Merge pull request #113 from bcgsc/release/v1.15.0_kbStatementRelated_genes

Release/v1.15.0 kb statement related genes

Author: dustinbleile

graphkb/genes.py

@@ -392,16 +392,18 @@ def get_gene_information(
 
     Function is originally from pori_ipr_python::annotate.py
 
-    Gene flags (categories) are: ['cancerGene', 'cancerRelated', 'knownFusionPartner', 'knownSmallMutation',
-                                  'oncogene', 'therapeuticAssociated', 'tumourSuppressor']
+    Gene flags (categories) are: [
+        'cancerGeneListMatch', 'kbStatementRelated', 'knownFusionPartner',
+        'knownSmallMutation', 'oncogene', 'therapeuticAssociated', 'tumourSuppressor'
+    ]
 
     Args:
         graphkb_conn ([type]): [description]
         gene_names ([type]): [description]
     Returns:
         List of gene_info dicts of form [{'name':<gene_str>, <flag>: True}]
         Keys of False values are simply omitted from ipr upload to reduce info transfer.
-            eg. [{'cancerRelated': True,
+            eg. [{'kbStatementRelated': True,
                   'knownFusionPartner': True,
                   'knownSmallMutation': True,
                   'name': 'TERT',
@@ -423,7 +425,7 @@ def get_gene_information(
     statements = [s for s in statements if s.get("reviewStatus") != FAILED_REVIEW_STATUS]
 
     gene_flags: Dict[str, Set[str]] = {
-        "cancerRelated": set(),
+        "kbStatementRelated": set(),
         "knownFusionPartner": set(),
         "knownSmallMutation": set(),
     }
@@ -432,9 +434,9 @@ def get_gene_information(
         for condition in statement["conditions"]:
             if not condition.get("reference1"):
                 continue
-            gene_flags["cancerRelated"].add(condition["reference1"])
+            gene_flags["kbStatementRelated"].add(condition["reference1"])
             if condition["reference2"]:
-                gene_flags["cancerRelated"].add(condition["reference2"])
+                gene_flags["kbStatementRelated"].add(condition["reference2"])
                 gene_flags["knownFusionPartner"].add(condition["reference1"])
                 gene_flags["knownFusionPartner"].add(condition["reference2"])
             elif condition["@class"] == "PositionalVariant":
@@ -444,8 +446,8 @@ def get_gene_information(
     gene_flags["oncogene"] = convert_to_rid_set(get_oncokb_oncogenes(graphkb_conn))
     logger.info("fetching tumour supressors list")
     gene_flags["tumourSuppressor"] = convert_to_rid_set(get_oncokb_tumour_supressors(graphkb_conn))
-    logger.info("fetching cancerGene list")
-    gene_flags["cancerGene"] = convert_to_rid_set(get_cancer_genes(graphkb_conn))
+    logger.info("fetching cancerGeneListMatch list")
+    gene_flags["cancerGeneListMatch"] = convert_to_rid_set(get_cancer_genes(graphkb_conn))
 
     logger.info("fetching therapeutic associated genes lists")
     gene_flags["therapeuticAssociated"] = convert_to_rid_set(

setup.cfg

@@ -10,7 +10,7 @@ include_trailing_comma = true
 [metadata]
 name = graphkb
 url = https://github.com/bcgsc/pori_graphkb_python
-version = 1.14.0
+version = 1.15.0
 author_email = graphkb@bcgsc.ca
 description = python adapter for interacting with the GraphKB API
 long_description = file: README.md

tests/test_genes.py

@@ -246,10 +246,10 @@ def test_get_gene_information(conn):
         + CANNONICAL_THERAPY_GENES
     ):
         assert gene in [
-            g["name"] for g in gene_info if g.get("cancerRelated")
-        ], f"Missed cancerRelated {gene}"
+            g["name"] for g in gene_info if g.get("kbStatementRelated")
+        ], f"Missed kbStatementRelated {gene}"
 
     for gene in CANONICAL_CG:
         assert gene in [
-            g["name"] for g in gene_info if g.get("cancerGene")
-        ], f"Missed cancerGene {gene}"
+            g["name"] for g in gene_info if g.get("cancerGeneListMatch")
+        ], f"Missed cancerGeneListMatch {gene}"

tests/test_statement.py

@@ -5,7 +5,9 @@
 
 from graphkb import statement
 
-from .test_match import conn
+from .test_match import (  # noqa - 'F401 imported but unused' is being fooled by pytest conventions
+    conn,
+)
 
 EXCLUDE_INTEGRATION_TESTS = os.environ.get("EXCLUDE_INTEGRATION_TESTS") == "1"
 
@@ -86,7 +88,7 @@ def test_custom_categories(self, graphkb_conn):
 
 @pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason="excluding long running integration tests")
 class TestStatementMatch:
-    def test_truncating_categories(self, conn):
+    def test_truncating_categories(self, conn):  # noqa - pytest fixture, not redefinition
         variant = {"@class": "CategoryVariant", "@rid": "#161:429", "displayName": "RB1 truncating"}
         statements = statement.get_statements_from_variants(conn, [variant])
         assert statements