Support native list params in filters

app/dependencies/filter.py

@@ -0,0 +1,55 @@
+from copy import deepcopy
+from typing import Any, get_args, get_origin
+
+from fastapi import Depends, Query, params
+from fastapi.exceptions import RequestValidationError
+from fastapi_filter.base.filter import BaseFilterModel
+from pydantic import ValidationError, create_model
+
+
+def _list_to_query_fields(filter_model: type[BaseFilterModel]):
+    fields = {}
+    for name, f in filter_model.model_fields.items():
+        field_info = deepcopy(f)
+        annotation = f.annotation
+
+        if (
+            annotation is list
+            or get_origin(annotation) is list
+            or any(get_origin(a) is list for a in get_args(annotation))
+        ) and type(field_info.default) is not params.Query:
+            field_info.default = Query(default=field_info.default)
+
+        fields[name] = (f.annotation, field_info)
+
+    return fields
+
+
+def FilterDepends(filter_model: type[BaseFilterModel], *, by_alias: bool = False, **_) -> Any:
+    """Use a hack to treat lists as query parameters.
+
+    What we do is loop through the fields of a filter and assign any `list` field a default value of
+    `Query` so that FastAPI knows it should be treated a query parameter and not body.
+
+    When we apply the filter, we build the original filter to properly validate the data (i.e. can
+    the string be parsed and formatted as a list of <type>?)
+    """
+    fields = _list_to_query_fields(filter_model)
+    GeneratedFilter = create_model(filter_model.__class__.__name__, **fields)  # noqa: N806
+
+    class FilterWrapper(GeneratedFilter):  # type: ignore[misc,valid-type]
+        def __new__(cls, *args, **kwargs):
+            try:
+                instance = GeneratedFilter(*args, **kwargs)
+                data = instance.model_dump(
+                    exclude_unset=True, exclude_defaults=True, by_alias=by_alias
+                )
+                if original_filter := getattr(filter_model.Constants, "original_filter", None):
+                    prefix = f"{filter_model.Constants.prefix}__"
+                    stripped = {k.removeprefix(prefix): v for k, v in data.items()}
+                    return original_filter(**stripped)
+                return filter_model(**data)
+            except ValidationError as e:
+                raise RequestValidationError(e.errors()) from e
+
+    return Depends(FilterWrapper)

app/filters/activity.py

@@ -1,8 +1,9 @@
 from datetime import datetime
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
+from app.dependencies.filter import FilterDepends
 from app.filters.common import (
     CreationFilterMixin,
     CreatorFilterMixin,

app/filters/base.py

@@ -8,6 +8,7 @@
 from sqlalchemy.orm import DeclarativeBase
 
 from app.db.model import Identifiable
+from app.logger import L
 
 Aliases = dict[type[Identifiable], type[Identifiable] | dict[str, type[Identifiable]]]
 
@@ -18,6 +19,33 @@ class CustomFilter[T: DeclarativeBase](Filter):
     class Constants(Filter.Constants):
         ordering_model_fields: list[str]
 
+    @field_validator("*", mode="before")
+    @classmethod
+    def split_str(cls, value, field):  # pyright: ignore reportIncompatibleMethodOverride
+        """Prevent splitting field logic from parent class."""
+        # backwards compatibility by splitting only comma separated single list elements that do not
+        # have space directly after the comma. e.g "a,b,c" will be split but not 'a, b, c'.
+        if (
+            field.field_name is not None  # noqa: PLR0916
+            and (
+                field.field_name == cls.Constants.ordering_field_name
+                or field.field_name.endswith("__in")
+                or field.field_name.endswith("__not_in")
+            )
+            and value
+            and len(value) == 1
+            and isinstance(value[0], str)
+            and "," in value[0]
+            and ", " not in value[0]
+        ):
+            msg = (
+                "Deprecated comma separated single-string IN query used instead of native list. "
+                f"Filter: field.config['title'] Field name: {field.field_name} Value: {value}"
+            )
+            L.warning(msg)
+            return value[0].split(",")
+        return value
+
     @field_validator("order_by", check_fields=False)
     @classmethod
     def restrict_sortable_fields(cls, value: list[str]):

app/filters/brain_atlas.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import BrainAtlas, BrainAtlasRegion
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import IdFilterMixin, NameFilterMixin, SpeciesFilterMixin
 

