diff --git a/Dockerfile b/Dockerfile index 8d029a0..5365bb7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 AS base-deps +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.11.10 AS base-deps SHELL ["/bin/bash", "-c"] diff --git a/README.md b/README.md index c776cb5..41840ca 100644 --- a/README.md +++ b/README.md @@ -87,11 +87,8 @@ Parameter: "tags": { "workflow_id": "...", // must correspond to the worflow_params namespace "workflow_metadata": { - "inputs": [{}], // must correspond to the .wdl input section - "outputs": [{}] // must correspond to the .wdl output section - }, - "project_id": "...", - "dataset_id": "..." + "inputs": [{}] // Defines setup for injecting values into the .wdl input section. IDs must align. + } } } ``` @@ -260,40 +257,10 @@ validity is disabled in Bento (see the corresponding Dockerfile). This script contains the routes definitions as [Flask's Blueprints](https://flask.palletsprojects.com/en/2.0.x/blueprints/) ### runner.py -This script contains the implementation of the workflows execution. -Of interest is the code handling the callbacks and -some service specific routines (i.e. code paths specific to Gohan or Katsu ingestions). - -The expected output files are -retrieved using the workflow metadata (Bento-specific) with a possibility -to map output files names to input files names. In the following example, -the property `map_from_input` refers to an `id` in the `inputs` section. This -maps the `value` property to use the input file name for string interpolation. -```json5 -{ - "workflow_name": { - // ... - }, - "inputs": [ - { - "id": "vcf_files", - "type": "file[]", - "required": true, - "extensions": [".vcf"] - }, - // ... - ], - "outputs": [ - { - "id": "vcf_gz_files", - "type": "file[]", - "map_from_input": "vcf_files", - "value": "{}.gz" - }, - // ... - ] -} -``` +This script contains the implementation of workflow execution. + +The expected inputs come from the workflow metadata (Bento-specific), which +also define how `bento_web` will render the workflow set-up UI. Another extension to the workflow metadata inputs is used to get values from the WES configuration variables. The special value `FROM_CONFIG` causes the interpolation diff --git a/bento_wes/app.py b/bento_wes/app.py index 3c8e270..a951e1f 100644 --- a/bento_wes/app.py +++ b/bento_wes/app.py @@ -103,14 +103,11 @@ def service_info(): try: if res_tag := subprocess.check_output(["git", "describe", "--tags", "--abbrev=0"]): - res_tag_str = res_tag.decode().rstrip() - info["bento"]["gitTag"] = res_tag_str + info["bento"]["gitTag"] = res_tag.decode().rstrip() if res_branch := subprocess.check_output(["git", "branch", "--show-current"]): - res_branch_str = res_branch.decode().rstrip() - info["bento"]["gitBranch"] = res_branch_str + info["bento"]["gitBranch"] = res_branch.decode().rstrip() if res_commit := subprocess.check_output(["git", "rev-parse", "HEAD"]): - res_commit_str = res_commit.decode().rstrip() - info["bento"]["gitCommit"] = res_commit_str + info["bento"]["gitCommit"] = res_commit.decode().rstrip() except Exception as e: except_name = type(e).__name__ current_app.logger.info(f"Could not retrieve git information: {str(except_name)}: {e}") diff --git a/bento_wes/authz.py b/bento_wes/authz.py index 3bd5ad0..8da3e3e 100644 --- a/bento_wes/authz.py +++ b/bento_wes/authz.py @@ -3,8 +3,6 @@ __all__ = [ "authz_middleware", - "PERMISSION_INGEST_DATA", - "PERMISSION_VIEW_RUNS", ] authz_middleware = FlaskAuthMiddleware( @@ -12,6 +10,3 @@ debug_mode=config.BENTO_DEBUG, enabled=config.AUTHZ_ENABLED, ) - -PERMISSION_INGEST_DATA = "ingest:data" -PERMISSION_VIEW_RUNS = "view:runs" diff --git a/bento_wes/backends/_wes_backend.py b/bento_wes/backends/_wes_backend.py index d00a67a..de39f35 100644 --- a/bento_wes/backends/_wes_backend.py +++ b/bento_wes/backends/_wes_backend.py @@ -10,13 +10,15 @@ from abc import ABC, abstractmethod from bento_lib.events import EventBus from bento_lib.events.types import EVENT_WES_RUN_FINISHED +from bento_lib.workflows.models import WorkflowSecretInput +from bento_lib.workflows.utils import namespaced_input from flask import current_app from typing import Any from bento_wes import states -from bento_wes.constants import SERVICE_ARTIFACT, RUN_PARAM_FROM_CONFIG +from bento_wes.constants import SERVICE_ARTIFACT from bento_wes.db import get_db, finish_run, update_run_state_and_commit -from bento_wes.models import Run, RunWithDetails, BentoWorkflowInputWithValue +from bento_wes.models import Run, RunWithDetails from bento_wes.states import STATE_EXECUTOR_ERROR, STATE_SYSTEM_ERROR from bento_wes.utils import iso_now from bento_wes.workflows import WorkflowType, WorkflowManager @@ -28,13 +30,8 @@ # Spec: https://software.broadinstitute.org/wdl/documentation/spec#whitespace-strings-identifiers-constants WDL_WORKSPACE_NAME_REGEX = re.compile(r"workflow\s+([a-zA-Z][a-zA-Z0-9_]+)") -PARAM_SECRET_PREFIX = "secret__" ParamDict = dict[str, str | int | float | bool] -FORBIDDEN_FROM_CONFIG_PARAMS = ( - "WES_CLIENT_SECRET", -) - class WESBackend(ABC): def __init__( @@ -305,14 +302,15 @@ def _initialize_run_and_get_command( self, run: RunWithDetails, celery_id: int, - access_token: str, + secrets: dict[str, str], ) -> tuple[Command, dict] | None: """ Performs "initialization" operations on the run, including setting states, downloading and validating the workflow file, and generating and logging the workflow-running command. :param run: The run to initialize :param celery_id: The Celery ID of the Celery task responsible for executing the run - :param access_token: An access token for talking with this Bento instance's services + :param secrets: A dictionary of secrets (e.g., tokens) to be injected as parameters (potentially) but not stored + in the database. :return: The command to execute, if no errors occurred; None otherwise """ @@ -320,114 +318,87 @@ def _initialize_run_and_get_command( run_dir = self.run_dir(run) - # -- Check that the run directory exists ------------------------------ + # -- Check that the run directory exists ----------------------------------------------------------------------- if not os.path.exists(run_dir): # TODO: Log error in run log self.log_error("Run directory not found") return self._finish_run_and_clean_up(run, states.STATE_SYSTEM_ERROR) - c = self.db.cursor() + run_req = run.request - workflow_id = run.request.tags.workflow_id - workflow_params: ParamDict = { - **run.request.workflow_params, - f"{workflow_id}.{PARAM_SECRET_PREFIX}access_token": access_token, - - # In export/analysis mode, as we rely on services located in different containers - # there is a need to have designated folders on shared volumes between - # WES and the other services, to write files to. - # This is possible because /wes/tmp is a volume mounted with the same - # path in each data service (except Gohan which mounts the dropbox - # data-x directory directly instead, to avoid massive duplicates). - # Also, the Toil library creates directories in the generic /tmp/ - # directory instead of the one that is configured for the job execution, - # to create the current working directories where tasks are executed. - # These files are inaccessible to other containers in the context of a - # task unless they are written arbitrarily to run_dir - f"{workflow_id}.run_dir": run_dir, - - # TODO: in the long run, we shouldn't tie workflow runs to a specific dataset ID inherently, necessarily - # - instead, they can be special input parameters that get translated to strings - f"{workflow_id}.project_id": run.request.tags.project_id, - f"{workflow_id}.dataset_id": run.request.tags.dataset_id, - # Don't use data_type from workflow metadata here - instead, workflows can say what they're ingesting - - # TODO: more special parameters: service URLs, system__run_dir... - } - - # Some workflow parameters depend on the WES application configuration - # and need to be added from there. - # The reserved keyword `FROM_CONFIG` is used to detect those inputs. - # All parameters in config are upper case. e.g. drs_url --> DRS_URL - for i in run.request.tags.workflow_metadata.inputs: - self.log_debug(f"Found workflow input for run {run.run_id}: {str(i)}") - if not isinstance(i, BentoWorkflowInputWithValue) or i.value != RUN_PARAM_FROM_CONFIG: - continue - input_id_upper = i.id.upper() - if input_id_upper in FORBIDDEN_FROM_CONFIG_PARAMS: # Cannot grab WES client secret, for example - self.log_warning(f"Cannot inject forbidden WES config item: {i.id}") - continue - param_val = current_app.config.get(input_id_upper, "") - workflow_params[f"{workflow_id}.{i.id}"] = param_val - self.log_debug(f"Injecting FROM_CONFIG param to {workflow_id}: {i.id}={param_val}") - - # -- Validate the workflow -------------------------------------------- + # run_req.workflow_params now includes non-secret injected values since it was read from the database after + # the run ID was passed to the runner: + workflow_params_with_secrets: ParamDict = {**run_req.workflow_params} + + # -- Find which inputs are secrets, which need to be injected here (so they don't end up in the database) ------ + for run_input in run_req.tags.workflow_metadata.inputs: + if isinstance(run_input, WorkflowSecretInput): + secret_value = secrets.get(run_input.key) + if secret_value is None: + err = f"Could not find injectable secret for key {run_input.key}" + self.log_error(err) + return self._finish_run_and_clean_up(run, STATE_EXECUTOR_ERROR) + workflow_params_with_secrets[namespaced_input(run_req.tags.workflow_id, run_input.id)] = secret_value + + # -- Validate the workflow ------------------------------------------------------------------------------------- error = self._check_workflow_and_type(run) if error is not None: self.log_error(error[0]) return self._finish_run_and_clean_up(run, error[1]) - # -- Find "real" workflow name from workflow file --------------------- + # -- Find "real" workflow name from workflow file -------------------------------------------------------------- workflow_name = self.get_workflow_name(self.workflow_path(run)) if workflow_name is None: # Invalid/non-workflow-specifying workflow file self.log_error("Could not find workflow name in workflow file") return self._finish_run_and_clean_up(run, states.STATE_SYSTEM_ERROR) + c = self.db.cursor() + # TODO: To avoid having multiple names, we should maybe only set this once? c.execute("UPDATE runs SET run_log__name = ? WHERE id = ?", (workflow_name, run.run_id)) self.db.commit() - # -- Store input for the workflow in a file in the temporary folder --- + # -- Store input for the workflow in a file in the temporary folder -------------------------------------------- with open(self._params_path(run), "w") as pf: - pf.write(self._serialize_params(workflow_params)) + pf.write(self._serialize_params(workflow_params_with_secrets)) - # -- Create the runner command based on inputs ------------------------ + # -- Create the runner command based on inputs ----------------------------------------------------------------- cmd = self._get_command(self.workflow_path(run), self._params_path(run), self.run_dir(run)) - # -- Update run log with command and Celery ID ------------------------ + # -- Update run log with command and Celery ID ----------------------------------------------------------------- c.execute( "UPDATE