern.__dict__.items(): + if isinstance(value, OMFilePathPattern): + fg_instance = FilePathPattern.from_jsonld(value.to_jsonld()) + fg_instance._space = FilePathPattern.default_space + setattr(FilePathPattern, key, fg_instance) +FilePathPattern.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_repository.py b/fairgraph/openminds/core/data/file_repository.py index 0b31d283..a6cbebf1 100644 --- a/fairgraph/openminds/core/data/file_repository.py +++ b/fairgraph/openminds/core/data/file_repository.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import FileRepository +from openminds.latest.core import FileRepository as OMFileRepository from fairgraph import KGObject from openminds import IRI -class FileRepository(KGObject, FileRepository): +class FileRepository(KGObject, OMFileRepository): """ Structured information on a file repository. """ @@ -97,3 +97,13 @@ def __init__( structure_pattern=structure_pattern, type=type, ) + + +# cast openMINDS instances to their fairgraph subclass +FileRepository.set_error_handling(None) +for key, value in OMFileRepository.__dict__.items(): + if isinstance(value, OMFileRepository): + fg_instance = FileRepository.from_jsonld(value.to_jsonld()) + fg_instance._space = FileRepository.default_space + setattr(FileRepository, key, fg_instance) +FileRepository.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_repository_structure.py b/fairgraph/openminds/core/data/file_repository_structure.py index 4b289f42..6bdade73 100644 --- a/fairgraph/openminds/core/data/file_repository_structure.py +++ b/fairgraph/openminds/core/data/file_repository_structure.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import FileRepositoryStructure +from openminds.latest.core import FileRepositoryStructure as OMFileRepositoryStructure from fairgraph import KGObject -class FileRepositoryStructure(KGObject, FileRepositoryStructure): +class FileRepositoryStructure(KGObject, OMFileRepositoryStructure): """ """ @@ -42,3 +42,13 @@ def __init__( file_path_patterns=file_path_patterns, structures=structures, ) + + +# cast openMINDS instances to their fairgraph subclass +FileRepositoryStructure.set_error_handling(None) +for key, value in OMFileRepositoryStructure.__dict__.items(): + if isinstance(value, OMFileRepositoryStructure): + fg_instance = FileRepositoryStructure.from_jsonld(value.to_jsonld()) + fg_instance._space = FileRepositoryStructure.default_space + setattr(FileRepositoryStructure, key, fg_instance) +FileRepositoryStructure.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/hash.py b/fairgraph/openminds/core/data/hash.py index 45f4eb8d..15453558 100644 --- a/fairgraph/openminds/core/data/hash.py +++ b/fairgraph/openminds/core/data/hash.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Hash +from openminds.latest.core import Hash as OMHash from fairgraph import EmbeddedMetadata -class Hash(EmbeddedMetadata, Hash): +class Hash(EmbeddedMetadata, OMHash): """ Structured information on a hash. """ @@ -20,3 +20,13 @@ class Hash(EmbeddedMetadata, Hash): def __init__(self, algorithm=None, digest=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, algorithm=algorithm, digest=digest) + + +# cast openMINDS instances to their fairgraph subclass +Hash.set_error_handling(None) +for key, value in OMHash.__dict__.items(): + if isinstance(value, OMHash): + fg_instance = Hash.from_jsonld(value.to_jsonld()) + fg_instance._space = Hash.default_space + setattr(Hash, key, fg_instance) +Hash.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/license.py b/fairgraph/openminds/core/data/license.py index 9e957c41..b95c74f7 100644 --- a/fairgraph/openminds/core/data/license.py +++ b/fairgraph/openminds/core/data/license.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import License +from openminds.latest.core import License as OMLicense from fairgraph import KGObject from openminds import IRI -class License(KGObject, License): +class License(KGObject, OMLicense): """ Structured information on a used license. """ @@ -75,3 +75,13 @@ def __init__( short_name=short_name, webpages=webpages, ) + + +# cast openMINDS instances to their fairgraph subclass +License.set_error_handling(None) +for key, value in OMLicense.__dict__.items(): + if isinstance(value, OMLicense): + fg_instance = License.from_jsonld(value.to_jsonld()) + fg_instance._space = License.default_space + setattr(License, key, fg_instance) +License.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/measurement.py b/fairgraph/openminds/core/data/measurement.py index afab14d7..e69d2521 100644 --- a/fairgraph/openminds/core/data/measurement.py +++ b/fairgraph/openminds/core/data/measurement.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Measurement +from openminds.latest.core import Measurement as OMMeasurement from fairgraph import EmbeddedMetadata from datetime import datetime -class Measurement(EmbeddedMetadata, Measurement): +class Measurement(EmbeddedMetadata, OMMeasurement): """ Structured information about a measurement performed during a scientific experiment. """ @@ -42,3 +42,13 @@ def __init__( timestamp=timestamp, values=values, ) + + +# cast openMINDS instances to their fairgraph subclass +Measurement.set_error_handling(None) +for key, value in OMMeasurement.__dict__.items(): + if isinstance(value, OMMeasurement): + fg_instance = Measurement.from_jsonld(value.to_jsonld()) + fg_instance._space = Measurement.default_space + setattr(Measurement, key, fg_instance) +Measurement.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/service_link.py b/fairgraph/openminds/core/data/service_link.py index 57a12eaf..c3c6dfc2 100644 --- a/fairgraph/openminds/core/data/service_link.py +++ b/fairgraph/openminds/core/data/service_link.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ServiceLink +from openminds.latest.core import ServiceLink as OMServiceLink from fairgraph import KGObject from openminds import IRI -class ServiceLink(KGObject, ServiceLink): +class ServiceLink(KGObject, OMServiceLink): """ """ @@ -47,3 +47,13 @@ def __init__( preview_image=preview_image, service=service, ) + + +# cast openMINDS instances to their fairgraph subclass +ServiceLink.set_error_handling(None) +for key, value in OMServiceLink.__dict__.items(): + if isinstance(value, OMServiceLink): + fg_instance = ServiceLink.from_jsonld(value.to_jsonld()) + fg_instance._space = ServiceLink.default_space + setattr(ServiceLink, key, fg_instance) +ServiceLink.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/doi.py b/fairgraph/openminds/core/digital_identifier/doi.py index a7fd5f8a..9f766774 100644 --- a/fairgraph/openminds/core/digital_identifier/doi.py +++ b/fairgraph/openminds/core/digital_identifier/doi.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import DOI +from openminds.latest.core import DOI as OMDOI from fairgraph import KGObject -class DOI(KGObject, DOI): +class DOI(KGObject, OMDOI): """ Structured information about a digital object identifier, as standardized by the International Organization for Standardization. """ @@ -96,3 +96,13 @@ def __init__( identifies=identifies, related_to=related_to, ) + + +# cast openMINDS instances to their fairgraph subclass +DOI.set_error_handling(None) +for key, value in OMDOI.__dict__.items(): + if isinstance(value, OMDOI): + fg_instance = DOI.from_jsonld(value.to_jsonld()) + fg_instance._space = DOI.default_space + setattr(DOI, key, fg_instance) +DOI.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/gridid.py b/fairgraph/openminds/core/digital_identifier/gridid.py index 2596321d..5024f226 100644 --- a/fairgraph/openminds/core/digital_identifier/gridid.py +++ b/fairgraph/openminds/core/digital_identifier/gridid.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import GRIDID +from openminds.latest.core import GRIDID as OMGRIDID from fairgraph import KGObject -class GRIDID(KGObject, GRIDID): +class GRIDID(KGObject, OMGRIDID): """ A GRID (Global Research Identifier Database) identifier. """ @@ -33,3 +33,13 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) + + +# cast openMINDS instances to their fairgraph subclass +GRIDID.set_error_handling(None) +for key, value in OMGRIDID.__dict__.items(): + if isinstance(value, OMGRIDID): + fg_instance = GRIDID.from_jsonld(value.to_jsonld()) + fg_instance._space = GRIDID.default_space + setattr(GRIDID, key, fg_instance) +GRIDID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/handle.py b/fairgraph/openminds/core/digital_identifier/handle.py index d9530dfc..64912c35 100644 --- a/fairgraph/openminds/core/digital_identifier/handle.py +++ b/fairgraph/openminds/core/digital_identifier/handle.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import HANDLE +from openminds.latest.core import HANDLE as OMHANDLE from fairgraph import KGObject -class HANDLE(KGObject, HANDLE): +class HANDLE(KGObject, OMHANDLE): """ A persistent identifier for an information resource provided by the Handle System of the Corporation for National Research Initiatives. """ @@ -44,3 +44,13 @@ def __init__(self, identifier=None, related_to=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, related_to=related_to ) + + +# cast openMINDS instances to their fairgraph subclass +HANDLE.set_error_handling(None) +for key, value in OMHANDLE.__dict__.items(): + if isinstance(value, OMHANDLE): + fg_instance = HANDLE.from_jsonld(value.to_jsonld()) + fg_instance._space = HANDLE.default_space + setattr(HANDLE, key, fg_instance) +HANDLE.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py index 29724ceb..7401f0a6 100644 --- a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py +++ b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import IdentifiersDotOrgID +from openminds.latest.core import IdentifiersDotOrgID as OMIdentifiersDotOrgID from fairgraph import KGObject -class IdentifiersDotOrgID(KGObject, IdentifiersDotOrgID): +class IdentifiersDotOrgID(KGObject, OMIdentifiersDotOrgID): """ """ @@ -33,3 +33,13 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) + + +# cast openMINDS instances to their fairgraph subclass +IdentifiersDotOrgID.set_error_handling(None) +for key, value in OMIdentifiersDotOrgID.__dict__.items(): + if isinstance(value, OMIdentifiersDotOrgID): + fg_instance = IdentifiersDotOrgID.from_jsonld(value.to_jsonld()) + fg_instance._space = IdentifiersDotOrgID.default_space + setattr(IdentifiersDotOrgID, key, fg_instance) +IdentifiersDotOrgID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/isbn.py b/fairgraph/openminds/core/digital_identifier/isbn.py index dcd1aa46..1046aff1 100644 --- a/fairgraph/openminds/core/digital_identifier/isbn.py +++ b/fairgraph/openminds/core/digital_identifier/isbn.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ISBN +from openminds.latest.core import ISBN as OMISBN from fairgraph import KGObject -class ISBN(KGObject, ISBN): +class ISBN(KGObject, OMISBN): """ An International Standard Book Number of the International ISBN Agency. """ @@ -86,3 +86,13 @@ def __init__( identifies=identifies, related_to=related_to, ) + + +# cast openMINDS instances to their fairgraph subclass +ISBN.set_error_handling(None) +for key, value in OMISBN.__dict__.items(): + if isinstance(value, OMISBN): + fg_instance = ISBN.from_jsonld(value.to_jsonld()) + fg_instance._space = ISBN.default_space + setattr(ISBN, key, fg_instance) +ISBN.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/issn.py b/fairgraph/openminds/core/digital_identifier/issn.py index b2d4d380..06f53402 100644 --- a/fairgraph/openminds/core/digital_identifier/issn.py +++ b/fairgraph/openminds/core/digital_identifier/issn.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ISSN +from openminds.latest.core import ISSN as OMISSN from fairgraph import KGObject -class ISSN(KGObject, ISSN): +class ISSN(KGObject, OMISSN): """ An International Standard Serial Number of the ISSN International Centre. """ @@ -59,3 +59,13 @@ def __init__(self, identifier=None, identifies=None, related_to=None, id=None, d identifies=identifies, related_to=related_to, ) + + +# cast openMINDS instances to their fairgraph subclass +ISSN.set_error_handling(None) +for key, value in OMISSN.__dict__.items(): + if isinstance(value, OMISSN): + fg_instance = ISSN.from_jsonld(value.to_jsonld()) + fg_instance._space = ISSN.default_space + setattr(ISSN, key, fg_instance) +ISSN.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/orcid.py b/fairgraph/openminds/core/digital_identifier/orcid.py index cf1a103d..961754ff 100644 --- a/fairgraph/openminds/core/digital_identifier/orcid.py +++ b/fairgraph/openminds/core/digital_identifier/orcid.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ORCID +from openminds.latest.core import ORCID as OMORCID from fairgraph import KGObject -class ORCID(KGObject, ORCID): +class ORCID(KGObject, OMORCID): """ A persistent identifier for a researcher provided by Open Researcher and Contributor ID, Inc. """ @@ -33,3 +33,13 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) + + +# cast openMINDS instances to their fairgraph subclass +ORCID.set_error_handling(None) +for key, value in OMORCID.__dict__.items(): + if isinstance(value, OMORCID): + fg_instance = ORCID.from_jsonld(value.to_jsonld()) + fg_instance._space = ORCID.default_space + setattr(ORCID, key, fg_instance) +ORCID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/rorid.py b/fairgraph/openminds/core/digital_identifier/rorid.py index 1be099ce..7a51d621 100644 --- a/fairgraph/openminds/core/digital_identifier/rorid.py +++ b/fairgraph/openminds/core/digital_identifier/rorid.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import RORID +from openminds.latest.core import RORID as OMRORID from fairgraph import KGObject -class RORID(KGObject, RORID): +class RORID(KGObject, OMRORID): """ A persistent identifier for a research organization, provided by the Research Organization Registry. """ @@ -33,3 +33,13 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) + + +# cast openMINDS instances to their fairgraph subclass +RORID.set_error_handling(None) +for key, value in OMRORID.__dict__.items(): + if isinstance(value, OMRORID): + fg_instance = RORID.from_jsonld(value.to_jsonld()) + fg_instance._space = RORID.default_space + setattr(RORID, key, fg_instance) +RORID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/rrid.py b/fairgraph/openminds/core/digital_identifier/rrid.py index 9a9164c9..454f0e66 100644 --- a/fairgraph/openminds/core/digital_identifier/rrid.py +++ b/fairgraph/openminds/core/digital_identifier/rrid.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import RRID +from openminds.latest.core import RRID as OMRRID from fairgraph import KGObject -class RRID(KGObject, RRID): +class RRID(KGObject, OMRRID): """ A persistent identifier for a research resource provided by the Resource Identification Initiative. """ @@ -47,3 +47,13 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) + + +# cast openMINDS instances to their fairgraph subclass +RRID.set_error_handling(None) +for key, value in OMRRID.__dict__.items(): + if isinstance(value, OMRRID): + fg_instance = RRID.from_jsonld(value.to_jsonld()) + fg_instance._space = RRID.default_space + setattr(RRID, key, fg_instance) +RRID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/stock_number.py b/fairgraph/openminds/core/digital_identifier/stock_number.py index bc62b583..da8189fb 100644 --- a/fairgraph/openminds/core/digital_identifier/stock_number.py +++ b/fairgraph/openminds/core/digital_identifier/stock_number.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import StockNumber +from openminds.latest.core import StockNumber as OMStockNumber from fairgraph import EmbeddedMetadata -class StockNumber(EmbeddedMetadata, StockNumber): +class StockNumber(EmbeddedMetadata, OMStockNumber): """ """ @@ -20,3 +20,13 @@ class StockNumber(EmbeddedMetadata, StockNumber): def __init__(self, identifier=None, vendor=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, identifier=identifier, vendor=vendor) + + +# cast openMINDS instances to their fairgraph subclass +StockNumber.set_error_handling(None) +for key, value in OMStockNumber.__dict__.items(): + if isinstance(value, OMStockNumber): + fg_instance = StockNumber.from_jsonld(value.to_jsonld()) + fg_instance._space = StockNumber.default_space + setattr(StockNumber, key, fg_instance) +StockNumber.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/swhid.py b/fairgraph/openminds/core/digital_identifier/swhid.py index 5eb9b473..901d0abd 100644 --- a/fairgraph/openminds/core/digital_identifier/swhid.py +++ b/fairgraph/openminds/core/digital_identifier/swhid.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import SWHID +from openminds.latest.core import SWHID as OMSWHID from fairgraph import KGObject -class SWHID(KGObject, SWHID): +class SWHID(KGObject, OMSWHID): """ """ @@ -40,3 +40,13 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) + + +# cast openMINDS instances to their fairgraph subclass +SWHID.set_error_handling(None) +for key, value in OMSWHID.__dict__.items(): + if isinstance(value, OMSWHID): + fg_instance = SWHID.from_jsonld(value.to_jsonld()) + fg_instance._space = SWHID.default_space + setattr(SWHID, key, fg_instance) +SWHID.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/comment.py b/fairgraph/openminds/core/miscellaneous/comment.py index f0f63086..1f740e4c 100644 --- a/fairgraph/openminds/core/miscellaneous/comment.py +++ b/fairgraph/openminds/core/miscellaneous/comment.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Comment +from openminds.latest.core import Comment as OMComment from fairgraph import KGObject from datetime import datetime -class Comment(KGObject, Comment): +class Comment(KGObject, OMComment): """ Structured information about a short text expressing an opinion on, or giving information about some entity. """ @@ -37,3 +37,13 @@ def __init__( commenter=commenter, timestamp=timestamp, ) + + +# cast openMINDS instances to their fairgraph subclass +Comment.set_error_handling(None) +for key, value in OMComment.__dict__.items(): + if isinstance(value, OMComment): + fg_instance = Comment.from_jsonld(value.to_jsonld()) + fg_instance._space = Comment.default_space + setattr(Comment, key, fg_instance) +Comment.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/funding.py b/fairgraph/openminds/core/miscellaneous/funding.py index af678517..1407571b 100644 --- a/fairgraph/openminds/core/miscellaneous/funding.py +++ b/fairgraph/openminds/core/miscellaneous/funding.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Funding +from openminds.latest.core import Funding as OMFunding from fairgraph import KGObject -class Funding(KGObject, Funding): +class Funding(KGObject, OMFunding): """ Structured information on used funding. """ @@ -68,3 +68,13 @@ def __init__( funded=funded, funder=funder, ) + + +# cast openMINDS instances to their fairgraph subclass +Funding.set_error_handling(None) +for key, value in OMFunding.__dict__.items(): + if isinstance(value, OMFunding): + fg_instance = Funding.from_jsonld(value.to_jsonld()) + fg_instance._space = Funding.default_space + setattr(Funding, key, fg_instance) +Funding.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value.py b/fairgraph/openminds/core/miscellaneous/quantitative_value.py index ae10032c..cb70ca0c 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import QuantitativeValue +from openminds.latest.core import QuantitativeValue as OMQuantitativeValue from fairgraph import EmbeddedMetadata from numbers import Real -class QuantitativeValue(EmbeddedMetadata, QuantitativeValue): +class QuantitativeValue(EmbeddedMetadata, OMQuantitativeValue): """ Structured information on a quantitative value. """ @@ -40,3 +40,13 @@ def __init__( unit=unit, value=value, ) + + +# cast openMINDS instances to their fairgraph subclass +QuantitativeValue.set_error_handling(None) +for key, value in OMQuantitativeValue.__dict__.items(): + if isinstance(value, OMQuantitativeValue): + fg_instance = QuantitativeValue.from_jsonld(value.to_jsonld()) + fg_instance._space = QuantitativeValue.default_space + setattr(QuantitativeValue, key, fg_instance) +QuantitativeValue.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py index 90fb8456..abdcb8e0 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import QuantitativeValueArray +from openminds.latest.core import QuantitativeValueArray as OMQuantitativeValueArray from fairgraph import KGObject from numbers import Real -class QuantitativeValueArray(KGObject, QuantitativeValueArray): +class QuantitativeValueArray(KGObject, OMQuantitativeValueArray): """ A representation of an array of quantitative values, optionally with uncertainties. """ @@ -47,3 +47,13 @@ def __init__( unit=unit, values=values, ) + + +# cast openMINDS instances to their fairgraph subclass +QuantitativeValueArray.set_error_handling(None) +for key, value in OMQuantitativeValueArray.__dict__.items(): + if isinstance(value, OMQuantitativeValueArray): + fg_instance = QuantitativeValueArray.from_jsonld(value.to_jsonld()) + fg_instance._space = QuantitativeValueArray.default_space + setattr(QuantitativeValueArray, key, fg_instance) +QuantitativeValueArray.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py index d9327ebd..40efd8d1 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import QuantitativeValueRange +from openminds.latest.core import QuantitativeValueRange as OMQuantitativeValueRange from fairgraph import EmbeddedMetadata from numbers import Real -class QuantitativeValueRange(EmbeddedMetadata, QuantitativeValueRange): +class QuantitativeValueRange(EmbeddedMetadata, OMQuantitativeValueRange): """ A representation of a range of quantitative values. """ @@ -40,3 +40,13 @@ def __init__( min_value=min_value, min_value_unit=min_value_unit, ) + + +# cast openMINDS instances to their fairgraph subclass +QuantitativeValueRange.set_error_handling(None) +for key, value in OMQuantitativeValueRange.__dict__.items(): + if isinstance(value, OMQuantitativeValueRange): + fg_instance = QuantitativeValueRange.from_jsonld(value.to_jsonld()) + fg_instance._space = QuantitativeValueRange.default_space + setattr(QuantitativeValueRange, key, fg_instance) +QuantitativeValueRange.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/research_product_group.py b/fairgraph/openminds/core/miscellaneous/research_product_group.py index 2a6cfb03..2461a4e3 100644 --- a/fairgraph/openminds/core/miscellaneous/research_product_group.py +++ b/fairgraph/openminds/core/miscellaneous/research_product_group.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ResearchProductGroup +from openminds.latest.core import ResearchProductGroup as OMResearchProductGroup from fairgraph import KGObject -class ResearchProductGroup(KGObject, ResearchProductGroup): +class ResearchProductGroup(KGObject, OMResearchProductGroup): """ """ @@ -24,3 +24,13 @@ def __init__(self, context=None, has_parts=None, id=None, data=None, space=None, return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, context=context, has_parts=has_parts ) + + +# cast openMINDS instances to their fairgraph subclass +ResearchProductGroup.set_error_handling(None) +for key, value in OMResearchProductGroup.__dict__.items(): + if isinstance(value, OMResearchProductGroup): + fg_instance = ResearchProductGroup.from_jsonld(value.to_jsonld()) + fg_instance._space = ResearchProductGroup.default_space + setattr(ResearchProductGroup, key, fg_instance) +ResearchProductGroup.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/web_resource.py b/fairgraph/openminds/core/miscellaneous/web_resource.py index ff57a6d4..36c761cf 100644 --- a/fairgraph/openminds/core/miscellaneous/web_resource.py +++ b/fairgraph/openminds/core/miscellaneous/web_resource.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import WebResource +from openminds.latest.core import WebResource as OMWebResource from fairgraph import KGObject from openminds import IRI -class WebResource(KGObject, WebResource): +class WebResource(KGObject, OMWebResource): """ """ @@ -102,3 +102,13 @@ def __init__( is_output_of=is_output_of, is_reference_for=is_reference_for, ) + + +# cast openMINDS instances to their fairgraph subclass +WebResource.set_error_handling(None) +for key, value in OMWebResource.__dict__.items(): + if isinstance(value, OMWebResource): + fg_instance = WebResource.from_jsonld(value.to_jsonld()) + fg_instance._space = WebResource.default_space + setattr(WebResource, key, fg_instance) +WebResource.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/dataset.py b/fairgraph/openminds/core/products/dataset.py index 639b597d..ed539b68 100644 --- a/fairgraph/openminds/core/products/dataset.py +++ b/fairgraph/openminds/core/products/dataset.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Dataset +from openminds.latest.core import Dataset as OMDataset from fairgraph import KGObject from openminds import IRI -class Dataset(KGObject, Dataset): +class Dataset(KGObject, OMDataset): """ Structured information on data originating from human/animal studies or simulations (concept level). """ @@ -93,3 +93,13 @@ def __init__( short_name=short_name, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +Dataset.set_error_handling(None) +for key, value in OMDataset.__dict__.items(): + if isinstance(value, OMDataset): + fg_instance = Dataset.from_jsonld(value.to_jsonld()) + fg_instance._space = Dataset.default_space + setattr(Dataset, key, fg_instance) +Dataset.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/dataset_version.py b/fairgraph/openminds/core/products/dataset_version.py index b5c82abf..c5606983 100644 --- a/fairgraph/openminds/core/products/dataset_version.py +++ b/fairgraph/openminds/core/products/dataset_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import DatasetVersion +from openminds.latest.core import DatasetVersion as OMDatasetVersion from fairgraph import KGObject from urllib.request import urlretrieve @@ -15,7 +15,7 @@ from openminds import IRI -class DatasetVersion(KGObject, DatasetVersion): +class DatasetVersion(KGObject, OMDatasetVersion): """ Structured information on data originating from human/animal studies or simulations (version level). """ @@ -218,3 +218,13 @@ def download(self, local_path, client, accept_terms_of_use=False): local_filename.parent.mkdir(parents=True, exist_ok=True) local_filename, headers = urlretrieve(zip_archive_url, local_filename) return local_filename, repo.iri.value + + +# cast openMINDS instances to their fairgraph subclass +DatasetVersion.set_error_handling(None) +for key, value in OMDatasetVersion.__dict__.items(): + if isinstance(value, OMDatasetVersion): + fg_instance = DatasetVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = DatasetVersion.default_space + setattr(DatasetVersion, key, fg_instance) +DatasetVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/meta_data_model.py b/fairgraph/openminds/core/products/meta_data_model.py index efb943d9..772f5cb8 100644 --- a/fairgraph/openminds/core/products/meta_data_model.py +++ b/fairgraph/openminds/core/products/meta_data_model.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import MetaDataModel +from openminds.latest.core import MetaDataModel as OMMetaDataModel from fairgraph import KGObject from openminds import IRI -class MetaDataModel(KGObject, MetaDataModel): +class MetaDataModel(KGObject, OMMetaDataModel): """ """ @@ -93,3 +93,13 @@ def __init__( short_name=short_name, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +MetaDataModel.set_error_handling(None) +for key, value in OMMetaDataModel.__dict__.items(): + if isinstance(value, OMMetaDataModel): + fg_instance = MetaDataModel.from_jsonld(value.to_jsonld()) + fg_instance._space = MetaDataModel.default_space + setattr(MetaDataModel, key, fg_instance) +MetaDataModel.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/meta_data_model_version.py b/fairgraph/openminds/core/products/meta_data_model_version.py index 4a5866e8..596d34b0 100644 --- a/fairgraph/openminds/core/products/meta_data_model_version.py +++ b/fairgraph/openminds/core/products/meta_data_model_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import MetaDataModelVersion +from openminds.latest.core import MetaDataModelVersion as OMMetaDataModelVersion from fairgraph import KGObject @@ -13,7 +13,7 @@ from openminds import IRI -class MetaDataModelVersion(KGObject, MetaDataModelVersion): +class MetaDataModelVersion(KGObject, OMMetaDataModelVersion): """ """ @@ -146,3 +146,13 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) + + +# cast openMINDS instances to their fairgraph subclass +MetaDataModelVersion.set_error_handling(None) +for key, value in OMMetaDataModelVersion.__dict__.items(): + if isinstance(value, OMMetaDataModelVersion): + fg_instance = MetaDataModelVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = MetaDataModelVersion.default_space + setattr(MetaDataModelVersion, key, fg_instance) +MetaDataModelVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/model.py b/fairgraph/openminds/core/products/model.py index a65a327f..83ace321 100644 --- a/fairgraph/openminds/core/products/model.py +++ b/fairgraph/openminds/core/products/model.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Model +from openminds.latest.core import Model as OMModel from fairgraph import KGObject from openminds import IRI -class Model(KGObject, Model): +class Model(KGObject, OMModel): """ Structured information on a computational model (concept level). """ @@ -99,3 +99,13 @@ def __init__( study_targets=study_targets, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +Model.set_error_handling(None) +for key, value in OMModel.__dict__.items(): + if isinstance(value, OMModel): + fg_instance = Model.from_jsonld(value.to_jsonld()) + fg_instance._space = Model.default_space + setattr(Model, key, fg_instance) +Model.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/model_version.py b/fairgraph/openminds/core/products/model_version.py index 7a3ac7a3..266b95c1 100644 --- a/fairgraph/openminds/core/products/model_version.py +++ b/fairgraph/openminds/core/products/model_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ModelVersion +from openminds.latest.core import ModelVersion as OMModelVersion from fairgraph import KGObject from fairgraph.errors import ResolutionFailure @@ -14,7 +14,7 @@ from openminds import IRI -class ModelVersion(KGObject, ModelVersion): +class ModelVersion(KGObject, OMModelVersion): """ Structured information on a computational model (version level). """ @@ -207,3 +207,13 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] + + +# cast openMINDS instances to their fairgraph subclass +ModelVersion.set_error_handling(None) +for key, value in OMModelVersion.__dict__.items(): + if isinstance(value, OMModelVersion): + fg_instance = ModelVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = ModelVersion.default_space + setattr(ModelVersion, key, fg_instance) +ModelVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/project.py b/fairgraph/openminds/core/products/project.py index 2d6e00a3..beb1ded9 100644 --- a/fairgraph/openminds/core/products/project.py +++ b/fairgraph/openminds/core/products/project.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Project +from openminds.latest.core import Project as OMProject from fairgraph import KGObject from openminds import IRI -class Project(KGObject, Project): +class Project(KGObject, OMProject): """ Structured information on a research project. """ @@ -54,3 +54,13 @@ def __init__( homepage=homepage, short_name=short_name, ) + + +# cast openMINDS instances to their fairgraph subclass +Project.set_error_handling(None) +for key, value in OMProject.__dict__.items(): + if isinstance(value, OMProject): + fg_instance = Project.from_jsonld(value.to_jsonld()) + fg_instance._space = Project.default_space + setattr(Project, key, fg_instance) +Project.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/setup.py b/fairgraph/openminds/core/products/setup.py index f08884b3..b2291efd 100644 --- a/fairgraph/openminds/core/products/setup.py +++ b/fairgraph/openminds/core/products/setup.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Setup +from openminds.latest.core import Setup as OMSetup from fairgraph import KGObject -class Setup(KGObject, Setup): +class Setup(KGObject, OMSetup): """ """ @@ -67,3 +67,13 @@ def __init__( types=types, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +Setup.set_error_handling(None) +for key, value in OMSetup.__dict__.items(): + if isinstance(value, OMSetup): + fg_instance = Setup.from_jsonld(value.to_jsonld()) + fg_instance._space = Setup.default_space + setattr(Setup, key, fg_instance) +Setup.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/software.py b/fairgraph/openminds/core/products/software.py index 53aea868..5da68e53 100644 --- a/fairgraph/openminds/core/products/software.py +++ b/fairgraph/openminds/core/products/software.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Software +from openminds.latest.core import Software as OMSoftware from fairgraph import KGObject from openminds import IRI -class Software(KGObject, Software): +class Software(KGObject, OMSoftware): """ Structured information on a software tool (concept level). """ @@ -93,3 +93,13 @@ def __init__( short_name=short_name, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +Software.set_error_handling(None) +for key, value in OMSoftware.__dict__.items(): + if isinstance(value, OMSoftware): + fg_instance = Software.from_jsonld(value.to_jsonld()) + fg_instance._space = Software.default_space + setattr(Software, key, fg_instance) +Software.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/software_version.py b/fairgraph/openminds/core/products/software_version.py index 8228a957..2214bff9 100644 --- a/fairgraph/openminds/core/products/software_version.py +++ b/fairgraph/openminds/core/products/software_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import SoftwareVersion +from openminds.latest.core import SoftwareVersion as OMSoftwareVersion from fairgraph import KGObject from fairgraph.errors import ResolutionFailure @@ -14,7 +14,7 @@ from openminds import IRI -class SoftwareVersion(KGObject, SoftwareVersion): +class SoftwareVersion(KGObject, OMSoftwareVersion): """ """ @@ -213,3 +213,13 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] + + +# cast openMINDS instances to their fairgraph subclass +SoftwareVersion.set_error_handling(None) +for key, value in OMSoftwareVersion.__dict__.items(): + if isinstance(value, OMSoftwareVersion): + fg_instance = SoftwareVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = SoftwareVersion.default_space + setattr(SoftwareVersion, key, fg_instance) +SoftwareVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/web_service.py b/fairgraph/openminds/core/products/web_service.py index 2105b61e..97ef9fb2 100644 --- a/fairgraph/openminds/core/products/web_service.py +++ b/fairgraph/openminds/core/products/web_service.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import WebService +from openminds.latest.core import WebService as OMWebService from fairgraph import KGObject from openminds import IRI -class WebService(KGObject, WebService): +class WebService(KGObject, OMWebService): """ """ @@ -111,3 +111,13 @@ def __init__( short_name=short_name, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +WebService.set_error_handling(None) +for key, value in OMWebService.__dict__.items(): + if isinstance(value, OMWebService): + fg_instance = WebService.from_jsonld(value.to_jsonld()) + fg_instance._space = WebService.default_space + setattr(WebService, key, fg_instance) +WebService.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/web_service_version.py b/fairgraph/openminds/core/products/web_service_version.py index 1b1b9c1e..31823614 100644 --- a/fairgraph/openminds/core/products/web_service_version.py +++ b/fairgraph/openminds/core/products/web_service_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import WebServiceVersion +from openminds.latest.core import WebServiceVersion as OMWebServiceVersion from fairgraph import KGObject from fairgraph.errors import ResolutionFailure @@ -14,7 +14,7 @@ from openminds import IRI -class WebServiceVersion(KGObject, WebServiceVersion): +class WebServiceVersion(KGObject, OMWebServiceVersion): """ """ @@ -169,3 +169,13 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] + + +# cast openMINDS instances to their fairgraph subclass +WebServiceVersion.set_error_handling(None) +for key, value in OMWebServiceVersion.__dict__.items(): + if isinstance(value, OMWebServiceVersion): + fg_instance = WebServiceVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = WebServiceVersion.default_space + setattr(WebServiceVersion, key, fg_instance) +WebServiceVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/behavioral_protocol.py b/fairgraph/openminds/core/research/behavioral_protocol.py index 986474a1..3764e50e 100644 --- a/fairgraph/openminds/core/research/behavioral_protocol.py +++ b/fairgraph/openminds/core/research/behavioral_protocol.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import BehavioralProtocol +from openminds.latest.core import BehavioralProtocol as OMBehavioralProtocol from fairgraph import KGObject -class BehavioralProtocol(KGObject, BehavioralProtocol): +class BehavioralProtocol(KGObject, OMBehavioralProtocol): """ Structured information about a protocol used in an experiment studying human or animal behavior. """ @@ -67,3 +67,13 @@ def __init__( stimulus_types=stimulus_types, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +BehavioralProtocol.set_error_handling(None) +for key, value in OMBehavioralProtocol.__dict__.items(): + if isinstance(value, OMBehavioralProtocol): + fg_instance = BehavioralProtocol.from_jsonld(value.to_jsonld()) + fg_instance._space = BehavioralProtocol.default_space + setattr(BehavioralProtocol, key, fg_instance) +BehavioralProtocol.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/configuration.py b/fairgraph/openminds/core/research/configuration.py index 98c1eb7d..6593f40c 100644 --- a/fairgraph/openminds/core/research/configuration.py +++ b/fairgraph/openminds/core/research/configuration.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Configuration +from openminds.latest.core import Configuration as OMConfiguration from fairgraph import KGObject -class Configuration(KGObject, Configuration): +class Configuration(KGObject, OMConfiguration): """ Structured information about the properties or parameters of an entity or process. """ @@ -66,3 +66,13 @@ def __init__( is_configuration_of=is_configuration_of, specifies=specifies, ) + + +# cast openMINDS instances to their fairgraph subclass +Configuration.set_error_handling(None) +for key, value in OMConfiguration.__dict__.items(): + if isinstance(value, OMConfiguration): + fg_instance = Configuration.from_jsonld(value.to_jsonld()) + fg_instance._space = Configuration.default_space + setattr(Configuration, key, fg_instance) +Configuration.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/custom_property_set.py b/fairgraph/openminds/core/research/custom_property_set.py index 58e18aca..bfa80faa 100644 --- a/fairgraph/openminds/core/research/custom_property_set.py +++ b/fairgraph/openminds/core/research/custom_property_set.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import CustomPropertySet +from openminds.latest.core import CustomPropertySet as OMCustomPropertySet from fairgraph import EmbeddedMetadata -class CustomPropertySet(EmbeddedMetadata, CustomPropertySet): +class CustomPropertySet(EmbeddedMetadata, OMCustomPropertySet): """ Structured information about properties of an entity that are not represented in an openMINDS schema. """ @@ -24,3 +24,13 @@ def __init__( return EmbeddedMetadata.__init__( self, data=data, context=context, data_location=data_location, relevant_for=relevant_for ) + + +# cast openMINDS instances to their fairgraph subclass +CustomPropertySet.set_error_handling(None) +for key, value in OMCustomPropertySet.__dict__.items(): + if isinstance(value, OMCustomPropertySet): + fg_instance = CustomPropertySet.from_jsonld(value.to_jsonld()) + fg_instance._space = CustomPropertySet.default_space + setattr(CustomPropertySet, key, fg_instance) +CustomPropertySet.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/numerical_property.py b/fairgraph/openminds/core/research/numerical_property.py index 5d4abe86..c8a6fc90 100644 --- a/fairgraph/openminds/core/research/numerical_property.py +++ b/fairgraph/openminds/core/research/numerical_property.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import NumericalProperty +from openminds.latest.core import NumericalProperty as OMNumericalProperty from fairgraph import EmbeddedMetadata -class NumericalProperty(EmbeddedMetadata, NumericalProperty): +class NumericalProperty(EmbeddedMetadata, OMNumericalProperty): """ Structured information about a property of some entity or process whose value is a number. """ @@ -20,3 +20,13 @@ class NumericalProperty(EmbeddedMetadata, NumericalProperty): def __init__(self, name=None, values=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, name=name, values=values) + + +# cast openMINDS instances to their fairgraph subclass +NumericalProperty.set_error_handling(None) +for key, value in OMNumericalProperty.__dict__.items(): + if isinstance(value, OMNumericalProperty): + fg_instance = NumericalProperty.from_jsonld(value.to_jsonld()) + fg_instance._space = NumericalProperty.default_space + setattr(NumericalProperty, key, fg_instance) +NumericalProperty.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/property_value_list.py b/fairgraph/openminds/core/research/property_value_list.py index 27f81b92..de59cb28 100644 --- a/fairgraph/openminds/core/research/property_value_list.py +++ b/fairgraph/openminds/core/research/property_value_list.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import PropertyValueList +from openminds.latest.core import PropertyValueList as OMPropertyValueList from fairgraph import KGObject -class PropertyValueList(KGObject, PropertyValueList): +class PropertyValueList(KGObject, OMPropertyValueList): """ An identifiable list of property-value pairs. """ @@ -69,3 +69,13 @@ def __init__( property_value_pairs=property_value_pairs, specifies=specifies, ) + + +# cast openMINDS instances to their fairgraph subclass +PropertyValueList.set_error_handling(None) +for key, value in OMPropertyValueList.