Cell types and other tests (#56)

* Added cell types and other tests * changelog * New cell types unittests * Fix fixture * Test merging utilities * Added missing test resolving tests * Added missing utils tests --------- Co-authored-by: kanesoban <[email protected]> Co-authored-by: Nicolas Frank <[email protected]>
BlueBrain · Dec 18, 2024 · 56a81ea · 56a81ea
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Tool implementations without langchain or langgraph dependencies
 - CRUDs.
 - BlueNaas CRUD tools
+- Cell types, resolving and utils tests
 - app unit tests
 - Tests of AgentsRoutine.
 - Unit tests for database

diff --git a/swarm_copy_tests/data/KG_brain_regions_hierarchy_test.json b/swarm_copy_tests/data/KG_brain_regions_hierarchy_test.json
@@ -0,0 +1,165 @@
+{
+    "@context": "https://neuroshapes.org",
+    "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/core/brainregion",
+    "@type": "Ontology",
+    "versionInfo": "R103",
+    "hasHierarchyView": [
+        {
+            "@id": "https://bbp.epfl.ch/ontologies/core/bmo/BrainLayer",
+            "label": "Layer",
+            "description": "Layer based hierarchy",
+            "hasParentHierarchyProperty": "isLayerPartOf",
+            "hasChildrenHierarchyProperty": "hasLayerPart",
+            "hasLeafHierarchyProperty": "hasLayerLeafRegionPart"
+        },
+        {
+            "@id": "https://neuroshapes.org/BrainRegion",
+            "label": "BrainRegion",
+            "description": "Atlas default brain region hierarchy",
+            "hasParentHierarchyProperty": "isPartOf",
+            "hasChildrenHierarchyProperty": "hasPart",
+            "hasLeafHierarchyProperty": "hasLeafRegionPart"
+        }
+    ],
+    "atlasRelease": {
+        "@id": "https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885",
+        "@type": "BrainAtlasRelease",
+        "_rev": 8
+    },
+    "defines": [
+        {
+            "@id": "http://api.brain-map.org/api/v2/data/Structure/1",
+            "@type": "Class",
+            "atlas_id": 424,
+            "color_hex_triplet": "FF4C3E",
+            "graph_order": 775,
+            "hemisphere_id": 3,
+            "st_level": 9,
+            "identifier": "1",
+            "isPartOf": [
+                "http://api.brain-map.org/api/v2/data/Structure/2"
+            ],
+            "isDefinedBy": "http://bbp.epfl.ch/neurosciencegraph/ontologies/core/brainregion",
+            "subClassOf": [
+                "https://neuroshapes.org/BrainRegion"
+            ],
+            "delineates": [
+                "http://purl.obolibrary.org/obo/UBERON_0014594"
+            ],
+            "regionVolume": {
+                "unitCode": "cubic micrometer",
+                "value": 108296875.0
+            },
+            "regionVolumeRatioToWholeBrain": {
+                "unitCode": "cubic micrometer",
+                "value": 0.00021400307558019888
+            },
+            "representedInAnnotation": true,
+            "hasHierarchyView": [
+                "https://neuroshapes.org/BrainRegion"
+            ],
+            "prefLabel": "Tuberomammillary nucleus, ventral part",
+            "label": "Tuberomammillary nucleus, ventral part",
+            "notation": "TMv",
+            "altLabel": "TMv",
+            "atlasRelease": {
+                "@id": "https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885",
+                "@type": "BrainAtlasRelease",
+                "_rev": 8
+            }
+        },
+        {
+            "@id": "http://api.brain-map.org/api/v2/data/Structure/2",
+            "@type": "Class",
+            "atlas_id": 425,
+            "color_hex_triplet": "FF90FF",
+            "graph_order": 834,
+            "hemisphere_id": 3,
+            "st_level": 9,
+            "hasPart": [
+                "http://api.brain-map.org/api/v2/data/Structure/503",
+                "http://api.brain-map.org/api/v2/data/Structure/511",
+                "http://api.brain-map.org/api/v2/data/Structure/614454425",
+                "http://api.brain-map.org/api/v2/data/Structure/494"
+            ],
+            "identifier": "2",
+            "isDefinedBy": "http://bbp.epfl.ch/neurosciencegraph/ontologies/core/brainregion",
+            "subClassOf": [
+                "https://neuroshapes.org/BrainRegion"
+            ],
+            "regionVolume": {
+                "unitCode": "cubic micrometer",
+                "value": 2036828125.0
+            },
+            "regionVolumeRatioToWholeBrain": {
+                "unitCode": "cubic micrometer",
+                "value": 0.004024931311990765
+            },
+            "representedInAnnotation": true,
+            "hasLeafRegionPart": [
+                "http://api.brain-map.org/api/v2/data/Structure/494",
+                "http://api.brain-map.org/api/v2/data/Structure/614454425",