runs SET run_log__cmd = ?, run_log__celery_id = ? WHERE id = ?", (" ".join(cmd), celery_id, run.run_id)) self.db.commit() - return cmd, workflow_params + return cmd, workflow_params_with_secrets @abstractmethod def get_workflow_outputs(self, run_dir: str) -> dict[str, Any]: pass - def _perform_run(self, run: RunWithDetails, cmd: Command, params_with_extras: ParamDict) -> ProcessResult | None: + def _perform_run(self, run: RunWithDetails, cmd: Command, params_with_secrets: ParamDict) -> ProcessResult | None: """ Performs a run based on a provided command and returns stdout, stderr, exit code, and whether the process timed out while running. :param run: The run to execute :param cmd: The command used to execute the run - :param params_with_extras: A dictionary of parameters, including secret values + :param params_with_secrets: A dictionary of parameters, including secret values :return: A ProcessResult tuple of (stdout, stderr, exit_code, timed_out) """ c = self.db.cursor() - # Perform run ========================================================= + # Perform run ================================================================================================== - # -- Start process running the generated command ---------------------- + # -- Start process running the generated command --------------------------------------------------------------- runner_process = subprocess.Popen( cmd, cwd=self.tmp_dir, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8") c.execute("UPDATE runs SET run_log__start_time = ? WHERE id = ?", (iso_now(), run.run_id)) self._update_run_state_and_commit(run.run_id, states.STATE_RUNNING) - # -- Wait for and capture output -------------------------------------- + # -- Wait for and capture output ------------------------------------------------------------------------------- timed_out = False @@ -442,26 +413,19 @@ def _perform_run(self, run: RunWithDetails, cmd: Command, params_with_extras: Pa finally: exit_code = runner_process.returncode - # -- Censor output in case it includes any secrets + # -- Censor output in case it includes any secrets ------------------------------------------------------------- - for k, v in params_with_extras.items(): - if PARAM_SECRET_PREFIX not in k: - continue - if isinstance(v, str) and len(v) >= 5: # redacted secrets must be somewhat lengthy + workflow_id = run.request.tags.workflow_id + req_secret_inputs = (i for i in run.request.tags.workflow_metadata.inputs if isinstance(i, WorkflowSecretInput)) + for req_secret_input in req_secret_inputs: + v = params_with_secrets.get(namespaced_input(workflow_id, req_secret_input.id)) + if isinstance(v, str) and len(v) > 1: # don't "censor" blank strings/single characters stdout = stdout.replace(v, "") stderr = stderr.replace(v, "") - # Complete run ======================================================== - - # -- Get various Bento-specific data from tags ------------------------ - - tags = run.request.tags - - workflow_metadata = tags.workflow_metadata - project_id: str = tags.project_id - dataset_id: str | None = tags.dataset_id + # Complete run ================================================================================================= - # -- Update run log with stdout/stderr, exit code --------------------- + # -- Update run log with stdout/stderr, exit code -------------------------------------------------------------- # - Explicitly don't commit here; sync with state update c.execute("UPDATE runs SET run_log__stdout = ?, run_log__stderr = ?, run_log__exit_code = ? WHERE id = ?", (stdout, stderr, exit_code, run.run_id)) @@ -471,7 +435,7 @@ def _perform_run(self, run: RunWithDetails, cmd: Command, params_with_extras: Pa self.log_error("Encountered timeout while performing run") return self._finish_run_and_clean_up(run, states.STATE_SYSTEM_ERROR) - # -- Final steps: check exit code and report results ------------------ + # -- Final steps: check exit code and report results ----------------------------------------------------------- if exit_code != 0: # TODO: Report error somehow @@ -488,31 +452,31 @@ def _perform_run(self, run: RunWithDetails, cmd: Command, params_with_extras: Pa # Explicitly don't commit here; sync with state update c.execute("UPDATE runs SET outputs = ? WHERE id = ?", (json.dumps(workflow_outputs), str(run.run_id))) - # Run result object - run_results = { - "project_id": project_id, - **({"dataset_id": dataset_id} if dataset_id else {}), - - "workflow_id": workflow_name, - "workflow_metadata": workflow_metadata.model_dump_json(), - "workflow_outputs": workflow_outputs, - "workflow_params": run.request.workflow_params, - } - # Emit event if possible - self.event_bus.publish_service_event(SERVICE_ARTIFACT, EVENT_WES_RUN_FINISHED, run_results) + self.event_bus.publish_service_event( + SERVICE_ARTIFACT, # TODO: bento_lib: replace with service kind + EVENT_WES_RUN_FINISHED, + # Run result object: + event_data={ + "workflow_id": workflow_name, + "workflow_metadata": run.request.tags.workflow_metadata.model_dump_json(), + "workflow_outputs": workflow_outputs, + "workflow_params": run.request.workflow_params, + }, + ) # Finally, set our state to COMPLETE + finish up the run. self._finish_run_and_clean_up(run, states.STATE_COMPLETE) return ProcessResult((stdout, stderr, exit_code, timed_out)) - def perform_run(self, run: RunWithDetails, celery_id: int, access_token: str) -> ProcessResult | None: + def perform_run(self, run: RunWithDetails, celery_id: int, secrets: dict[str, str]) -> ProcessResult | None: """ Executes a run from start to finish (initialization, startup, and completion / cleanup.) :param run: The run to execute :param celery_id: The ID of the Celery task responsible for executing the workflow - :param access_token: An access token for talking with this Bento instance's services + :param secrets: A dictionary of secrets (e.g., tokens) to be injected as parameters (potentially) but not stored + in the database. :return: A ProcessResult tuple of (stdout, stderr, exit_code, timed_out) """ @@ -523,12 +487,12 @@ def perform_run(self, run: RunWithDetails, celery_id: int, access_token: str) -> self._runs[run.run_id] = run - # Initialization (loading / downloading files) ------------------------ - init_vals = self._initialize_run_and_get_command(run, celery_id, access_token) + # Initialization (loading / downloading files + secrets injection) --------------------------------------------- + init_vals = self._initialize_run_and_get_command(run, celery_id, secrets) if init_vals is None: return - cmd, params_with_extras = init_vals + cmd, params_with_secrets = init_vals - # Perform, finish, and clean up run ----------------------------------- - return self._perform_run(run, cmd, params_with_extras) + # Perform, finish, and clean up run ---------------------------------------------------------------------------- + return self._perform_run(run, cmd, params_with_secrets) diff --git a/bento_wes/config.py b/bento_wes/config.py index d9b6c33..cb39378 100644 --- a/bento_wes/config.py +++ b/bento_wes/config.py @@ -20,18 +20,16 @@ def _get_from_environ_or_fail(var: str) -> str: return val +def _to_bool(val: str) -> bool: + return val.strip().lower() in TRUTH_VALUES + + TRUTH_VALUES = ("true", "1") AUTHZ_ENABLED = os.environ.get("AUTHZ_ENABLED", "true").strip().lower() in TRUTH_VALUES -BENTO_DEBUG: bool = os.environ.get( - "BENTO_DEBUG", - os.environ.get("FLASK_DEBUG", "false") -).strip().lower() in TRUTH_VALUES - -CELERY_DEBUG: bool = os.environ.get( - "CELERY_DEBUG", "" -).strip().lower() in TRUTH_VALUES +BENTO_DEBUG: bool = _to_bool(os.environ.get("BENTO_DEBUG", os.environ.get("FLASK_DEBUG", "false"))) +CELERY_DEBUG: bool = _to_bool(os.environ.get("CELERY_DEBUG", "")) AUTHZ_URL: str = _get_from_environ_or_fail("BENTO_AUTHZ_SERVICE_URL").strip().rstrip("/") SERVICE_REGISTRY_URL: str = _get_from_environ_or_fail("SERVICE_REGISTRY_URL").strip().rstrip("/") @@ -47,8 +45,7 @@ class Config: BENTO_URL: str = os.environ.get("BENTO_URL", "http://127.0.0.1:5000/") BENTO_DEBUG: bool = BENTO_DEBUG - BENTO_VALIDATE_SSL: bool = os.environ.get( - "BENTO_VALIDATE_SSL", str(not BENTO_DEBUG)).strip().lower() in TRUTH_VALUES + BENTO_VALIDATE_SSL: bool = _to_bool(os.environ.get("BENTO_VALIDATE_SSL", str(not BENTO_DEBUG))) DATABASE: str = os.environ.get("DATABASE", "bento_wes.db") SERVICE_ID = SERVICE_ID @@ -74,10 +71,7 @@ class Config: WES_CLIENT_ID: str = os.environ.get("WES_CLIENT_ID", "bento_wes") WES_CLIENT_SECRET: str = os.environ.get("WES_CLIENT_SECRET", "") - # Other services, used for interpolating workflow variables and ( - DRS_URL: str = os.environ.get("DRS_URL", "").strip().rstrip("/") - GOHAN_URL: str = os.environ.get("GOHAN_URL", "").strip().rstrip("/") - KATSU_URL: str = os.environ.get("KATSU_URL", "").strip().rstrip("/") + # Service registry URL, used for looking up service kinds to inject as workflow input SERVICE_REGISTRY_URL: str = SERVICE_REGISTRY_URL # VEP-related configuration diff --git a/bento_wes/constants.py b/bento_wes/constants.py index 981c8a2..80ee099 100644 --- a/bento_wes/constants.py +++ b/bento_wes/constants.py @@ -1,8 +1,6 @@ import bento_wes import os -from typing import Literal - __all__ = [ "BENTO_SERVICE_KIND", @@ -10,7 +8,6 @@ "SERVICE_TYPE", "SERVICE_ID", "SERVICE_NAME", - "RUN_PARAM_FROM_CONFIG", ] BENTO_SERVICE_KIND = "wes" @@ -22,5 +19,3 @@ } SERVICE_ID = os.environ.get("SERVICE_ID", ":".join(SERVICE_TYPE.values())) SERVICE_NAME = "Bento WES" - -RUN_PARAM_FROM_CONFIG: Literal["FROM_CONFIG"] = "FROM_CONFIG" diff --git a/bento_wes/models.py b/bento_wes/models.py index 5ff1840..8e4e1f3 100644 --- a/bento_wes/models.py +++ b/bento_wes/models.py @@ -1,12 +1,9 @@ +from bento_lib.workflows.models import WorkflowDefinition from datetime import datetime from pydantic import BaseModel, ConfigDict, AnyUrl, Json from typing import Literal __all__ = [ - "BentoWorkflowInput", - "BentoWorkflowInputWithValue", - "BentoWorkflowOutput", - "BentoWorkflowMetadata", "BentoRunRequestTags", "RunRequest", "RunLog", @@ -16,48 +13,11 @@ ] -class BentoWorkflowInput(BaseModel): - id: str - type: Literal["string", "string[]", "number", "number[]", "enum", "enum[]", "file", "file[]"] - required: bool = False, - extensions: list[str] | None = None - - -class BentoWorkflowInputWithFileExtensions(BentoWorkflowInput): - type: Literal["file", "file[]"] - extensions: list[str] | None = None - - -class BentoWorkflowInputWithValue(BentoWorkflowInput): - value: Literal["FROM_CONFIG"] - hidden: bool = True - - -class BentoWorkflowOutput(BaseModel): - id: str - type: Literal["string", "string[]", "number", "number[]", "enum", "enum[]", "file", "file[]"] - value: str - - -# TODO: Move to bento_lib -class BentoWorkflowMetadata(BaseModel): - name: str - description: str - action: Literal["ingestion", "analysis", "export"] - data_type: str | None = None - file: str - inputs: list[BentoWorkflowInputWithValue | BentoWorkflowInputWithFileExtensions | BentoWorkflowInput] - outputs: list[BentoWorkflowOutput] - - class BentoRunRequestTags(BaseModel): model_config = ConfigDict(extra="allow") workflow_id: str - workflow_metadata: BentoWorkflowMetadata - - project_id: str - dataset_id: str | None = None + workflow_metadata: WorkflowDefinition class