Update instructions for local development (#10)

.github/workflows/docs.yaml

@@ -35,7 +35,7 @@ jobs:
         poetry install -vv --no-interaction
         poetry show -vv
     - name: Build docs
-      run: AUDIT_SERVICE_CONFIG_PATH=src/audit/config-default.yaml poetry run python run.py openapi
+      run: poetry run python run.py openapi
 
     - uses: stefanzweifel/[email protected]
       with:

cfg_help.py

@@ -99,9 +99,7 @@ def create_config_file(file_name, full_path=None):
     if dir_name and not os.path.exists(dir_name):
         os.makedirs(os.path.dirname(config_path))
 
-    copyfile(
-        os.path.join(ROOT_DIR, "src/gen3workflow/config-default.yaml"), config_path
-    )
+    copyfile(os.path.join(ROOT_DIR, "gen3workflow/config-default.yaml"), config_path)
 
     return config_path
 

docs/local_installation.md

@@ -42,25 +42,44 @@ To use a configuration file in a custom location, you can set the `GEN3WORKFLOW_
 
 ## Run Gen3Workflow
 
-Update your configuration file to set `LOCAL_MIGRATION` to `true`, so that no attempts to interact with Arborist are made.
+You will need to run a TES server for Gen3Workflow to talk to. For example, you can start a local Funnel server: https://ohsu-comp-bio.github.io/funnel/#intro.
 
-Run database schema migration:
+Update your configuration file:
+- set `TES_SERVER_URL` to the TES server URL
+- set `MOCK_AUTH` to `true`, so that no attempts to interact with Arborist are made.
+
+Start the Gen3Workflow app:
 
 ```bash
-alembic upgrade head
+python run.py
 ```
 
-Run the server with auto-reloading:
+Try out the API at <http://localhost:8080/_status> or <http://localhost:8080/docs> (you might have to set `DOCS_URL_PREFIX` to `""` in your configuration file for the docs endpoint to work).
 