+                "http://api.brain-map.org/api/v2/data/Structure/511",
+                "http://api.brain-map.org/api/v2/data/Structure/503"
+            ],
+            "hasHierarchyView": [
+                "https://neuroshapes.org/BrainRegion"
+            ],
+            "prefLabel": "Superior colliculus, motor related, intermediate gray layer",
+            "label": "Superior colliculus, motor related, intermediate gray layer",
+            "notation": "SCig",
+            "altLabel": "SCig",
+            "atlasRelease": {
+                "@id": "https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885",
+                "@type": "BrainAtlasRelease",
+                "_rev": 8
+            }
+        },
+        {
+            "@id": "http://api.brain-map.org/api/v2/data/Structure/3",
+            "@type": "Class",
+            "atlas_id": 424,
+            "color_hex_triplet": "FF4C3E",
+            "graph_order": 775,
+            "hemisphere_id": 3,
+            "st_level": 9,
+            "identifier": "3",
+            "isPartOf": [
+                "http://api.brain-map.org/api/v2/data/Structure/2"
+            ],
+            "isDefinedBy": "http://bbp.epfl.ch/neurosciencegraph/ontologies/core/brainregion",
+            "subClassOf": [
+                "https://neuroshapes.org/BrainRegion"
+            ],
+            "delineates": [
+                "http://purl.obolibrary.org/obo/UBERON_0014594"
+            ],
+            "regionVolume": {
+                "unitCode": "cubic micrometer",
+                "value": 108296875.0
+            },
+            "regionVolumeRatioToWholeBrain": {
+                "unitCode": "cubic micrometer",
+                "value": 0.00021400307558019888
+            },
+            "representedInAnnotation": true,
+            "hasHierarchyView": [
+                "https://neuroshapes.org/BrainRegion"
+            ],
+            "prefLabel": "Tuberomammillary nucleus, ventral part",
+            "label": "Primary Motor Cortex",
+            "notation": "TMv",
+            "altLabel": "TMv",
+            "atlasRelease": {
+                "@id": "https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885",
+                "@type": "BrainAtlasRelease",
+                "_rev": 8
+            }
+        }
+    ],
+    "derivation": [
+        {},
+        {}
+    ],
+    "label": "Brain Region Ontology"
+}
diff --git a/swarm_copy_tests/data/brainregion_hierarchy.json b/swarm_copy_tests/data/brainregion_hierarchy.json
diff --git a/swarm_copy_tests/data/kg_cell_types_hierarchy_test.json b/swarm_copy_tests/data/kg_cell_types_hierarchy_test.json
@@ -0,0 +1,13 @@
+{
+  "@context": "https://neuroshapes.org",
+  "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/core/celltypes",
+  "@type": "Ontology",
+  "preferredNamespacePrefix": "celltypes",
+  "versionInfo": "R1660",
+  "defines": [
+    {"@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint", "@type": "Class", "label": "cACint", "subClassOf": ["https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType", "https://neuroshapes.org/EType", "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType"], "definition": "Continuous accommodating interneuron electrical type", "color": "#108b8b", "prefLabel": "Continuous accommodating interneuron electrical type", "notation": "cACint", "atlasRelease": {"@id": "https://bbp.epfl.ch/neurosciencegraph/data/brainatlasrelease/c96c71a8-4c0d-4bc1-8a1a-141d9ed6693d", "@type": "BrainAtlasRelease", "_rev": 45}},
+    {"@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/GCL_GC", "@type": "Class", "label": "GCL_GC", "subClassOf": ["https://bbp.epfl.ch/ontologies/core/mtypes/HippocampusMType", "https://bbp.epfl.ch/ontologies/core/bmo/NeuronMorphologicalType", "https://neuroshapes.org/MType", "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType"], "atlasRelease": {"@id": "https://bbp.epfl.ch/neurosciencegraph/data/brainatlasrelease/c96c71a8-4c0d-4bc1-8a1a-141d9ed6693d", "@type": "BrainAtlasRelease", "_rev": 45}},
+    {"@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/L23_PTPC", "@type": "Class", "label": "L23_PTPC", "subClassOf": ["https://bbp.epfl.ch/ontologies/core/bmo/HumanNeocortexMType", "https://neuroshapes.org/PyramidalNeuron", "https://bbp.epfl.ch/ontologies/core/bmo/NeuronMorphologicalType", "https://neuroshapes.org/MType", "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType"], "notation": "L2_MC", "atlasRelease": {"@id": "https://bbp.epfl.ch/neurosciencegraph/data/brainatlasrelease/c96c71a8-4c0d-4bc1-8a1a-141d9ed6693d", "@type": "BrainAtlasRelease", "_rev": 45}}
+  ],
+  "label": "Cell Types Ontology"
+}
diff --git a/swarm_copy_tests/test_cell_types.py b/swarm_copy_tests/test_cell_types.py
@@ -0,0 +1,190 @@
+"""Test cell types meta functions."""
