make it run locally

Makefile

@@ -51,4 +51,19 @@ dev-app da:
 .PHONY: dev-celery dc
 dev-celery dc:
 	@echo "Starting Celery worker..."
-	cd pro_wes && celery -A celery_worker worker -E --loglevel=info
+	cd pro_wes && celery -A celery_worker worker -E --loglevel=info
+
+.PHONY: lint fl
+lint fl:
+
+	@echo "1.Formatting with black..."
+	black --exclude .venv pro_wes/ setup.py tests/
+	@echo "\n\n2.Checking style with flake8..."
+	black --exclude .venv pro_wes/ setup.py tests/
+	@echo "\n\n3.Running pylint..."
+	pylint pro_wes/ setup.py
+
+.PHONY: type-check tc
+type-check tc:
+	@echo "Running mypy..."
+	mypy pro_wes/ setup.py

docker-compose.dev.yaml

@@ -11,7 +11,7 @@ services:
     image: mongo:3.2
     restart: unless-stopped
     volumes:
-      - ${PROWES_DATA_DIR:-../data/pro_wes}/db:${PWD}/data/db
+      - ${PROWES_DATA_DIR:-../data/pro_wes}/db:/data/db
     ports:
       - "27017:27017"
 

docker-compose.yaml

@@ -33,15 +33,15 @@ services:
     links:
       - mongodb
     ports:
-      - "5682:5672"
+      - "5672:5672"
 
   mongodb:
     image: mongo:3.2
     restart: unless-stopped
     volumes:
       - ${PROWES_DATA_DIR:-../data/pro_wes}/db:/data/db
     ports:
-      - "27027:27017"
+      - "27017:27017"
 
   flower:
     image: mher/flower:0.9.7
@@ -50,4 +50,4 @@ services:
       - prowes-worker
     command: flower --broker=amqp://guest:guest@rabbitmq:5672// --port=5555
     ports:
-      - "5565:5555"
+      - "5555:5555"

pro_wes/app.py

@@ -1,6 +1,5 @@
 """proWES application entry point."""
 
-import os
 from pathlib import Path
 
 from connexion import App
@@ -17,13 +16,8 @@ def init_app() -> App:
     Returns:
         FOCA application.
     """
-    _parent_dir = Path(__file__).resolve().parent
-    if os.environ.get("ENVIRONMENT") == "DEV":
-        config_file = _parent_dir / "config.dev.yaml"
-    else:
-        config_file = _parent_dir / "config.yaml"
     foca = Foca(
-        config_file=config_file,
+        config_file=Path(__file__).resolve().parent / "config.yaml",
         custom_config_model="pro_wes.config_models.CustomConfig",
     )
     app = foca.create_app()
@@ -53,6 +47,5 @@ def run_app(app: App) -> None:
 
 
 if __name__ == "__main__":
-    os.environ.setdefault("ENVIRONMENT", "DEV")
     foca_app = init_app()
     run_app(app=foca_app)

pro_wes/config.yaml

@@ -30,7 +30,7 @@ security:
 # Database configuration
 # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.DBConfig
 db:
-  host: mongodb
+  host: localhost
   port: 27017
   dbs:
     runStore:
@@ -92,7 +92,7 @@ log:
 # Background job configuration
 # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.JobsConfig
 jobs:
-  host: rabbitmq
+  host: localhost
   port: 5672
   backend: "rpc://"
   include:
@@ -116,7 +116,7 @@ custom:
     id_length: 6
     polling_attempts: 100
     polling_wait: 3
-    storage_path: "/data"
+    storage_path: "./data"
     timeout_job: null
     timeout_post: null
   list_runs:

pro_wes/ga4gh/wes/workflow_runs.py

@@ -482,7 +482,9 @@ def _validate_run_request(
         """
         dict_of_lists = form_data.to_dict(flat=False)
         # flatten single item lists
-        dict_atomic = {k: v[0] if len(v) == 1 else v for k, v in dict_of_lists.items()}
+        dict_atomic: dict = {
+            k: v[0] if len(v) == 1 else v for k, v in dict_of_lists.items()
+        }
         # remove 'workflow_attachment' field
         dict_atomic.pop("workflow_attachment", None)
         model_instance = RunRequest(**dict_atomic)

requirements.txt

@@ -1,5 +1,4 @@
 connexion<3
 email-validator>=2.1.0,<3
-foca>=0.12.1
+foca==0.12.1
 gunicorn>=20.1.0,<21
-pymongo==4.7  # Cf. https://github.com/elixir-cloud-aai/foca/issues/246