RunRequest(BaseModel): diff --git a/bento_wes/runner.py b/bento_wes/runner.py index d8927ff..9cc11b1 100644 --- a/bento_wes/runner.py +++ b/bento_wes/runner.py @@ -51,7 +51,8 @@ def run_workflow(self, run_id: uuid.UUID): debug=current_app.config["BENTO_DEBUG"], ) - access_token: str = "" + secrets: dict[str, str] = {"access_token": ""} + # If we have credentials, obtain access token for use inside workflow to ingest data try: if (client_id := current_app.config["WES_CLIENT_ID"]) and \ @@ -70,7 +71,7 @@ def run_workflow(self, run_id: uuid.UUID): "client_id": client_id, "client_secret": client_secret, }) - access_token = token_res.json()["access_token"] + secrets["access_token"] = token_res.json()["access_token"] else: logger.warning( "Missing WES credentials: WES_CLIENT_ID and/or WES_CLIENT_SECRET; setting job access token to ''") @@ -83,7 +84,7 @@ def run_workflow(self, run_id: uuid.UUID): # Perform the run try: logger.info("Starting workflow execution...") - backend.perform_run(run, self.request.id, access_token) + backend.perform_run(run, self.request.id, secrets) except Exception as e: # Intercept any uncaught exceptions and finish with an error state logger.error(f"Uncaught exception while performing run: {type(e).__name__} {e}") diff --git a/bento_wes/runs.py b/bento_wes/runs.py index a6da2c9..900752b 100644 --- a/bento_wes/runs.py +++ b/bento_wes/runs.py @@ -7,6 +7,10 @@ import traceback import uuid +from bento_lib.auth.permissions import P_INGEST_DATA, P_VIEW_RUNS +from bento_lib.auth.resources import RESOURCE_EVERYTHING, build_resource +from bento_lib.workflows.models import WorkflowProjectDatasetInput, WorkflowConfigInput, WorkflowServiceUrlInput +from bento_lib.workflows.utils import namespaced_input from bento_lib.responses.flask_errors import ( flask_bad_request_error, flask_internal_server_error, @@ -14,11 +18,11 @@ flask_forbidden_error, ) from flask import Blueprint, Response, current_app, jsonify, request -from typing import Callable +from typing import Callable, Iterator from werkzeug.utils import secure_filename from . import states -from .authz import authz_middleware, PERMISSION_INGEST_DATA, PERMISSION_VIEW_RUNS +from .authz import authz_middleware from .celery import celery from .db import ( get_db, @@ -31,6 +35,7 @@ from .logger import logger from .models import RunRequest from .runner import run_workflow +from .service_registry import get_bento_services from .states import STATE_COMPLETE from .types import RunStream from .workflows import ( @@ -45,45 +50,81 @@ bp_runs = Blueprint("runs", __name__) -def _check_runs_permission(run_requests: list[RunRequest], permission: str) -> tuple[bool, ...]: - if not current_app.config["AUTHZ_ENABLED"]: - return tuple([True] * len(run_requests)) # Assume we have permission for everything if authz disabled +def _get_resource_for_run_request(run_req: RunRequest) -> dict: + wi = run_req.tags.workflow_id + wm = run_req.tags.workflow_metadata - # /policy/evaluate returns a LIST of booleans when a LIST of requested_resource[s] is passed. Thus, we can - # return this list directly *rather* than wrapping it like the above case where authz was disabled. - return authz_middleware.authz_post(request, "/policy/evaluate", body={ - "requested_resource": [ - { - "project": run_request.tags.project_id, - **({"dataset": run_request.tags.dataset_id} if run_request.tags.dataset_id else {}), - } - for run_request in run_requests - ], - "required_permissions": [permission], - })["result"] + resource = RESOURCE_EVERYTHING + + project_dataset_inputs = [i for i in wm.inputs if isinstance(i, WorkflowProjectDatasetInput)] + if len(project_dataset_inputs) == 1: + inp = project_dataset_inputs[0] + if inp_val := run_req.workflow_params.get(namespaced_input(wi, inp.id)): + project, dataset = inp_val.split(":") + resource = build_resource(project, dataset, data_type=wm.data_type) + + return resource + + +def authz_enabled() -> bool: + return current_app.config["AUTHZ_ENABLED"] + + +def _check_runs_permission(run_requests: list[RunRequest], permission: str) -> Iterator[bool]: + if not authz_enabled(): + yield from [True] * len(run_requests) # Assume we have permission for everything if authz disabled + return + + # /policy/evaluate returns a matrix of booleans of row: resource, col: permission. Thus, we can + # return permission booleans by resource by flattening it, since there is only one column. + yield from (r[0] for r in authz_middleware.evaluate( + request, + [_get_resource_for_run_request(run_request) for run_request in run_requests], + [permission], + )) def _check_single_run_permission_and_mark(run_req: RunRequest, permission: str) -> bool: - p_res = _check_runs_permission([run_req], permission) # By calling this, the developer indicates that they will have handled permissions adequately: - authz_middleware.mark_authz_done(request) - return p_res and p_res[0] + return authz_middleware.evaluate_one( + request, _get_resource_for_run_request(run_req), permission, mark_authz_done=True + ) if authz_enabled() else True + + +def _config_for_run(run_dir: str) -> dict[str, str | None]: + return { + # In export/analysis mode, as we rely on services located in different containers + # there is a need to have designated folders on shared volumes between + # WES and the other services, to write files to. + # This is possible because /wes/tmp is a volume mounted with the same + # path in each data service (except Gohan which mounts the dropbox + # data-x directory directly instead, to avoid massive duplicates). + # Also, the Toil library creates directories in the generic /tmp/ + # directory instead of the one that is configured