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Add test_ensembl_protein
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‎tests/test_match.py‎

Lines changed: 129 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -79,6 +79,135 @@ def test_checks_by_source_id_kras(self, conn):
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]
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assert "KRAS" in kras
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# KBDEV-1163
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# Testing if the addition of Ensembl protein Features are limiting results
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# returned by get_equivalent_features() since SimilatTo queryType queries
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# aren't traversing the graph to it's whole depth.
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@pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason="excluding data-specific test")
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def test_ensembl_protein(self, conn):
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for feature, expected in [
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# Sample
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(
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'EGFR',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NM_001346897',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NM_001346897.2',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NP_001333826',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NP_001333826.1',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'ENSG00000146648',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
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],
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),
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(
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'ENSG00000146648.17',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
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],
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),
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(
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'ENST00000275493',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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],
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),
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(
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'ENST00000275493.6',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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],
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),
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]:
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equivalent_features = match.get_equivalent_features(conn, feature)
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equivalent_features = [el['displayName'] for el in equivalent_features]
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for equivalent_feature in expected:
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assert equivalent_feature in equivalent_features
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class TestMatchCopyVariant:
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def test_bad_category(self, conn):

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