diff --git a/pori_python/ipr/content.spec.json b/pori_python/ipr/content.spec.json index c994ba6..f35b15b 100644 --- a/pori_python/ipr/content.spec.json +++ b/pori_python/ipr/content.spec.json @@ -564,6 +564,10 @@ "hrd": { "properties": { "kbCategory": { + "examples": [ + "homologous recombination deficiency strong signature", + "homologous recombination deficiency moderate signature" + ], "type": "string" }, "score": { diff --git a/tests/test_ipr/test_annotate.py b/tests/test_ipr/test_annotate.py index 43de421..79eb54c 100644 --- a/tests/test_ipr/test_annotate.py +++ b/tests/test_ipr/test_annotate.py @@ -6,6 +6,7 @@ from pori_python.ipr.constants import ( COSMIC_SIGNATURE_VARIANT_TYPE, HLA_SIGNATURE_VARIANT_TYPE, + HRD_MAPPING, MSI_MAPPING, TMB_SIGNATURE, TMB_SIGNATURE_VARIANT_TYPE, @@ -13,7 +14,7 @@ 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' @@ -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'