lint

bcgsc · Jul 18, 2024 · aabd8bb · aabd8bb
1 parent a44ec03
commit aabd8bb
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Showing 2 changed files with 14 additions and 24 deletions.
diff --git a/pori_python/ipr/connection.py b/pori_python/ipr/connection.py
@@ -87,9 +87,7 @@ def upload_report(
             def check_status_result(result):
                 if result.get("report", False):
                     return "upload complete"
-                if result.get("jobStatus", False) and result["jobStatus"].get(
-                    "state", False
-                ):
+                if result.get("jobStatus", False) and result["jobStatus"].get("state", False):
                     return result["jobStatus"]["state"]
                 raise Exception(
                     f"async report get returned with no report or jobStatus, or unexpected jobStatus type"
@@ -157,9 +155,7 @@ def set_analyst_comments(self, report_id: str, data: Dict) -> Dict:
             data=zlib.compress(json.dumps(data, allow_nan=False).encode("utf-8")),
         )
 
-    def post_images(
-        self, report_id: str, files: Dict[str, str], data: Dict[str, str] = {}
-    ) -> None:
+    def post_images(self, report_id: str, files: Dict[str, str], data: Dict[str, str] = {}) -> None:
         """
         Post images to the report
         """
@@ -190,9 +186,7 @@ def post_images(
                     handler.close()
             start_index += IMAGE_MAX
         if image_errors:
-            raise ValueError(
-                f'Error uploading images ({", ".join(sorted(list(image_errors)))})'
-            )
+            raise ValueError(f'Error uploading images ({", ".join(sorted(list(image_errors)))})')
 
     def get_spec(self) -> Dict:
         """

diff --git a/tests/test_ipr/test_upload.py b/tests/test_ipr/test_upload.py
@@ -50,25 +50,23 @@ def loaded_report(tmp_path_factory) -> Dict:
                 "patientId": patient_id,
                 "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,
@@ -117,9 +115,7 @@ def get_section(loaded_report, section_name):
 @pytest.mark.skipif(
     not INCLUDE_UPLOAD_TESTS, reason="excluding tests of upload to live ipr instance"
 )
-@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_patient_id_loaded_once(self, loaded_report: Tuple) -> None:
         patient_id = loaded_report[0]