__dict__.items(): + if isinstance(value, OMPropertyValueList): + fg_instance = PropertyValueList.from_jsonld(value.to_jsonld()) + fg_instance._space = PropertyValueList.default_space + setattr(PropertyValueList, key, fg_instance) +PropertyValueList.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/protocol.py b/fairgraph/openminds/core/research/protocol.py index 16af0ad7..89863840 100644 --- a/fairgraph/openminds/core/research/protocol.py +++ b/fairgraph/openminds/core/research/protocol.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Protocol +from openminds.latest.core import Protocol as OMProtocol from fairgraph import KGObject -class Protocol(KGObject, Protocol): +class Protocol(KGObject, OMProtocol): """ Structured information on a research project. """ @@ -65,3 +65,13 @@ def __init__( techniques=techniques, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +Protocol.set_error_handling(None) +for key, value in OMProtocol.__dict__.items(): + if isinstance(value, OMProtocol): + fg_instance = Protocol.from_jsonld(value.to_jsonld()) + fg_instance._space = Protocol.default_space + setattr(Protocol, key, fg_instance) +Protocol.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/protocol_execution.py b/fairgraph/openminds/core/research/protocol_execution.py index 1b6bfddd..ef4c9c3c 100644 --- a/fairgraph/openminds/core/research/protocol_execution.py +++ b/fairgraph/openminds/core/research/protocol_execution.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import ProtocolExecution +from openminds.latest.core import ProtocolExecution as OMProtocolExecution from fairgraph import KGObject from datetime import datetime, time -class ProtocolExecution(KGObject, ProtocolExecution): +class ProtocolExecution(KGObject, OMProtocolExecution): """ Structured information on a protocol execution. """ @@ -74,3 +74,13 @@ def __init__( start_time=start_time, study_targets=study_targets, ) + + +# cast openMINDS instances to their fairgraph subclass +ProtocolExecution.set_error_handling(None) +for key, value in OMProtocolExecution.__dict__.items(): + if isinstance(value, OMProtocolExecution): + fg_instance = ProtocolExecution.from_jsonld(value.to_jsonld()) + fg_instance._space = ProtocolExecution.default_space + setattr(ProtocolExecution, key, fg_instance) +ProtocolExecution.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/strain.py b/fairgraph/openminds/core/research/strain.py index b57b3086..5575d2b4 100644 --- a/fairgraph/openminds/core/research/strain.py +++ b/fairgraph/openminds/core/research/strain.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Strain +from openminds.latest.core import Strain as OMStrain from fairgraph import KGObject -class Strain(KGObject, Strain): +class Strain(KGObject, OMStrain): """ """ @@ -88,3 +88,13 @@ def __init__( stock_number=stock_number, synonyms=synonyms, ) + + +# cast openMINDS instances to their fairgraph subclass +Strain.set_error_handling(None) +for key, value in OMStrain.__dict__.items(): + if isinstance(value, OMStrain): + fg_instance = Strain.from_jsonld(value.to_jsonld()) + fg_instance._space = Strain.default_space + setattr(Strain, key, fg_instance) +Strain.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/string_property.py b/fairgraph/openminds/core/research/string_property.py index 9f69c4b8..5eb14f98 100644 --- a/fairgraph/openminds/core/research/string_property.py +++ b/fairgraph/openminds/core/research/string_property.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import StringProperty +from openminds.latest.core import StringProperty as OMStringProperty from fairgraph import EmbeddedMetadata -class StringProperty(EmbeddedMetadata, StringProperty): +class StringProperty(EmbeddedMetadata, OMStringProperty): """ """ @@ -20,3 +20,13 @@ class StringProperty(EmbeddedMetadata, StringProperty): def __init__(self, name=None, value=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, name=name, value=value) + + +# cast openMINDS instances to their fairgraph subclass +StringProperty.set_error_handling(None) +for key, value in OMStringProperty.__dict__.items(): + if isinstance(value, OMStringProperty): + fg_instance = StringProperty.from_jsonld(value.to_jsonld()) + fg_instance._space = StringProperty.default_space + setattr(StringProperty, key, fg_instance) +StringProperty.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject.py b/fairgraph/openminds/core/research/subject.py index ff15c1ba..4b8d83db 100644 --- a/fairgraph/openminds/core/research/subject.py +++ b/fairgraph/openminds/core/research/subject.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import Subject +from openminds.latest.core import Subject as OMSubject from fairgraph import KGObject -class Subject(KGObject, Subject): +class Subject(KGObject, OMSubject): """ Structured information on a subject. """ @@ -77,3 +77,13 @@ def __init__( studied_states=studied_states, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +Subject.set_error_handling(None) +for key, value in OMSubject.__dict__.items(): + if isinstance(value, OMSubject): + fg_instance = Subject.from_jsonld(value.to_jsonld()) + fg_instance._space = Subject.default_space + setattr(Subject, key, fg_instance) +Subject.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject_group.py b/fairgraph/openminds/core/research/subject_group.py index 06dec4d0..6d817bef 100644 --- a/fairgraph/openminds/core/research/subject_group.py +++ b/fairgraph/openminds/core/research/subject_group.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import SubjectGroup +from openminds.latest.core import SubjectGroup as OMSubjectGroup from fairgraph import KGObject -class SubjectGroup(KGObject, SubjectGroup): +class SubjectGroup(KGObject, OMSubjectGroup): """ """ @@ -89,3 +89,13 @@ def __init__( studied_states=studied_states, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +SubjectGroup.set_error_handling(None) +for key, value in OMSubjectGroup.__dict__.items(): + if isinstance(value, OMSubjectGroup): + fg_instance = SubjectGroup.from_jsonld(value.to_jsonld()) + fg_instance._space = SubjectGroup.default_space + setattr(SubjectGroup, key, fg_instance) +SubjectGroup.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject_group_state.py b/fairgraph/openminds/core/research/subject_group_state.py index a416d31c..1a9b91da 100644 --- a/fairgraph/openminds/core/research/subject_group_state.py +++ b/fairgraph/openminds/core/research/subject_group_state.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import SubjectGroupState +from openminds.latest.core import SubjectGroupState as OMSubjectGroupState from fairgraph import KGObject -class SubjectGroupState(KGObject, SubjectGroupState): +class SubjectGroupState(KGObject, OMSubjectGroupState): """ """ @@ -111,3 +111,13 @@ def __init__( relative_time_indication=relative_time_indication, weight=weight, ) + + +# cast openMINDS instances to their fairgraph subclass +SubjectGroupState.set_error_handling(None) +for key, value in OMSubjectGroupState.__dict__.items(): + if isinstance(value, OMSubjectGroupState): + fg_instance = SubjectGroupState.from_jsonld(value.to_jsonld()) + fg_instance._space = SubjectGroupState.default_space + setattr(SubjectGroupState, key, fg_instance) +SubjectGroupState.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject_state.py b/fairgraph/openminds/core/research/subject_state.py index 2322c444..5214f619 100644 --- a/fairgraph/openminds/core/research/subject_state.py +++ b/fairgraph/openminds/core/research/subject_state.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import SubjectState +from openminds.latest.core import SubjectState as OMSubjectState from fairgraph import KGObject -class SubjectState(KGObject, SubjectState): +class SubjectState(KGObject, OMSubjectState): """ Structured information on a temporary state of a subject. """ @@ -136,3 +136,13 @@ def __init__( used_in=used_in, weight=weight, ) + + +# cast openMINDS instances to their fairgraph subclass +SubjectState.set_error_handling(None) +for key, value in OMSubjectState.__dict__.items(): + if isinstance(value, OMSubjectState): + fg_instance = SubjectState.from_jsonld(value.to_jsonld()) + fg_instance._space = SubjectState.default_space + setattr(SubjectState, key, fg_instance) +SubjectState.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample.py b/fairgraph/openminds/core/research/tissue_sample.py index d045e94d..88fea5c7 100644 --- a/fairgraph/openminds/core/research/tissue_sample.py +++ b/fairgraph/openminds/core/research/tissue_sample.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import TissueSample +from openminds.latest.core import TissueSample as OMTissueSample from fairgraph import KGObject -class TissueSample(KGObject, TissueSample): +class TissueSample(KGObject, OMTissueSample): """ Structured information on a tissue sample. """ @@ -85,3 +85,13 @@ def __init__( type=type, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueSample.set_error_handling(None) +for key, value in OMTissueSample.__dict__.items(): + if isinstance(value, OMTissueSample): + fg_instance = TissueSample.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueSample.default_space + setattr(TissueSample, key, fg_instance) +TissueSample.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample_collection.py b/fairgraph/openminds/core/research/tissue_sample_collection.py index 743cf91f..76aef615 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import TissueSampleCollection +from openminds.latest.core import TissueSampleCollection as OMTissueSampleCollection from fairgraph import KGObject -class TissueSampleCollection(KGObject, TissueSampleCollection): +class TissueSampleCollection(KGObject, OMTissueSampleCollection): """ """ @@ -97,3 +97,13 @@ def __init__( types=types, used_in=used_in, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueSampleCollection.set_error_handling(None) +for key, value in OMTissueSampleCollection.__dict__.items(): + if isinstance(value, OMTissueSampleCollection): + fg_instance = TissueSampleCollection.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueSampleCollection.default_space + setattr(TissueSampleCollection, key, fg_instance) +TissueSampleCollection.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample_collection_state.py b/fairgraph/openminds/core/research/tissue_sample_collection_state.py index 44232354..6675e5de 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection_state.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import TissueSampleCollectionState +from openminds.latest.core import TissueSampleCollectionState as OMTissueSampleCollectionState from fairgraph import KGObject -class TissueSampleCollectionState(KGObject, TissueSampleCollectionState): +class TissueSampleCollectionState(KGObject, OMTissueSampleCollectionState): """ """ @@ -107,3 +107,13 @@ def __init__( relative_time_indication=relative_time_indication, weight=weight, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueSampleCollectionState.set_error_handling(None) +for key, value in OMTissueSampleCollectionState.__dict__.items(): + if isinstance(value, OMTissueSampleCollectionState): + fg_instance = TissueSampleCollectionState.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueSampleCollectionState.default_space + setattr(TissueSampleCollectionState, key, fg_instance) +TissueSampleCollectionState.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample_state.py b/fairgraph/openminds/core/research/tissue_sample_state.py index 950343ab..0c5325a6 100644 --- a/fairgraph/openminds/core/research/tissue_sample_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_state.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.core import TissueSampleState +from openminds.latest.core import TissueSampleState as OMTissueSampleState from fairgraph import KGObject -class TissueSampleState(KGObject, TissueSampleState): +class TissueSampleState(KGObject, OMTissueSampleState): """ Structured information on a temporary state of a tissue sample. """ @@ -125,3 +125,13 @@ def __init__( used_in=used_in, weight=weight, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueSampleState.set_error_handling(None) +for key, value in OMTissueSampleState.__dict__.items(): + if isinstance(value, OMTissueSampleState): + fg_instance = TissueSampleState.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueSampleState.default_space + setattr(TissueSampleState, key, fg_instance) +TissueSampleState.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/activity/cell_patching.py b/fairgraph/openminds/ephys/activity/cell_patching.py index 5a13c81b..fc1576c6 100644 --- a/fairgraph/openminds/ephys/activity/cell_patching.py +++ b/fairgraph/openminds/ephys/activity/cell_patching.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import CellPatching +from openminds.latest.ephys import CellPatching as OMCellPatching from fairgraph import KGObject from datetime import datetime, time -class CellPatching(KGObject, CellPatching): +class CellPatching(KGObject, OMCellPatching): """ """ @@ -71,3 +71,13 @@ def __init__( tissue_bath_solution=tissue_bath_solution, variation=variation, ) + + +# cast openMINDS instances to their fairgraph subclass +CellPatching.set_error_handling(None) +for key, value in OMCellPatching.__dict__.items(): + if isinstance(value, OMCellPatching): + fg_instance = CellPatching.from_jsonld(value.to_jsonld()) + fg_instance._space = CellPatching.default_space + setattr(CellPatching, key, fg_instance) +CellPatching.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/activity/electrode_placement.py b/fairgraph/openminds/ephys/activity/electrode_placement.py index 33307898..3d211d7f 100644 --- a/fairgraph/openminds/ephys/activity/electrode_placement.py +++ b/fairgraph/openminds/ephys/activity/electrode_placement.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import ElectrodePlacement +from openminds.latest.ephys import ElectrodePlacement as OMElectrodePlacement from fairgraph import KGObject from datetime import datetime, time -class ElectrodePlacement(KGObject, ElectrodePlacement): +class ElectrodePlacement(KGObject, OMElectrodePlacement): """ """ @@ -65,3 +65,13 @@ def __init__( study_targets=study_targets, target_position=target_position, ) + + +# cast openMINDS instances to their fairgraph subclass +ElectrodePlacement.set_error_handling(None) +for key, value in OMElectrodePlacement.__dict__.items(): + if isinstance(value, OMElectrodePlacement): + fg_instance = ElectrodePlacement.from_jsonld(value.to_jsonld()) + fg_instance._space = ElectrodePlacement.default_space + setattr(ElectrodePlacement, key, fg_instance) +ElectrodePlacement.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/activity/recording_activity.py b/fairgraph/openminds/ephys/activity/recording_activity.py index e7e09d7e..d80b14f0 100644 --- a/fairgraph/openminds/ephys/activity/recording_activity.py +++ b/fairgraph/openminds/ephys/activity/recording_activity.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import RecordingActivity +from openminds.latest.ephys import RecordingActivity as OMRecordingActivity from fairgraph import KGObject from datetime import datetime, time -class RecordingActivity(KGObject, RecordingActivity): +class RecordingActivity(KGObject, OMRecordingActivity): """ """ @@ -65,3 +65,13 @@ def __init__( start_time=start_time, study_targets=study_targets, ) + + +# cast openMINDS instances to their fairgraph subclass +RecordingActivity.set_error_handling(None) +for key, value in OMRecordingActivity.__dict__.items(): + if isinstance(value, OMRecordingActivity): + fg_instance = RecordingActivity.from_jsonld(value.to_jsonld()) + fg_instance._space = RecordingActivity.default_space + setattr(RecordingActivity, key, fg_instance) +RecordingActivity.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode.py b/fairgraph/openminds/ephys/device/electrode.py index cdb2c892..d5bb1c42 100644 --- a/fairgraph/openminds/ephys/device/electrode.py +++ b/fairgraph/openminds/ephys/device/electrode.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import Electrode +from openminds.latest.ephys import Electrode as OMElectrode from fairgraph import KGObject -class Electrode(KGObject, Electrode): +class Electrode(KGObject, OMElectrode): """ Structured information on an electrode. """ @@ -79,3 +79,13 @@ def __init__( serial_number=serial_number, usage=usage, ) + + +# cast openMINDS instances to their fairgraph subclass +Electrode.set_error_handling(None) +for key, value in OMElectrode.__dict__.items(): + if isinstance(value, OMElectrode): + fg_instance = Electrode.from_jsonld(value.to_jsonld()) + fg_instance._space = Electrode.default_space + setattr(Electrode, key, fg_instance) +Electrode.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode_array.py b/fairgraph/openminds/ephys/device/electrode_array.py index 896362d1..3c476b14 100644 --- a/fairgraph/openminds/ephys/device/electrode_array.py +++ b/fairgraph/openminds/ephys/device/electrode_array.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import ElectrodeArray +from openminds.latest.ephys import ElectrodeArray as OMElectrodeArray from fairgraph import KGObject -class ElectrodeArray(KGObject, ElectrodeArray): +class ElectrodeArray(KGObject, OMElectrodeArray): """ Structured information on an electrode array. """ @@ -83,3 +83,13 @@ def __init__( serial_number=serial_number, usage=usage, ) + + +# cast openMINDS instances to their fairgraph subclass +ElectrodeArray.set_error_handling(None) +for key, value in OMElectrodeArray.__dict__.items(): + if isinstance(value, OMElectrodeArray): + fg_instance = ElectrodeArray.from_jsonld(value.to_jsonld()) + fg_instance._space = ElectrodeArray.default_space + setattr(ElectrodeArray, key, fg_instance) +ElectrodeArray.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode_array_usage.py b/fairgraph/openminds/ephys/device/electrode_array_usage.py index b0c528c5..0d93fffb 100644 --- a/fairgraph/openminds/ephys/device/electrode_array_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_array_usage.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import ElectrodeArrayUsage +from openminds.latest.ephys import ElectrodeArrayUsage as OMElectrodeArrayUsage from fairgraph import KGObject -class ElectrodeArrayUsage(KGObject, ElectrodeArrayUsage): +class ElectrodeArrayUsage(KGObject, OMElectrodeArrayUsage): """ """ @@ -103,3 +103,13 @@ def __init__( used_to_measure=used_to_measure, used_to_record=used_to_record, ) + + +# cast openMINDS instances to their fairgraph subclass +ElectrodeArrayUsage.set_error_handling(None) +for key, value in OMElectrodeArrayUsage.__dict__.items(): + if isinstance(value, OMElectrodeArrayUsage): + fg_instance = ElectrodeArrayUsage.from_jsonld(value.to_jsonld()) + fg_instance._space = ElectrodeArrayUsage.default_space + setattr(ElectrodeArrayUsage, key, fg_instance) +ElectrodeArrayUsage.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode_usage.py b/fairgraph/openminds/ephys/device/electrode_usage.py index 8eddce21..1b377c13 100644 --- a/fairgraph/openminds/ephys/device/electrode_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_usage.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import ElectrodeUsage +from openminds.latest.ephys import ElectrodeUsage as OMElectrodeUsage from fairgraph import KGObject -class ElectrodeUsage(KGObject, ElectrodeUsage): +class ElectrodeUsage(KGObject, OMElectrodeUsage): """ """ @@ -99,3 +99,13 @@ def __init__( used_to_measure=used_to_measure, used_to_record=used_to_record, ) + + +# cast openMINDS instances to their fairgraph subclass +ElectrodeUsage.set_error_handling(None) +for key, value in OMElectrodeUsage.__dict__.items(): + if isinstance(value, OMElectrodeUsage): + fg_instance = ElectrodeUsage.from_jsonld(value.to_jsonld()) + fg_instance._space = ElectrodeUsage.default_space + setattr(ElectrodeUsage, key, fg_instance) +ElectrodeUsage.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/pipette.py b/fairgraph/openminds/ephys/device/pipette.py index 5a6febc5..2f9e6a4a 100644 --- a/fairgraph/openminds/ephys/device/pipette.py +++ b/fairgraph/openminds/ephys/device/pipette.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import Pipette +from openminds.latest.ephys import Pipette as OMPipette from fairgraph import KGObject -class Pipette(KGObject, Pipette): +class Pipette(KGObject, OMPipette): """ """ @@ -79,3 +79,13 @@ def __init__( serial_number=serial_number, usage=usage, ) + + +# cast openMINDS instances to their fairgraph subclass +Pipette.set_error_handling(None) +for key, value in OMPipette.__dict__.items(): + if isinstance(value, OMPipette): + fg_instance = Pipette.from_jsonld(value.to_jsonld()) + fg_instance._space = Pipette.default_space + setattr(Pipette, key, fg_instance) +Pipette.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/pipette_usage.py b/fairgraph/openminds/ephys/device/pipette_usage.py index fd2fa196..90d3882f 100644 --- a/fairgraph/openminds/ephys/device/pipette_usage.py +++ b/fairgraph/openminds/ephys/device/pipette_usage.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import PipetteUsage +from openminds.latest.ephys import PipetteUsage as OMPipetteUsage from fairgraph import KGObject -class PipetteUsage(KGObject, PipetteUsage): +class PipetteUsage(KGObject, OMPipetteUsage): """ """ @@ -121,3 +121,13 @@ def __init__( used_to_measure=used_to_measure, used_to_record=used_to_record, ) + + +# cast openMINDS instances to their fairgraph subclass +PipetteUsage.set_error_handling(None) +for key, value in OMPipetteUsage.__dict__.items(): + if isinstance(value, OMPipetteUsage): + fg_instance = PipetteUsage.from_jsonld(value.to_jsonld()) + fg_instance._space = PipetteUsage.default_space + setattr(PipetteUsage, key, fg_instance) +PipetteUsage.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/entity/channel.py b/fairgraph/openminds/ephys/entity/channel.py index ee1f0109..95be349e 100644 --- a/fairgraph/openminds/ephys/entity/channel.py +++ b/fairgraph/openminds/ephys/entity/channel.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import Channel +from openminds.latest.ephys import Channel as OMChannel from fairgraph import EmbeddedMetadata -class Channel(EmbeddedMetadata, Channel): +class Channel(EmbeddedMetadata, OMChannel): """ """ @@ -20,3 +20,13 @@ class Channel(EmbeddedMetadata, Channel): def __init__(self, internal_identifier=None, unit=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, internal_identifier=internal_identifier, unit=unit) + + +# cast openMINDS instances to their fairgraph subclass +Channel.set_error_handling(None) +for key, value in OMChannel.__dict__.items(): + if isinstance(value, OMChannel): + fg_instance = Channel.from_jsonld(value.to_jsonld()) + fg_instance._space = Channel.default_space + setattr(Channel, key, fg_instance) +Channel.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/entity/recording.py b/fairgraph/openminds/ephys/entity/recording.py index 621d2ffe..be750ea3 100644 --- a/fairgraph/openminds/ephys/entity/recording.py +++ b/fairgraph/openminds/ephys/entity/recording.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.ephys import Recording +from openminds.latest.ephys import Recording as OMRecording from fairgraph import KGObject -class Recording(KGObject, Recording): +class Recording(KGObject, OMRecording): """ """ @@ -61,3 +61,13 @@ def __init__( recorded_with=recorded_with, sampling_frequency=sampling_frequency, ) + + +# cast openMINDS instances to their fairgraph subclass +Recording.set_error_handling(None) +for key, value in OMRecording.__dict__.items(): + if isinstance(value, OMRecording): + fg_instance = Recording.from_jsonld(value.to_jsonld()) + fg_instance._space = Recording.default_space + setattr(Recording, key, fg_instance) +Recording.set_error_handling("log") diff --git a/fairgraph/openminds/publications/book.py b/fairgraph/openminds/publications/book.py index 3fe1fdd6..5c42e4f4 100644 --- a/fairgraph/openminds/publications/book.py +++ b/fairgraph/openminds/publications/book.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import Book +from openminds.latest.publications import Book as OMBook from fairgraph import KGObject @@ -13,7 +13,7 @@ from openminds import IRI -class Book(KGObject, Book): +class Book(KGObject, OMBook): """ """ @@ -104,3 +104,13 @@ def __init__( related_to=related_to, version_identifier=version_identifier, ) + + +# cast openMINDS instances to their fairgraph subclass +Book.set_error_handling(None) +for key, value in OMBook.__dict__.items(): + if isinstance(value, OMBook): + fg_instance = Book.from_jsonld(value.to_jsonld()) + fg_instance._space = Book.default_space + setattr(Book, key, fg_instance) +Book.set_error_handling("log") diff --git a/fairgraph/openminds/publications/chapter.py b/fairgraph/openminds/publications/chapter.py index 65b97c5a..371a6f7a 100644 --- a/fairgraph/openminds/publications/chapter.py +++ b/fairgraph/openminds/publications/chapter.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import Chapter +from openminds.latest.publications import Chapter as OMChapter from fairgraph import KGObject @@ -13,7 +13,7 @@ from openminds import IRI -class Chapter(KGObject, Chapter): +class Chapter(KGObject, OMChapter): """ """ @@ -98,3 +98,13 @@ def __init__( related_to=related_to, version_identifier=version_identifier, ) + + +# cast openMINDS instances to their fairgraph subclass +Chapter.set_error_handling(None) +for key, value in OMChapter.__dict__.items(): + if isinstance(value, OMChapter): + fg_instance = Chapter.from_jsonld(value.to_jsonld()) + fg_instance._space = Chapter.default_space + setattr(Chapter, key, fg_instance) +Chapter.set_error_handling("log") diff --git a/fairgraph/openminds/publications/learning_resource.py b/fairgraph/openminds/publications/learning_resource.py index fdbf4e87..46f53f23 100644 --- a/fairgraph/openminds/publications/learning_resource.py +++ b/fairgraph/openminds/publications/learning_resource.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import LearningResource +from openminds.latest.publications import LearningResource as OMLearningResource from fairgraph import KGObject @@ -13,7 +13,7 @@ from openminds import IRI -class LearningResource(KGObject, LearningResource): +class LearningResource(KGObject, OMLearningResource): """ """ @@ -88,3 +88,13 @@ def __init__( type=type, version_identifier=version_identifier, ) + + +# cast openMINDS instances to their fairgraph subclass +LearningResource.set_error_handling(None) +for key, value in OMLearningResource.__dict__.items(): + if isinstance(value, OMLearningResource): + fg_instance = LearningResource.from_jsonld(value.to_jsonld()) + fg_instance._space = LearningResource.default_space + setattr(LearningResource, key, fg_instance) +LearningResource.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper.py b/fairgraph/openminds/publications/live_paper.py index ffbf5c8f..d99a0299 100644 --- a/fairgraph/openminds/publications/live_paper.py +++ b/fairgraph/openminds/publications/live_paper.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import LivePaper +from openminds.latest.publications import LivePaper as OMLivePaper from fairgraph import KGObject from openminds import IRI -class LivePaper(KGObject, LivePaper): +class LivePaper(KGObject, OMLivePaper): """ """ @@ -93,3 +93,13 @@ def __init__( short_name=short_name, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +LivePaper.set_error_handling(None) +for key, value in OMLivePaper.__dict__.items(): + if isinstance(value, OMLivePaper): + fg_instance = LivePaper.from_jsonld(value.to_jsonld()) + fg_instance._space = LivePaper.default_space + setattr(LivePaper, key, fg_instance) +LivePaper.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper_resource_item.py b/fairgraph/openminds/publications/live_paper_resource_item.py index cb009609..45f7791a 100644 --- a/fairgraph/openminds/publications/live_paper_resource_item.py +++ b/fairgraph/openminds/publications/live_paper_resource_item.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import LivePaperResourceItem +from openminds.latest.publications import LivePaperResourceItem as OMLivePaperResourceItem from fairgraph import KGObject from openminds import IRI -class LivePaperResourceItem(KGObject, LivePaperResourceItem): +class LivePaperResourceItem(KGObject, OMLivePaperResourceItem): """ """ @@ -56,3 +56,13 @@ def __init__( is_location_of=is_location_of, is_part_of=is_part_of, ) + + +# cast openMINDS instances to their fairgraph subclass +LivePaperResourceItem.set_error_handling(None) +for key, value in OMLivePaperResourceItem.__dict__.items(): + if isinstance(value, OMLivePaperResourceItem): + fg_instance = LivePaperResourceItem.from_jsonld(value.to_jsonld()) + fg_instance._space = LivePaperResourceItem.default_space + setattr(LivePaperResourceItem, key, fg_instance) +LivePaperResourceItem.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper_section.py b/fairgraph/openminds/publications/live_paper_section.py index b7a10943..bdb44ca6 100644 --- a/fairgraph/openminds/publications/live_paper_section.py +++ b/fairgraph/openminds/publications/live_paper_section.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import LivePaperSection +from openminds.latest.publications import LivePaperSection as OMLivePaperSection from fairgraph import KGObject -class LivePaperSection(KGObject, LivePaperSection): +class LivePaperSection(KGObject, OMLivePaperSection): """ """ @@ -55,3 +55,13 @@ def __init__( order=order, type=type, ) + + +# cast openMINDS instances to their fairgraph subclass +LivePaperSection.set_error_handling(None) +for key, value in OMLivePaperSection.__dict__.items(): + if isinstance(value, OMLivePaperSection): + fg_instance = LivePaperSection.from_jsonld(value.to_jsonld()) + fg_instance._space = LivePaperSection.default_space + setattr(LivePaperSection, key, fg_instance) +LivePaperSection.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper_version.py b/fairgraph/openminds/publications/live_paper_version.py index 5878a162..50edd0c9 100644 --- a/fairgraph/openminds/publications/live_paper_version.py +++ b/fairgraph/openminds/publications/live_paper_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import LivePaperVersion +from openminds.latest.publications import LivePaperVersion as OMLivePaperVersion from fairgraph import KGObject from fairgraph.errors import ResolutionFailure @@ -15,7 +15,7 @@ from openminds import IRI -class LivePaperVersion(KGObject, LivePaperVersion): +class LivePaperVersion(KGObject, OMLivePaperVersion): """ """ @@ -164,3 +164,13 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] + + +# cast openMINDS instances to their fairgraph subclass +LivePaperVersion.set_error_handling(None) +for key, value in OMLivePaperVersion.__dict__.items(): + if isinstance(value, OMLivePaperVersion): + fg_instance = LivePaperVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = LivePaperVersion.default_space + setattr(LivePaperVersion, key, fg_instance) +LivePaperVersion.set_error_handling("log") diff --git a/fairgraph/openminds/publications/periodical.py b/fairgraph/openminds/publications/periodical.py index b3f6e956..36dfa5f3 100644 --- a/fairgraph/openminds/publications/periodical.py +++ b/fairgraph/openminds/publications/periodical.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import Periodical +from openminds.latest.publications import Periodical as OMPeriodical from fairgraph import KGObject -class Periodical(KGObject, Periodical): +class Periodical(KGObject, OMPeriodical): """ """ @@ -51,3 +51,13 @@ def __init__( digital_identifier=digital_identifier, has_parts=has_parts, ) + + +# cast openMINDS instances to their fairgraph subclass +Periodical.set_error_handling(None) +for key, value in OMPeriodical.__dict__.items(): + if isinstance(value, OMPeriodical): + fg_instance = Periodical.from_jsonld(value.to_jsonld()) + fg_instance._space = Periodical.default_space + setattr(Periodical, key, fg_instance) +Periodical.set_error_handling("log") diff --git a/fairgraph/openminds/publications/publication_issue.py b/fairgraph/openminds/publications/publication_issue.py index a5bf707a..71de45da 100644 --- a/fairgraph/openminds/publications/publication_issue.py +++ b/fairgraph/openminds/publications/publication_issue.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import PublicationIssue +from openminds.latest.publications import PublicationIssue as OMPublicationIssue from fairgraph import KGObject -class PublicationIssue(KGObject, PublicationIssue): +class PublicationIssue(KGObject, OMPublicationIssue): """ """ @@ -40,3 +40,13 @@ def __init__(self, has_parts=None, is_part_of=None, issue_number=None, id=None, is_part_of=is_part_of, issue_number=issue_number, ) + + +# cast openMINDS instances to their fairgraph subclass +PublicationIssue.set_error_handling(None) +for key, value in OMPublicationIssue.__dict__.items(): + if isinstance(value, OMPublicationIssue): + fg_instance = PublicationIssue.from_jsonld(value.to_jsonld()) + fg_instance._space = PublicationIssue.default_space + setattr(PublicationIssue, key, fg_instance) +PublicationIssue.set_error_handling("log") diff --git a/fairgraph/openminds/publications/publication_volume.py b/fairgraph/openminds/publications/publication_volume.py index 98e0aa4c..b8282fc8 100644 --- a/fairgraph/openminds/publications/publication_volume.py +++ b/fairgraph/openminds/publications/publication_volume.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import PublicationVolume +from openminds.latest.publications import PublicationVolume as OMPublicationVolume from fairgraph import KGObject -class PublicationVolume(KGObject, PublicationVolume): +class PublicationVolume(KGObject, OMPublicationVolume): """ """ @@ -42,3 +42,13 @@ def __init__( is_part_of=is_part_of, volume_number=volume_number, ) + + +# cast openMINDS instances to their fairgraph subclass +PublicationVolume.set_error_handling(None) +for key, value in OMPublicationVolume.__dict__.items(): + if isinstance(value, OMPublicationVolume): + fg_instance = PublicationVolume.from_jsonld(value.to_jsonld()) + fg_instance._space = PublicationVolume.default_space + setattr(PublicationVolume, key, fg_instance) +PublicationVolume.set_error_handling("log") diff --git a/fairgraph/openminds/publications/scholarly_article.py b/fairgraph/openminds/publications/scholarly_article.py index 0b04b8a9..4668b07c 100644 --- a/fairgraph/openminds/publications/scholarly_article.py +++ b/fairgraph/openminds/publications/scholarly_article.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.publications import ScholarlyArticle +from openminds.latest.publications import ScholarlyArticle as OMScholarlyArticle from fairgraph import KGObject from fairgraph.utility import as_list @@ -15,7 +15,7 @@ from openminds import IRI -class ScholarlyArticle(KGObject, ScholarlyArticle): +class ScholarlyArticle(KGObject, OMScholarlyArticle): """ """ @@ -142,3 +142,13 @@ def get_citation_string(self, client): journal_name = journal.name if journal else "" volume_number = f"{volume.volume_number}: " if (volume and volume.volume_number != "placeholder") else "" return f"{author_str} ({self.publication_date.year}). {title} {journal_name}, {volume_number}{self.pagination or ''}." + + +# cast openMINDS instances to their fairgraph subclass +ScholarlyArticle.set_error_handling(None) +for key, value in OMScholarlyArticle.__dict__.items(): + if isinstance(value, OMScholarlyArticle): + fg_instance = ScholarlyArticle.from_jsonld(value.to_jsonld()) + fg_instance._space = ScholarlyArticle.default_space + setattr(ScholarlyArticle, key, fg_instance) +ScholarlyArticle.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/atlas_annotation.py b/fairgraph/openminds/sands/atlas/atlas_annotation.py index e955671b..766f72e2 100644 --- a/fairgraph/openminds/sands/atlas/atlas_annotation.py +++ b/fairgraph/openminds/sands/atlas/atlas_annotation.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import AtlasAnnotation +from openminds.latest.sands import AtlasAnnotation as OMAtlasAnnotation from fairgraph import EmbeddedMetadata -class AtlasAnnotation(EmbeddedMetadata, AtlasAnnotation): +class AtlasAnnotation(EmbeddedMetadata, OMAtlasAnnotation): """ """ @@ -49,3 +49,13 @@ def __init__( specification=specification, type=type, ) + + +# cast openMINDS instances to their fairgraph subclass +AtlasAnnotation.set_error_handling(None) +for key, value in OMAtlasAnnotation.__dict__.items(): + if isinstance(value, OMAtlasAnnotation): + fg_instance = AtlasAnnotation.from_jsonld(value.to_jsonld()) + fg_instance._space = AtlasAnnotation.default_space + setattr(AtlasAnnotation, key, fg_instance) +AtlasAnnotation.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/brain_atlas.py b/fairgraph/openminds/sands/atlas/brain_atlas.py index 24ca08d8..c5731677 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import BrainAtlas +from openminds.latest.sands import BrainAtlas as OMBrainAtlas from fairgraph import KGObject from openminds import IRI -class BrainAtlas(KGObject, BrainAtlas): +class BrainAtlas(KGObject, OMBrainAtlas): """ """ @@ -111,3 +111,13 @@ def __init__( used_species=used_species, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +BrainAtlas.set_error_handling(None) +for key, value in OMBrainAtlas.__dict__.items(): + if isinstance(value, OMBrainAtlas): + fg_instance = BrainAtlas.from_jsonld(value.to_jsonld()) + fg_instance._space = BrainAtlas.default_space + setattr(BrainAtlas, key, fg_instance) +BrainAtlas.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/brain_atlas_version.py b/fairgraph/openminds/sands/atlas/brain_atlas_version.py index b8ebb8af..3ab54494 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas_version.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import BrainAtlasVersion +from openminds.latest.sands import BrainAtlasVersion as OMBrainAtlasVersion from fairgraph import KGObject @@ -13,7 +13,7 @@ from openminds import IRI -class BrainAtlasVersion(KGObject, BrainAtlasVersion): +class BrainAtlasVersion(KGObject, OMBrainAtlasVersion): """ """ @@ -172,3 +172,13 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) + + +# cast openMINDS instances to their fairgraph subclass +BrainAtlasVersion.set_error_handling(None) +for key, value in OMBrainAtlasVersion.__dict__.items(): + if isinstance(value, OMBrainAtlasVersion): + fg_instance = BrainAtlasVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = BrainAtlasVersion.default_space + setattr(BrainAtlasVersion, key, fg_instance) +BrainAtlasVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space.py b/fairgraph/openminds/sands/atlas/common_coordinate_space.py index 2577c88a..f1073b56 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import CommonCoordinateSpace +from openminds.latest.sands import CommonCoordinateSpace as OMCommonCoordinateSpace from fairgraph import KGObject from openminds import IRI -class CommonCoordinateSpace(KGObject, CommonCoordinateSpace): +class CommonCoordinateSpace(KGObject, OMCommonCoordinateSpace): """ """ @@ -119,3 +119,13 @@ def __init__( used_species=used_species, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +CommonCoordinateSpace.set_error_handling(None) +for key, value in OMCommonCoordinateSpace.__dict__.items(): + if isinstance(value, OMCommonCoordinateSpace): + fg_instance = CommonCoordinateSpace.from_jsonld(value.to_jsonld()) + fg_instance._space = CommonCoordinateSpace.default_space + setattr(CommonCoordinateSpace, key, fg_instance) +CommonCoordinateSpace.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py index dbd1786e..c5ebaaeb 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import CommonCoordinateSpaceVersion +from openminds.latest.sands import CommonCoordinateSpaceVersion as OMCommonCoordinateSpaceVersion from fairgraph import KGObject @@ -13,7 +13,7 @@ from openminds import IRI -class CommonCoordinateSpaceVersion(KGObject, CommonCoordinateSpaceVersion): +class CommonCoordinateSpaceVersion(KGObject, OMCommonCoordinateSpaceVersion): """ """ @@ -202,3 +202,13 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) + + +# cast openMINDS instances to their fairgraph subclass +CommonCoordinateSpaceVersion.set_error_handling(None) +for key, value in OMCommonCoordinateSpaceVersion.__dict__.items(): + if isinstance(value, OMCommonCoordinateSpaceVersion): + fg_instance = CommonCoordinateSpaceVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = CommonCoordinateSpaceVersion.default_space + setattr(CommonCoordinateSpaceVersion, key, fg_instance) +CommonCoordinateSpaceVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity.py b/fairgraph/openminds/sands/atlas/parcellation_entity.py index 804e6fc0..01fa298d 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import ParcellationEntity +from openminds.latest.sands import ParcellationEntity as OMParcellationEntity from fairgraph import KGObject -class ParcellationEntity(KGObject, ParcellationEntity): +class ParcellationEntity(KGObject, OMParcellationEntity): """ """ @@ -131,3 +131,13 @@ def __init__( studied_in=studied_in, versions=versions, ) + + +# cast openMINDS instances to their fairgraph subclass +ParcellationEntity.set_error_handling(None) +for key, value in OMParcellationEntity.__dict__.items(): + if isinstance(value, OMParcellationEntity): + fg_instance = ParcellationEntity.from_jsonld(value.to_jsonld()) + fg_instance._space = ParcellationEntity.default_space + setattr(ParcellationEntity, key, fg_instance) +ParcellationEntity.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py index a7b8eb72..9105989c 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import ParcellationEntityVersion +from openminds.latest.sands import ParcellationEntityVersion as OMParcellationEntityVersion from fairgraph import KGObject -class ParcellationEntityVersion(KGObject, ParcellationEntityVersion): +class ParcellationEntityVersion(KGObject, OMParcellationEntityVersion): """ """ @@ -160,3 +160,13 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) + + +# cast openMINDS instances to their fairgraph subclass +ParcellationEntityVersion.set_error_handling(None) +for key, value in OMParcellationEntityVersion.