app/filters/brain_region.py

@@ -2,10 +2,10 @@
 from typing import Annotated
 
 import sqlalchemy as sa
-from fastapi_filter import FilterDepends
 from sqlalchemy.orm import aliased
 
 from app.db.model import BrainRegion, BrainRegionHierarchy
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import NameFilterMixin
 

app/filters/brain_region_hierarchy.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import BrainRegionHierarchy
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import IdFilterMixin, NameFilterMixin
 

app/filters/cell_composition.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import CellComposition
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     EntityFilterMixin,

app/filters/circuit.py

@@ -2,9 +2,8 @@
 from datetime import datetime
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import Circuit
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/common.py

@@ -2,7 +2,7 @@
 from datetime import datetime
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import (
     Agent,
@@ -15,12 +15,17 @@
     Strain,
     Subject,
 )
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 
 
 class IdFilterMixin:
     id: uuid.UUID | None = None
-    id__in: list[uuid.UUID] | None = None
+
+    # id__in needs to be a str for backwards compatibility when instead of a native list a comma
+    # separated string is provided, e.g. 'id1,id2' . With list[UUID] backwards compatibility would
+    # fail because of validation of the field which would be expected to be a UUID.
+    id__in: list[str] | None = None
 
 
 class NameFilterMixin:

app/filters/density.py

@@ -1,12 +1,11 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import (
     ExperimentalBoutonDensity,
     ExperimentalNeuronDensity,
     ExperimentalSynapsesPerConnection,
 )
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilter,

app/filters/electrical_cell_recording.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import ElectricalCellRecording
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/emodel.py

@@ -1,8 +1,9 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import EModel
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/entity.py

@@ -1,9 +1,8 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import Entity
 from app.db.types import EntityType
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 
 

app/filters/ion_channel_model.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import IonChannelModel
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/measurement_annotation.py

@@ -1,11 +1,12 @@
 import uuid
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import MeasurementAnnotation, MeasurementItem, MeasurementKind
 from app.db.types import MeasurementStatistic, MeasurementUnit, StructuralDomain
 from app.db.utils import MeasurableEntityType
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import CreationFilterMixin
 

app/filters/memodel.py

@@ -1,8 +1,9 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import MEModel, ValidationStatus
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/memodel_calibration_result.py

@@ -1,9 +1,8 @@
 import uuid
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import MEModelCalibrationResult
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import EntityFilterMixin
 

app/filters/morphology.py

@@ -1,8 +1,9 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import ReconstructionMorphology
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/person.py

@@ -1,9 +1,8 @@
 import uuid
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import Person
+from app.dependencies.filter import FilterDepends
 from app.filters.common import AgentFilter, CreatorFilterMixin
 
 

app/filters/simulation.py

@@ -1,9 +1,10 @@
 import uuid
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import Simulation
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     ContributionFilterMixin,

app/filters/simulation_campaign.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import SimulationCampaign
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import EntityFilterMixin, NameFilterMixin
 from app.filters.simulation import NestedSimulationFilter, NestedSimulationFilterDep

app/filters/simulation_execution.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import SimulationExecution
+from app.dependencies.filter import FilterDepends
 from app.filters.activity import ActivityFilterMixin
 from app.filters.base import CustomFilter
 

app/filters/simulation_generation.py

@@ -1,8 +1,7 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import SimulationGeneration
+from app.dependencies.filter import FilterDepends
 from app.filters.activity import ActivityFilterMixin
 from app.filters.base import CustomFilter
 

app/filters/simulation_result.py

@@ -1,8 +1,9 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import SimulationResult
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     ContributionFilterMixin,

app/filters/single_neuron_simulation.py

@@ -1,9 +1,8 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import SingleNeuronSimulation
 from app.db.types import SingleNeuronSimulationStatus
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/single_neuron_synaptome.py

@@ -1,8 +1,9 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends, with_prefix
+from fastapi_filter import with_prefix
 
 from app.db.model import SingleNeuronSynaptome
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,

app/filters/single_neuron_synaptome_simulation.py

@@ -1,9 +1,8 @@
 from typing import Annotated
 
-from fastapi_filter import FilterDepends
-
 from app.db.model import SingleNeuronSynaptomeSimulation
 from app.db.types import SingleNeuronSimulationStatus
+from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
 from app.filters.common import (
     BrainRegionFilterMixin,