-```bash
-python run.py
-OR
-uvicorn gen3workflow.app:app --reload
+## Run Nextflow workflows with Gen3Workflow
+
+Example Nextflow configuration:
+```
+plugins {
+	id 'nf-ga4gh'
+}
+process {
+	executor = 'tes'
+	container = 'quay.io/nextflow/bash'
+}
+tes {
+	endpoint = 'http://localhost:8080/ga4gh-tes'
+}
+```
+> `http://localhost:8080/ga4gh-tes` is where Gen3Workflow runs by default when started with `python run.py`.
+
+Run a workflow:
+```
+nextflow run hello
 ```
 
-Try out the API at <http://localhost:8000/_status> or <http://localhost:8000/docs> (you might have to set `DOCS_URL_PREFIX` to `""` in your configuration file for the docs endpoint to work).
 
-### Quickstart with Helm
+## Quickstart with Helm
 
 You can now deploy individual services via Helm!
 

gen3workflow/app.py

@@ -33,6 +33,10 @@ def get_app(httpx_client=None) -> FastAPI:
     get_logger("gen3workflow", log_level=log_level)
 
     logger.info("Initializing Arborist client")
+    if config["MOCK_AUTH"]:
+        logger.warning(
+            "Mock authentication and authorization are enabled! 'MOCK_AUTH' should NOT be enabled in production!"
+        )
     custom_arborist_url = os.environ.get("ARBORIST_URL", config["ARBORIST_URL"])
     if custom_arborist_url:
         app.arborist_client = ArboristClient(

gen3workflow/auth.py

@@ -11,6 +11,7 @@
 from gen3authz.client.arborist.errors import ArboristError
 
 from gen3workflow import logger
+from gen3workflow.config import config
 
 
 # auto_error=False prevents FastAPI from raising a 403 when the request
@@ -29,13 +30,19 @@ def __init__(
         self.bearer_token = bearer_token
 
     def get_access_token(self):
+        if config["MOCK_AUTH"]:
+            return "123"
+
         return (
             self.bearer_token.credentials
             if self.bearer_token and hasattr(self.bearer_token, "credentials")
             else None
         )
 
     async def get_token_claims(self) -> dict:
+        if config["MOCK_AUTH"]:
+            return {"sub": 64, "context": {"user": {"name": "mocked-user"}}}
+
         if not self.bearer_token:
             err_msg = "Must provide an access token"
             logger.error(err_msg)
@@ -64,8 +71,10 @@ async def authorize(
         resources: list,
         throw: bool = True,
     ) -> bool:
-        token = self.get_access_token()
+        if config["MOCK_AUTH"]:
+            return True
 
+        token = self.get_access_token()
         try:
             authorized = await self.arborist_client.auth_request(
                 token, "gen3-workflow", method, resources

gen3workflow/config-default.yaml

@@ -8,6 +8,9 @@ DOCS_URL_PREFIX: /gen3workflow
 # override the default Arborist URL; ignored if already set as an environment variable
 ARBORIST_URL:
 
+# /!\ only use for development! Allows running gen3workflow locally without Arborist interaction
+MOCK_AUTH: false
+
 ####################
 # GA4GH TES        #
 ####################

gen3workflow/routes/ga4gh_tes.py

@@ -31,9 +31,10 @@ async def get_request_body(request: Request):
 
 @router.get("/service-info", status_code=HTTP_200_OK)
 async def service_info(request: Request):
-    res = await request.app.async_client.get(f"{config['TES_SERVER_URL']}/service-info")
+    url = f"{config['TES_SERVER_URL']}/service-info"
+    res = await request.app.async_client.get(url)
     if res.status_code != HTTP_200_OK:
-        logger.error(f"TES server error: {res.status_code} {res.text}")
+        logger.error(f"TES server error at '{url}': {res.status_code} {res.text}")
         raise HTTPException(res.status_code, res.text)
     return res.json()
 
@@ -68,11 +69,10 @@ async def create_task(request: Request, auth=Depends(Auth)):
         body["tags"] = {}
     body["tags"]["AUTHZ"] = f"/users/{user_id}/gen3-workflow/tasks/TASK_ID_PLACEHOLDER"
 
-    res = await request.app.async_client.post(
-        f"{config['TES_SERVER_URL']}/tasks", json=body
-    )
+    url = f"{config['TES_SERVER_URL']}/tasks"
+    res = await request.app.async_client.post(url, json=body)
     if res.status_code != HTTP_200_OK:
-        logger.error(f"TES server error: {res.status_code} {res.text}")
+        logger.error(f"TES server error at '{url}': {res.status_code} {res.text}")
         raise HTTPException(res.status_code, res.text)
 
     try:
@@ -128,11 +128,10 @@ async def list_tasks(request: Request, auth=Depends(Auth)):
     query_params["view"] = "FULL"
 
     # get all the tasks, regardless of access
-    res = await request.app.async_client.get(
-        f"{config['TES_SERVER_URL']}/tasks", params=query_params
-    )
+    url = f"{config['TES_SERVER_URL']}/tasks"
+    res = await request.app.async_client.get(url, params=query_params)
     if res.status_code != HTTP_200_OK:
-        logger.error(f"TES server error: {res.status_code} {res.text}")
+        logger.error(f"TES server error at '{url}': {res.status_code} {res.text}")
         raise HTTPException(res.status_code, res.text)
     listed_tasks = res.json()
 
@@ -179,11 +178,10 @@ async def get_task(request: Request, task_id: str, auth=Depends(Auth)):
     requested_view = query_params.get("view")
     query_params["view"] = "FULL"
 
-    res = await request.app.async_client.get(
-        f"{config['TES_SERVER_URL']}/tasks/{task_id}", params=query_params
-    )
+    url = f"{config['TES_SERVER_URL']}/tasks/{task_id}"
+    res = await request.app.async_client.get(url, params=query_params)
     if res.status_code != HTTP_200_OK:
-        logger.error(f"TES server error: {res.status_code} {res.text}")
+        logger.error(f"TES server error at '{url}': {res.status_code} {res.text}")
         raise HTTPException(res.status_code, res.text)
 
     # check if this user has access to see this task
@@ -202,11 +200,10 @@ async def get_task(request: Request, task_id: str, auth=Depends(Auth)):
 @router.post("/tasks/{task_id}:cancel", status_code=HTTP_200_OK)
 async def cancel_task(request: Request, task_id: str, auth=Depends(Auth)):
     # check if this user has access to delete this task
-    res = await request.app.async_client.get(
-        f"{config['TES_SERVER_URL']}/tasks/{task_id}?view=FULL"
-    )
+    url = f"{config['TES_SERVER_URL']}/tasks/{task_id}?view=FULL"
+    res = await request.app.async_client.get(url)
     if res.status_code != HTTP_200_OK:
-        logger.error(f"TES server error: {res.status_code} {res.text}")
+        logger.error(f"TES server error at '{url}': {res.status_code} {res.text}")
         raise HTTPException(res.status_code, res.text)
     body = res.json()
     authz_path = body.get("tags", {}).get("AUTHZ")
@@ -218,11 +215,10 @@ async def cancel_task(request: Request, task_id: str, auth=Depends(Auth)):
     await auth.authorize("delete", [authz_path])
 
     # the user has access: delete the task
-    res = await request.app.async_client.post(
-        f"{config['TES_SERVER_URL']}/tasks/{task_id}:cancel"
-    )
+    url = f"{config['TES_SERVER_URL']}/tasks/{task_id}:cancel"
+    res = await request.app.async_client.post(url)
     if res.status_code != HTTP_200_OK:
-        logger.error(f"TES server error: {res.status_code} {res.text}")
+        logger.error(f"TES server error at '{url}': {res.status_code} {res.text}")
         raise HTTPException(res.status_code, res.text)
 
     return res.json()