diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 523f17b..a0fd235 100644 --- a/.github/workflows/docs.yaml +++ b/.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/git-auto-commit-action@v4.1.2 with: diff --git a/cfg_help.py b/cfg_help.py index 149c0dc..6bc11aa 100644 --- a/cfg_help.py +++ b/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 diff --git a/docs/local_installation.md b/docs/local_installation.md index cebfdea..fdde8c3 100644 --- a/docs/local_installation.md +++ b/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 or (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 or (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! diff --git a/gen3workflow/app.py b/gen3workflow/app.py index d6fbfda..5b0d49d 100644 --- a/gen3workflow/app.py +++ b/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( diff --git a/gen3workflow/auth.py b/gen3workflow/auth.py index c1ea359..09b3965 100644 --- a/gen3workflow/auth.py +++ b/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 @@ -29,6 +30,9 @@ 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") @@ -36,6 +40,9 @@ def get_access_token(self): ) 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 diff --git a/gen3workflow/config-default.yaml b/gen3workflow/config-default.yaml index a23d1c2..d3cf9fa 100644 --- a/gen3workflow/config-default.yaml +++ b/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 # #################### diff --git a/gen3workflow/routes/ga4gh_tes.py b/gen3workflow/routes/ga4gh_tes.py index ba20aa2..1f28248 100644 --- a/gen3workflow/routes/ga4gh_tes.py +++ b/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() @@ -60,11 +61,10 @@ 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: @@ -121,11 +121,10 @@ 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() @@ -172,11 +171,10 @@ 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 @@ -195,11 +193,10 @@ 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") @@ -211,11 +208,10 @@ 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() diff --git a/poetry.lock b/poetry.lock index 5fb6db6..bca3fc6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,24 +1,5 @@ # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. -[[package]] -name = "alembic" -version = "1.13.3" -description = "A database migration tool for SQLAlchemy." -optional = false -python-versions = ">=3.8" -files = [ - {file = "alembic-1.13.3-py3-none-any.whl", hash = "sha256:908e905976d15235fae59c9ac42c4c5b75cfcefe3d27c0fbf7ae15a37715d80e"}, - {file = "alembic-1.13.3.tar.gz", hash = "sha256:203503117415561e203aa14541740643a611f641517f0209fcae63e9fa09f1a2"}, -] - -[package.dependencies] 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