Add tests for registration

src/blue_cwl/registering.py

@@ -14,7 +14,7 @@
  METypeDensity,
 )
 from entity_management.base import BrainLocation, Derivation, OntologyTerm
-from entity_management.core import DataDownload, Subject
+from entity_management.core import DataDownload, Entity, Subject
 from entity_management.simulation import DetailedCircuit
 from entity_management.util import get_entity
 
@@ -62,11 +62,12 @@ def register_partial_circuit(
 
 
 def register_cell_composition_summary(
+ *,
  name: str,
+ description: str,
  distribution_file: StrOrPath,
- atlas_release,
- derivation_entity,
- *,
+ atlas_release: AtlasRelease,
+ derivation_entity: Entity,
  base=None,
  org=None,
  proj=None,
@@ -84,8 +85,8 @@ def register_cell_composition_summary(
  derivation = Derivation(entity=derivation_entity)
  summary = CellCompositionSummary(
  name=name,
+ description=description,
  about=["nsg:Neuron", "nsg:Glia"],
- description="Statistical summary of the model cell composition.",
  atlasRelease=atlas_release,
  brainLocation=atlas_release.brainLocation,
  distribution=distribution,
@@ -96,11 +97,12 @@ def register_cell_composition_summary(
 
 
 def register_cell_composition_volume(
+ *,
  name: str,
+ description: str,
  distribution_file: StrOrPath,
- atlas_release,
- derivation_entity,
- *,
+ atlas_release: AtlasRelease,
+ derivation_entity: Entity,
  base=None,
  org=None,
  proj=None,
@@ -118,8 +120,8 @@ def register_cell_composition_volume(
  derivation = Derivation(entity=derivation_entity)
  volume = CellCompositionVolume(
  name=name,
+ description=description,
  about=["nsg:Neuron", "nsg:Glia"],
- description="NRRD volume distribution of the cell composition.",
  atlasRelease=atlas_release,
  brainLocation=atlas_release.brainLocation,
  distribution=distribution,
@@ -129,9 +131,18 @@ def register_cell_composition_volume(
  return volume.publish(base=base, org=org, proj=proj, use_auth=token)
 
 
-def register_densities(atlas_release, cell_composition_volume_file, output_file=None):
+def register_densities(
+ *,
+ atlas_release: AtlasRelease,
+ distribution_file: StrOrPath,
+ output_file: StrOrPath | None = None,
+ base: str | None = None,
+ org: str | None = None,
+ proj: str | None = None,
+ token: str | None = None,
+) -> dict:
  """Register METypeDensity volumes."""
- volumes_dict = load_json(cell_composition_volume_file)
+ volumes_dict = load_json(distribution_file)
 
  derivation = Derivation(entity=atlas_release)
  subject = atlas_release.subject
@@ -147,6 +158,10 @@ def register_densities(atlas_release, cell_composition_volume_file, output_file=
  brain_location=brain_location,
  derivation=derivation,
  subject=subject,
+ base=base,
+ org=org,
+ proj=proj,
+ token=token,
  )
 
  nrrd_data["@id"] = me_density.get_id()
@@ -161,14 +176,16 @@ def register_densities(atlas_release, cell_composition_volume_file, output_file=
  if output_file is not None:
  write_json(data=volumes_dict, filepath=output_file)
 
+ return volumes_dict
+
 
 def _register_me_density(
- distribution_file: StrOrPath,
- atlas_release,
- brain_location,
- derivation,
- subject,
  *,
+ distribution_file: StrOrPath,
+ atlas_release: AtlasRelease,
+ brain_location: BrainLocation,
+ derivation: Derivation,
+ subject: Subject,
  base=None,
  org=None,
  proj=None,
@@ -195,10 +212,12 @@ def _register_me_density(
 
 
 def register_cell_composition(
- atlas_release,
+ *,
+ name: str,
+ description: str,
+ atlas_release: AtlasRelease,
  cell_composition_volume_file: StrOrPath,
  cell_composition_summary_file: StrOrPath,
- *,
  base=None,
  org=None,
  proj=None,
@@ -207,6 +226,7 @@ def register_cell_composition(
  """Register CellComposition."""
  summary = register_cell_composition_summary(
  name="Cell Composition Summary",
+ description="Cell Composition Summary Distribution",
  distribution_file=cell_composition_summary_file,
  atlas_release=atlas_release,
  derivation_entity=atlas_release,
@@ -217,6 +237,7 @@ def register_cell_composition(
  )
  volume = register_cell_composition_volume(
  name="Cell Composition Volume",
+ description="Cell Composition Volume Distribution",
  distribution_file=cell_composition_volume_file,
  atlas_release=atlas_release,
  derivation_entity=atlas_release,
@@ -226,7 +247,8 @@ def register_cell_composition(
  token=token,
  )
  cell_composition = CellComposition(
- name="Cell Composition",
+ name=name,
+ description=description,
  about=["nsg:Neuron", "nsg:Glia"],
  atlasRelease=atlas_release,
  atlasSpatialReferenceSystem=atlas_release.spatialReferenceSystem,

src/blue_cwl/wrappers/cell_composition_manipulation.py

@@ -267,10 +267,12 @@ def register(
  )
  registering.register_densities(
  atlas_release=atlas_release,
- cell_composition_volume_file=cell_composition_volume_file,
+ distribution_file=cell_composition_volume_file,
  output_file=registered_cell_composition_volume_file,
  )
  cell_composition = registering.register_cell_composition(
+ name="Cell Composition",
+ description="Manipulated Cell Composition",
  atlas_release=atlas_release,
  cell_composition_volume_file=registered_cell_composition_volume_file,
  cell_composition_summary_file=cell_composition_summary_file,

src/blue_cwl/wrappers/cell_composition_summary.py

@@ -59,7 +59,8 @@ def from_density_distribution(
 
  # pylint: disable=no-member
  registering.register_cell_composition_summary(
- name="Cell composition summary",
+ name="Cell Composition Summary",
+ description="Cell Composition Summary from density distribution",
  distribution_file=composition_summary_file,
  atlas_release=get_entity(atlas_release, cls=AtlasRelease),
  derivation_entity=cell_composition_volume,

src/blue_cwl/wrappers/neurons_cell_position.py

@@ -347,7 +347,8 @@ def _register(
  )
  # pylint: disable=no-member
  registering.register_cell_composition_summary(
- name="Cell composition summary",
+ name="Cell Composition Summary",
+ description="Cell Composition Summary of Node Population",
  distribution_file=generated_data["composition-summary-file"],
  atlas_release=get_entity(generated_data["atlas-id"], cls=AtlasRelease),
  derivation_entity=circuit_resource,