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Merged
mathieulemieux merged 3 commits into from
May 29, 2026
Merged

Task/sdev 5403 hrd kb category #116

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1d05cdd
Add to enum values to hrd kbCategory specs
mathieulemieux May 26, 2026
4107b24
Add hrd tests for annotate_signature_variants()
mathieulemieux May 26, 2026
bb9c6ae
Change enum values into examples for hrd kbCategory specs
mathieulemieux May 26, 2026
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4 changes: 4 additions & 0 deletions pori_python/ipr/content.spec.json
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Original file line number Diff line number Diff line change
Expand Up @@ -564,6 +564,10 @@
"hrd": {
"properties": {
"kbCategory": {
"examples": [
"homologous recombination deficiency strong signature",
"homologous recombination deficiency moderate signature"
],
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"type": "string"
},
"score": {
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26 changes: 25 additions & 1 deletion tests/test_ipr/test_annotate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,15 @@
from pori_python.ipr.constants import (
COSMIC_SIGNATURE_VARIANT_TYPE,
HLA_SIGNATURE_VARIANT_TYPE,
HRD_MAPPING,
MSI_MAPPING,
TMB_SIGNATURE,
TMB_SIGNATURE_VARIANT_TYPE,
)
from pori_python.ipr.inputs import preprocess_signature_variants
from pori_python.types import IprSmallMutationVariant

from .test_ipr import DISEASE_RIDS
from .test_ipr import DISEASE_RIDS # dummy RIDs; will always result in matchedCancer == false

EXCLUDE_BCGSC_TESTS = os.environ.get('EXCLUDE_BCGSC_TESTS') == '1'

Expand Down Expand Up @@ -203,6 +204,29 @@ def test_annotate_signature_variants_msi(self, graphkb_conn):
)
assert len(msi) != 0

def test_annotate_signature_variants_hrd_strong(self, graphkb_conn):
"""Test HRD strong signature"""
hrd = annotate_signature_variants(
graphkb_conn,
DISEASE_RIDS,
preprocess_signature_variants(
[HRD_MAPPING['homologous recombination deficiency strong signature']]
),
)
assert len(hrd) != 0

@pytest.mark.skip(reason='no GKB statement for HRD moderate Signature CVs yet')
def test_annotate_signature_variants_hrd_moderate(self, graphkb_conn):
"""Test HRD moderate signature"""
hrd = annotate_signature_variants(
graphkb_conn,
DISEASE_RIDS,
preprocess_signature_variants(
[HRD_MAPPING['homologous recombination deficiency moderate signature']]
),
)
assert len(hrd) != 0

def test_annotate_structural_variants_tp53(self, graphkb_conn):
"""Verify alternate TP53 variants match."""
ref_key = 'prot_only'
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