From df44701c93f30a0721e2c60860da2b9f98b64653 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 3 Nov 2025 12:49:36 +0100 Subject: [PATCH 1/2] Rename "scope" to "release_status" and "model_scope" to "scope" --- README.md | 10 +-- .../additional_methods/DatasetVersion.py.txt | 2 +- builder/additional_methods/Person.py.txt | 2 +- .../ScholarlyArticle.py.txt | 2 +- builder/fairgraph_module_template.py.txt | 2 +- builder/update_openminds.py | 34 +++----- fairgraph/base.py | 2 +- fairgraph/client.py | 64 +++++++------- fairgraph/kgobject.py | 70 +++++++-------- fairgraph/kgproxy.py | 20 ++--- fairgraph/kgquery.py | 24 +++--- fairgraph/node.py | 25 +++--- .../openminds/chemicals/amount_of_chemical.py | 2 +- .../openminds/chemicals/chemical_mixture.py | 4 +- .../openminds/chemicals/chemical_substance.py | 4 +- .../openminds/chemicals/product_source.py | 4 +- .../openminds/computation/data_analysis.py | 4 +- fairgraph/openminds/computation/data_copy.py | 4 +- .../openminds/computation/environment.py | 4 +- .../computation/generic_computation.py | 4 +- .../openminds/computation/hardware_system.py | 4 +- .../computation/launch_configuration.py | 4 +- fairgraph/openminds/computation/local_file.py | 4 +- .../openminds/computation/model_validation.py | 4 +- .../openminds/computation/optimization.py | 4 +- fairgraph/openminds/computation/simulation.py | 4 +- .../openminds/computation/software_agent.py | 4 +- .../openminds/computation/validation_test.py | 8 +- .../computation/validation_test_version.py | 4 +- .../openminds/computation/visualization.py | 4 +- .../computation/workflow_execution.py | 12 ++- .../openminds/computation/workflow_recipe.py | 4 +- .../computation/workflow_recipe_version.py | 4 +- .../controlled_terms/action_status_type.py | 4 +- .../controlled_terms/age_category.py | 4 +- .../controlled_terms/analysis_technique.py | 4 +- .../anatomical_axes_orientation.py | 4 +- .../anatomical_identification_type.py | 4 +- .../controlled_terms/anatomical_plane.py | 4 +- .../annotation_criteria_type.py | 4 +- .../controlled_terms/annotation_type.py | 4 +- .../openminds/controlled_terms/atlas_type.py | 4 +- .../auditory_stimulus_type.py | 4 +- .../controlled_terms/biological_order.py | 4 +- .../controlled_terms/biological_process.py | 4 +- .../controlled_terms/biological_sex.py | 4 +- .../controlled_terms/breeding_type.py | 4 +- .../controlled_terms/cell_culture_type.py | 4 +- .../openminds/controlled_terms/cell_type.py | 4 +- .../controlled_terms/chemical_mixture_type.py | 4 +- .../openminds/controlled_terms/colormap.py | 4 +- .../controlled_terms/contribution_type.py | 4 +- .../cranial_window_construction_type.py | 4 +- .../cranial_window_reinforcement_type.py | 4 +- .../controlled_terms/criteria_quality_type.py | 4 +- .../openminds/controlled_terms/data_type.py | 4 +- .../openminds/controlled_terms/device_type.py | 4 +- .../controlled_terms/difference_measure.py | 4 +- .../openminds/controlled_terms/disease.py | 4 +- .../controlled_terms/disease_model.py | 4 +- .../controlled_terms/educational_level.py | 4 +- .../electrical_stimulus_type.py | 4 +- .../controlled_terms/ethics_assessment.py | 4 +- .../controlled_terms/experimental_approach.py | 4 +- .../controlled_terms/file_bundle_grouping.py | 4 +- .../controlled_terms/file_repository_type.py | 4 +- .../controlled_terms/file_usage_role.py | 4 +- .../controlled_terms/genetic_strain_type.py | 4 +- .../gustatory_stimulus_type.py | 4 +- .../openminds/controlled_terms/handedness.py | 4 +- .../openminds/controlled_terms/language.py | 4 +- .../openminds/controlled_terms/laterality.py | 4 +- .../learning_resource_type.py | 4 +- .../controlled_terms/measured_quantity.py | 4 +- .../controlled_terms/measured_signal_type.py | 4 +- .../controlled_terms/meta_data_model_type.py | 4 +- .../model_abstraction_level.py | 4 +- .../openminds/controlled_terms/model_scope.py | 8 +- .../controlled_terms/molecular_entity.py | 4 +- .../controlled_terms/mr_spatial_encoding.py | 4 +- .../controlled_terms/mri_pulse_sequence.py | 4 +- .../controlled_terms/mri_weighting.py | 4 +- .../olfactory_stimulus_type.py | 4 +- .../controlled_terms/operating_device.py | 4 +- .../controlled_terms/operating_system.py | 4 +- .../controlled_terms/optical_stimulus_type.py | 4 +- fairgraph/openminds/controlled_terms/organ.py | 4 +- .../controlled_terms/organism_substance.py | 4 +- .../controlled_terms/organism_system.py | 4 +- .../controlled_terms/patch_clamp_variation.py | 4 +- .../controlled_terms/preparation_type.py | 4 +- .../controlled_terms/product_accessibility.py | 4 +- .../controlled_terms/programming_language.py | 4 +- .../controlled_terms/qualitative_overlap.py | 4 +- .../controlled_terms/semantic_data_type.py | 4 +- .../openminds/controlled_terms/service.py | 4 +- .../openminds/controlled_terms/setup_type.py | 4 +- .../software_application_category.py | 4 +- .../controlled_terms/software_feature.py | 4 +- .../openminds/controlled_terms/species.py | 4 +- .../controlled_terms/stimulation_approach.py | 4 +- .../controlled_terms/stimulation_technique.py | 4 +- .../controlled_terms/subcellular_entity.py | 4 +- .../controlled_terms/subject_attribute.py | 4 +- .../controlled_terms/tactile_stimulus_type.py | 4 +- .../openminds/controlled_terms/technique.py | 4 +- .../controlled_terms/term_suggestion.py | 4 +- .../openminds/controlled_terms/terminology.py | 4 +- .../tissue_sample_attribute.py | 4 +- .../controlled_terms/tissue_sample_type.py | 4 +- .../controlled_terms/type_of_uncertainty.py | 4 +- .../controlled_terms/uberon_parcellation.py | 4 +- .../controlled_terms/unit_of_measurement.py | 4 +- .../controlled_terms/visual_stimulus_type.py | 4 +- .../core/actors/account_information.py | 6 +- .../openminds/core/actors/affiliation.py | 4 +- fairgraph/openminds/core/actors/consortium.py | 4 +- .../core/actors/contact_information.py | 6 +- .../openminds/core/actors/contribution.py | 2 +- .../openminds/core/actors/organization.py | 4 +- fairgraph/openminds/core/actors/person.py | 6 +- fairgraph/openminds/core/data/content_type.py | 4 +- .../core/data/content_type_pattern.py | 4 +- fairgraph/openminds/core/data/copyright.py | 2 +- fairgraph/openminds/core/data/file.py | 4 +- fairgraph/openminds/core/data/file_archive.py | 4 +- fairgraph/openminds/core/data/file_bundle.py | 4 +- .../openminds/core/data/file_path_pattern.py | 2 +- .../openminds/core/data/file_repository.py | 4 +- .../core/data/file_repository_structure.py | 11 ++- fairgraph/openminds/core/data/hash.py | 2 +- fairgraph/openminds/core/data/license.py | 4 +- fairgraph/openminds/core/data/measurement.py | 2 +- fairgraph/openminds/core/data/service_link.py | 4 +- .../openminds/core/digital_identifier/doi.py | 4 +- .../core/digital_identifier/gridid.py | 10 ++- .../core/digital_identifier/handle.py | 10 ++- .../identifiers_dot_org_id.py | 10 ++- .../openminds/core/digital_identifier/isbn.py | 4 +- .../openminds/core/digital_identifier/issn.py | 6 +- .../core/digital_identifier/orcid.py | 10 ++- .../core/digital_identifier/rorid.py | 10 ++- .../openminds/core/digital_identifier/rrid.py | 10 ++- .../core/digital_identifier/stock_number.py | 2 +- .../core/digital_identifier/swhid.py | 10 ++- .../openminds/core/miscellaneous/comment.py | 12 ++- .../openminds/core/miscellaneous/funding.py | 4 +- .../core/miscellaneous/quantitative_value.py | 2 +- .../miscellaneous/quantitative_value_array.py | 4 +- .../miscellaneous/quantitative_value_range.py | 2 +- .../miscellaneous/research_product_group.py | 4 +- .../core/miscellaneous/web_resource.py | 4 +- fairgraph/openminds/core/products/dataset.py | 4 +- .../core/products/dataset_version.py | 6 +- .../core/products/meta_data_model.py | 4 +- .../core/products/meta_data_model_version.py | 4 +- fairgraph/openminds/core/products/model.py | 8 +- .../openminds/core/products/model_version.py | 4 +- fairgraph/openminds/core/products/project.py | 4 +- fairgraph/openminds/core/products/setup.py | 4 +- fairgraph/openminds/core/products/software.py | 4 +- .../core/products/software_version.py | 4 +- .../openminds/core/products/web_service.py | 4 +- .../core/products/web_service_version.py | 4 +- .../core/research/behavioral_protocol.py | 4 +- .../openminds/core/research/configuration.py | 4 +- .../core/research/custom_property_set.py | 2 +- .../core/research/numerical_property.py | 2 +- .../core/research/property_value_list.py | 4 +- fairgraph/openminds/core/research/protocol.py | 4 +- .../core/research/protocol_execution.py | 4 +- fairgraph/openminds/core/research/strain.py | 4 +- .../core/research/string_property.py | 2 +- fairgraph/openminds/core/research/subject.py | 4 +- .../openminds/core/research/subject_group.py | 4 +- .../core/research/subject_group_state.py | 4 +- .../openminds/core/research/subject_state.py | 4 +- .../openminds/core/research/tissue_sample.py | 4 +- .../core/research/tissue_sample_collection.py | 4 +- .../tissue_sample_collection_state.py | 4 +- .../core/research/tissue_sample_state.py | 4 +- .../openminds/ephys/activity/cell_patching.py | 4 +- .../ephys/activity/electrode_placement.py | 4 +- .../ephys/activity/recording_activity.py | 4 +- fairgraph/openminds/ephys/device/electrode.py | 4 +- .../openminds/ephys/device/electrode_array.py | 4 +- .../ephys/device/electrode_array_usage.py | 4 +- .../openminds/ephys/device/electrode_usage.py | 4 +- fairgraph/openminds/ephys/device/pipette.py | 4 +- .../openminds/ephys/device/pipette_usage.py | 4 +- fairgraph/openminds/ephys/entity/channel.py | 2 +- fairgraph/openminds/ephys/entity/recording.py | 4 +- fairgraph/openminds/publications/book.py | 4 +- fairgraph/openminds/publications/chapter.py | 4 +- .../publications/learning_resource.py | 4 +- .../openminds/publications/live_paper.py | 4 +- .../publications/live_paper_resource_item.py | 4 +- .../publications/live_paper_section.py | 4 +- .../publications/live_paper_version.py | 4 +- .../openminds/publications/periodical.py | 4 +- .../publications/publication_issue.py | 6 +- .../publications/publication_volume.py | 4 +- .../publications/scholarly_article.py | 8 +- .../openminds/sands/atlas/atlas_annotation.py | 2 +- .../openminds/sands/atlas/brain_atlas.py | 4 +- .../sands/atlas/brain_atlas_version.py | 4 +- .../sands/atlas/common_coordinate_space.py | 4 +- .../atlas/common_coordinate_space_version.py | 4 +- .../sands/atlas/parcellation_entity.py | 4 +- .../atlas/parcellation_entity_version.py | 4 +- .../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 | 9 +- .../quantitative_relation_assessment.py | 9 +- .../sands/miscellaneous/single_color.py | 4 +- .../miscellaneous/viewer_specification.py | 2 +- .../non_atlas/custom_anatomical_entity.py | 4 +- .../sands/non_atlas/custom_annotation.py | 2 +- .../non_atlas/custom_coordinate_space.py | 4 +- .../activity/cranial_window_preparation.py | 4 +- .../activity/tissue_culture_preparation.py | 4 +- .../activity/tissue_sample_slicing.py | 4 +- .../specimen_prep/device/slicing_device.py | 4 +- .../device/slicing_device_usage.py | 4 +- .../activity/stimulation_activity.py | 4 +- .../stimulation/stimulus/ephys_stimulus.py | 4 +- fairgraph/registry.py | 2 +- test/test_base.py | 2 +- test/test_client.py | 8 +- .../openminds/core/model_vf_query.json | 4 +- test/test_openminds_core.py | 86 +++++++++---------- test/utils.py | 4 +- 237 files changed, 686 insertions(+), 610 deletions(-) diff --git a/README.md b/README.md index 2d4242de..442ffdbb 100644 --- a/README.md +++ b/README.md @@ -80,28 +80,28 @@ Using these classes, it is possible to list all metadata matching a particular c ``` ``` ->>> datasets = DatasetVersion.list(client, techniques=whole_cell_patch, scope="in progress") +>>> datasets = DatasetVersion.list(client, techniques=whole_cell_patch, release_status="in progress") ``` For research products that are versioned, such as datasets, models, and software, certain attributes may be inherited from the parent (e.g. a DatasetVersion generally inherits its name from a Dataset). In this case, we have a convenience method to retrieve the parent's name: ``` ->>> print(datasets[0].get_name(client, scope="in progress")) +>>> print(datasets[0].get_name(client, release_status="in progress")) 'Cholinergic interneurons in the striatum - Single cell patch clamp recordings' ``` If you know the unique identifier of an object, you can retrieve it directly: ``` ->>> dataset = DatasetVersion.from_id("17196b79-04db-4ea4-bb69-d20aab6f1d62", client, scope="in progress") +>>> dataset = DatasetVersion.from_id("17196b79-04db-4ea4-bb69-d20aab6f1d62", client, release_status="in progress") ``` Links between metadata in the Knowledge Graph are not followed automatically, to avoid unnecessary network traffic, but can be followed with the `resolve()` method: ``` ->>> license = dataset.license.resolve(client, scope="in progress") ->>> authors = [author.resolve(client, scope="in progress") for author in dataset.authors] +>>> license = dataset.license.resolve(client, release_status="in progress") +>>> authors = [author.resolve(client, release_status="in progress") for author in dataset.authors] ``` The associated metadata is accessible as attributes of the Python objects, e.g.: diff --git a/builder/additional_methods/DatasetVersion.py.txt b/builder/additional_methods/DatasetVersion.py.txt index 73fcafc6..e96f796a 100644 --- a/builder/additional_methods/DatasetVersion.py.txt +++ b/builder/additional_methods/DatasetVersion.py.txt @@ -1,6 +1,6 @@ def download(self, local_path, client, accept_terms_of_use=False): if accepted_terms_of_use(client, accept_terms_of_use=accept_terms_of_use): - repo = self.repository.resolve(client, scope=self.scope or None) + repo = self.repository.resolve(client, release_status=self.release_status or None) if (repo.iri.value.startswith("https://object.cscs.ch/v1/AUTH") or repo.iri.value.startswith("https://data-proxy.ebrains.eu/api/v1/public") ): diff --git a/builder/additional_methods/Person.py.txt b/builder/additional_methods/Person.py.txt index 9a4ad145..8dc1fd08 100644 --- a/builder/additional_methods/Person.py.txt +++ b/builder/additional_methods/Person.py.txt @@ -6,7 +6,7 @@ def me(cls, client, allow_multiple=False, follow_links=None): user_info = client.user_info() possible_matches = cls.list( - client, scope="in progress", space="common", + client, release_status="in progress", space="common", follow_links=follow_links, family_name=user_info.family_name, given_name=user_info.given_name diff --git a/builder/additional_methods/ScholarlyArticle.py.txt b/builder/additional_methods/ScholarlyArticle.py.txt index 96aaa636..466029b8 100644 --- a/builder/additional_methods/ScholarlyArticle.py.txt +++ b/builder/additional_methods/ScholarlyArticle.py.txt @@ -1,7 +1,7 @@ def get_journal(self, client, with_volume=False, with_issue=False): journal = volume = issue = None if self.is_part_of: - issue_or_volume = self.is_part_of.resolve(client, scope=self.scope, follow_links={"is_part_of": {}}) + issue_or_volume = self.is_part_of.resolve(client, release_status=self.release_status, follow_links={"is_part_of": {}}) if isinstance(issue_or_volume, PublicationIssue): volume = issue_or_volume.is_part_of issue = issue_or_volume diff --git a/builder/fairgraph_module_template.py.txt b/builder/fairgraph_module_template.py.txt index 7b7e9335..c15c43ba 100644 --- a/builder/fairgraph_module_template.py.txt +++ b/builder/fairgraph_module_template.py.txt @@ -46,6 +46,6 @@ class {{ class_name }}({{base_class}}, OM{{ class_name }}): existence_query_properties = {{ existence_query_properties }} {%- endif %} - def __init__(self {%- for arg in constructor_arguments -%}, {{arg}}=None{%- endfor -%}, id=None, data=None, space=None, scope=None): + def __init__(self {%- for arg in constructor_arguments -%}, {{arg}}=None{%- endfor -%}, id=None, data=None, space=None, release_status=None): 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 192dc44f..ed9bc929 100644 --- a/builder/update_openminds.py +++ b/builder/update_openminds.py @@ -13,13 +13,6 @@ OPENMINDS_VERSION = "latest" -name_map = { - "scope": "model_scope", # this is because 'scope' is already a keyword - # we could rename the 'scope' keyword to 'stage' - # but we would have the same problem, as there is - # a property named 'stage' - # Suggested resolution: rename the property "scope" in openMINDS to "hasScope" -} global_aliases = { "short_name": "alias", @@ -235,20 +228,17 @@ } def generate_python_name(json_name): - if json_name in name_map: - python_name = name_map[json_name] - else: - python_name = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", json_name.strip()) - python_name = re.sub("([a-z0-9])([A-Z])", r"\1_\2", python_name).lower() - replacements = [ - ("-", "_"), (".", "_"), ("+", "plus"), ("#", "sharp"), (",", "comma"), ("(", ""), (")", "") - ] - for before, after in replacements: - python_name = python_name.replace(before, after) - if python_name[0] in number_names: # Python variables can't start with a number - python_name = number_names[python_name[0]] + python_name[1:] - if not python_name.isidentifier(): - raise NameError(f"Cannot generate a valid Python name from '{json_name}'") + python_name = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", json_name.strip()) + python_name = re.sub("([a-z0-9])([A-Z])", r"\1_\2", python_name).lower() + replacements = [ + ("-", "_"), (".", "_"), ("+", "plus"), ("#", "sharp"), (",", "comma"), ("(", ""), (")", "") + ] + for before, after in replacements: + python_name = python_name.replace(before, after) + if python_name[0] in number_names: # Python variables can't start with a number + python_name = number_names[python_name[0]] + python_name[1:] + if not python_name.isidentifier(): + raise NameError(f"Cannot generate a valid Python name from '{json_name}'") return python_name @@ -665,7 +655,7 @@ def get_type(prop): else: base_class = "KGObject" default_space = get_default_space(module_name, class_name) - standard_init_properties = "id=id, space=space, scope=scope, " + standard_init_properties = "id=id, space=space, release_status=release_status, " properties = [] plurals_special_cases = { # because this is a single item (PropertyValueList), but that item contains a list diff --git a/fairgraph/base.py b/fairgraph/base.py index 0559fb64..658155ab 100644 --- a/fairgraph/base.py +++ b/fairgraph/base.py @@ -56,7 +56,7 @@ class Resolvable: # all def resolve( self, client: KGClient, - scope: Optional[str] = None, + release_status: Optional[str] = None, use_cache: bool = True, follow_links: Optional[Dict[str, Any]] = None, ): diff --git a/fairgraph/client.py b/fairgraph/client.py index 971a903c..e5b02972 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -197,7 +197,7 @@ def migrated(self): 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") + result = self.instance_from_full_uri("https://kg.ebrains.eu/api/instances/92631f2e-fc6e-4122-8015-a0731c67f66c", release_status="released") if "om-i.org" in result["@type"]: self._migrated = True else: @@ -211,7 +211,7 @@ def query( instance_id: Optional[str] = None, from_index: int = 0, size: int = 100, - scope: str = "released", + release_status: str = "released", id_key: str = "@id", use_stored_query: bool = False, restrict_to_spaces: Optional[List[str]] = None @@ -226,7 +226,7 @@ def query( instance_id (Optional[URI]): The URI of a specific KG instance