lint with black

Author: elewis2

pori_python/ipr/summary.py

@@ -86,15 +86,7 @@ def merge_diseases(
         [d["@class"] == "Disease" for d in diseases]
     ):
         words = sorted(
-            list(
-                set(
-                    [
-                        get_displayname(s)
-                        for s in diseases
-                        if s["@rid"] in disease_matches
-                    ]
-                )
-            )
+            list(set([get_displayname(s) for s in diseases if s["@rid"] in disease_matches]))
         )
         words.append(OTHER_DISEASES)
         return natural_join(words)
@@ -132,18 +124,12 @@ def substitute_sentence_template(
         # remove subject from the conditions replacements
         subjects_ids = convert_to_rid_set(subjects)
         disease_conditions = [
-            cast(Ontology, d)
-            for d in disease_conditions
-            if d["@rid"] not in subjects_ids
+            cast(Ontology, d) for d in disease_conditions if d["@rid"] not in subjects_ids
         ]
         variant_conditions = [
-            cast(Ontology, d)
-            for d in variant_conditions
-            if d["@rid"] not in subjects_ids
-        ]
-        other_conditions = [
-            d for d in other_conditions if d["@rid"] not in subjects_ids
+            cast(Ontology, d) for d in variant_conditions if d["@rid"] not in subjects_ids
         ]
+        other_conditions = [d for d in other_conditions if d["@rid"] not in subjects_ids]
 
         result = result.replace(r"{subject}", merge_diseases(subjects, disease_matches))
 
@@ -155,9 +141,7 @@ def substitute_sentence_template(
         other_conditions.extend(disease_conditions)
 
     if r"{conditions:variant}" in template:
-        result = result.replace(
-            r"{conditions:variant}", natural_join_records(variant_conditions)
-        )
+        result = result.replace(r"{conditions:variant}", natural_join_records(variant_conditions))
     else:
         other_conditions.extend(variant_conditions)
 
@@ -188,9 +172,7 @@ def aggregate_statements(
     def generate_key(statement: Statement) -> Tuple:
         result = [
             cond.get("displayName", cond["@rid"])
-            for cond in filter_by_record_class(
-                statement["conditions"], "Disease", exclude=True
-            )
+            for cond in filter_by_record_class(statement["conditions"], "Disease", exclude=True)
             if cond["@rid"] != statement["subject"]["@rid"]
         ]
         if statement.get("subject", {}).get("@class", "Disease") != "Disease":
@@ -250,9 +232,7 @@ def display_variant(variant: IprVariant) -> str:
     # Use chosen legacy 'proteinChange' or an hgvs description of lowest detail.
     hgvs = variant.get(
         "proteinChange",
-        variant.get(
-            "hgvsProtein", variant.get("hgvsCds", variant.get("hgvsGenomic", ""))
-        ),
+        variant.get("hgvsProtein", variant.get("hgvsCds", variant.get("hgvsGenomic", ""))),
     )
 
     if gene and hgvs:
@@ -264,16 +244,14 @@ def display_variant(variant: IprVariant) -> str:
 
 
 def display_variants(gene_name: str, variants: List[IprVariant]) -> str:
-    result = sorted(
-        list({v for v in [display_variant(e) for e in variants] if gene_name in v})
-    )
+    result = sorted(list({v for v in [display_variant(e) for e in variants] if gene_name in v}))
     variants_text = natural_join(result)
     if len(result) > 1:
-        return f"Multiple variants of the gene {gene_name} were observed in this case: {variants_text}"
-    elif result:
         return (
-            f"{variants_text[0].upper()}{variants_text[1:]} was observed in this case."
+            f"Multiple variants of the gene {gene_name} were observed in this case: {variants_text}"
         )
+    elif result:
+        return f"{variants_text[0].upper()}{variants_text[1:]} was observed in this case."
     return ""
 
