ci: check code format with Black (#74)

elixir-cloud-aai · Nov 5, 2023 · f739d49 · f739d49
1 parent 8e9ab93
commit f739d49
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Showing 17 changed files with 219 additions and 227 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -9,7 +9,7 @@ on:
 
 jobs:
   lint:
-    name: Run linting
+    name: Run static code analysis
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -24,6 +24,8 @@ jobs:
           pip install .
       - name: Lint with Flake8
         run: flake8
+      - name: Check code format with Black
+        run: black --check setup.py pro_wes/ tests/
   test:
     name: Run tests
     runs-on: ubuntu-latest

diff --git a/pro_wes/client_wes.py b/pro_wes/client_wes.py
@@ -69,18 +69,14 @@ def get_service_info(
         try:
             response_unvalidated = self.session.get(url, **kwargs).json()
         except (RequestException, ValueError) as exc:
-            raise EngineUnavailable(
-                "external workflow engine unavailable"
-            ) from exc
+            raise EngineUnavailable("external workflow engine unavailable") from exc
         try:
             response = ServiceInfo(**response_unvalidated)
         except Exception:
             try:
                 response = ErrorResponse(**response_unvalidated)
             except Exception as exc:
-                raise ValueError(
-                    f"invalid response: {response_unvalidated}"
-                ) from exc
+                raise ValueError(f"invalid response: {response_unvalidated}") from exc
         return response
 
     def post_run(
@@ -133,18 +129,14 @@ def post_run(
                 **kwargs,
             ).json()
         except (RequestException, ValueError) as exc:
-            raise EngineUnavailable(
-                "external workflow engine unavailable"
-            ) from exc
+            raise EngineUnavailable("external workflow engine unavailable") from exc
         try:
             response = RunId(**response_unvalidated)
         except Exception:
             try:
                 response = ErrorResponse(**response_unvalidated)
             except Exception as exc:
-                raise ValueError(
-                    f"invalid response: {response_unvalidated}"
-                ) from exc
+                raise ValueError(f"invalid response: {response_unvalidated}") from exc
         return response
 
     def get_runs(
@@ -171,18 +163,14 @@ def get_runs(
         try:
             response_unvalidated = self.session.get(url, **kwargs).json()
         except (RequestException, ValueError) as exc:
-            raise EngineUnavailable(
-                "external workflow engine unavailable"
-            ) from exc
+            raise EngineUnavailable("external workflow engine unavailable") from exc
         try:
             response = RunListResponse(**response_unvalidated)
         except Exception:
             try:
                 response = ErrorResponse(**response_unvalidated)
             except Exception as exc:
-                raise ValueError(
-                    f"invalid response: {response_unvalidated}"
-                ) from exc
+                raise ValueError(f"invalid response: {response_unvalidated}") from exc
         return response
 
     def get_run(
@@ -211,9 +199,7 @@ def get_run(
         try:
             response_unvalidated = self.session.get(url, **kwargs).json()
         except (RequestException, ValueError) as exc:
-            raise EngineUnavailable(
-                "external workflow engine unavailable"
-            ) from exc
+            raise EngineUnavailable("external workflow engine unavailable") from exc
         # skip validation; workaround for cwl-WES
         return response_unvalidated
         try:
@@ -222,9 +208,7 @@ def get_run(
             try:
                 response = ErrorResponse(**response_unvalidated)
             except Exception as exc:
-                raise ValueError(
-                    f"invalid response: {response_unvalidated}"
-                ) from exc
+                raise ValueError(f"invalid response: {response_unvalidated}") from exc
         return response
 
     def get_run_status(
@@ -252,18 +236,14 @@ def get_run_status(
         try:
             response_unvalidated = self.session.get(url, **kwargs).json()
         except (RequestException, ValueError) as exc:
-            raise EngineUnavailable(
-                "external workflow engine unavailable"
-            ) from exc
+            raise EngineUnavailable("external workflow engine unavailable") from exc
         try:
             response = RunStatus(**response_unvalidated)
         except Exception:
             try:
                 response = ErrorResponse(**response_unvalidated)
             except Exception as exc:
-                raise ValueError(
-                    f"invalid response: {response_unvalidated}"
-                ) from exc
+                raise ValueError(f"invalid response: {response_unvalidated}") from exc
         return response
 
     def cancel_run(
@@ -291,18 +271,14 @@ def cancel_run(
         try:
             response_unvalidated = self.session.post(url, **kwargs).json()
         except (RequestException, ValueError) as exc:
-            raise EngineUnavailable(
-                "external workflow engine unavailable"
-            ) from exc
+            raise EngineUnavailable("external workflow engine unavailable") from exc
         try:
             response = RunId(**response_unvalidated)
         except Exception:
             try:
                 response = ErrorResponse(**response_unvalidated)
             except Exception as exc:
-                raise ValueError(
-                    f"invalid response: {response_unvalidated}"
-                ) from exc
+                raise ValueError(f"invalid response: {response_unvalidated}") from exc
         return response
 
     def set_token(

diff --git a/pro_wes/config_models.py b/pro_wes/config_models.py
@@ -23,6 +23,7 @@ class Defaults(BaseModel):
         timeout: Timeout for outgoing requests. May be overridden by more
         specific parameters for each endpoint.
     """
+
     timeout: Optional[int] = 3
 