to retrieve. from_index (int): The index of the first result to return (0-based). size (int): The maximum number of results to return. - scope (str): The scope of the query. Valid values are "released", "in progress", or "any". Default is "released". + release_status (str): The scope of the query. Valid values are "released", "in progress", or "any". Default is "released". id_key (str): The key that identifies the ID of a JSON-LD document. Default is "@id". use_stored_query (bool): Whether to use a stored query with the given query_id instead of a dynamic query. Default is False. @@ -239,16 +239,16 @@ def query( if use_stored_query: - def _query(scope, from_index, size): + def _query(release_status, from_index, size): response = self._kg_client.queries.execute_query_by_id( query_id=self.uuid_from_uri(query_id), additional_request_params=filter or {}, - stage=STAGE_MAP[scope], + stage=STAGE_MAP[release_status], pagination=Pagination(start=from_index, size=size), instance_id=instance_id, restrict_to_spaces=restrict_to_spaces ) - error_context = f"_query(scope={scope} query_id={query_id} filter={filter} instance_id={instance_id} size={size} from_index={from_index})" + error_context = f"_query(release_status={release_status} query_id={query_id} filter={filter} instance_id={instance_id} size={size} from_index={from_index})" return self._check_response( response, error_context=error_context, expected_instance_id=instance_id, ignore_not_found=True ) @@ -257,21 +257,21 @@ def _query(scope, from_index, size): if self.migrated is False: query = adapt_namespaces_for_query(query) - def _query(scope, from_index, size): + def _query(release_status, from_index, size): response = self._kg_client.queries.test_query( query, additional_request_params=filter or {}, - stage=STAGE_MAP[scope], + stage=STAGE_MAP[release_status], pagination=Pagination(start=from_index, size=size), instance_id=instance_id, restrict_to_spaces=restrict_to_spaces ) - error_context = f"_query(scope={scope} query_id={query_id} filter={filter} instance_id={instance_id} size={size} from_index={from_index})" + error_context = f"_query(release_status={release_status} query_id={query_id} filter={filter} instance_id={instance_id} size={size} from_index={from_index})" return self._check_response( response, error_context=error_context, expected_instance_id=instance_id, ignore_not_found=True ) - if scope == "any": + if release_status == "any": # the following implementation is simple but very inefficient # because we retrieve _all_ instances and then apply the limits # from_index and size. @@ -291,7 +291,7 @@ def _query(scope, from_index, size): response.size = len(response.data) response.total = len(instances) else: - response = _query(scope, from_index, size) + response = _query(release_status, from_index, size) return response def list( @@ -300,7 +300,7 @@ def list( space: Optional[str] = None, from_index: int = 0, size: int = 100, - scope: str = "released", + release_status: str = "released", ) -> ResultPage[JsonLdDocument]: """ List KG instances of a given type. @@ -310,7 +310,7 @@ def list( space: If specified, restricts the search to the given space. from_index: The index of the first result to include in the response. size: The maximum number of results to include in the response. - scope: The scope of instances to include in the response. Valid values are + release_status: The scope of instances to include in the response. Valid values are 'released', 'in progress', 'any'. If 'any' is specified, all accessible instances are included in the response, but this may be slow where there are large numbers of instances. @@ -322,20 +322,20 @@ def list( if self.migrated is False: target_type = adapt_type_4to3(target_type) - def _list(scope, from_index, size): + def _list(release_status, from_index, size): response = self._kg_client.instances.list( - stage=STAGE_MAP[scope], + stage=STAGE_MAP[release_status], target_type=target_type, space=space, response_configuration=default_response_configuration, pagination=Pagination(start=from_index, size=size), ) error_context = ( - f"_list(scope={scope} space={space} target_type={target_type} size={size} from_index={from_index})" + f"_list(release_status={release_status} space={space} target_type={target_type} size={size} from_index={from_index})" ) return self._check_response(response, error_context=error_context) - if scope == "any": + if release_status == "any": # see comments in query() about this implementation instances = {} # first we get the released instances @@ -352,13 +352,13 @@ def _list(scope, from_index, size): response.total = len(instances) return response else: - return _list(scope, from_index, size) + return _list(release_status, from_index, size) def instance_from_full_uri( self, uri: str, use_cache: bool = True, - scope: str = "released", + release_status: str = "released", require_full_data: bool = True, ) -> JsonLdDocument: """ @@ -367,7 +367,7 @@ def instance_from_full_uri( Args: uri: The global identifier of the instance use_cache: whether to use cached data if they exist. Defaults to True. - scope: The scope of instances to include in the response. + release_status: The release_status of instances to include in the response. Valid values are 'released', 'in progress', 'any'. require_full_data: Whether to only return instances for which the user has full read access. """ @@ -377,8 +377,8 @@ def instance_from_full_uri( logger.debug("Retrieving instance {} from cache".format(uri)) data = self.cache[uri] else: - def _get_instance(scope): - error_context = f"_get_instance(scope={scope} uri={uri})" + def _get_instance(release_status): + error_context = f"_get_instance(release_status={release_status} uri={uri})" # 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) @@ -387,7 +387,7 @@ def _get_instance(scope): 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], + stage=STAGE_MAP[release_status], instance_id=self.uuid_from_uri(uri), extended_response_configuration=default_response_configuration, ) @@ -405,7 +405,7 @@ def _get_instance(scope): else: payload = [uri] response = self._kg_client.instances.get_by_identifiers( - stage=STAGE_MAP[scope], + stage=STAGE_MAP[release_status], payload=payload, extended_response_configuration=default_response_configuration, ) @@ -421,14 +421,14 @@ def _get_instance(scope): data = None return data - if scope == "any": + if release_status == "any": data_ip = _get_instance("in progress") data_rel = _get_instance("released") data = data_rel or data_ip if data_ip is not None: data.update(data_ip) else: - data = _get_instance(scope) + data = _get_instance(release_status) if data: self.cache[uri] = data @@ -706,7 +706,7 @@ def move_to_space(self, uri: str, destination_space: str): if response.error: raise Exception(response.error) - def space_info(self, space_name: str, scope: str = "released", ignore_errors: bool = False): + def space_info(self, space_name: str, release_status: str = "released", ignore_errors: bool = False): """ Return information about the types and number of instances in a space. @@ -714,7 +714,7 @@ def space_info(self, space_name: str, scope: str = "released", ignore_errors: bo 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]) + result = self._kg_client.types.list(space=space_name, stage=STAGE_MAP[release_status]) if result.error: raise Exception(result.error) response = {} @@ -745,7 +745,7 @@ def clean_space(self, space_name): """Delete all instances from a given space.""" # todo: check for released instances, they must be unreleased # before deletion. - space_info = self.space_info(space_name, scope="in progress", ignore_errors=True) + space_info = self.space_info(space_name, release_status="in progress", ignore_errors=True) if sum(space_info.values()) > 0: print(f"The space '{space_name}' contains the following instances:\n") for cls, count in space_info.items(): @@ -757,7 +757,7 @@ 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="") - response = self.list(cls.type_, scope="in progress", space=space_name) + response = self.list(cls.type_, release_status="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 @@ -772,7 +772,7 @@ def move_all_to_space(self, source_space: str, destination_space: str): Move all the KG instances in one space to another. """ assert source_space != destination_space - space_info = self.space_info(source_space, scope="in progress") + space_info = self.space_info(source_space, release_status="in progress") if sum(space_info.values()) > 0: print(f"The space '{source_space}' contains the following instances:\n") for cls, count in space_info.items(): @@ -784,7 +784,7 @@ def move_all_to_space(self, source_space: str, destination_space: str): for cls, count in space_info.items(): if count > 0 and hasattr(cls, "list"): # exclude embedded metadata instances print(f"Moving {cls.__name__} instances", end="") - instances = cls.list(self, scope="in progress", space=source_space) + instances = cls.list(self, release_status="in progress", space=source_space) assert len(instances) <= count for instance in instances: assert instance.space == source_space diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index e4c9a47a..cc60a4f5 100644 --- a/fairgraph/kgobject.py +++ b/fairgraph/kgobject.py @@ -72,12 +72,12 @@ def __init__( id: Optional[str] = None, data: Optional[JSONdict] = None, space: Optional[str] = None, - scope: Optional[str] = None, + release_status: Optional[str] = None, **properties, ): self.id = id self._space = space - self.scope = scope + self.release_status = release_status self.allow_update = True super().__init__(data=data, **properties) for prop in self.reverse_properties: @@ -106,10 +106,10 @@ def space(self) -> Union[str, None]: return self._space @classmethod - def from_jsonld(cls, data: JSONdict, scope: Optional[str] = None) -> KGObject: + def from_jsonld(cls, data: JSONdict, release_status: Optional[str] = None) -> KGObject: """Create an instance of the class from a JSON-LD document.""" deserialized_data = cls._deserialize_data(data, include_id=True) - return cls(id=data["@id"], data=data, scope=scope, **deserialized_data) + return cls(id=data["@id"], data=data, release_status=release_status, **deserialized_data) # @classmethod # def _fix_keys(cls, data): @@ -136,7 +136,7 @@ def from_uri( uri: str, client: KGClient, use_cache: bool = True, - scope: str = "released", + release_status: str = "released", follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, ): @@ -146,7 +146,7 @@ def from_uri( Args: uri (str): long-form identifier for the KG instance (a full URI) client: a KGClient - scope (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". + release_status (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". 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. @@ -160,17 +160,17 @@ def from_uri( 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 + results = client.query(query, instance_id=client.uuid_from_uri(uri), size=1, release_status=release_status).data if results: data = results[0] else: data = None else: - data = client.instance_from_full_uri(uri, use_cache=use_cache, scope=scope) + data = client.instance_from_full_uri(uri, use_cache=use_cache, release_status=release_status) if data is None: return None else: - return cls.from_jsonld(data, scope=scope) + return cls.from_jsonld(data, release_status=release_status) @classmethod def from_uuid( @@ -178,7 +178,7 @@ def from_uuid( uuid: str, client: KGClient, use_cache: bool = True, - scope: str = "released", + release_status: str = "released", follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, ): @@ -188,7 +188,7 @@ def from_uuid( Args: uuid (str): short-form identifier for the KG instance (a UUID). client: a KGClient - scope (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". + release_status (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". 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. @@ -207,7 +207,7 @@ def from_uuid( uri, client, use_cache=use_cache, - scope=scope, + release_status=release_status, follow_links=follow_links, with_reverse_properties=with_reverse_properties, ) @@ -218,7 +218,7 @@ def from_id( id: str, client: KGClient, use_cache: bool = True, - scope: str = "released", + release_status: str = "released", follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, ): @@ -228,7 +228,7 @@ def from_id( Args: id (str): short-form (UUID) or long-form (URI) identifier for the KG instance. client: a KGClient - scope (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". + release_status (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". 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. @@ -248,7 +248,7 @@ def from_id( id, client, use_cache=use_cache, - scope=scope, + release_status=release_status, follow_links=follow_links, with_reverse_properties=with_reverse_properties, ) @@ -260,13 +260,13 @@ def from_id( uri = client.uri_from_uuid(id) if follow_links is not None: raise NotImplementedError - data = client.instance_from_full_uri(uri, use_cache=use_cache, scope=scope) + data = client.instance_from_full_uri(uri, use_cache=use_cache, release_status=release_status) type_ = data["@type"] if isinstance(type_, list): assert len(type_) == 1 type_ = type_[0] cls_from_data = lookup_type(type_, OPENMINDS_VERSION) - return cls_from_data.from_jsonld(data, scope=scope) + return cls_from_data.from_jsonld(data, release_status=release_status) @classmethod def from_alias( @@ -274,7 +274,7 @@ def from_alias( alias: str, client: KGClient, space: Optional[str] = None, - scope: str = "released", + release_status: str = "released", follow_links: Optional[Dict[str, Any]] = None, ): """ @@ -286,7 +286,7 @@ def from_alias( alias (str): a short name used to identify a KG instance. client: a KGClient space (str, optional): the KG space to look in. Default is to look in all available spaces. - scope (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". + release_status (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". Defaults to "released". follow_links (dict): The links in the graph to follow. Defaults to None. @@ -302,7 +302,7 @@ def from_alias( size=20, from_index=0, api="query", - scope=scope, + release_status=release_status, space=space, alias=alias, follow_links=follow_links, @@ -341,7 +341,7 @@ def list( size: int = 100, from_index: int = 0, api: str = "auto", - scope: str = "released", + release_status: str = "released", space: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, @@ -355,7 +355,7 @@ def list( size (int, optional): The maximum number of instances to return. Default is 100. from_index (int, optional): The index of the first instance to return. Default is 0. api (str): The KG API to use for the query. Can be 'query', 'core', or 'auto'. Default is 'auto'. - scope (str, optional): The scope to use for the query. Can be 'released', 'in progress', or 'all'. Default is 'released'. + release_status (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. @@ -400,24 +400,24 @@ def list( query=query, from_index=from_index, size=size, - scope=scope, + release_status=release_status, ).data elif api == "core": if filters: raise ValueError("Cannot use filters with api='core'") if follow_links: raise NotImplementedError("Following links with api='core' not yet implemented") - instances = client.list(cls.type_, space=space, from_index=from_index, size=size, scope=scope).data + instances = client.list(cls.type_, space=space, from_index=from_index, size=size, release_status=release_status).data else: raise ValueError("'api' must be either 'query', 'core', or 'auto'") - return [cls.from_jsonld(data=instance, scope=scope) for instance in instances] + return [cls.from_jsonld(data=instance, release_status=release_status) for instance in instances] @classmethod def count( cls, client: KGClient, api: str = "auto", - scope: str = "released", + release_status: str = "released", space: Optional[str] = None, **filters, ) -> int: @@ -427,7 +427,7 @@ def count( Args: client: KGClient object that handles the communication with the KG. api (str): The KG API to use for the query. Can be 'query', 'core', or 'auto'. Default is 'auto'. - scope (str, optional): The scope to use for the query. Can be 'released', 'in progress', or 'all'. Default is 'released'. + release_status (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 counted. filters: Optional keyword arguments representing filters to apply to the query. @@ -454,11 +454,11 @@ def count( api = "core" if api == "query": query = cls.generate_query(space=space, client=client, filters=filters) - response = client.query(query=query, from_index=0, size=1, scope=scope) + response = client.query(query=query, from_index=0, size=1, release_status=release_status) elif api == "core": if filters: raise ValueError("Cannot use filters with api='core'") - response = client.list(cls.type_, space=space, scope=scope, from_index=0, size=1) + response = client.list(cls.type_, space=space, release_status=release_status, from_index=0, size=1) return response.total def _update_empty_properties(self, data: JSONdict): @@ -522,7 +522,7 @@ def exists( # Since the KG now allows user-specified IDs we can't assume that the presence of # an id means the object exists data = client.instance_from_full_uri( - self.id, use_cache=True, scope=self.scope or "any", require_full_data=False + self.id, use_cache=True, release_status=self.release_status or "any", require_full_data=False ) if self._raw_remote_data is None: self._raw_remote_data = data @@ -559,7 +559,7 @@ def exists( filters=query_filter, ) - instances = client.query(query=query, size=2, scope="any", restrict_to_spaces=in_spaces).data + instances = client.query(query=query, size=2, release_status="any", restrict_to_spaces=in_spaces).data if instances: if len(instances) > 1 and not ignore_duplicates: @@ -568,7 +568,7 @@ def exists( # it seems that sometimes the "query" endpoint returns instances # which the "instances" endpoint doesn't know about, so here we double check that # the instance can be found - instance = client.instance_from_full_uri(instances[0]["@id"], scope="any") + instance = client.instance_from_full_uri(instances[0]["@id"], release_status="any") if instance is None: return False @@ -791,7 +791,7 @@ def by_name( match: str = "equals", all: bool = False, space: Optional[str] = None, - scope: str = "released", + release_status: str = "released", follow_links: Optional[Dict[str, Any]] = None, ) -> Union[KGObject, List[KGObject], None]: """ @@ -805,7 +805,7 @@ def by_name( match (str, optional): either "equals" (exact match - default) or "contains". all (bool, optional): Whether to return all objects that match the name, or only the first. Defaults to False. space (str, optional): the KG space to search in. Default is to search in all available spaces. - scope (str, optional): The scope of the search. Valid values are "released", "in progress", or "any". + release_status (str, optional): The scope of the search. Valid values are "released", "in progress", or "any". Defaults to "released". follow_links (dict): The links in the graph to follow. Defaults to None. @@ -813,7 +813,7 @@ def by_name( # todo: move this to openminds generation, and include only in those subclasses # that have a name # todo: also count 'lookup_name', "family_name", "given_name" as a name - objects = cls.list(client, space=space, scope=scope, api="query", name=name, follow_links=follow_links) + objects = cls.list(client, space=space, release_status=release_status, api="query", name=name, follow_links=follow_links) if match == "equals": objects = [obj for obj in objects if hasattr(obj, "name") and obj.name == name] if len(objects) == 0: diff --git a/fairgraph/kgproxy.py b/fairgraph/kgproxy.py index d7a711bd..1c76c8b0 100644 --- a/fairgraph/kgproxy.py +++ b/fairgraph/kgproxy.py @@ -46,7 +46,7 @@ class KGProxy(RepresentsSingleObject, Link): 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. + preferred_release_status (str, optional): The preferred scope used to resolve the proxy. Valid values are "released", "in progress", or "any". Example: @@ -65,7 +65,7 @@ def __init__( self, classes: Union[str, KGObject, List[KGObject], Tuple[KGObject]], uri: str, - preferred_scope: str = "released" + preferred_release_status: str = "released" ): self.classes: List[KGObject] # todo: make this a set? if isinstance(classes, str): @@ -80,7 +80,7 @@ def __init__( if TYPE_CHECKING: assert all(isinstance(cls, KGObject) for cls in self.classes) self.id = uri - self.preferred_scope = preferred_scope + self.preferred_release_status = preferred_release_status self.remote_data = None Link.