__dict__.items(): + if isinstance(value, OMParcellationEntityVersion): + fg_instance = ParcellationEntityVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = ParcellationEntityVersion.default_space + setattr(ParcellationEntityVersion, key, fg_instance) +ParcellationEntityVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology.py b/fairgraph/openminds/sands/atlas/parcellation_terminology.py index d174142e..066fed1c 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import ParcellationTerminology +from openminds.latest.sands import ParcellationTerminology as OMParcellationTerminology from fairgraph import EmbeddedMetadata -class ParcellationTerminology(EmbeddedMetadata, ParcellationTerminology): +class ParcellationTerminology(EmbeddedMetadata, OMParcellationTerminology): """ """ @@ -35,3 +35,13 @@ def __init__( has_entities=has_entities, ontology_identifiers=ontology_identifiers, ) + + +# cast openMINDS instances to their fairgraph subclass +ParcellationTerminology.set_error_handling(None) +for key, value in OMParcellationTerminology.__dict__.items(): + if isinstance(value, OMParcellationTerminology): + fg_instance = ParcellationTerminology.from_jsonld(value.to_jsonld()) + fg_instance._space = ParcellationTerminology.default_space + setattr(ParcellationTerminology, key, fg_instance) +ParcellationTerminology.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py index 3cfa19d6..bc3bb851 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import ParcellationTerminologyVersion +from openminds.latest.sands import ParcellationTerminologyVersion as OMParcellationTerminologyVersion from fairgraph import EmbeddedMetadata -class ParcellationTerminologyVersion(EmbeddedMetadata, ParcellationTerminologyVersion): +class ParcellationTerminologyVersion(EmbeddedMetadata, OMParcellationTerminologyVersion): """ """ @@ -35,3 +35,13 @@ def __init__( has_entities=has_entities, ontology_identifiers=ontology_identifiers, ) + + +# cast openMINDS instances to their fairgraph subclass +ParcellationTerminologyVersion.set_error_handling(None) +for key, value in OMParcellationTerminologyVersion.__dict__.items(): + if isinstance(value, OMParcellationTerminologyVersion): + fg_instance = ParcellationTerminologyVersion.from_jsonld(value.to_jsonld()) + fg_instance._space = ParcellationTerminologyVersion.default_space + setattr(ParcellationTerminologyVersion, key, fg_instance) +ParcellationTerminologyVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/mathematical_shapes/circle.py b/fairgraph/openminds/sands/mathematical_shapes/circle.py index 67a42260..8092a2c8 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/circle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/circle.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import Circle +from openminds.latest.sands import Circle as OMCircle from fairgraph import EmbeddedMetadata -class Circle(EmbeddedMetadata, Circle): +class Circle(EmbeddedMetadata, OMCircle): """ """ @@ -20,3 +20,13 @@ class Circle(EmbeddedMetadata, Circle): def __init__(self, radius=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, radius=radius) + + +# cast openMINDS instances to their fairgraph subclass +Circle.set_error_handling(None) +for key, value in OMCircle.__dict__.items(): + if isinstance(value, OMCircle): + fg_instance = Circle.from_jsonld(value.to_jsonld()) + fg_instance._space = Circle.default_space + setattr(Circle, key, fg_instance) +Circle.set_error_handling("log") diff --git a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py index 9baeb5b0..29267dfa 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py +++ b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import Ellipse +from openminds.latest.sands import Ellipse as OMEllipse from fairgraph import EmbeddedMetadata -class Ellipse(EmbeddedMetadata, Ellipse): +class Ellipse(EmbeddedMetadata, OMEllipse): """ """ @@ -22,3 +22,13 @@ def __init__(self, semi_major_axis=None, semi_minor_axis=None, id=None, data=Non return EmbeddedMetadata.__init__( self, data=data, semi_major_axis=semi_major_axis, semi_minor_axis=semi_minor_axis ) + + +# cast openMINDS instances to their fairgraph subclass +Ellipse.set_error_handling(None) +for key, value in OMEllipse.__dict__.items(): + if isinstance(value, OMEllipse): + fg_instance = Ellipse.from_jsonld(value.to_jsonld()) + fg_instance._space = Ellipse.default_space + setattr(Ellipse, key, fg_instance) +Ellipse.set_error_handling("log") diff --git a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py index 157c227c..bcc2bbeb 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import Rectangle +from openminds.latest.sands import Rectangle as OMRectangle from fairgraph import EmbeddedMetadata -class Rectangle(EmbeddedMetadata, Rectangle): +class Rectangle(EmbeddedMetadata, OMRectangle): """ """ @@ -20,3 +20,13 @@ class Rectangle(EmbeddedMetadata, Rectangle): def __init__(self, length=None, width=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, length=length, width=width) + + +# cast openMINDS instances to their fairgraph subclass +Rectangle.set_error_handling(None) +for key, value in OMRectangle.__dict__.items(): + if isinstance(value, OMRectangle): + fg_instance = Rectangle.from_jsonld(value.to_jsonld()) + fg_instance._space = Rectangle.default_space + setattr(Rectangle, key, fg_instance) +Rectangle.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py index 0a8ede02..092134d0 100644 --- a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py +++ b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import AnatomicalTargetPosition +from openminds.latest.sands import AnatomicalTargetPosition as OMAnatomicalTargetPosition from fairgraph import EmbeddedMetadata -class AnatomicalTargetPosition(EmbeddedMetadata, AnatomicalTargetPosition): +class AnatomicalTargetPosition(EmbeddedMetadata, OMAnatomicalTargetPosition): """ """ @@ -37,3 +37,13 @@ def __init__( spatial_locations=spatial_locations, target_identification_type=target_identification_type, ) + + +# cast openMINDS instances to their fairgraph subclass +AnatomicalTargetPosition.set_error_handling(None) +for key, value in OMAnatomicalTargetPosition.__dict__.items(): + if isinstance(value, OMAnatomicalTargetPosition): + fg_instance = AnatomicalTargetPosition.from_jsonld(value.to_jsonld()) + fg_instance._space = AnatomicalTargetPosition.default_space + setattr(AnatomicalTargetPosition, key, fg_instance) +AnatomicalTargetPosition.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py index f2414511..ff5ff1ab 100644 --- a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py +++ b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import CoordinatePoint +from openminds.latest.sands import CoordinatePoint as OMCoordinatePoint from fairgraph import EmbeddedMetadata -class CoordinatePoint(EmbeddedMetadata, CoordinatePoint): +class CoordinatePoint(EmbeddedMetadata, OMCoordinatePoint): """ """ @@ -20,3 +20,13 @@ class CoordinatePoint(EmbeddedMetadata, CoordinatePoint): def __init__(self, coordinate_space=None, coordinates=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, coordinate_space=coordinate_space, coordinates=coordinates) + + +# cast openMINDS instances to their fairgraph subclass +CoordinatePoint.set_error_handling(None) +for key, value in OMCoordinatePoint.__dict__.items(): + if isinstance(value, OMCoordinatePoint): + fg_instance = CoordinatePoint.from_jsonld(value.to_jsonld()) + fg_instance._space = CoordinatePoint.default_space + setattr(CoordinatePoint, key, fg_instance) +CoordinatePoint.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py index 4926d1c3..257ffbc1 100644 --- a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import QualitativeRelationAssessment +from openminds.latest.sands import QualitativeRelationAssessment as OMQualitativeRelationAssessment from fairgraph import EmbeddedMetadata -class QualitativeRelationAssessment(EmbeddedMetadata, QualitativeRelationAssessment): +class QualitativeRelationAssessment(EmbeddedMetadata, OMQualitativeRelationAssessment): """ """ @@ -24,3 +24,13 @@ def __init__( return EmbeddedMetadata.__init__( self, data=data, criteria=criteria, in_relation_to=in_relation_to, qualitative_overlap=qualitative_overlap ) + + +# cast openMINDS instances to their fairgraph subclass +QualitativeRelationAssessment.set_error_handling(None) +for key, value in OMQualitativeRelationAssessment.__dict__.items(): + if isinstance(value, OMQualitativeRelationAssessment): + fg_instance = QualitativeRelationAssessment.from_jsonld(value.to_jsonld()) + fg_instance._space = QualitativeRelationAssessment.default_space + setattr(QualitativeRelationAssessment, key, fg_instance) +QualitativeRelationAssessment.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py index dcf99412..0fe9369f 100644 --- a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import QuantitativeRelationAssessment +from openminds.latest.sands import QuantitativeRelationAssessment as OMQuantitativeRelationAssessment from fairgraph import EmbeddedMetadata -class QuantitativeRelationAssessment(EmbeddedMetadata, QuantitativeRelationAssessment): +class QuantitativeRelationAssessment(EmbeddedMetadata, OMQuantitativeRelationAssessment): """ """ @@ -28,3 +28,13 @@ def __init__( in_relation_to=in_relation_to, quantitative_overlap=quantitative_overlap, ) + + +# cast openMINDS instances to their fairgraph subclass +QuantitativeRelationAssessment.set_error_handling(None) +for key, value in OMQuantitativeRelationAssessment.__dict__.items(): + if isinstance(value, OMQuantitativeRelationAssessment): + fg_instance = QuantitativeRelationAssessment.from_jsonld(value.to_jsonld()) + fg_instance._space = QuantitativeRelationAssessment.default_space + setattr(QuantitativeRelationAssessment, key, fg_instance) +QuantitativeRelationAssessment.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/single_color.py b/fairgraph/openminds/sands/miscellaneous/single_color.py index 19067931..fc4db8f1 100644 --- a/fairgraph/openminds/sands/miscellaneous/single_color.py +++ b/fairgraph/openminds/sands/miscellaneous/single_color.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import SingleColor +from openminds.latest.sands import SingleColor as OMSingleColor from fairgraph import KGObject -class SingleColor(KGObject, SingleColor): +class SingleColor(KGObject, OMSingleColor): """ """ @@ -22,3 +22,13 @@ class SingleColor(KGObject, SingleColor): def __init__(self, value=None, id=None, data=None, space=None, scope=None): return KGObject.__init__(self, id=id, space=space, scope=scope, data=data, value=value) + + +# cast openMINDS instances to their fairgraph subclass +SingleColor.set_error_handling(None) +for key, value in OMSingleColor.__dict__.items(): + if isinstance(value, OMSingleColor): + fg_instance = SingleColor.from_jsonld(value.to_jsonld()) + fg_instance._space = SingleColor.default_space + setattr(SingleColor, key, fg_instance) +SingleColor.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py index 802986f6..c13961d6 100644 --- a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py +++ b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import ViewerSpecification +from openminds.latest.sands import ViewerSpecification as OMViewerSpecification from fairgraph import EmbeddedMetadata -class ViewerSpecification(EmbeddedMetadata, ViewerSpecification): +class ViewerSpecification(EmbeddedMetadata, OMViewerSpecification): """ """ @@ -37,3 +37,13 @@ def __init__( camera_position=camera_position, preferred_display_color=preferred_display_color, ) + + +# cast openMINDS instances to their fairgraph subclass +ViewerSpecification.set_error_handling(None) +for key, value in OMViewerSpecification.__dict__.items(): + if isinstance(value, OMViewerSpecification): + fg_instance = ViewerSpecification.from_jsonld(value.to_jsonld()) + fg_instance._space = ViewerSpecification.default_space + setattr(ViewerSpecification, key, fg_instance) +ViewerSpecification.set_error_handling("log") diff --git a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py index 139f005b..29201b5b 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py +++ b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import CustomAnatomicalEntity +from openminds.latest.sands import CustomAnatomicalEntity as OMCustomAnatomicalEntity from fairgraph import KGObject -class CustomAnatomicalEntity(KGObject, CustomAnatomicalEntity): +class CustomAnatomicalEntity(KGObject, OMCustomAnatomicalEntity): """ """ @@ -108,3 +108,13 @@ def __init__( relation_assessments=relation_assessments, studied_in=studied_in, ) + + +# cast openMINDS instances to their fairgraph subclass +CustomAnatomicalEntity.set_error_handling(None) +for key, value in OMCustomAnatomicalEntity.__dict__.items(): + if isinstance(value, OMCustomAnatomicalEntity): + fg_instance = CustomAnatomicalEntity.from_jsonld(value.to_jsonld()) + fg_instance._space = CustomAnatomicalEntity.default_space + setattr(CustomAnatomicalEntity, key, fg_instance) +CustomAnatomicalEntity.set_error_handling("log") diff --git a/fairgraph/openminds/sands/non_atlas/custom_annotation.py b/fairgraph/openminds/sands/non_atlas/custom_annotation.py index ce0e4c5e..61677df2 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_annotation.py +++ b/fairgraph/openminds/sands/non_atlas/custom_annotation.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import CustomAnnotation +from openminds.latest.sands import CustomAnnotation as OMCustomAnnotation from fairgraph import EmbeddedMetadata -class CustomAnnotation(EmbeddedMetadata, CustomAnnotation): +class CustomAnnotation(EmbeddedMetadata, OMCustomAnnotation): """ """ @@ -51,3 +51,13 @@ def __init__( specification=specification, type=type, ) + + +# cast openMINDS instances to their fairgraph subclass +CustomAnnotation.set_error_handling(None) +for key, value in OMCustomAnnotation.__dict__.items(): + if isinstance(value, OMCustomAnnotation): + fg_instance = CustomAnnotation.from_jsonld(value.to_jsonld()) + fg_instance._space = CustomAnnotation.default_space + setattr(CustomAnnotation, key, fg_instance) +CustomAnnotation.set_error_handling("log") diff --git a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py index 6b463fb8..955cf594 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py +++ b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.sands import CustomCoordinateSpace +from openminds.latest.sands import CustomCoordinateSpace as OMCustomCoordinateSpace from fairgraph import KGObject -class CustomCoordinateSpace(KGObject, CustomCoordinateSpace): +class CustomCoordinateSpace(KGObject, OMCustomCoordinateSpace): """ """ @@ -65,3 +65,13 @@ def __init__( is_used_to_group=is_used_to_group, native_unit=native_unit, ) + + +# cast openMINDS instances to their fairgraph subclass +CustomCoordinateSpace.set_error_handling(None) +for key, value in OMCustomCoordinateSpace.__dict__.items(): + if isinstance(value, OMCustomCoordinateSpace): + fg_instance = CustomCoordinateSpace.from_jsonld(value.to_jsonld()) + fg_instance._space = CustomCoordinateSpace.default_space + setattr(CustomCoordinateSpace, key, fg_instance) +CustomCoordinateSpace.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py index a777469a..f1682ccc 100644 --- a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.specimen_prep import CranialWindowPreparation +from openminds.latest.specimen_prep import CranialWindowPreparation as OMCranialWindowPreparation from fairgraph import KGObject from datetime import datetime, time -class CranialWindowPreparation(KGObject, CranialWindowPreparation): +class CranialWindowPreparation(KGObject, OMCranialWindowPreparation): """ """ @@ -67,3 +67,13 @@ def __init__( start_time=start_time, study_targets=study_targets, ) + + +# cast openMINDS instances to their fairgraph subclass +CranialWindowPreparation.set_error_handling(None) +for key, value in OMCranialWindowPreparation.__dict__.items(): + if isinstance(value, OMCranialWindowPreparation): + fg_instance = CranialWindowPreparation.from_jsonld(value.to_jsonld()) + fg_instance._space = CranialWindowPreparation.default_space + setattr(CranialWindowPreparation, key, fg_instance) +CranialWindowPreparation.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py index 20f64fa1..c339b1bd 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.specimen_prep import TissueCulturePreparation +from openminds.latest.specimen_prep import TissueCulturePreparation as OMTissueCulturePreparation from fairgraph import KGObject from datetime import datetime, time -class TissueCulturePreparation(KGObject, TissueCulturePreparation): +class TissueCulturePreparation(KGObject, OMTissueCulturePreparation): """ """ @@ -65,3 +65,13 @@ def __init__( start_time=start_time, study_targets=study_targets, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueCulturePreparation.set_error_handling(None) +for key, value in OMTissueCulturePreparation.__dict__.items(): + if isinstance(value, OMTissueCulturePreparation): + fg_instance = TissueCulturePreparation.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueCulturePreparation.default_space + setattr(TissueCulturePreparation, key, fg_instance) +TissueCulturePreparation.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py index 5665be21..dd6d5442 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.specimen_prep import TissueSampleSlicing +from openminds.latest.specimen_prep import TissueSampleSlicing as OMTissueSampleSlicing from fairgraph import KGObject from datetime import datetime, time -class TissueSampleSlicing(KGObject, TissueSampleSlicing): +class TissueSampleSlicing(KGObject, OMTissueSampleSlicing): """ """ @@ -67,3 +67,13 @@ def __init__( temperature=temperature, tissue_bath_solution=tissue_bath_solution, ) + + +# cast openMINDS instances to their fairgraph subclass +TissueSampleSlicing.set_error_handling(None) +for key, value in OMTissueSampleSlicing.__dict__.items(): + if isinstance(value, OMTissueSampleSlicing): + fg_instance = TissueSampleSlicing.from_jsonld(value.to_jsonld()) + fg_instance._space = TissueSampleSlicing.default_space + setattr(TissueSampleSlicing, key, fg_instance) +TissueSampleSlicing.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device.py b/fairgraph/openminds/specimen_prep/device/slicing_device.py index ce094a77..f68c5b12 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.specimen_prep import SlicingDevice +from openminds.latest.specimen_prep import SlicingDevice as OMSlicingDevice from fairgraph import KGObject -class SlicingDevice(KGObject, SlicingDevice): +class SlicingDevice(KGObject, OMSlicingDevice): """ """ @@ -71,3 +71,13 @@ def __init__( serial_number=serial_number, usage=usage, ) + + +# cast openMINDS instances to their fairgraph subclass +SlicingDevice.set_error_handling(None) +for key, value in OMSlicingDevice.__dict__.items(): + if isinstance(value, OMSlicingDevice): + fg_instance = SlicingDevice.from_jsonld(value.to_jsonld()) + fg_instance._space = SlicingDevice.default_space + setattr(SlicingDevice, key, fg_instance) +SlicingDevice.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py index ace49eb3..0baa6761 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.specimen_prep import SlicingDeviceUsage +from openminds.latest.specimen_prep import SlicingDeviceUsage as OMSlicingDeviceUsage from fairgraph import KGObject -class SlicingDeviceUsage(KGObject, SlicingDeviceUsage): +class SlicingDeviceUsage(KGObject, OMSlicingDeviceUsage): """ """ @@ -115,3 +115,13 @@ def __init__( used_to_record=used_to_record, vibration_frequency=vibration_frequency, ) + + +# cast openMINDS instances to their fairgraph subclass +SlicingDeviceUsage.set_error_handling(None) +for key, value in OMSlicingDeviceUsage.__dict__.items(): + if isinstance(value, OMSlicingDeviceUsage): + fg_instance = SlicingDeviceUsage.from_jsonld(value.to_jsonld()) + fg_instance._space = SlicingDeviceUsage.default_space + setattr(SlicingDeviceUsage, key, fg_instance) +SlicingDeviceUsage.set_error_handling("log") diff --git a/fairgraph/openminds/stimulation/activity/stimulation_activity.py b/fairgraph/openminds/stimulation/activity/stimulation_activity.py index c178c7f2..35da518b 100644 --- a/fairgraph/openminds/stimulation/activity/stimulation_activity.py +++ b/fairgraph/openminds/stimulation/activity/stimulation_activity.py @@ -5,14 +5,14 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.stimulation import StimulationActivity +from openminds.latest.stimulation import StimulationActivity as OMStimulationActivity from fairgraph import KGObject from datetime import datetime, time -class StimulationActivity(KGObject, StimulationActivity): +class StimulationActivity(KGObject, OMStimulationActivity): """ """ @@ -65,3 +65,13 @@ def __init__( stimuli=stimuli, study_targets=study_targets, ) + + +# cast openMINDS instances to their fairgraph subclass +StimulationActivity.set_error_handling(None) +for key, value in OMStimulationActivity.__dict__.items(): + if isinstance(value, OMStimulationActivity): + fg_instance = StimulationActivity.from_jsonld(value.to_jsonld()) + fg_instance._space = StimulationActivity.default_space + setattr(StimulationActivity, key, fg_instance) +StimulationActivity.set_error_handling("log") diff --git a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py index 4b9cef7d..5e3cbb8e 100644 --- a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py +++ b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py @@ -5,11 +5,11 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.stimulation import EphysStimulus +from openminds.latest.stimulation import EphysStimulus as OMEphysStimulus from fairgraph import KGObject -class EphysStimulus(KGObject, EphysStimulus): +class EphysStimulus(KGObject, OMEphysStimulus): """ """ @@ -61,3 +61,13 @@ def __init__( specifications=specifications, type=type, ) + + +# cast openMINDS instances to their fairgraph subclass +EphysStimulus.set_error_handling(None) +for key, value in OMEphysStimulus.__dict__.items(): + if isinstance(value, OMEphysStimulus): + fg_instance = EphysStimulus.from_jsonld(value.to_jsonld()) + fg_instance._space = EphysStimulus.default_space + setattr(EphysStimulus, key, fg_instance) +EphysStimulus.set_error_handling("log") From e35e8bec1f2ae9eed4523a8204bca6543445c612 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Tue, 9 Sep 2025 10:55:19 +0200 Subject: [PATCH 11/25] Fix __repr__ for the case when not all properties have been set --- fairgraph/embedded.py | 2 +- fairgraph/kgobject.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/fairgraph/embedded.py b/fairgraph/embedded.py index 8d1951c4..abe61d33 100644 --- a/fairgraph/embedded.py +++ b/fairgraph/embedded.py @@ -60,7 +60,7 @@ def __repr__(self): template_parts = ( "{}={{self.{}!r}}".format(prop.name, prop.name) for prop in self.properties - if getattr(self, prop.name) is not None + if getattr(self, prop.name, None) is not None ) template = "{self.__class__.__name__}(" + ", ".join(template_parts) + ")" return template.format(self=self) diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index c06b6e5d..1b5f6dd8 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -91,7 +91,7 @@ def __repr__(self): template_parts = ( "{}={{self.{}!r}}".format(prop.name, prop.name) for prop in self.__class__.all_properties - if getattr(self, prop.name) is not None + if getattr(self, prop.name, None) is not None ) template = "{self.__class__.__name__}(" + ", ".join(template_parts) + ", space={self.space}, id={self.id})" return template.format(self=self) From 00f98bf033018c31cc90dba62cf2a8e13aceb5fa Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Tue, 9 Sep 2025 10:56:00 +0200 Subject: [PATCH 12/25] When setting error handling for a class, set the same value for all embedded metadata. --- fairgraph/node.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/fairgraph/node.py b/fairgraph/node.py index d90241ed..01f5ed07 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -153,9 +153,16 @@ def set_error_handling( the mode will be applied only to those properties. """ if value is None: - cls.error_handling = ErrorHandling.none + value = ErrorHandling.none else: - cls.error_handling = ErrorHandling(value) + value = ErrorHandling(value) + cls.error_handling = value + # set the same action for all embedded types + for prop in cls.properties: + for type_ in prop.types: + if issubclass(type_, ContainsMetadata) and not issubclass(type_, RepresentsSingleObject): + # i.e., is EmbeddedMetadata + type_.set_error_handling(value) @classmethod def normalize_filter(cls, filter_dict: Dict[str, Any]) -> Dict[str, Any]: From 5853d18f6935c26e2ab0982ecde5f38e4aee09fe Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 15 Sep 2025 17:14:43 +0200 Subject: [PATCH 13/25] In query generation, cast openMINDS classes (in property definitions) to their fairgraph subclasses --- fairgraph/queries.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/fairgraph/queries.py b/fairgraph/queries.py index d1f5c25c..a07c88bc 100644 --- a/fairgraph/queries.py +++ b/fairgraph/queries.py @@ -24,7 +24,7 @@ from warnings import warn from openminds.base import IRI, EmbeddedMetadata, LinkedMetadata, Node - +from openminds.registry import lookup_type from .utility import as_list, expand_uri @@ -315,6 +315,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any else: property_name = property.path type_filter = None + fg_cls = lookup_type(cls.type_) # get the fairgraph version of cls properties.append( QueryProperty( expanded_path, @@ -323,7 +324,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any type_filter=type_filter, ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, - properties=cls.generate_query_properties(follow_links), + properties=fg_cls.generate_query_properties(follow_links), ) ) elif any(issubclass(_type, LinkedMetadata) for _type in property.types): @@ -337,7 +338,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any type_filter = cls.type_ else: type_filter = None - + fg_cls = lookup_type(cls.type_) properties.append( QueryProperty( expanded_path, @@ -346,7 +347,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any type_filter=type_filter, ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, - properties=[QueryProperty("@id"), *cls.generate_query_properties(follow_links)], + properties=[QueryProperty("@id"), *fg_cls.generate_query_properties(follow_links)], ) ) else: From 0411a3f2c195c7bc38033fa54eda08a602b6d573 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 15 Sep 2025 17:16:50 +0200 Subject: [PATCH 14/25] Fix `KGClient.configure_space()` and `KGClient.space_info()` to work with both v3 and v4 type IRIs --- fairgraph/client.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/fairgraph/client.py b/fairgraph/client.py index 5f0fd410..41e94c73 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -659,11 +659,15 @@ def configure_space(self, space_name: Optional[str] = None, types: Optional[List result = self._kg_admin_client.create_space_definition(space=space_name) if result: # error err_msg = f"Unable to configure KG space for space '{space_name}': {result}" - if not space_name.startswith("collab="): + if not space_name.startswith("collab-"): err_msg += f". If you are trying to configure a collab space, ensure the space name starts with 'collab-'" raise Exception(err_msg) for cls in types: - result = self._kg_admin_client.assign_type_to_space(space=space_name, target_type=cls.type_) + if self.migrated: + target_type = cls.type_ + else: + target_type = adapt_type_4to3(cls.type_) + result = self._kg_admin_client.assign_type_to_space(space=space_name, target_type=target_type) if result: # error raise Exception(f"Unable to assign {cls.__name__} to space {space_name}: {result}") return space_name @@ -686,13 +690,20 @@ def space_info(self, space_name: str, scope: str = "released", ignore_errors: bo The return format is a dictionary whose keys are classes and the values are the number of instances of each class in the given spaces. """ + # todo: if not self.migrated, adapt type before lookup result = self._kg_client.types.list(space=space_name, stage=STAGE_MAP[scope]) if result.error: raise Exception(result.error) response = {} for item in result.data: + if self.migrated: + type_iri = item.identifier + else: + type_ = {"@type": item.identifier} + adapt_namespaces_3to4(type_) + type_iri = type_["@type"] try: - cls = lookup_type(item.identifier) + cls = lookup_type(type_iri) except KeyError as err: ignore_list = [ "https://core.kg.ebrains.eu/vocab/type/Bookmark", From 181318426e7afc23bee5fbd956c5d15e9b68e564 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Tue, 16 Sep 2025 12:51:42 +0200 Subject: [PATCH 15/25] Handle retrieving KG-independent (openMINDS) URIs for controlled terms --- fairgraph/client.py | 45 ++++++++++++++++++++++++++++++++++----------- 1 file changed, 34 insertions(+), 11 deletions(-) diff --git a/fairgraph/client.py b/fairgraph/client.py index 41e94c73..7eec9f98 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -377,20 +377,43 @@ def instance_from_full_uri( logger.debug("Retrieving instance {} from cache".format(uri)) data = self.cache[uri] else: - def _get_instance(scope): - response = self._kg_client.instances.get_by_id( - stage=STAGE_MAP[scope], - instance_id=self.uuid_from_uri(uri), - extended_response_configuration=default_response_configuration, - ) error_context = f"_get_instance(scope={scope} uri={uri})" - response = self._check_response(response, error_context=error_context, ignore_not_found=True) - if response.error: - assert response.error.code == 404 # all other errors should have been trapped by the check - data = None + # Normal KG URIs start with https://kg.ebrains.eu/api/instances/ with a UUID + # but for openMINDS controlled terms we may have the openMINDS URI + # of the form https://openminds.ebrains.eu/instances/ageCategory/juvenile (v3) + # or https://openminds.om-i.org/instances/ageCategory/juvenile (v4) + # We use different query methods for these different cases. + kg_namespace = self._kg_client.instances._kg_config.id_namespace + if uri.startswith(kg_namespace): + response = self._kg_client.instances.get_by_id( + stage=STAGE_MAP[scope], + instance_id=self.uuid_from_uri(uri), + extended_response_configuration=default_response_configuration, + ) + response = self._check_response(response, error_context=error_context, ignore_not_found=True) + if response.error: + assert response.error.code == 404 # all other errors should have been trapped by the check + data = None + else: + data = response.data + elif uri.startswith("https://openminds.om-i.org/instances") or uri.startswith("https://openminds.ebrains.eu/instances"): + if self.migrated and uri.startswith("https://openminds.ebrains.eu"): + payload = [uri.replace("ebrains.eu", "om-i.org")] + elif uri.startswith("https://openminds.om-i.org"): + payload = [uri.replace("om-i.org", "ebrains.eu")] + else: + payload = [uri] + response = self._kg_client.instances.get_by_identifiers( + stage=STAGE_MAP[scope], + payload=payload, + extended_response_configuration=default_response_configuration, + ) + # todo: handle errors + data = response.data[payload[0]].data else: - data = response.data + raise Exception(f"This client cannot retrieve instances from {uri}") + # in some circumstances, the KG returns "minimal" metadata, # e.g. with just the id and fullName properties # this means the user does not have full access, so we count this as no data From 3d1e23688ddef59be3b0834ed50f4e368ec4487b Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Tue, 16 Sep 2025 12:52:29 +0200 Subject: [PATCH 16/25] Avoid instantiating nodes as KGObjects when cleaning an entire space --- fairgraph/client.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/fairgraph/client.py b/fairgraph/client.py index 7eec9f98..e114ce7e 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -757,12 +757,12 @@ def clean_space(self, space_name): for cls, count in space_info.items(): if count > 0 and hasattr(cls, "list"): # exclude embedded metadata instances print(f"Deleting {cls.__name__} instances", end="") - instances = cls.list(self, scope="in progress", space=space_name) - assert len(instances) <= count - for instance in instances: - assert instance.space == space_name + response = self.list(cls.type_, scope="in progress", space=space_name) + assert response.size <= count + for instance in response.data: + assert instance["https://core.kg.ebrains.eu/vocab/meta/space"] == space_name print(".", end="") - instance.delete(self, ignore_not_found=False) + self.delete_instance(self.uuid_from_uri(instance["@id"]), ignore_not_found=False) print() else: print(f"The space '{space_name}' is already clean") From cb7107d4bbda7b42723b5d8083711e9bbe0d4c2d Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Tue, 16 Sep 2025 15:26:35 +0200 Subject: [PATCH 17/25] Fix more bugs relating to the openMINDS v3-v4 transition --- fairgraph/kgobject.py | 2 +- fairgraph/utility.py | 28 +++++++++++++++++++++------- 2 files changed, 22 insertions(+), 8 deletions(-) diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index 1b5f6dd8..b46d6942 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -710,7 +710,7 @@ def save( activity_log.update(item=self, delta=None, space=space, entry_type="no-op") else: # create new - local_data = self.to_jsonld(embed_linked_nodes=False) + local_data = normalize_data(self.to_jsonld(embed_linked_nodes=False), self.context) logger.info(" - creating instance with data {}".format(local_data)) try: instance_data = client.create_new_instance( diff --git a/fairgraph/utility.py b/fairgraph/utility.py index 520323a7..c843453f 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -446,19 +446,21 @@ def types_match(a, b): return False -def _adapt_namespaces(data, adapt_keys, adapt_type): +def _adapt_namespaces(data, adapt_keys, adapt_type, adapt_instance_uri): if isinstance(data, list): for item in data: - _adapt_namespaces(item, adapt_keys, adapt_type) + _adapt_namespaces(item, adapt_keys, adapt_type, adapt_instance_uri) elif isinstance(data, dict): # adapt property URIs old_keys = tuple(data.keys()) new_keys = adapt_keys(old_keys) for old_key, new_key in zip(old_keys, new_keys): data[new_key] = data.pop(old_key) - for value in data.values(): - if isinstance(value, (list, dict)): - _adapt_namespaces(value, adapt_keys, adapt_type) + for key, value in data.items(): + if key == "@id": + data[key] = adapt_instance_uri(value) + elif isinstance(value, (list, dict)): + _adapt_namespaces(value, adapt_keys, adapt_type, adapt_instance_uri) # adapt @type URIs if "@type" in data: data["@type"] = adapt_type(data["@type"]) @@ -478,7 +480,13 @@ def adapt_type_3to4(uri): uri = uri[0] return f"https://openminds.om-i.org/types/{uri.split('/')[-1]}" - return _adapt_namespaces(data, adapt_keys_3to4, adapt_type_3to4) + def adapt_instance_uri_3to4(uri): + if uri.startswith("https://openminds"): + return uri.replace("ebrains.eu", "om-i.org") + else: + return uri + + return _adapt_namespaces(data, adapt_keys_3to4, adapt_type_3to4, adapt_instance_uri_3to4) def adapt_type_4to3(uri): @@ -500,7 +508,13 @@ def adapt_keys_4to3(uri_list): replacement = ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab") return (uri.replace(*replacement) for uri in uri_list) - return _adapt_namespaces(data, adapt_keys_4to3, adapt_type_4to3) + def adapt_instance_uri_4to3(uri): + if uri.startswith("https://openminds"): + return uri.replace("om-i.org", "ebrains.eu") + else: + return uri + + return _adapt_namespaces(data, adapt_keys_4to3, adapt_type_4to3, adapt_instance_uri_4to3) def adapt_namespaces_for_query(query): From 9f4738e18e06d55d711e1cee00bde021cbfd0573 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 17 Sep 2025 10:50:06 +0200 Subject: [PATCH 18/25] A better way to make openMINDS terminology instances available as fairgraph instances. The previous approach of initialising the instances as each module was imported, implemented in [b25091a5] and [e4df6ff0], has the problem that it prematurely triggers the resolution of types (in Property definitions) from strings to classes, and so the properties retain the openMINDS classes rather than getting the fairgraph ones. The new approach leaves initialisation of instances until after all modules have been imported and the registry correctly set up. This also reverts [5853d18f], since those changes are not needed if all classes are properly initialised. --- builder/fairgraph_module_template.py.txt | 10 ---------- builder/update_openminds.py | 5 +---- fairgraph/__init__.py | 15 ++++++++++++--- fairgraph/kgobject.py | 2 -- fairgraph/node.py | 1 - .../openminds/chemicals/amount_of_chemical.py | 10 ---------- .../openminds/chemicals/chemical_mixture.py | 10 ---------- .../openminds/chemicals/chemical_substance.py | 10 ---------- fairgraph/openminds/chemicals/product_source.py | 10 ---------- .../openminds/computation/data_analysis.py | 10 ---------- fairgraph/openminds/computation/data_copy.py | 10 ---------- fairgraph/openminds/computation/environment.py | 10 ---------- .../computation/generic_computation.py | 10 ---------- .../openminds/computation/hardware_system.py | 10 ---------- .../computation/launch_configuration.py | 10 ---------- fairgraph/openminds/computation/local_file.py | 10 ---------- .../openminds/computation/model_validation.py | 10 ---------- fairgraph/openminds/computation/optimization.py | 10 ---------- fairgraph/openminds/computation/simulation.py | 10 ---------- .../openminds/computation/software_agent.py | 10 ---------- .../openminds/computation/validation_test.py | 10 ---------- .../computation/validation_test_version.py | 10 ---------- .../openminds/computation/visualization.py | 10 ---------- .../openminds/computation/workflow_execution.py | 10 ---------- .../openminds/computation/workflow_recipe.py | 10 ---------- .../computation/workflow_recipe_version.py | 10 ---------- .../openminds/controlled_terms/__init__.py | 2 +- .../controlled_terms/action_status_type.py | 10 ---------- .../openminds/controlled_terms/age_category.py | 10 ---------- .../controlled_terms/analysis_technique.py | 10 ---------- .../anatomical_axes_orientation.py | 10 ---------- .../anatomical_identification_type.py | 10 ---------- .../controlled_terms/anatomical_plane.py | 10 ---------- .../annotation_criteria_type.py | 10 ---------- .../controlled_terms/annotation_type.py | 10 ---------- .../openminds/controlled_terms/atlas_type.py | 10 ---------- .../controlled_terms/auditory_stimulus_type.py | 10 ---------- .../controlled_terms/biological_order.py | 10 ---------- .../controlled_terms/biological_process.py | 10 ---------- .../controlled_terms/biological_sex.py | 10 ---------- .../openminds/controlled_terms/breeding_type.py | 10 ---------- .../controlled_terms/cell_culture_type.py | 10 ---------- .../openminds/controlled_terms/cell_type.py | 10 ---------- .../controlled_terms/chemical_mixture_type.py | 10 ---------- .../openminds/controlled_terms/colormap.py | 10 ---------- .../controlled_terms/contribution_type.py | 10 ---------- .../cranial_window_construction_type.py | 10 ---------- .../cranial_window_reinforcement_type.py | 10 ---------- .../controlled_terms/criteria_quality_type.py | 10 ---------- .../openminds/controlled_terms/data_type.py | 10 ---------- .../openminds/controlled_terms/device_type.py | 10 ---------- .../controlled_terms/difference_measure.py | 10 ---------- fairgraph/openminds/controlled_terms/disease.py | 10 ---------- .../openminds/controlled_terms/disease_model.py | 10 ---------- .../controlled_terms/educational_level.py | 10 ---------- .../electrical_stimulus_type.py | 10 ---------- .../controlled_terms/ethics_assessment.py | 10 ---------- .../controlled_terms/experimental_approach.py | 10 ---------- .../controlled_terms/file_bundle_grouping.py | 10 ---------- .../controlled_terms/file_repository_type.py | 10 ---------- .../controlled_terms/file_usage_role.py | 10 ---------- .../controlled_terms/genetic_strain_type.py | 10 ---------- .../controlled_terms/gustatory_stimulus_type.py | 10 ---------- .../openminds/controlled_terms/handedness.py | 10 ---------- .../openminds/controlled_terms/language.py | 10 ---------- .../openminds/controlled_terms/laterality.py | 10 ---------- .../controlled_terms/learning_resource_type.py | 10 ---------- .../controlled_terms/measured_quantity.py | 10 ---------- .../controlled_terms/measured_signal_type.py | 10 ---------- .../controlled_terms/meta_data_model_type.py | 10 ---------- .../controlled_terms/model_abstraction_level.py | 10 ---------- .../openminds/controlled_terms/model_scope.py | 10 ---------- .../controlled_terms/molecular_entity.py | 10 ---------- ...quisition_type.py => mr_spatial_encoding.py} | 16 +++------------- .../controlled_terms/mri_pulse_sequence.py | 10 ---------- .../openminds/controlled_terms/mri_weighting.py | 10 ---------- .../controlled_terms/olfactory_stimulus_type.py | 10 ---------- .../controlled_terms/operating_device.py | 10 ---------- .../controlled_terms/operating_system.py | 10 ---------- .../controlled_terms/optical_stimulus_type.py | 10 ---------- fairgraph/openminds/controlled_terms/organ.py | 10 ---------- .../controlled_terms/organism_substance.py | 10 ---------- .../controlled_terms/organism_system.py | 10 ---------- .../controlled_terms/patch_clamp_variation.py | 10 ---------- .../controlled_terms/preparation_type.py | 10 ---------- .../controlled_terms/product_accessibility.py | 10 ---------- .../controlled_terms/programming_language.py | 10 ---------- .../controlled_terms/qualitative_overlap.py | 10 ---------- .../controlled_terms/semantic_data_type.py | 10 ---------- fairgraph/openminds/controlled_terms/service.py | 10 ---------- .../openminds/controlled_terms/setup_type.py | 10 ---------- .../software_application_category.py | 10 ---------- .../controlled_terms/software_feature.py | 10 ---------- fairgraph/openminds/controlled_terms/species.py | 10 ---------- .../controlled_terms/stimulation_approach.py | 10 ---------- .../controlled_terms/stimulation_technique.py | 10 ---------- .../controlled_terms/subcellular_entity.py | 10 ---------- .../controlled_terms/subject_attribute.py | 10 ---------- .../controlled_terms/tactile_stimulus_type.py | 10 ---------- .../openminds/controlled_terms/technique.py | 10 ---------- .../controlled_terms/term_suggestion.py | 10 ---------- .../openminds/controlled_terms/terminology.py | 10 ---------- .../controlled_terms/tissue_sample_attribute.py | 10 ---------- .../controlled_terms/tissue_sample_type.py | 10 ---------- .../controlled_terms/type_of_uncertainty.py | 10 ---------- .../controlled_terms/uberon_parcellation.py | 10 ---------- .../controlled_terms/unit_of_measurement.py | 10 ---------- .../controlled_terms/visual_stimulus_type.py | 10 ---------- .../core/actors/account_information.py | 10 ---------- fairgraph/openminds/core/actors/affiliation.py | 10 ---------- fairgraph/openminds/core/actors/consortium.py | 10 ---------- .../core/actors/contact_information.py | 10 ---------- fairgraph/openminds/core/actors/contribution.py | 10 ---------- fairgraph/openminds/core/actors/organization.py | 10 ---------- fairgraph/openminds/core/actors/person.py | 10 ---------- fairgraph/openminds/core/data/content_type.py | 10 ---------- .../openminds/core/data/content_type_pattern.py | 10 ---------- fairgraph/openminds/core/data/copyright.py | 10 ---------- fairgraph/openminds/core/data/file.py | 10 ---------- fairgraph/openminds/core/data/file_archive.py | 10 ---------- fairgraph/openminds/core/data/file_bundle.py | 10 ---------- .../openminds/core/data/file_path_pattern.py | 10 ---------- .../openminds/core/data/file_repository.py | 10 ---------- .../core/data/file_repository_structure.py | 10 ---------- fairgraph/openminds/core/data/hash.py | 10 ---------- fairgraph/openminds/core/data/license.py | 10 ---------- fairgraph/openminds/core/data/measurement.py | 10 ---------- fairgraph/openminds/core/data/service_link.py | 10 ---------- .../openminds/core/digital_identifier/doi.py | 10 ---------- .../openminds/core/digital_identifier/gridid.py | 10 ---------- .../openminds/core/digital_identifier/handle.py | 10 ---------- .../identifiers_dot_org_id.py | 10 ---------- .../openminds/core/digital_identifier/isbn.py | 10 ---------- .../openminds/core/digital_identifier/issn.py | 10 ---------- .../openminds/core/digital_identifier/orcid.py | 10 ---------- .../openminds/core/digital_identifier/rorid.py | 10 ---------- .../openminds/core/digital_identifier/rrid.py | 10 ---------- .../core/digital_identifier/stock_number.py | 10 ---------- .../openminds/core/digital_identifier/swhid.py | 10 ---------- .../openminds/core/miscellaneous/comment.py | 10 ---------- .../openminds/core/miscellaneous/funding.py | 10 ---------- .../core/miscellaneous/quantitative_value.py | 10 ---------- .../miscellaneous/quantitative_value_array.py | 10 ---------- .../miscellaneous/quantitative_value_range.py | 10 ---------- .../miscellaneous/research_product_group.py | 10 ---------- .../core/miscellaneous/web_resource.py | 10 ---------- fairgraph/openminds/core/products/dataset.py | 10 ---------- .../openminds/core/products/dataset_version.py | 10 ---------- .../openminds/core/products/meta_data_model.py | 10 ---------- .../core/products/meta_data_model_version.py | 10 ---------- fairgraph/openminds/core/products/model.py | 10 ---------- .../openminds/core/products/model_version.py | 10 ---------- fairgraph/openminds/core/products/project.py | 10 ---------- fairgraph/openminds/core/products/setup.py | 10 ---------- fairgraph/openminds/core/products/software.py | 10 ---------- .../openminds/core/products/software_version.py | 10 ---------- .../openminds/core/products/web_service.py | 10 ---------- .../core/products/web_service_version.py | 10 ---------- .../core/research/behavioral_protocol.py | 10 ---------- .../openminds/core/research/configuration.py | 10 ---------- .../core/research/custom_property_set.py | 10 ---------- .../core/research/numerical_property.py | 10 ---------- .../core/research/property_value_list.py | 10 ---------- fairgraph/openminds/core/research/protocol.py | 10 ---------- .../core/research/protocol_execution.py | 10 ---------- fairgraph/openminds/core/research/strain.py | 10 ---------- .../openminds/core/research/string_property.py | 10 ---------- fairgraph/openminds/core/research/subject.py | 10 ---------- .../openminds/core/research/subject_group.py | 10 ---------- .../core/research/subject_group_state.py | 10 ---------- .../openminds/core/research/subject_state.py | 10 ---------- .../openminds/core/research/tissue_sample.py | 10 ---------- .../core/research/tissue_sample_collection.py | 10 ---------- .../research/tissue_sample_collection_state.py | 10 ---------- .../core/research/tissue_sample_state.py | 10 ---------- .../openminds/ephys/activity/cell_patching.py | 10 ---------- .../ephys/activity/electrode_placement.py | 10 ---------- .../ephys/activity/recording_activity.py | 10 ---------- fairgraph/openminds/ephys/device/electrode.py | 10 ---------- .../openminds/ephys/device/electrode_array.py | 10 ---------- .../ephys/device/electrode_array_usage.py | 10 ---------- .../openminds/ephys/device/electrode_usage.py | 10 ---------- fairgraph/openminds/ephys/device/pipette.py | 10 ---------- .../openminds/ephys/device/pipette_usage.py | 10 ---------- fairgraph/openminds/ephys/entity/channel.py | 10 ---------- fairgraph/openminds/ephys/entity/recording.py | 10 ---------- fairgraph/openminds/publications/book.py | 10 ---------- fairgraph/openminds/publications/chapter.py | 10 ---------- .../openminds/publications/learning_resource.py | 10 ---------- fairgraph/openminds/publications/live_paper.py | 10 ---------- .../publications/live_paper_resource_item.py | 10 ---------- .../publications/live_paper_section.py | 10 ---------- .../publications/live_paper_version.py | 10 ---------- fairgraph/openminds/publications/periodical.py | 10 ---------- .../openminds/publications/publication_issue.py | 10 ---------- .../publications/publication_volume.py | 10 ---------- .../openminds/publications/scholarly_article.py | 10 ---------- .../openminds/sands/atlas/atlas_annotation.py | 10 ---------- fairgraph/openminds/sands/atlas/brain_atlas.py | 10 ---------- .../sands/atlas/brain_atlas_version.py | 10 ---------- .../sands/atlas/common_coordinate_space.py | 10 ---------- .../atlas/common_coordinate_space_version.py | 10 ---------- .../sands/atlas/parcellation_entity.py | 10 ---------- .../sands/atlas/parcellation_entity_version.py | 10 ---------- .../sands/atlas/parcellation_terminology.py | 10 ---------- .../atlas/parcellation_terminology_version.py | 10 ---------- .../sands/mathematical_shapes/circle.py | 10 ---------- .../sands/mathematical_shapes/ellipse.py | 10 ---------- .../sands/mathematical_shapes/rectangle.py | 10 ---------- .../miscellaneous/anatomical_target_position.py | 10 ---------- .../sands/miscellaneous/coordinate_point.py | 10 ---------- .../qualitative_relation_assessment.py | 10 ---------- .../quantitative_relation_assessment.py | 10 ---------- .../sands/miscellaneous/single_color.py | 10 ---------- .../sands/miscellaneous/viewer_specification.py | 10 ---------- .../sands/non_atlas/custom_anatomical_entity.py | 10 ---------- .../sands/non_atlas/custom_annotation.py | 10 ---------- .../sands/non_atlas/custom_coordinate_space.py | 10 ---------- .../activity/cranial_window_preparation.py | 10 ---------- .../activity/tissue_culture_preparation.py | 10 ---------- .../activity/tissue_sample_slicing.py | 10 ---------- .../specimen_prep/device/slicing_device.py | 10 ---------- .../device/slicing_device_usage.py | 10 ---------- .../activity/stimulation_activity.py | 10 ---------- .../stimulation/stimulus/ephys_stimulus.py | 10 ---------- fairgraph/queries.py | 6 ++---- fairgraph/utility.py | 17 +++++++++++++++++ 227 files changed, 36 insertions(+), 2218 deletions(-) rename fairgraph/openminds/controlled_terms/{mr_acquisition_type.py => mr_spatial_encoding.py} (78%) diff --git a/builder/fairgraph_module_template.py.txt b/builder/fairgraph_module_template.py.txt index 3717ea4f..70beedac 100644 --- a/builder/fairgraph_module_template.py.txt +++ b/builder/fairgraph_module_template.py.txt @@ -49,13 +49,3 @@ class {{ class_name }}({{base_class}}, OM{{ class_name }}): def __init__(self {%- for arg in constructor_arguments -%}, {{arg}}=None{%- endfor -%}, id=None, data=None, space=None, scope=None): return {{ base_class }}.__init__(self, {{ standard_init_properties }}data=data {%- for arg in constructor_arguments -%}, {{arg}}={{arg}}{%- endfor -%}) {{ additional_methods }} - - -# cast openMINDS instances to their fairgraph subclass -{{ class_name }}.set_error_handling(None) -for key, value in OM{{ class_name }}.__dict__.items(): - if isinstance(value, OM{{ class_name }}): - fg_instance = {{ class_name }}.from_jsonld(value.to_jsonld()) - fg_instance._space = {{ class_name }}.default_space - setattr({{ class_name }}, key, fg_instance) -{{ class_name }}.set_error_handling("log") diff --git a/builder/update_openminds.py b/builder/update_openminds.py index b8f0b990..6186593e 100644 --- a/builder/update_openminds.py +++ b/builder/update_openminds.py @@ -275,7 +275,7 @@ def invert_dict(D): DEFAULT_SPACES = { - "chemicals": {"default": "dataset"}, + "chemicals": {"default": "in-depth"}, "core": invert_dict( { "common": [ @@ -387,7 +387,6 @@ def invert_dict(D): ), "publications": {"default": "livepapers"}, "ephys": {"default": "in-depth"}, - "chemicals": {"default": "in-depth"}, "specimen_prep": {"default": "in-depth"}, "stimulation": {"default": "in-depth"}, } @@ -620,7 +619,6 @@ def get_type(prop): "email": "str", # todo: add an Email class for validation? "ECMA262": "str", # ... } - #breakpoint() if "_linkedTypes" in prop: types = [] for item in prop["_linkedTypes"]: @@ -839,7 +837,6 @@ def get_edges(self): reverse_link_name, ) # linked from (cls, prop name, prop name plural, reverse name) # if self._schema_payload["_type"].endswith("File"): - # breakpoint() return embedded, linked def get_module_map(self): diff --git a/fairgraph/__init__.py b/fairgraph/__init__.py index 01458227..8c809144 100644 --- a/fairgraph/__init__.py +++ b/fairgraph/__init__.py @@ -25,9 +25,18 @@ from .embedded import EmbeddedMetadata from .kgproxy import KGProxy from .kgquery import KGQuery - +from . import client, errors, openminds, utility __version__ = "0.12.2" -# from . import ( -# base, client, errors, utility, openminds) +utility.initialise_instances([ + openminds.sands.BrainAtlas, + openminds.sands.BrainAtlasVersion, + openminds.sands.CommonCoordinateSpace, + openminds.sands.CommonCoordinateSpaceVersion, + openminds.core.ContentType, + openminds.core.License, + openminds.sands.ParcellationEntity, + openminds.sands.ParcellationEntityVersion] + + openminds.controlled_terms.list_kg_classes() +) diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index b46d6942..7cc5b66c 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -456,8 +456,6 @@ def __ne__(self, other): val_self = getattr(self, prop.name) val_other = getattr(other, prop.name) if val_self != val_other: - #if self.uuid == "ab532423-1fd7-4255-8c6f-f99dc6df814f": - # raise Exception("breakpoint") return True return False diff --git a/fairgraph/node.py b/fairgraph/node.py index 01f5ed07..5d70238c 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -110,7 +110,6 @@ def __setattr__(self, name, value): failures = prop.validate(value) if failures: errmsg = str(failures) # todo: create a nicer error message - breakpoint() ErrorHandling.handle_violation(self.error_handling, errmsg) super().__setattr__(name, value) diff --git a/fairgraph/openminds/chemicals/amount_of_chemical.py b/fairgraph/openminds/chemicals/amount_of_chemical.py index 2b18efb5..40d34019 100644 --- a/fairgraph/openminds/chemicals/amount_of_chemical.py +++ b/fairgraph/openminds/chemicals/amount_of_chemical.py @@ -20,13 +20,3 @@ class AmountOfChemical(EmbeddedMetadata, OMAmountOfChemical): def __init__(self, amount=None, chemical_product=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, amount=amount, chemical_product=chemical_product) - - -# cast openMINDS instances to their fairgraph subclass -AmountOfChemical.set_error_handling(None) -for key, value in OMAmountOfChemical.__dict__.items(): - if isinstance(value, OMAmountOfChemical): - fg_instance = AmountOfChemical.from_jsonld(value.to_jsonld()) - fg_instance._space = AmountOfChemical.default_space - setattr(AmountOfChemical, key, fg_instance) -AmountOfChemical.set_error_handling("log") diff --git a/fairgraph/openminds/chemicals/chemical_mixture.py b/fairgraph/openminds/chemicals/chemical_mixture.py index 1b51361c..e8f60976 100644 --- a/fairgraph/openminds/chemicals/chemical_mixture.py +++ b/fairgraph/openminds/chemicals/chemical_mixture.py @@ -74,13 +74,3 @@ def __init__( type=type, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -ChemicalMixture.set_error_handling(None) -for key, value in OMChemicalMixture.__dict__.items(): - if isinstance(value, OMChemicalMixture): - fg_instance = ChemicalMixture.from_jsonld(value.to_jsonld()) - fg_instance._space = ChemicalMixture.default_space - setattr(ChemicalMixture, key, fg_instance) -ChemicalMixture.set_error_handling("log") diff --git a/fairgraph/openminds/chemicals/chemical_substance.py b/fairgraph/openminds/chemicals/chemical_substance.py index f1a6d77c..0d6d0161 100644 --- a/fairgraph/openminds/chemicals/chemical_substance.py +++ b/fairgraph/openminds/chemicals/chemical_substance.py @@ -69,13 +69,3 @@ def __init__( product_source=product_source, purity=purity, ) - - -# cast openMINDS instances to their fairgraph subclass -ChemicalSubstance.set_error_handling(None) -for key, value in OMChemicalSubstance.__dict__.items(): - if isinstance(value, OMChemicalSubstance): - fg_instance = ChemicalSubstance.from_jsonld(value.to_jsonld()) - fg_instance._space = ChemicalSubstance.default_space - setattr(ChemicalSubstance, key, fg_instance) -ChemicalSubstance.set_error_handling("log") diff --git a/fairgraph/openminds/chemicals/product_source.py b/fairgraph/openminds/chemicals/product_source.py index 73f559cb..d10e141e 100644 --- a/fairgraph/openminds/chemicals/product_source.py +++ b/fairgraph/openminds/chemicals/product_source.py @@ -55,13 +55,3 @@ def __init__( provider=provider, purity=purity, ) - - -# cast openMINDS instances to their fairgraph subclass -ProductSource.set_error_handling(None) -for key, value in OMProductSource.__dict__.items(): - if isinstance(value, OMProductSource): - fg_instance = ProductSource.from_jsonld(value.to_jsonld()) - fg_instance._space = ProductSource.default_space - setattr(ProductSource, key, fg_instance) -ProductSource.set_error_handling("log") diff --git a/fairgraph/openminds/computation/data_analysis.py b/fairgraph/openminds/computation/data_analysis.py index 3ba130d6..a936edff 100644 --- a/fairgraph/openminds/computation/data_analysis.py +++ b/fairgraph/openminds/computation/data_analysis.py @@ -102,13 +102,3 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) - - -# cast openMINDS instances to their fairgraph subclass -DataAnalysis.set_error_handling(None) -for key, value in OMDataAnalysis.__dict__.items(): - if isinstance(value, OMDataAnalysis): - fg_instance = DataAnalysis.from_jsonld(value.to_jsonld()) - fg_instance._space = DataAnalysis.default_space - setattr(DataAnalysis, key, fg_instance) -DataAnalysis.set_error_handling("log") diff --git a/fairgraph/openminds/computation/data_copy.py b/fairgraph/openminds/computation/data_copy.py index 13313ac0..65c86639 100644 --- a/fairgraph/openminds/computation/data_copy.py +++ b/fairgraph/openminds/computation/data_copy.py @@ -102,13 +102,3 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) - - -# cast openMINDS instances to their fairgraph subclass -DataCopy.set_error_handling(None) -for key, value in OMDataCopy.__dict__.items(): - if isinstance(value, OMDataCopy): - fg_instance = DataCopy.from_jsonld(value.to_jsonld()) - fg_instance._space = DataCopy.default_space - setattr(DataCopy, key, fg_instance) -DataCopy.set_error_handling("log") diff --git a/fairgraph/openminds/computation/environment.py b/fairgraph/openminds/computation/environment.py index bd043ae9..297cecf2 100644 --- a/fairgraph/openminds/computation/environment.py +++ b/fairgraph/openminds/computation/environment.py @@ -64,13 +64,3 @@ def __init__( software=software, used_for=used_for, ) - - -# cast openMINDS instances to their fairgraph subclass -Environment.set_error_handling(None) -for key, value in OMEnvironment.__dict__.items(): - if isinstance(value, OMEnvironment): - fg_instance = Environment.from_jsonld(value.to_jsonld()) - fg_instance._space = Environment.default_space - setattr(Environment, key, fg_instance) -Environment.set_error_handling("log") diff --git a/fairgraph/openminds/computation/generic_computation.py b/fairgraph/openminds/computation/generic_computation.py index 048a442c..c321cd2c 100644 --- a/fairgraph/openminds/computation/generic_computation.py +++ b/fairgraph/openminds/computation/generic_computation.py @@ -102,13 +102,3 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) - - -# cast openMINDS instances to their fairgraph subclass -GenericComputation.set_error_handling(None) -for key, value in OMGenericComputation.__dict__.items(): - if isinstance(value, OMGenericComputation): - fg_instance = GenericComputation.from_jsonld(value.to_jsonld()) - fg_instance._space = GenericComputation.default_space - setattr(GenericComputation, key, fg_instance) -GenericComputation.set_error_handling("log") diff --git a/fairgraph/openminds/computation/hardware_system.py b/fairgraph/openminds/computation/hardware_system.py index e62f240a..73a0799d 100644 --- a/fairgraph/openminds/computation/hardware_system.py +++ b/fairgraph/openminds/computation/hardware_system.py @@ -51,13 +51,3 @@ def __init__( used_by=used_by, version_identifier=version_identifier, ) - - -# cast openMINDS instances to their fairgraph subclass -HardwareSystem.set_error_handling(None) -for key, value in OMHardwareSystem.__dict__.items(): - if isinstance(value, OMHardwareSystem): - fg_instance = HardwareSystem.from_jsonld(value.to_jsonld()) - fg_instance._space = HardwareSystem.default_space - setattr(HardwareSystem, key, fg_instance) -HardwareSystem.set_error_handling("log") diff --git a/fairgraph/openminds/computation/launch_configuration.py b/fairgraph/openminds/computation/launch_configuration.py index 3e5f3ca4..990e9991 100644 --- a/fairgraph/openminds/computation/launch_configuration.py +++ b/fairgraph/openminds/computation/launch_configuration.py @@ -63,13 +63,3 @@ def __init__( executable=executable, is_launch_configuration_of=is_launch_configuration_of, ) - - -# cast openMINDS instances to their fairgraph subclass -LaunchConfiguration.set_error_handling(None) -for key, value in OMLaunchConfiguration.__dict__.items(): - if isinstance(value, OMLaunchConfiguration): - fg_instance = LaunchConfiguration.from_jsonld(value.to_jsonld()) - fg_instance._space = LaunchConfiguration.default_space - setattr(LaunchConfiguration, key, fg_instance) -LaunchConfiguration.set_error_handling("log") diff --git a/fairgraph/openminds/computation/local_file.py b/fairgraph/openminds/computation/local_file.py index eefe436b..fd4c4001 100644 --- a/fairgraph/openminds/computation/local_file.py +++ b/fairgraph/openminds/computation/local_file.py @@ -81,13 +81,3 @@ def __init__( special_usage_role=special_usage_role, storage_size=storage_size, ) - - -# cast openMINDS instances to their fairgraph subclass -LocalFile.set_error_handling(None) -for key, value in OMLocalFile.__dict__.items(): - if isinstance(value, OMLocalFile): - fg_instance = LocalFile.from_jsonld(value.to_jsonld()) - fg_instance._space = LocalFile.default_space - setattr(LocalFile, key, fg_instance) -LocalFile.set_error_handling("log") diff --git a/fairgraph/openminds/computation/model_validation.py b/fairgraph/openminds/computation/model_validation.py index 96dda549..69b78647 100644 --- a/fairgraph/openminds/computation/model_validation.py +++ b/fairgraph/openminds/computation/model_validation.py @@ -105,13 +105,3 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) - - -# cast openMINDS instances to their fairgraph subclass -ModelValidation.set_error_handling(None) -for key, value in OMModelValidation.__dict__.items(): - if isinstance(value, OMModelValidation): - fg_instance = ModelValidation.from_jsonld(value.to_jsonld()) - fg_instance._space = ModelValidation.default_space - setattr(ModelValidation, key, fg_instance) -ModelValidation.set_error_handling("log") diff --git a/fairgraph/openminds/computation/optimization.py b/fairgraph/openminds/computation/optimization.py index 11cad8ad..1c3420a2 100644 --- a/fairgraph/openminds/computation/optimization.py +++ b/fairgraph/openminds/computation/optimization.py @@ -102,13 +102,3 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) - - -# cast openMINDS instances to their fairgraph subclass -Optimization.set_error_handling(None) -for key, value in OMOptimization.__dict__.items(): - if isinstance(value, OMOptimization): - fg_instance = Optimization.from_jsonld(value.to_jsonld()) - fg_instance._space = Optimization.default_space - setattr(Optimization, key, fg_instance) -Optimization.set_error_handling("log") diff --git a/fairgraph/openminds/computation/simulation.py b/fairgraph/openminds/computation/simulation.py index a49f4dae..d3ecbfcd 100644 --- a/fairgraph/openminds/computation/simulation.py +++ b/fairgraph/openminds/computation/simulation.py @@ -102,13 +102,3 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) - - -# cast openMINDS instances to their fairgraph subclass -Simulation.set_error_handling(None) -for key, value in OMSimulation.__dict__.items(): - if isinstance(value, OMSimulation): - fg_instance = Simulation.from_jsonld(value.to_jsonld()) - fg_instance._space = Simulation.default_space - setattr(Simulation, key, fg_instance) -Simulation.set_error_handling("log") diff --git a/fairgraph/openminds/computation/software_agent.py b/fairgraph/openminds/computation/software_agent.py index 4f980100..5aec43dc 100644 --- a/fairgraph/openminds/computation/software_agent.py +++ b/fairgraph/openminds/computation/software_agent.py @@ -79,13 +79,3 @@ def __init__( software=software, started=started, ) - - -# cast openMINDS instances to their fairgraph subclass -SoftwareAgent.set_error_handling(None) -for key, value in OMSoftwareAgent.__dict__.items(): - if isinstance(value, OMSoftwareAgent): - fg_instance = SoftwareAgent.from_jsonld(value.to_jsonld()) - fg_instance._space = SoftwareAgent.default_space - setattr(SoftwareAgent, key, fg_instance) -SoftwareAgent.set_error_handling("log") diff --git a/fairgraph/openminds/computation/validation_test.py b/fairgraph/openminds/computation/validation_test.py index 92afb712..c7fceea3 100644 --- a/fairgraph/openminds/computation/validation_test.py +++ b/fairgraph/openminds/computation/validation_test.py @@ -101,13 +101,3 @@ def __init__( study_targets=study_targets, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -ValidationTest.set_error_handling(None) -for key, value in OMValidationTest.__dict__.items(): - if isinstance(value, OMValidationTest): - fg_instance = ValidationTest.from_jsonld(value.to_jsonld()) - fg_instance._space = ValidationTest.default_space - setattr(ValidationTest, key, fg_instance) -ValidationTest.set_error_handling("log") diff --git a/fairgraph/openminds/computation/validation_test_version.py b/fairgraph/openminds/computation/validation_test_version.py index 2219b059..014216b1 100644 --- a/fairgraph/openminds/computation/validation_test_version.py +++ b/fairgraph/openminds/computation/validation_test_version.py @@ -167,13 +167,3 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] - - -# cast openMINDS instances to their fairgraph subclass -ValidationTestVersion.set_error_handling(None) -for key, value in OMValidationTestVersion.__dict__.items(): - if isinstance(value, OMValidationTestVersion): - fg_instance = ValidationTestVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = ValidationTestVersion.default_space - setattr(ValidationTestVersion, key, fg_instance) -ValidationTestVersion.set_error_handling("log") diff --git a/fairgraph/openminds/computation/visualization.py b/fairgraph/openminds/computation/visualization.py index 7ab6565a..145f068d 100644 --- a/fairgraph/openminds/computation/visualization.py +++ b/fairgraph/openminds/computation/visualization.py @@ -102,13 +102,3 @@ def __init__( techniques=techniques, was_informed_by=was_informed_by, ) - - -# cast openMINDS instances to their fairgraph subclass -Visualization.set_error_handling(None) -for key, value in OMVisualization.__dict__.items(): - if isinstance(value, OMVisualization): - fg_instance = Visualization.from_jsonld(value.to_jsonld()) - fg_instance._space = Visualization.default_space - setattr(Visualization, key, fg_instance) -Visualization.set_error_handling("log") diff --git a/fairgraph/openminds/computation/workflow_execution.py b/fairgraph/openminds/computation/workflow_execution.py index 74e53c66..617b2140 100644 --- a/fairgraph/openminds/computation/workflow_execution.py +++ b/fairgraph/openminds/computation/workflow_execution.py @@ -34,13 +34,3 @@ def __init__( stages=stages, started_by=started_by, ) - - -# cast openMINDS instances to their fairgraph subclass -WorkflowExecution.set_error_handling(None) -for key, value in OMWorkflowExecution.__dict__.items(): - if isinstance(value, OMWorkflowExecution): - fg_instance = WorkflowExecution.from_jsonld(value.to_jsonld()) - fg_instance._space = WorkflowExecution.default_space - setattr(WorkflowExecution, key, fg_instance) -WorkflowExecution.set_error_handling("log") diff --git a/fairgraph/openminds/computation/workflow_recipe.py b/fairgraph/openminds/computation/workflow_recipe.py index 497b24e4..2cb39253 100644 --- a/fairgraph/openminds/computation/workflow_recipe.py +++ b/fairgraph/openminds/computation/workflow_recipe.py @@ -93,13 +93,3 @@ def __init__( short_name=short_name, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -WorkflowRecipe.set_error_handling(None) -for key, value in OMWorkflowRecipe.__dict__.items(): - if isinstance(value, OMWorkflowRecipe): - fg_instance = WorkflowRecipe.from_jsonld(value.to_jsonld()) - fg_instance._space = WorkflowRecipe.default_space - setattr(WorkflowRecipe, key, fg_instance) -WorkflowRecipe.set_error_handling("log") diff --git a/fairgraph/openminds/computation/workflow_recipe_version.py b/fairgraph/openminds/computation/workflow_recipe_version.py index 852f67e9..76e7ed84 100644 --- a/fairgraph/openminds/computation/workflow_recipe_version.py +++ b/fairgraph/openminds/computation/workflow_recipe_version.py @@ -163,13 +163,3 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) - - -# cast openMINDS instances to their fairgraph subclass -WorkflowRecipeVersion.set_error_handling(None) -for key, value in OMWorkflowRecipeVersion.__dict__.items(): - if isinstance(value, OMWorkflowRecipeVersion): - fg_instance = WorkflowRecipeVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = WorkflowRecipeVersion.default_space - setattr(WorkflowRecipeVersion, key, fg_instance) -WorkflowRecipeVersion.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/__init__.py b/fairgraph/openminds/controlled_terms/__init__.py index 403a50b7..958b3cae 100644 --- a/fairgraph/openminds/controlled_terms/__init__.py +++ b/fairgraph/openminds/controlled_terms/__init__.py @@ -49,7 +49,7 @@ from .model_abstraction_level import ModelAbstractionLevel from .model_scope import ModelScope from .molecular_entity import MolecularEntity -from .mr_acquisition_type import MRAcquisitionType +from .mr_spatial_encoding import MRSpatialEncoding from .mri_pulse_sequence import MRIPulseSequence from .mri_weighting import MRIWeighting from .olfactory_stimulus_type import OlfactoryStimulusType diff --git a/fairgraph/openminds/controlled_terms/action_status_type.py b/fairgraph/openminds/controlled_terms/action_status_type.py index a010d55d..10af58df 100644 --- a/fairgraph/openminds/controlled_terms/action_status_type.py +++ b/fairgraph/openminds/controlled_terms/action_status_type.py @@ -95,13 +95,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ActionStatusType.set_error_handling(None) -for key, value in OMActionStatusType.__dict__.items(): - if isinstance(value, OMActionStatusType): - fg_instance = ActionStatusType.from_jsonld(value.to_jsonld()) - fg_instance._space = ActionStatusType.default_space - setattr(ActionStatusType, key, fg_instance) -ActionStatusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/age_category.py b/fairgraph/openminds/controlled_terms/age_category.py index 6d348775..3cfc05fe 100644 --- a/fairgraph/openminds/controlled_terms/age_category.py +++ b/fairgraph/openminds/controlled_terms/age_category.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -AgeCategory.set_error_handling(None) -for key, value in OMAgeCategory.__dict__.items(): - if isinstance(value, OMAgeCategory): - fg_instance = AgeCategory.from_jsonld(value.to_jsonld()) - fg_instance._space = AgeCategory.default_space - setattr(AgeCategory, key, fg_instance) -AgeCategory.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/analysis_technique.py b/fairgraph/openminds/controlled_terms/analysis_technique.py index 3636e029..08ab551d 100644 --- a/fairgraph/openminds/controlled_terms/analysis_technique.py +++ b/fairgraph/openminds/controlled_terms/analysis_technique.py @@ -106,13 +106,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -AnalysisTechnique.set_error_handling(None) -for key, value in OMAnalysisTechnique.__dict__.items(): - if isinstance(value, OMAnalysisTechnique): - fg_instance = AnalysisTechnique.from_jsonld(value.to_jsonld()) - fg_instance._space = AnalysisTechnique.default_space - setattr(AnalysisTechnique, key, fg_instance) -AnalysisTechnique.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py index 7f813d19..c2354c2d 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py +++ b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -AnatomicalAxesOrientation.set_error_handling(None) -for key, value in OMAnatomicalAxesOrientation.__dict__.items(): - if isinstance(value, OMAnatomicalAxesOrientation): - fg_instance = AnatomicalAxesOrientation.from_jsonld(value.to_jsonld()) - fg_instance._space = AnatomicalAxesOrientation.default_space - setattr(AnatomicalAxesOrientation, key, fg_instance) -AnatomicalAxesOrientation.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py index 9e61fcd2..8fcc906e 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py +++ b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -AnatomicalIdentificationType.set_error_handling(None) -for key, value in OMAnatomicalIdentificationType.__dict__.items(): - if isinstance(value, OMAnatomicalIdentificationType): - fg_instance = AnatomicalIdentificationType.from_jsonld(value.to_jsonld()) - fg_instance._space = AnatomicalIdentificationType.default_space - setattr(AnatomicalIdentificationType, key, fg_instance) -AnatomicalIdentificationType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/anatomical_plane.py b/fairgraph/openminds/controlled_terms/anatomical_plane.py index ea5adad1..6851bdc9 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_plane.py +++ b/fairgraph/openminds/controlled_terms/anatomical_plane.py @@ -87,13 +87,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -AnatomicalPlane.set_error_handling(None) -for key, value in OMAnatomicalPlane.__dict__.items(): - if isinstance(value, OMAnatomicalPlane): - fg_instance = AnatomicalPlane.from_jsonld(value.to_jsonld()) - fg_instance._space = AnatomicalPlane.default_space - setattr(AnatomicalPlane, key, fg_instance) -AnatomicalPlane.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py index 87bc8f20..378f7b53 100644 --- a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py @@ -87,13 +87,3 @@ def __init__( synonyms=synonyms, used_by_annotation=used_by_annotation, ) - - -# cast openMINDS instances to their fairgraph subclass -AnnotationCriteriaType.set_error_handling(None) -for key, value in OMAnnotationCriteriaType.__dict__.items(): - if isinstance(value, OMAnnotationCriteriaType): - fg_instance = AnnotationCriteriaType.from_jsonld(value.to_jsonld()) - fg_instance._space = AnnotationCriteriaType.default_space - setattr(AnnotationCriteriaType, key, fg_instance) -AnnotationCriteriaType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/annotation_type.py b/fairgraph/openminds/controlled_terms/annotation_type.py index aadcd822..812a06a4 100644 --- a/fairgraph/openminds/controlled_terms/annotation_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_type.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -AnnotationType.set_error_handling(None) -for key, value in OMAnnotationType.__dict__.items(): - if isinstance(value, OMAnnotationType): - fg_instance = AnnotationType.from_jsonld(value.to_jsonld()) - fg_instance._space = AnnotationType.default_space - setattr(AnnotationType, key, fg_instance) -AnnotationType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/atlas_type.py b/fairgraph/openminds/controlled_terms/atlas_type.py index a1b8af57..fee26948 100644 --- a/fairgraph/openminds/controlled_terms/atlas_type.py +++ b/fairgraph/openminds/controlled_terms/atlas_type.py @@ -86,13 +86,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -AtlasType.set_error_handling(None) -for key, value in OMAtlasType.__dict__.items(): - if isinstance(value, OMAtlasType): - fg_instance = AtlasType.from_jsonld(value.to_jsonld()) - fg_instance._space = AtlasType.default_space - setattr(AtlasType, key, fg_instance) -AtlasType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py index 49cac42d..1101086e 100644 --- a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py @@ -125,13 +125,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -AuditoryStimulusType.set_error_handling(None) -for key, value in OMAuditoryStimulusType.__dict__.items(): - if isinstance(value, OMAuditoryStimulusType): - fg_instance = AuditoryStimulusType.from_jsonld(value.to_jsonld()) - fg_instance._space = AuditoryStimulusType.default_space - setattr(AuditoryStimulusType, key, fg_instance) -AuditoryStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/biological_order.py b/fairgraph/openminds/controlled_terms/biological_order.py index 6d0c9298..43920ff6 100644 --- a/fairgraph/openminds/controlled_terms/biological_order.py +++ b/fairgraph/openminds/controlled_terms/biological_order.py @@ -115,13 +115,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -BiologicalOrder.set_error_handling(None) -for key, value in OMBiologicalOrder.__dict__.items(): - if isinstance(value, OMBiologicalOrder): - fg_instance = BiologicalOrder.from_jsonld(value.to_jsonld()) - fg_instance._space = BiologicalOrder.default_space - setattr(BiologicalOrder, key, fg_instance) -BiologicalOrder.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/biological_process.py b/fairgraph/openminds/controlled_terms/biological_process.py index b10b959c..d3fdea70 100644 --- a/fairgraph/openminds/controlled_terms/biological_process.py +++ b/fairgraph/openminds/controlled_terms/biological_process.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -BiologicalProcess.set_error_handling(None) -for key, value in OMBiologicalProcess.__dict__.items(): - if isinstance(value, OMBiologicalProcess): - fg_instance = BiologicalProcess.from_jsonld(value.to_jsonld()) - fg_instance._space = BiologicalProcess.default_space - setattr(BiologicalProcess, key, fg_instance) -BiologicalProcess.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/biological_sex.py b/fairgraph/openminds/controlled_terms/biological_sex.py index 441cf625..f44cc1f3 100644 --- a/fairgraph/openminds/controlled_terms/biological_sex.py +++ b/fairgraph/openminds/controlled_terms/biological_sex.py @@ -130,13 +130,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -BiologicalSex.set_error_handling(None) -for key, value in OMBiologicalSex.__dict__.items(): - if isinstance(value, OMBiologicalSex): - fg_instance = BiologicalSex.from_jsonld(value.to_jsonld()) - fg_instance._space = BiologicalSex.default_space - setattr(BiologicalSex, key, fg_instance) -BiologicalSex.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/breeding_type.py b/fairgraph/openminds/controlled_terms/breeding_type.py index 09c1f674..bf7e932b 100644 --- a/fairgraph/openminds/controlled_terms/breeding_type.py +++ b/fairgraph/openminds/controlled_terms/breeding_type.py @@ -125,13 +125,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -BreedingType.set_error_handling(None) -for key, value in OMBreedingType.__dict__.items(): - if isinstance(value, OMBreedingType): - fg_instance = BreedingType.from_jsonld(value.to_jsonld()) - fg_instance._space = BreedingType.default_space - setattr(BreedingType, key, fg_instance) -BreedingType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cell_culture_type.py b/fairgraph/openminds/controlled_terms/cell_culture_type.py index 65439d30..b67b3372 100644 --- a/fairgraph/openminds/controlled_terms/cell_culture_type.py +++ b/fairgraph/openminds/controlled_terms/cell_culture_type.py @@ -115,13 +115,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -CellCultureType.set_error_handling(None) -for key, value in OMCellCultureType.__dict__.items(): - if isinstance(value, OMCellCultureType): - fg_instance = CellCultureType.from_jsonld(value.to_jsonld()) - fg_instance._space = CellCultureType.default_space - setattr(CellCultureType, key, fg_instance) -CellCultureType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cell_type.py b/fairgraph/openminds/controlled_terms/cell_type.py index 5bc6b89c..58173b54 100644 --- a/fairgraph/openminds/controlled_terms/cell_type.py +++ b/fairgraph/openminds/controlled_terms/cell_type.py @@ -149,13 +149,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -CellType.set_error_handling(None) -for key, value in OMCellType.__dict__.items(): - if isinstance(value, OMCellType): - fg_instance = CellType.from_jsonld(value.to_jsonld()) - fg_instance._space = CellType.default_space - setattr(CellType, key, fg_instance) -CellType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py index b4c8544c..286df5cb 100644 --- a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py +++ b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ChemicalMixtureType.set_error_handling(None) -for key, value in OMChemicalMixtureType.__dict__.items(): - if isinstance(value, OMChemicalMixtureType): - fg_instance = ChemicalMixtureType.from_jsonld(value.to_jsonld()) - fg_instance._space = ChemicalMixtureType.default_space - setattr(ChemicalMixtureType, key, fg_instance) -ChemicalMixtureType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/colormap.py b/fairgraph/openminds/controlled_terms/colormap.py index d2b016a8..3962225f 100644 --- a/fairgraph/openminds/controlled_terms/colormap.py +++ b/fairgraph/openminds/controlled_terms/colormap.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Colormap.set_error_handling(None) -for key, value in OMColormap.__dict__.items(): - if isinstance(value, OMColormap): - fg_instance = Colormap.from_jsonld(value.to_jsonld()) - fg_instance._space = Colormap.default_space - setattr(Colormap, key, fg_instance) -Colormap.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/contribution_type.py b/fairgraph/openminds/controlled_terms/contribution_type.py index 0a86a1d7..c8851727 100644 --- a/fairgraph/openminds/controlled_terms/contribution_type.py +++ b/fairgraph/openminds/controlled_terms/contribution_type.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ContributionType.set_error_handling(None) -for key, value in OMContributionType.__dict__.items(): - if isinstance(value, OMContributionType): - fg_instance = ContributionType.from_jsonld(value.to_jsonld()) - fg_instance._space = ContributionType.default_space - setattr(ContributionType, key, fg_instance) -ContributionType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py index 8a49118c..3fc80254 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py @@ -87,13 +87,3 @@ def __init__( synonyms=synonyms, used_for=used_for, ) - - -# cast openMINDS instances to their fairgraph subclass -CranialWindowConstructionType.set_error_handling(None) -for key, value in OMCranialWindowConstructionType.__dict__.items(): - if isinstance(value, OMCranialWindowConstructionType): - fg_instance = CranialWindowConstructionType.from_jsonld(value.to_jsonld()) - fg_instance._space = CranialWindowConstructionType.default_space - setattr(CranialWindowConstructionType, key, fg_instance) -CranialWindowConstructionType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py index 1d9a8bab..0f12b5de 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py @@ -87,13 +87,3 @@ def __init__( synonyms=synonyms, used_for=used_for, ) - - -# cast openMINDS instances to their fairgraph subclass -CranialWindowReinforcementType.set_error_handling(None) -for key, value in OMCranialWindowReinforcementType.__dict__.items(): - if isinstance(value, OMCranialWindowReinforcementType): - fg_instance = CranialWindowReinforcementType.from_jsonld(value.to_jsonld()) - fg_instance._space = CranialWindowReinforcementType.default_space - setattr(CranialWindowReinforcementType, key, fg_instance) -CranialWindowReinforcementType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/criteria_quality_type.py b/fairgraph/openminds/controlled_terms/criteria_quality_type.py index 1ba335be..9a312d11 100644 --- a/fairgraph/openminds/controlled_terms/criteria_quality_type.py +++ b/fairgraph/openminds/controlled_terms/criteria_quality_type.py @@ -87,13 +87,3 @@ def __init__( synonyms=synonyms, used_by_annotation=used_by_annotation, ) - - -# cast openMINDS instances to their fairgraph subclass -CriteriaQualityType.set_error_handling(None) -for key, value in OMCriteriaQualityType.