 
@@ -344,11 +322,7 @@ def create_section_html(
     for section in [
         {s for (s, v) in sentence_categories.items() if v == "diagnostic"},
         {s for (s, v) in sentence_categories.items() if v == "biological"},
-        {
-            s
-            for (s, v) in sentence_categories.items()
-            if v in ["therapeutic", "prognostic"]
-        },
+        {s for (s, v) in sentence_categories.items() if v in ["therapeutic", "prognostic"]},
         {
             s
             for (s, v) in sentence_categories.items()
@@ -490,14 +464,10 @@ def auto_analyst_comments(
     # aggregate similar sentences
     sentences = {}
     for template, group in templates.items():
-        sentences.update(
-            aggregate_statements(graphkb_conn, template, group, disease_matches)
-        )
+        sentences.update(aggregate_statements(graphkb_conn, template, group, disease_matches))
 
     # section statements by genes
-    statements_by_genes = section_statements_by_genes(
-        graphkb_conn, list(statements.values())
-    )
+    statements_by_genes = section_statements_by_genes(graphkb_conn, list(statements.values()))
 
     output: List[str] = [
         "<h3>The comments below were automatically generated from matches to GraphKB and have not been manually reviewed</h3>"

tests/test_ipr/test_main.py

@@ -48,25 +48,23 @@ def report_upload_content(tmp_path_factory) -> Dict:
                 "patientId": "PATIENT001",
                 "project": "TEST",
                 "expressionVariants": json.loads(
-                    pd.read_csv(
-                        get_test_file("expression.short.tab"), sep="\t"
-                    ).to_json(orient="records")
+                    pd.read_csv(get_test_file("expression.short.tab"), sep="\t").to_json(
+                        orient="records"
+                    )
                 ),
                 "smallMutations": json.loads(
-                    pd.read_csv(
-                        get_test_file("small_mutations.short.tab"), sep="\t"
-                    ).to_json(orient="records")
+                    pd.read_csv(get_test_file("small_mutations.short.tab"), sep="\t").to_json(
+                        orient="records"
+                    )
                 ),
                 "copyVariants": json.loads(
-                    pd.read_csv(
-                        get_test_file("copy_variants.short.tab"), sep="\t"
-                    ).to_json(orient="records")
-                ),
-                "structuralVariants": json.loads(
-                    pd.read_csv(get_test_file("fusions.tab"), sep="\t").to_json(
+                    pd.read_csv(get_test_file("copy_variants.short.tab"), sep="\t").to_json(
                         orient="records"
                     )
                 ),
+                "structuralVariants": json.loads(
+                    pd.read_csv(get_test_file("fusions.tab"), sep="\t").to_json(orient="records")
+                ),
                 "kbDiseaseMatch": "colorectal cancer",
             },
             allow_nan=False,
@@ -105,9 +103,7 @@ def side_effect_function(*args, **kwargs):
     ):
         with patch.object(IprConnection, "upload_report", new=mock):
             with patch.object(IprConnection, "get_spec", return_value=get_test_spec()):
-                with patch.object(
-                    IprConnection, "get", side_effect=side_effect_function
-                ):
+                with patch.object(IprConnection, "get", side_effect=side_effect_function):
                     command_interface()
 
     assert mock.called
@@ -116,9 +112,7 @@ def side_effect_function(*args, **kwargs):
     return report_content
 
 
-@pytest.mark.skipif(
-    EXCLUDE_INTEGRATION_TESTS, reason="excluding long running integration tests"
-)
+@pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason="excluding long running integration tests")
 class TestCreateReport:
     def test_main_sections_present(self, report_upload_content: Dict) -> None:
         sections = set(report_upload_content.keys())
@@ -134,10 +128,7 @@ def test_main_sections_present(self, report_upload_content: Dict) -> None:
             assert section in sections
 
     def test_kept_low_quality_fusion(self, report_upload_content: Dict) -> None:
-        fusions = [
-            (sv["gene1"], sv["gene2"])
-            for sv in report_upload_content["structuralVariants"]
-        ]
+        fusions = [(sv["gene1"], sv["gene2"]) for sv in report_upload_content["structuralVariants"]]
         if (
             EXCLUDE_BCGSC_TESTS
         ):  # may be missing statements assoc with SUZ12 if no access to bcgsc data
@@ -154,17 +145,13 @@ def test_found_fusion_partner_gene(self, report_upload_content: Dict) -> None:
         # eg, A1BG
         assert any([g.get("knownFusionPartner", False) for g in genes])
 