__init__(self, self.id, allowed_types=self.classes) @@ -112,7 +112,7 @@ def to_jsonld(self, **kwargs): def resolve( self, client: KGClient, - scope: Optional[str] = None, + release_status: Optional[str] = None, use_cache: bool = True, follow_links: Optional[Dict[str, Any]] = None, ): @@ -121,8 +121,8 @@ def resolve( Args: client: a KGClient - scope (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". - If not provided, the "preferred_scope" provided when creating the proxy object will be used. + release_status (str, optional): The scope of the lookup. Valid values are "released", "in progress", or "any". + If not provided, the "preferred_release_status" 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. @@ -132,12 +132,12 @@ def resolve( if use_cache and self.id in object_cache: obj = object_cache[self.id] else: - scope = scope or self.preferred_scope + release_status = release_status or self.preferred_release_status 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) + obj = cls.from_uri(self.id, client, release_status=release_status) except TypeError: pass else: @@ -146,7 +146,7 @@ def resolve( 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) + return obj.resolve(client, release_status=release_status, use_cache=use_cache, follow_links=follow_links) else: return obj @@ -170,7 +170,7 @@ def uuid(self) -> str: def delete(self, client: KGClient, ignore_not_found: bool = True): """Delete the instance which this proxy represents""" try: - obj = self.resolve(client, scope="in progress") + obj = self.resolve(client, release_status="in progress") except ResolutionFailure as err: logger.warning(str(err)) obj = None diff --git a/fairgraph/kgquery.py b/fairgraph/kgquery.py index 4be12e4c..0ba2513a 100644 --- a/fairgraph/kgquery.py +++ b/fairgraph/kgquery.py @@ -45,7 +45,7 @@ class KGQuery(Resolvable, SupportsQuerying): Args: classes (list of KGObject subclasses): a list of types to query. filter (dict): key:value pairs that should be matched. All pairs must match. - preferred_scope (str): The preferred scope used to resolve the query. + preferred_release_status (str): The preferred scope used to resolve the query. Valid values are "released", "in progress", or "any". Example: @@ -63,7 +63,7 @@ def __init__( self, classes: Union[str, KGObject, List[Union[str, KGObject]]], filter: Dict[str, str], - preferred_scope: str = "released", + preferred_release_status: str = "released", ): self.classes: List[KGObject] = [] for cls in as_list(classes): @@ -74,7 +74,7 @@ def __init__( else: self.classes.append(cls) self.filter = filter - self.preferred_scope = preferred_scope + self.preferred_release_status = preferred_release_status def __repr__(self): return "{self.__class__.__name__}(" "{self.classes!r}, {self.filter!r})".format(self=self) @@ -85,7 +85,7 @@ def resolve( size: int = 10000, from_index: int = 0, space: Optional[str] = None, - scope: Optional[str] = None, + release_status: Optional[str] = None, use_cache: bool = True, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, @@ -98,8 +98,8 @@ def resolve( from_index: The index of the first result to include in the response. size: The maximum number of results to include in the response. space: If specified, queries only in the given space. - scope (str, optional): The scope of the query. Valid values are "released", "in progress", or "any". - If not provided, the "preferred_scope" provided when creating the proxy object will be used. + release_status (str, optional): The scope of the query. Valid values are "released", "in progress", or "any". + If not provided, the "preferred_release_status" 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. @@ -107,7 +107,7 @@ def resolve( Returns: a KGObject instance, of the appropriate subclass. """ - scope = scope or self.preferred_scope + release_status = release_status or self.preferred_release_status objects: List[KGObject] = [] for cls in self.classes: if hasattr(cls, "generate_query"): @@ -123,7 +123,7 @@ def resolve( query=query, size=size, from_index=from_index, - scope=scope, + release_status=release_status, ).data objects.extend(cls.from_jsonld(instance_data, client) for instance_data in instances) for obj in objects: @@ -131,19 +131,19 @@ def resolve( if follow_links: for obj in objects: - obj.resolve(client, scope=scope, use_cache=use_cache, follow_links=follow_links) + obj.resolve(client, release_status=release_status, use_cache=use_cache, follow_links=follow_links) if len(objects) == 1: return objects[0] else: return objects - def count(self, client: KGClient, space: Optional[str] = None, scope: Optional[str] = None): + def count(self, client: KGClient, space: Optional[str] = None, release_status: Optional[str] = None): """ Return the number of objects that would be returned by resolving this query. """ - scope = scope or self.preferred_scope + release_status = release_status or self.preferred_release_status n = 0 for cls in self.classes: - n += cls.count(client, api="query", scope=scope, space=space, **self.filter) + n += cls.count(client, api="query", release_status=release_status, space=space, **self.filter) return n diff --git a/fairgraph/node.py b/fairgraph/node.py index 0ec5f62d..bfe65a69 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -41,7 +41,7 @@ class ContainsMetadata(Resolvable, metaclass=Node): # KGObject and EmbeddedMeta reverse_properties: List[Property] = [] context: Dict[str, str] type_: str - scope: Optional[str] + release_status: Optional[str] space: Union[str, None] default_space: Union[str, None] remote_data: Optional[JSONdict] @@ -119,7 +119,7 @@ def get_property(cls, name): return cls._property_lookup[name] @classmethod - def from_jsonld(cls, data: JSONdict, scope: Optional[str] = None) -> ContainsMetadata: + def from_jsonld(cls, data: JSONdict, release_status: Optional[str] = None) -> ContainsMetadata: """ Create an instance of the class from a JSON-LD document. """ @@ -371,21 +371,16 @@ def _normalize_type(data_item): 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: try: value = prop.deserialize(data_item) @@ -397,14 +392,14 @@ def _normalize_type(data_item): 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 + deserialized_data[prop.name] = value return deserialized_data def resolve( self, client: KGClient, - scope: Optional[str] = None, + release_status: Optional[str] = None, use_cache: bool = True, follow_links: Optional[Dict[str, Any]] = None, ): @@ -413,14 +408,14 @@ def resolve( Args: client: KGClient object that handles the communication with the KG. - scope (str): The scope of instances to include in the response. + release_status (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" + use_release_status = release_status or self.release_status or "released" if follow_links: reverse_aliases = invert_dict(self.__class__.aliases) for prop in self.__class__.all_properties: @@ -444,7 +439,7 @@ def resolve( try: resolved_value = value.resolve( client, - scope=use_scope, + release_status=use_release_status, use_cache=use_cache, follow_links=follow_links[follow_name], ) diff --git a/fairgraph/openminds/chemicals/amount_of_chemical.py b/fairgraph/openminds/chemicals/amount_of_chemical.py index 40d34019..021a10cf 100644 --- a/fairgraph/openminds/chemicals/amount_of_chemical.py +++ b/fairgraph/openminds/chemicals/amount_of_chemical.py @@ -18,5 +18,5 @@ class AmountOfChemical(EmbeddedMetadata, OMAmountOfChemical): # 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): + def __init__(self, amount=None, chemical_product=None, id=None, data=None, space=None, release_status=None): 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 e8f60976..718a82d9 100644 --- a/fairgraph/openminds/chemicals/chemical_mixture.py +++ b/fairgraph/openminds/chemicals/chemical_mixture.py @@ -58,13 +58,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/chemicals/chemical_substance.py b/fairgraph/openminds/chemicals/chemical_substance.py index 0d6d0161..c12fdcf6 100644 --- a/fairgraph/openminds/chemicals/chemical_substance.py +++ b/fairgraph/openminds/chemicals/chemical_substance.py @@ -53,13 +53,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/chemicals/product_source.py b/fairgraph/openminds/chemicals/product_source.py index d10e141e..6b8b5204 100644 --- a/fairgraph/openminds/chemicals/product_source.py +++ b/fairgraph/openminds/chemicals/product_source.py @@ -40,13 +40,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, digital_identifier=digital_identifier, identifier=identifier, diff --git a/fairgraph/openminds/computation/data_analysis.py b/fairgraph/openminds/computation/data_analysis.py index a936edff..a0d22b0c 100644 --- a/fairgraph/openminds/computation/data_analysis.py +++ b/fairgraph/openminds/computation/data_analysis.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/computation/data_copy.py b/fairgraph/openminds/computation/data_copy.py index 65c86639..2e0dd226 100644 --- a/fairgraph/openminds/computation/data_copy.py +++ b/fairgraph/openminds/computation/data_copy.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/computation/environment.py b/fairgraph/openminds/computation/environment.py index 297cecf2..47332db6 100644 --- a/fairgraph/openminds/computation/environment.py +++ b/fairgraph/openminds/computation/environment.py @@ -49,13 +49,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, configuration=configuration, diff --git a/fairgraph/openminds/computation/generic_computation.py b/fairgraph/openminds/computation/generic_computation.py index c321cd2c..1c6ade1b 100644 --- a/fairgraph/openminds/computation/generic_computation.py +++ b/fairgraph/openminds/computation/generic_computation.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/computation/hardware_system.py b/fairgraph/openminds/computation/hardware_system.py index 73a0799d..6f07936d 100644 --- a/fairgraph/openminds/computation/hardware_system.py +++ b/fairgraph/openminds/computation/hardware_system.py @@ -38,13 +38,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, description=description, diff --git a/fairgraph/openminds/computation/launch_configuration.py b/fairgraph/openminds/computation/launch_configuration.py index 990e9991..1caea4e0 100644 --- a/fairgraph/openminds/computation/launch_configuration.py +++ b/fairgraph/openminds/computation/launch_configuration.py @@ -48,13 +48,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, arguments=arguments, diff --git a/fairgraph/openminds/computation/local_file.py b/fairgraph/openminds/computation/local_file.py index fd4c4001..47c4189f 100644 --- a/fairgraph/openminds/computation/local_file.py +++ b/fairgraph/openminds/computation/local_file.py @@ -61,13 +61,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, content_description=content_description, diff --git a/fairgraph/openminds/computation/model_validation.py b/fairgraph/openminds/computation/model_validation.py index 69b78647..8b4f5af7 100644 --- a/fairgraph/openminds/computation/model_validation.py +++ b/fairgraph/openminds/computation/model_validation.py @@ -75,13 +75,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/computation/optimization.py b/fairgraph/openminds/computation/optimization.py index 1c3420a2..1fec2c5c 100644 --- a/fairgraph/openminds/computation/optimization.py +++ b/fairgraph/openminds/computation/optimization.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/computation/simulation.py b/fairgraph/openminds/computation/simulation.py index d3ecbfcd..9365252f 100644 --- a/fairgraph/openminds/computation/simulation.py +++ b/fairgraph/openminds/computation/simulation.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/computation/software_agent.py b/fairgraph/openminds/computation/software_agent.py index 5aec43dc..c1dd7163 100644 --- a/fairgraph/openminds/computation/software_agent.py +++ b/fairgraph/openminds/computation/software_agent.py @@ -65,13 +65,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, activities=activities, diff --git a/fairgraph/openminds/computation/validation_test.py b/fairgraph/openminds/computation/validation_test.py index c7fceea3..c41a20fc 100644 --- a/fairgraph/openminds/computation/validation_test.py +++ b/fairgraph/openminds/computation/validation_test.py @@ -64,8 +64,8 @@ def __init__( how_to_cite=None, is_part_of=None, learning_resources=None, - model_scope=None, reference_data_acquisitions=None, + scope=None, score_type=None, short_name=None, study_targets=None, @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, @@ -94,8 +94,8 @@ def __init__( how_to_cite=how_to_cite, is_part_of=is_part_of, learning_resources=learning_resources, - model_scope=model_scope, reference_data_acquisitions=reference_data_acquisitions, + scope=scope, score_type=score_type, short_name=short_name, study_targets=study_targets, diff --git a/fairgraph/openminds/computation/validation_test_version.py b/fairgraph/openminds/computation/validation_test_version.py index 7e10e5eb..5f60cf4a 100644 --- a/fairgraph/openminds/computation/validation_test_version.py +++ b/fairgraph/openminds/computation/validation_test_version.py @@ -115,13 +115,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/computation/visualization.py b/fairgraph/openminds/computation/visualization.py index 145f068d..5580d3c3 100644 --- a/fairgraph/openminds/computation/visualization.py +++ b/fairgraph/openminds/computation/visualization.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/computation/workflow_execution.py b/fairgraph/openminds/computation/workflow_execution.py index 617b2140..7e1a9335 100644 --- a/fairgraph/openminds/computation/workflow_execution.py +++ b/fairgraph/openminds/computation/workflow_execution.py @@ -21,13 +21,21 @@ class WorkflowExecution(KGObject, OMWorkflowExecution): existence_query_properties = ("stages",) def __init__( - self, configuration=None, recipe=None, stages=None, started_by=None, id=None, data=None, space=None, scope=None + self, + configuration=None, + recipe=None, + stages=None, + started_by=None, + id=None, + data=None, + space=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, configuration=configuration, recipe=recipe, diff --git a/fairgraph/openminds/computation/workflow_recipe.py b/fairgraph/openminds/computation/workflow_recipe.py index 2cb39253..40b0761f 100644 --- a/fairgraph/openminds/computation/workflow_recipe.py +++ b/fairgraph/openminds/computation/workflow_recipe.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/computation/workflow_recipe_version.py b/fairgraph/openminds/computation/workflow_recipe_version.py index 76e7ed84..4a4851bf 100644 --- a/fairgraph/openminds/computation/workflow_recipe_version.py +++ b/fairgraph/openminds/computation/workflow_recipe_version.py @@ -121,13 +121,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/controlled_terms/action_status_type.py b/fairgraph/openminds/controlled_terms/action_status_type.py index 10af58df..2bbb25fc 100644 --- a/fairgraph/openminds/controlled_terms/action_status_type.py +++ b/fairgraph/openminds/controlled_terms/action_status_type.py @@ -77,13 +77,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/age_category.py b/fairgraph/openminds/controlled_terms/age_category.py index 3cfc05fe..9ee17cba 100644 --- a/fairgraph/openminds/controlled_terms/age_category.py +++ b/fairgraph/openminds/controlled_terms/age_category.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/analysis_technique.py b/fairgraph/openminds/controlled_terms/analysis_technique.py index 08ab551d..10696de6 100644 --- a/fairgraph/openminds/controlled_terms/analysis_technique.py +++ b/fairgraph/openminds/controlled_terms/analysis_technique.py @@ -87,13 +87,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py index c2354c2d..b3261ce9 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py +++ b/fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py index 8fcc906e..fa68d757 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_identification_type.py +++ b/fairgraph/openminds/controlled_terms/anatomical_identification_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/anatomical_plane.py b/fairgraph/openminds/controlled_terms/anatomical_plane.py index 6851bdc9..45402058 100644 --- a/fairgraph/openminds/controlled_terms/anatomical_plane.py +++ b/fairgraph/openminds/controlled_terms/anatomical_plane.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py index 378f7b53..87d6854b 100644 --- a/fairgraph/openminds/controlled_terms/annotation_criteria_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_criteria_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/annotation_type.py b/fairgraph/openminds/controlled_terms/annotation_type.py index 812a06a4..64c3823e 100644 --- a/fairgraph/openminds/controlled_terms/annotation_type.py +++ b/fairgraph/openminds/controlled_terms/annotation_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/atlas_type.py b/fairgraph/openminds/controlled_terms/atlas_type.py index fee26948..5787f6d7 100644 --- a/fairgraph/openminds/controlled_terms/atlas_type.py +++ b/fairgraph/openminds/controlled_terms/atlas_type.py @@ -68,13 +68,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py index 1101086e..ff16a539 100644 --- a/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/auditory_stimulus_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/biological_order.py b/fairgraph/openminds/controlled_terms/biological_order.py index 43920ff6..04452120 100644 --- a/fairgraph/openminds/controlled_terms/biological_order.py +++ b/fairgraph/openminds/controlled_terms/biological_order.py @@ -96,13 +96,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/biological_process.py b/fairgraph/openminds/controlled_terms/biological_process.py index d3fdea70..6096ef3f 100644 --- a/fairgraph/openminds/controlled_terms/biological_process.py +++ b/fairgraph/openminds/controlled_terms/biological_process.