CI fix

.safety-policy.yml

@@ -10,7 +10,9 @@ scanning-settings:
 
 security:
   ignore-vulnerabilities:
-<<<<<<< HEAD
+      62019:
+          reason: 'Foca needs to update werkzeug to >=2.3.8.'
+          expires: '2025-5-27'
       65213:
           reason: 'Fix is downgrading the pyopenssl package to 21.0.0, doing that breaks all the test.'
           expires: '2025-5-18'
@@ -20,23 +22,9 @@ security:
       70612:
           reason: 'No fix available.'
           expires: '2025-5-18'
-      62019:
-          reason: 'Foca needs to update werkzeug to >=2.3.8.'
-          expires: '2025-5-27'
       70624:
           reason: 'No fix available.'
           expires: '2025-5-27'
-=======
-    65213:
-      reason: 'Need the pyopenssl== 21.0.0, which breaks the test.'
-      expires: '2025-5-18'
-    67599:
-      reason: 'No fix available.'
-      expires: '2025-5-18'
-    70612:
-      reason: 'No fix available.'
-      expires: '2025-5-18'
->>>>>>> main
 
 report:
   dependency-vulnerabilities:

tesk/api/__init__.py

@@ -0,0 +1 @@
+"""TESK API package."""

tesk/api/ga4gh/__init__.py

@@ -0,0 +1 @@
+"""TESK API GA4GH package."""

tesk/api/ga4gh/tes/__init__.py

@@ -0,0 +1 @@
+"""TESK API GA4GH TES package."""

tesk/api/ga4gh/tes/controllers.py

@@ -12,28 +12,60 @@
 # POST /tasks/{id}:cancel
 @log_traffic
 def CancelTask(id, *args, **kwargs) -> dict:  # type: ignore
+	"""Cancel unfinished task.
+
+	Args:
+			id: Task identifier.
+			*args: Variable length argument list.
+			**kwargs: Arbitrary keyword arguments.
+	"""
 	pass
 
 
 # POST /tasks
 @log_traffic
 def CreateTask(*args, **kwargs) -> dict:  # type: ignore
+	"""Create task.
+
+	Args:
+			*args: Variable length argument list.
+			**kwargs: Arbitrary keyword arguments.
+	"""
 	pass
 
 
 # GET /tasks/service-info
 @log_traffic
 def GetServiceInfo(*args, **kwargs) -> dict:  # type: ignore
+	"""Get service info.
+
+	Args:
+			*args: Variable length argument list.
+			**kwargs: Arbitrary keyword arguments.
+	"""
 	pass
 
 
 # GET /tasks
 @log_traffic
 def ListTasks(*args, **kwargs) -> dict:  # type: ignore
+	"""List all available tasks.
+
+	Args:
+			*args: Variable length argument list.
+			**kwargs: Arbitrary keyword arguments.
+	"""
 	pass
 
 
 # GET /tasks
 @log_traffic
 def GetTask(*args, **kwargs) -> dict:  # type: ignore
+	"""Get info for individual task.
+
+	Args:
+			id: Task identifier.
+			*args: Variable length argument list.
+			**kwargs: Arbitrary keyword arguments.
+	"""
 	pass

tesk/app.py

@@ -12,7 +12,6 @@
 
 def init_app() -> FlaskApp:
 	"""Initialize the FOCA app."""
-
 	# Use environment variables, this will be useful for docker
 	config_path_env = os.getenv('TESK_FOCA_CONFIG_PATH')
 	config_filename_env = os.getenv('TESK_FOCA_CONFIG_FILENAME', 'config.yaml')