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@kanesoban
kanesoban committed Dec 18, 2024
2 parents 52be9a5 + 56a81ea commit e1a9095
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Unit tests for the migrated tools
- CRUDs.
- BlueNaas CRUD tools
- Cell types, resolving and utils tests
- app unit tests
- Tests of AgentsRoutine.
- Unit tests for database
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2 changes: 1 addition & 1 deletion swarm_copy_tests/data/kg_cell_types_hierarchy_test.json
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Expand Up @@ -10,4 +10,4 @@
{"@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"
}
}
190 changes: 190 additions & 0 deletions swarm_copy_tests/test_cell_types.py
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"""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
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