technical debt: run black for schematic api and test and modify pre-commit

.pre-commit-config.yaml

@@ -10,4 +10,4 @@ repos:
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
         language_version: python3.10
-        files: schematic/
+        files: ^(tests|schematic|schematic_api)/

schematic_api/api/__main__.py

@@ -2,7 +2,7 @@
 from schematic_api.api import app
 
 
-def main(): 
+def main():
     # Get app configuration
     host = os.environ.get("APP_HOST", "0.0.0.0")
     port = os.environ.get("APP_PORT", "3001")
@@ -11,5 +11,6 @@ def main():
     # Launch app
     app.run(host=host, port=port, debug=False)
 
+
 if __name__ == "__main__":
-    main()
+    main()

schematic_api/api/routes.py

@@ -39,7 +39,10 @@
     SynapseTimeoutError,
 )
 from schematic.utils.general import entity_type_mapping
-from schematic.utils.schema_utils import get_property_label_from_display_name, DisplayLabelType
+from schematic.utils.schema_utils import (
+    get_property_label_from_display_name,
+    DisplayLabelType,
+)
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.DEBUG)
@@ -210,6 +213,7 @@ def save_file(file_key="csv_file"):
 
     return temp_path
 
+
 def initalize_metadata_model(schema_url, data_model_labels):
     # get path to temp data model file (csv or jsonld) as appropriate
     data_model = get_temp_model_path(schema_url)
@@ -393,7 +397,7 @@ def submit_manifest_route(
     project_scope=None,
     table_column_names=None,
     annotation_keys=None,
-    file_annotations_upload:bool=True,
+    file_annotations_upload: bool = True,
 ):
     # call config_handler()
     config_handler(asset_view=asset_view)
@@ -450,7 +454,7 @@ def submit_manifest_route(
         project_scope=project_scope,
         table_column_names=table_column_names,
         annotation_keys=annotation_keys,
-        file_annotations_upload=file_annotations_upload
+        file_annotations_upload=file_annotations_upload,
     )
 
     return manifest_id
@@ -729,6 +733,7 @@ def get_asset_view_table(asset_view, return_type):
         file_view_table_df.to_csv(export_path, index=False)
         return export_path
 
+
 def get_project_manifests(project_id, asset_view):
     # Access token now stored in request header
     access_token = get_access_token()
@@ -1022,4 +1027,4 @@ def get_schematic_version() -> str:
         raise NotImplementedError(
             "Using this endpoint to check the version of schematic is only supported when the API is running in a docker container."
         )
-    return version
+    return version

schematic_api/api/security_controller_.py

@@ -11,4 +11,4 @@ def info_from_bearerAuth(token):
     :return: Decoded token information or None if token is invalid
     :rtype: dict | None
     """
-    return {"uid": "user_id"}
+    return {"uid": "user_id"}

tests/conftest.py

@@ -128,19 +128,22 @@ def synapse_store(request):
 
 
 # These fixtures make copies of existing test manifests.
-# These copies can the be altered by a given test, and the copy will eb destroyed at the 
+# These copies can the be altered by a given test, and the copy will eb destroyed at the
 # end of the test
 
+
 @pytest.fixture(scope="function")
 def temporary_file_copy(request, helpers: Helpers) -> Generator[str, None, None]:
     file_name = request.param
     # original file copy
     original_test_path = helpers.get_data_path(f"mock_manifests/{file_name}")
     # get filename without extension
-    file_name_no_extension=file_name.split(".")[0]
+    file_name_no_extension = file_name.split(".")[0]
     # Copy the original CSV file to a temporary directory
-    temp_csv_path = helpers.get_data_path(f"mock_manifests/{file_name_no_extension}_copy.csv")
-
+    temp_csv_path = helpers.get_data_path(
+        f"mock_manifests/{file_name_no_extension}_copy.csv"
+    )
+
     shutil.copyfile(original_test_path, temp_csv_path)
     yield temp_csv_path
     # Teardown

tests/test_api.py

@@ -78,7 +78,7 @@ def test_manifest_json(helpers):
 
 @pytest.fixture(scope="class")
 def data_model_jsonld():
-    data_model_jsonld ="https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld"
+    data_model_jsonld = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld"
     yield data_model_jsonld
 
 
@@ -143,15 +143,15 @@ class TestSynapseStorage:
     def test_invalid_authentication(self, client, request_invalid_headers):
         response = client.get(
             "http://localhost:3001/v1/storage/assets/tables",
-            query_string = {"asset_view": "syn23643253", "return_type": "csv"},
+            query_string={"asset_view": "syn23643253", "return_type": "csv"},
             headers=request_invalid_headers,
         )
         assert response.status_code == 401
 