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/biological_sex.py b/fairgraph/openminds/controlled_terms/biological_sex.py index f44cc1f3..d27a0f50 100644 --- a/fairgraph/openminds/controlled_terms/biological_sex.py +++ b/fairgraph/openminds/controlled_terms/biological_sex.py @@ -110,13 +110,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/breeding_type.py b/fairgraph/openminds/controlled_terms/breeding_type.py index bf7e932b..3046db88 100644 --- a/fairgraph/openminds/controlled_terms/breeding_type.py +++ b/fairgraph/openminds/controlled_terms/breeding_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/cell_culture_type.py b/fairgraph/openminds/controlled_terms/cell_culture_type.py index b67b3372..d9f1e1be 100644 --- a/fairgraph/openminds/controlled_terms/cell_culture_type.py +++ b/fairgraph/openminds/controlled_terms/cell_culture_type.py @@ -96,13 +96,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/cell_type.py b/fairgraph/openminds/controlled_terms/cell_type.py index 58173b54..0bd71c77 100644 --- a/fairgraph/openminds/controlled_terms/cell_type.py +++ b/fairgraph/openminds/controlled_terms/cell_type.py @@ -127,13 +127,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py index 286df5cb..143e511f 100644 --- a/fairgraph/openminds/controlled_terms/chemical_mixture_type.py +++ b/fairgraph/openminds/controlled_terms/chemical_mixture_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/colormap.py b/fairgraph/openminds/controlled_terms/colormap.py index 3962225f..b23fe509 100644 --- a/fairgraph/openminds/controlled_terms/colormap.py +++ b/fairgraph/openminds/controlled_terms/colormap.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/contribution_type.py b/fairgraph/openminds/controlled_terms/contribution_type.py index c8851727..b375d1b7 100644 --- a/fairgraph/openminds/controlled_terms/contribution_type.py +++ b/fairgraph/openminds/controlled_terms/contribution_type.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py index 3fc80254..3220c52c 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_construction_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py index 0f12b5de..9689b317 100644 --- a/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py +++ b/fairgraph/openminds/controlled_terms/cranial_window_reinforcement_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/criteria_quality_type.py b/fairgraph/openminds/controlled_terms/criteria_quality_type.py index 9a312d11..86b70fff 100644 --- a/fairgraph/openminds/controlled_terms/criteria_quality_type.py +++ b/fairgraph/openminds/controlled_terms/criteria_quality_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/data_type.py b/fairgraph/openminds/controlled_terms/data_type.py index b014fd35..e71d5d4b 100644 --- a/fairgraph/openminds/controlled_terms/data_type.py +++ b/fairgraph/openminds/controlled_terms/data_type.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/device_type.py b/fairgraph/openminds/controlled_terms/device_type.py index 74c156a4..c60b0d00 100644 --- a/fairgraph/openminds/controlled_terms/device_type.py +++ b/fairgraph/openminds/controlled_terms/device_type.py @@ -74,13 +74,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/difference_measure.py b/fairgraph/openminds/controlled_terms/difference_measure.py index 3b89443e..1076303b 100644 --- a/fairgraph/openminds/controlled_terms/difference_measure.py +++ b/fairgraph/openminds/controlled_terms/difference_measure.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/disease.py b/fairgraph/openminds/controlled_terms/disease.py index 700a2b68..38aa1234 100644 --- a/fairgraph/openminds/controlled_terms/disease.py +++ b/fairgraph/openminds/controlled_terms/disease.py @@ -119,13 +119,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/disease_model.py b/fairgraph/openminds/controlled_terms/disease_model.py index 005bdf2d..23b43d2c 100644 --- a/fairgraph/openminds/controlled_terms/disease_model.py +++ b/fairgraph/openminds/controlled_terms/disease_model.py @@ -119,13 +119,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/educational_level.py b/fairgraph/openminds/controlled_terms/educational_level.py index 7a4b5686..bd0deae0 100644 --- a/fairgraph/openminds/controlled_terms/educational_level.py +++ b/fairgraph/openminds/controlled_terms/educational_level.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py index 67c1263f..bcdb5fe9 100644 --- a/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/electrical_stimulus_type.py @@ -114,13 +114,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/ethics_assessment.py b/fairgraph/openminds/controlled_terms/ethics_assessment.py index 08db38c8..f454fc1c 100644 --- a/fairgraph/openminds/controlled_terms/ethics_assessment.py +++ b/fairgraph/openminds/controlled_terms/ethics_assessment.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/experimental_approach.py b/fairgraph/openminds/controlled_terms/experimental_approach.py index 4453010b..e70fb1d5 100644 --- a/fairgraph/openminds/controlled_terms/experimental_approach.py +++ b/fairgraph/openminds/controlled_terms/experimental_approach.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py index 6159d0e6..f5fa4533 100644 --- a/fairgraph/openminds/controlled_terms/file_bundle_grouping.py +++ b/fairgraph/openminds/controlled_terms/file_bundle_grouping.py @@ -78,13 +78,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/file_repository_type.py b/fairgraph/openminds/controlled_terms/file_repository_type.py index 404e6550..434088f5 100644 --- a/fairgraph/openminds/controlled_terms/file_repository_type.py +++ b/fairgraph/openminds/controlled_terms/file_repository_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/file_usage_role.py b/fairgraph/openminds/controlled_terms/file_usage_role.py index 7a1d7ac8..75682992 100644 --- a/fairgraph/openminds/controlled_terms/file_usage_role.py +++ b/fairgraph/openminds/controlled_terms/file_usage_role.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/genetic_strain_type.py b/fairgraph/openminds/controlled_terms/genetic_strain_type.py index 56ad7273..49fdff82 100644 --- a/fairgraph/openminds/controlled_terms/genetic_strain_type.py +++ b/fairgraph/openminds/controlled_terms/genetic_strain_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py index a217fdb9..88b97cca 100644 --- a/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/gustatory_stimulus_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/handedness.py b/fairgraph/openminds/controlled_terms/handedness.py index d63ed91a..21607239 100644 --- a/fairgraph/openminds/controlled_terms/handedness.py +++ b/fairgraph/openminds/controlled_terms/handedness.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/language.py b/fairgraph/openminds/controlled_terms/language.py index 93a85143..8f5cd69a 100644 --- a/fairgraph/openminds/controlled_terms/language.py +++ b/fairgraph/openminds/controlled_terms/language.py @@ -68,13 +68,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/laterality.py b/fairgraph/openminds/controlled_terms/laterality.py index 239909fb..a0a4a47e 100644 --- a/fairgraph/openminds/controlled_terms/laterality.py +++ b/fairgraph/openminds/controlled_terms/laterality.py @@ -74,13 +74,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/learning_resource_type.py b/fairgraph/openminds/controlled_terms/learning_resource_type.py index 5b1adbee..a6977614 100644 --- a/fairgraph/openminds/controlled_terms/learning_resource_type.py +++ b/fairgraph/openminds/controlled_terms/learning_resource_type.py @@ -68,13 +68,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/measured_quantity.py b/fairgraph/openminds/controlled_terms/measured_quantity.py index 73897cae..fcf62788 100644 --- a/fairgraph/openminds/controlled_terms/measured_quantity.py +++ b/fairgraph/openminds/controlled_terms/measured_quantity.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/measured_signal_type.py b/fairgraph/openminds/controlled_terms/measured_signal_type.py index a5590d57..c71f1443 100644 --- a/fairgraph/openminds/controlled_terms/measured_signal_type.py +++ b/fairgraph/openminds/controlled_terms/measured_signal_type.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/meta_data_model_type.py b/fairgraph/openminds/controlled_terms/meta_data_model_type.py index f397896b..aa8933f9 100644 --- a/fairgraph/openminds/controlled_terms/meta_data_model_type.py +++ b/fairgraph/openminds/controlled_terms/meta_data_model_type.py @@ -68,13 +68,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/model_abstraction_level.py b/fairgraph/openminds/controlled_terms/model_abstraction_level.py index cffe8f7e..514709d5 100644 --- a/fairgraph/openminds/controlled_terms/model_abstraction_level.py +++ b/fairgraph/openminds/controlled_terms/model_abstraction_level.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/model_scope.py b/fairgraph/openminds/controlled_terms/model_scope.py index e927abf2..a993be81 100644 --- a/fairgraph/openminds/controlled_terms/model_scope.py +++ b/fairgraph/openminds/controlled_terms/model_scope.py @@ -48,9 +48,9 @@ class ModelScope(KGObject, OMModelScope): "is_scope_of", ["openminds.latest.computation.ValidationTest", "openminds.latest.core.Model"], "scope", - reverse="model_scope", + reverse="scope", multiple=True, - description="reverse of 'model_scope'", + description="reverse of 'scope'", ), ] existence_query_properties = ("name",) @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/molecular_entity.py b/fairgraph/openminds/controlled_terms/molecular_entity.py index e243b551..6366a668 100644 --- a/fairgraph/openminds/controlled_terms/molecular_entity.py +++ b/fairgraph/openminds/controlled_terms/molecular_entity.py @@ -119,13 +119,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, composes=composes, diff --git a/fairgraph/openminds/controlled_terms/mr_spatial_encoding.py b/fairgraph/openminds/controlled_terms/mr_spatial_encoding.py index 4a19306f..c8eafba0 100644 --- a/fairgraph/openminds/controlled_terms/mr_spatial_encoding.py +++ b/fairgraph/openminds/controlled_terms/mr_spatial_encoding.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py index 6fdc534b..800e806f 100644 --- a/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py +++ b/fairgraph/openminds/controlled_terms/mri_pulse_sequence.py @@ -77,13 +77,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/mri_weighting.py b/fairgraph/openminds/controlled_terms/mri_weighting.py index 3f52530a..0037dc1c 100644 --- a/fairgraph/openminds/controlled_terms/mri_weighting.py +++ b/fairgraph/openminds/controlled_terms/mri_weighting.py @@ -77,13 +77,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py index 34fe3c10..5a603cdf 100644 --- a/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/olfactory_stimulus_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/operating_device.py b/fairgraph/openminds/controlled_terms/operating_device.py index 38559641..9f813298 100644 --- a/fairgraph/openminds/controlled_terms/operating_device.py +++ b/fairgraph/openminds/controlled_terms/operating_device.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/operating_system.py b/fairgraph/openminds/controlled_terms/operating_system.py index dd985fec..8bdab69a 100644 --- a/fairgraph/openminds/controlled_terms/operating_system.py +++ b/fairgraph/openminds/controlled_terms/operating_system.py @@ -68,13 +68,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py index 9ab9f9ae..672ce1aa 100644 --- a/fairgraph/openminds/controlled_terms/optical_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/optical_stimulus_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/organ.py b/fairgraph/openminds/controlled_terms/organ.py index 6ea20fef..470326f6 100644 --- a/fairgraph/openminds/controlled_terms/organ.py +++ b/fairgraph/openminds/controlled_terms/organ.py @@ -136,13 +136,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, defines=defines, diff --git a/fairgraph/openminds/controlled_terms/organism_substance.py b/fairgraph/openminds/controlled_terms/organism_substance.py index 00eb2721..6ae9f68c 100644 --- a/fairgraph/openminds/controlled_terms/organism_substance.py +++ b/fairgraph/openminds/controlled_terms/organism_substance.py @@ -127,13 +127,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/organism_system.py b/fairgraph/openminds/controlled_terms/organism_system.py index 70ecea72..aa8050fc 100644 --- a/fairgraph/openminds/controlled_terms/organism_system.py +++ b/fairgraph/openminds/controlled_terms/organism_system.py @@ -96,13 +96,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py index 67eb0ebe..986a3a6a 100644 --- a/fairgraph/openminds/controlled_terms/patch_clamp_variation.py +++ b/fairgraph/openminds/controlled_terms/patch_clamp_variation.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/preparation_type.py b/fairgraph/openminds/controlled_terms/preparation_type.py index 7172cffa..34e70027 100644 --- a/fairgraph/openminds/controlled_terms/preparation_type.py +++ b/fairgraph/openminds/controlled_terms/preparation_type.py @@ -78,13 +78,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/product_accessibility.py b/fairgraph/openminds/controlled_terms/product_accessibility.py index e9858d27..aaedceef 100644 --- a/fairgraph/openminds/controlled_terms/product_accessibility.py +++ b/fairgraph/openminds/controlled_terms/product_accessibility.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/programming_language.py b/fairgraph/openminds/controlled_terms/programming_language.py index 6d53c829..e49b197c 100644 --- a/fairgraph/openminds/controlled_terms/programming_language.py +++ b/fairgraph/openminds/controlled_terms/programming_language.py @@ -68,13 +68,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/qualitative_overlap.py b/fairgraph/openminds/controlled_terms/qualitative_overlap.py index 3a6afd24..7198824d 100644 --- a/fairgraph/openminds/controlled_terms/qualitative_overlap.py +++ b/fairgraph/openminds/controlled_terms/qualitative_overlap.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/semantic_data_type.py b/fairgraph/openminds/controlled_terms/semantic_data_type.py index 53bfabba..acd89c7c 100644 --- a/fairgraph/openminds/controlled_terms/semantic_data_type.py +++ b/fairgraph/openminds/controlled_terms/semantic_data_type.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/service.py b/fairgraph/openminds/controlled_terms/service.py index 99db60a4..bc43eac8 100644 --- a/fairgraph/openminds/controlled_terms/service.py +++ b/fairgraph/openminds/controlled_terms/service.py @@ -78,13 +78,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/setup_type.py b/fairgraph/openminds/controlled_terms/setup_type.py index ffcfc574..d0575fdf 100644 --- a/fairgraph/openminds/controlled_terms/setup_type.py +++ b/fairgraph/openminds/controlled_terms/setup_type.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/software_application_category.py b/fairgraph/openminds/controlled_terms/software_application_category.py index 9e423469..f6fcc1c3 100644 --- a/fairgraph/openminds/controlled_terms/software_application_category.py +++ b/fairgraph/openminds/controlled_terms/software_application_category.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/software_feature.py b/fairgraph/openminds/controlled_terms/software_feature.py index 237274dc..dacb668f 100644 --- a/fairgraph/openminds/controlled_terms/software_feature.py +++ b/fairgraph/openminds/controlled_terms/software_feature.py @@ -60,13 +60,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/species.py b/fairgraph/openminds/controlled_terms/species.py index 40237ca8..da34cca4 100644 --- a/fairgraph/openminds/controlled_terms/species.py +++ b/fairgraph/openminds/controlled_terms/species.py @@ -120,13 +120,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, common_coordinate_space=common_coordinate_space, diff --git a/fairgraph/openminds/controlled_terms/stimulation_approach.py b/fairgraph/openminds/controlled_terms/stimulation_approach.py index d68d6632..2640a1e2 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_approach.py +++ b/fairgraph/openminds/controlled_terms/stimulation_approach.py @@ -81,13 +81,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/stimulation_technique.py b/fairgraph/openminds/controlled_terms/stimulation_technique.py index b6fa19aa..42e19f01 100644 --- a/fairgraph/openminds/controlled_terms/stimulation_technique.py +++ b/fairgraph/openminds/controlled_terms/stimulation_technique.py @@ -81,13 +81,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/subcellular_entity.py b/fairgraph/openminds/controlled_terms/subcellular_entity.py index 57511019..ae8e2ee6 100644 --- a/fairgraph/openminds/controlled_terms/subcellular_entity.py +++ b/fairgraph/openminds/controlled_terms/subcellular_entity.py @@ -120,13 +120,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/subject_attribute.py b/fairgraph/openminds/controlled_terms/subject_attribute.py index 1f45f764..da461b68 100644 --- a/fairgraph/openminds/controlled_terms/subject_attribute.py +++ b/fairgraph/openminds/controlled_terms/subject_attribute.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py index 683614a1..5e167a09 100644 --- a/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/tactile_stimulus_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/technique.py b/fairgraph/openminds/controlled_terms/technique.py index 49283ba7..f8ac782e 100644 --- a/fairgraph/openminds/controlled_terms/technique.py +++ b/fairgraph/openminds/controlled_terms/technique.py @@ -86,13 +86,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/term_suggestion.py b/fairgraph/openminds/controlled_terms/term_suggestion.py index 7036c6c4..fa57d920 100644 --- a/fairgraph/openminds/controlled_terms/term_suggestion.py +++ b/fairgraph/openminds/controlled_terms/term_suggestion.py @@ -98,13 +98,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, add_existing_terminology=add_existing_terminology, diff --git a/fairgraph/openminds/controlled_terms/terminology.py b/fairgraph/openminds/controlled_terms/terminology.py index c9a4e45b..cb43262c 100644 --- a/fairgraph/openminds/controlled_terms/terminology.py +++ b/fairgraph/openminds/controlled_terms/terminology.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py index 9bba66cb..6e22ee38 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_attribute.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/tissue_sample_type.py b/fairgraph/openminds/controlled_terms/tissue_sample_type.py index 2aff27b3..acba542e 100644 --- a/fairgraph/openminds/controlled_terms/tissue_sample_type.py +++ b/fairgraph/openminds/controlled_terms/tissue_sample_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py index 7699ab81..ea3c1321 100644 --- a/fairgraph/openminds/controlled_terms/type_of_uncertainty.py +++ b/fairgraph/openminds/controlled_terms/type_of_uncertainty.