Additional tests

tests/test_transform.py

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+"""
+An example test file for the transform script.
+
+It uses pytest fixtures to define the input data and the mock koza transform.
+The test_example function then tests the output of the transform script.
+
+See the Koza documentation for more information on testing transforms:
+https://koza.monarchinitiative.org/Usage/testing/
+"""
+
+import pytest
+from koza.utils.testing_utils import mock_koza
+
+# Define the ingest name and transform script path
+INGEST_NAME = "alliance_disease"
+TRANSFORM_SCRIPT = "./src/alliance_disease_association_ingest/transform.py"
+
+# Define the mock koza transform on an example row
+@pytest.fixture
+def mgi_agm(mock_koza):
+    row = {'Taxon': 'NCBITaxon:10090', 'SpeciesName': 'Mus musculus', 'DBobjectType': 'affected_genomic_model',
+            'DBObjectID': 'MGI:3799157', 'DBObjectSymbol': 'None [background:] C58/J', 'AssociationType': 'is_model_of',
+            'DOID': 'DOID:0060041', 'DOtermName': 'autism spectrum disorder', 'WithOrtholog': '', 'InferredFromID': '',
+            'InferredFromSymbol': '', 'ExperimentalCondition': '', 'Modifier': '', 'EvidenceCode': 'ECO:0000033',
+            'EvidenceCodeName': 'author statement supported by traceable reference', 'Reference': 'PMID:29885454',
+            'Date': '20181028', 'Source': 'MGI'}
+    return mock_koza(
+        INGEST_NAME,
+        [row],
+        TRANSFORM_SCRIPT,
+    )
+
+
+def test_mgi_agm(mgi_agm):
+    entities = mgi_agm
+    assert len(entities) == 1
+    association = entities[0]
+    assert association
+    assert association.category == ['biolink:GenotypeToDiseaseAssociation']
+    assert association.subject == 'MGI:3799157'
+    assert association.predicate == 'biolink:model_of'
+    assert association.object == 'DOID:0060041'
+    assert association.has_evidence == ['ECO:0000033']
+    assert association.publications == ['PMID:29885454']
+
+@pytest.fixture
+def zfin_agm(mock_koza):
+    row = {'Taxon': 'NCBITaxon:7955', 'SpeciesName': 'Danio rerio', 'DBobjectType': 'affected_genomic_model', 'DBObjectID': 'ZFIN:ZDB-FISH-160908-10', 'DBObjectSymbol': 'TU + MO2-mybpc2b', 'AssociationType': 'is_model_of', 'DOID': 'DOID:423', 'DOtermName': 'myopathy', 'WithOrtholog': '', 'InferredFromID': '', 'InferredFromSymbol': '', 'ExperimentalCondition': 'Has Condition: standard conditions', 'Modifier': '', 'EvidenceCode': 'ECO:0000305', 'EvidenceCodeName': 'curator inference used in manual assertion', 'Reference': 'PMID:27022191', 'Date': '20240314', 'Source': 'ZFIN'}
+    return mock_koza(
+        INGEST_NAME,
+        [row],
+        TRANSFORM_SCRIPT,
+    )
+
+def test_zfin_agm(zfin_agm):
+    entities = zfin_agm
+    assert len(entities) == 1
+    association = entities[0]
+    assert association
+    assert association.category == ['biolink:GenotypeToDiseaseAssociation']
+    assert association.subject == 'ZFIN:ZDB-FISH-160908-10'
+    assert association.predicate == 'biolink:model_of'
+    assert association.object == 'DOID:423'
+    assert association.has_evidence == ['ECO:0000305']
+    assert association.publications == ['PMID:27022191']
+
+@pytest.fixture
+def zfin_agm_chemical_environment(mock_koza):
+    row = {'Taxon': 'NCBITaxon:7955', 'SpeciesName': 'Danio rerio', 'DBobjectType': 'affected_genomic_model', 'DBObjectID': 'ZFIN:ZDB-FISH-150901-29105', 'DBObjectSymbol': 'WT', 'AssociationType': 'is_model_of', 'DOID': 'DOID:0060668', 'DOtermName': 'anencephaly', 'WithOrtholog': '', 'InferredFromID': '', 'InferredFromSymbol': '', 'ExperimentalCondition': 'Has Condition: chemical treatment by environment: SU5402', 'Modifier': '', 'EvidenceCode': 'ECO:0000305', 'EvidenceCodeName': 'curator inference used in manual assertion', 'Reference': 'PMID:29488319', 'Date': '20240314', 'Source': 'ZFIN'}
+    return mock_koza(
+        INGEST_NAME,
+        [row],
+        TRANSFORM_SCRIPT,
+    )
+
+def test_zfin_agm_chemical_environment(zfin_agm_chemical_environment):
+    entities = zfin_agm_chemical_environment
+    assert len(entities) == 0
+    assert entities == []