add query parameters to morphology metrics. Fix openapi.json generation

app/endpoints/declared_endpoints.py

@@ -1,5 +1,5 @@
 from http import HTTPStatus
-from typing import Annotated
+from typing import Annotated, Literal
 
 import entitysdk.client
 import entitysdk.exception
@@ -17,6 +17,7 @@
     get_electrophysiology_metrics,
 )
 from obi_one.scientific.morphology_metrics.morphology_metrics import (
+    MORPHOLOGY_METRICS,
     MorphologyMetricsOutput,
     get_morphology_metrics,
 )
@@ -30,15 +31,27 @@ def activate_declared_endpoints(router: APIRouter) -> APIRouter:
                     morphology.",
     )
     def neuron_morphology_metrics_endpoint(
-        db_client: Annotated[entitysdk.client.Client, Depends(get_client)],
         reconstruction_morphology_id: str,
+        db_client: Annotated[entitysdk.client.Client, Depends(get_client)],
+        requested_metrics: Annotated[
+            list[Literal[*MORPHOLOGY_METRICS]] | None,  # type: ignore[misc]
+            Query(
+                description="List of requested metrics",
+            ),
+        ] = None,
     ) -> MorphologyMetricsOutput:
+        """Calculates neuron morphology metrics for a given reconstruction morphology.
+
+        - **reconstruction_morphology_id**: ID of the reconstruction morphology.
+        - **requested_metrics**: List of requested metrics (optional).
+        """
         L.info("get_morphology_metrics")
 
         try:
             metrics = get_morphology_metrics(
                 reconstruction_morphology_id=reconstruction_morphology_id,
                 db_client=db_client,
+                requested_metrics=requested_metrics,
             )
         except entitysdk.exception.EntitySDKError as err:
             raise HTTPException(

obi_one/core/block_reference.py

@@ -28,7 +28,18 @@ class Config:
         @staticmethod
         def json_schema_extra(schema: dict, model: "BlockReference") -> None:
             # Dynamically get allowed_block_types from subclass
-            schema["allowed_block_types"] = [t.__name__ for t in model.allowed_block_types_union()]
+            allowed_types = model.allowed_block_types_union()
+            if isinstance(allowed_types, tuple):
+                schema["allowed_block_types"] = [t.__name__ for t in allowed_types]
+            elif hasattr(allowed_types, "__name__"):
+                schema["allowed_block_types"] = [allowed_types.__name__]
+            else:
+                # Handle UnionType or other types without __name__
+                schema["allowed_block_types"] = [
+                    t.__name__
+                    for t in get_args(model.allowed_block_types)
+                    if hasattr(t, "__name__")
+                ]
             schema["is_block_reference"] = True
 
     @property

obi_one/scientific/morphology_metrics/morphology_metrics.py

@@ -16,6 +16,31 @@
 
 L = logging.getLogger(__name__)
 
+MORPHOLOGY_METRICS = [
+    "aspect_ratio",
+    "circularity",
+    "length_fraction_above_soma",
+    "max_radial_distance",
+    "number_of_neurites",
+    "soma_radius",
+    "soma_surface_area",
+    "total_length",
+    "total_height",
+    "total_width",
+    "total_depth",
+    "total_area",
+    "total_volume",
+    "section_lengths",
+    "segment_radii",
+    "number_of_sections",
+    "local_bifurcation_angles",
+    "remote_bifurcation_angles",
+    "section_path_distances",
+    "section_radial_distances",
+    "section_branch_orders",
+    "section_strahler_orders",
+]
+
 
 class MorphologyMetricsForm(Form):
     single_coord_class_name: ClassVar[str] = "MorphologyMetrics"
@@ -32,182 +57,190 @@ class Initialize(Block):
 