+import logging
+from pathlib import Path
+
+import pytest
+
+from swarm_copy.cell_types import CellTypesMeta, get_celltypes_descendants
+
+CELL_TYPES_FILE = Path(__file__).parent / "data" / "kg_cell_types_hierarchy_test.json"
+
+
+@pytest.mark.parametrize(
+    "cell_type_id,expected_descendants",
+    [
+        (
+            "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType",
+            {
+                "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/L23_PTPC",
+                "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+                "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/GCL_GC",
+                "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType",
+            },
+        ),
+        (
+            "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+            {
+                "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+                "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+            },
+        ),
+        (
+            "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+            {
+                "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+            },
+        ),
+    ],
+)
+def test_get_celltypes_descendants(cell_type_id, expected_descendants, tmp_path):
+    cell_types_meta = CellTypesMeta.from_json(CELL_TYPES_FILE)
+    save_file = tmp_path / "tmp_config_cell_types_meta.json"
+    cell_types_meta.save_config(save_file)
+
+    descendants = get_celltypes_descendants(cell_type_id, json_path=save_file)
+    assert expected_descendants == descendants
+
+
+class TestCellTypesMeta:
+    def test_from_json(self):
+        ct_meta = CellTypesMeta.from_json(CELL_TYPES_FILE)
+        assert isinstance(ct_meta.name_, dict)
+        assert isinstance(ct_meta.descendants_ids, dict)
+
+        expected_names = {
+            "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint": "cACint",
+            "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/GCL_GC": "GCL_GC",
+            "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/L23_PTPC": (
+                "L23_PTPC"
+            ),
+        }
+
+        assert ct_meta.name_ == expected_names
+        assert ct_meta.descendants_ids[
+            "https://bbp.epfl.ch/ontologies/core/mtypes/HippocampusMType"
+        ] == {"http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/GCL_GC"}
+        assert ct_meta.descendants_ids[
+            "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType"
+        ] == {
+            "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/L23_PTPC",
+            "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+            "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/GCL_GC",
+        }
+
+    def test_from_dict(self):
+        test_dict = {
+            "defines": [
+                {
+                    "@id": "id1",
+                    "label": "cell1",
+                    "subClassOf": []
+                },
+                {
+                    "@id": "id2",
+                    "label": "cell2",
+                    "subClassOf": ["id1"]
+                },
+                {
+                    "@id": "id3",
+                    "subClassOf": ["id2"]
+                }
+            ]
+        }
+        cell_meta = CellTypesMeta.from_dict(test_dict)
+        assert isinstance(cell_meta, CellTypesMeta)
+        assert cell_meta.name_ == {"id1": "cell1", "id2": "cell2", "id3": None}
+        assert cell_meta.descendants_ids == {"id1": {"id2", "id3"}, "id2": {"id3"}}
+
+    def test_from_dict_missing_label(self):
+        test_dict = {
+            "defines": [
+                {
+                    "@id": "id1",
+                    "subClassOf": []
+                },
+                {
+                    "@id": "id2",
+                    "subClassOf": ["id1"]
+                }
+            ]
+        }
+        cell_meta = CellTypesMeta.from_dict(test_dict)
+        assert cell_meta.name_ == {"id1": None, "id2": None}
+        assert cell_meta.descendants_ids == {"id1": {"id2"}}
+
+    def test_from_dict_missing_subClassOf(self):
+        test_dict = {
+            "defines": [
+                {
+                    "@id": "id1",
+                    "label": "cell1",
+                },
+                {
+                    "@id": "id2",
+                    "label": "cell2",
+                    "subClassOf": ["id1"]
+                }
+            ]
+        }
+        cell_meta = CellTypesMeta.from_dict(test_dict)
+        assert cell_meta.name_ == {"id1": "cell1", "id2": "cell2"}
+        assert cell_meta.descendants_ids == {"id1": {"id2"}}
+
+    @pytest.mark.parametrize(
+        "cell_type_id,expected_descendants",
+        [
+            (
+                "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType",
+                {
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/L23_PTPC",
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/GCL_GC",
+                    "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType",
+                },
+            ),
+            (
+                "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+                {
+                    "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+                },
+            ),
+            (
+                [
+                    "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType",
+                    "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+                ],
+                {
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/L23_PTPC",
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/mtypes/GCL_GC",
+                    "https://bbp.epfl.ch/ontologies/core/bmo/BrainCellType",
+                    "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+                },
+            ),
+            (
+                "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+                {
+                    "https://bbp.epfl.ch/ontologies/core/bmo/NeuronElectricalType",
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+                },
+            ),
+            (
+                "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+                {
+                    "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/cACint",
+                },
+            ),
+        ],
+    )
+    def test_descendants(self, cell_type_id, expected_descendants):
+        ct_meta = CellTypesMeta.from_json(CELL_TYPES_FILE)
+        assert ct_meta.descendants(cell_type_id) == expected_descendants
+
+    def test_load_and_save_config(self, tmp_path):
+        ct_meta = CellTypesMeta.from_json(CELL_TYPES_FILE)
+        file_path = tmp_path / "ct_meta_tmp.json"
+        ct_meta.save_config(file_path)
+        ct_meta2 = CellTypesMeta.load_config(file_path)
+        assert ct_meta.name_ == ct_meta2.name_
+        assert ct_meta.descendants_ids == ct_meta2.descendants_ids