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mathieulemieuxmathieulemieux
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Merge branch 'develop' into feature/KBDEV-1306-fix-disease-matching-with-subgraphs
2 parents fba0f5f + dc19024 commit 8dacdb4

2 files changed

Lines changed: 140 additions & 8 deletions

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‎tests/test_graphkb/data.py‎

Lines changed: 127 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,10 @@
1-
"""_summary_
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matches:
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Array of variants (diplayName and type) that MUST be matching, but not restricted to
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does_not_matches:
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Array of variants (diplayName and type) that MUST NOT be matching, but not restricted to
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"""
7-
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# Screening structural variant to rule out small events [KBDEV_1056]
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#
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# matches:
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# Array of variants (diplayName and type) that MUST be matching, but not restricted to
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# does_not_matches:
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# Array of variants (diplayName and type) that MUST NOT be matching, but not restricted to
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#
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structuralVariants = {
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# Unambiguous structural variations
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"(FGFR3,BRCA2):fusion(g.1234567,g.1234567)": {
@@ -76,3 +75,124 @@
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"does_not_matches": {"displayName": ["FGFR3 rearrangement"], "type": ["rearrangement"]},
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},
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}
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# KBDEV-1163.
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# pos 0: a feature
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# pos 1: expected equivalences
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ensemblProteinSample = [
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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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]

‎tests/test_graphkb/test_match.py‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
from pori_python.graphkb.util import FeatureNotFoundError
1414

1515
# Test datasets
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from .data import structuralVariants
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from .data import ensemblProteinSample, structuralVariants
1717

1818
EXCLUDE_BCGSC_TESTS = os.environ.get("EXCLUDE_BCGSC_TESTS") == "1"
1919
EXCLUDE_INTEGRATION_TESTS = os.environ.get("EXCLUDE_INTEGRATION_TESTS") == "1"
@@ -101,6 +101,18 @@ def test_checks_by_source_id_kras(self, conn):
101101
]
102102
assert "KRAS" in kras
103103

104+
# KBDEV-1163
105+
# Testing if the addition of Ensembl protein Features are limiting results
106+
# returned by get_equivalent_features() since SimilatTo queryType queries
107+
# aren't traversing the graph to it's whole depth.
108+
@pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason="excluding data-specific test")
109+
def test_ensembl_protein(self, conn):
110+
for feature, expected in ensemblProteinSample:
111+
equivalent_features = match.get_equivalent_features(conn, feature)
112+
equivalent_features = [el['displayName'] for el in equivalent_features]
113+
for equivalent_feature in expected:
114+
assert equivalent_feature in equivalent_features
115+
104116

105117
class TestMatchCopyVariant:
106118
def test_bad_category(self, conn):

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