 class MorphologyMetricsOutput(BaseModel):
     aspect_ratio: Annotated[
-        float,
+        float | None,
         Field(
             title="aspect_ratio",
             description="Calculates the min/max ratio of the principal direction extents \
                 along the plane.",
+            default=None,
         ),
     ]
     circularity: Annotated[
-        float,
+        float | None,
         Field(
             title="circularity",
             description="Calculates the circularity of the morphology points along the plane.",
+            default=None,
         ),
     ]
     length_fraction_above_soma: Annotated[
-        float,
+        float | None,
         Field(
             title="length_fraction_above_soma",
             description="Returns the length fraction of the segments that have their midpoints \
                             higher than the soma.",
+            default=None,
         ),
     ]
     max_radial_distance: Annotated[
-        float,
+        float | None,
         Field(
             title="max_radial_distance",
             description="The maximum radial distance from the soma in micrometers.",
+            default=None,
         ),
     ]
     number_of_neurites: Annotated[
-        int, Field(title="number_of_neurites", description="Number of neurites in a morphology.")
+        int | None,
+        Field(
+            title="number_of_neurites",
+            description="Number of neurites in a morphology.",
+            default=None,
+        ),
     ]
 
     soma_radius: Annotated[
-        float, Field(title="soma_radius [μm]", description="The radius of the soma in micrometers.")
+        float | None,
+        Field(
+            title="soma_radius [μm]",
+            description="The radius of the soma in micrometers.",
+            default=None,
+        ),
     ]
     soma_surface_area: Annotated[
-        float,
+        float | None,
         Field(
             title="soma_surface_area [μm^2]",
             description="The surface area of the soma in square micrometers.",
+            default=None,
         ),
     ]
     total_length: Annotated[
-        float,
+        float | None,
         Field(
             title="total_length [μm]",
             description="The total length of the morphology neurites in micrometers.",
+            default=None,
         ),
     ]
     total_height: Annotated[
-        float,
+        float | None,
         Field(
             title="total_height [μm]",
             description="The total height (Y-range) of the morphology in micrometers.",
+            default=None,
         ),
     ]
     total_height: Annotated[
-        float,
+        float | None,
         Field(
             title="total_width [μm]",
             description="The total width (X-range) of the morphology in micrometers.",
+            default=None,
         ),
     ]
     total_depth: Annotated[
-        float,
+        float | None,
         Field(
             title="total_depth [μm]",
             description="The total depth (Z-range) of the morphology in micrometers.",
+            default=None,
         ),
     ]
     total_area: Annotated[
-        float,
+        float | None,
         Field(
             title="total_area [μm^2]",
             description="The total surface area of all sections in square micrometers.",
+            default=None,
         ),
     ]
     total_volume: Annotated[
-        float,
+        float | None,
         Field(
             title="total_volume [μm^3]",
             description="The total volume of all sections in cubic micrometers.",
+            default=None,
         ),
     ]
     section_lengths: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="section_lengths [μm]",
             description="The distribution of lengths per section in micrometers.",
+            default=None,
         ),
     ]
     segment_radii: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="segment_radii [μm]",
             description="The distribution of radii of the morphology in micrometers.",
+            default=None,
         ),
     ]
     number_of_sections: Annotated[
-        float,
+        float | None,
         Field(
             title="number_of_sections",
             description="The number of sections in the morphology.",
+            default=None,
         ),
     ]
     local_bifurcation_angles: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="local_bifurcation_angles [rad]",
             description="Angles between two sections computed at the bifurcation (local).",
+            default=None,
         ),
     ]
     remote_bifurcation_angles: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="remote_bifurcation_angles [rad]",
             description="Angles between two sections computed at the end of the sections (remote).",
+            default=None,
         ),
     ]
     section_path_distances: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="section_path_distances [μm]",
             description="Path distances from the soma to section endpoints in micrometers.",
+            default=None,
         ),
     ]
     section_radial_distances: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="section_radial_distances [μm]",
             description="Radial distance from the soma to section endpoints in micrometers.",
+            default=None,
         ),
     ]
     section_branch_orders: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="section_branch_orders",
             description="The distribution of branch orders of sections, computed from soma.",
+            default=None,
         ),
     ]
     section_strahler_orders: Annotated[
-        list[float],
+        list[float] | None,
         Field(
             title="section_strahler_orders",
             description="The distribution of strahler branch orders of sections, computed from \
                 terminals.",
+            default=None,
         ),
     ]
 