     def test_insufficent_auth(self, client, request_headers):
         response = client.get(
             "http://localhost:3001/v1/storage/assets/tables",
-            query_string = {"asset_view": "syn23643252", "return_type": "csv"},
+            query_string={"asset_view": "syn23643252", "return_type": "csv"},
             headers=request_headers,
         )
         assert response.status_code == 403
@@ -370,8 +370,7 @@ def test_get_property_label_from_display_name(self, client, strict_camel_case):
 @pytest.mark.schematic_api
 class TestDataModelGraphExplorerOperation:
     def test_get_schema(self, client, data_model_jsonld):
-        params = {"schema_url": data_model_jsonld,
-                  "data_model_labels": 'class_label'}
+        params = {"schema_url": data_model_jsonld, "data_model_labels": "class_label"}
         response = client.get(
             "http://localhost:3001/v1/schemas/get/schema", query_string=params
         )
@@ -385,7 +384,11 @@ def test_get_schema(self, client, data_model_jsonld):
             os.remove(response_dt)
 
     def test_if_node_required(test, client, data_model_jsonld):
-        params = {"schema_url": data_model_jsonld, "node_display_name": "FamilyHistory", "data_model_labels": "class_label"}
+        params = {
+            "schema_url": data_model_jsonld,
+            "node_display_name": "FamilyHistory",
+            "data_model_labels": "class_label",
+        }
 
         response = client.get(
             "http://localhost:3001/v1/schemas/is_node_required", query_string=params
@@ -1121,7 +1124,11 @@ def test_submit_manifest_file_only_replace(
             elif python_version == "3.9":
                 dataset_id = "syn52656104"
 
-            specific_params = {"asset_view": "syn23643253", "dataset_id": dataset_id, "project_scope":["syn54126707"]}
+            specific_params = {
+                "asset_view": "syn23643253",
+                "dataset_id": dataset_id,
+                "project_scope": ["syn54126707"],
+            }
 
         params.update(specific_params)
 

tests/test_manifest.py

@@ -61,7 +61,9 @@ def manifest_generator(helpers, request):
 
     # Get graph data model
     graph_data_model = generate_graph_data_model(
-        helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+        helpers,
+        path_to_data_model=path_to_data_model,
+        data_model_labels="class_label",
     )
 
     manifest_generator = ManifestGenerator(
@@ -111,18 +113,22 @@ def manifest(dataset_id, manifest_generator, request):
 
     yield manifest, use_annotations, data_type, sheet_url
 
+
 @pytest.fixture(scope="class")
 def app():
     app = create_app()
     yield app
 
+
 class TestManifestGenerator:
     def test_init(self, helpers):
         path_to_data_model = helpers.get_data_path("example.model.jsonld")
 
         # Get graph data model
         graph_data_model = generate_graph_data_model(
-            helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+            helpers,
+            path_to_data_model=path_to_data_model,
+            data_model_labels="class_label",
         )
 
         generator = ManifestGenerator(
@@ -157,7 +163,9 @@ def test_missing_root_error(self, helpers, data_type, exc, exc_message):
 
         # Get graph data model
         graph_data_model = generate_graph_data_model(
-            helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+            helpers,
+            path_to_data_model=path_to_data_model,
+            data_model_labels="class_label",
         )
 
         # A LookupError should be raised and include message when the component cannot be found
@@ -242,7 +250,9 @@ def test_get_manifest_excel(self, helpers, sheet_url, output_format, dataset_id)
 
         # Get graph data model
         graph_data_model = generate_graph_data_model(
-            helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+            helpers,
+            path_to_data_model=path_to_data_model,
+            data_model_labels="class_label",
         )
 
         generator = ManifestGenerator(
@@ -300,7 +310,9 @@ def test_get_manifest_no_annos(self, helpers, dataset_id):
 
         # Get graph data model
         graph_data_model = generate_graph_data_model(
-            helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+            helpers,
+            path_to_data_model=path_to_data_model,
+            data_model_labels="class_label",
         )
 
         # Instantiate object with use_annotations set to True
@@ -416,7 +428,9 @@ def test_add_root_to_component_without_additional_metadata(
 
         # Get graph data model
         graph_data_model = generate_graph_data_model(
-            helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+            helpers,
+            path_to_data_model=path_to_data_model,
+            data_model_labels="class_label",
         )
 
         manifest_generator = ManifestGenerator(
@@ -453,7 +467,9 @@ def test_add_root_to_component_with_additional_metadata(
 
         # Get graph data model
         graph_data_model = generate_graph_data_model(
-            helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+            helpers,
+            path_to_data_model=path_to_data_model,
+            data_model_labels="class_label",
         )
 
         manifest_generator = ManifestGenerator(
@@ -537,7 +553,9 @@ def test_update_dataframe_with_existing_df(self, helpers, existing_manifest):
 
         # Get graph data model
         graph_data_model = generate_graph_data_model(
-            helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label',
+            helpers,
+            path_to_data_model=path_to_data_model,
+            data_model_labels="class_label",
         )
 
         # Instantiate the Manifest Generator.
@@ -661,34 +679,85 @@ def test_populate_existing_excel_spreadsheet(
 
         # remove file
         os.remove(dummy_output_path)
-
-    @pytest.mark.parametrize("return_output", ["Mock excel file path", "Mock google sheet link"])
-    def test_create_single_manifest(self, simple_manifest_generator, helpers, return_output):
-        with patch("schematic.manifest.generator.ManifestGenerator.get_manifest", return_value=return_output):
+
+    @pytest.mark.parametrize(
+        "return_output", ["Mock excel file path", "Mock google sheet link"]
+    )
+    def test_create_single_manifest(
+        self, simple_manifest_generator, helpers, return_output
+    ):
+        with patch(
+            "schematic.manifest.generator.ManifestGenerator.get_manifest",
+            return_value=return_output,
+        ):
             json_ld_path = helpers.get_data_path("example.model.jsonld")
             data_type = "Patient"
 