for the job execution, + # to create the current working directories where tasks are executed. + # These files are inaccessible to other containers in the context of a + # task unless they are written arbitrarily to run_dir + "run_dir": run_dir, + + "vep_cache_dir": current_app.config["VEP_CACHE_DIR"], + } def _create_run(db: sqlite3.Connection, c: sqlite3.Cursor) -> Response: - run_req = RunRequest(**request.form) - - # TODO: Use this fully - # - files inside the workflow - # - workflow_url can refer to an attachment - workflow_attachment_list = request.files.getlist("workflow_attachment") + run_req = RunRequest.model_validate(request.form.to_dict()) # Check ingest permissions before continuing - if not _check_single_run_permission_and_mark(run_req, PERMISSION_INGEST_DATA): + if not _check_single_run_permission_and_mark(run_req, P_INGEST_DATA): return flask_forbidden_error("Forbidden") # We have permission - so continue --------- + logger.info(f"Starting run creation for workflow {run_req.tags.workflow_id}") + + # TODO: Use this fully + # - files inside the workflow + # - workflow_url can refer to an attachment + workflow_attachment_list = request.files.getlist("workflow_attachment") # Get list of allowed workflow hosts from configuration for any checks inside the runner # If it's blank, assume that means "any host is allowed" and pass None to the runner @@ -141,6 +182,35 @@ def _create_run(db: sqlite3.Connection, c: sqlite3.Cursor) -> Response: # TODO: Support WDL uploads for workflows attachment.save(os.path.join(run_dir, secure_filename(attachment.filename))) + # Process parameters & inject non-secret values + # - Get injectable run config for processing inputs + run_injectable_config = _config_for_run(run_dir) + # - Set up parameters + run_params = {**run_req.workflow_params} + bento_services_data = None + for run_input in run_req.tags.workflow_metadata.inputs: + input_key = namespaced_input(run_req.tags.workflow_id, run_input.id) + if isinstance(run_input, WorkflowConfigInput): + config_value = run_injectable_config.get(run_input.key) + if config_value is None: + err = f"Could not find injectable configuration value for key {run_input.key}" + logger.error(err) + return flask_bad_request_error(err) + logger.debug( + f"Injecting configuration parameter '{run_input.key}' into run {run_id}: {run_input.id}={config_value}") + run_params[input_key] = config_value + elif isinstance(run_input, WorkflowServiceUrlInput): + bento_services_data = bento_services_data or get_bento_services() + config_value: str | None = bento_services_data.get(run_input.service_kind).get("url") + sk = run_input.service_kind + if config_value is None: + err = f"Could not find URL/service record for service kind '{sk}'" + logger.error(err) + return flask_bad_request_error(err) + logger.debug( + f"Injecting URL for service kind '{sk}' into run {run_id}: {run_input.id}={config_value}") + run_params[input_key] = config_value + # Will be updated to STATE_QUEUED once submitted c.execute(""" INSERT INTO runs ( @@ -162,7 +232,7 @@ def _create_run(db: sqlite3.Connection, c: sqlite3.Cursor) -> Response: states.STATE_UNKNOWN, json.dumps({}), - json.dumps(run_req.workflow_params), + json.dumps(run_params), run_req.workflow_type, run_req.workflow_type_version, json.dumps(run_req.workflow_engine_parameters), @@ -217,10 +287,11 @@ def run_list(): try: return _create_run(db, c) except pydantic.ValidationError: # TODO: Better error messages + logger.error(f"Encountered validation error during run creation: {traceback.format_exc()}") authz_middleware.mark_authz_done(request) - logger.error(f"Encountered validation error: {traceback.format_exc()}") return flask_bad_request_error("Validation error: bad run request format") except ValueError: + logger.error(f"Encountered value error during run creation: {traceback.format_exc()}") authz_middleware.mark_authz_done(request) return flask_bad_request_error("Value error") @@ -254,8 +325,7 @@ def run_list(): if not public_endpoint: # Filter runs to just those which we have permission to view - p_res = _check_runs_permission(perms_list, PERMISSION_VIEW_RUNS) - res_list = [v for v, p in zip(res_list, p_res) if p] + res_list = [v for v, p in zip(res_list, _check_runs_permission(perms_list, P_VIEW_RUNS)) if p] authz_middleware.mark_authz_done(request) @@ -264,16 +334,15 @@ def run_list(): @bp_runs.route("/runs/", methods=["GET"]) def run_detail(run_id: uuid.UUID): - authz_enabled = current_app.config["AUTHZ_ENABLED"] run_details = get_run_with_details(get_db().cursor(), run_id, stream_content=False) if run_details is None: - if authz_enabled: + if authz_enabled(): return flask_forbidden_error("Forbidden") else: return flask_not_found_error(f"Run {run_id} not found") - if not _check_single_run_permission_and_mark(run_details.request, PERMISSION_VIEW_RUNS): + if not _check_single_run_permission_and_mark(run_details.request, P_VIEW_RUNS): return flask_forbidden_error("Forbidden") return jsonify(run_details.model_dump(mode="json")) @@ -300,12 +369,12 @@ def check_run_authz_then_return_response( c: sqlite3.Cursor, run_id: uuid.UUID, cb: Callable[[], Response | dict], - permission: str = PERMISSION_VIEW_RUNS, + permission: str = P_VIEW_RUNS, ): run = get_run_with_details(c, run_id, stream_content=False) if run is None: - if current_app.config["AUTHZ_ENABLED"]: + if authz_enabled(): # Without the required permissions, don't even leak if this run exists - just return forbidden authz_middleware.mark_authz_done(request) return flask_forbidden_error("Forbidden") diff --git a/bento_wes/service_registry.py b/bento_wes/service_registry.py new file mode 100644 