__dict__.items(): - if isinstance(value, OMCriteriaQualityType): - fg_instance = CriteriaQualityType.from_jsonld(value.to_jsonld()) - fg_instance._space = CriteriaQualityType.default_space - setattr(CriteriaQualityType, key, fg_instance) -CriteriaQualityType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/data_type.py b/fairgraph/openminds/controlled_terms/data_type.py index 0aea9114..b014fd35 100644 --- a/fairgraph/openminds/controlled_terms/data_type.py +++ b/fairgraph/openminds/controlled_terms/data_type.py @@ -91,13 +91,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -DataType.set_error_handling(None) -for key, value in OMDataType.__dict__.items(): - if isinstance(value, OMDataType): - fg_instance = DataType.from_jsonld(value.to_jsonld()) - fg_instance._space = DataType.default_space - setattr(DataType, key, fg_instance) -DataType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/device_type.py b/fairgraph/openminds/controlled_terms/device_type.py index bc8ba967..74c156a4 100644 --- a/fairgraph/openminds/controlled_terms/device_type.py +++ b/fairgraph/openminds/controlled_terms/device_type.py @@ -92,13 +92,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -DeviceType.set_error_handling(None) -for key, value in OMDeviceType.__dict__.items(): - if isinstance(value, OMDeviceType): - fg_instance = DeviceType.from_jsonld(value.to_jsonld()) - fg_instance._space = DeviceType.default_space - setattr(DeviceType, key, fg_instance) -DeviceType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/difference_measure.py b/fairgraph/openminds/controlled_terms/difference_measure.py index 93900878..3b89443e 100644 --- a/fairgraph/openminds/controlled_terms/difference_measure.py +++ b/fairgraph/openminds/controlled_terms/difference_measure.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -DifferenceMeasure.set_error_handling(None) -for key, value in OMDifferenceMeasure.__dict__.items(): - if isinstance(value, OMDifferenceMeasure): - fg_instance = DifferenceMeasure.from_jsonld(value.to_jsonld()) - fg_instance._space = DifferenceMeasure.default_space - setattr(DifferenceMeasure, key, fg_instance) -DifferenceMeasure.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/disease.py b/fairgraph/openminds/controlled_terms/disease.py index 5c039783..700a2b68 100644 --- a/fairgraph/openminds/controlled_terms/disease.py +++ b/fairgraph/openminds/controlled_terms/disease.py @@ -140,13 +140,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Disease.set_error_handling(None) -for key, value in OMDisease.__dict__.items(): - if isinstance(value, OMDisease): - fg_instance = Disease.from_jsonld(value.to_jsonld()) - fg_instance._space = Disease.default_space - setattr(Disease, key, fg_instance) -Disease.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/disease_model.py b/fairgraph/openminds/controlled_terms/disease_model.py index fa29baaa..005bdf2d 100644 --- a/fairgraph/openminds/controlled_terms/disease_model.py +++ b/fairgraph/openminds/controlled_terms/disease_model.py @@ -140,13 +140,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -DiseaseModel.set_error_handling(None) -for key, value in OMDiseaseModel.__dict__.items(): - if isinstance(value, OMDiseaseModel): - fg_instance = DiseaseModel.from_jsonld(value.to_jsonld()) - fg_instance._space = DiseaseModel.default_space - setattr(DiseaseModel, key, fg_instance) -DiseaseModel.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/educational_level.py b/fairgraph/openminds/controlled_terms/educational_level.py index 96b3b024..7a4b5686 100644 --- a/fairgraph/openminds/controlled_terms/educational_level.py +++ b/fairgraph/openminds/controlled_terms/educational_level.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -EducationalLevel.set_error_handling(None) -for key, value in OMEducationalLevel.__dict__.items(): - if isinstance(value, OMEducationalLevel): - fg_instance = EducationalLevel.from_jsonld(value.to_jsonld()) - fg_instance._space = EducationalLevel.default_space - setattr(EducationalLevel, key, fg_instance) -EducationalLevel.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py index d13ac4e0..67c1263f 100644 --- a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py @@ -135,13 +135,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -ElectricalStimulusType.set_error_handling(None) -for key, value in OMElectricalStimulusType.__dict__.items(): - if isinstance(value, OMElectricalStimulusType): - fg_instance = ElectricalStimulusType.from_jsonld(value.to_jsonld()) - fg_instance._space = ElectricalStimulusType.default_space - setattr(ElectricalStimulusType, key, fg_instance) -ElectricalStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/ethics_assessment.py b/fairgraph/openminds/controlled_terms/ethics_assessment.py index 563d1f4a..08db38c8 100644 --- a/fairgraph/openminds/controlled_terms/ethics_assessment.py +++ b/fairgraph/openminds/controlled_terms/ethics_assessment.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -EthicsAssessment.set_error_handling(None) -for key, value in OMEthicsAssessment.__dict__.items(): - if isinstance(value, OMEthicsAssessment): - fg_instance = EthicsAssessment.from_jsonld(value.to_jsonld()) - fg_instance._space = EthicsAssessment.default_space - setattr(EthicsAssessment, key, fg_instance) -EthicsAssessment.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/experimental_approach.py b/fairgraph/openminds/controlled_terms/experimental_approach.py index 62466140..4453010b 100644 --- a/fairgraph/openminds/controlled_terms/experimental_approach.py +++ b/fairgraph/openminds/controlled_terms/experimental_approach.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ExperimentalApproach.set_error_handling(None) -for key, value in OMExperimentalApproach.__dict__.items(): - if isinstance(value, OMExperimentalApproach): - fg_instance = ExperimentalApproach.from_jsonld(value.to_jsonld()) - fg_instance._space = ExperimentalApproach.default_space - setattr(ExperimentalApproach, key, fg_instance) -ExperimentalApproach.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py index 0b002bd5..6159d0e6 100644 --- a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py +++ b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py @@ -97,13 +97,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -FileBundleGrouping.set_error_handling(None) -for key, value in OMFileBundleGrouping.__dict__.items(): - if isinstance(value, OMFileBundleGrouping): - fg_instance = FileBundleGrouping.from_jsonld(value.to_jsonld()) - fg_instance._space = FileBundleGrouping.default_space - setattr(FileBundleGrouping, key, fg_instance) -FileBundleGrouping.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/file_repository_type.py b/fairgraph/openminds/controlled_terms/file_repository_type.py index 5f41dc63..404e6550 100644 --- a/fairgraph/openminds/controlled_terms/file_repository_type.py +++ b/fairgraph/openminds/controlled_terms/file_repository_type.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -FileRepositoryType.set_error_handling(None) -for key, value in OMFileRepositoryType.__dict__.items(): - if isinstance(value, OMFileRepositoryType): - fg_instance = FileRepositoryType.from_jsonld(value.to_jsonld()) - fg_instance._space = FileRepositoryType.default_space - setattr(FileRepositoryType, key, fg_instance) -FileRepositoryType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/file_usage_role.py b/fairgraph/openminds/controlled_terms/file_usage_role.py index 15bda2aa..7a1d7ac8 100644 --- a/fairgraph/openminds/controlled_terms/file_usage_role.py +++ b/fairgraph/openminds/controlled_terms/file_usage_role.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -FileUsageRole.set_error_handling(None) -for key, value in OMFileUsageRole.__dict__.items(): - if isinstance(value, OMFileUsageRole): - fg_instance = FileUsageRole.from_jsonld(value.to_jsonld()) - fg_instance._space = FileUsageRole.default_space - setattr(FileUsageRole, key, fg_instance) -FileUsageRole.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/genetic_strain_type.py b/fairgraph/openminds/controlled_terms/genetic_strain_type.py index 256af37a..56ad7273 100644 --- a/fairgraph/openminds/controlled_terms/genetic_strain_type.py +++ b/fairgraph/openminds/controlled_terms/genetic_strain_type.py @@ -125,13 +125,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -GeneticStrainType.set_error_handling(None) -for key, value in OMGeneticStrainType.__dict__.items(): - if isinstance(value, OMGeneticStrainType): - fg_instance = GeneticStrainType.from_jsonld(value.to_jsonld()) - fg_instance._space = GeneticStrainType.default_space - setattr(GeneticStrainType, key, fg_instance) -GeneticStrainType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py index 88fc7159..a217fdb9 100644 --- a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py @@ -125,13 +125,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -GustatoryStimulusType.set_error_handling(None) -for key, value in OMGustatoryStimulusType.__dict__.items(): - if isinstance(value, OMGustatoryStimulusType): - fg_instance = GustatoryStimulusType.from_jsonld(value.to_jsonld()) - fg_instance._space = GustatoryStimulusType.default_space - setattr(GustatoryStimulusType, key, fg_instance) -GustatoryStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/handedness.py b/fairgraph/openminds/controlled_terms/handedness.py index 52674ccb..d63ed91a 100644 --- a/fairgraph/openminds/controlled_terms/handedness.py +++ b/fairgraph/openminds/controlled_terms/handedness.py @@ -125,13 +125,3 @@ def __init__( subject_states=subject_states, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Handedness.set_error_handling(None) -for key, value in OMHandedness.__dict__.items(): - if isinstance(value, OMHandedness): - fg_instance = Handedness.from_jsonld(value.to_jsonld()) - fg_instance._space = Handedness.default_space - setattr(Handedness, key, fg_instance) -Handedness.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/language.py b/fairgraph/openminds/controlled_terms/language.py index 12d628a0..93a85143 100644 --- a/fairgraph/openminds/controlled_terms/language.py +++ b/fairgraph/openminds/controlled_terms/language.py @@ -86,13 +86,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -Language.set_error_handling(None) -for key, value in OMLanguage.__dict__.items(): - if isinstance(value, OMLanguage): - fg_instance = Language.from_jsonld(value.to_jsonld()) - fg_instance._space = Language.default_space - setattr(Language, key, fg_instance) -Language.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/laterality.py b/fairgraph/openminds/controlled_terms/laterality.py index 6d208f61..239909fb 100644 --- a/fairgraph/openminds/controlled_terms/laterality.py +++ b/fairgraph/openminds/controlled_terms/laterality.py @@ -92,13 +92,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Laterality.set_error_handling(None) -for key, value in OMLaterality.__dict__.items(): - if isinstance(value, OMLaterality): - fg_instance = Laterality.from_jsonld(value.to_jsonld()) - fg_instance._space = Laterality.default_space - setattr(Laterality, key, fg_instance) -Laterality.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/learning_resource_type.py b/fairgraph/openminds/controlled_terms/learning_resource_type.py index 3cd55cba..5b1adbee 100644 --- a/fairgraph/openminds/controlled_terms/learning_resource_type.py +++ b/fairgraph/openminds/controlled_terms/learning_resource_type.py @@ -86,13 +86,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -LearningResourceType.set_error_handling(None) -for key, value in OMLearningResourceType.__dict__.items(): - if isinstance(value, OMLearningResourceType): - fg_instance = LearningResourceType.from_jsonld(value.to_jsonld()) - fg_instance._space = LearningResourceType.default_space - setattr(LearningResourceType, key, fg_instance) -LearningResourceType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/measured_quantity.py b/fairgraph/openminds/controlled_terms/measured_quantity.py index 6c355b6e..73897cae 100644 --- a/fairgraph/openminds/controlled_terms/measured_quantity.py +++ b/fairgraph/openminds/controlled_terms/measured_quantity.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -MeasuredQuantity.set_error_handling(None) -for key, value in OMMeasuredQuantity.__dict__.items(): - if isinstance(value, OMMeasuredQuantity): - fg_instance = MeasuredQuantity.from_jsonld(value.to_jsonld()) - fg_instance._space = MeasuredQuantity.default_space - setattr(MeasuredQuantity, key, fg_instance) -MeasuredQuantity.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/measured_signal_type.py b/fairgraph/openminds/controlled_terms/measured_signal_type.py index acf30a5a..a5590d57 100644 --- a/fairgraph/openminds/controlled_terms/measured_signal_type.py +++ b/fairgraph/openminds/controlled_terms/measured_signal_type.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -MeasuredSignalType.set_error_handling(None) -for key, value in OMMeasuredSignalType.__dict__.items(): - if isinstance(value, OMMeasuredSignalType): - fg_instance = MeasuredSignalType.from_jsonld(value.to_jsonld()) - fg_instance._space = MeasuredSignalType.default_space - setattr(MeasuredSignalType, key, fg_instance) -MeasuredSignalType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/meta_data_model_type.py b/fairgraph/openminds/controlled_terms/meta_data_model_type.py index 2ff6aa67..f397896b 100644 --- a/fairgraph/openminds/controlled_terms/meta_data_model_type.py +++ b/fairgraph/openminds/controlled_terms/meta_data_model_type.py @@ -86,13 +86,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -MetaDataModelType.set_error_handling(None) -for key, value in OMMetaDataModelType.__dict__.items(): - if isinstance(value, OMMetaDataModelType): - fg_instance = MetaDataModelType.from_jsonld(value.to_jsonld()) - fg_instance._space = MetaDataModelType.default_space - setattr(MetaDataModelType, key, fg_instance) -MetaDataModelType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/model_abstraction_level.py b/fairgraph/openminds/controlled_terms/model_abstraction_level.py index 134fdd04..cffe8f7e 100644 --- a/fairgraph/openminds/controlled_terms/model_abstraction_level.py +++ b/fairgraph/openminds/controlled_terms/model_abstraction_level.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ModelAbstractionLevel.set_error_handling(None) -for key, value in OMModelAbstractionLevel.__dict__.items(): - if isinstance(value, OMModelAbstractionLevel): - fg_instance = ModelAbstractionLevel.from_jsonld(value.to_jsonld()) - fg_instance._space = ModelAbstractionLevel.default_space - setattr(ModelAbstractionLevel, key, fg_instance) -ModelAbstractionLevel.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/model_scope.py b/fairgraph/openminds/controlled_terms/model_scope.py index 1af6c6e1..e927abf2 100644 --- a/fairgraph/openminds/controlled_terms/model_scope.py +++ b/fairgraph/openminds/controlled_terms/model_scope.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ModelScope.set_error_handling(None) -for key, value in OMModelScope.__dict__.items(): - if isinstance(value, OMModelScope): - fg_instance = ModelScope.from_jsonld(value.to_jsonld()) - fg_instance._space = ModelScope.default_space - setattr(ModelScope, key, fg_instance) -ModelScope.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/molecular_entity.py b/fairgraph/openminds/controlled_terms/molecular_entity.py index 5f1ede72..e243b551 100644 --- a/fairgraph/openminds/controlled_terms/molecular_entity.py +++ b/fairgraph/openminds/controlled_terms/molecular_entity.py @@ -140,13 +140,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -MolecularEntity.set_error_handling(None) -for key, value in OMMolecularEntity.__dict__.items(): - if isinstance(value, OMMolecularEntity): - fg_instance = MolecularEntity.from_jsonld(value.to_jsonld()) - fg_instance._space = MolecularEntity.default_space - setattr(MolecularEntity, key, fg_instance) -MolecularEntity.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py b/fairgraph/openminds/controlled_terms/mr_spatial_encoding.py similarity index 78% rename from fairgraph/openminds/controlled_terms/mr_acquisition_type.py rename to fairgraph/openminds/controlled_terms/mr_spatial_encoding.py index b91b1dde..4a19306f 100644 --- a/fairgraph/openminds/controlled_terms/mr_acquisition_type.py +++ b/fairgraph/openminds/controlled_terms/mr_spatial_encoding.py @@ -5,19 +5,19 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.controlled_terms import MRAcquisitionType as OMMRAcquisitionType +from openminds.latest.controlled_terms import MRSpatialEncoding as OMMRSpatialEncoding from fairgraph import KGObject from openminds import IRI -class MRAcquisitionType(KGObject, OMMRAcquisitionType): +class MRSpatialEncoding(KGObject, OMMRSpatialEncoding): """ """ - type_ = "https://openminds.om-i.org/types/MRAcquisitionType" + type_ = "https://openminds.om-i.org/types/MRSpatialEncoding" default_space = "controlled" # forward properties are defined in the parent class (in openMINDS-Python) reverse_properties = [ @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -MRAcquisitionType.set_error_handling(None) -for key, value in OMMRAcquisitionType.__dict__.items(): - if isinstance(value, OMMRAcquisitionType): - fg_instance = MRAcquisitionType.from_jsonld(value.to_jsonld()) - fg_instance._space = MRAcquisitionType.default_space - setattr(MRAcquisitionType, key, fg_instance) -MRAcquisitionType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py index dff20b25..6fdc534b 100644 --- a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py +++ b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py @@ -96,13 +96,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -MRIPulseSequence.set_error_handling(None) -for key, value in OMMRIPulseSequence.__dict__.items(): - if isinstance(value, OMMRIPulseSequence): - fg_instance = MRIPulseSequence.from_jsonld(value.to_jsonld()) - fg_instance._space = MRIPulseSequence.default_space - setattr(MRIPulseSequence, key, fg_instance) -MRIPulseSequence.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/mri_weighting.py b/fairgraph/openminds/controlled_terms/mri_weighting.py index 45fe4994..3f52530a 100644 --- a/fairgraph/openminds/controlled_terms/mri_weighting.py +++ b/fairgraph/openminds/controlled_terms/mri_weighting.py @@ -96,13 +96,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -MRIWeighting.set_error_handling(None) -for key, value in OMMRIWeighting.__dict__.items(): - if isinstance(value, OMMRIWeighting): - fg_instance = MRIWeighting.from_jsonld(value.to_jsonld()) - fg_instance._space = MRIWeighting.default_space - setattr(MRIWeighting, key, fg_instance) -MRIWeighting.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py index 6691b79c..34fe3c10 100644 --- a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py @@ -125,13 +125,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -OlfactoryStimulusType.set_error_handling(None) -for key, value in OMOlfactoryStimulusType.__dict__.items(): - if isinstance(value, OMOlfactoryStimulusType): - fg_instance = OlfactoryStimulusType.from_jsonld(value.to_jsonld()) - fg_instance._space = OlfactoryStimulusType.default_space - setattr(OlfactoryStimulusType, key, fg_instance) -OlfactoryStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/operating_device.py b/fairgraph/openminds/controlled_terms/operating_device.py index 03f8a2c3..38559641 100644 --- a/fairgraph/openminds/controlled_terms/operating_device.py +++ b/fairgraph/openminds/controlled_terms/operating_device.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -OperatingDevice.set_error_handling(None) -for key, value in OMOperatingDevice.__dict__.items(): - if isinstance(value, OMOperatingDevice): - fg_instance = OperatingDevice.from_jsonld(value.to_jsonld()) - fg_instance._space = OperatingDevice.default_space - setattr(OperatingDevice, key, fg_instance) -OperatingDevice.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/operating_system.py b/fairgraph/openminds/controlled_terms/operating_system.py index dde6d146..dd985fec 100644 --- a/fairgraph/openminds/controlled_terms/operating_system.py +++ b/fairgraph/openminds/controlled_terms/operating_system.py @@ -86,13 +86,3 @@ def __init__( synonyms=synonyms, used_by=used_by, ) - - -# cast openMINDS instances to their fairgraph subclass -OperatingSystem.set_error_handling(None) -for key, value in OMOperatingSystem.__dict__.items(): - if isinstance(value, OMOperatingSystem): - fg_instance = OperatingSystem.from_jsonld(value.to_jsonld()) - fg_instance._space = OperatingSystem.default_space - setattr(OperatingSystem, key, fg_instance) -OperatingSystem.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py index 2298d05f..9ab9f9ae 100644 --- a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py @@ -125,13 +125,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -OpticalStimulusType.set_error_handling(None) -for key, value in OMOpticalStimulusType.__dict__.items(): - if isinstance(value, OMOpticalStimulusType): - fg_instance = OpticalStimulusType.from_jsonld(value.to_jsonld()) - fg_instance._space = OpticalStimulusType.default_space - setattr(OpticalStimulusType, key, fg_instance) -OpticalStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/organ.py b/fairgraph/openminds/controlled_terms/organ.py index 3ffc7576..6ea20fef 100644 --- a/fairgraph/openminds/controlled_terms/organ.py +++ b/fairgraph/openminds/controlled_terms/organ.py @@ -159,13 +159,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Organ.set_error_handling(None) -for key, value in OMOrgan.__dict__.items(): - if isinstance(value, OMOrgan): - fg_instance = Organ.from_jsonld(value.to_jsonld()) - fg_instance._space = Organ.default_space - setattr(Organ, key, fg_instance) -Organ.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/organism_substance.py b/fairgraph/openminds/controlled_terms/organism_substance.py index bc586006..00eb2721 100644 --- a/fairgraph/openminds/controlled_terms/organism_substance.py +++ b/fairgraph/openminds/controlled_terms/organism_substance.py @@ -149,13 +149,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -OrganismSubstance.set_error_handling(None) -for key, value in OMOrganismSubstance.__dict__.items(): - if isinstance(value, OMOrganismSubstance): - fg_instance = OrganismSubstance.from_jsonld(value.to_jsonld()) - fg_instance._space = OrganismSubstance.default_space - setattr(OrganismSubstance, key, fg_instance) -OrganismSubstance.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/organism_system.py b/fairgraph/openminds/controlled_terms/organism_system.py index e9233611..70ecea72 100644 --- a/fairgraph/openminds/controlled_terms/organism_system.py +++ b/fairgraph/openminds/controlled_terms/organism_system.py @@ -115,13 +115,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -OrganismSystem.set_error_handling(None) -for key, value in OMOrganismSystem.__dict__.items(): - if isinstance(value, OMOrganismSystem): - fg_instance = OrganismSystem.from_jsonld(value.to_jsonld()) - fg_instance._space = OrganismSystem.default_space - setattr(OrganismSystem, key, fg_instance) -OrganismSystem.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py index 74909adf..67eb0ebe 100644 --- a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py +++ b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py @@ -87,13 +87,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -PatchClampVariation.set_error_handling(None) -for key, value in OMPatchClampVariation.__dict__.items(): - if isinstance(value, OMPatchClampVariation): - fg_instance = PatchClampVariation.from_jsonld(value.to_jsonld()) - fg_instance._space = PatchClampVariation.default_space - setattr(PatchClampVariation, key, fg_instance) -PatchClampVariation.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/preparation_type.py b/fairgraph/openminds/controlled_terms/preparation_type.py index 17c77f69..7172cffa 100644 --- a/fairgraph/openminds/controlled_terms/preparation_type.py +++ b/fairgraph/openminds/controlled_terms/preparation_type.py @@ -96,13 +96,3 @@ def __init__( synonyms=synonyms, used_for=used_for, ) - - -# cast openMINDS instances to their fairgraph subclass -PreparationType.set_error_handling(None) -for key, value in OMPreparationType.__dict__.items(): - if isinstance(value, OMPreparationType): - fg_instance = PreparationType.from_jsonld(value.to_jsonld()) - fg_instance._space = PreparationType.default_space - setattr(PreparationType, key, fg_instance) -PreparationType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/product_accessibility.py b/fairgraph/openminds/controlled_terms/product_accessibility.py index 850d544b..e9858d27 100644 --- a/fairgraph/openminds/controlled_terms/product_accessibility.py +++ b/fairgraph/openminds/controlled_terms/product_accessibility.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ProductAccessibility.set_error_handling(None) -for key, value in OMProductAccessibility.__dict__.items(): - if isinstance(value, OMProductAccessibility): - fg_instance = ProductAccessibility.from_jsonld(value.to_jsonld()) - fg_instance._space = ProductAccessibility.default_space - setattr(ProductAccessibility, key, fg_instance) -ProductAccessibility.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/programming_language.py b/fairgraph/openminds/controlled_terms/programming_language.py index c28368a6..6d53c829 100644 --- a/fairgraph/openminds/controlled_terms/programming_language.py +++ b/fairgraph/openminds/controlled_terms/programming_language.py @@ -86,13 +86,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -ProgrammingLanguage.set_error_handling(None) -for key, value in OMProgrammingLanguage.__dict__.items(): - if isinstance(value, OMProgrammingLanguage): - fg_instance = ProgrammingLanguage.from_jsonld(value.to_jsonld()) - fg_instance._space = ProgrammingLanguage.default_space - setattr(ProgrammingLanguage, key, fg_instance) -ProgrammingLanguage.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/qualitative_overlap.py b/fairgraph/openminds/controlled_terms/qualitative_overlap.py index bd760a5e..3a6afd24 100644 --- a/fairgraph/openminds/controlled_terms/qualitative_overlap.py +++ b/fairgraph/openminds/controlled_terms/qualitative_overlap.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -QualitativeOverlap.set_error_handling(None) -for key, value in OMQualitativeOverlap.__dict__.items(): - if isinstance(value, OMQualitativeOverlap): - fg_instance = QualitativeOverlap.from_jsonld(value.to_jsonld()) - fg_instance._space = QualitativeOverlap.default_space - setattr(QualitativeOverlap, key, fg_instance) -QualitativeOverlap.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/semantic_data_type.py b/fairgraph/openminds/controlled_terms/semantic_data_type.py index 1efe5331..53bfabba 100644 --- a/fairgraph/openminds/controlled_terms/semantic_data_type.py +++ b/fairgraph/openminds/controlled_terms/semantic_data_type.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -SemanticDataType.set_error_handling(None) -for key, value in OMSemanticDataType.__dict__.items(): - if isinstance(value, OMSemanticDataType): - fg_instance = SemanticDataType.from_jsonld(value.to_jsonld()) - fg_instance._space = SemanticDataType.default_space - setattr(SemanticDataType, key, fg_instance) -SemanticDataType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/service.py b/fairgraph/openminds/controlled_terms/service.py index 1243a95f..99db60a4 100644 --- a/fairgraph/openminds/controlled_terms/service.py +++ b/fairgraph/openminds/controlled_terms/service.py @@ -97,13 +97,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Service.set_error_handling(None) -for key, value in OMService.__dict__.items(): - if isinstance(value, OMService): - fg_instance = Service.from_jsonld(value.to_jsonld()) - fg_instance._space = Service.default_space - setattr(Service, key, fg_instance) -Service.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/setup_type.py b/fairgraph/openminds/controlled_terms/setup_type.py index 05c1d73f..ffcfc574 100644 --- a/fairgraph/openminds/controlled_terms/setup_type.py +++ b/fairgraph/openminds/controlled_terms/setup_type.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -SetupType.set_error_handling(None) -for key, value in OMSetupType.__dict__.items(): - if isinstance(value, OMSetupType): - fg_instance = SetupType.from_jsonld(value.to_jsonld()) - fg_instance._space = SetupType.default_space - setattr(SetupType, key, fg_instance) -SetupType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/software_application_category.py b/fairgraph/openminds/controlled_terms/software_application_category.py index 2270e95c..9e423469 100644 --- a/fairgraph/openminds/controlled_terms/software_application_category.py +++ b/fairgraph/openminds/controlled_terms/software_application_category.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -SoftwareApplicationCategory.set_error_handling(None) -for key, value in OMSoftwareApplicationCategory.__dict__.items(): - if isinstance(value, OMSoftwareApplicationCategory): - fg_instance = SoftwareApplicationCategory.from_jsonld(value.to_jsonld()) - fg_instance._space = SoftwareApplicationCategory.default_space - setattr(SoftwareApplicationCategory, key, fg_instance) -SoftwareApplicationCategory.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/software_feature.py b/fairgraph/openminds/controlled_terms/software_feature.py index d5d47f19..237274dc 100644 --- a/fairgraph/openminds/controlled_terms/software_feature.py +++ b/fairgraph/openminds/controlled_terms/software_feature.py @@ -77,13 +77,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -SoftwareFeature.set_error_handling(None) -for key, value in OMSoftwareFeature.__dict__.items(): - if isinstance(value, OMSoftwareFeature): - fg_instance = SoftwareFeature.from_jsonld(value.to_jsonld()) - fg_instance._space = SoftwareFeature.default_space - setattr(SoftwareFeature, key, fg_instance) -SoftwareFeature.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/species.py b/fairgraph/openminds/controlled_terms/species.py index 9b492c8d..40237ca8 100644 --- a/fairgraph/openminds/controlled_terms/species.py +++ b/fairgraph/openminds/controlled_terms/species.py @@ -141,13 +141,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Species.set_error_handling(None) -for key, value in OMSpecies.__dict__.items(): - if isinstance(value, OMSpecies): - fg_instance = Species.from_jsonld(value.to_jsonld()) - fg_instance._space = Species.default_space - setattr(Species, key, fg_instance) -Species.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/stimulation_approach.py b/fairgraph/openminds/controlled_terms/stimulation_approach.py index b0a08927..d68d6632 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_approach.py +++ b/fairgraph/openminds/controlled_terms/stimulation_approach.py @@ -100,13 +100,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -StimulationApproach.set_error_handling(None) -for key, value in OMStimulationApproach.__dict__.items(): - if isinstance(value, OMStimulationApproach): - fg_instance = StimulationApproach.from_jsonld(value.to_jsonld()) - fg_instance._space = StimulationApproach.default_space - setattr(StimulationApproach, key, fg_instance) -StimulationApproach.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/stimulation_technique.py b/fairgraph/openminds/controlled_terms/stimulation_technique.py index 339af597..b6fa19aa 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_technique.py +++ b/fairgraph/openminds/controlled_terms/stimulation_technique.py @@ -100,13 +100,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -StimulationTechnique.set_error_handling(None) -for key, value in OMStimulationTechnique.__dict__.items(): - if isinstance(value, OMStimulationTechnique): - fg_instance = StimulationTechnique.from_jsonld(value.to_jsonld()) - fg_instance._space = StimulationTechnique.default_space - setattr(StimulationTechnique, key, fg_instance) -StimulationTechnique.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/subcellular_entity.py b/fairgraph/openminds/controlled_terms/subcellular_entity.py index 35b0f5d4..57511019 100644 --- a/fairgraph/openminds/controlled_terms/subcellular_entity.py +++ b/fairgraph/openminds/controlled_terms/subcellular_entity.py @@ -141,13 +141,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -SubcellularEntity.set_error_handling(None) -for key, value in OMSubcellularEntity.__dict__.items(): - if isinstance(value, OMSubcellularEntity): - fg_instance = SubcellularEntity.from_jsonld(value.to_jsonld()) - fg_instance._space = SubcellularEntity.default_space - setattr(SubcellularEntity, key, fg_instance) -SubcellularEntity.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/subject_attribute.py b/fairgraph/openminds/controlled_terms/subject_attribute.py index a89798d9..1f45f764 100644 --- a/fairgraph/openminds/controlled_terms/subject_attribute.py +++ b/fairgraph/openminds/controlled_terms/subject_attribute.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -SubjectAttribute.set_error_handling(None) -for key, value in OMSubjectAttribute.__dict__.items(): - if isinstance(value, OMSubjectAttribute): - fg_instance = SubjectAttribute.from_jsonld(value.to_jsonld()) - fg_instance._space = SubjectAttribute.default_space - setattr(SubjectAttribute, key, fg_instance) -SubjectAttribute.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py index 06ab6d8d..683614a1 100644 --- a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py @@ -125,13 +125,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -TactileStimulusType.set_error_handling(None) -for key, value in OMTactileStimulusType.__dict__.items(): - if isinstance(value, OMTactileStimulusType): - fg_instance = TactileStimulusType.from_jsonld(value.to_jsonld()) - fg_instance._space = TactileStimulusType.default_space - setattr(TactileStimulusType, key, fg_instance) -TactileStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/technique.py b/fairgraph/openminds/controlled_terms/technique.py index 045abf5e..49283ba7 100644 --- a/fairgraph/openminds/controlled_terms/technique.py +++ b/fairgraph/openminds/controlled_terms/technique.py @@ -106,13 +106,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -Technique.set_error_handling(None) -for key, value in OMTechnique.__dict__.items(): - if isinstance(value, OMTechnique): - fg_instance = Technique.from_jsonld(value.to_jsonld()) - fg_instance._space = Technique.default_space - setattr(Technique, key, fg_instance) -Technique.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/term_suggestion.py b/fairgraph/openminds/controlled_terms/term_suggestion.py index 43f23f79..7036c6c4 100644 --- a/fairgraph/openminds/controlled_terms/term_suggestion.py +++ b/fairgraph/openminds/controlled_terms/term_suggestion.py @@ -119,13 +119,3 @@ def __init__( suggest_new_terminology=suggest_new_terminology, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -TermSuggestion.set_error_handling(None) -for key, value in OMTermSuggestion.__dict__.items(): - if isinstance(value, OMTermSuggestion): - fg_instance = TermSuggestion.from_jsonld(value.to_jsonld()) - fg_instance._space = TermSuggestion.default_space - setattr(TermSuggestion, key, fg_instance) -TermSuggestion.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/terminology.py b/fairgraph/openminds/controlled_terms/terminology.py index fb0e542f..c9a4e45b 100644 --- a/fairgraph/openminds/controlled_terms/terminology.py +++ b/fairgraph/openminds/controlled_terms/terminology.py @@ -87,13 +87,3 @@ def __init__( suggested_in=suggested_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Terminology.set_error_handling(None) -for key, value in OMTerminology.__dict__.items(): - if isinstance(value, OMTerminology): - fg_instance = Terminology.from_jsonld(value.to_jsonld()) - fg_instance._space = Terminology.default_space - setattr(Terminology, key, fg_instance) -Terminology.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py index 603cea09..9bba66cb 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py @@ -87,13 +87,3 @@ def __init__( preferred_ontology_identifier=preferred_ontology_identifier, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueSampleAttribute.set_error_handling(None) -for key, value in OMTissueSampleAttribute.__dict__.items(): - if isinstance(value, OMTissueSampleAttribute): - fg_instance = TissueSampleAttribute.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueSampleAttribute.default_space - setattr(TissueSampleAttribute, key, fg_instance) -TissueSampleAttribute.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_type.py b/fairgraph/openminds/controlled_terms/tissue_sample_type.py index da33c8e7..2aff27b3 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_type.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_type.py @@ -125,13 +125,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueSampleType.set_error_handling(None) -for key, value in OMTissueSampleType.__dict__.items(): - if isinstance(value, OMTissueSampleType): - fg_instance = TissueSampleType.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueSampleType.default_space - setattr(TissueSampleType, key, fg_instance) -TissueSampleType.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py index c3defc8e..7699ab81 100644 --- a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py +++ b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py @@ -87,13 +87,3 @@ def __init__( synonyms=synonyms, value=value, ) - - -# cast openMINDS instances to their fairgraph subclass -TypeOfUncertainty.set_error_handling(None) -for key, value in OMTypeOfUncertainty.__dict__.items(): - if isinstance(value, OMTypeOfUncertainty): - fg_instance = TypeOfUncertainty.from_jsonld(value.to_jsonld()) - fg_instance._space = TypeOfUncertainty.default_space - setattr(TypeOfUncertainty, key, fg_instance) -TypeOfUncertainty.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/uberon_parcellation.py b/fairgraph/openminds/controlled_terms/uberon_parcellation.py index dd63ae70..1c494ef8 100644 --- a/fairgraph/openminds/controlled_terms/uberon_parcellation.py +++ b/fairgraph/openminds/controlled_terms/uberon_parcellation.py @@ -151,13 +151,3 @@ def __init__( studied_in=studied_in, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -UBERONParcellation.set_error_handling(None) -for key, value in OMUBERONParcellation.__dict__.items(): - if isinstance(value, OMUBERONParcellation): - fg_instance = UBERONParcellation.from_jsonld(value.to_jsonld()) - fg_instance._space = UBERONParcellation.default_space - setattr(UBERONParcellation, key, fg_instance) -UBERONParcellation.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/unit_of_measurement.py b/fairgraph/openminds/controlled_terms/unit_of_measurement.py index e3253364..f453c1e4 100644 --- a/fairgraph/openminds/controlled_terms/unit_of_measurement.py +++ b/fairgraph/openminds/controlled_terms/unit_of_measurement.py @@ -106,13 +106,3 @@ def __init__( used_in=used_in, value=value, ) - - -# cast openMINDS instances to their fairgraph subclass -UnitOfMeasurement.set_error_handling(None) -for key, value in OMUnitOfMeasurement.__dict__.items(): - if isinstance(value, OMUnitOfMeasurement): - fg_instance = UnitOfMeasurement.from_jsonld(value.to_jsonld()) - fg_instance._space = UnitOfMeasurement.default_space - setattr(UnitOfMeasurement, key, fg_instance) -UnitOfMeasurement.set_error_handling("log") diff --git a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py index daf03550..d4bc63b3 100644 --- a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py @@ -125,13 +125,3 @@ def __init__( synonyms=synonyms, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -VisualStimulusType.set_error_handling(None) -for key, value in OMVisualStimulusType.__dict__.items(): - if isinstance(value, OMVisualStimulusType): - fg_instance = VisualStimulusType.from_jsonld(value.to_jsonld()) - fg_instance._space = VisualStimulusType.default_space - setattr(VisualStimulusType, key, fg_instance) -VisualStimulusType.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/account_information.py b/fairgraph/openminds/core/actors/account_information.py index f4a70c5c..9ae32bef 100644 --- a/fairgraph/openminds/core/actors/account_information.py +++ b/fairgraph/openminds/core/actors/account_information.py @@ -40,13 +40,3 @@ def __init__(self, belongs_to=None, service=None, user_name=None, id=None, data= service=service, user_name=user_name, ) - - -# cast openMINDS instances to their fairgraph subclass -AccountInformation.set_error_handling(None) -for key, value in OMAccountInformation.__dict__.items(): - if isinstance(value, OMAccountInformation): - fg_instance = AccountInformation.from_jsonld(value.to_jsonld()) - fg_instance._space = AccountInformation.default_space - setattr(AccountInformation, key, fg_instance) -AccountInformation.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/affiliation.py b/fairgraph/openminds/core/actors/affiliation.py index 84a68910..15dc25ae 100644 --- a/fairgraph/openminds/core/actors/affiliation.py +++ b/fairgraph/openminds/core/actors/affiliation.py @@ -25,13 +25,3 @@ def __init__(self, end_date=None, member_of=None, start_date=None, id=None, data return EmbeddedMetadata.__init__( self, data=data, end_date=end_date, member_of=member_of, start_date=start_date ) - - -# cast openMINDS instances to their fairgraph subclass -Affiliation.set_error_handling(None) -for key, value in OMAffiliation.__dict__.items(): - if isinstance(value, OMAffiliation): - fg_instance = Affiliation.from_jsonld(value.to_jsonld()) - fg_instance._space = Affiliation.default_space - setattr(Affiliation, key, fg_instance) -Affiliation.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/consortium.py b/fairgraph/openminds/core/actors/consortium.py index 60be5b94..c3f81f30 100644 --- a/fairgraph/openminds/core/actors/consortium.py +++ b/fairgraph/openminds/core/actors/consortium.py @@ -173,13 +173,3 @@ def __init__( published=published, short_name=short_name, ) - - -# cast openMINDS instances to their fairgraph subclass -Consortium.set_error_handling(None) -for key, value in OMConsortium.