 
@@ -46,9 +47,10 @@ class PostRuns(BaseModel):
         raised and the job is set to state `SYSTEM_ERROR`. Once a valid
         response is obtained, the counter is reset to 1.
     """
-    storage_path: Path = Path('/data')
+
+    storage_path: Path = Path("/data")
     db_insert_attempts: int = 10
-    id_charset: str = 'string.ascii_uppercase + string.digits'
+    id_charset: str = "string.ascii_uppercase + string.digits"
     id_length: int = 6
     timeout_post: Optional[int] = None
     timeout_job: Optional[int] = None
@@ -65,6 +67,7 @@ class ListRuns(BaseModel):
     Attributes:
         default_page_size: Default page size for response pagination.
     """
+
     default_page_size: int = 5
 
 
@@ -75,6 +78,7 @@ class WorkflowTypeVersion(BaseModel):
         workflow_type_version: List of one or more acceptable versions for the
             workflow type.
     """
+
     workflow_type_version: Optional[List[str]] = []
 
 
@@ -91,6 +95,7 @@ class DefaultWorkflowEngineParameter(BaseModel):
         type: Parameter type.
         default_value: Stringified version of default parameter.
     """
+
     name: Optional[str]
     type: Optional[str]
     default_value: Optional[str]
@@ -129,25 +134,20 @@ class ServiceInfo(BaseModel):
             on how to get an authorization token for use with this service.
         tags: Additional information about this service as key-value pairs.
     """
+
     workflow_type_versions: Dict[str, WorkflowTypeVersion] = {
-        'CWL': WorkflowTypeVersion(workflow_type_version=['v1.0']),
+        "CWL": WorkflowTypeVersion(workflow_type_version=["v1.0"]),
     }
     supported_wes_versions: List[str] = [
-        '1.0.0',
+        "1.0.0",
     ]
     supported_filesystem_protocols: List[str] = [
-        'http',
+        "http",
     ]
     workflow_engine_versions: Dict[str, str] = {}
-    default_workflow_engine_parameters: List[
-        DefaultWorkflowEngineParameter
-    ] = []
-    auth_instructions_url: AnyUrl = (
-        'https://lifescience-ri.eu/ls-login/'
-    )
-    tags: Dict[str, str] = {
-        'service_repo': 'https://github.com/elixir-europe/proWES'
-    }
+    default_workflow_engine_parameters: List[DefaultWorkflowEngineParameter] = []
+    auth_instructions_url: AnyUrl = "https://lifescience-ri.eu/ls-login/"
+    tags: Dict[str, str] = {"service_repo": "https://github.com/elixir-europe/proWES"}
 
 
 class CustomConfig(BaseModel):
@@ -167,6 +167,7 @@ class CustomConfig(BaseModel):
         service_info: Configuration parameters for initiliazing the service
             info.
     """
+
     defaults: Defaults = Defaults()
     post_runs: PostRuns = PostRuns()
     list_runs: ListRuns = ListRuns()

diff --git a/pro_wes/exceptions.py b/pro_wes/exceptions.py
@@ -15,93 +15,99 @@
 
 class EngineProblem(InternalServerError):
     """The external workflow engine appears to experience problems."""
+
     pass
 
 
 class EngineUnavailable(EngineProblem):
     """The external workflow engine is not available."""
+
     pass
 
 
 class NoSuitableEngine(BadRequest):
     """Raised when the service does not know of a suitable engine to process
     the requested workflow run.
     """
+
     pass
 
 
 class RunNotFound(NotFound):
     """Raised when workflow run with given run identifier was not found."""
+
     pass
 
 
 class IdsUnavailableProblem(PyMongoError):
     """Raised when no unique run identifier could be found for insertion into
     the database collection.
     """
+
     pass
 
 
 class StorageUnavailableProblem(OSError):
     """Raised when storage is not available for OS operations."""
+
     pass
 
 
 exceptions = {
     Exception: {
         "message": "An unexpected error occurred.",
-        "code": '500',
+        "code": "500",
     },
     BadRequest: {
         "message": "The request is malformed.",
-        "code": '400',
+        "code": "400",
     },
     BadRequestProblem: {
         "message": "The request is malformed.",
-        "code": '400',
+        "code": "400",
     },
     ExtraParameterProblem: {
         "message": "The request is malformed.",
-        "code": '400',
+        "code": "400",
     },
     NoSuitableEngine: {
         "message": "No suitable workflow engine known.",
-        "code": '400',
+        "code": "400",
     },
     ValidationError: {
         "message": "The request is malformed.",
-        "code": '400',
+        "code": "400",
     },
     Unauthorized: {
         "message": " The request is unauthorized.",
-        "code": '401',
+        "code": "401",
     },
     Forbidden: {
         "message": "The requester is not authorized to perform this action.",
-        "code": '403',
+        "code": "403",
     },
     NotFound: {
         "message": "The requested resource wasn't found.",
-        "code": '404',
+        "code": "404",
     },
     RunNotFound: {
         "message": "The requested run wasn't found.",
-        "code": '404',
+        "code": "404",
     },
     EngineUnavailable: {
         "message": "Could not reach remote WES service.",
-        "code": '500',
+        "code": "500",
     },
     InternalServerError: {
         "message": "An unexpected error occurred.",
-        "code": '500',
+        "code": "500",
     },
     IdsUnavailableProblem: {
         "message": "No/few unique run identifiers available.",
-        "code": '500',
+        "code": "500",
     },
     StorageUnavailableProblem: {
         "message": "Storage is not accessible.",
-        "code": '500',
+        "code": "500",
     },
 }
diff --git a/pro_wes/ga4gh/wes/controllers.py b/pro_wes/ga4gh/wes/controllers.py
@@ -41,7 +41,7 @@ def postServiceInfo(**kwargs) -> Tuple[None, str, Dict]:
     """
     service_info = ServiceInfo()
     headers = service_info.set_service_info(data=request.json)
-    return (None, '201', headers)
+    return (None, "201", headers)
 
 
 # controller for `POST /runs`