index 0000000..cf6d05b --- /dev/null +++ b/bento_wes/service_registry.py @@ -0,0 +1,34 @@ +import requests +from datetime import datetime +from flask import current_app + +__all__ = [ + "get_bento_services", +] + + +# TODO: this will need to be re-done without a global cache for any async implementation + +_bento_services_cache: dict | None = None +_bento_services_last_updated: datetime | None = None + +_cache_ttl: int = 30 # seconds + + +def get_bento_services() -> dict: + global _bento_services_cache + global _bento_services_last_updated + + if not ( + _bento_services_cache and + _bento_services_last_updated and + (datetime.now() - _bento_services_last_updated).total_seconds() < _cache_ttl + ): + validate_ssl = current_app.config["BENTO_VALIDATE_SSL"] + res = requests.get( + current_app.config["SERVICE_REGISTRY_URL"].rstrip("/") + "/bento-services", verify=validate_ssl) + res.raise_for_status() + _bento_services_cache = {v["service_kind"]: v for v in res.json().values()} + _bento_services_last_updated = datetime.now() + + return _bento_services_cache diff --git a/dev.Dockerfile b/dev.Dockerfile index 23d60d1..2fb72c9 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 AS base-deps +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.11.10 AS base-deps LABEL org.opencontainers.image.description="Local development image for Bento WES." LABEL devcontainer.metadata='[{ \ diff --git a/poetry.lock b/poetry.lock index 56a32c9..59ac947 100644 --- a/poetry.lock +++ b/poetry.lock @@ -124,17 +124,17 @@ frozenlist = ">=1.1.0" [[package]] name = "amqp" -version = "5.1.1" +version = "5.2.0" description = "Low-level AMQP client for Python (fork of amqplib)." optional = false python-versions = ">=3.6" files = [ - {file = "amqp-5.1.1-py3-none-any.whl", hash = "sha256:6f0956d2c23d8fa6e7691934d8c3930eadb44972cbbd1a7ae3a520f735d43359"}, - {file = "amqp-5.1.1.tar.gz", hash = "sha256:2c1b13fecc0893e946c65cbd5f36427861cffa4ea2201d8f6fca22e2a373b5e2"}, + {file = "amqp-5.2.0-py3-none-any.whl", hash = "sha256:827cb12fb0baa892aad844fd95258143bce4027fdac4fccddbc43330fd281637"}, + {file = "amqp-5.2.0.tar.gz", hash = "sha256:a1ecff425ad063ad42a486c902807d1482311481c8ad95a72694b2975e75f7fd"}, ] [package.dependencies] -vine = ">=5.0.0" +vine = ">=5.0.0,<6.0.0" [[package]] name = "annotated-types" @@ -178,89 +178,41 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "bento-lib" -version = "7.2.2" +version = "9.2.0" description = "A set of common utilities and helpers for Bento platform services." optional = false python-versions = ">=3.10.0" files = [ - {file = "bento_lib-7.2.2-py3-none-any.whl", hash = "sha256:195f09e0aaf5101f51e381f7d713f48a351e30fd3f5cca04b352ba9bbf66fa88"}, - {file = "bento_lib-7.2.2.tar.gz", hash = "sha256:8bdb30b0befb1cfe49206a3bf884eeb2821a1a54181eac9a80e33398e9c66edc"}, + {file = "bento_lib-9.2.0-py3-none-any.whl", hash = "sha256:7b7f38ce216b0c0d1fe2a51b4616aebbb8c5cc16c970cac1ae6d9c2ed5b18ca1"}, + {file = "bento_lib-9.2.0.tar.gz", hash = "sha256:4a269b5c23d96eeae1cced814a52e02ba3b981636f6338e49f102f54370cc155"}, ] [package.dependencies] aiohttp = ">=3.8.4,<4" -Flask = {version = ">=2.2.5,<3", optional = true, markers = "extra == \"flask\""} +Flask = {version = ">=2.2.5,<4", optional = true, markers = "extra == \"flask\""} jsonschema = ">=4.17.3,<5" psycopg2-binary = ">=2.9.5,<3.0" +pydantic = ">=2.3.0,<3" redis = ">=4.5.4,<5.0" requests = ">=2.28.1,<3" -Werkzeug = ">=2.2.3,<3" +Werkzeug = ">=2.2.3,<4" [package.extras] django = ["Django (>=4.2.1,<5)", "djangorestframework (>=3.14.0,<3.15)"] -fastapi = ["fastapi (>=0.95.2,<0.102)"] -flask = ["Flask (>=2.2.5,<3)"] +fastapi = ["fastapi (>=0.100,<0.105)"] +flask = ["Flask (>=2.2.5,<4)"] [[package]] name = "billiard" -version = "4.1.0" +version = "4.2.0" description = "Python multiprocessing fork with improvements and bugfixes" optional = false python-versions = ">=3.7" files = [ - {file = "billiard-4.1.0-py3-none-any.whl", hash = "sha256:0f50d6be051c6b2b75bfbc8bfd85af195c5739c281d3f5b86a5640c65563614a"}, - {file = "billiard-4.1.0.tar.gz", hash = "sha256:1ad2eeae8e28053d729ba3373d34d9d6e210f6e4d8bf0a9c64f92bd053f1edf5"}, -] - -[[package]] -name = "boto" -version = "2.49.0" -description = "Amazon Web Services Library" -optional = false -python-versions = "*" -files = [ - {file = "boto-2.49.0-py2.py3-none-any.whl", hash = "sha256:147758d41ae7240dc989f0039f27da8ca0d53734be0eb869ef16e3adcfa462e8"}, - {file = "boto-2.49.0.tar.gz", hash = "sha256:ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a"}, -] - -[[package]] -name = "boto3" -version = "1.28.73" -description = "The AWS SDK for Python" -optional = false -python-versions = ">= 3.7" -files = [ - {file = "boto3-1.28.73-py3-none-any.whl", hash = "sha256:bbe377a288b6b12b526fae3b3d743318c6868626cf67e1e97f104345a5194b1e"}, - {file = "boto3-1.28.73.tar.gz", hash = "sha256:a61cf96f7e196b1450afdf4856b7ea0e58080752e687b0011157be96934489be"}, -] - 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-[package.extras] -crt = ["awscrt (==0.16.26)"] - [[package]] name = "cachetools" version = "5.3.2" @@ -274,30 +226,30 @@ files = [ [[package]] name = "celery" -version = "5.3.4" +version = "5.3.5" description = "Distributed Task Queue." optional = false python-versions = ">=3.8" files = [ - {file = "celery-5.3.4-py3-none-any.whl", hash = "sha256:1e6ed40af72695464ce98ca2c201ad0ef8fd192246f6c9eac8bba343b980ad34"}, - {file = "celery-5.3.4.tar.gz", hash = "sha256:9023df6a8962da79eb30c0c84d5f4863d9793a466354cc931d7f72423996de28"}, + {file = "celery-5.3.5-py3-none-any.whl", hash = "sha256:30b75ac60fb081c2d9f8881382c148ed7c9052031a75a1e8743ff4b4b071f184"}, + {file = "celery-5.3.5.tar.gz", hash = "sha256:6b65d8dd5db499dd6190c45aa6398e171b99592f2af62c312f7391587feb5458"}, ] [package.dependencies] -billiard = ">=4.1.0,<5.0" +billiard = ">=4.2.0,<5.0" click = ">=8.1.2,<9.0" click-didyoumean = ">=0.3.0" click-plugins = ">=1.1.1" click-repl = ">=0.2.0" -kombu = ">=5.3.2,<6.0" +kombu = ">=5.3.3,<6.0" python-dateutil = ">=2.8.2" -redis = {version = ">=4.5.2,<4.5.5 || >4.5.5,<5.0.0", optional = true, markers = "extra == \"redis\""} +redis = {version = ">=4.5.2,<4.5.5 || >4.5.5,<6.0.0", optional = true, markers = "extra == \"redis\""} tzdata = ">=2022.7" -vine = ">=5.0.0,<6.0" +vine = ">=5.1.0,<6.0" [package.extras] arangodb = ["pyArango (>=2.0.2)"] -auth = ["cryptography (==41.0.3)"] +auth = ["cryptography (==41.0.5)"] azureblockblob = ["azure-storage-blob (>=12.15.0)"] brotli = ["brotli (>=1.0.0)", "brotlipy (>=0.7.0)"] cassandra = ["cassandra-driver (>=3.25.0,<4)"] @@ -307,26 +259,26 @@ couchbase = ["couchbase (>=3.0.0)"] couchdb = ["pycouchdb (==1.14.2)"] django = ["Django (>=2.2.28)"] dynamodb = ["boto3 (>=1.26.143)"] -elasticsearch = ["elasticsearch (<8.0)"] +elasticsearch = ["elastic-transport (<=8.10.0)", "elasticsearch (<=8.10.1)"] eventlet = ["eventlet (>=0.32.0)"] gevent = ["gevent (>=1.5.0)"] librabbitmq = ["librabbitmq (>=2.0.0)"] memcache = ["pylibmc (==1.6.3)"] mongodb = ["pymongo[srv] (>=4.0.2)"] -msgpack = ["msgpack (==1.0.5)"] +msgpack = ["msgpack (==1.0.7)"] pymemcache = ["python-memcached (==1.59)"] pyro = ["pyro4 (==4.82)"] pytest = ["pytest-celery (==0.0.0)"] -redis = ["redis (>=4.5.2,!=4.5.5,<5.0.0)"] +redis = ["redis (>=4.5.2,!=4.5.5,<6.0.0)"] s3 = ["boto3 (>=1.26.143)"] slmq = ["softlayer-messaging (>=1.0.3)"] -solar = ["ephem (==4.1.4)"] +solar = ["ephem (==4.1.5)"] sqlalchemy = ["sqlalchemy (>=1.4.48,<2.1)"] sqs = ["boto3 (>=1.26.143)", "kombu[sqs] (>=5.3.0)", "pycurl (>=7.43.0.5)", "urllib3 (>=1.26.16)"] tblib = ["tblib (>=1.3.0)", "tblib (>=1.5.0)"] yaml = ["PyYAML (>=3.10)"] zookeeper = ["kazoo (>=1.3.1)"] -zstd = ["zstandard (==0.21.0)"] +zstd = ["zstandard (==0.22.0)"] [[package]] name = "certifi" @@ -352,101 +304,101 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.3.1" +version = "3.3.2" description = "The Real First Universal Charset Detector. 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"^3.10.0" -content-hash = "6540ae90a913088f6a7625e71438ea9105ce19dfb6df58fbafebc480d0ae3d9e" +content-hash = "3f7068876da974fe90203217d368c88a6a804f4eb124d92b679d2d882521ba39" diff --git a/pyproject.toml b/pyproject.toml index 80112cf..c6ad6a9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "bento_wes" -version = "0.11.0" +version = "0.12.0" description = "Workflow execution service for the Bento platform." authors = [ "David Lougheed ", @@ -24,17 +24,13 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.10.0" -bento-lib = {extras = ["flask"], version = "^7.2.0"} +bento-lib = {version = "^9.1.0", extras = ["flask"]} celery = {extras = ["redis"], version = "^5.2.7"} requests = "^2.28.1" -Flask = "~2.2.2" -# Don't actually need boto3/boto, but Toil errors without it... >:( -# Related: https://github.com/DataBiosphere/toil/issues/4314 -boto3 = "^1.26.50" -boto = "^2.49.0" +Flask = "~2.2.5" pydantic = "^2.0.2" flask-cors = "^4.0.0" -werkzeug = "~2.2.3" # debugpy is broken with werkzeug 2.3.x so pin this manually +werkzeug = "~2.2.2" # debugpy is broken with werkzeug 2.3.x so pin this manually [tool.poetry.group.dev.dependencies] coverage = "^7.2.2" diff --git a/run.dev.bash b/run.dev.bash index 3224f0e..7899334 100644 --- a/run.dev.bash +++ b/run.dev.bash @@ -28,6 +28,6 @@ celery --app bento_wes.app worker --loglevel="${celery_log_level}" & # Start API server echo "[bento_wes] [entrypoint] Starting Flask server" -python -m debugpy --listen 0.0.0.0:${DEBUGGER_PORT} -m flask run \ +python -Xfrozen_modules=off -m debugpy --listen 0.0.0.0:${DEBUGGER_PORT} -m flask run \ --host 0.0.0.0 \ --port "${INTERNAL_PORT}" diff --git a/tests/constants.py b/tests/constants.py index 796dc46..9e29548 100644 --- a/tests/constants.py +++ b/tests/constants.py @@ -12,6 +12,7 @@ EXAMPLE_RUN = { "workflow_params": { + "phenopackets_json.project_dataset": f"{EXAMPLE_PROJECT_ID}:{EXAMPLE_DATASET_ID}", "phenopackets_json.json_document": "http://my-server.local/test.json", }, "workflow_type": "WDL", @@ -24,27 +25,24 @@ "name": "Bento Phenopackets-Compatible JSON", "description": "This ingestion workflow will validate and import a Phenopackets schema-compatible " "JSON document.", - "action": "ingestion", + "type": "ingestion", "data_type": "phenopacket", + "tags": ["phenopacket"], "file": "phenopackets_json.wdl", "inputs": [ { - "id": "json_document", - "type": "file", + "id": "project_dataset", + "type": "project:dataset", "required": True, - "extensions": [".json"] - } - ], - "outputs": [ + }, { "id": "json_document", "type": "file", - "value": "{json_document}" + "required": True, + "pattern": r"^.json$", } ], - }, - "project_id": EXAMPLE_PROJECT_ID, - "dataset_id": EXAMPLE_DATASET_ID, + } }, } diff --git a/tests/test_runs.py b/tests/test_runs.py index 13fab98..fdeeffd 100644 --- a/tests/test_runs.py +++ b/tests/test_runs.py @@ -195,7 +195,7 @@ def test_runs_public_endpoint(client, mocked_responses): expected_keys = ["run_id", "state", "details"] expected_details_keys = ["request", "run_id", "run_log", "state"] expected_request_keys = ["tags", "workflow_type"] - expected_tags_keys = ["workflow_id", "workflow_metadata", "project_id", "dataset_id"] + expected_tags_keys = ["workflow_id", "workflow_metadata"] expected_metadata_keys = ["data_type"] expected_run_log_keys = ["end_time", "start_time"]