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/uberon_parcellation.py b/fairgraph/openminds/controlled_terms/uberon_parcellation.py index 1c494ef8..6e990838 100644 --- a/fairgraph/openminds/controlled_terms/uberon_parcellation.py +++ b/fairgraph/openminds/controlled_terms/uberon_parcellation.py @@ -129,13 +129,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, defines=defines, diff --git a/fairgraph/openminds/controlled_terms/unit_of_measurement.py b/fairgraph/openminds/controlled_terms/unit_of_measurement.py index f453c1e4..3b6def06 100644 --- a/fairgraph/openminds/controlled_terms/unit_of_measurement.py +++ b/fairgraph/openminds/controlled_terms/unit_of_measurement.py @@ -86,13 +86,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py index d4bc63b3..988d0e52 100644 --- a/fairgraph/openminds/controlled_terms/visual_stimulus_type.py +++ b/fairgraph/openminds/controlled_terms/visual_stimulus_type.py @@ -105,13 +105,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, definition=definition, diff --git a/fairgraph/openminds/core/actors/account_information.py b/fairgraph/openminds/core/actors/account_information.py index 9ae32bef..40b76299 100644 --- a/fairgraph/openminds/core/actors/account_information.py +++ b/fairgraph/openminds/core/actors/account_information.py @@ -29,12 +29,14 @@ class AccountInformation(KGObject, OMAccountInformation): ] 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): + def __init__( + self, belongs_to=None, service=None, user_name=None, id=None, data=None, space=None, release_status=None + ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, belongs_to=belongs_to, service=service, diff --git a/fairgraph/openminds/core/actors/affiliation.py b/fairgraph/openminds/core/actors/affiliation.py index 15dc25ae..858f3c47 100644 --- a/fairgraph/openminds/core/actors/affiliation.py +++ b/fairgraph/openminds/core/actors/affiliation.py @@ -21,7 +21,9 @@ class Affiliation(EmbeddedMetadata, OMAffiliation): # 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): + def __init__( + self, end_date=None, member_of=None, start_date=None, id=None, data=None, space=None, release_status=None + ): 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 c3f81f30..f38c6500 100644 --- a/fairgraph/openminds/core/actors/consortium.py +++ b/fairgraph/openminds/core/actors/consortium.py @@ -149,13 +149,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/actors/contact_information.py b/fairgraph/openminds/core/actors/contact_information.py index f2860485..d71a971d 100644 --- a/fairgraph/openminds/core/actors/contact_information.py +++ b/fairgraph/openminds/core/actors/contact_information.py @@ -29,12 +29,14 @@ class ContactInformation(KGObject, OMContactInformation): ] existence_query_properties = ("email",) - def __init__(self, email=None, is_contact_information_of=None, id=None, data=None, space=None, scope=None): + def __init__( + self, email=None, is_contact_information_of=None, id=None, data=None, space=None, release_status=None + ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, email=email, is_contact_information_of=is_contact_information_of, diff --git a/fairgraph/openminds/core/actors/contribution.py b/fairgraph/openminds/core/actors/contribution.py index 1404679a..ced887bb 100644 --- a/fairgraph/openminds/core/actors/contribution.py +++ b/fairgraph/openminds/core/actors/contribution.py @@ -18,5 +18,5 @@ class Contribution(EmbeddedMetadata, OMContribution): # 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): + def __init__(self, contributor=None, types=None, id=None, data=None, space=None, release_status=None): 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 e31b0b6d..0008da20 100644 --- a/fairgraph/openminds/core/actors/organization.py +++ b/fairgraph/openminds/core/actors/organization.py @@ -169,13 +169,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/actors/person.py b/fairgraph/openminds/core/actors/person.py index 3e215bba..047e81ad 100644 --- a/fairgraph/openminds/core/actors/person.py +++ b/fairgraph/openminds/core/actors/person.py @@ -182,13 +182,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, activities=activities, affiliations=affiliations, @@ -219,7 +219,7 @@ def me(cls, client, allow_multiple=False, follow_links=None): user_info = client.user_info() possible_matches = cls.list( client, - scope="in progress", + release_status="in progress", space="common", follow_links=follow_links, family_name=user_info.family_name, diff --git a/fairgraph/openminds/core/data/content_type.py b/fairgraph/openminds/core/data/content_type.py index 78f0e252..c1a2effe 100644 --- a/fairgraph/openminds/core/data/content_type.py +++ b/fairgraph/openminds/core/data/content_type.py @@ -84,13 +84,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, data_types=data_types, diff --git a/fairgraph/openminds/core/data/content_type_pattern.py b/fairgraph/openminds/core/data/content_type_pattern.py index 5f7617a1..5eab93a6 100644 --- a/fairgraph/openminds/core/data/content_type_pattern.py +++ b/fairgraph/openminds/core/data/content_type_pattern.py @@ -38,13 +38,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, content_type=content_type, diff --git a/fairgraph/openminds/core/data/copyright.py b/fairgraph/openminds/core/data/copyright.py index 6a80398e..688f69bc 100644 --- a/fairgraph/openminds/core/data/copyright.py +++ b/fairgraph/openminds/core/data/copyright.py @@ -18,5 +18,5 @@ class Copyright(EmbeddedMetadata, OMCopyright): # 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): + def __init__(self, holders=None, years=None, id=None, data=None, space=None, release_status=None): 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 d36c02dc..06052b91 100644 --- a/fairgraph/openminds/core/data/file.py +++ b/fairgraph/openminds/core/data/file.py @@ -208,13 +208,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, content_description=content_description, diff --git a/fairgraph/openminds/core/data/file_archive.py b/fairgraph/openminds/core/data/file_archive.py index f4b13981..f11d8467 100644 --- a/fairgraph/openminds/core/data/file_archive.py +++ b/fairgraph/openminds/core/data/file_archive.py @@ -55,13 +55,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, format=format, iri=iri, diff --git a/fairgraph/openminds/core/data/file_bundle.py b/fairgraph/openminds/core/data/file_bundle.py index 40fd5ad4..f46312d8 100644 --- a/fairgraph/openminds/core/data/file_bundle.py +++ b/fairgraph/openminds/core/data/file_bundle.py @@ -123,13 +123,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, content_description=content_description, diff --git a/fairgraph/openminds/core/data/file_path_pattern.py b/fairgraph/openminds/core/data/file_path_pattern.py index 1b7c4f28..5a092f7a 100644 --- a/fairgraph/openminds/core/data/file_path_pattern.py +++ b/fairgraph/openminds/core/data/file_path_pattern.py @@ -18,5 +18,5 @@ class FilePathPattern(EmbeddedMetadata, OMFilePathPattern): # 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): + def __init__(self, grouping_types=None, regex=None, id=None, data=None, space=None, release_status=None): 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 a35a31b8..dbf03d79 100644 --- a/fairgraph/openminds/core/data/file_repository.py +++ b/fairgraph/openminds/core/data/file_repository.py @@ -76,13 +76,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, contains_content_of=contains_content_of, diff --git a/fairgraph/openminds/core/data/file_repository_structure.py b/fairgraph/openminds/core/data/file_repository_structure.py index 37fbf59c..4e02f681 100644 --- a/fairgraph/openminds/core/data/file_repository_structure.py +++ b/fairgraph/openminds/core/data/file_repository_structure.py @@ -30,13 +30,20 @@ class FileRepositoryStructure(KGObject, OMFileRepositoryStructure): existence_query_properties = ("lookup_label",) def __init__( - self, lookup_label=None, file_path_patterns=None, structures=None, id=None, data=None, space=None, scope=None + self, + lookup_label=None, + file_path_patterns=None, + structures=None, + id=None, + data=None, + space=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, file_path_patterns=file_path_patterns, diff --git a/fairgraph/openminds/core/data/hash.py b/fairgraph/openminds/core/data/hash.py index 1696f580..f68bd6bc 100644 --- a/fairgraph/openminds/core/data/hash.py +++ b/fairgraph/openminds/core/data/hash.py @@ -18,5 +18,5 @@ class Hash(EmbeddedMetadata, OMHash): # 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): + def __init__(self, algorithm=None, digest=None, id=None, data=None, space=None, release_status=None): 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 6be0b2a3..d06ba7b5 100644 --- a/fairgraph/openminds/core/data/license.py +++ b/fairgraph/openminds/core/data/license.py @@ -59,13 +59,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/data/measurement.py b/fairgraph/openminds/core/data/measurement.py index 5e7e7eeb..064ba0ea 100644 --- a/fairgraph/openminds/core/data/measurement.py +++ b/fairgraph/openminds/core/data/measurement.py @@ -31,7 +31,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/core/data/service_link.py b/fairgraph/openminds/core/data/service_link.py index 1b4c9779..8e8fa8b5 100644 --- a/fairgraph/openminds/core/data/service_link.py +++ b/fairgraph/openminds/core/data/service_link.py @@ -33,13 +33,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, data_location=data_location, display_label=display_label, diff --git a/fairgraph/openminds/core/digital_identifier/doi.py b/fairgraph/openminds/core/digital_identifier/doi.py index 3c6ed9d5..e2619a26 100644 --- a/fairgraph/openminds/core/digital_identifier/doi.py +++ b/fairgraph/openminds/core/digital_identifier/doi.py @@ -83,13 +83,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, describes=describes, identifier=identifier, diff --git a/fairgraph/openminds/core/digital_identifier/gridid.py b/fairgraph/openminds/core/digital_identifier/gridid.py index 7dafc960..26b92d2e 100644 --- a/fairgraph/openminds/core/digital_identifier/gridid.py +++ b/fairgraph/openminds/core/digital_identifier/gridid.py @@ -29,7 +29,13 @@ class GRIDID(KGObject, OMGRIDID): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): + def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + self, + id=id, + space=space, + release_status=release_status, + 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 34733855..c1a1b5dd 100644 --- a/fairgraph/openminds/core/digital_identifier/handle.py +++ b/fairgraph/openminds/core/digital_identifier/handle.py @@ -40,7 +40,13 @@ class HANDLE(KGObject, OMHANDLE): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, related_to=None, id=None, data=None, space=None, scope=None): + def __init__(self, identifier=None, related_to=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, identifier=identifier, related_to=related_to + self, + id=id, + space=space, + release_status=release_status, + 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 cdfc44aa..7c05a736 100644 --- a/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py +++ b/fairgraph/openminds/core/digital_identifier/identifiers_dot_org_id.py @@ -29,7 +29,13 @@ class IdentifiersDotOrgID(KGObject, OMIdentifiersDotOrgID): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): + def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + self, + id=id, + space=space, + release_status=release_status, + 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 2fb1e3c2..19cbc030 100644 --- a/fairgraph/openminds/core/digital_identifier/isbn.py +++ b/fairgraph/openminds/core/digital_identifier/isbn.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, cited_in=cited_in, identifier=identifier, diff --git a/fairgraph/openminds/core/digital_identifier/issn.py b/fairgraph/openminds/core/digital_identifier/issn.py index 1c69a4b6..35f0f1af 100644 --- a/fairgraph/openminds/core/digital_identifier/issn.py +++ b/fairgraph/openminds/core/digital_identifier/issn.py @@ -48,12 +48,14 @@ class ISSN(KGObject, OMISSN): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, identifies=None, related_to=None, id=None, data=None, space=None, scope=None): + def __init__( + self, identifier=None, identifies=None, related_to=None, id=None, data=None, space=None, release_status=None + ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, identifier=identifier, identifies=identifies, diff --git a/fairgraph/openminds/core/digital_identifier/orcid.py b/fairgraph/openminds/core/digital_identifier/orcid.py index f35616fc..7e0ed2ff 100644 --- a/fairgraph/openminds/core/digital_identifier/orcid.py +++ b/fairgraph/openminds/core/digital_identifier/orcid.py @@ -29,7 +29,13 @@ class ORCID(KGObject, OMORCID): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): + def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + self, + id=id, + space=space, + release_status=release_status, + 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 8d7944af..0b68d9df 100644 --- a/fairgraph/openminds/core/digital_identifier/rorid.py +++ b/fairgraph/openminds/core/digital_identifier/rorid.py @@ -29,7 +29,13 @@ class RORID(KGObject, OMRORID): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): + def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + self, + id=id, + space=space, + release_status=release_status, + 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 772a797a..2e29d9f9 100644 --- a/fairgraph/openminds/core/digital_identifier/rrid.py +++ b/fairgraph/openminds/core/digital_identifier/rrid.py @@ -43,7 +43,13 @@ class RRID(KGObject, OMRRID): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): + def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + self, + id=id, + space=space, + release_status=release_status, + 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 cbd5962d..c3b323cb 100644 --- a/fairgraph/openminds/core/digital_identifier/stock_number.py +++ b/fairgraph/openminds/core/digital_identifier/stock_number.py @@ -18,5 +18,5 @@ class StockNumber(EmbeddedMetadata, OMStockNumber): # 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): + def __init__(self, identifier=None, vendor=None, id=None, data=None, space=None, release_status=None): 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 83e0d78c..46744af7 100644 --- a/fairgraph/openminds/core/digital_identifier/swhid.py +++ b/fairgraph/openminds/core/digital_identifier/swhid.py @@ -36,7 +36,13 @@ class SWHID(KGObject, OMSWHID): ] existence_query_properties = ("identifier",) - def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, scope=None): + def __init__(self, identifier=None, identifies=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, identifier=identifier, identifies=identifies + self, + id=id, + space=space, + release_status=release_status, + data=data, + identifier=identifier, + identifies=identifies, ) diff --git a/fairgraph/openminds/core/miscellaneous/comment.py b/fairgraph/openminds/core/miscellaneous/comment.py index 0ecae0f7..c8cd81c9 100644 --- a/fairgraph/openminds/core/miscellaneous/comment.py +++ b/fairgraph/openminds/core/miscellaneous/comment.py @@ -24,13 +24,21 @@ class Comment(KGObject, OMComment): 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 + self, + about=None, + comment=None, + commenter=None, + timestamp=None, + id=None, + data=None, + space=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, about=about, comment=comment, diff --git a/fairgraph/openminds/core/miscellaneous/funding.py b/fairgraph/openminds/core/miscellaneous/funding.py index b9636c2d..5df60507 100644 --- a/fairgraph/openminds/core/miscellaneous/funding.py +++ b/fairgraph/openminds/core/miscellaneous/funding.py @@ -54,13 +54,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, acknowledgement=acknowledgement, award_number=award_number, diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value.py b/fairgraph/openminds/core/miscellaneous/quantitative_value.py index 11a27be1..668fbb3a 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value.py @@ -30,7 +30,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py index 8f75b201..93584d54 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_array.py @@ -33,13 +33,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, negative_uncertainties=negative_uncertainties, positive_uncertainties=positive_uncertainties, diff --git a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py index 7d877c19..9e30a552 100644 --- a/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py +++ b/fairgraph/openminds/core/miscellaneous/quantitative_value_range.py @@ -30,7 +30,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/core/miscellaneous/research_product_group.py b/fairgraph/openminds/core/miscellaneous/research_product_group.py index 13bd6356..15570cae 100644 --- a/fairgraph/openminds/core/miscellaneous/research_product_group.py +++ b/fairgraph/openminds/core/miscellaneous/research_product_group.py @@ -20,7 +20,7 @@ class ResearchProductGroup(KGObject, OMResearchProductGroup): reverse_properties = [] existence_query_properties = ("context", "has_parts") - def __init__(self, context=None, has_parts=None, id=None, data=None, space=None, scope=None): + def __init__(self, context=None, has_parts=None, id=None, data=None, space=None, release_status=None): return KGObject.__init__( - self, id=id, space=space, scope=scope, data=data, context=context, has_parts=has_parts + self, id=id, space=space, release_status=release_status, 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 9a5cca47..f5ef4958 100644 --- a/fairgraph/openminds/core/miscellaneous/web_resource.py +++ b/fairgraph/openminds/core/miscellaneous/web_resource.py @@ -85,13 +85,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, content_description=content_description, describes=describes, diff --git a/fairgraph/openminds/core/products/dataset.py b/fairgraph/openminds/core/products/dataset.py index e92b6fe1..fb7d4436 100644 --- a/fairgraph/openminds/core/products/dataset.py +++ b/fairgraph/openminds/core/products/dataset.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/dataset_version.py b/fairgraph/openminds/core/products/dataset_version.py index 44b60141..f06fc1bb 100644 --- a/fairgraph/openminds/core/products/dataset_version.py +++ b/fairgraph/openminds/core/products/dataset_version.py @@ -149,13 +149,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, @@ -204,7 +204,7 @@ def __init__( def download(self, local_path, client, accept_terms_of_use=False): if accepted_terms_of_use(client, accept_terms_of_use=accept_terms_of_use): - repo = self.repository.resolve(client, scope=self.scope or None) + repo = self.repository.resolve(client, release_status=self.release_status or None) if repo.iri.value.startswith("https://object.cscs.ch/v1/AUTH") or repo.iri.value.startswith( "https://data-proxy.ebrains.eu/api/v1/public" ): diff --git a/fairgraph/openminds/core/products/meta_data_model.py b/fairgraph/openminds/core/products/meta_data_model.py index a98d188b..b14b4dad 100644 --- a/fairgraph/openminds/core/products/meta_data_model.py +++ b/fairgraph/openminds/core/products/meta_data_model.