__dict__.items(): - if isinstance(value, OMConsortium): - fg_instance = Consortium.from_jsonld(value.to_jsonld()) - fg_instance._space = Consortium.default_space - setattr(Consortium, key, fg_instance) -Consortium.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/contact_information.py b/fairgraph/openminds/core/actors/contact_information.py index 70631b9c..f2860485 100644 --- a/fairgraph/openminds/core/actors/contact_information.py +++ b/fairgraph/openminds/core/actors/contact_information.py @@ -39,13 +39,3 @@ def __init__(self, email=None, is_contact_information_of=None, id=None, data=Non email=email, is_contact_information_of=is_contact_information_of, ) - - -# cast openMINDS instances to their fairgraph subclass -ContactInformation.set_error_handling(None) -for key, value in OMContactInformation.__dict__.items(): - if isinstance(value, OMContactInformation): - fg_instance = ContactInformation.from_jsonld(value.to_jsonld()) - fg_instance._space = ContactInformation.default_space - setattr(ContactInformation, key, fg_instance) -ContactInformation.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/contribution.py b/fairgraph/openminds/core/actors/contribution.py index 4756ba13..1404679a 100644 --- a/fairgraph/openminds/core/actors/contribution.py +++ b/fairgraph/openminds/core/actors/contribution.py @@ -20,13 +20,3 @@ class Contribution(EmbeddedMetadata, OMContribution): def __init__(self, contributor=None, types=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, contributor=contributor, types=types) - - -# cast openMINDS instances to their fairgraph subclass -Contribution.set_error_handling(None) -for key, value in OMContribution.__dict__.items(): - if isinstance(value, OMContribution): - fg_instance = Contribution.from_jsonld(value.to_jsonld()) - fg_instance._space = Contribution.default_space - setattr(Contribution, key, fg_instance) -Contribution.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/organization.py b/fairgraph/openminds/core/actors/organization.py index 6e312ca2..e31b0b6d 100644 --- a/fairgraph/openminds/core/actors/organization.py +++ b/fairgraph/openminds/core/actors/organization.py @@ -197,13 +197,3 @@ def __init__( published=published, short_name=short_name, ) - - -# cast openMINDS instances to their fairgraph subclass -Organization.set_error_handling(None) -for key, value in OMOrganization.__dict__.items(): - if isinstance(value, OMOrganization): - fg_instance = Organization.from_jsonld(value.to_jsonld()) - fg_instance._space = Organization.default_space - setattr(Organization, key, fg_instance) -Organization.set_error_handling("log") diff --git a/fairgraph/openminds/core/actors/person.py b/fairgraph/openminds/core/actors/person.py index d9206bb5..3e215bba 100644 --- a/fairgraph/openminds/core/actors/person.py +++ b/fairgraph/openminds/core/actors/person.py @@ -234,13 +234,3 @@ def me(cls, client, allow_multiple=False, follow_links=None): else: raise Exception("Found multiple matches") return person - - -# cast openMINDS instances to their fairgraph subclass -Person.set_error_handling(None) -for key, value in OMPerson.__dict__.items(): - if isinstance(value, OMPerson): - fg_instance = Person.from_jsonld(value.to_jsonld()) - fg_instance._space = Person.default_space - setattr(Person, key, fg_instance) -Person.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/content_type.py b/fairgraph/openminds/core/data/content_type.py index da36b408..78f0e252 100644 --- a/fairgraph/openminds/core/data/content_type.py +++ b/fairgraph/openminds/core/data/content_type.py @@ -105,13 +105,3 @@ def __init__( specification=specification, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -ContentType.set_error_handling(None) -for key, value in OMContentType.__dict__.items(): - if isinstance(value, OMContentType): - fg_instance = ContentType.from_jsonld(value.to_jsonld()) - fg_instance._space = ContentType.default_space - setattr(ContentType, key, fg_instance) -ContentType.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/content_type_pattern.py b/fairgraph/openminds/core/data/content_type_pattern.py index 854fb761..5f7617a1 100644 --- a/fairgraph/openminds/core/data/content_type_pattern.py +++ b/fairgraph/openminds/core/data/content_type_pattern.py @@ -51,13 +51,3 @@ def __init__( identifies_content_of=identifies_content_of, regex=regex, ) - - -# cast openMINDS instances to their fairgraph subclass -ContentTypePattern.set_error_handling(None) -for key, value in OMContentTypePattern.__dict__.items(): - if isinstance(value, OMContentTypePattern): - fg_instance = ContentTypePattern.from_jsonld(value.to_jsonld()) - fg_instance._space = ContentTypePattern.default_space - setattr(ContentTypePattern, key, fg_instance) -ContentTypePattern.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/copyright.py b/fairgraph/openminds/core/data/copyright.py index 6b77a5a2..6a80398e 100644 --- a/fairgraph/openminds/core/data/copyright.py +++ b/fairgraph/openminds/core/data/copyright.py @@ -20,13 +20,3 @@ class Copyright(EmbeddedMetadata, OMCopyright): def __init__(self, holders=None, years=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, holders=holders, years=years) - - -# cast openMINDS instances to their fairgraph subclass -Copyright.set_error_handling(None) -for key, value in OMCopyright.__dict__.items(): - if isinstance(value, OMCopyright): - fg_instance = Copyright.from_jsonld(value.to_jsonld()) - fg_instance._space = Copyright.default_space - setattr(Copyright, key, fg_instance) -Copyright.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file.py b/fairgraph/openminds/core/data/file.py index 3d8254c4..d36c02dc 100644 --- a/fairgraph/openminds/core/data/file.py +++ b/fairgraph/openminds/core/data/file.py @@ -273,13 +273,3 @@ def download(self, local_path, client, accept_terms_of_use=False): # rather than a filename, create that directory and save a file called self.name # within it return local_filename - - -# cast openMINDS instances to their fairgraph subclass -File.set_error_handling(None) -for key, value in OMFile.__dict__.items(): - if isinstance(value, OMFile): - fg_instance = File.from_jsonld(value.to_jsonld()) - fg_instance._space = File.default_space - setattr(File, key, fg_instance) -File.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_archive.py b/fairgraph/openminds/core/data/file_archive.py index e563a976..f4b13981 100644 --- a/fairgraph/openminds/core/data/file_archive.py +++ b/fairgraph/openminds/core/data/file_archive.py @@ -69,13 +69,3 @@ def __init__( is_output_of=is_output_of, source_data=source_data, ) - - -# cast openMINDS instances to their fairgraph subclass -FileArchive.set_error_handling(None) -for key, value in OMFileArchive.__dict__.items(): - if isinstance(value, OMFileArchive): - fg_instance = FileArchive.from_jsonld(value.to_jsonld()) - fg_instance._space = FileArchive.default_space - setattr(FileArchive, key, fg_instance) -FileArchive.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_bundle.py b/fairgraph/openminds/core/data/file_bundle.py index 1c146327..40fd5ad4 100644 --- a/fairgraph/openminds/core/data/file_bundle.py +++ b/fairgraph/openminds/core/data/file_bundle.py @@ -148,13 +148,3 @@ def __init__( specifies=specifies, storage_size=storage_size, ) - - -# cast openMINDS instances to their fairgraph subclass -FileBundle.set_error_handling(None) -for key, value in OMFileBundle.__dict__.items(): - if isinstance(value, OMFileBundle): - fg_instance = FileBundle.from_jsonld(value.to_jsonld()) - fg_instance._space = FileBundle.default_space - setattr(FileBundle, key, fg_instance) -FileBundle.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_path_pattern.py b/fairgraph/openminds/core/data/file_path_pattern.py index f92d3d8b..1b7c4f28 100644 --- a/fairgraph/openminds/core/data/file_path_pattern.py +++ b/fairgraph/openminds/core/data/file_path_pattern.py @@ -20,13 +20,3 @@ class FilePathPattern(EmbeddedMetadata, OMFilePathPattern): def __init__(self, grouping_types=None, regex=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, grouping_types=grouping_types, regex=regex) - - -# cast openMINDS instances to their fairgraph subclass -FilePathPattern.set_error_handling(None) -for key, value in OMFilePathPattern.__dict__.items(): - if isinstance(value, OMFilePathPattern): - fg_instance = FilePathPattern.from_jsonld(value.to_jsonld()) - fg_instance._space = FilePathPattern.default_space - setattr(FilePathPattern, key, fg_instance) -FilePathPattern.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_repository.py b/fairgraph/openminds/core/data/file_repository.py index a6cbebf1..a35a31b8 100644 --- a/fairgraph/openminds/core/data/file_repository.py +++ b/fairgraph/openminds/core/data/file_repository.py @@ -97,13 +97,3 @@ def __init__( structure_pattern=structure_pattern, type=type, ) - - -# cast openMINDS instances to their fairgraph subclass -FileRepository.set_error_handling(None) -for key, value in OMFileRepository.__dict__.items(): - if isinstance(value, OMFileRepository): - fg_instance = FileRepository.from_jsonld(value.to_jsonld()) - fg_instance._space = FileRepository.default_space - setattr(FileRepository, key, fg_instance) -FileRepository.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/file_repository_structure.py b/fairgraph/openminds/core/data/file_repository_structure.py index 6bdade73..37fbf59c 100644 --- a/fairgraph/openminds/core/data/file_repository_structure.py +++ b/fairgraph/openminds/core/data/file_repository_structure.py @@ -42,13 +42,3 @@ def __init__( file_path_patterns=file_path_patterns, structures=structures, ) - - -# cast openMINDS instances to their fairgraph subclass -FileRepositoryStructure.set_error_handling(None) -for key, value in OMFileRepositoryStructure.__dict__.items(): - if isinstance(value, OMFileRepositoryStructure): - fg_instance = FileRepositoryStructure.from_jsonld(value.to_jsonld()) - fg_instance._space = FileRepositoryStructure.default_space - setattr(FileRepositoryStructure, key, fg_instance) -FileRepositoryStructure.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/hash.py b/fairgraph/openminds/core/data/hash.py index 15453558..1696f580 100644 --- a/fairgraph/openminds/core/data/hash.py +++ b/fairgraph/openminds/core/data/hash.py @@ -20,13 +20,3 @@ class Hash(EmbeddedMetadata, OMHash): def __init__(self, algorithm=None, digest=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, algorithm=algorithm, digest=digest) - - -# cast openMINDS instances to their fairgraph subclass -Hash.set_error_handling(None) -for key, value in OMHash.__dict__.items(): - if isinstance(value, OMHash): - fg_instance = Hash.from_jsonld(value.to_jsonld()) - fg_instance._space = Hash.default_space - setattr(Hash, key, fg_instance) -Hash.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/license.py b/fairgraph/openminds/core/data/license.py index b95c74f7..6be0b2a3 100644 --- a/fairgraph/openminds/core/data/license.py +++ b/fairgraph/openminds/core/data/license.py @@ -75,13 +75,3 @@ def __init__( short_name=short_name, webpages=webpages, ) - - -# cast openMINDS instances to their fairgraph subclass -License.set_error_handling(None) -for key, value in OMLicense.__dict__.items(): - if isinstance(value, OMLicense): - fg_instance = License.from_jsonld(value.to_jsonld()) - fg_instance._space = License.default_space - setattr(License, key, fg_instance) -License.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/measurement.py b/fairgraph/openminds/core/data/measurement.py index e69d2521..5e7e7eeb 100644 --- a/fairgraph/openminds/core/data/measurement.py +++ b/fairgraph/openminds/core/data/measurement.py @@ -42,13 +42,3 @@ def __init__( timestamp=timestamp, values=values, ) - - -# cast openMINDS instances to their fairgraph subclass -Measurement.set_error_handling(None) -for key, value in OMMeasurement.__dict__.items(): - if isinstance(value, OMMeasurement): - fg_instance = Measurement.from_jsonld(value.to_jsonld()) - fg_instance._space = Measurement.default_space - setattr(Measurement, key, fg_instance) -Measurement.set_error_handling("log") diff --git a/fairgraph/openminds/core/data/service_link.py b/fairgraph/openminds/core/data/service_link.py index c3c6dfc2..1b4c9779 100644 --- a/fairgraph/openminds/core/data/service_link.py +++ b/fairgraph/openminds/core/data/service_link.py @@ -47,13 +47,3 @@ def __init__( preview_image=preview_image, service=service, ) - - -# cast openMINDS instances to their fairgraph subclass -ServiceLink.set_error_handling(None) -for key, value in OMServiceLink.__dict__.items(): - if isinstance(value, OMServiceLink): - fg_instance = ServiceLink.from_jsonld(value.to_jsonld()) - fg_instance._space = ServiceLink.default_space - setattr(ServiceLink, key, fg_instance) -ServiceLink.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/doi.py b/fairgraph/openminds/core/digital_identifier/doi.py index 9f766774..3c6ed9d5 100644 --- a/fairgraph/openminds/core/digital_identifier/doi.py +++ b/fairgraph/openminds/core/digital_identifier/doi.py @@ -96,13 +96,3 @@ def __init__( identifies=identifies, related_to=related_to, ) - - -# cast openMINDS instances to their fairgraph subclass -DOI.set_error_handling(None) -for key, value in OMDOI.__dict__.items(): - if isinstance(value, OMDOI): - fg_instance = DOI.from_jsonld(value.to_jsonld()) - fg_instance._space = DOI.default_space - setattr(DOI, key, fg_instance) -DOI.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/gridid.py b/fairgraph/openminds/core/digital_identifier/gridid.py index 5024f226..7dafc960 100644 --- a/fairgraph/openminds/core/digital_identifier/gridid.py +++ b/fairgraph/openminds/core/digital_identifier/gridid.py @@ -33,13 +33,3 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) - - -# cast openMINDS instances to their fairgraph subclass -GRIDID.set_error_handling(None) -for key, value in OMGRIDID.__dict__.items(): - if isinstance(value, OMGRIDID): - fg_instance = GRIDID.from_jsonld(value.to_jsonld()) - fg_instance._space = GRIDID.default_space - setattr(GRIDID, key, fg_instance) -GRIDID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/handle.py b/fairgraph/openminds/core/digital_identifier/handle.py index 64912c35..34733855 100644 --- a/fairgraph/openminds/core/digital_identifier/handle.py +++ b/fairgraph/openminds/core/digital_identifier/handle.py @@ -44,13 +44,3 @@ def __init__(self, identifier=None, related_to=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, related_to=related_to ) - - -# cast openMINDS instances to their fairgraph subclass -HANDLE.set_error_handling(None) -for key, value in OMHANDLE.__dict__.items(): - if isinstance(value, OMHANDLE): - fg_instance = HANDLE.from_jsonld(value.to_jsonld()) - fg_instance._space = HANDLE.default_space - setattr(HANDLE, key, fg_instance) -HANDLE.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py index 7401f0a6..cdfc44aa 100644 --- a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py +++ b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py @@ -33,13 +33,3 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) - - -# cast openMINDS instances to their fairgraph subclass -IdentifiersDotOrgID.set_error_handling(None) -for key, value in OMIdentifiersDotOrgID.__dict__.items(): - if isinstance(value, OMIdentifiersDotOrgID): - fg_instance = IdentifiersDotOrgID.from_jsonld(value.to_jsonld()) - fg_instance._space = IdentifiersDotOrgID.default_space - setattr(IdentifiersDotOrgID, key, fg_instance) -IdentifiersDotOrgID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/isbn.py b/fairgraph/openminds/core/digital_identifier/isbn.py index 1046aff1..2fb1e3c2 100644 --- a/fairgraph/openminds/core/digital_identifier/isbn.py +++ b/fairgraph/openminds/core/digital_identifier/isbn.py @@ -86,13 +86,3 @@ def __init__( identifies=identifies, related_to=related_to, ) - - -# cast openMINDS instances to their fairgraph subclass -ISBN.set_error_handling(None) -for key, value in OMISBN.__dict__.items(): - if isinstance(value, OMISBN): - fg_instance = ISBN.from_jsonld(value.to_jsonld()) - fg_instance._space = ISBN.default_space - setattr(ISBN, key, fg_instance) -ISBN.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/issn.py b/fairgraph/openminds/core/digital_identifier/issn.py index 06f53402..1c69a4b6 100644 --- a/fairgraph/openminds/core/digital_identifier/issn.py +++ b/fairgraph/openminds/core/digital_identifier/issn.py @@ -59,13 +59,3 @@ def __init__(self, identifier=None, identifies=None, related_to=None, id=None, d identifies=identifies, related_to=related_to, ) - - -# cast openMINDS instances to their fairgraph subclass -ISSN.set_error_handling(None) -for key, value in OMISSN.__dict__.items(): - if isinstance(value, OMISSN): - fg_instance = ISSN.from_jsonld(value.to_jsonld()) - fg_instance._space = ISSN.default_space - setattr(ISSN, key, fg_instance) -ISSN.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/orcid.py b/fairgraph/openminds/core/digital_identifier/orcid.py index 961754ff..f35616fc 100644 --- a/fairgraph/openminds/core/digital_identifier/orcid.py +++ b/fairgraph/openminds/core/digital_identifier/orcid.py @@ -33,13 +33,3 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) - - -# cast openMINDS instances to their fairgraph subclass -ORCID.set_error_handling(None) -for key, value in OMORCID.__dict__.items(): - if isinstance(value, OMORCID): - fg_instance = ORCID.from_jsonld(value.to_jsonld()) - fg_instance._space = ORCID.default_space - setattr(ORCID, key, fg_instance) -ORCID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/rorid.py b/fairgraph/openminds/core/digital_identifier/rorid.py index 7a51d621..8d7944af 100644 --- a/fairgraph/openminds/core/digital_identifier/rorid.py +++ b/fairgraph/openminds/core/digital_identifier/rorid.py @@ -33,13 +33,3 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) - - -# cast openMINDS instances to their fairgraph subclass -RORID.set_error_handling(None) -for key, value in OMRORID.__dict__.items(): - if isinstance(value, OMRORID): - fg_instance = RORID.from_jsonld(value.to_jsonld()) - fg_instance._space = RORID.default_space - setattr(RORID, key, fg_instance) -RORID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/rrid.py b/fairgraph/openminds/core/digital_identifier/rrid.py index 454f0e66..772a797a 100644 --- a/fairgraph/openminds/core/digital_identifier/rrid.py +++ b/fairgraph/openminds/core/digital_identifier/rrid.py @@ -47,13 +47,3 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) - - -# cast openMINDS instances to their fairgraph subclass -RRID.set_error_handling(None) -for key, value in OMRRID.__dict__.items(): - if isinstance(value, OMRRID): - fg_instance = RRID.from_jsonld(value.to_jsonld()) - fg_instance._space = RRID.default_space - setattr(RRID, key, fg_instance) -RRID.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/stock_number.py b/fairgraph/openminds/core/digital_identifier/stock_number.py index da8189fb..cbd5962d 100644 --- a/fairgraph/openminds/core/digital_identifier/stock_number.py +++ b/fairgraph/openminds/core/digital_identifier/stock_number.py @@ -20,13 +20,3 @@ class StockNumber(EmbeddedMetadata, OMStockNumber): def __init__(self, identifier=None, vendor=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, identifier=identifier, vendor=vendor) - - -# cast openMINDS instances to their fairgraph subclass -StockNumber.set_error_handling(None) -for key, value in OMStockNumber.__dict__.items(): - if isinstance(value, OMStockNumber): - fg_instance = StockNumber.from_jsonld(value.to_jsonld()) - fg_instance._space = StockNumber.default_space - setattr(StockNumber, key, fg_instance) -StockNumber.set_error_handling("log") diff --git a/fairgraph/openminds/core/digital_identifier/swhid.py b/fairgraph/openminds/core/digital_identifier/swhid.py index 901d0abd..83e0d78c 100644 --- a/fairgraph/openminds/core/digital_identifier/swhid.py +++ b/fairgraph/openminds/core/digital_identifier/swhid.py @@ -40,13 +40,3 @@ def __init__(self, identifier=None, identifies=None, id=None, data=None, space=N return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies ) - - -# cast openMINDS instances to their fairgraph subclass -SWHID.set_error_handling(None) -for key, value in OMSWHID.__dict__.items(): - if isinstance(value, OMSWHID): - fg_instance = SWHID.from_jsonld(value.to_jsonld()) - fg_instance._space = SWHID.default_space - setattr(SWHID, key, fg_instance) -SWHID.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/comment.py b/fairgraph/openminds/core/miscellaneous/comment.py index 1f740e4c..0ecae0f7 100644 --- a/fairgraph/openminds/core/miscellaneous/comment.py +++ b/fairgraph/openminds/core/miscellaneous/comment.py @@ -37,13 +37,3 @@ def __init__( commenter=commenter, timestamp=timestamp, ) - - -# cast openMINDS instances to their fairgraph subclass -Comment.set_error_handling(None) -for key, value in OMComment.__dict__.items(): - if isinstance(value, OMComment): - fg_instance = Comment.from_jsonld(value.to_jsonld()) - fg_instance._space = Comment.default_space - setattr(Comment, key, fg_instance) -Comment.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/funding.py b/fairgraph/openminds/core/miscellaneous/funding.py index 1407571b..b9636c2d 100644 --- a/fairgraph/openminds/core/miscellaneous/funding.py +++ b/fairgraph/openminds/core/miscellaneous/funding.py @@ -68,13 +68,3 @@ def __init__( funded=funded, funder=funder, ) - - -# cast openMINDS instances to their fairgraph subclass -Funding.set_error_handling(None) -for key, value in OMFunding.__dict__.items(): - if isinstance(value, OMFunding): - fg_instance = Funding.from_jsonld(value.to_jsonld()) - fg_instance._space = Funding.default_space - setattr(Funding, key, fg_instance) -Funding.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value.py b/fairgraph/openminds/core/miscellaneous/quantitative_value.py index cb70ca0c..11a27be1 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value.py @@ -40,13 +40,3 @@ def __init__( unit=unit, value=value, ) - - -# cast openMINDS instances to their fairgraph subclass -QuantitativeValue.set_error_handling(None) -for key, value in OMQuantitativeValue.__dict__.items(): - if isinstance(value, OMQuantitativeValue): - fg_instance = QuantitativeValue.from_jsonld(value.to_jsonld()) - fg_instance._space = QuantitativeValue.default_space - setattr(QuantitativeValue, key, fg_instance) -QuantitativeValue.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py index abdcb8e0..8f75b201 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py @@ -47,13 +47,3 @@ def __init__( unit=unit, values=values, ) - - -# cast openMINDS instances to their fairgraph subclass -QuantitativeValueArray.set_error_handling(None) -for key, value in OMQuantitativeValueArray.__dict__.items(): - if isinstance(value, OMQuantitativeValueArray): - fg_instance = QuantitativeValueArray.from_jsonld(value.to_jsonld()) - fg_instance._space = QuantitativeValueArray.default_space - setattr(QuantitativeValueArray, key, fg_instance) -QuantitativeValueArray.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py index 40efd8d1..7d877c19 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py @@ -40,13 +40,3 @@ def __init__( min_value=min_value, min_value_unit=min_value_unit, ) - - -# cast openMINDS instances to their fairgraph subclass -QuantitativeValueRange.set_error_handling(None) -for key, value in OMQuantitativeValueRange.__dict__.items(): - if isinstance(value, OMQuantitativeValueRange): - fg_instance = QuantitativeValueRange.from_jsonld(value.to_jsonld()) - fg_instance._space = QuantitativeValueRange.default_space - setattr(QuantitativeValueRange, key, fg_instance) -QuantitativeValueRange.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/research_product_group.py b/fairgraph/openminds/core/miscellaneous/research_product_group.py index 2461a4e3..13bd6356 100644 --- a/fairgraph/openminds/core/miscellaneous/research_product_group.py +++ b/fairgraph/openminds/core/miscellaneous/research_product_group.py @@ -24,13 +24,3 @@ def __init__(self, context=None, has_parts=None, id=None, data=None, space=None, return KGObject.__init__( self, id=id, space=space, scope=scope, data=data, context=context, has_parts=has_parts ) - - -# cast openMINDS instances to their fairgraph subclass -ResearchProductGroup.set_error_handling(None) -for key, value in OMResearchProductGroup.__dict__.items(): - if isinstance(value, OMResearchProductGroup): - fg_instance = ResearchProductGroup.from_jsonld(value.to_jsonld()) - fg_instance._space = ResearchProductGroup.default_space - setattr(ResearchProductGroup, key, fg_instance) -ResearchProductGroup.set_error_handling("log") diff --git a/fairgraph/openminds/core/miscellaneous/web_resource.py b/fairgraph/openminds/core/miscellaneous/web_resource.py index 36c761cf..9a5cca47 100644 --- a/fairgraph/openminds/core/miscellaneous/web_resource.py +++ b/fairgraph/openminds/core/miscellaneous/web_resource.py @@ -102,13 +102,3 @@ def __init__( is_output_of=is_output_of, is_reference_for=is_reference_for, ) - - -# cast openMINDS instances to their fairgraph subclass -WebResource.set_error_handling(None) -for key, value in OMWebResource.__dict__.items(): - if isinstance(value, OMWebResource): - fg_instance = WebResource.from_jsonld(value.to_jsonld()) - fg_instance._space = WebResource.default_space - setattr(WebResource, key, fg_instance) -WebResource.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/dataset.py b/fairgraph/openminds/core/products/dataset.py index ed539b68..e92b6fe1 100644 --- a/fairgraph/openminds/core/products/dataset.py +++ b/fairgraph/openminds/core/products/dataset.py @@ -93,13 +93,3 @@ def __init__( short_name=short_name, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -Dataset.set_error_handling(None) -for key, value in OMDataset.__dict__.items(): - if isinstance(value, OMDataset): - fg_instance = Dataset.from_jsonld(value.to_jsonld()) - fg_instance._space = Dataset.default_space - setattr(Dataset, key, fg_instance) -Dataset.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/dataset_version.py b/fairgraph/openminds/core/products/dataset_version.py index c5606983..44b60141 100644 --- a/fairgraph/openminds/core/products/dataset_version.py +++ b/fairgraph/openminds/core/products/dataset_version.py @@ -218,13 +218,3 @@ def download(self, local_path, client, accept_terms_of_use=False): local_filename.parent.mkdir(parents=True, exist_ok=True) local_filename, headers = urlretrieve(zip_archive_url, local_filename) return local_filename, repo.iri.value - - -# cast openMINDS instances to their fairgraph subclass -DatasetVersion.set_error_handling(None) -for key, value in OMDatasetVersion.__dict__.items(): - if isinstance(value, OMDatasetVersion): - fg_instance = DatasetVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = DatasetVersion.default_space - setattr(DatasetVersion, key, fg_instance) -DatasetVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/meta_data_model.py b/fairgraph/openminds/core/products/meta_data_model.py index 772f5cb8..a98d188b 100644 --- a/fairgraph/openminds/core/products/meta_data_model.py +++ b/fairgraph/openminds/core/products/meta_data_model.py @@ -93,13 +93,3 @@ def __init__( short_name=short_name, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -MetaDataModel.set_error_handling(None) -for key, value in OMMetaDataModel.__dict__.items(): - if isinstance(value, OMMetaDataModel): - fg_instance = MetaDataModel.from_jsonld(value.to_jsonld()) - fg_instance._space = MetaDataModel.default_space - setattr(MetaDataModel, key, fg_instance) -MetaDataModel.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/meta_data_model_version.py b/fairgraph/openminds/core/products/meta_data_model_version.py index 596d34b0..3126b1cf 100644 --- a/fairgraph/openminds/core/products/meta_data_model_version.py +++ b/fairgraph/openminds/core/products/meta_data_model_version.py @@ -146,13 +146,3 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) - - -# cast openMINDS instances to their fairgraph subclass -MetaDataModelVersion.set_error_handling(None) -for key, value in OMMetaDataModelVersion.__dict__.items(): - if isinstance(value, OMMetaDataModelVersion): - fg_instance = MetaDataModelVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = MetaDataModelVersion.default_space - setattr(MetaDataModelVersion, key, fg_instance) -MetaDataModelVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/model.py b/fairgraph/openminds/core/products/model.py index 83ace321..281023de 100644 --- a/fairgraph/openminds/core/products/model.py +++ b/fairgraph/openminds/core/products/model.py @@ -99,13 +99,3 @@ def __init__( study_targets=study_targets, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -Model.set_error_handling(None) -for key, value in OMModel.__dict__.items(): - if isinstance(value, OMModel): - fg_instance = Model.from_jsonld(value.to_jsonld()) - fg_instance._space = Model.default_space - setattr(Model, key, fg_instance) -Model.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/model_version.py b/fairgraph/openminds/core/products/model_version.py index 266b95c1..4bc0d66a 100644 --- a/fairgraph/openminds/core/products/model_version.py +++ b/fairgraph/openminds/core/products/model_version.py @@ -207,13 +207,3 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] - - -# cast openMINDS instances to their fairgraph subclass -ModelVersion.set_error_handling(None) -for key, value in OMModelVersion.__dict__.items(): - if isinstance(value, OMModelVersion): - fg_instance = ModelVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = ModelVersion.default_space - setattr(ModelVersion, key, fg_instance) -ModelVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/project.py b/fairgraph/openminds/core/products/project.py index beb1ded9..e83904d1 100644 --- a/fairgraph/openminds/core/products/project.py +++ b/fairgraph/openminds/core/products/project.py @@ -54,13 +54,3 @@ def __init__( homepage=homepage, short_name=short_name, ) - - -# cast openMINDS instances to their fairgraph subclass -Project.set_error_handling(None) -for key, value in OMProject.__dict__.items(): - if isinstance(value, OMProject): - fg_instance = Project.from_jsonld(value.to_jsonld()) - fg_instance._space = Project.default_space - setattr(Project, key, fg_instance) -Project.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/setup.py b/fairgraph/openminds/core/products/setup.py index b2291efd..eb5c5e6e 100644 --- a/fairgraph/openminds/core/products/setup.py +++ b/fairgraph/openminds/core/products/setup.py @@ -67,13 +67,3 @@ def __init__( types=types, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -Setup.set_error_handling(None) -for key, value in OMSetup.__dict__.items(): - if isinstance(value, OMSetup): - fg_instance = Setup.from_jsonld(value.to_jsonld()) - fg_instance._space = Setup.default_space - setattr(Setup, key, fg_instance) -Setup.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/software.py b/fairgraph/openminds/core/products/software.py index 5da68e53..8e25880d 100644 --- a/fairgraph/openminds/core/products/software.py +++ b/fairgraph/openminds/core/products/software.py @@ -93,13 +93,3 @@ def __init__( short_name=short_name, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -Software.set_error_handling(None) -for key, value in OMSoftware.__dict__.items(): - if isinstance(value, OMSoftware): - fg_instance = Software.from_jsonld(value.to_jsonld()) - fg_instance._space = Software.default_space - setattr(Software, key, fg_instance) -Software.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/software_version.py b/fairgraph/openminds/core/products/software_version.py index 2214bff9..2860f42c 100644 --- a/fairgraph/openminds/core/products/software_version.py +++ b/fairgraph/openminds/core/products/software_version.py @@ -213,13 +213,3 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] - - -# cast openMINDS instances to their fairgraph subclass -SoftwareVersion.set_error_handling(None) -for key, value in OMSoftwareVersion.__dict__.items(): - if isinstance(value, OMSoftwareVersion): - fg_instance = SoftwareVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = SoftwareVersion.default_space - setattr(SoftwareVersion, key, fg_instance) -SoftwareVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/web_service.py b/fairgraph/openminds/core/products/web_service.py index 97ef9fb2..e105e110 100644 --- a/fairgraph/openminds/core/products/web_service.py +++ b/fairgraph/openminds/core/products/web_service.py @@ -111,13 +111,3 @@ def __init__( short_name=short_name, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -WebService.set_error_handling(None) -for key, value in OMWebService.__dict__.items(): - if isinstance(value, OMWebService): - fg_instance = WebService.from_jsonld(value.to_jsonld()) - fg_instance._space = WebService.default_space - setattr(WebService, key, fg_instance) -WebService.set_error_handling("log") diff --git a/fairgraph/openminds/core/products/web_service_version.py b/fairgraph/openminds/core/products/web_service_version.py index 31823614..ca52b1ca 100644 --- a/fairgraph/openminds/core/products/web_service_version.py +++ b/fairgraph/openminds/core/products/web_service_version.py @@ -169,13 +169,3 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] - - -# cast openMINDS instances to their fairgraph subclass -WebServiceVersion.set_error_handling(None) -for key, value in OMWebServiceVersion.__dict__.items(): - if isinstance(value, OMWebServiceVersion): - fg_instance = WebServiceVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = WebServiceVersion.default_space - setattr(WebServiceVersion, key, fg_instance) -WebServiceVersion.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/behavioral_protocol.py b/fairgraph/openminds/core/research/behavioral_protocol.py index 3764e50e..abb5ddc7 100644 --- a/fairgraph/openminds/core/research/behavioral_protocol.py +++ b/fairgraph/openminds/core/research/behavioral_protocol.py @@ -67,13 +67,3 @@ def __init__( stimulus_types=stimulus_types, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -BehavioralProtocol.set_error_handling(None) -for key, value in OMBehavioralProtocol.__dict__.items(): - if isinstance(value, OMBehavioralProtocol): - fg_instance = BehavioralProtocol.from_jsonld(value.to_jsonld()) - fg_instance._space = BehavioralProtocol.default_space - setattr(BehavioralProtocol, key, fg_instance) -BehavioralProtocol.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/configuration.py b/fairgraph/openminds/core/research/configuration.py index 6593f40c..1ed89c7f 100644 --- a/fairgraph/openminds/core/research/configuration.py +++ b/fairgraph/openminds/core/research/configuration.py @@ -66,13 +66,3 @@ def __init__( is_configuration_of=is_configuration_of, specifies=specifies, ) - - -# cast openMINDS instances to their fairgraph subclass -Configuration.set_error_handling(None) -for key, value in OMConfiguration.__dict__.items(): - if isinstance(value, OMConfiguration): - fg_instance = Configuration.from_jsonld(value.to_jsonld()) - fg_instance._space = Configuration.default_space - setattr(Configuration, key, fg_instance) -Configuration.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/custom_property_set.py b/fairgraph/openminds/core/research/custom_property_set.py index bfa80faa..9cbd6b88 100644 --- a/fairgraph/openminds/core/research/custom_property_set.py +++ b/fairgraph/openminds/core/research/custom_property_set.py @@ -24,13 +24,3 @@ def __init__( return EmbeddedMetadata.__init__( self, data=data, context=context, data_location=data_location, relevant_for=relevant_for ) - - -# cast openMINDS instances to their fairgraph subclass -CustomPropertySet.set_error_handling(None) -for key, value in OMCustomPropertySet.__dict__.items(): - if isinstance(value, OMCustomPropertySet): - fg_instance = CustomPropertySet.from_jsonld(value.to_jsonld()) - fg_instance._space = CustomPropertySet.default_space - setattr(CustomPropertySet, key, fg_instance) -CustomPropertySet.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/numerical_property.py b/fairgraph/openminds/core/research/numerical_property.py index c8a6fc90..0d3e0a10 100644 --- a/fairgraph/openminds/core/research/numerical_property.py +++ b/fairgraph/openminds/core/research/numerical_property.py @@ -20,13 +20,3 @@ class NumericalProperty(EmbeddedMetadata, OMNumericalProperty): def __init__(self, name=None, values=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, name=name, values=values) - - -# cast openMINDS instances to their fairgraph subclass -NumericalProperty.set_error_handling(None) -for key, value in OMNumericalProperty.__dict__.items(): - if isinstance(value, OMNumericalProperty): - fg_instance = NumericalProperty.from_jsonld(value.to_jsonld()) - fg_instance._space = NumericalProperty.default_space - setattr(NumericalProperty, key, fg_instance) -NumericalProperty.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/property_value_list.py b/fairgraph/openminds/core/research/property_value_list.py index de59cb28..89f5552e 100644 --- a/fairgraph/openminds/core/research/property_value_list.py +++ b/fairgraph/openminds/core/research/property_value_list.py @@ -69,13 +69,3 @@ def __init__( property_value_pairs=property_value_pairs, specifies=specifies, ) - - -# cast openMINDS instances to their fairgraph subclass -PropertyValueList.set_error_handling(None) -for key, value in OMPropertyValueList.__dict__.items(): - if isinstance(value, OMPropertyValueList): - fg_instance = PropertyValueList.from_jsonld(value.to_jsonld()) - fg_instance._space = PropertyValueList.default_space - setattr(PropertyValueList, key, fg_instance) -PropertyValueList.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/protocol.py b/fairgraph/openminds/core/research/protocol.py index 89863840..017853ed 100644 --- a/fairgraph/openminds/core/research/protocol.py +++ b/fairgraph/openminds/core/research/protocol.py @@ -65,13 +65,3 @@ def __init__( techniques=techniques, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -Protocol.set_error_handling(None) -for key, value in OMProtocol.__dict__.items(): - if isinstance(value, OMProtocol): - fg_instance = Protocol.from_jsonld(value.to_jsonld()) - fg_instance._space = Protocol.default_space - setattr(Protocol, key, fg_instance) -Protocol.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/protocol_execution.py b/fairgraph/openminds/core/research/protocol_execution.py index ef4c9c3c..96667d3e 100644 --- a/fairgraph/openminds/core/research/protocol_execution.py +++ b/fairgraph/openminds/core/research/protocol_execution.py @@ -74,13 +74,3 @@ def __init__( start_time=start_time, study_targets=study_targets, ) - - -# cast openMINDS instances to their fairgraph subclass -ProtocolExecution.set_error_handling(None) -for key, value in OMProtocolExecution.__dict__.items(): - if isinstance(value, OMProtocolExecution): - fg_instance = ProtocolExecution.from_jsonld(value.to_jsonld()) - fg_instance._space = ProtocolExecution.default_space - setattr(ProtocolExecution, key, fg_instance) -ProtocolExecution.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/strain.py b/fairgraph/openminds/core/research/strain.py index 5575d2b4..b3a0b3f2 100644 --- a/fairgraph/openminds/core/research/strain.py +++ b/fairgraph/openminds/core/research/strain.py @@ -88,13 +88,3 @@ def __init__( stock_number=stock_number, synonyms=synonyms, ) - - -# cast openMINDS instances to their fairgraph subclass -Strain.set_error_handling(None) -for key, value in OMStrain.__dict__.items(): - if isinstance(value, OMStrain): - fg_instance = Strain.from_jsonld(value.to_jsonld()) - fg_instance._space = Strain.default_space - setattr(Strain, key, fg_instance) -Strain.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/string_property.py b/fairgraph/openminds/core/research/string_property.py index 5eb14f98..47a1b773 100644 --- a/fairgraph/openminds/core/research/string_property.py +++ b/fairgraph/openminds/core/research/string_property.py @@ -20,13 +20,3 @@ class StringProperty(EmbeddedMetadata, OMStringProperty): def __init__(self, name=None, value=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, name=name, value=value) - - -# cast openMINDS instances to their fairgraph subclass -StringProperty.set_error_handling(None) -for key, value in OMStringProperty.__dict__.items(): - if isinstance(value, OMStringProperty): - fg_instance = StringProperty.from_jsonld(value.to_jsonld()) - fg_instance._space = StringProperty.default_space - setattr(StringProperty, key, fg_instance) -StringProperty.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject.py b/fairgraph/openminds/core/research/subject.py index 4b8d83db..07adc1f3 100644 --- a/fairgraph/openminds/core/research/subject.py +++ b/fairgraph/openminds/core/research/subject.py @@ -77,13 +77,3 @@ def __init__( studied_states=studied_states, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -Subject.set_error_handling(None) -for key, value in OMSubject.__dict__.items(): - if isinstance(value, OMSubject): - fg_instance = Subject.from_jsonld(value.to_jsonld()) - fg_instance._space = Subject.default_space - setattr(Subject, key, fg_instance) -Subject.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject_group.py b/fairgraph/openminds/core/research/subject_group.py index 6d817bef..72780ed1 100644 --- a/fairgraph/openminds/core/research/subject_group.py +++ b/fairgraph/openminds/core/research/subject_group.py @@ -89,13 +89,3 @@ def __init__( studied_states=studied_states, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -SubjectGroup.set_error_handling(None) -for key, value in OMSubjectGroup.__dict__.items(): - if isinstance(value, OMSubjectGroup): - fg_instance = SubjectGroup.from_jsonld(value.to_jsonld()) - fg_instance._space = SubjectGroup.default_space - setattr(SubjectGroup, key, fg_instance) -SubjectGroup.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject_group_state.py b/fairgraph/openminds/core/research/subject_group_state.py index 1a9b91da..f89225e0 100644 --- a/fairgraph/openminds/core/research/subject_group_state.py +++ b/fairgraph/openminds/core/research/subject_group_state.py @@ -111,13 +111,3 @@ def __init__( relative_time_indication=relative_time_indication, weight=weight, ) - - -# cast openMINDS instances to their fairgraph subclass -SubjectGroupState.set_error_handling(None) -for key, value in OMSubjectGroupState.