minor lint - isort inputs & quotes

Author: dustinbleile

pori_python/ipr/ipr.py

@@ -295,10 +295,10 @@ def create_key_alterations(
     counts: Dict[str, Set] = {v: set() for v in type_mapping.values()}
     skipped_variant_types = []
 
-    included_kbvariant_ids = list(set([item['kbVariantId'] for item in included_kb_matches]))
+    included_kbvariant_ids = list(set([item["kbVariantId"] for item in included_kb_matches]))
 
     for kb_match in kb_matches:
-        if kb_match['kbVariantId'] not in included_kbvariant_ids:
+        if kb_match["kbVariantId"] not in included_kbvariant_ids:
             continue
         variant_type = kb_match["variantType"]
         variant_key = kb_match["variant"]
@@ -646,13 +646,13 @@ def get_kb_matches_sections(
         unique_kb_variant_ids = list(
             set(
                 [
-                    item['kbVariantId']
+                    item["kbVariantId"]
                     for conditionSet in kb_statement_matched_conditions
-                    for item in conditionSet['matchedConditions']
+                    for item in conditionSet["matchedConditions"]
                 ]
             )
         )
-        kb_variants = [item for item in kb_variants if item['kbVariantId'] in unique_kb_variant_ids]
+        kb_variants = [item for item in kb_variants if item["kbVariantId"] in unique_kb_variant_ids]
 
     return {
         "kbMatches": kb_variants,

pori_python/ipr/main.py

@@ -525,7 +525,7 @@ def ipr_report(
 
     # KEY ALTERATIONS
     key_alterations, variant_counts = create_key_alterations(
-        gkb_matches, all_variants, kb_matched_sections['kbMatches']
+        gkb_matches, all_variants, kb_matched_sections["kbMatches"]
     )
 
     # OUTPUT CONTENT

tests/test_ipr/test_ipr.py

@@ -5,13 +5,13 @@
 from pori_python.graphkb import vocab as gkb_vocab
 from pori_python.ipr.ipr import (
     convert_statements_to_alterations,
+    create_key_alterations,
     germline_kb_matches,
     get_kb_disease_matches,
     get_kb_matched_statements,
+    get_kb_matches_sections,
     get_kb_statement_matched_conditions,
     get_kb_variants,
-    get_kb_matches_sections,
-    create_key_alterations,
 )
 from pori_python.types import Statement
 
@@ -497,10 +497,10 @@ def test_germline_kb_matches(self):
 ]
 
 ALL_VARIANTS = [
-    {"variant": "var1", "key": '1', "variantType": 'mut'},
-    {"variant": "var2", "key": '2', "variantType": 'mut'},
-    {"variant": "var3", "key": '3', "variantType": 'mut'},
-    {"variant": "var4", "key": '4', "variantType": 'mut'},
+    {"variant": "var1", "key": "1", "variantType": "mut"},
+    {"variant": "var2", "key": "2", "variantType": "mut"},
+    {"variant": "var3", "key": "3", "variantType": "mut"},
+    {"variant": "var4", "key": "4", "variantType": "mut"},
 ]
 
 BASIC_GKB_MATCH = {
@@ -709,8 +709,8 @@ def test_partial_matches_omitted(self):
         gkb_matches = create_gkb_matches(input_fields)
         sections = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)
 
-        stmts = sections['kbMatchedStatements']
-        kbcs = sections['kbStatementMatchedConditions']
+        stmts = sections["kbMatchedStatements"]
+        kbcs = sections["kbStatementMatchedConditions"]
         assert len(stmts) == 2
         assert len(kbcs) == 1  # X only
         assert kbcs[0]["kbStatementId"] == "X"
@@ -796,14 +796,14 @@ def test_kbvariants_removed_from_set_when_not_part_of_full_conditionset_match(se
             item["kbVariant"] = "test"
         gkb_matches = create_gkb_matches(input_fields)
         sections1 = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)
-        kbcs1 = sections1['kbStatementMatchedConditions']
-        kbvars1 = sections1['kbMatches']
+        kbcs1 = sections1["kbStatementMatchedConditions"]
+        kbvars1 = sections1["kbMatches"]
         assert len(kbcs1) == 1  # only fully matched condition sets included
         assert len(kbvars1) == 2  # therefore, kbvars associated with stmt X are pruned
 
         sections2 = get_kb_matches_sections(gkb_matches, allow_partial_matches=True)
-        kbcs2 = sections2['kbStatementMatchedConditions']
-        kbvars2 = sections2['kbMatches']
+        kbcs2 = sections2["kbStatementMatchedConditions"]
+        kbvars2 = sections2["kbMatches"]
         assert len(kbcs2) == 2  # all condition sets included
         assert len(kbvars2) == 3  # therefore, no pruning
 
@@ -844,12 +844,12 @@ def test_create_key_alterations_includes_only_pruned_kbmatches(self):
 
         sections1 = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)
         key_alts1, counts1 = create_key_alterations(
-            gkb_matches, ALL_VARIANTS, sections1['kbMatches']
+            gkb_matches, ALL_VARIANTS, sections1["kbMatches"]
         )
 
         sections2 = get_kb_matches_sections(gkb_matches, allow_partial_matches=True)
         key_alts2, counts2 = create_key_alterations(
-            gkb_matches, ALL_VARIANTS, sections2['kbMatches']
+            gkb_matches, ALL_VARIANTS, sections2["kbMatches"]
         )
 
         # check partial-match-only variants are not included in key alterations when