feat(ci): add mypy type checking

.github/workflows/checks.yaml

@@ -25,6 +25,8 @@ jobs:
         run: flake8 pro_tes/ setup.py
       - name: Lint with Pylint
         run: pylint pro_tes/ setup.py
+      - name: Type check with mypy
+        run: mypy pro_tes/
   test:
     name: Run tests
     runs-on: ubuntu-latest

pro_tes/ga4gh/tes/models.py

@@ -300,7 +300,7 @@ class ServiceType(CustomBaseModel):
         ),
         example="org.ga4gh",
     )
-    artifact: str = Field(
+    artifact: Enum = Field(
         ...,
         description=(
             "Name of the API or GA4GH specification implemented.            "
@@ -349,7 +349,7 @@ class Service(CustomBaseModel):
         description="Name of this service. Should be human readable.",
         example="My project",
     )
-    type: ServiceType
+    type: Optional[ServiceType]
     description: Optional[str] = Field(
         None,
         description=(
@@ -601,6 +601,7 @@ class TesTask(CustomBaseModel):
         ),
         example={"WORKFLOW_ID": "cwl-01234", "PROJECT_GROUP": "alice-lab"},
     )
+
     logs: Optional[list[TesTaskLog]] = Field(
         None,
         description=(
@@ -708,8 +709,8 @@ class DbDocument(CustomBaseModel):
         tes_endpoint: External TES endpoint.
     """
 
-    task: TesTask = TesTask()
-    task_original: TesTask = TesTask(executors=[])
+    task: TesTask = TesTask()   # type: ignore
+    task_original: TesTask = TesTask(executors=[])  # type: ignore
     user_id: Optional[str] = None
     worker_id: str = ""
     basic_auth: BasicAuth = BasicAuth()

pro_tes/ga4gh/tes/service_info.py

@@ -24,7 +24,7 @@ class ServiceInfo:
     def __init__(self) -> None:
         """Construct class instance."""
         self.db_client: Collection = (
-            current_app.config.foca.db.dbs["taskStore"]
+            current_app.config.foca.db.dbs["taskStore"]  # type: ignore
             .collections["service_info"]
             .client
         )
@@ -65,7 +65,7 @@ def init_service_info_from_config(self) -> None:
 
         Set service info only if it does not yet exist.
         """
-        service_info_conf = current_app.config.foca.serviceInfo
+        service_info_conf = current_app.config.foca.serviceInfo  # type: ignore
         try:
             service_info_db = self.get_service_info()
         except NotFound:

pro_tes/ga4gh/tes/task_runs.py

@@ -57,7 +57,7 @@ class TaskRuns:
 
     def __init__(self) -> None:
         """Construct object instance."""
-        self.foca_config: Config = current_app.config.foca
+        self.foca_config: Config = current_app.config.foca  # type: ignore
         self.db_client: Collection = (
             self.foca_config.db.dbs["taskStore"].collections["tasks"].client
         )
@@ -84,7 +84,9 @@ def create_task(  # pylint: disable=too-many-statements,too-many-branches
 
         # apply middlewares
         mw_handler = MiddlewareHandler()
-        mw_handler.set_middlewares(paths=current_app.config.foca.middlewares)
+        mw_handler.set_middlewares(
+            paths=current_app.config.foca.middlewares   # type: ignore
+        )
         logger.debug(f"Middlewares registered: {mw_handler.middlewares}")
         request_modified = mw_handler.apply_middlewares(request=request)
 
@@ -276,7 +278,7 @@ def list_tasks(self, **kwargs) -> dict:
         view = kwargs.get("view", "BASIC")
         projection = self._set_projection(view=view)
 
-        name_prefix: str = kwargs.get("name_prefix")
+        name_prefix: str = str(kwargs.get("name_prefix"))
 
         if name_prefix is not None:
             filter_dict["task_original.name"] = {"$regex": f"^{name_prefix}"}
@@ -355,7 +357,7 @@ def cancel_task(self, id: str, **kwargs) -> dict:
         if document is None:
             logger.error(f"task '{id}' not found.")
             raise TaskNotFound
-        db_document = DbDocument(**document)
+        db_document: DbDocument = DbDocument(**document)
 
         if db_document.task.state in States.CANCELABLE:
             db_connector = DbDocumentConnector(
@@ -366,10 +368,17 @@ def cancel_task(self, id: str, **kwargs) -> dict:
                 f"{db_document.tes_endpoint.host.rstrip('/')}/"
                 f"{db_document.tes_endpoint.base_path.strip('/')}"
             )
-            if self.store_logs:
-                task_id = db_document.task.logs[0].metadata.forwarded_to.id
+
+            assert db_document.task.logs is not None
+            logs: list[TesTaskLog] = db_document.task.logs
+
+            if (self.store_logs and logs and logs[0].metadata and
+                    logs[0].metadata.forwarded_to):
+                task_id = logs[0].metadata.forwarded_to.id
+                task_id = logs[0].metadata.forwarded_to.id
             else:
-                task_id = db_document.task.logs[0].metadata["remote_task_id"]
+                task_id = logs[0].metadata["remote_task_id"]    # type: ignore
+
             logger.info(
                 "Trying to cancel task with task identifier"
                 f" '{task_id}' and worker job"
@@ -421,6 +430,7 @@ def _write_doc_to_db(
             except DuplicateKeyError:
                 continue
             assert document is not None
+            assert document.task.id is not None
             return document.task.id, document.worker_id
         raise DuplicateKeyError("Could not insert document into database.")
 
@@ -603,10 +613,13 @@ def _update_task_metadata(
         Returns:
             The updated database document.
         """
-        for logs in db_document.task.logs:
+        assert db_document.task.logs is not None
+        logs: list[TesTaskLog] = db_document.task.logs
+        for log in logs:
+            assert log.metadata is not None
             tesNextTes_obj = TesNextTes(id=remote_task_id, url=tes_url)
-            if logs.metadata.forwarded_to is None:
-                logs.metadata.forwarded_to = tesNextTes_obj
+            if log.metadata.forwarded_to is None:
+                log.metadata.forwarded_to = tesNextTes_obj
         return db_document
 
     @staticmethod

pro_tes/tasks/track_task_progress.py

@@ -50,7 +50,7 @@ def task__track_task_progress(  # pylint: disable=too-many-arguments
         user: User-name for basic authentication.
         password: Password for basic authentication.
     """
-    foca_config: Config = current_app.config.foca
+    foca_config: Config = current_app.config.foca   # type: ignore
     controller_config: dict = foca_config.controllers["post_task"]
 
     # create database client
@@ -110,6 +110,8 @@ def task__track_task_progress(  # pylint: disable=too-many-arguments
 
     # updating task after task is finished
     document.task.state = task_converted.state
+    assert task_converted.logs is not None
+    assert document.task.logs is not None
     for index, logs in enumerate(task_converted.logs):
         document.task.logs[index].logs = logs.logs
         document.task.logs[index].outputs = logs.outputs

requirements_dev.txt

@@ -7,3 +7,5 @@ mypy>=0.990
 pylint>=2.15.5
 pytest>=7.2.0
 python-semantic-release>=7.32.2
+mypy>=1.8.0
+types-python-dateutil>=2.8.19.20240106