__dict__.items(): - if isinstance(value, OMSubjectGroupState): - fg_instance = SubjectGroupState.from_jsonld(value.to_jsonld()) - fg_instance._space = SubjectGroupState.default_space - setattr(SubjectGroupState, key, fg_instance) -SubjectGroupState.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/subject_state.py b/fairgraph/openminds/core/research/subject_state.py index 5214f619..13662b89 100644 --- a/fairgraph/openminds/core/research/subject_state.py +++ b/fairgraph/openminds/core/research/subject_state.py @@ -136,13 +136,3 @@ def __init__( used_in=used_in, weight=weight, ) - - -# cast openMINDS instances to their fairgraph subclass -SubjectState.set_error_handling(None) -for key, value in OMSubjectState.__dict__.items(): - if isinstance(value, OMSubjectState): - fg_instance = SubjectState.from_jsonld(value.to_jsonld()) - fg_instance._space = SubjectState.default_space - setattr(SubjectState, key, fg_instance) -SubjectState.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample.py b/fairgraph/openminds/core/research/tissue_sample.py index 88fea5c7..18051e86 100644 --- a/fairgraph/openminds/core/research/tissue_sample.py +++ b/fairgraph/openminds/core/research/tissue_sample.py @@ -85,13 +85,3 @@ def __init__( type=type, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueSample.set_error_handling(None) -for key, value in OMTissueSample.__dict__.items(): - if isinstance(value, OMTissueSample): - fg_instance = TissueSample.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueSample.default_space - setattr(TissueSample, key, fg_instance) -TissueSample.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample_collection.py b/fairgraph/openminds/core/research/tissue_sample_collection.py index 76aef615..9f20aae1 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection.py @@ -97,13 +97,3 @@ def __init__( types=types, used_in=used_in, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueSampleCollection.set_error_handling(None) -for key, value in OMTissueSampleCollection.__dict__.items(): - if isinstance(value, OMTissueSampleCollection): - fg_instance = TissueSampleCollection.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueSampleCollection.default_space - setattr(TissueSampleCollection, key, fg_instance) -TissueSampleCollection.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample_collection_state.py b/fairgraph/openminds/core/research/tissue_sample_collection_state.py index 6675e5de..fa992f84 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection_state.py @@ -107,13 +107,3 @@ def __init__( relative_time_indication=relative_time_indication, weight=weight, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueSampleCollectionState.set_error_handling(None) -for key, value in OMTissueSampleCollectionState.__dict__.items(): - if isinstance(value, OMTissueSampleCollectionState): - fg_instance = TissueSampleCollectionState.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueSampleCollectionState.default_space - setattr(TissueSampleCollectionState, key, fg_instance) -TissueSampleCollectionState.set_error_handling("log") diff --git a/fairgraph/openminds/core/research/tissue_sample_state.py b/fairgraph/openminds/core/research/tissue_sample_state.py index 0c5325a6..f32a0352 100644 --- a/fairgraph/openminds/core/research/tissue_sample_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_state.py @@ -125,13 +125,3 @@ def __init__( used_in=used_in, weight=weight, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueSampleState.set_error_handling(None) -for key, value in OMTissueSampleState.__dict__.items(): - if isinstance(value, OMTissueSampleState): - fg_instance = TissueSampleState.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueSampleState.default_space - setattr(TissueSampleState, key, fg_instance) -TissueSampleState.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/activity/cell_patching.py b/fairgraph/openminds/ephys/activity/cell_patching.py index fc1576c6..1eb72779 100644 --- a/fairgraph/openminds/ephys/activity/cell_patching.py +++ b/fairgraph/openminds/ephys/activity/cell_patching.py @@ -71,13 +71,3 @@ def __init__( tissue_bath_solution=tissue_bath_solution, variation=variation, ) - - -# cast openMINDS instances to their fairgraph subclass -CellPatching.set_error_handling(None) -for key, value in OMCellPatching.__dict__.items(): - if isinstance(value, OMCellPatching): - fg_instance = CellPatching.from_jsonld(value.to_jsonld()) - fg_instance._space = CellPatching.default_space - setattr(CellPatching, key, fg_instance) -CellPatching.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/activity/electrode_placement.py b/fairgraph/openminds/ephys/activity/electrode_placement.py index 3d211d7f..b405c65c 100644 --- a/fairgraph/openminds/ephys/activity/electrode_placement.py +++ b/fairgraph/openminds/ephys/activity/electrode_placement.py @@ -65,13 +65,3 @@ def __init__( study_targets=study_targets, target_position=target_position, ) - - -# cast openMINDS instances to their fairgraph subclass -ElectrodePlacement.set_error_handling(None) -for key, value in OMElectrodePlacement.__dict__.items(): - if isinstance(value, OMElectrodePlacement): - fg_instance = ElectrodePlacement.from_jsonld(value.to_jsonld()) - fg_instance._space = ElectrodePlacement.default_space - setattr(ElectrodePlacement, key, fg_instance) -ElectrodePlacement.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/activity/recording_activity.py b/fairgraph/openminds/ephys/activity/recording_activity.py index d80b14f0..bf8cc1e5 100644 --- a/fairgraph/openminds/ephys/activity/recording_activity.py +++ b/fairgraph/openminds/ephys/activity/recording_activity.py @@ -65,13 +65,3 @@ def __init__( start_time=start_time, study_targets=study_targets, ) - - -# cast openMINDS instances to their fairgraph subclass -RecordingActivity.set_error_handling(None) -for key, value in OMRecordingActivity.__dict__.items(): - if isinstance(value, OMRecordingActivity): - fg_instance = RecordingActivity.from_jsonld(value.to_jsonld()) - fg_instance._space = RecordingActivity.default_space - setattr(RecordingActivity, key, fg_instance) -RecordingActivity.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode.py b/fairgraph/openminds/ephys/device/electrode.py index d5bb1c42..7bebeb6b 100644 --- a/fairgraph/openminds/ephys/device/electrode.py +++ b/fairgraph/openminds/ephys/device/electrode.py @@ -79,13 +79,3 @@ def __init__( serial_number=serial_number, usage=usage, ) - - -# cast openMINDS instances to their fairgraph subclass -Electrode.set_error_handling(None) -for key, value in OMElectrode.__dict__.items(): - if isinstance(value, OMElectrode): - fg_instance = Electrode.from_jsonld(value.to_jsonld()) - fg_instance._space = Electrode.default_space - setattr(Electrode, key, fg_instance) -Electrode.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode_array.py b/fairgraph/openminds/ephys/device/electrode_array.py index 3c476b14..f7d4d1dd 100644 --- a/fairgraph/openminds/ephys/device/electrode_array.py +++ b/fairgraph/openminds/ephys/device/electrode_array.py @@ -83,13 +83,3 @@ def __init__( serial_number=serial_number, usage=usage, ) - - -# cast openMINDS instances to their fairgraph subclass -ElectrodeArray.set_error_handling(None) -for key, value in OMElectrodeArray.__dict__.items(): - if isinstance(value, OMElectrodeArray): - fg_instance = ElectrodeArray.from_jsonld(value.to_jsonld()) - fg_instance._space = ElectrodeArray.default_space - setattr(ElectrodeArray, key, fg_instance) -ElectrodeArray.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode_array_usage.py b/fairgraph/openminds/ephys/device/electrode_array_usage.py index 0d93fffb..0746202d 100644 --- a/fairgraph/openminds/ephys/device/electrode_array_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_array_usage.py @@ -103,13 +103,3 @@ def __init__( used_to_measure=used_to_measure, used_to_record=used_to_record, ) - - -# cast openMINDS instances to their fairgraph subclass -ElectrodeArrayUsage.set_error_handling(None) -for key, value in OMElectrodeArrayUsage.__dict__.items(): - if isinstance(value, OMElectrodeArrayUsage): - fg_instance = ElectrodeArrayUsage.from_jsonld(value.to_jsonld()) - fg_instance._space = ElectrodeArrayUsage.default_space - setattr(ElectrodeArrayUsage, key, fg_instance) -ElectrodeArrayUsage.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/electrode_usage.py b/fairgraph/openminds/ephys/device/electrode_usage.py index 1b377c13..3b2ce02a 100644 --- a/fairgraph/openminds/ephys/device/electrode_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_usage.py @@ -99,13 +99,3 @@ def __init__( used_to_measure=used_to_measure, used_to_record=used_to_record, ) - - -# cast openMINDS instances to their fairgraph subclass -ElectrodeUsage.set_error_handling(None) -for key, value in OMElectrodeUsage.__dict__.items(): - if isinstance(value, OMElectrodeUsage): - fg_instance = ElectrodeUsage.from_jsonld(value.to_jsonld()) - fg_instance._space = ElectrodeUsage.default_space - setattr(ElectrodeUsage, key, fg_instance) -ElectrodeUsage.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/pipette.py b/fairgraph/openminds/ephys/device/pipette.py index 2f9e6a4a..ee39a7fe 100644 --- a/fairgraph/openminds/ephys/device/pipette.py +++ b/fairgraph/openminds/ephys/device/pipette.py @@ -79,13 +79,3 @@ def __init__( serial_number=serial_number, usage=usage, ) - - -# cast openMINDS instances to their fairgraph subclass -Pipette.set_error_handling(None) -for key, value in OMPipette.__dict__.items(): - if isinstance(value, OMPipette): - fg_instance = Pipette.from_jsonld(value.to_jsonld()) - fg_instance._space = Pipette.default_space - setattr(Pipette, key, fg_instance) -Pipette.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/device/pipette_usage.py b/fairgraph/openminds/ephys/device/pipette_usage.py index 90d3882f..ad1198d5 100644 --- a/fairgraph/openminds/ephys/device/pipette_usage.py +++ b/fairgraph/openminds/ephys/device/pipette_usage.py @@ -121,13 +121,3 @@ def __init__( used_to_measure=used_to_measure, used_to_record=used_to_record, ) - - -# cast openMINDS instances to their fairgraph subclass -PipetteUsage.set_error_handling(None) -for key, value in OMPipetteUsage.__dict__.items(): - if isinstance(value, OMPipetteUsage): - fg_instance = PipetteUsage.from_jsonld(value.to_jsonld()) - fg_instance._space = PipetteUsage.default_space - setattr(PipetteUsage, key, fg_instance) -PipetteUsage.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/entity/channel.py b/fairgraph/openminds/ephys/entity/channel.py index 95be349e..69943189 100644 --- a/fairgraph/openminds/ephys/entity/channel.py +++ b/fairgraph/openminds/ephys/entity/channel.py @@ -20,13 +20,3 @@ class Channel(EmbeddedMetadata, OMChannel): def __init__(self, internal_identifier=None, unit=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, internal_identifier=internal_identifier, unit=unit) - - -# cast openMINDS instances to their fairgraph subclass -Channel.set_error_handling(None) -for key, value in OMChannel.__dict__.items(): - if isinstance(value, OMChannel): - fg_instance = Channel.from_jsonld(value.to_jsonld()) - fg_instance._space = Channel.default_space - setattr(Channel, key, fg_instance) -Channel.set_error_handling("log") diff --git a/fairgraph/openminds/ephys/entity/recording.py b/fairgraph/openminds/ephys/entity/recording.py index be750ea3..f63def75 100644 --- a/fairgraph/openminds/ephys/entity/recording.py +++ b/fairgraph/openminds/ephys/entity/recording.py @@ -61,13 +61,3 @@ def __init__( recorded_with=recorded_with, sampling_frequency=sampling_frequency, ) - - -# cast openMINDS instances to their fairgraph subclass -Recording.set_error_handling(None) -for key, value in OMRecording.__dict__.items(): - if isinstance(value, OMRecording): - fg_instance = Recording.from_jsonld(value.to_jsonld()) - fg_instance._space = Recording.default_space - setattr(Recording, key, fg_instance) -Recording.set_error_handling("log") diff --git a/fairgraph/openminds/publications/book.py b/fairgraph/openminds/publications/book.py index 5c42e4f4..8c69fc6c 100644 --- a/fairgraph/openminds/publications/book.py +++ b/fairgraph/openminds/publications/book.py @@ -104,13 +104,3 @@ def __init__( related_to=related_to, version_identifier=version_identifier, ) - - -# cast openMINDS instances to their fairgraph subclass -Book.set_error_handling(None) -for key, value in OMBook.__dict__.items(): - if isinstance(value, OMBook): - fg_instance = Book.from_jsonld(value.to_jsonld()) - fg_instance._space = Book.default_space - setattr(Book, key, fg_instance) -Book.set_error_handling("log") diff --git a/fairgraph/openminds/publications/chapter.py b/fairgraph/openminds/publications/chapter.py index 371a6f7a..5e4fd59f 100644 --- a/fairgraph/openminds/publications/chapter.py +++ b/fairgraph/openminds/publications/chapter.py @@ -98,13 +98,3 @@ def __init__( related_to=related_to, version_identifier=version_identifier, ) - - -# cast openMINDS instances to their fairgraph subclass -Chapter.set_error_handling(None) -for key, value in OMChapter.__dict__.items(): - if isinstance(value, OMChapter): - fg_instance = Chapter.from_jsonld(value.to_jsonld()) - fg_instance._space = Chapter.default_space - setattr(Chapter, key, fg_instance) -Chapter.set_error_handling("log") diff --git a/fairgraph/openminds/publications/learning_resource.py b/fairgraph/openminds/publications/learning_resource.py index 46f53f23..80c7ca1b 100644 --- a/fairgraph/openminds/publications/learning_resource.py +++ b/fairgraph/openminds/publications/learning_resource.py @@ -88,13 +88,3 @@ def __init__( type=type, version_identifier=version_identifier, ) - - -# cast openMINDS instances to their fairgraph subclass -LearningResource.set_error_handling(None) -for key, value in OMLearningResource.__dict__.items(): - if isinstance(value, OMLearningResource): - fg_instance = LearningResource.from_jsonld(value.to_jsonld()) - fg_instance._space = LearningResource.default_space - setattr(LearningResource, key, fg_instance) -LearningResource.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper.py b/fairgraph/openminds/publications/live_paper.py index d99a0299..3dbc5a28 100644 --- a/fairgraph/openminds/publications/live_paper.py +++ b/fairgraph/openminds/publications/live_paper.py @@ -93,13 +93,3 @@ def __init__( short_name=short_name, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -LivePaper.set_error_handling(None) -for key, value in OMLivePaper.__dict__.items(): - if isinstance(value, OMLivePaper): - fg_instance = LivePaper.from_jsonld(value.to_jsonld()) - fg_instance._space = LivePaper.default_space - setattr(LivePaper, key, fg_instance) -LivePaper.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper_resource_item.py b/fairgraph/openminds/publications/live_paper_resource_item.py index 45f7791a..9a17c907 100644 --- a/fairgraph/openminds/publications/live_paper_resource_item.py +++ b/fairgraph/openminds/publications/live_paper_resource_item.py @@ -56,13 +56,3 @@ def __init__( is_location_of=is_location_of, is_part_of=is_part_of, ) - - -# cast openMINDS instances to their fairgraph subclass -LivePaperResourceItem.set_error_handling(None) -for key, value in OMLivePaperResourceItem.__dict__.items(): - if isinstance(value, OMLivePaperResourceItem): - fg_instance = LivePaperResourceItem.from_jsonld(value.to_jsonld()) - fg_instance._space = LivePaperResourceItem.default_space - setattr(LivePaperResourceItem, key, fg_instance) -LivePaperResourceItem.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper_section.py b/fairgraph/openminds/publications/live_paper_section.py index bdb44ca6..b8200eeb 100644 --- a/fairgraph/openminds/publications/live_paper_section.py +++ b/fairgraph/openminds/publications/live_paper_section.py @@ -55,13 +55,3 @@ def __init__( order=order, type=type, ) - - -# cast openMINDS instances to their fairgraph subclass -LivePaperSection.set_error_handling(None) -for key, value in OMLivePaperSection.__dict__.items(): - if isinstance(value, OMLivePaperSection): - fg_instance = LivePaperSection.from_jsonld(value.to_jsonld()) - fg_instance._space = LivePaperSection.default_space - setattr(LivePaperSection, key, fg_instance) -LivePaperSection.set_error_handling("log") diff --git a/fairgraph/openminds/publications/live_paper_version.py b/fairgraph/openminds/publications/live_paper_version.py index 50edd0c9..10c86baf 100644 --- a/fairgraph/openminds/publications/live_paper_version.py +++ b/fairgraph/openminds/publications/live_paper_version.py @@ -164,13 +164,3 @@ def is_version_of(self, client): else: assert len(parents) == 1 return parents[0] - - -# cast openMINDS instances to their fairgraph subclass -LivePaperVersion.set_error_handling(None) -for key, value in OMLivePaperVersion.__dict__.items(): - if isinstance(value, OMLivePaperVersion): - fg_instance = LivePaperVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = LivePaperVersion.default_space - setattr(LivePaperVersion, key, fg_instance) -LivePaperVersion.set_error_handling("log") diff --git a/fairgraph/openminds/publications/periodical.py b/fairgraph/openminds/publications/periodical.py index 36dfa5f3..5138a30a 100644 --- a/fairgraph/openminds/publications/periodical.py +++ b/fairgraph/openminds/publications/periodical.py @@ -51,13 +51,3 @@ def __init__( digital_identifier=digital_identifier, has_parts=has_parts, ) - - -# cast openMINDS instances to their fairgraph subclass -Periodical.set_error_handling(None) -for key, value in OMPeriodical.__dict__.items(): - if isinstance(value, OMPeriodical): - fg_instance = Periodical.from_jsonld(value.to_jsonld()) - fg_instance._space = Periodical.default_space - setattr(Periodical, key, fg_instance) -Periodical.set_error_handling("log") diff --git a/fairgraph/openminds/publications/publication_issue.py b/fairgraph/openminds/publications/publication_issue.py index 71de45da..d4c4e714 100644 --- a/fairgraph/openminds/publications/publication_issue.py +++ b/fairgraph/openminds/publications/publication_issue.py @@ -40,13 +40,3 @@ def __init__(self, has_parts=None, is_part_of=None, issue_number=None, id=None, is_part_of=is_part_of, issue_number=issue_number, ) - - -# cast openMINDS instances to their fairgraph subclass -PublicationIssue.set_error_handling(None) -for key, value in OMPublicationIssue.__dict__.items(): - if isinstance(value, OMPublicationIssue): - fg_instance = PublicationIssue.from_jsonld(value.to_jsonld()) - fg_instance._space = PublicationIssue.default_space - setattr(PublicationIssue, key, fg_instance) -PublicationIssue.set_error_handling("log") diff --git a/fairgraph/openminds/publications/publication_volume.py b/fairgraph/openminds/publications/publication_volume.py index b8282fc8..a132a231 100644 --- a/fairgraph/openminds/publications/publication_volume.py +++ b/fairgraph/openminds/publications/publication_volume.py @@ -42,13 +42,3 @@ def __init__( is_part_of=is_part_of, volume_number=volume_number, ) - - -# cast openMINDS instances to their fairgraph subclass -PublicationVolume.set_error_handling(None) -for key, value in OMPublicationVolume.__dict__.items(): - if isinstance(value, OMPublicationVolume): - fg_instance = PublicationVolume.from_jsonld(value.to_jsonld()) - fg_instance._space = PublicationVolume.default_space - setattr(PublicationVolume, key, fg_instance) -PublicationVolume.set_error_handling("log") diff --git a/fairgraph/openminds/publications/scholarly_article.py b/fairgraph/openminds/publications/scholarly_article.py index 4668b07c..ae2ce1b9 100644 --- a/fairgraph/openminds/publications/scholarly_article.py +++ b/fairgraph/openminds/publications/scholarly_article.py @@ -142,13 +142,3 @@ def get_citation_string(self, client): journal_name = journal.name if journal else "" volume_number = f"{volume.volume_number}: " if (volume and volume.volume_number != "placeholder") else "" return f"{author_str} ({self.publication_date.year}). {title} {journal_name}, {volume_number}{self.pagination or ''}." - - -# cast openMINDS instances to their fairgraph subclass -ScholarlyArticle.set_error_handling(None) -for key, value in OMScholarlyArticle.__dict__.items(): - if isinstance(value, OMScholarlyArticle): - fg_instance = ScholarlyArticle.from_jsonld(value.to_jsonld()) - fg_instance._space = ScholarlyArticle.default_space - setattr(ScholarlyArticle, key, fg_instance) -ScholarlyArticle.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/atlas_annotation.py b/fairgraph/openminds/sands/atlas/atlas_annotation.py index 766f72e2..21b4ff50 100644 --- a/fairgraph/openminds/sands/atlas/atlas_annotation.py +++ b/fairgraph/openminds/sands/atlas/atlas_annotation.py @@ -49,13 +49,3 @@ def __init__( specification=specification, type=type, ) - - -# cast openMINDS instances to their fairgraph subclass -AtlasAnnotation.set_error_handling(None) -for key, value in OMAtlasAnnotation.__dict__.items(): - if isinstance(value, OMAtlasAnnotation): - fg_instance = AtlasAnnotation.from_jsonld(value.to_jsonld()) - fg_instance._space = AtlasAnnotation.default_space - setattr(AtlasAnnotation, key, fg_instance) -AtlasAnnotation.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/brain_atlas.py b/fairgraph/openminds/sands/atlas/brain_atlas.py index c5731677..ca9d1350 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas.py @@ -111,13 +111,3 @@ def __init__( used_species=used_species, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -BrainAtlas.set_error_handling(None) -for key, value in OMBrainAtlas.__dict__.items(): - if isinstance(value, OMBrainAtlas): - fg_instance = BrainAtlas.from_jsonld(value.to_jsonld()) - fg_instance._space = BrainAtlas.default_space - setattr(BrainAtlas, key, fg_instance) -BrainAtlas.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/brain_atlas_version.py b/fairgraph/openminds/sands/atlas/brain_atlas_version.py index 3ab54494..8acd3abb 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas_version.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas_version.py @@ -172,13 +172,3 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) - - -# cast openMINDS instances to their fairgraph subclass -BrainAtlasVersion.set_error_handling(None) -for key, value in OMBrainAtlasVersion.__dict__.items(): - if isinstance(value, OMBrainAtlasVersion): - fg_instance = BrainAtlasVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = BrainAtlasVersion.default_space - setattr(BrainAtlasVersion, key, fg_instance) -BrainAtlasVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space.py b/fairgraph/openminds/sands/atlas/common_coordinate_space.py index f1073b56..a374bf06 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space.py @@ -119,13 +119,3 @@ def __init__( used_species=used_species, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -CommonCoordinateSpace.set_error_handling(None) -for key, value in OMCommonCoordinateSpace.__dict__.items(): - if isinstance(value, OMCommonCoordinateSpace): - fg_instance = CommonCoordinateSpace.from_jsonld(value.to_jsonld()) - fg_instance._space = CommonCoordinateSpace.default_space - setattr(CommonCoordinateSpace, key, fg_instance) -CommonCoordinateSpace.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py index c5ebaaeb..0dae2548 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py @@ -202,13 +202,3 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) - - -# cast openMINDS instances to their fairgraph subclass -CommonCoordinateSpaceVersion.set_error_handling(None) -for key, value in OMCommonCoordinateSpaceVersion.__dict__.items(): - if isinstance(value, OMCommonCoordinateSpaceVersion): - fg_instance = CommonCoordinateSpaceVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = CommonCoordinateSpaceVersion.default_space - setattr(CommonCoordinateSpaceVersion, key, fg_instance) -CommonCoordinateSpaceVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity.py b/fairgraph/openminds/sands/atlas/parcellation_entity.py index 01fa298d..ed489a6d 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity.py @@ -131,13 +131,3 @@ def __init__( studied_in=studied_in, versions=versions, ) - - -# cast openMINDS instances to their fairgraph subclass -ParcellationEntity.set_error_handling(None) -for key, value in OMParcellationEntity.__dict__.items(): - if isinstance(value, OMParcellationEntity): - fg_instance = ParcellationEntity.from_jsonld(value.to_jsonld()) - fg_instance._space = ParcellationEntity.default_space - setattr(ParcellationEntity, key, fg_instance) -ParcellationEntity.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py index 9105989c..9ad33086 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py @@ -160,13 +160,3 @@ def __init__( version_identifier=version_identifier, version_innovation=version_innovation, ) - - -# cast openMINDS instances to their fairgraph subclass -ParcellationEntityVersion.set_error_handling(None) -for key, value in OMParcellationEntityVersion.__dict__.items(): - if isinstance(value, OMParcellationEntityVersion): - fg_instance = ParcellationEntityVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = ParcellationEntityVersion.default_space - setattr(ParcellationEntityVersion, key, fg_instance) -ParcellationEntityVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology.py b/fairgraph/openminds/sands/atlas/parcellation_terminology.py index 066fed1c..fa7ad8b9 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology.py @@ -35,13 +35,3 @@ def __init__( has_entities=has_entities, ontology_identifiers=ontology_identifiers, ) - - -# cast openMINDS instances to their fairgraph subclass -ParcellationTerminology.set_error_handling(None) -for key, value in OMParcellationTerminology.__dict__.items(): - if isinstance(value, OMParcellationTerminology): - fg_instance = ParcellationTerminology.from_jsonld(value.to_jsonld()) - fg_instance._space = ParcellationTerminology.default_space - setattr(ParcellationTerminology, key, fg_instance) -ParcellationTerminology.set_error_handling("log") diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py index bc3bb851..93ca650b 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py @@ -35,13 +35,3 @@ def __init__( has_entities=has_entities, ontology_identifiers=ontology_identifiers, ) - - -# cast openMINDS instances to their fairgraph subclass -ParcellationTerminologyVersion.set_error_handling(None) -for key, value in OMParcellationTerminologyVersion.__dict__.items(): - if isinstance(value, OMParcellationTerminologyVersion): - fg_instance = ParcellationTerminologyVersion.from_jsonld(value.to_jsonld()) - fg_instance._space = ParcellationTerminologyVersion.default_space - setattr(ParcellationTerminologyVersion, key, fg_instance) -ParcellationTerminologyVersion.set_error_handling("log") diff --git a/fairgraph/openminds/sands/mathematical_shapes/circle.py b/fairgraph/openminds/sands/mathematical_shapes/circle.py index 8092a2c8..1951488b 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/circle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/circle.py @@ -20,13 +20,3 @@ class Circle(EmbeddedMetadata, OMCircle): def __init__(self, radius=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, radius=radius) - - -# cast openMINDS instances to their fairgraph subclass -Circle.set_error_handling(None) -for key, value in OMCircle.__dict__.items(): - if isinstance(value, OMCircle): - fg_instance = Circle.from_jsonld(value.to_jsonld()) - fg_instance._space = Circle.default_space - setattr(Circle, key, fg_instance) -Circle.set_error_handling("log") diff --git a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py index 29267dfa..567b40b1 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py +++ b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py @@ -22,13 +22,3 @@ def __init__(self, semi_major_axis=None, semi_minor_axis=None, id=None, data=Non return EmbeddedMetadata.__init__( self, data=data, semi_major_axis=semi_major_axis, semi_minor_axis=semi_minor_axis ) - - -# cast openMINDS instances to their fairgraph subclass -Ellipse.set_error_handling(None) -for key, value in OMEllipse.__dict__.items(): - if isinstance(value, OMEllipse): - fg_instance = Ellipse.from_jsonld(value.to_jsonld()) - fg_instance._space = Ellipse.default_space - setattr(Ellipse, key, fg_instance) -Ellipse.set_error_handling("log") diff --git a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py index bcc2bbeb..8894f237 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py @@ -20,13 +20,3 @@ class Rectangle(EmbeddedMetadata, OMRectangle): def __init__(self, length=None, width=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, length=length, width=width) - - -# cast openMINDS instances to their fairgraph subclass -Rectangle.set_error_handling(None) -for key, value in OMRectangle.__dict__.items(): - if isinstance(value, OMRectangle): - fg_instance = Rectangle.from_jsonld(value.to_jsonld()) - fg_instance._space = Rectangle.default_space - setattr(Rectangle, key, fg_instance) -Rectangle.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py index 092134d0..57139a50 100644 --- a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py +++ b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py @@ -37,13 +37,3 @@ def __init__( spatial_locations=spatial_locations, target_identification_type=target_identification_type, ) - - -# cast openMINDS instances to their fairgraph subclass -AnatomicalTargetPosition.set_error_handling(None) -for key, value in OMAnatomicalTargetPosition.__dict__.items(): - if isinstance(value, OMAnatomicalTargetPosition): - fg_instance = AnatomicalTargetPosition.from_jsonld(value.to_jsonld()) - fg_instance._space = AnatomicalTargetPosition.default_space - setattr(AnatomicalTargetPosition, key, fg_instance) -AnatomicalTargetPosition.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py index ff5ff1ab..06c643f3 100644 --- a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py +++ b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py @@ -20,13 +20,3 @@ class CoordinatePoint(EmbeddedMetadata, OMCoordinatePoint): def __init__(self, coordinate_space=None, coordinates=None, id=None, data=None, space=None, scope=None): return EmbeddedMetadata.__init__(self, data=data, coordinate_space=coordinate_space, coordinates=coordinates) - - -# cast openMINDS instances to their fairgraph subclass -CoordinatePoint.set_error_handling(None) -for key, value in OMCoordinatePoint.__dict__.items(): - if isinstance(value, OMCoordinatePoint): - fg_instance = CoordinatePoint.from_jsonld(value.to_jsonld()) - fg_instance._space = CoordinatePoint.default_space - setattr(CoordinatePoint, key, fg_instance) -CoordinatePoint.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py index 257ffbc1..d822bb33 100644 --- a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py @@ -24,13 +24,3 @@ def __init__( return EmbeddedMetadata.__init__( self, data=data, criteria=criteria, in_relation_to=in_relation_to, qualitative_overlap=qualitative_overlap ) - - -# cast openMINDS instances to their fairgraph subclass -QualitativeRelationAssessment.set_error_handling(None) -for key, value in OMQualitativeRelationAssessment.__dict__.items(): - if isinstance(value, OMQualitativeRelationAssessment): - fg_instance = QualitativeRelationAssessment.from_jsonld(value.to_jsonld()) - fg_instance._space = QualitativeRelationAssessment.default_space - setattr(QualitativeRelationAssessment, key, fg_instance) -QualitativeRelationAssessment.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py index 0fe9369f..4d1a6166 100644 --- a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py @@ -28,13 +28,3 @@ def __init__( in_relation_to=in_relation_to, quantitative_overlap=quantitative_overlap, ) - - -# cast openMINDS instances to their fairgraph subclass -QuantitativeRelationAssessment.set_error_handling(None) -for key, value in OMQuantitativeRelationAssessment.__dict__.items(): - if isinstance(value, OMQuantitativeRelationAssessment): - fg_instance = QuantitativeRelationAssessment.from_jsonld(value.to_jsonld()) - fg_instance._space = QuantitativeRelationAssessment.default_space - setattr(QuantitativeRelationAssessment, key, fg_instance) -QuantitativeRelationAssessment.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/single_color.py b/fairgraph/openminds/sands/miscellaneous/single_color.py index fc4db8f1..e3980294 100644 --- a/fairgraph/openminds/sands/miscellaneous/single_color.py +++ b/fairgraph/openminds/sands/miscellaneous/single_color.py @@ -22,13 +22,3 @@ class SingleColor(KGObject, OMSingleColor): def __init__(self, value=None, id=None, data=None, space=None, scope=None): return KGObject.__init__(self, id=id, space=space, scope=scope, data=data, value=value) - - -# cast openMINDS instances to their fairgraph subclass -SingleColor.set_error_handling(None) -for key, value in OMSingleColor.__dict__.items(): - if isinstance(value, OMSingleColor): - fg_instance = SingleColor.from_jsonld(value.to_jsonld()) - fg_instance._space = SingleColor.default_space - setattr(SingleColor, key, fg_instance) -SingleColor.set_error_handling("log") diff --git a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py index c13961d6..9965a0d8 100644 --- a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py +++ b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py @@ -37,13 +37,3 @@ def __init__( camera_position=camera_position, preferred_display_color=preferred_display_color, ) - - -# cast openMINDS instances to their fairgraph subclass -ViewerSpecification.set_error_handling(None) -for key, value in OMViewerSpecification.__dict__.items(): - if isinstance(value, OMViewerSpecification): - fg_instance = ViewerSpecification.from_jsonld(value.to_jsonld()) - fg_instance._space = ViewerSpecification.default_space - setattr(ViewerSpecification, key, fg_instance) -ViewerSpecification.set_error_handling("log") diff --git a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py index 29201b5b..61b876d8 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py +++ b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py @@ -108,13 +108,3 @@ def __init__( relation_assessments=relation_assessments, studied_in=studied_in, ) - - -# cast openMINDS instances to their fairgraph subclass -CustomAnatomicalEntity.set_error_handling(None) -for key, value in OMCustomAnatomicalEntity.__dict__.items(): - if isinstance(value, OMCustomAnatomicalEntity): - fg_instance = CustomAnatomicalEntity.from_jsonld(value.to_jsonld()) - fg_instance._space = CustomAnatomicalEntity.default_space - setattr(CustomAnatomicalEntity, key, fg_instance) -CustomAnatomicalEntity.set_error_handling("log") diff --git a/fairgraph/openminds/sands/non_atlas/custom_annotation.py b/fairgraph/openminds/sands/non_atlas/custom_annotation.py index 61677df2..8f2d86dd 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_annotation.py +++ b/fairgraph/openminds/sands/non_atlas/custom_annotation.py @@ -51,13 +51,3 @@ def __init__( specification=specification, type=type, ) - - -# cast openMINDS instances to their fairgraph subclass -CustomAnnotation.set_error_handling(None) -for key, value in OMCustomAnnotation.__dict__.items(): - if isinstance(value, OMCustomAnnotation): - fg_instance = CustomAnnotation.from_jsonld(value.to_jsonld()) - fg_instance._space = CustomAnnotation.default_space - setattr(CustomAnnotation, key, fg_instance) -CustomAnnotation.set_error_handling("log") diff --git a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py index 955cf594..cc2fb703 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py +++ b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py @@ -65,13 +65,3 @@ def __init__( is_used_to_group=is_used_to_group, native_unit=native_unit, ) - - -# cast openMINDS instances to their fairgraph subclass -CustomCoordinateSpace.set_error_handling(None) -for key, value in OMCustomCoordinateSpace.__dict__.items(): - if isinstance(value, OMCustomCoordinateSpace): - fg_instance = CustomCoordinateSpace.from_jsonld(value.to_jsonld()) - fg_instance._space = CustomCoordinateSpace.default_space - setattr(CustomCoordinateSpace, key, fg_instance) -CustomCoordinateSpace.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py index f1682ccc..5df9fb4a 100644 --- a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py @@ -67,13 +67,3 @@ def __init__( start_time=start_time, study_targets=study_targets, ) - - -# cast openMINDS instances to their fairgraph subclass -CranialWindowPreparation.set_error_handling(None) -for key, value in OMCranialWindowPreparation.__dict__.items(): - if isinstance(value, OMCranialWindowPreparation): - fg_instance = CranialWindowPreparation.from_jsonld(value.to_jsonld()) - fg_instance._space = CranialWindowPreparation.default_space - setattr(CranialWindowPreparation, key, fg_instance) -CranialWindowPreparation.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py index c339b1bd..84a83e9d 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py @@ -65,13 +65,3 @@ def __init__( start_time=start_time, study_targets=study_targets, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueCulturePreparation.set_error_handling(None) -for key, value in OMTissueCulturePreparation.__dict__.items(): - if isinstance(value, OMTissueCulturePreparation): - fg_instance = TissueCulturePreparation.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueCulturePreparation.default_space - setattr(TissueCulturePreparation, key, fg_instance) -TissueCulturePreparation.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py index dd6d5442..4dcec1f3 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py @@ -67,13 +67,3 @@ def __init__( temperature=temperature, tissue_bath_solution=tissue_bath_solution, ) - - -# cast openMINDS instances to their fairgraph subclass -TissueSampleSlicing.set_error_handling(None) -for key, value in OMTissueSampleSlicing.__dict__.items(): - if isinstance(value, OMTissueSampleSlicing): - fg_instance = TissueSampleSlicing.from_jsonld(value.to_jsonld()) - fg_instance._space = TissueSampleSlicing.default_space - setattr(TissueSampleSlicing, key, fg_instance) -TissueSampleSlicing.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device.py b/fairgraph/openminds/specimen_prep/device/slicing_device.py index f68c5b12..9fa935d7 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device.py @@ -71,13 +71,3 @@ def __init__( serial_number=serial_number, usage=usage, ) - - -# cast openMINDS instances to their fairgraph subclass -SlicingDevice.set_error_handling(None) -for key, value in OMSlicingDevice.__dict__.items(): - if isinstance(value, OMSlicingDevice): - fg_instance = SlicingDevice.from_jsonld(value.to_jsonld()) - fg_instance._space = SlicingDevice.default_space - setattr(SlicingDevice, key, fg_instance) -SlicingDevice.set_error_handling("log") diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py index 0baa6761..8613e1f9 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py @@ -115,13 +115,3 @@ def __init__( used_to_record=used_to_record, vibration_frequency=vibration_frequency, ) - - -# cast openMINDS instances to their fairgraph subclass -SlicingDeviceUsage.set_error_handling(None) -for key, value in OMSlicingDeviceUsage.__dict__.items(): - if isinstance(value, OMSlicingDeviceUsage): - fg_instance = SlicingDeviceUsage.from_jsonld(value.to_jsonld()) - fg_instance._space = SlicingDeviceUsage.default_space - setattr(SlicingDeviceUsage, key, fg_instance) -SlicingDeviceUsage.set_error_handling("log") diff --git a/fairgraph/openminds/stimulation/activity/stimulation_activity.py b/fairgraph/openminds/stimulation/activity/stimulation_activity.py index 35da518b..f2a4268e 100644 --- a/fairgraph/openminds/stimulation/activity/stimulation_activity.py +++ b/fairgraph/openminds/stimulation/activity/stimulation_activity.py @@ -65,13 +65,3 @@ def __init__( stimuli=stimuli, study_targets=study_targets, ) - - -# cast openMINDS instances to their fairgraph subclass -StimulationActivity.set_error_handling(None) -for key, value in OMStimulationActivity.__dict__.items(): - if isinstance(value, OMStimulationActivity): - fg_instance = StimulationActivity.from_jsonld(value.to_jsonld()) - fg_instance._space = StimulationActivity.default_space - setattr(StimulationActivity, key, fg_instance) -StimulationActivity.set_error_handling("log") diff --git a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py index 5e3cbb8e..2f900b8e 100644 --- a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py +++ b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py @@ -61,13 +61,3 @@ def __init__( specifications=specifications, type=type, ) - - -# cast openMINDS instances to their fairgraph subclass -EphysStimulus.set_error_handling(None) -for key, value in OMEphysStimulus.__dict__.items(): - if isinstance(value, OMEphysStimulus): - fg_instance = EphysStimulus.from_jsonld(value.to_jsonld()) - fg_instance._space = EphysStimulus.default_space - setattr(EphysStimulus, key, fg_instance) -EphysStimulus.set_error_handling("log") diff --git a/fairgraph/queries.py b/fairgraph/queries.py index a07c88bc..c1a83d5e 100644 --- a/fairgraph/queries.py +++ b/fairgraph/queries.py @@ -315,7 +315,6 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any else: property_name = property.path type_filter = None - fg_cls = lookup_type(cls.type_) # get the fairgraph version of cls properties.append( QueryProperty( expanded_path, @@ -324,7 +323,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any type_filter=type_filter, ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, - properties=fg_cls.generate_query_properties(follow_links), + properties=cls.generate_query_properties(follow_links), ) ) elif any(issubclass(_type, LinkedMetadata) for _type in property.types): @@ -338,7 +337,6 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any type_filter = cls.type_ else: type_filter = None - fg_cls = lookup_type(cls.type_) properties.append( QueryProperty( expanded_path, @@ -347,7 +345,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any type_filter=type_filter, ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, - properties=[QueryProperty("@id"), *fg_cls.generate_query_properties(follow_links)], + properties=[QueryProperty("@id"), *cls.generate_query_properties(follow_links)], ) ) else: diff --git a/fairgraph/utility.py b/fairgraph/utility.py index c843453f..992318f7 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -540,3 +540,20 @@ def adapt_structure(structure, replacement): replacement = ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab") adapt_structure(migrated_query["structure"], replacement) return migrated_query + + +def initialise_instances(class_list): + """Cast openMINDS instances to their fairgraph subclass""" + for cls in class_list: + cls.set_error_handling(None) + # find parent openMINDS class + for parent_cls in cls.