-            graph_data_model = generate_graph_data_model(helpers, path_to_data_model=json_ld_path, data_model_labels='class_label')
+            graph_data_model = generate_graph_data_model(
+                helpers,
+                path_to_data_model=json_ld_path,
+                data_model_labels="class_label",
+            )
 
-            result = simple_manifest_generator.create_single_manifest(path_to_data_model=json_ld_path, graph_data_model=graph_data_model, data_type=data_type, output_format="google_sheet", use_annotations=False)
+            result = simple_manifest_generator.create_single_manifest(
+                path_to_data_model=json_ld_path,
+                graph_data_model=graph_data_model,
+                data_type=data_type,
+                output_format="google_sheet",
+                use_annotations=False,
+            )
             assert result == return_output
-
-    @pytest.mark.parametrize("test_data_types", [["Patient", "Biospecimen"], ["all manifests"]])
-    def test_create_manifests_raise_errors(self, simple_manifest_generator, helpers, test_data_types):
-        with pytest.raises(ValueError) as exception_info: 
+
+    @pytest.mark.parametrize(
+        "test_data_types", [["Patient", "Biospecimen"], ["all manifests"]]
+    )
+    def test_create_manifests_raise_errors(
+        self, simple_manifest_generator, helpers, test_data_types
+    ):
+        with pytest.raises(ValueError) as exception_info:
             json_ld_path = helpers.get_data_path("example.model.jsonld")
             data_types = test_data_types
-            dataset_ids=["syn123456"]
-
-            simple_manifest_generator.create_manifests(path_to_data_model=json_ld_path, data_types=data_types, dataset_ids=dataset_ids, output_format="google_sheet", use_annotations=False, data_model_labels='class_label')
-
-    @pytest.mark.parametrize("test_data_types, dataset_ids, expected_result", [
-        (["Patient", "Biospecimen"], ["mock dataset id1", "mock dataset id2"], ["mock google sheet link", "mock google sheet link"]),
-        (["Patient"], ["mock dataset id1"], ["mock google sheet link"]),
-        ])
-    def test_create_manifests(self, simple_manifest_generator, helpers, test_data_types, dataset_ids, expected_result):
-        with patch("schematic.manifest.generator.ManifestGenerator.create_single_manifest", return_value="mock google sheet link"):
+            dataset_ids = ["syn123456"]
+
+            simple_manifest_generator.create_manifests(
+                path_to_data_model=json_ld_path,
+                data_types=data_types,
+                dataset_ids=dataset_ids,
+                output_format="google_sheet",
+                use_annotations=False,
+                data_model_labels="class_label",
+            )
+
+    @pytest.mark.parametrize(
+        "test_data_types, dataset_ids, expected_result",
+        [
+            (
+                ["Patient", "Biospecimen"],
+                ["mock dataset id1", "mock dataset id2"],
+                ["mock google sheet link", "mock google sheet link"],
+            ),
+            (["Patient"], ["mock dataset id1"], ["mock google sheet link"]),
+        ],
+    )
+    def test_create_manifests(
+        self,
+        simple_manifest_generator,
+        helpers,
+        test_data_types,
+        dataset_ids,
+        expected_result,
+    ):
+        with patch(
+            "schematic.manifest.generator.ManifestGenerator.create_single_manifest",
+            return_value="mock google sheet link",
+        ):
             json_ld_path = helpers.get_data_path("example.model.jsonld")
-            all_results = simple_manifest_generator.create_manifests(path_to_data_model=json_ld_path, data_types=test_data_types, dataset_ids=dataset_ids, output_format="google_sheet", use_annotations=False, data_model_labels='class_label')
+            all_results = simple_manifest_generator.create_manifests(
+                path_to_data_model=json_ld_path,
+                data_types=test_data_types,
+                dataset_ids=dataset_ids,
+                output_format="google_sheet",
+                use_annotations=False,
+                data_model_labels="class_label",
+            )
             assert all_results == expected_result
-

tests/test_metadata.py

@@ -109,10 +109,12 @@ def test_populate_manifest(self, helpers, return_excel, data_model_labels):
         ids=["data_model_labels-display_label", "data_model_labels-class_label"],
     )
     @pytest.mark.parametrize("validate_component", [None, "BulkRNA-seqAssay"])
-    @pytest.mark.parametrize("temporary_file_copy", ["test_BulkRNAseq.csv"], indirect=True)
+    @pytest.mark.parametrize(
+        "temporary_file_copy", ["test_BulkRNAseq.csv"], indirect=True
+    )
     def test_submit_metadata_manifest(
         self,
-        temporary_file_copy: Generator[str, None, None], 
+        temporary_file_copy: Generator[str, None, None],
         helpers: Helpers,
         file_annotations_upload: bool,
         restrict_rules: bool,