Add tests

src/blue_cwl/wrappers/cell_composition_manipulation.py

@@ -8,12 +8,12 @@
 import click
 import pandas as pd
 import voxcell
+from entity_management import nexus
 from entity_management.atlas import CellComposition
 from entity_management.config import BrainRegionSelectorConfig, CellCompositionConfig
 
 # pylint: disable=no-name-in-module
 from entity_management.core import Entity
-from entity_management.nexus import load_by_id
 from entity_management.util import get_entity
 
 from blue_cwl import density_manipulation, registering, staging, statistics, utils
@@ -256,9 +256,7 @@ def register(
  cell_composition_summary_file: Summary file to create the new CellComposition from.
  output_dir: Output directory to write outputs.
  """
- base_cell_composition = get_entity(
- base_cell_composition_id, cls=CellComposition, resolve_context=True
- )
+ base_cell_composition = get_entity(base_cell_composition_id, cls=CellComposition)
 
  atlas_release = base_cell_composition.atlasRelease
 
@@ -281,7 +279,7 @@ def register(
  _validate_cell_composition_schemas(cell_composition)
 
  utils.write_json(
- data=load_by_id(cell_composition.get_id()),
+ data=nexus.load_by_id(cell_composition.get_id()),
  filepath=Path(output_dir, "resource.json"),
  )
 

tests/unit/cell_composition/data/base_cell_composition_summary_distribution.json

@@ -0,0 +1,30 @@
+{
+ "version": 1,
+ "unitCode": {
+ "density": "mm^-3"
+ },
+ "hasPart": {
+ "http://api.brain-map.org/api/v2/data/Structure/614454292": {
+ "label": "Primary somatosensory area, barrel field, layer 2",
+ "about": "BrainRegion",
+ "hasPart": {
+ "http://uri.interlex.org/base/ilx_0381367": {
+ "label": "L2_TPC:B",
+ "about": "MType",
+ "hasPart": {
+ "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cADpyr": {
+ "label": "cADpyr",
+ "about": "EType",
+ "composition": {
+ "neuron": {
+ "density": 41061.716478599694,
+ "count": 8059
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+}

tests/unit/cell_composition/data/base_cell_composition_volume_distribution.json

@@ -0,0 +1,32 @@
+{
+ "hasPart": [
+ {
+ "@id": "http://uri.interlex.org/base/ilx_0381367",
+ "label": "L2_TPC:B",
+ "about": [
+ "https://neuroshapes.org/MType"
+ ],
+ "hasPart": [
+ {
+ "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cADpyr",
+ "label": "cADpyr",
+ "about": [
+ "https://neuroshapes.org/EType"
+ ],
+ "hasPart": [
+ {
+ "@id": "nrrd-id",
+ "@type": [
+ "METypeDensity",
+ "NeuronDensity",
+ "VolumetricDataLayer",
+ "CellDensityDataLayer"
+ ],
+ "_rev": 2
+ }
+ ]
+ }
+ ]
+ }
+ ]
+}

tests/unit/cell_composition/data/configuration_distribution.json

@@ -0,0 +1,47 @@
+{
+ "version": 1,
+ "unitCode": {
+ "density": "mm^-3"
+ },
+ "overrides": {
+ "http://api.brain-map.org/api/v2/data/Structure/614454292": {
+ "label": "Primary somatosensory area, barrel field, layer 2",
+ "about": "BrainRegion",
+ "hasPart": {
+ "http://uri.interlex.org/base/ilx_0381367": {
+ "label": "L2_TPC:B",
+ "about": "MType",
+ "hasPart": {
+ "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cADpyr": {
+ "label": "cADpyr",
+ "about": "EType",
+ "composition": {
+ "neuron": {
+ "density": 203.9132207910741,
+ "count": 8059
+ }
+ },
+ "density": 203.9132207910741
+ }
+ },
+ "composition": {
+ "neuron": {
+ "density": 203.91322079107408
+ },
+ "glia": {
+ "density": 0
+ }
+ }
+ }
+ },
+ "composition": {
+ "neuron": {
+ "density": 203.91322079107408
+ },
+ "glia": {
+ "density": 0
+ }
+ }
+ }
+ }
+}