     @classmethod
     def from_morphology(cls, neurom_morphology: neurom.core.Morphology) -> Self:
-        return cls(
-            aspect_ratio=neurom.get("aspect_ratio", neurom_morphology),
-            circularity=neurom.get("circularity", neurom_morphology),
-            length_fraction_above_soma=neurom.get("length_fraction_above_soma", neurom_morphology),
-            max_radial_distance=neurom.get("max_radial_distance", neurom_morphology),
-            number_of_neurites=neurom.get("number_of_neurites", neurom_morphology),
-            soma_radius=neurom.get("soma_radius", neurom_morphology),
-            soma_surface_area=neurom.get("soma_surface_area", neurom_morphology),
-            total_length=neurom.get("total_length", neurom_morphology),
-            total_height=neurom.get("total_height", neurom_morphology),
-            total_width=neurom.get("total_width", neurom_morphology),
-            total_depth=neurom.get("total_depth", neurom_morphology),
-            total_area=neurom.get("total_area", neurom_morphology),
-            total_volume=neurom.get("total_volume", neurom_morphology),
-            section_lengths=neurom.get("section_lengths", neurom_morphology),
-            segment_radii=neurom.get("segment_radii", neurom_morphology),
-            number_of_sections=neurom.get("number_of_sections", neurom_morphology),
-            local_bifurcation_angles=neurom.get("local_bifurcation_angles", neurom_morphology),
-            remote_bifurcation_angles=neurom.get("remote_bifurcation_angles", neurom_morphology),
-            section_path_distances=neurom.get("section_path_distances", neurom_morphology),
-            section_radial_distances=neurom.get("section_radial_distances", neurom_morphology),
-            section_branch_orders=neurom.get("section_branch_orders", neurom_morphology),
-            section_strahler_orders=neurom.get("section_strahler_orders", neurom_morphology),
-        )
+        values = {metric: neurom.get(metric, neurom_morphology) for metric in MORPHOLOGY_METRICS}
+        return cls(**values)
 
 
 class MorphologyMetrics(MorphologyMetricsForm, SingleCoordinateMixin):
@@ -226,28 +259,28 @@ def run(self, db_client: entitysdk.client.Client = None) -> MorphologyMetricsOut
 
 
 def get_morphology_metrics(
-    reconstruction_morphology_id: str, db_client: entitysdk.client.Client
+    reconstruction_morphology_id: str,
+    db_client: entitysdk.client.Client,
+    requested_metrics: list[str] | None = None,
 ) -> MorphologyMetricsOutput:
     morphology = db_client.get_entity(
         entity_id=reconstruction_morphology_id, entity_type=ReconstructionMorphology
     )
 
-    # Iterate through the assets of the morphology to find the one with content
-    # type "application/asc"
     for asset in morphology.assets:
         if asset.content_type == "application/swc":
-            # Download the content into memory
             content = db_client.download_content(
                 entity_id=morphology.id,
                 entity_type=ReconstructionMorphology,
                 asset_id=asset.id,
             ).decode(encoding="utf-8")
 
-            # Use StringIO to create a file-like object in memory from the string content
             neurom_morphology = load_morphology(io.StringIO(content), reader="swc")
 
-            # Calculate the metrics using neurom
-            morphology_metrics = MorphologyMetricsOutput.from_morphology(neurom_morphology)
-
-            return morphology_metrics
+            if requested_metrics:
+                values = {
+                    metric: neurom.get(metric, neurom_morphology) for metric in requested_metrics
+                }
+                return MorphologyMetricsOutput(**values)
+            return MorphologyMetricsOutput.from_morphology(neurom_morphology)
     return None