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/meta_data_model_version.py b/fairgraph/openminds/core/products/meta_data_model_version.py index 3126b1cf..a2193ed4 100644 --- a/fairgraph/openminds/core/products/meta_data_model_version.py +++ b/fairgraph/openminds/core/products/meta_data_model_version.py @@ -104,13 +104,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/model.py b/fairgraph/openminds/core/products/model.py index 281023de..f7d8e42a 100644 --- a/fairgraph/openminds/core/products/model.py +++ b/fairgraph/openminds/core/products/model.py @@ -65,20 +65,20 @@ def __init__( how_to_cite=None, is_part_of=None, learning_resources=None, - model_scope=None, + scope=None, short_name=None, study_targets=None, versions=None, id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, @@ -94,7 +94,7 @@ def __init__( how_to_cite=how_to_cite, is_part_of=is_part_of, learning_resources=learning_resources, - model_scope=model_scope, + scope=scope, short_name=short_name, study_targets=study_targets, versions=versions, diff --git a/fairgraph/openminds/core/products/model_version.py b/fairgraph/openminds/core/products/model_version.py index a069a5f2..1f212a0b 100644 --- a/fairgraph/openminds/core/products/model_version.py +++ b/fairgraph/openminds/core/products/model_version.py @@ -151,13 +151,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/project.py b/fairgraph/openminds/core/products/project.py index e83904d1..a02e54f6 100644 --- a/fairgraph/openminds/core/products/project.py +++ b/fairgraph/openminds/core/products/project.py @@ -37,13 +37,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/setup.py b/fairgraph/openminds/core/products/setup.py index eb5c5e6e..31401a6f 100644 --- a/fairgraph/openminds/core/products/setup.py +++ b/fairgraph/openminds/core/products/setup.py @@ -50,13 +50,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, description=description, diff --git a/fairgraph/openminds/core/products/software.py b/fairgraph/openminds/core/products/software.py index 8e25880d..6083f805 100644 --- a/fairgraph/openminds/core/products/software.py +++ b/fairgraph/openminds/core/products/software.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/software_version.py b/fairgraph/openminds/core/products/software_version.py index 4e5facd2..7f64ec0a 100644 --- a/fairgraph/openminds/core/products/software_version.py +++ b/fairgraph/openminds/core/products/software_version.py @@ -153,13 +153,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/web_service.py b/fairgraph/openminds/core/products/web_service.py index e105e110..e9544e45 100644 --- a/fairgraph/openminds/core/products/web_service.py +++ b/fairgraph/openminds/core/products/web_service.py @@ -86,13 +86,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/products/web_service_version.py b/fairgraph/openminds/core/products/web_service_version.py index 86f23d2e..44d21f5b 100644 --- a/fairgraph/openminds/core/products/web_service_version.py +++ b/fairgraph/openminds/core/products/web_service_version.py @@ -120,13 +120,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/core/research/behavioral_protocol.py b/fairgraph/openminds/core/research/behavioral_protocol.py index abb5ddc7..d2c98a66 100644 --- a/fairgraph/openminds/core/research/behavioral_protocol.py +++ b/fairgraph/openminds/core/research/behavioral_protocol.py @@ -50,13 +50,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, described_in=described_in, diff --git a/fairgraph/openminds/core/research/configuration.py b/fairgraph/openminds/core/research/configuration.py index 1ed89c7f..45306556 100644 --- a/fairgraph/openminds/core/research/configuration.py +++ b/fairgraph/openminds/core/research/configuration.py @@ -52,13 +52,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, configuration=configuration, diff --git a/fairgraph/openminds/core/research/custom_property_set.py b/fairgraph/openminds/core/research/custom_property_set.py index 9cbd6b88..a86cd36a 100644 --- a/fairgraph/openminds/core/research/custom_property_set.py +++ b/fairgraph/openminds/core/research/custom_property_set.py @@ -19,7 +19,7 @@ class CustomPropertySet(EmbeddedMetadata, OMCustomPropertySet): reverse_properties = [] def __init__( - self, context=None, data_location=None, relevant_for=None, id=None, data=None, space=None, scope=None + self, context=None, data_location=None, relevant_for=None, id=None, data=None, space=None, release_status=None ): 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 0d3e0a10..ad54ef82 100644 --- a/fairgraph/openminds/core/research/numerical_property.py +++ b/fairgraph/openminds/core/research/numerical_property.py @@ -18,5 +18,5 @@ class NumericalProperty(EmbeddedMetadata, OMNumericalProperty): # 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): + def __init__(self, name=None, values=None, id=None, data=None, space=None, release_status=None): 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 89f5552e..be4aa839 100644 --- a/fairgraph/openminds/core/research/property_value_list.py +++ b/fairgraph/openminds/core/research/property_value_list.py @@ -55,13 +55,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, defines_environment_of=defines_environment_of, diff --git a/fairgraph/openminds/core/research/protocol.py b/fairgraph/openminds/core/research/protocol.py index 017853ed..d6f5dca6 100644 --- a/fairgraph/openminds/core/research/protocol.py +++ b/fairgraph/openminds/core/research/protocol.py @@ -50,13 +50,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, described_in=described_in, diff --git a/fairgraph/openminds/core/research/protocol_execution.py b/fairgraph/openminds/core/research/protocol_execution.py index 96667d3e..f29eeab1 100644 --- a/fairgraph/openminds/core/research/protocol_execution.py +++ b/fairgraph/openminds/core/research/protocol_execution.py @@ -51,13 +51,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, based_on_protocol_execution=based_on_protocol_execution, diff --git a/fairgraph/openminds/core/research/strain.py b/fairgraph/openminds/core/research/strain.py index b3a0b3f2..20a52087 100644 --- a/fairgraph/openminds/core/research/strain.py +++ b/fairgraph/openminds/core/research/strain.py @@ -63,13 +63,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alternate_identifiers=alternate_identifiers, diff --git a/fairgraph/openminds/core/research/string_property.py b/fairgraph/openminds/core/research/string_property.py index 47a1b773..7bb3cf49 100644 --- a/fairgraph/openminds/core/research/string_property.py +++ b/fairgraph/openminds/core/research/string_property.py @@ -18,5 +18,5 @@ class StringProperty(EmbeddedMetadata, OMStringProperty): # 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): + def __init__(self, name=None, value=None, id=None, data=None, space=None, release_status=None): 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 07adc1f3..efe3e0f3 100644 --- a/fairgraph/openminds/core/research/subject.py +++ b/fairgraph/openminds/core/research/subject.py @@ -59,13 +59,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, biological_sex=biological_sex, diff --git a/fairgraph/openminds/core/research/subject_group.py b/fairgraph/openminds/core/research/subject_group.py index 72780ed1..6d39c430 100644 --- a/fairgraph/openminds/core/research/subject_group.py +++ b/fairgraph/openminds/core/research/subject_group.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/core/research/subject_group_state.py b/fairgraph/openminds/core/research/subject_group_state.py index f89225e0..e4afb20d 100644 --- a/fairgraph/openminds/core/research/subject_group_state.py +++ b/fairgraph/openminds/core/research/subject_group_state.py @@ -86,13 +86,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/core/research/subject_state.py b/fairgraph/openminds/core/research/subject_state.py index 13662b89..c0d32b83 100644 --- a/fairgraph/openminds/core/research/subject_state.py +++ b/fairgraph/openminds/core/research/subject_state.py @@ -110,13 +110,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/core/research/tissue_sample.py b/fairgraph/openminds/core/research/tissue_sample.py index 18051e86..a73fe5bb 100644 --- a/fairgraph/openminds/core/research/tissue_sample.py +++ b/fairgraph/openminds/core/research/tissue_sample.py @@ -63,13 +63,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, anatomical_locations=anatomical_locations, diff --git a/fairgraph/openminds/core/research/tissue_sample_collection.py b/fairgraph/openminds/core/research/tissue_sample_collection.py index 9f20aae1..27679e27 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection.py @@ -73,13 +73,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/core/research/tissue_sample_collection_state.py b/fairgraph/openminds/core/research/tissue_sample_collection_state.py index fa992f84..24736749 100644 --- a/fairgraph/openminds/core/research/tissue_sample_collection_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_collection_state.py @@ -84,13 +84,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/core/research/tissue_sample_state.py b/fairgraph/openminds/core/research/tissue_sample_state.py index f32a0352..adfe5be3 100644 --- a/fairgraph/openminds/core/research/tissue_sample_state.py +++ b/fairgraph/openminds/core/research/tissue_sample_state.py @@ -101,13 +101,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/ephys/activity/cell_patching.py b/fairgraph/openminds/ephys/activity/cell_patching.py index 1eb72779..81f7ba30 100644 --- a/fairgraph/openminds/ephys/activity/cell_patching.py +++ b/fairgraph/openminds/ephys/activity/cell_patching.py @@ -45,13 +45,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, bath_temperature=bath_temperature, diff --git a/fairgraph/openminds/ephys/activity/electrode_placement.py b/fairgraph/openminds/ephys/activity/electrode_placement.py index b405c65c..3f20043a 100644 --- a/fairgraph/openminds/ephys/activity/electrode_placement.py +++ b/fairgraph/openminds/ephys/activity/electrode_placement.py @@ -42,13 +42,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/ephys/activity/recording_activity.py b/fairgraph/openminds/ephys/activity/recording_activity.py index bf8cc1e5..30d71975 100644 --- a/fairgraph/openminds/ephys/activity/recording_activity.py +++ b/fairgraph/openminds/ephys/activity/recording_activity.py @@ -42,13 +42,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/ephys/device/electrode.py b/fairgraph/openminds/ephys/device/electrode.py index 7bebeb6b..5e386913 100644 --- a/fairgraph/openminds/ephys/device/electrode.py +++ b/fairgraph/openminds/ephys/device/electrode.py @@ -56,13 +56,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, lookup_label=lookup_label, diff --git a/fairgraph/openminds/ephys/device/electrode_array.py b/fairgraph/openminds/ephys/device/electrode_array.py index f7d4d1dd..e877af8f 100644 --- a/fairgraph/openminds/ephys/device/electrode_array.py +++ b/fairgraph/openminds/ephys/device/electrode_array.py @@ -58,13 +58,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, lookup_label=lookup_label, diff --git a/fairgraph/openminds/ephys/device/electrode_array_usage.py b/fairgraph/openminds/ephys/device/electrode_array_usage.py index 0746202d..a6950478 100644 --- a/fairgraph/openminds/ephys/device/electrode_array_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_array_usage.py @@ -80,13 +80,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, anatomical_locations_of_arrays=anatomical_locations_of_arrays, diff --git a/fairgraph/openminds/ephys/device/electrode_usage.py b/fairgraph/openminds/ephys/device/electrode_usage.py index 3b2ce02a..138c6f8f 100644 --- a/fairgraph/openminds/ephys/device/electrode_usage.py +++ b/fairgraph/openminds/ephys/device/electrode_usage.py @@ -78,13 +78,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, anatomical_location=anatomical_location, diff --git a/fairgraph/openminds/ephys/device/pipette.py b/fairgraph/openminds/ephys/device/pipette.py index ee39a7fe..79c2dd3c 100644 --- a/fairgraph/openminds/ephys/device/pipette.py +++ b/fairgraph/openminds/ephys/device/pipette.py @@ -56,13 +56,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, lookup_label=lookup_label, diff --git a/fairgraph/openminds/ephys/device/pipette_usage.py b/fairgraph/openminds/ephys/device/pipette_usage.py index ad1198d5..ad352bc7 100644 --- a/fairgraph/openminds/ephys/device/pipette_usage.py +++ b/fairgraph/openminds/ephys/device/pipette_usage.py @@ -89,13 +89,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, anatomical_location=anatomical_location, diff --git a/fairgraph/openminds/ephys/entity/channel.py b/fairgraph/openminds/ephys/entity/channel.py index 69943189..690f2e3c 100644 --- a/fairgraph/openminds/ephys/entity/channel.py +++ b/fairgraph/openminds/ephys/entity/channel.py @@ -18,5 +18,5 @@ class Channel(EmbeddedMetadata, OMChannel): # 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): + def __init__(self, internal_identifier=None, unit=None, id=None, data=None, space=None, release_status=None): 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 f63def75..894ed0d5 100644 --- a/fairgraph/openminds/ephys/entity/recording.py +++ b/fairgraph/openminds/ephys/entity/recording.py @@ -43,13 +43,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, additional_remarks=additional_remarks, diff --git a/fairgraph/openminds/publications/book.py b/fairgraph/openminds/publications/book.py index 8c69fc6c..3dbffd76 100644 --- a/fairgraph/openminds/publications/book.py +++ b/fairgraph/openminds/publications/book.py @@ -76,13 +76,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, abstract=abstract, diff --git a/fairgraph/openminds/publications/chapter.py b/fairgraph/openminds/publications/chapter.py index 5e4fd59f..6834c210 100644 --- a/fairgraph/openminds/publications/chapter.py +++ b/fairgraph/openminds/publications/chapter.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, abstract=abstract, diff --git a/fairgraph/openminds/publications/learning_resource.py b/fairgraph/openminds/publications/learning_resource.py index 80c7ca1b..9f6d1a64 100644 --- a/fairgraph/openminds/publications/learning_resource.py +++ b/fairgraph/openminds/publications/learning_resource.py @@ -54,13 +54,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, about=about, diff --git a/fairgraph/openminds/publications/live_paper.py b/fairgraph/openminds/publications/live_paper.py index 3dbc5a28..5e5cf312 100644 --- a/fairgraph/openminds/publications/live_paper.py +++ b/fairgraph/openminds/publications/live_paper.py @@ -69,13 +69,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/publications/live_paper_resource_item.py b/fairgraph/openminds/publications/live_paper_resource_item.py index 9a17c907..af845059 100644 --- a/fairgraph/openminds/publications/live_paper_resource_item.py +++ b/fairgraph/openminds/publications/live_paper_resource_item.py @@ -42,13 +42,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, hosted_by=hosted_by, diff --git a/fairgraph/openminds/publications/live_paper_section.py b/fairgraph/openminds/publications/live_paper_section.py index b8200eeb..a0ed99d1 100644 --- a/fairgraph/openminds/publications/live_paper_section.py +++ b/fairgraph/openminds/publications/live_paper_section.py @@ -40,13 +40,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, description=description, diff --git a/fairgraph/openminds/publications/live_paper_version.py b/fairgraph/openminds/publications/live_paper_version.py index 536f3edf..02b9d9ad 100644 --- a/fairgraph/openminds/publications/live_paper_version.py +++ b/fairgraph/openminds/publications/live_paper_version.py @@ -114,13 +114,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/publications/periodical.py b/fairgraph/openminds/publications/periodical.py index 5138a30a..b7097a5f 100644 --- a/fairgraph/openminds/publications/periodical.py +++ b/fairgraph/openminds/publications/periodical.py @@ -38,13 +38,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, abbreviation=abbreviation, diff --git a/fairgraph/openminds/publications/publication_issue.py b/fairgraph/openminds/publications/publication_issue.py index d4c4e714..95c636ca 100644 --- a/fairgraph/openminds/publications/publication_issue.py +++ b/fairgraph/openminds/publications/publication_issue.py @@ -29,12 +29,14 @@ class PublicationIssue(KGObject, OMPublicationIssue): ] 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): + def __init__( + self, has_parts=None, is_part_of=None, issue_number=None, id=None, data=None, space=None, release_status=None + ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, has_parts=has_parts, is_part_of=is_part_of, diff --git a/fairgraph/openminds/publications/publication_volume.py b/fairgraph/openminds/publications/publication_volume.py index a132a231..2f162807 100644 --- a/fairgraph/openminds/publications/publication_volume.py +++ b/fairgraph/openminds/publications/publication_volume.py @@ -30,13 +30,13 @@ class PublicationVolume(KGObject, OMPublicationVolume): existence_query_properties = ("is_part_of", "volume_number") def __init__( - self, has_parts=None, is_part_of=None, volume_number=None, id=None, data=None, space=None, scope=None + self, has_parts=None, is_part_of=None, volume_number=None, id=None, data=None, space=None, release_status=None ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, has_parts=has_parts, is_part_of=is_part_of, diff --git a/fairgraph/openminds/publications/scholarly_article.py b/fairgraph/openminds/publications/scholarly_article.py index ae2ce1b9..c17104cf 100644 --- a/fairgraph/openminds/publications/scholarly_article.py +++ b/fairgraph/openminds/publications/scholarly_article.py @@ -71,13 +71,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, abstract=abstract, @@ -104,7 +104,9 @@ def __init__( def get_journal(self, client, with_volume=False, with_issue=False): journal = volume = issue = None if self.is_part_of: - issue_or_volume = self.is_part_of.resolve(client, scope=self.scope, follow_links={"is_part_of": {}}) + issue_or_volume = self.is_part_of.resolve( + client, release_status=self.release_status, follow_links={"is_part_of": {}} + ) if isinstance(issue_or_volume, PublicationIssue): volume = issue_or_volume.is_part_of issue = issue_or_volume diff --git a/fairgraph/openminds/sands/atlas/atlas_annotation.py b/fairgraph/openminds/sands/atlas/atlas_annotation.py index 21b4ff50..657f5041 100644 --- a/fairgraph/openminds/sands/atlas/atlas_annotation.py +++ b/fairgraph/openminds/sands/atlas/atlas_annotation.py @@ -33,7 +33,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/sands/atlas/brain_atlas.py b/fairgraph/openminds/sands/atlas/brain_atlas.py index ca9d1350..a71dbb7d 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas.py @@ -82,13 +82,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/sands/atlas/brain_atlas_version.py b/fairgraph/openminds/sands/atlas/brain_atlas_version.py index 8acd3abb..f8de269e 100644 --- a/fairgraph/openminds/sands/atlas/brain_atlas_version.py +++ b/fairgraph/openminds/sands/atlas/brain_atlas_version.py @@ -125,13 +125,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space.py b/fairgraph/openminds/sands/atlas/common_coordinate_space.py index a374bf06..73518fb0 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space.py @@ -90,13 +90,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py index 0dae2548..9e645aa0 100644 --- a/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py +++ b/fairgraph/openminds/sands/atlas/common_coordinate_space_version.py @@ -153,13 +153,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, alias=alias, diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity.py b/fairgraph/openminds/sands/atlas/parcellation_entity.py index ed489a6d..7d3985d3 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity.py @@ -107,13 +107,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, lookup_label=lookup_label, diff --git a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py index 9ad33086..de02aa20 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_entity_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_entity_version.py @@ -132,13 +132,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, lookup_label=lookup_label, diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology.py