__mro__[1:]: + if parent_cls.__name__ == cls.__name__: + # could also do this by looking for issubclass(parent_cls, openminds.Node) + break + for key, value in parent_cls.__dict__.items(): + if isinstance(value, parent_cls): + fg_instance = cls.from_jsonld(value.to_jsonld()) + fg_instance._space = cls.default_space + setattr(cls, key, fg_instance) + cls.set_error_handling("log") \ No newline at end of file From 314a0bcabfa695f8646543548751afae286aed4b Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 17 Sep 2025 11:19:33 +0200 Subject: [PATCH 19/25] Adapt unit tests to work with a non-privileged user token (i.e., not a curator) --- fairgraph/utility.py | 4 ++++ test/test_client.py | 17 +++++++++-------- test/test_openminds_core.py | 10 +++++----- test/test_queries.py | 26 +++++++++++++------------- test/utils.py | 9 +++++++++ 5 files changed, 40 insertions(+), 26 deletions(-) diff --git a/fairgraph/utility.py b/fairgraph/utility.py index 992318f7..0278ca5e 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -494,6 +494,10 @@ def adapt_type_4to3(uri): assert len(uri) == 1 uri = uri[0] cls = lookup_type(uri) + + if cls.__module__ == "test.test_client": + return cls.type_ + module_name = cls.__module__.split(".")[2] # e.g., 'fairgraph.openminds.core.actors.person' -> "core" module_name = { "controlled_terms": "controlledTerms", diff --git a/test/test_client.py b/test/test_client.py index bed42958..f56ce44d 100644 --- a/test/test_client.py +++ b/test/test_client.py @@ -1,11 +1,11 @@ import os -import json import pytest from kg_core.response import Error as KGError +from fairgraph.kgobject import KGObject from fairgraph.queries import Query, QueryProperty, Filter from fairgraph.errors import AuthenticationError, AuthorizationError, ResourceExistsError -from .utils import kg_client, skip_if_no_connection, MockKGResponse +from .utils import kg_client, kg_client_curator, skip_if_no_connection, MockKGResponse @skip_if_no_connection @@ -42,7 +42,6 @@ def test_spaces_names_only(kg_client): @skip_if_no_connection def test_query_filter_by_space(kg_client): - import fairgraph.openminds.core # needed to populate registry query = Query( node_type="https://openminds.om-i.org/types/Model", @@ -96,7 +95,6 @@ def test_get_admin_client(kg_client): @skip_if_no_connection def test_list_scopes(kg_client): - import fairgraph.openminds.core def _get_models(scope): return kg_client.list( @@ -177,7 +175,8 @@ def test_store_and_retrieve_query(kg_client, mocker): @skip_if_no_connection def test_configure_space(kg_client, mocker): - class MockType: + class MockType(KGObject): + schema_version = "latest" type_ = "hello" mocker.patch.object(kg_client._kg_admin_client, "create_space_definition", lambda space: None) @@ -188,10 +187,12 @@ class MockType: @skip_if_no_connection -def test_is_released(kg_client): +def test_is_released(kg_client_curator): + if kg_client_curator is None: + pytest.skip("Need to set environment variable KG_AUTH_TOKEN_CURATOR") instance_id = "https://kg.ebrains.eu/api/instances/5ed1e9f9-482d-41c7-affd-f1aa887bd618" - kg_client.is_released(instance_id, with_children=True) - kg_client.is_released(instance_id, with_children=False) + kg_client_curator.is_released(instance_id, with_children=True) + kg_client_curator.is_released(instance_id, with_children=False) @skip_if_no_connection diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index d0eb5163..0d16ada5 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -144,13 +144,13 @@ def test_resolve_model(kg_client): assert model.name == "Scaffold Model of Cerebellum microcircuit version 2.0" assert isinstance(model.versions, KGProxy) resolved_model2 = deepcopy(model).resolve( - kg_client, scope="in progress", follow_links={"versions": {}, "custodians": {"affiliations": {}}} + kg_client, scope="released", follow_links={"versions": {}, "custodians": {"affiliations": {}}} ) assert isinstance(resolved_model2.versions, omcore.ModelVersion) assert isinstance(resolved_model2.custodians[0].affiliations[0].member_of, KGProxy) resolved_model4 = deepcopy(model).resolve( - kg_client, scope="in progress", follow_links={"custodians": {"affiliations": {"member_of": {}}}} + kg_client, scope="released", follow_links={"custodians": {"affiliations": {"member_of": {}}}} ) assert isinstance(resolved_model4.custodians[0].affiliations[0].member_of, omcore.Organization) @@ -292,7 +292,7 @@ def test_retrieve_released_model_versions_follow_reverse_links(kg_client): def test_query_across_links(kg_client): models = omcore.Model.list( kg_client, - scope="in progress", + scope="released", space="model", api="query", follow_links={"developers": {"affiliations": {"member_of": {}}}}, @@ -311,7 +311,7 @@ def test_query_across_links(kg_client): # check that "follow_links" is not needed for the cross-link filter to work models2 = omcore.Model.list( kg_client, - scope="in progress", + scope="released", space="model", api="query", follow_links=None, @@ -326,7 +326,7 @@ def test_query_across_links(kg_client): def test_query_across_reverse_links(kg_client): versions = omcore.ModelVersion.list( kg_client, - scope="in progress", + scope="released", space="model", api="query", follow_links={"is_version_of": {"developers": {"affiliations": {"member_of": {}}}}}, diff --git a/test/test_queries.py b/test/test_queries.py index 0e283e40..b4e4eec9 100644 --- a/test/test_queries.py +++ b/test/test_queries.py @@ -376,7 +376,7 @@ def test_execute_query(kg_client, example_query_model_version): query = adapt_namespaces_for_query(query) response = kg_client._kg_client.queries.test_query( payload=query, - stage=Stage.IN_PROGRESS, + stage=Stage.RELEASED, pagination=Pagination(start=0, size=3), ) data = response.data @@ -412,7 +412,7 @@ def test_execute_query_with_id_filter(kg_client, example_query_model): response = kg_client._kg_client.queries.test_query( payload=query, instance_id=kg_client.uuid_from_uri(target_id), - stage=Stage.IN_PROGRESS, + stage=Stage.RELEASED, pagination=Pagination(start=0, size=10), ) data = response.data @@ -424,24 +424,24 @@ def test_execute_query_with_id_filter(kg_client, example_query_model): @skip_if_no_connection def test_execute_query_with_reverse_properties_and_instance_id(kg_client, example_query_repository_with_reverse): - target_id = "https://kg.ebrains.eu/api/instances/2f8d64f3-d848-49bd-baa6-a2c7080c98da" + target_id = "https://kg.ebrains.eu/api/instances/1c846a5f-eac2-477a-9dc3-d2e51b00fda9" query = example_query_repository_with_reverse.serialize() if kg_client.migrated is False: query = adapt_namespaces_for_query(query) response = kg_client._kg_client.queries.test_query( payload=query, instance_id=kg_client.uuid_from_uri(target_id), - stage=Stage.IN_PROGRESS, + stage=Stage.RELEASED, pagination=Pagination(start=0, size=10), ) data = response.data assert len(data) == 1 assert ( data[0]["location"] - == "https://data-proxy.ebrains.eu/api/v1/buckets/p7e415-brette-etal-2007?prefix=Benchmark2" + == "https://data-proxy.ebrains.eu/api/v1/buckets/p63ea6-Angelo_SGA1_1.2.4?prefix=hbp-00810/EPSC/" ) - assert "VAbenchmarks" in data[0]["files"][0]["filename"] - assert data[0]["files"][5]["hash"][0]["algorithm"] == "MD5" + assert "hbp-00810_ESPC" in data[0]["files"][0]["filename"] + assert data[0]["files"][4]["hash"][0]["algorithm"] == "MD5" @skip_if_no_connection @@ -451,19 +451,19 @@ def test_execute_query_with_reverse_properties_and_filter(kg_client, example_que query = adapt_namespaces_for_query(query) response = kg_client._kg_client.queries.test_query( payload=query, - additional_request_params={"dataset_alias": "data-brette-etal-2007-benchmark2-v1"}, - stage=Stage.IN_PROGRESS, + additional_request_params={"dataset_alias": "Recordings of excitatory postsynaptic currents from cerebellar neurons"}, + stage=Stage.RELEASED, pagination=Pagination(start=0, size=10), ) data = response.data assert len(data) == 1 assert ( data[0]["location"] - == "https://data-proxy.ebrains.eu/api/v1/buckets/p7e415-brette-etal-2007?prefix=Benchmark2" + == "https://data-proxy.ebrains.eu/api/v1/buckets/p63ea6-Angelo_SGA1_1.2.4?prefix=hbp-00810/EPSC/" ) - assert "VAbenchmarks" in data[0]["files"][0]["filename"] - assert data[0]["files"][5]["hash"][0]["algorithm"] == "MD5" - assert data[0]["contains_dataset_version"][0]["alias"] == "data-brette-etal-2007-benchmark2-v1" + assert "hbp-00810_ESPC" in data[0]["files"][0]["filename"] + assert data[0]["files"][4]["hash"][0]["algorithm"] == "MD5" + assert data[0]["contains_dataset_version"][0]["alias"] == "Recordings of excitatory postsynaptic currents from cerebellar neurons" def test_openminds_core_queries(mock_client): diff --git a/test/utils.py b/test/utils.py index 21dc6c29..3e21f5ca 100644 --- a/test/utils.py +++ b/test/utils.py @@ -1,4 +1,5 @@ from copy import deepcopy +import os from uuid import uuid4 from requests.exceptions import SSLError from fairgraph.client import KGClient @@ -40,6 +41,14 @@ def kg_client(): return client +@pytest.fixture(scope="session") +def kg_client_curator(): + if "KG_AUTH_TOKEN_CURATOR" in os.environ: + return KGClient(host=kg_host, allow_interactive=False, token=os.environ["KG_AUTH_TOKEN_CURATOR"]) + else: + return None + + class MockKGResponse: def __init__(self, data, error=None): self.data = data From 5f40f4a5f565d19a9de8213cf1037c5b6eb3b7ac Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 17 Sep 2025 13:22:55 +0200 Subject: [PATCH 20/25] Preparations for tying fairgraph.openminds to a stable openMINDS version --- builder/fairgraph_module_template.py.txt | 2 +- builder/update_openminds.py | 4 +++- fairgraph/base.py | 2 ++ fairgraph/client.py | 3 ++- fairgraph/kgobject.py | 4 ++-- fairgraph/queries.py | 1 - fairgraph/registry.py | 6 ++++-- fairgraph/utility.py | 4 +++- test/test_client.py | 3 ++- 9 files changed, 19 insertions(+), 10 deletions(-) diff --git a/builder/fairgraph_module_template.py.txt b/builder/fairgraph_module_template.py.txt index 70beedac..7b7e9335 100644 --- a/builder/fairgraph_module_template.py.txt +++ b/builder/fairgraph_module_template.py.txt @@ -5,7 +5,7 @@ # this file was auto-generated from openminds.properties import Property -from openminds.latest.{{ module_name }} import {{ class_name }} as OM{{ class_name }} +from openminds.{{ openminds_version }}.{{ module_name }} import {{ class_name }} as OM{{ class_name }} from fairgraph import {{ base_class }} {{preamble}} diff --git a/builder/update_openminds.py b/builder/update_openminds.py index 6186593e..192dc44f 100644 --- a/builder/update_openminds.py +++ b/builder/update_openminds.py @@ -11,6 +11,7 @@ from jinja2 import Environment, select_autoescape, FileSystemLoader +OPENMINDS_VERSION = "latest" name_map = { "scope": "model_scope", # this is because 'scope' is already a keyword @@ -488,7 +489,7 @@ def generate_class_name(iri, module_map=None): assert isinstance(iri, str) class_name = iri.split("/")[-1] module_name = generate_python_name(module_map[iri]) - return f"openminds.latest.{module_name}.{class_name}" + return f"openminds.{OPENMINDS_VERSION}.{module_name}.{class_name}" def get_controlled_terms_table(type_): @@ -764,6 +765,7 @@ def get_type(prop): with open(f"additional_methods/{class_name}.py.txt") as fp: additional_methods = fp.read() self.context = { + "openminds_version": OPENMINDS_VERSION, "docstring": self._schema_payload.get("description", ""), "base_class": base_class, "preamble": preamble.get(class_name, ""), # default value, may be updated below diff --git a/fairgraph/base.py b/fairgraph/base.py index b588974c..0559fb64 100644 --- a/fairgraph/base.py +++ b/fairgraph/base.py @@ -29,6 +29,8 @@ if TYPE_CHECKING: from .client import KGClient +OPENMINDS_VERSION = "latest" + logger = logging.getLogger("fairgraph") JSONdict = Dict[str, Any] # see https://github.com/python/typing/issues/182 for some possible improvements diff --git a/fairgraph/client.py b/fairgraph/client.py index e114ce7e..d1f63dd4 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -38,6 +38,7 @@ from .errors import AuthenticationError, AuthorizationError, ResourceExistsError from .utility import adapt_namespaces_for_query, adapt_namespaces_3to4, adapt_namespaces_4to3, adapt_type_4to3 +from .base import OPENMINDS_VERSION if TYPE_CHECKING: from .kgobject import KGObject @@ -726,7 +727,7 @@ def space_info(self, space_name: str, scope: str = "released", ignore_errors: bo adapt_namespaces_3to4(type_) type_iri = type_["@type"] try: - cls = lookup_type(type_iri) + cls = lookup_type(type_iri, OPENMINDS_VERSION) except KeyError as err: ignore_list = [ "https://core.kg.ebrains.eu/vocab/type/Bookmark", diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index 7cc5b66c..e6ae5112 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -41,7 +41,7 @@ from .queries import Query, QueryProperty from .errors import AuthorizationError, ResourceExistsError, CannotBuildExistenceQuery from .caching import object_cache, save_cache, generate_cache_key -from .base import RepresentsSingleObject, SupportsQuerying, JSONdict +from .base import RepresentsSingleObject, SupportsQuerying, JSONdict, OPENMINDS_VERSION from .node import ContainsMetadata from .kgproxy import KGProxy from .kgquery import KGQuery @@ -239,7 +239,7 @@ def from_id( if isinstance(type_, list): assert len(type_) == 1 type_ = type_[0] - cls_from_data = lookup_type(type_) + cls_from_data = lookup_type(type_, OPENMINDS_VERSION) return cls_from_data.from_jsonld(data, scope=scope) @classmethod diff --git a/fairgraph/queries.py b/fairgraph/queries.py index c1a83d5e..c9822a9a 100644 --- a/fairgraph/queries.py +++ b/fairgraph/queries.py @@ -24,7 +24,6 @@ from warnings import warn from openminds.base import IRI, EmbeddedMetadata, LinkedMetadata, Node -from openminds.registry import lookup_type from .utility import as_list, expand_uri diff --git a/fairgraph/registry.py b/fairgraph/registry.py index 95349c3b..036facc0 100644 --- a/fairgraph/registry.py +++ b/fairgraph/registry.py @@ -12,6 +12,8 @@ from openminds.properties import Property from openminds.registry import Registry +from .base import OPENMINDS_VERSION + if TYPE_CHECKING: from .node import ContainsMetadata @@ -38,9 +40,9 @@ def __new__(meta, name, bases, class_dict): # set class_name so that the fairgraph class replaces the equivalent openminds class # in the registry # e.g. 'fairgraph.openminds.sands.miscellaneous.anatomical_target_position' - # --> 'openminds.latest.sands.AnatomicalTargetPosition' + # --> 'openminds.v4.sands.AnatomicalTargetPosition' class_dict["class_name"] = ".".join( - class_dict["__module__"].replace("fairgraph.openminds", "openminds.latest").split(".")[:3] + [name] + class_dict["__module__"].replace("fairgraph.openminds", f"openminds.{OPENMINDS_VERSION}").split(".")[:3] + [name] ) class_dict["preferred_import_path"] = class_dict["class_name"] cls = Registry.__new__(meta, name, bases, class_dict) diff --git a/fairgraph/utility.py b/fairgraph/utility.py index 0278ca5e..e3fd196e 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -26,6 +26,8 @@ from openminds.registry import lookup_type +from .base import OPENMINDS_VERSION + if TYPE_CHECKING: from .client import KGClient from .kgobject import KGObject @@ -493,7 +495,7 @@ def adapt_type_4to3(uri): if isinstance(uri, list): assert len(uri) == 1 uri = uri[0] - cls = lookup_type(uri) + cls = lookup_type(uri, OPENMINDS_VERSION) if cls.__module__ == "test.test_client": return cls.type_ diff --git a/test/test_client.py b/test/test_client.py index f56ce44d..6c2da548 100644 --- a/test/test_client.py +++ b/test/test_client.py @@ -5,6 +5,7 @@ from fairgraph.kgobject import KGObject from fairgraph.queries import Query, QueryProperty, Filter from fairgraph.errors import AuthenticationError, AuthorizationError, ResourceExistsError +from fairgraph.base import OPENMINDS_VERSION from .utils import kg_client, kg_client_curator, skip_if_no_connection, MockKGResponse @@ -176,7 +177,7 @@ def test_store_and_retrieve_query(kg_client, mocker): @skip_if_no_connection def test_configure_space(kg_client, mocker): class MockType(KGObject): - schema_version = "latest" + schema_version = OPENMINDS_VERSION type_ = "hello" mocker.patch.object(kg_client._kg_admin_client, "create_space_definition", lambda space: None) From d75c6869e6b0f7df05108368b53dfe4985f2d249 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Fri, 26 Sep 2025 12:04:54 +0200 Subject: [PATCH 21/25] When constructing filters, check that the keys actually correspond to property names. This catches the common case of mis-spelling property names, or wrongly guessing, e.g., using "authors" when it should be "developers" --- fairgraph/node.py | 19 +++++++++++++++++-- test/test_openminds_core.py | 14 ++++++++++++++ 2 files changed, 31 insertions(+), 2 deletions(-) diff --git a/fairgraph/node.py b/fairgraph/node.py index 5d70238c..4695764d 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -1,6 +1,7 @@ from __future__ import annotations from typing import TYPE_CHECKING, Optional, Dict, List, Union, Any from copy import copy +from itertools import chain import logging from warnings import warn @@ -164,7 +165,7 @@ def set_error_handling( type_.set_error_handling(value) @classmethod - def normalize_filter(cls, filter_dict: Dict[str, Any]) -> Dict[str, Any]: + def normalize_filter(cls, filter_dict: Dict[str, Any], check_validity: bool = True) -> Dict[str, Any]: """ Normalize a dict containing filter key:value pairs so that it can be used in a call to the KG query API. @@ -185,15 +186,29 @@ def normalize_filter(cls, filter_dict: Dict[str, Any]) -> Dict[str, Any]: if name_ in filter_dict_copy: filter_dict_copy[alias_] = filter_dict_copy.pop(name_) + def _check_validity(filters, property_names): + invalid_filters = set(filters).difference(property_names) + if invalid_filters: + if len(invalid_filters) == 1: + msg = f"Invalid filter: " + else: + msg = f"Invalid filters: " + raise ValueError(msg + ", ".join(invalid_filters)) + + if check_validity: + _check_validity(filter_dict_copy, cls.property_names) + for prop in cls.all_properties: if prop.name in filter_dict_copy: value = filter_dict_copy[prop.name] if isinstance(value, dict): + _check_validity(value, set(chain(*(child_cls.property_names for child_cls in prop.types)))) normalized[prop.name] = {} for child_cls in prop.types: - normalized[prop.name].update(child_cls.normalize_filter(value)) + normalized[prop.name].update(child_cls.normalize_filter(value, check_validity=False)) else: normalized[prop.name] = get_filter_value(prop, value) + return normalized @classmethod diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index 0d16ada5..4be99be5 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -696,6 +696,20 @@ def test_normalize_filter(): assert result == expected +def test_normalize_filter_with_invalid_keys(): + with pytest.raises(ValueError) as excinfo: + omcore.ModelVersion.normalize_filter({ + "authors": {"given_name": "Zaphod"}, + "documentation": {"iri": "http://example.org"} + }) # should be "developers", "full_documentation" + assert str(excinfo.value) == "Invalid filters: authors, documentation" + with pytest.raises(ValueError) as excinfo: + omcore.ModelVersion.normalize_filter({ + "developers": {"digital_identifiers": {"id": "https://orcid.org/some-id"}} + }) # should be "identifier", not "id" + assert str(excinfo.value) == "Invalid filter: id" + + def test_class_docstring(): assert "email address" in omcore.Person.__doc__ From 65b503419195b40c85487d879b566b2c74997932 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Fri, 3 Oct 2025 17:00:31 +0200 Subject: [PATCH 22/25] Assorted fixes --- fairgraph/client.py | 5 ++--- fairgraph/node.py | 8 ++++---- fairgraph/utility.py | 30 ++++++++++++++++++++---------- 3 files changed, 26 insertions(+), 17 deletions(-) diff --git a/fairgraph/client.py b/fairgraph/client.py index d1f63dd4..971a903c 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -235,9 +235,6 @@ def query( along with metadata about the query results such as total number of instances, and pagination information. """ - if self.migrated is False: - query = adapt_namespaces_for_query(query) - query_id = query.get("@id", None) if use_stored_query: @@ -257,6 +254,8 @@ def _query(scope, from_index, size): ) else: + if self.migrated is False: + query = adapt_namespaces_for_query(query) def _query(scope, from_index, size): response = self._kg_client.queries.test_query( diff --git a/fairgraph/node.py b/fairgraph/node.py index 4695764d..79e090c2 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -148,9 +148,6 @@ def set_error_handling( value (str): action to follow when there is a validation failure. (e.g. if a required property is not provided). Possible values: "error", "warning", "log", None - property_names (str or list of str, optional): If not provided, the error handling - mode will be applied to all properties. If a property name or list of names is given, - the mode will be applied only to those properties. """ if value is None: value = ErrorHandling.none @@ -298,7 +295,10 @@ def _normalize_type(data_item): normalised_key = expand_uri(key, cls.context) value = [item for item in as_list(value) if _get_type_from_data(item).endswith(type_filter)] if normalised_key in D: - D[normalised_key].extend(value) + if isinstance(D[normalised_key], list): + D[normalised_key].extend(value) + else: + D[normalised_key] = [D[normalised_key]] + value else: D[normalised_key] = value elif key.startswith("Q"): # for 'Q' properties in data from queries diff --git a/fairgraph/utility.py b/fairgraph/utility.py index e3fd196e..66ff3b8b 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -526,18 +526,28 @@ def adapt_instance_uri_4to3(uri): def adapt_namespaces_for_query(query): """Map from v4+ to v3 openMINDS namespace""" + def adapt_path(item_path, replacement): + if isinstance(item_path, str): + return item_path.replace(*replacement) + elif isinstance(item_path, list): + return [adapt_path(part, replacement) for part in item_path] + else: + assert isinstance(item_path, dict) + new_item_path = item_path.copy() + new_item_path["@id"] = item_path["@id"].replace(*replacement) + if "typeFilter" in item_path: + if isinstance(item_path["typeFilter"], list): + new_item_path["typeFilter"] = [ + {"@id": adapt_type_4to3(subitem["@id"])} + for subitem in item_path["typeFilter"] + ] + else: + new_item_path["typeFilter"]["@id"] = adapt_type_4to3(item_path["typeFilter"]["@id"]) + return new_item_path + def adapt_structure(structure, replacement): for item in structure: - if isinstance(item["path"], str): - item["path"] = item["path"].replace(*replacement) - elif isinstance(item["path"], list): - item["path"] = [part.replace(*replacement) for part in item["path"]] - # todo: individual parts could be dicts with "@id", "typeFilter" - else: - assert isinstance(item["path"], dict) - item["path"]["@id"] = item["path"]["@id"].replace(*replacement) - if "typeFilter" in item["path"]: - item["path"]["typeFilter"]["@id"] = adapt_type_4to3(item["path"]["typeFilter"]["@id"]) + item["path"] = adapt_path(item["path"], replacement) if "structure" in item: adapt_structure(item["structure"], replacement) From 461a0a5b712de2658029c0b3294c49a3858a1069 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Sun, 2 Nov 2025 22:52:11 +0100 Subject: [PATCH 23/25] Do not add values for reverse properties (as KGProxy instances) unless requested Fixes #102 --- fairgraph/kgobject.py | 50 ++++++++++++-- fairgraph/kgquery.py | 10 ++- fairgraph/node.py | 68 +++++++++++++++---- .../openminds/core/products/model_version.py | 1 + fairgraph/queries.py | 19 ++++-- fairgraph/registry.py | 4 ++ test/test_openminds_computation.py | 1 + test/test_openminds_core.py | 7 +- test/test_queries.py | 3 + 9 files changed, 133 insertions(+), 30 deletions(-) diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index e6ae5112..e4c9a47a 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -138,6 +138,7 @@ def from_uri( use_cache: bool = True, scope: str = "released", follow_links: Optional[Dict[str, Any]] = None, + with_reverse_properties: Optional[bool] = False, ): """ Retrieve an instance from the Knowledge Graph based on its URI. @@ -149,10 +150,16 @@ def from_uri( Defaults to "released". use_cache (bool): Whether to use cached data if they exist. Defaults to True. follow_links (dict): The links in the graph to follow. Defaults to None. - + with_reverse_properties (bool): Whether to include reverse properties. Defaults to False. """ if follow_links: - query = cls.generate_query(space=None, client=client, filters=None, follow_links=follow_links) + query = cls.generate_query( + space=None, + client=client, + filters=None, + follow_links=follow_links, + with_reverse_properties=with_reverse_properties, + ) results = client.query(query, instance_id=client.uuid_from_uri(uri), size=1, scope=scope).data if results: data = results[0] @@ -173,6 +180,7 @@ def from_uuid( use_cache: bool = True, scope: str = "released", follow_links: Optional[Dict[str, Any]] = None, + with_reverse_properties: Optional[bool] = False, ): """ Retrieve an instance from the Knowledge Graph based on its UUID. @@ -184,6 +192,7 @@ def from_uuid( Defaults to "released". use_cache (bool): Whether to use cached data if they exist. Defaults to True. follow_links (dict): The links in the graph to follow. Defaults to None. + with_reverse_properties (bool): Whether to include reverse properties. Defaults to False. """ logger.info("Attempting to retrieve {} with uuid {}".format(cls.__name__, uuid)) @@ -194,7 +203,14 @@ def from_uuid( except ValueError as err: raise ValueError("{} - {}".format(err, uuid)) uri = cls.uri_from_uuid(uuid, client) - return cls.from_uri(uri, client, use_cache=use_cache, scope=scope, follow_links=follow_links) + return cls.from_uri( + uri, + client, + use_cache=use_cache, + scope=scope, + follow_links=follow_links, + with_reverse_properties=with_reverse_properties, + ) @classmethod def from_id( @@ -204,6 +220,7 @@ def from_id( use_cache: bool = True, scope: str = "released", follow_links: Optional[Dict[str, Any]] = None, + with_reverse_properties: Optional[bool] = False, ): """ Retrieve an instance from the Knowledge Graph based on either its URI or UUID. @@ -215,6 +232,7 @@ def from_id( Defaults to "released". use_cache (bool): Whether to use cached data if they exist. Defaults to True. follow_links (dict): The links in the graph to follow. Defaults to None. + with_reverse_properties (bool): Whether to include reverse properties. Defaults to False. Returns: Either a KGObject of the correct type, or None. @@ -223,9 +241,17 @@ def from_id( """ if hasattr(cls, "type_") and cls.type_: if id.startswith("http"): - return cls.from_uri(id, client, use_cache=use_cache, scope=scope, follow_links=follow_links) + fn = cls.from_uri else: - return cls.from_uuid(id, client, use_cache=use_cache, scope=scope, follow_links=follow_links) + fn = cls.from_uuid + return fn( + id, + client, + use_cache=use_cache, + scope=scope, + follow_links=follow_links, + with_reverse_properties=with_reverse_properties, + ) else: # if we don't know the type if id.startswith("http"): @@ -318,6 +344,7 @@ def list( scope: str = "released", space: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, + with_reverse_properties: Optional[bool] = False, **filters, ) -> List[KGObject]: """ @@ -331,6 +358,7 @@ def list( scope (str, optional): The scope to use for the query. Can be 'released', 'in progress', or 'all'. Default is 'released'. space (str, optional): The KG space to be queried. If not specified, results from all accessible spaces will be included. follow_links (dict): The links in the graph to follow. Defaults to None. + with_reverse_properties (bool): Whether to include reverse properties. Defaults to False. filters: Optional keyword arguments representing filters to apply to the query. Returns: @@ -361,7 +389,13 @@ def list( api = "core" if api == "query": - query = cls.generate_query(space=space, client=client, filters=filters, follow_links=follow_links) + query = cls.generate_query( + space=space, + client=client, + filters=filters, + follow_links=follow_links, + with_reverse_properties=with_reverse_properties, + ) instances = client.query( query=query, from_index=from_index, @@ -827,6 +861,7 @@ def generate_query( space: Union[str, None], filters: Optional[Dict[str, Any]] = None, follow_links: Optional[Dict[str, Any]] = None, + with_reverse_properties: Optional[bool] = False, label: Optional[str] = None, ) -> Union[Dict[str, Any], None]: """ @@ -837,6 +872,7 @@ def generate_query( space (str, optional): if provided, restrict the query to metadata stored in the given KG space. filters (dict): A dictonary defining search parameters for the query. follow_links (dict): The links in the graph to follow. Defaults to None. + with_reverse_properties (dict): Whether to include reverse properties. Default False. label (str, optional): a label for the query Returns: @@ -857,7 +893,7 @@ def generate_query( node_type=cls.type_, label=label, space=real_space, - properties=cls.generate_query_properties(follow_links), + properties=cls.generate_query_properties(follow_links, with_reverse_properties), ) # second pass, we add filters query.properties.extend(cls.generate_query_filter_properties(normalized_filters)) diff --git a/fairgraph/kgquery.py b/fairgraph/kgquery.py index f6bed9f8..4be12e4c 100644 --- a/fairgraph/kgquery.py +++ b/fairgraph/kgquery.py @@ -88,6 +88,7 @@ def resolve( scope: Optional[str] = None, use_cache: bool = True, follow_links: Optional[Dict[str, Any]] = None, + with_reverse_properties: Optional[bool] = False, ): """ Retrieve the full metadata for the KGObject(s) represented by this query object. @@ -101,6 +102,7 @@ def resolve( If not provided, the "preferred_scope" provided when creating the proxy object will be used. use_cache (bool): Whether to use cached data if they exist. Defaults to True. follow_links (dict): The links in the graph to follow. Defaults to None. + with_reverse_properties (dict): Whether to include reverse properties. Defaults to False. Returns: a KGObject instance, of the appropriate subclass. @@ -110,7 +112,13 @@ def resolve( for cls in self.classes: if hasattr(cls, "generate_query"): # if cls is EmbeddedMetadata we cannot query it - query = cls.generate_query(client=client, filters=self.filter, space=space, follow_links=follow_links) + query = cls.generate_query( + client=client, + filters=self.filter, + space=space, + follow_links=follow_links, + with_reverse_properties=with_reverse_properties, + ) instances = client.query( query=query, size=size, diff --git a/fairgraph/node.py b/fairgraph/node.py index 79e090c2..0ec5f62d 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -190,16 +190,26 @@ def _check_validity(filters, property_names): msg = f"Invalid filter: " else: msg = f"Invalid filters: " - raise ValueError(msg + ", ".join(invalid_filters)) + raise ValueError(msg + ", ".join(sorted(invalid_filters))) if check_validity: - _check_validity(filter_dict_copy, cls.property_names) + _check_validity(filter_dict_copy, cls.all_property_names) for prop in cls.all_properties: if prop.name in filter_dict_copy: value = filter_dict_copy[prop.name] if isinstance(value, dict): - _check_validity(value, set(chain(*(child_cls.property_names for child_cls in prop.types)))) + _check_validity( + value, + set( + chain( + *( + child_cls.property_names + list(child_cls.aliases.keys()) + for child_cls in prop.types + ) + ) + ), + ) normalized[prop.name] = {} for child_cls in prop.types: normalized[prop.name].update(child_cls.normalize_filter(value, check_validity=False)) @@ -209,33 +219,65 @@ def _check_validity(filters, property_names): return normalized @classmethod - def generate_query_properties(cls, follow_links: Optional[Dict[str, Any]] = None): + def generate_query_properties( + cls, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False + ): """ Generate a list of QueryProperty instances for this class for use in constructing a KG query definition. Args: - follow_links (dict): The links in the graph to follow when constructing the query. Defaults to None. + follow_links (dict): The links in the graph to follow when constructing the query. + Defaults to None. + with_reverse_properties (bool): Whether to include reverse properties. + Defaults to False.` """ if issubclass(cls, RepresentsSingleObject): # KGObject - properties = [ + query_properties = [ QueryProperty("https://core.kg.ebrains.eu/vocab/meta/space", name="query:space"), QueryProperty("@type"), ] else: # EmbeddedMetadata - properties = [QueryProperty("@type")] + query_properties = [QueryProperty("@type")] reverse_aliases = invert_dict(cls.aliases) - for prop in cls.all_properties: + + if with_reverse_properties: + included_properties = cls.all_properties + else: + included_properties = cls.properties[:] # need to make a copy because we may be appending to it + if follow_links: + for prop_name in follow_links: + try: + prop = cls.get_property(prop_name) + # where a property can be of multiple types, + # not all types may be relevant to follow_links + except KeyError: + pass + else: + if prop.reverse: + included_properties.append(prop) + + for prop in included_properties: if prop.is_link and follow_links: if prop.name in follow_links: - properties.extend(get_query_properties(prop, cls.context, follow_links[prop.name])) + query_properties.extend( + get_query_properties(prop, cls.context, follow_links[prop.name], with_reverse_properties) + ) elif reverse_aliases.get(prop.name, None) in follow_links: - properties.extend(get_query_properties(prop, cls.context, follow_links[reverse_aliases[prop.name]])) + query_properties.extend( + get_query_properties( + prop, cls.context, follow_links[reverse_aliases[prop.name]], with_reverse_properties + ) + ) else: - properties.extend(get_query_properties(prop, cls.context)) + query_properties.extend( + get_query_properties(prop, cls.context, with_reverse_properties=with_reverse_properties) + ) else: - properties.extend(get_query_properties(prop, cls.context)) - return properties + query_properties.extend( + get_query_properties(prop, cls.context, with_reverse_properties=with_reverse_properties) + ) + return query_properties @classmethod def generate_query_filter_properties( diff --git a/fairgraph/openminds/core/products/model_version.py b/fairgraph/openminds/core/products/model_version.py index 4bc0d66a..be01c810 100644 --- a/fairgraph/openminds/core/products/model_version.py +++ b/fairgraph/openminds/core/products/model_version.py @@ -201,6 +201,7 @@ def __init__( ) def is_version_of(self, client): + # ??this method name shadows or overwrites the reverse property name "is_version_of" parents = Model.list(client, scope=self.scope, space=self.space, versions=self) if len(parents) == 0: raise ResolutionFailure("Unable to find parent") diff --git a/fairgraph/queries.py b/fairgraph/queries.py index c9822a9a..857ee335 100644 --- a/fairgraph/queries.py +++ b/fairgraph/queries.py @@ -294,7 +294,9 @@ def _get_query_property_name(property, possible_classes): return property_name -def get_query_properties(property, context, follow_links: Optional[Dict[str, Any]] = None) -> List[QueryProperty]: +def get_query_properties( + property, context, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False +) -> List[QueryProperty]: """ Generate one or more QueryProperty instances for this property, for use in constructing a KG query definition. @@ -318,11 +320,11 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any QueryProperty( expanded_path, name=property_name, - reverse=property.reverse, + reverse=bool(property.reverse), type_filter=type_filter, ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, - properties=cls.generate_query_properties(follow_links), + properties=cls.generate_query_properties(follow_links, with_reverse_properties), ) ) elif any(issubclass(_type, LinkedMetadata) for _type in property.types): @@ -340,11 +342,14 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any QueryProperty( expanded_path, name=property_name, - reverse=property.reverse, + reverse=bool(property.reverse), type_filter=type_filter, ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, - properties=[QueryProperty("@id"), *cls.generate_query_properties(follow_links)], + properties=[ + QueryProperty("@id"), + *cls.generate_query_properties(follow_links, with_reverse_properties), + ], ) ) else: @@ -354,7 +359,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any QueryProperty( expanded_path, name=property_name, - reverse=property.reverse, + reverse=bool(property.reverse), type_filter=None, ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, @@ -373,7 +378,7 @@ def get_query_properties(property, context, follow_links: Optional[Dict[str, Any QueryProperty( expanded_path, name=property.path, - reverse=property.reverse, + reverse=bool(property.reverse), ensure_order=property.multiple, expect_single=property.is_link and not property.multiple, ) diff --git a/fairgraph/registry.py b/fairgraph/registry.py index 036facc0..5d2b1cd1 100644 --- a/fairgraph/registry.py +++ b/fairgraph/registry.py @@ -77,6 +77,10 @@ def gen_path(type_): def all_properties(cls): return chain(cls.properties, cls.reverse_properties) + @property + def all_property_names(cls): + return [p.name for p in cls.all_properties] + @property def reverse_property_names(cls): return [p.name for p in cls.reverse_properties] diff --git a/test/test_openminds_computation.py b/test/test_openminds_computation.py index 5a2e7f22..dd3b0ebf 100644 --- a/test/test_openminds_computation.py +++ b/test/test_openminds_computation.py @@ -15,6 +15,7 @@ def test_generate_query(self, mock_client): "description": "bar", "software": SoftwareVersion(id="another_id"), }, + with_reverse_properties=True ) expected = { "@context": { diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index 4be99be5..c8c59816 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -25,7 +25,7 @@ def test_query_generation(mock_client): for cls in omcore.list_kg_classes(): - generated = cls.generate_query(space="collab-foobar", client=mock_client) + generated = cls.generate_query(space="collab-foobar", client=mock_client, with_reverse_properties=True) filename = f"test/test_data/queries/openminds/core/{cls.__name__.lower()}_simple_query.json" with open(filename, "r") as fp: expected = json.load(fp) @@ -164,7 +164,8 @@ def test_retrieve_released_models_follow_links(kg_client): api="query", size=5, from_index=randint(0, 80), - follow_links={"versions": {}, "developers": {"affiliation": {"member_of": {}}}, "abstraction_level": {}}, + follow_links={"versions": {}, "developers": {"affiliations": {"member_of": {}}}, "abstraction_level": {}}, + with_reverse_properties=True ) assert len(models) == 5 for model in models: @@ -193,6 +194,7 @@ def test_retrieve_released_model_versions_no_follow(kg_client): api=api, size=5, from_index=randint(0, 80), + with_reverse_properties=True ) for ver in versions: if ver.formats: @@ -225,6 +227,7 @@ def test_retrieve_released_model_versions_follow_reverse_links(kg_client): "developers": {"affiliation": {"member_of": {}}}, }, }, + with_reverse_properties=True ) for ver in versions: # check first level forward links have been resolved diff --git a/test/test_queries.py b/test/test_queries.py index b4e4eec9..ed8cc787 100644 --- a/test/test_queries.py +++ b/test/test_queries.py @@ -480,6 +480,7 @@ def test_openminds_core_queries(mock_client): space="collab-foobar", client=mock_client, follow_links=None, + with_reverse_properties=True ) with open(path_expected) as fp: expected = json.load(fp) @@ -506,6 +507,7 @@ def test_generate_query_with_follow_one_link(mock_client): "contact_information": {}, "digital_identifiers": {}, }, + with_reverse_properties=True ) with open(path_expected) as fp: expected = json.load(fp) @@ -527,6 +529,7 @@ def test_generate_query_with_follow_named_links(mock_client): client=mock_client, filters={"affiliations__member_of__has_parents__alias": "FZJ"}, follow_links={"affiliations": {"member_of": {"has_parents": {}}}, "contact_information": {}}, + with_reverse_properties=True ) with open(path_expected) as fp: expected = json.load(fp) From 52c49296bfe4285eedd124f4338e7f1e91d39c82 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 3 Nov 2025 10:42:51 +0100 Subject: [PATCH 24/25] Add openMINDS Python as a dependency to pyproject.toml and requirements.txt --- pyproject.toml | 1 + requirements.txt | 1 + 2 files changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 4626b53f..9da3fe3c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,7 @@ classifiers = [ keywords = ["ebrains", "hbp", "metadata", "electrophysiology", "knowledge-graph"] dependencies=[ "ebrains-kg-core", + "openminds", "python-dateutil", "tabulate", "requests" diff --git a/requirements.txt b/requirements.txt index 09fd6328..7d2404ea 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,5 @@ ebrains-kg-core +openminds @ git+https://github.com/apdavison/openMINDS_Python@custom python-dateutil tabulate requests From 39f9fcdf04cbf0c1c9e11c12f1785a193afb4397 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 3 Nov 2025 11:09:20 +0100 Subject: [PATCH 25/25] Update CI test matrix --- .github/workflows/tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d5c875cb..3b142f71 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -8,12 +8,12 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} - name: Install dependencies