-    @pytest.mark.skipif(
-        EXCLUDE_ONCOKB_TESTS, reason="excluding tests that depend on oncokb data"
-    )
+    @pytest.mark.skipif(EXCLUDE_ONCOKB_TESTS, reason="excluding tests that depend on oncokb data")
     def test_found_oncogene(self, report_upload_content: Dict) -> None:
         genes = report_upload_content["genes"]
         # eg, ZBTB20
         assert any([g.get("oncogene", False) for g in genes])
 
-    @pytest.mark.skipif(
-        EXCLUDE_ONCOKB_TESTS, reason="excluding tests that depend on oncokb data)"
-    )
+    @pytest.mark.skipif(EXCLUDE_ONCOKB_TESTS, reason="excluding tests that depend on oncokb data)")
     def test_found_tumour_supressor(self, report_upload_content: Dict) -> None:
         genes = report_upload_content["genes"]
         # eg, ZNRF3
@@ -174,11 +161,7 @@ def test_found_kb_statement_related_gene(self, report_upload_content: Dict) -> N
         genes = report_upload_content["genes"]
         assert any([g.get("kbStatementRelated", False) for g in genes])
 
-    @pytest.mark.skipif(
-        EXCLUDE_ONCOKB_TESTS, reason="excluding tests that depend on oncokb data"
-    )
-    def test_found_cancer_gene_list_match_gene(
-        self, report_upload_content: Dict
-    ) -> None:
+    @pytest.mark.skipif(EXCLUDE_ONCOKB_TESTS, reason="excluding tests that depend on oncokb data")
+    def test_found_cancer_gene_list_match_gene(self, report_upload_content: Dict) -> None:
         genes = report_upload_content["genes"]
         assert any([g.get("cancerGeneListMatch", False) for g in genes])

tests/test_ipr/test_probe.py

@@ -50,12 +50,8 @@ def side_effect_function(*args, **kwargs):
                     password=os.environ["IPR_PASS"],
                     log_level="info",
                     ipr_url="http://fake.url.ca",
-                    graphkb_username=os.environ.get(
-                        "GRAPHKB_USER", os.environ["IPR_USER"]
-                    ),
-                    graphkb_password=os.environ.get(
-                        "GRAPHKB_PASS", os.environ["IPR_PASS"]
-                    ),
+                    graphkb_username=os.environ.get("GRAPHKB_USER", os.environ["IPR_USER"]),
+                    graphkb_password=os.environ.get("GRAPHKB_PASS", os.environ["IPR_PASS"]),
                     graphkb_url=os.environ.get("GRAPHKB_URL", False),
                 )
 
@@ -65,19 +61,15 @@ def side_effect_function(*args, **kwargs):
     return report_content
 
 
-@pytest.mark.skipif(
-    EXCLUDE_INTEGRATION_TESTS, reason="excluding long running integration tests"
-)
+@pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason="excluding long running integration tests")
 class TestCreateReport:
     def test_found_probe_small_mutations(self, probe_upload_content: Dict) -> None:
         assert probe_upload_content["smallMutations"]
 
     @pytest.mark.skipif(
         EXCLUDE_BCGSC_TESTS, reason="excluding tests that depend on BCGSC-specific data"
     )
-    def test_found_probe_small_mutations_match(
-        self, probe_upload_content: Dict
-    ) -> None:
+    def test_found_probe_small_mutations_match(self, probe_upload_content: Dict) -> None:
         # verify each probe had a KB match
         for sm_probe in probe_upload_content["smallMutations"]:
             match_list = [