b/fairgraph/openminds/sands/atlas/parcellation_terminology.py index fa7ad8b9..464664e3 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology.py @@ -26,7 +26,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py index 93ca650b..e79f510f 100644 --- a/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py +++ b/fairgraph/openminds/sands/atlas/parcellation_terminology_version.py @@ -26,7 +26,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/sands/mathematical_shapes/circle.py b/fairgraph/openminds/sands/mathematical_shapes/circle.py index 1951488b..734ad239 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/circle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/circle.py @@ -18,5 +18,5 @@ class Circle(EmbeddedMetadata, OMCircle): # 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): + def __init__(self, radius=None, id=None, data=None, space=None, release_status=None): 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 567b40b1..1e0102bb 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/ellipse.py +++ b/fairgraph/openminds/sands/mathematical_shapes/ellipse.py @@ -18,7 +18,7 @@ class Ellipse(EmbeddedMetadata, OMEllipse): # 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): + def __init__(self, semi_major_axis=None, semi_minor_axis=None, id=None, data=None, space=None, release_status=None): 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 8894f237..6b6f82f4 100644 --- a/fairgraph/openminds/sands/mathematical_shapes/rectangle.py +++ b/fairgraph/openminds/sands/mathematical_shapes/rectangle.py @@ -18,5 +18,5 @@ class Rectangle(EmbeddedMetadata, OMRectangle): # 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): + def __init__(self, length=None, width=None, id=None, data=None, space=None, release_status=None): 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 57139a50..ffae9615 100644 --- a/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py +++ b/fairgraph/openminds/sands/miscellaneous/anatomical_target_position.py @@ -27,7 +27,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py index 06c643f3..4c1fe90d 100644 --- a/fairgraph/openminds/sands/miscellaneous/coordinate_point.py +++ b/fairgraph/openminds/sands/miscellaneous/coordinate_point.py @@ -18,5 +18,5 @@ class CoordinatePoint(EmbeddedMetadata, OMCoordinatePoint): # 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): + def __init__(self, coordinate_space=None, coordinates=None, id=None, data=None, space=None, release_status=None): 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 d822bb33..a7f578a1 100644 --- a/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/qualitative_relation_assessment.py @@ -19,7 +19,14 @@ class QualitativeRelationAssessment(EmbeddedMetadata, OMQualitativeRelationAsses reverse_properties = [] def __init__( - self, criteria=None, in_relation_to=None, qualitative_overlap=None, id=None, data=None, space=None, scope=None + self, + criteria=None, + in_relation_to=None, + qualitative_overlap=None, + id=None, + data=None, + space=None, + release_status=None, ): 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 4d1a6166..68bd8802 100644 --- a/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py +++ b/fairgraph/openminds/sands/miscellaneous/quantitative_relation_assessment.py @@ -19,7 +19,14 @@ class QuantitativeRelationAssessment(EmbeddedMetadata, OMQuantitativeRelationAss reverse_properties = [] def __init__( - self, criteria=None, in_relation_to=None, quantitative_overlap=None, id=None, data=None, space=None, scope=None + self, + criteria=None, + in_relation_to=None, + quantitative_overlap=None, + id=None, + data=None, + space=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/sands/miscellaneous/single_color.py b/fairgraph/openminds/sands/miscellaneous/single_color.py index e3980294..843be06b 100644 --- a/fairgraph/openminds/sands/miscellaneous/single_color.py +++ b/fairgraph/openminds/sands/miscellaneous/single_color.py @@ -20,5 +20,5 @@ class SingleColor(KGObject, OMSingleColor): reverse_properties = [] existence_query_properties = ("value",) - 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) + def __init__(self, value=None, id=None, data=None, space=None, release_status=None): + return KGObject.__init__(self, id=id, space=space, release_status=release_status, data=data, value=value) diff --git a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py index 9965a0d8..b04d1aa5 100644 --- a/fairgraph/openminds/sands/miscellaneous/viewer_specification.py +++ b/fairgraph/openminds/sands/miscellaneous/viewer_specification.py @@ -27,7 +27,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py index 61b876d8..cb506b8f 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py +++ b/fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py @@ -91,13 +91,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, has_annotations=has_annotations, diff --git a/fairgraph/openminds/sands/non_atlas/custom_annotation.py b/fairgraph/openminds/sands/non_atlas/custom_annotation.py index 8f2d86dd..ba9ea271 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_annotation.py +++ b/fairgraph/openminds/sands/non_atlas/custom_annotation.py @@ -34,7 +34,7 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return EmbeddedMetadata.__init__( self, diff --git a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py index cc2fb703..eac08012 100644 --- a/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py +++ b/fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py @@ -49,13 +49,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, anatomical_axes_orientation=anatomical_axes_orientation, diff --git a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py index 5df9fb4a..cf52e6a6 100644 --- a/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py @@ -43,13 +43,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, construction_type=construction_type, diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py index 84a83e9d..4d637c26 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py @@ -42,13 +42,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, culture_medium=culture_medium, diff --git a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py index 4dcec1f3..56a71c19 100644 --- a/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py +++ b/fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py @@ -43,13 +43,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device.py b/fairgraph/openminds/specimen_prep/device/slicing_device.py index 9fa935d7..03fa9800 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device.py @@ -52,13 +52,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, name=name, lookup_label=lookup_label, diff --git a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py index 8613e1f9..4d1cf6c5 100644 --- a/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py +++ b/fairgraph/openminds/specimen_prep/device/slicing_device_usage.py @@ -90,13 +90,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, device=device, diff --git a/fairgraph/openminds/stimulation/activity/stimulation_activity.py b/fairgraph/openminds/stimulation/activity/stimulation_activity.py index f2a4268e..38d5118c 100644 --- a/fairgraph/openminds/stimulation/activity/stimulation_activity.py +++ b/fairgraph/openminds/stimulation/activity/stimulation_activity.py @@ -42,13 +42,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, custom_property_sets=custom_property_sets, diff --git a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py index 2f900b8e..3557d49c 100644 --- a/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py +++ b/fairgraph/openminds/stimulation/stimulus/ephys_stimulus.py @@ -43,13 +43,13 @@ def __init__( id=None, data=None, space=None, - scope=None, + release_status=None, ): return KGObject.__init__( self, id=id, space=space, - scope=scope, + release_status=release_status, data=data, lookup_label=lookup_label, delivered_by=delivered_by, diff --git a/fairgraph/registry.py b/fairgraph/registry.py index 5d2b1cd1..b9db1fb7 100644 --- a/fairgraph/registry.py +++ b/fairgraph/registry.py @@ -68,7 +68,7 @@ def gen_path(type_): ) # todo: add property.instructions if present field_docs.append(doc) - # todo: also document id, data, space, scope + # todo: also document id, data, space, release_status return docstring_template.format(base=cls._base_docstring, args="\n".join(field_docs)) __doc__ = property(_get_doc) # type: ignore[assignment] diff --git a/test/test_base.py b/test/test_base.py index 86774205..feb20c69 100644 --- a/test/test_base.py +++ b/test/test_base.py @@ -518,7 +518,7 @@ def test_exists__it_does_exist(self): orig_object = self._construct_object_required_properties() class MockClient: - def instance_from_full_uri(self, id, use_cache=True, scope="in progress", require_full_data=True): + def instance_from_full_uri(self, id, use_cache=True, release_status="in progress", require_full_data=True): 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 diff --git a/test/test_client.py b/test/test_client.py index 6c2da548..81a7e979 100644 --- a/test/test_client.py +++ b/test/test_client.py @@ -80,7 +80,7 @@ def test_query_filter_by_space(kg_client): instance_id=None, from_index=0, size=1000, - scope="in progress", + release_status="in progress", id_key="uri", ) spaces = set(result["project_id"] for result in results.data) @@ -97,13 +97,13 @@ def test_get_admin_client(kg_client): @skip_if_no_connection def test_list_scopes(kg_client): - def _get_models(scope): + def _get_models(release_status): return kg_client.list( target_type="https://openminds.om-i.org/types/Model", space="model", from_index=0, size=10000, - scope=scope, + release_status=release_status, ) released_models = _get_models("released") @@ -150,7 +150,7 @@ def test_get_instance_from_cache(kg_client): @skip_if_no_connection def test_get_instance_no_cache(kg_client): instance_id = "https://kg.ebrains.eu/api/instances/5ed1e9f9-482d-41c7-affd-f1aa887bd618" - instance1 = kg_client.instance_from_full_uri(instance_id, use_cache=False, scope="any") + instance1 = kg_client.instance_from_full_uri(instance_id, use_cache=False, release_status="any") instance2 = kg_client.instance_from_full_uri(instance_id, use_cache=False) assert instance2 is not instance1 diff --git a/test/test_data/queries/openminds/core/model_vf_query.json b/test/test_data/queries/openminds/core/model_vf_query.json index 4d84f481..adfd8390 100644 --- a/test/test_data/queries/openminds/core/model_vf_query.json +++ b/test/test_data/queries/openminds/core/model_vf_query.json @@ -195,12 +195,12 @@ }, { "https://core.kg.ebrains.eu/vocab/query/propertyName": { - "@id": "https://schema.hbp.eu/myQuery/model_scope" + "@id": "https://schema.hbp.eu/myQuery/scope" }, "https://core.kg.ebrains.eu/vocab/query/singleValue": "FIRST", "https://core.kg.ebrains.eu/vocab/query/filter": { "https://core.kg.ebrains.eu/vocab/query/op": "CONTAINS", - "https://core.kg.ebrains.eu/vocab/query/parameter": "model_scope" + "https://core.kg.ebrains.eu/vocab/query/parameter": "scope" }, "https://core.kg.ebrains.eu/vocab/query/path": [ { diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index c8c59816..1d418468 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -35,7 +35,7 @@ def test_query_generation(mock_client): @skip_if_no_connection def test_retrieve_released_models_no_filter_api_core(kg_client): models = omcore.Model.list( - kg_client, scope="released", space="model", api="core", size=20, from_index=randint(0, 80) + kg_client, release_status="released", space="model", api="core", size=20, from_index=randint(0, 80) ) assert len(models) == 20 for m in models: @@ -45,7 +45,7 @@ def test_retrieve_released_models_no_filter_api_core(kg_client): @skip_if_no_connection def test_retrieve_released_models_no_filter_api_query(kg_client): models = omcore.Model.list( - kg_client, scope="released", space="model", api="query", size=20, from_index=randint(0, 80) + kg_client, release_status="released", space="model", api="query", size=20, from_index=randint(0, 80) ) assert len(models) == 20 @@ -53,17 +53,17 @@ def test_retrieve_released_models_no_filter_api_query(kg_client): @skip_if_no_connection def test_retrieve_released_models_with_filter_api_core(kg_client): with pytest.raises(ValueError): - models = omcore.Model.list(kg_client, scope="released", api="core", name="foo") + models = omcore.Model.list(kg_client, release_status="released", api="core", name="foo") @skip_if_no_connection def test_retrieve_released_models_filter_species_by_obj(kg_client): rat = omterms.Species.by_name("Rattus norvegicus", kg_client) assert rat.name == "Rattus norvegicus" - models = omcore.Model.list(kg_client, scope="released", space="model", api="query", study_targets=rat) + models = omcore.Model.list(kg_client, release_status="released", space="model", api="query", study_targets=rat) assert len(models) > 0 for model in models: - study_targets = [st.resolve(kg_client, scope="released") for st in as_list(model.study_targets)] + study_targets = [st.resolve(kg_client, release_status="released") for st in as_list(model.study_targets)] if study_targets: assert rat in study_targets @@ -71,7 +71,7 @@ def test_retrieve_released_models_filter_species_by_obj(kg_client): @skip_if_no_connection def test_retrieve_released_models_filter_species_by_uuid(kg_client): human = omterms.Species.by_name("Homo sapiens", kg_client) - models = omcore.Model.list(kg_client, scope="released", space="model", api="query", study_targets=UUID(human.uuid)) + models = omcore.Model.list(kg_client, release_status="released", space="model", api="query", study_targets=UUID(human.uuid)) assert len(models) > 0 for model in models: if model.study_targets: @@ -81,7 +81,7 @@ def test_retrieve_released_models_filter_species_by_uuid(kg_client): @skip_if_no_connection def test_retrieve_released_models_filter_species_by_id(kg_client): mouse = omterms.Species.by_name("Mus musculus", kg_client) - models = omcore.Model.list(kg_client, scope="released", space="model", api="query", study_targets=IRI(mouse.id)) + models = omcore.Model.list(kg_client, release_status="released", space="model", api="query", study_targets=IRI(mouse.id)) # todo: fix so that don't need to wrap the id in an IRI assert len(models) > 0 for model in models: @@ -93,7 +93,7 @@ def test_retrieve_released_models_filter_species_by_id(kg_client): def test_retrieve_released_models_filter_custodian(kg_client): alain = omcore.Person.list(kg_client, family_name="Destexhe", given_name="Alain")[0] assert alain.given_name == "Alain" - models = omcore.Model.list(kg_client, scope="released", space="model", api="query", custodians=alain) + models = omcore.Model.list(kg_client, release_status="released", space="model", api="query", custodians=alain) assert len(models) > 0 for model in models: assert alain.id in [c.id for c in as_list(model.custodians)] @@ -101,9 +101,9 @@ def test_retrieve_released_models_filter_custodian(kg_client): @skip_if_no_connection def test_retrieve_models_filter_by_space(kg_client): - all_models = omcore.Model.list(kg_client, scope="in progress", space=None, size=10000) - n_models_in_model_space_core = omcore.Model.count(kg_client, scope="in progress", space="model", api="core") - n_models_in_model_space_query = omcore.Model.count(kg_client, scope="in progress", space="model", api="query") + all_models = omcore.Model.list(kg_client, release_status="in progress", space=None, size=10000) + n_models_in_model_space_core = omcore.Model.count(kg_client, release_status="in progress", space="model", api="core") + n_models_in_model_space_query = omcore.Model.count(kg_client, release_status="in progress", space="model", api="query") assert n_models_in_model_space_core == n_models_in_model_space_query assert len(all_models) > n_models_in_model_space_core assert len([m for m in all_models if m.space == "model"]) == n_models_in_model_space_query @@ -117,7 +117,7 @@ def test_retrieve_single_model_with_followed_links(kg_client): follow_links={"abstraction_level": {}}, ) assert isinstance(model.abstraction_level, omterms.ModelAbstractionLevel) # followed - assert isinstance(model.model_scope, KGProxy) # not followed + assert isinstance(model.scope, KGProxy) # not followed @skip_if_no_connection @@ -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="released", follow_links={"versions": {}, "custodians": {"affiliations": {}}} + kg_client, release_status="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="released", follow_links={"custodians": {"affiliations": {"member_of": {}}}} + kg_client, release_status="released", follow_links={"custodians": {"affiliations": {"member_of": {}}}} ) assert isinstance(resolved_model4.custodians[0].affiliations[0].member_of, omcore.Organization) @@ -159,7 +159,7 @@ def test_resolve_model(kg_client): def test_retrieve_released_models_follow_links(kg_client): models = omcore.Model.list( kg_client, - scope="released", + release_status="released", space="model", api="query", size=5, @@ -189,7 +189,7 @@ def test_retrieve_released_model_versions_no_follow(kg_client): for api in ("query", "core"): versions = omcore.ModelVersion.list( kg_client, - scope="released", + release_status="released", space="model", api=api, size=5, @@ -213,7 +213,7 @@ def test_retrieve_released_model_versions_no_follow(kg_client): def test_retrieve_released_model_versions_follow_reverse_links(kg_client): versions = omcore.ModelVersion.list( kg_client, - scope="released", + release_status="released", space="model", api="query", size=5, @@ -243,8 +243,8 @@ def test_retrieve_released_model_versions_follow_reverse_links(kg_client): assert ver.id in [ver2.id for ver2 in as_list(model.versions)] if model.abstraction_level: assert isinstance(model.abstraction_level, omterms.ModelAbstractionLevel) - if model.model_scope: - assert isinstance(model.model_scope, KGProxy) + if model.scope: + assert isinstance(model.scope, KGProxy) for developer in as_list(model.developers): assert isinstance(developer, (omcore.Person, omcore.Organization, omcore.Consortium)) @@ -253,7 +253,7 @@ def test_retrieve_released_model_versions_follow_reverse_links(kg_client): # def test_retrieve_released_people_resolve_two_steps(kg_client): # people = omcore.Person.list( # kg_client, -# scope="released", +# release_status="released", # space="common", # api="query", # size=5, @@ -265,7 +265,7 @@ def test_retrieve_released_model_versions_follow_reverse_links(kg_client): # @skip_if_no_connection # def test_retrieve_released_models_resolve_two_steps(kg_client): -# models = omcore.Model.list(kg_client, scope="released", space="model", +# models = omcore.Model.list(kg_client, release_status="released", space="model", # api="query", size=10, from_index=randint(0, 80), # follow_links=2) # assert len(models) == 10 @@ -295,7 +295,7 @@ 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="released", + release_status="released", space="model", api="query", follow_links={"developers": {"affiliations": {"member_of": {}}}}, @@ -314,7 +314,7 @@ 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="released", + release_status="released", space="model", api="query", follow_links=None, @@ -329,7 +329,7 @@ def test_query_across_links(kg_client): def test_query_across_reverse_links(kg_client): versions = omcore.ModelVersion.list( kg_client, - scope="released", + release_status="released", space="model", api="query", follow_links={"is_version_of": {"developers": {"affiliations": {"member_of": {}}}}}, @@ -356,8 +356,8 @@ def test_resolve_reverse_link(kg_client): @skip_if_no_connection def test_count_released_models(kg_client): - models = omcore.Model.list(kg_client, scope="released", space="model", api="core", size=1000) - n_models = omcore.Model.count(kg_client, scope="released", space="model", api="core") + models = omcore.Model.list(kg_client, release_status="released", space="model", api="core", size=1000) + n_models = omcore.Model.count(kg_client, release_status="released", space="model", api="core") assert len(models) == n_models assert n_models > 100 @@ -370,19 +370,19 @@ def test_count_models_with_filters(kg_client): models = omcore.Model.list( kg_client, - scope="released", + release_status="released", space="model", api="auto", study_targets=ca1, - model_scope=single_cell, + scope=single_cell, ) n_models = omcore.Model.count( kg_client, - scope="released", + release_status="released", space="model", api="auto", study_targets=ca1, - model_scope=single_cell, + scope=single_cell, ) assert len(models) == n_models assert n_models > 1 @@ -434,7 +434,7 @@ def test__update(): "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") + person = omcore.Person.from_jsonld(example_data, release_status="in progress") for key in ( "http://schema.org/identifier", "https://core.kg.ebrains.eu/vocab/meta/revision", @@ -451,10 +451,10 @@ def test__update(): def test_KGQuery_resolve(kg_client): ca1 = omterms.UBERONParcellation.by_name("CA1 field of hippocampus", kg_client) single_cell = omterms.ModelScope.by_name("single cell", kg_client) - filters = {"study_targets": ca1, "model_scope": single_cell} + filters = {"study_targets": ca1, "scope": single_cell} q = KGQuery(omcore.Model, filters) - models_q = q.resolve(kg_client, scope="released") - models_direct = omcore.Model.list(kg_client, scope="released", space="model", api="query", **filters) + models_q = q.resolve(kg_client, release_status="released") + models_direct = omcore.Model.list(kg_client, release_status="released", space="model", api="query", **filters) assert models_q == models_direct @@ -462,10 +462,10 @@ def test_KGQuery_resolve(kg_client): def test_KGQuery_count(kg_client): ca1 = omterms.UBERONParcellation.by_name("CA1 field of hippocampus", kg_client) single_cell = omterms.ModelScope.by_name("single cell", kg_client) - filters = {"study_targets": ca1, "model_scope": single_cell} + filters = {"study_targets": ca1, "scope": single_cell} q = KGQuery(omcore.Model, filters) - n_models_q = q.count(kg_client, space="model", scope="released") - n_models_direct = omcore.Model.count(kg_client, scope="released", space="model", api="query", **filters) + n_models_q = q.count(kg_client, space="model", release_status="released") + n_models_direct = omcore.Model.count(kg_client, release_status="released", space="model", api="query", **filters) assert n_models_q == n_models_direct assert n_models_q > 1 @@ -552,7 +552,7 @@ def test_save_new_mock(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - model_scope=omterms.ModelScope.by_name("subcellular", mock_client), + release_status=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), @@ -582,7 +582,7 @@ def test_save_existing_mock(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - model_scope=omterms.ModelScope.by_name("subcellular", mock_client), + release_status=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), @@ -613,7 +613,7 @@ def test_save_existing_mock_no_updates_allowed(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - model_scope=omterms.ModelScope.by_name("subcellular", mock_client), + release_status=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), @@ -645,7 +645,7 @@ def test_save_replace_existing_mock(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - model_scope=omterms.ModelScope.by_name("subcellular", mock_client), + release_status=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), @@ -878,7 +878,7 @@ 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_jsonld(data, scope="released") + obj = omcore.Model.from_jsonld(data, release_status="released") assert obj.abstraction_level assert len(obj.developers) == 5 omcore.Model.type_ = orig_type @@ -968,7 +968,7 @@ def test_with_new_namespace_from_query(): } #omcore.set_error_handling("error") orig_types = (omcore.Model.type_, omcore.Person.type_) - obj = omcore.Model.from_jsonld(data, scope="released") + obj = omcore.Model.from_jsonld(data, release_status="released") assert obj.abstraction_level assert len(obj.developers) == 5 omcore.Model.type_, omcore.Person.type_ = orig_types diff --git a/test/utils.py b/test/utils.py index 3e21f5ca..b522e4c5 100644 --- a/test/utils.py +++ b/test/utils.py @@ -69,7 +69,7 @@ def instance_from_full_uri( self, uri: str, use_cache: bool = True, - scope: str = "released", + release_status: str = "released", require_full_data: bool = True, ): if uri == "0000": @@ -77,7 +77,7 @@ def instance_from_full_uri( else: raise NotImplementedError - def query(self, query, filter=None, space=None, size=100, from_index=0, scope="released", restrict_to_spaces=None): + def query(self, query, filter=None, space=None, size=100, from_index=0, release_status="released", restrict_to_spaces=None): for prop in query["structure"]: if prop.get("propertyName", "") in ("Qname", "Qfull_name"): filter_value = prop["filter"]["value"] From d456a1e3523f4bf945dbad2f735578d52ef54d72 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 3 Nov 2025 15:55:05 +0100 Subject: [PATCH 2/2] Restore "scope" as a deprecated keyword for non-constructor methods; add "model_scope" as an alias. --- builder/update_openminds.py | 3 ++- fairgraph/client.py | 12 +++++++++--- fairgraph/kgobject.py | 16 +++++++++++++++- fairgraph/node.py | 4 ++-- .../openminds/computation/validation_test.py | 4 +++- fairgraph/openminds/core/products/model.py | 4 +++- fairgraph/utility.py | 14 +++++++++++++- test/test_openminds_core.py | 14 +++++++------- test/utils.py | 2 ++ 9 files changed, 56 insertions(+), 17 deletions(-) diff --git a/builder/update_openminds.py b/builder/update_openminds.py index ed9bc929..9a9b23a8 100644 --- a/builder/update_openminds.py +++ b/builder/update_openminds.py @@ -19,7 +19,8 @@ "full_name": "name", "has_versions": "versions", "has_entity": "entities", - "hashes": "hash" + "hashes": "hash", + "scope": "model_scope" } diff --git a/fairgraph/client.py b/fairgraph/client.py index e5b02972..692bb7bd 100644 --- a/fairgraph/client.py +++ b/fairgraph/client.py @@ -37,7 +37,7 @@ from openminds.registry import lookup_type from .errors import AuthenticationError, AuthorizationError, ResourceExistsError -from .utility import adapt_namespaces_for_query, adapt_namespaces_3to4, adapt_namespaces_4to3, adapt_type_4to3 +from .utility import adapt_namespaces_for_query, adapt_namespaces_3to4, adapt_namespaces_4to3, adapt_type_4to3, handle_scope_keyword from .base import OPENMINDS_VERSION if TYPE_CHECKING: @@ -212,6 +212,7 @@ def query( from_index: int = 0, size: int = 100, release_status: str = "released", + scope: Optional[str] = None, id_key: str = "@id", use_stored_query: bool = False, restrict_to_spaces: Optional[List[str]] = None @@ -234,7 +235,7 @@ def query( A ResultPage object containing a list of JSON-LD instances that satisfy the query, along with metadata about the query results such as total number of instances, and pagination information. """ - + release_status = handle_scope_keyword(scope, release_status) query_id = query.get("@id", None) if use_stored_query: @@ -301,6 +302,7 @@ def list( from_index: int = 0, size: int = 100, release_status: str = "released", + scope: Optional[str] = None, ) -> ResultPage[JsonLdDocument]: """ List KG instances of a given type. @@ -318,6 +320,7 @@ def list( A ResultPage object containing the list of JSON-LD instances, along with metadata about the query results such as total number of instances, and pagination information. """ + release_status = handle_scope_keyword(scope, release_status) if self.migrated is False: target_type = adapt_type_4to3(target_type) @@ -359,6 +362,7 @@ def instance_from_full_uri( uri: str, use_cache: bool = True, release_status: str = "released", + scope: Optional[str] = None, require_full_data: bool = True, ) -> JsonLdDocument: """ @@ -371,6 +375,7 @@ def instance_from_full_uri( Valid values are 'released', 'in progress', 'any'. require_full_data: Whether to only return instances for which the user has full read access. """ + release_status = handle_scope_keyword(scope, release_status) logger.debug("Retrieving instance from {}, api='core' use_cache={}".format(uri, use_cache)) data: JsonLdDocument if use_cache and uri in self.cache: @@ -706,13 +711,14 @@ def move_to_space(self, uri: str, destination_space: str): if response.error: raise Exception(response.error) - def space_info(self, space_name: str, release_status: str = "released", ignore_errors: bool = False): + def space_info(self, space_name: str, release_status: str = "released", scope: Optional[str] = None, ignore_errors: bool = False): """ Return information about the types and number of instances in a space. 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. """ + release_status = handle_scope_keyword(scope, release_status) # todo: if not self.migrated, adapt type before lookup result = self._kg_client.types.list(space=space_name, stage=STAGE_MAP[release_status]) if result.error: diff --git a/fairgraph/kgobject.py b/fairgraph/kgobject.py index cc60a4f5..94e5bc25 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, normalize_data +from .utility import expand_uri, as_list, expand_filter, ActivityLog, normalize_data, handle_scope_keyword from .queries import Query, QueryProperty from .errors import AuthorizationError, ResourceExistsError, CannotBuildExistenceQuery from .caching import object_cache, save_cache, generate_cache_key @@ -137,6 +137,7 @@ def from_uri( client: KGClient, use_cache: bool = True, release_status: str = "released", + scope: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, ): @@ -152,6 +153,7 @@ def from_uri( 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. """ + release_status = handle_scope_keyword(scope, release_status) if follow_links: query = cls.generate_query( space=None, @@ -179,6 +181,7 @@ def from_uuid( client: KGClient, use_cache: bool = True, release_status: str = "released", + scope: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, ): @@ -195,6 +198,7 @@ def from_uuid( with_reverse_properties (bool): Whether to include reverse properties. Defaults to False. """ + release_status = handle_scope_keyword(scope, release_status) logger.info("Attempting to retrieve {} with uuid {}".format(cls.__name__, uuid)) if len(uuid) == 0: raise ValueError("Empty UUID") @@ -219,6 +223,7 @@ def from_id( client: KGClient, use_cache: bool = True, release_status: str = "released", + scope: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, ): @@ -239,6 +244,7 @@ def from_id( A return value of None means either the object doesn't exist or the user doesn't have permission to access it. """ + release_status = handle_scope_keyword(scope, release_status) if hasattr(cls, "type_") and cls.type_: if id.startswith("http"): fn = cls.from_uri @@ -275,6 +281,7 @@ def from_alias( client: KGClient, space: Optional[str] = None, release_status: str = "released", + scope: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, ): """ @@ -291,6 +298,7 @@ def from_alias( follow_links (dict): The links in the graph to follow. Defaults to None. """ + release_status = handle_scope_keyword(scope, release_status) # todo: move this to openminds generation, and include only in those subclasses # that have an alias # todo: also count 'lookup_name' as an alias @@ -342,6 +350,7 @@ def list( from_index: int = 0, api: str = "auto", release_status: str = "released", + scope: Optional[str] = None, space: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, with_reverse_properties: Optional[bool] = False, @@ -381,6 +390,7 @@ def list( fast spiking interneuron A parvalbumin positive GABAergic interneuron with a high-frequency firing pattern. """ + release_status = handle_scope_keyword(scope, release_status) if api == "auto": if filters: @@ -418,6 +428,7 @@ def count( client: KGClient, api: str = "auto", release_status: str = "released", + scope: Optional[str] = None, space: Optional[str] = None, **filters, ) -> int: @@ -447,6 +458,7 @@ def count( 8 """ + release_status = handle_scope_keyword(scope, release_status) if api == "auto": if filters: api = "query" @@ -792,6 +804,7 @@ def by_name( all: bool = False, space: Optional[str] = None, release_status: str = "released", + scope: Optional[str] = None, follow_links: Optional[Dict[str, Any]] = None, ) -> Union[KGObject, List[KGObject], None]: """ @@ -810,6 +823,7 @@ def by_name( follow_links (dict): The links in the graph to follow. Defaults to None. """ + release_status = handle_scope_keyword(scope, release_status) # todo: move this to openminds generation, and include only in those subclasses # that have a name # todo: also count 'lookup_name', "family_name", "given_name" as a name diff --git a/fairgraph/node.py b/fairgraph/node.py index bfe65a69..74675ed2 100644 --- a/fairgraph/node.py +++ b/fairgraph/node.py @@ -193,7 +193,7 @@ def _check_validity(filters, property_names): raise ValueError(msg + ", ".join(sorted(invalid_filters))) if check_validity: - _check_validity(filter_dict_copy, cls.all_property_names) + _check_validity(filter_dict_copy, cls.all_property_names + list(cls.aliases.keys())) for prop in cls.all_properties: if prop.name in filter_dict_copy: @@ -204,7 +204,7 @@ def _check_validity(filters, property_names): set( chain( *( - child_cls.property_names + list(child_cls.aliases.keys()) + child_cls.all_property_names + list(child_cls.aliases.keys()) for child_cls in prop.types ) ) diff --git a/fairgraph/openminds/computation/validation_test.py b/fairgraph/openminds/computation/validation_test.py index c41a20fc..7d783d5b 100644 --- a/fairgraph/openminds/computation/validation_test.py +++ b/fairgraph/openminds/computation/validation_test.py @@ -46,7 +46,7 @@ class ValidationTest(KGObject, OMValidationTest): description="reverse of 'about'", ), ] - aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} + aliases = {"name": "full_name", "versions": "has_versions", "model_scope": "scope", "alias": "short_name"} existence_query_properties = ("full_name", "short_name") def __init__( @@ -64,6 +64,7 @@ def __init__( how_to_cite=None, is_part_of=None, learning_resources=None, + model_scope=None, reference_data_acquisitions=None, scope=None, score_type=None, @@ -94,6 +95,7 @@ def __init__( how_to_cite=how_to_cite, is_part_of=is_part_of, learning_resources=learning_resources, + model_scope=model_scope, reference_data_acquisitions=reference_data_acquisitions, scope=scope, score_type=score_type, diff --git a/fairgraph/openminds/core/products/model.py b/fairgraph/openminds/core/products/model.py index f7d8e42a..02bcd0d0 100644 --- a/fairgraph/openminds/core/products/model.py +++ b/fairgraph/openminds/core/products/model.py @@ -46,7 +46,7 @@ class Model(KGObject, OMModel): description="reverse of 'about'", ), ] - aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"} + aliases = {"name": "full_name", "versions": "has_versions", "model_scope": "scope", "alias": "short_name"} existence_query_properties = ("full_name",) def __init__( @@ -65,6 +65,7 @@ def __init__( how_to_cite=None, is_part_of=None, learning_resources=None, + model_scope=None, scope=None, short_name=None, study_targets=None, @@ -94,6 +95,7 @@ def __init__( how_to_cite=how_to_cite, is_part_of=is_part_of, learning_resources=learning_resources, + model_scope=model_scope, scope=scope, short_name=short_name, study_targets=study_targets, diff --git a/fairgraph/utility.py b/fairgraph/utility.py index 66ff3b8b..e87f42db 100644 --- a/fairgraph/utility.py +++ b/fairgraph/utility.py @@ -572,4 +572,16 @@ def initialise_instances(class_list): 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 + cls.set_error_handling("log") + + +def handle_scope_keyword(scope, release_status): + """ + The keyword 'scope' has been renamed 'release_status', + use of 'scope' is deprecated but still accepted. + """ + if scope in ("released", "in progress", "any"): + warnings.warn("The keyword 'scope' is deprecated, and will be removed in version 1.0; it has been renamed to 'release_status'", DeprecationWarning, stacklevel=2) + return scope + else: + return release_status diff --git a/test/test_openminds_core.py b/test/test_openminds_core.py index 1d418468..dac34e5a 100644 --- a/test/test_openminds_core.py +++ b/test/test_openminds_core.py @@ -374,7 +374,7 @@ def test_count_models_with_filters(kg_client): space="model", api="auto", study_targets=ca1, - scope=single_cell, + model_scope=single_cell, # note that 'model_scope' is an alias for 'scope' ) n_models = omcore.Model.count( kg_client, @@ -382,7 +382,7 @@ def test_count_models_with_filters(kg_client): space="model", api="auto", study_targets=ca1, - scope=single_cell, + model_scope=single_cell, ) assert len(models) == n_models assert n_models > 1 @@ -451,7 +451,7 @@ def test__update(): def test_KGQuery_resolve(kg_client): ca1 = omterms.UBERONParcellation.by_name("CA1 field of hippocampus", kg_client) single_cell = omterms.ModelScope.by_name("single cell", kg_client) - filters = {"study_targets": ca1, "scope": single_cell} + filters = {"study_targets": ca1, "model_scope": single_cell} q = KGQuery(omcore.Model, filters) models_q = q.resolve(kg_client, release_status="released") models_direct = omcore.Model.list(kg_client, release_status="released", space="model", api="query", **filters) @@ -552,7 +552,7 @@ def test_save_new_mock(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - release_status=omterms.ModelScope.by_name("subcellular", mock_client), + scope=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), @@ -582,7 +582,7 @@ def test_save_existing_mock(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - release_status=omterms.ModelScope.by_name("subcellular", mock_client), + scope=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), @@ -613,7 +613,7 @@ def test_save_existing_mock_no_updates_allowed(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - release_status=omterms.ModelScope.by_name("subcellular", mock_client), + scope=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), @@ -645,7 +645,7 @@ def test_save_replace_existing_mock(mock_client): versions=None, homepage=IRI("http://example.com"), how_to_cite=None, - release_status=omterms.ModelScope.by_name("subcellular", mock_client), + scope=omterms.ModelScope.by_name("subcellular", mock_client), study_targets=[ omterms.Species.by_name("Mus musculus", mock_client), omterms.CellType.by_name("astrocyte", mock_client), diff --git a/test/utils.py b/test/utils.py index b522e4c5..90647a17 100644 --- a/test/utils.py +++ b/test/utils.py @@ -1,6 +1,8 @@ from copy import deepcopy import os from uuid import uuid4 +from typing import Optional + from requests.exceptions import SSLError from fairgraph.client import KGClient from fairgraph.errors import AuthenticationError, AuthorizationError