Add test_ensembl_protein

bcgsc · Mar 1, 2024 · f37e4ad · f37e4ad
1 parent f3a17ae
commit f37e4ad
Showing 1 changed file with 104 additions and 0 deletions.
diff --git a/tests/test_match.py b/tests/test_match.py
@@ -79,6 +79,110 @@ def test_checks_by_source_id_kras(self, conn):
         ]
         assert "KRAS" in kras
 
+    # KBDEV-1163
+    # Testing if the addition of Ensembl protein Features are limiting results
+    # returned by get_equivalent_features() since SimilatTo queryType queries
+    # aren't traversing the graph to it's whole depth.
+    @pytest.mark.skipif(
+        EXCLUDE_INTEGRATION_TESTS, reason="excluding data-specific test"
+    )
+    def test_ensembl_protein(self, conn):
+        for (feature, expected) in [
+            # Sample
+            ('EGFR', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648',
+                'ENSG00000146648.17',
+                'ENST00000275493',
+                'ENST00000275493.6',
+                'NM_001346897',
+                'NM_001346897.2',
+                'NP_001333826',
+                'NP_001333826.1',
+            ]),
+            ('NM_001346897', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648',
+                'ENSG00000146648.17',
+                'NM_001346897',
+                'NM_001346897.2',
+                'NP_001333826',
+                'NP_001333826.1',
+            ]),
+            ('NM_001346897.2', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648',
+                'ENSG00000146648.17',
+                'NM_001346897',
+                'NM_001346897.2',
+                'NP_001333826',
+                'NP_001333826.1',
+            ]),
+            ('NP_001333826', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
+                'NM_001346897',
+                'NM_001346897.2',
+                'NP_001333826',
+                'NP_001333826.1',
+            ]),
+            ('NP_001333826.1', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
+                'NM_001346897',
+                'NM_001346897.2',
+                'NP_001333826',
+                'NP_001333826.1',
+            ]),
+            ('ENSG00000146648', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648',
+                'ENSG00000146648.17',
+                'ENST00000275493',
+                'ENST00000275493.6',
+                'NM_001346897',
+                'NM_001346897.2',
+                'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
+            ]),
+            ('ENSG00000146648.17', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648',
+                'ENSG00000146648.17',
+                'ENST00000275493',
+                'ENST00000275493.6',
+                'NM_001346897',
+                'NM_001346897.2',
+                'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
+            ]),
+            ('ENST00000275493', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648',
+                'ENSG00000146648.17',
+                'ENST00000275493',
+                'ENST00000275493.6',
+            ]),
+            ('ENST00000275493.6', [
+                'EGFR',
+                'ERBB',
+                'ENSG00000146648',
+                'ENSG00000146648.17',
+                'ENST00000275493',
+                'ENST00000275493.6',
+            ]),
+        ]:
+            equivalent_features = match.get_equivalent_features(conn, feature)
+            equivalent_features = [el['displayName'] for el in equivalent_features]
+            for equivalent_feature in expected:
+                assert equivalent_feature in equivalent_features
+
 
 class TestMatchCopyVariant:
     def test_bad_category(self, conn):