linting - isort and black

bcgsc · Jul 12, 2024 · 7e67692 · 7e67692
1 parent a15f56e
commit 7e67692
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Showing 34 changed files with 1,787 additions and 1,350 deletions.
diff --git a/pori_python/__init__.py b/pori_python/__init__.py
@@ -1,2 +1 @@
-from . import ipr
-from . import graphkb
+from . import graphkb, ipr
diff --git a/pori_python/graphkb/constants.py b/pori_python/graphkb/constants.py
@@ -177,7 +177,7 @@ def __getitem__(self, key):
 }
 
 # For match.type_screening() [KBDEV-1056]
-DEFAULT_NON_STRUCTURAL_VARIANT_TYPE = 'mutation'
+DEFAULT_NON_STRUCTURAL_VARIANT_TYPE = "mutation"
 STRUCTURAL_VARIANT_SIZE_THRESHOLD = 48  # bp
 STRUCTURAL_VARIANT_TYPES = [
     "structural variant",

diff --git a/pori_python/graphkb/genes.py b/pori_python/graphkb/genes.py
@@ -24,7 +24,10 @@
 
 
 def _get_tumourigenesis_genes_list(
-    conn: GraphKBConnection, relevance: str, sources: List[str], ignore_cache: bool = False
+    conn: GraphKBConnection,
+    relevance: str,
+    sources: List[str],
+    ignore_cache: bool = False,
 ) -> List[Ontology]:
     statements = cast(
         List[Statement],
@@ -34,10 +37,17 @@ def _get_tumourigenesis_genes_list(
                 "filters": {
                     "AND": [
                         {"source": {"target": "Source", "filters": {"name": sources}}},
-                        {"relevance": {"target": "Vocabulary", "filters": {"name": relevance}}},
+                        {
+                            "relevance": {
+                                "target": "Vocabulary",
+                                "filters": {"name": relevance},
+                            }
+                        },
                     ]
                 },
-                "returnProperties": [f"subject.{prop}" for prop in GENE_RETURN_PROPERTIES],
+                "returnProperties": [
+                    f"subject.{prop}" for prop in GENE_RETURN_PROPERTIES
+                ],
             },
             ignore_cache=ignore_cache,
         ),
@@ -74,7 +84,9 @@ def get_oncokb_tumour_supressors(conn: GraphKBConnection) -> List[Ontology]:
     Returns:
         gene (Feature) records
     """
-    return _get_tumourigenesis_genes_list(conn, TUMOUR_SUPPRESSIVE, [ONCOKB_SOURCE_NAME])
+    return _get_tumourigenesis_genes_list(
+        conn, TUMOUR_SUPPRESSIVE, [ONCOKB_SOURCE_NAME]
+    )
 
 
 def get_cancer_genes(conn: GraphKBConnection) -> List[Ontology]:
@@ -147,7 +159,12 @@ def get_genes_from_variant_types(
     filters: List[Dict[str, Any]] = []
     if types:
         filters.append(
-            {"type": {"target": "Vocabulary", "filters": {"name": types, "operator": "IN"}}}
+            {
+                "type": {
+                    "target": "Vocabulary",
+                    "filters": {"name": types, "operator": "IN"},
+                }
+            }
         )
 
     variants = cast(
@@ -177,7 +194,11 @@ def get_genes_from_variant_types(
     result = cast(
         List[Ontology],
         conn.query(
-            {"target": list(genes), "returnProperties": GENE_RETURN_PROPERTIES, "filters": filters},
+            {
+                "target": list(genes),
+                "returnProperties": GENE_RETURN_PROPERTIES,
+                "filters": filters,
+            },
             ignore_cache=ignore_cache,
         ),
     )
@@ -273,7 +294,12 @@ def get_gene_linked_cancer_predisposition_info(
                             "filters": {"@rid": get_rid(conn, "Source", "CGL")},
                         }
                     },
-                    {"relevance": {"target": "Vocabulary", "filters": {"@rid": relevance_rids}}},
+                    {
+                        "relevance": {
+                            "target": "Vocabulary",
+                            "filters": {"@rid": relevance_rids},
+                        }
+                    },
                 ]
             },
             "returnProperties": [
@@ -307,7 +333,10 @@ def get_gene_linked_cancer_predisposition_info(
                             logger.error(
                                 f"Non-gene cancer predisposition {biotype}: {name} for {condition['displayName']}"
                             )
-                variants[condition["@rid"]] = [condition["displayName"], assoc_gene_list]
+                variants[condition["@rid"]] = [
+                    condition["displayName"],
+                    assoc_gene_list,
+                ]
 
     for gene, name, biotype in infer_genes:
         logger.debug(f"Found gene '{gene}' for '{name}' ({biotype})")
@@ -359,7 +388,12 @@ def get_gene_linked_pharmacogenomic_info(
         {
             "target": "Statement",
             "filters": [
-                {"relevance": {"target": "Vocabulary", "filters": {"@rid": relevance_rids}}}
+                {
+                    "relevance": {
+                        "target": "Vocabulary",
+                        "filters": {"@rid": relevance_rids},
+                    }
+                }
             ],
             "returnProperties": [
                 "conditions.@class",
@@ -397,7 +431,10 @@ def get_gene_linked_pharmacogenomic_info(
                             logger.error(
                                 f"Non-gene pharmacogenomic {biotype}: {name} for {condition['displayName']}"
                             )
-                variants[condition["@rid"]] = [condition["displayName"], assoc_gene_list]
+                variants[condition["@rid"]] = [
+                    condition["displayName"],
+                    assoc_gene_list,
+                ]
     for gene, name, biotype in infer_genes:
         logger.debug(f"Found gene '{gene}' for '{name}' ({biotype})")
         genes.add(gene)
@@ -449,7 +486,9 @@ def get_gene_information(
 
     gene_names = sorted(set(gene_names))
     statements = graphkb_conn.query(body)
-    statements = [s for s in statements if s.get("reviewStatus") != FAILED_REVIEW_STATUS]
+    statements = [
+        s for s in statements if s.get("reviewStatus") != FAILED_REVIEW_STATUS
+    ]
 
     gene_flags: Dict[str, Set[str]] = {
         "kbStatementRelated": set(),
@@ -472,9 +511,13 @@ def get_gene_information(
     logger.info("fetching oncogenes list")
     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))
+    gene_flags["tumourSuppressor"] = convert_to_rid_set(
+        get_oncokb_tumour_supressors(graphkb_conn)
+    )
     logger.info("fetching cancerGeneListMatch list")
-    gene_flags["cancerGeneListMatch"] = convert_to_rid_set(get_cancer_genes(graphkb_conn))
+    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(
@@ -484,7 +527,9 @@ def get_gene_information(
     logger.info(f"Setting gene_info flags on {len(gene_names)} genes")
     result = []
     for gene_name in gene_names:
-        equivalent = convert_to_rid_set(get_equivalent_features(graphkb_conn, gene_name))
+        equivalent = convert_to_rid_set(
+            get_equivalent_features(graphkb_conn, gene_name)
+        )
         row = {"name": gene_name}
         flagged = False
         for flag in gene_flags: