From e9548a38dade9a4317e45c4eedd7b01a3f42a7b6 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 6 Sep 2023 15:06:41 -0400 Subject: [PATCH 01/13] refact!: remove expectation for workflow outputs and project/dataset tags --- README.md | 45 ++++-------------------------- bento_wes/backends/_wes_backend.py | 40 ++++++++++---------------- bento_wes/models.py | 12 -------- bento_wes/runs.py | 1 + tests/constants.py | 17 +++++------ tests/test_runs.py | 2 +- 6 files changed, 29 insertions(+), 88 deletions(-) diff --git a/README.md b/README.md index c776cb5e..41840ca2 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/backends/_wes_backend.py b/bento_wes/backends/_wes_backend.py index d00a67a9..e7549939 100644 --- a/bento_wes/backends/_wes_backend.py +++ b/bento_wes/backends/_wes_backend.py @@ -331,6 +331,8 @@ def _initialize_run_and_get_command( workflow_id = run.request.tags.workflow_id workflow_params: ParamDict = { **run.request.workflow_params, + + # TODO: only if requested in inputs f"{workflow_id}.{PARAM_SECRET_PREFIX}access_token": access_token, # In export/analysis mode, as we rely on services located in different containers @@ -344,14 +346,9 @@ def _initialize_run_and_get_command( # 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 + # TODO: only if requested in inputs 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... } @@ -453,14 +450,6 @@ def _perform_run(self, run: RunWithDetails, cmd: Command, params_with_extras: Pa # 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 - # -- 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 = ?", @@ -488,19 +477,18 @@ 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) diff --git a/bento_wes/models.py b/bento_wes/models.py index 0aee8f5d..a356abd5 100644 --- a/bento_wes/models.py +++ b/bento_wes/models.py @@ -5,7 +5,6 @@ __all__ = [ "BentoWorkflowInput", "BentoWorkflowInputWithValue", - "BentoWorkflowOutput", "BentoWorkflowMetadata", "BentoRunRequestTags", "RunRequest", @@ -33,21 +32,13 @@ class BentoWorkflowInputWithValue(BentoWorkflowInput): 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): @@ -56,9 +47,6 @@ class BentoRunRequestTags(BaseModel): workflow_id: str workflow_metadata: BentoWorkflowMetadata - project_id: str - dataset_id: str | None = None - class RunRequest(BaseModel): workflow_params: Json[dict[str, str | int | float | bool | list[str]]] diff --git a/bento_wes/runs.py b/bento_wes/runs.py index a6da2c97..1d382d60 100644 --- a/bento_wes/runs.py +++ b/bento_wes/runs.py @@ -54,6 +54,7 @@ def _check_runs_permission(run_requests: list[RunRequest], permission: str) -> t return authz_middleware.authz_post(request, "/policy/evaluate", body={ "requested_resource": [ { + # TODO: pull from inputs, or if not found, default to whole node "project": run_request.tags.project_id, **({"dataset": run_request.tags.dataset_id} if run_request.tags.dataset_id else {}), } diff --git a/tests/constants.py b/tests/constants.py index 796dc461..d14e4322 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", @@ -29,22 +30,18 @@ "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, + "extensions": [".json"] } ], - }, - "project_id": EXAMPLE_PROJECT_ID, - "dataset_id": EXAMPLE_DATASET_ID, + } }, } diff --git a/tests/test_runs.py b/tests/test_runs.py index 13fab984..fdeeffd1 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"] From 217974d181b7aa40d4e6d15806d35d591b7f3822 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 23 Oct 2023 17:13:50 -0400 Subject: [PATCH 02/13] feat: start implementing injectable config + new bento_lib/authz stuff --- bento_wes/app.py | 9 +- bento_wes/authz.py | 5 -- bento_wes/backends/_wes_backend.py | 132 ++++++++++++----------------- bento_wes/config.py | 22 ++--- bento_wes/constants.py | 3 - bento_wes/models.py | 32 +------ bento_wes/runner.py | 7 +- bento_wes/runs.py | 108 ++++++++++++++++------- poetry.lock | 11 +-- pyproject.toml | 2 +- 10 files changed, 157 insertions(+), 174 deletions(-) diff --git a/bento_wes/app.py b/bento_wes/app.py index 3c8e2705..a951e1f5 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 3bd5ad08..8da3e3e6 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 e7549939..de39f35c 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 """ @@ -320,111 +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, - - # TODO: only if requested in inputs - 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 - # TODO: only if requested in inputs - f"{workflow_id}.run_dir": run_dir, - - # 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 @@ -439,18 +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 ======================================================== + # 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)) @@ -460,7 +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 @@ -495,12 +470,13 @@ def _perform_run(self, run: RunWithDetails, cmd: Command, params_with_extras: Pa 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) """ @@ -511,12 +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 d9b6c332..cb393789 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 981c8a20..275e86d7 100644 --- a/bento_wes/constants.py +++ b/bento_wes/constants.py @@ -10,7 +10,6 @@ "SERVICE_TYPE", "SERVICE_ID", "SERVICE_NAME", - "RUN_PARAM_FROM_CONFIG", ] BENTO_SERVICE_KIND = "wes" @@ -22,5 +21,3 @@ } 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 a356abd5..01f416d0 100644 --- a/bento_wes/models.py +++ b/bento_wes/models.py @@ -1,11 +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", - "BentoWorkflowMetadata", "BentoRunRequestTags", "RunRequest", "RunLog", @@ -15,37 +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 - - -# TODO: Move to bento_lib -class BentoWorkflowMetadata(BaseModel): - name: str - description: str - action: Literal["ingestion", "analysis", "export"] - file: str - inputs: list[BentoWorkflowInputWithValue | BentoWorkflowInputWithFileExtensions | BentoWorkflowInput] - - class BentoRunRequestTags(BaseModel): model_config = ConfigDict(extra="allow") workflow_id: str - workflow_metadata: BentoWorkflowMetadata + workflow_metadata: WorkflowDefinition class RunRequest(BaseModel): diff --git a/bento_wes/runner.py b/bento_wes/runner.py index d8927ffe..9cc11b14 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 1d382d60..c79d2f6e 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 +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, @@ -45,30 +49,61 @@ bp_runs = Blueprint("runs", __name__) -def _check_runs_permission(run_requests: list[RunRequest], permission: str) -> tuple[bool, ...]: - if not current_app.config["AUTHZ_ENABLED"]: +def _get_resource_for_run_request(run_req: RunRequest) -> dict: + wm = run_req.tags.workflow_metadata + + 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] + project, dataset = run_req.workflow_params[inp.id] + 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(): return tuple([True] * len(run_requests)) # Assume we have permission for everything if authz disabled - # /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": [ - { - # TODO: pull from inputs, or if not found, default to whole node - "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"] + # /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: @@ -81,7 +116,7 @@ def _create_run(db: sqlite3.Connection, c: sqlite3.Cursor) -> Response: # 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 --------- @@ -142,6 +177,23 @@ 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} + for run_input in run_req.tags.workflow_metadata.inputs: + # TODO: service input + 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[namespaced_input(run_req.tags.workflow_id, run_input.id)] = config_value + # Will be updated to STATE_QUEUED once submitted c.execute(""" INSERT INTO runs ( @@ -163,7 +215,7 @@ 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), @@ -255,8 +307,7 @@ 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) @@ -265,16 +316,15 @@ 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")) @@ -301,12 +351,12 @@ 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/poetry.lock b/poetry.lock index 28c48362..3f1cb969 100644 --- a/poetry.lock +++ b/poetry.lock @@ -178,13 +178,13 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "bento-lib" -version = "7.2.2" +version = "9.0.0a5" 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-9.0.0a5-py3-none-any.whl", hash = "sha256:c03eb897ba3e3da217981f4a2ce4ea98129596f7d6058b32c0f1a03e79b8c1ab"}, + {file = "bento_lib-9.0.0a5.tar.gz", hash = "sha256:e7a689f03eda59e1f2ad29ec83e1da68688df35b50796a60835faa81c19a984c"}, ] [package.dependencies] @@ -192,13 +192,14 @@ aiohttp = ">=3.8.4,<4" Flask = {version = ">=2.2.5,<3", 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" [package.extras] django = ["Django (>=4.2.1,<5)", "djangorestframework (>=3.14.0,<3.15)"] -fastapi = ["fastapi (>=0.95.2,<0.102)"] +fastapi = ["fastapi (>=0.100,<0.105)"] flask = ["Flask (>=2.2.5,<3)"] [[package]] @@ -1920,4 +1921,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "^3.10.0" -content-hash = "6540ae90a913088f6a7625e71438ea9105ce19dfb6df58fbafebc480d0ae3d9e" +content-hash = "8b63ef6234dfe579f42f31d30a29029c40869598842bde6af6c1367e0e464f4f" diff --git a/pyproject.toml b/pyproject.toml index 80112cf2..9b1196c5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.10.0" -bento-lib = {extras = ["flask"], version = "^7.2.0"} +bento-lib = {version = "9.0.0a5", extras = ["flask"]} celery = {extras = ["redis"], version = "^5.2.7"} requests = "^2.28.1" Flask = "~2.2.2" From 14a96f6d48da21822d78b519aabc8a32a74d3a25 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 24 Oct 2023 10:13:02 -0400 Subject: [PATCH 03/13] chore: update bento_lib --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index 3f1cb969..b20ad75e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -178,13 +178,13 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "bento-lib" -version = "9.0.0a5" +version = "9.0.0a6" description = "A set of common utilities and helpers for Bento platform services." optional = false python-versions = ">=3.10.0" files = [ - {file = "bento_lib-9.0.0a5-py3-none-any.whl", hash = "sha256:c03eb897ba3e3da217981f4a2ce4ea98129596f7d6058b32c0f1a03e79b8c1ab"}, - {file = "bento_lib-9.0.0a5.tar.gz", hash = "sha256:e7a689f03eda59e1f2ad29ec83e1da68688df35b50796a60835faa81c19a984c"}, + {file = "bento_lib-9.0.0a6-py3-none-any.whl", hash = "sha256:d0afacb7de3edad4f687e2185c71ee4442c5bbe13a9ee2de61beeb3299bd51f4"}, + {file = "bento_lib-9.0.0a6.tar.gz", hash = "sha256:1a9717490dcf3101397b3293eef3c13ff717b4bff92de04a5c77463907c22042"}, ] [package.dependencies] @@ -1921,4 +1921,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "^3.10.0" -content-hash = "8b63ef6234dfe579f42f31d30a29029c40869598842bde6af6c1367e0e464f4f" +content-hash = "290cf7bf2e3311abd59550754b6addd8f3a27d014da36b541671142c84ee1817" diff --git a/pyproject.toml b/pyproject.toml index 9b1196c5..504d4ef5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.10.0" -bento-lib = {version = "9.0.0a5", extras = ["flask"]} +bento-lib = {version = "9.0.0a6", extras = ["flask"]} celery = {extras = ["redis"], version = "^5.2.7"} requests = "^2.28.1" Flask = "~2.2.2" From 2312fb448ccfd2c50c4e0903972312e651a11792 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 24 Oct 2023 10:13:16 -0400 Subject: [PATCH 04/13] test: fix tests for new WES setup + lint --- bento_wes/constants.py | 2 -- bento_wes/runs.py | 14 ++++++++------ tests/constants.py | 5 +++-- 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/bento_wes/constants.py b/bento_wes/constants.py index 275e86d7..80ee0994 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", diff --git a/bento_wes/runs.py b/bento_wes/runs.py index c79d2f6e..40b88042 100644 --- a/bento_wes/runs.py +++ b/bento_wes/runs.py @@ -69,7 +69,8 @@ def authz_enabled() -> bool: def _check_runs_permission(run_requests: list[RunRequest], permission: str) -> Iterator[bool]: if not authz_enabled(): - return tuple([True] * len(run_requests)) # Assume we have permission for everything if authz disabled + 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. @@ -109,17 +110,18 @@ def _config_for_run(run_dir: str) -> dict[str, str | None]: 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") - # Check ingest permissions before continuing 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 diff --git a/tests/constants.py b/tests/constants.py index d14e4322..9e29548d 100644 --- a/tests/constants.py +++ b/tests/constants.py @@ -25,8 +25,9 @@ "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": [ { @@ -38,7 +39,7 @@ "id": "json_document", "type": "file", "required": True, - "extensions": [".json"] + "pattern": r"^.json$", } ], } From b20aeefad3b7e88fa9729fbe83a34439fe00d439 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 13 Nov 2023 11:52:19 -0500 Subject: [PATCH 05/13] chore: use prod bento_lib 9.x and update lockfile deps --- poetry.lock | 494 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 248 insertions(+), 248 deletions(-) diff --git a/poetry.lock b/poetry.lock index 299045ba..1fdcefb3 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"}, - 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project, dataset = run_req.workflow_params[inp.id] - resource = build_resource(project, dataset, data_type=wm.data_type) + 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 @@ -108,7 +110,7 @@ def _config_for_run(run_dir: str) -> dict[str, str | None]: def _create_run(db: sqlite3.Connection, c: sqlite3.Cursor) -> Response: - run_req = RunRequest(**request.form) + run_req = RunRequest.model_validate(request.form.to_dict()) # Check ingest permissions before continuing From eb92ccd20a699aa9f42425eca019aa2d64714ac9 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 14 Nov 2023 10:11:25 -0500 Subject: [PATCH 07/13] chore: properly log value errors during run creation --- bento_wes/runs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bento_wes/runs.py b/bento_wes/runs.py index fb807a99..078c6f0c 100644 --- a/bento_wes/runs.py +++ b/bento_wes/runs.py @@ -274,12 +274,13 @@ 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") + return flask_bad_request_error(f"Value error") # GET # Bento Extension: Include run public details with /runs request From 3bcf3a70e8829b876143ec463990919c87896b22 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 14 Nov 2023 10:11:46 -0500 Subject: [PATCH 08/13] chore: update dependencies and rm unneeded dependencies --- 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529fc74e..16e04f0d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,14 +27,10 @@ python = "^3.10.0" 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" From 3605de34d5f427b588475beba6264ca3b05576dd Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 14 Nov 2023 10:12:16 -0500 Subject: [PATCH 09/13] chore: turn python frozen modules off when debugging --- run.dev.bash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/run.dev.bash b/run.dev.bash index 3224f0e0..78993343 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}" From 00eff7769b5437748e1def5af12cee2a2a618c5c Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 14 Nov 2023 12:03:24 -0500 Subject: [PATCH 10/13] chore: implement service URL injection --- bento_wes/runs.py | 21 +++++++++++++++++---- bento_wes/service_registry.py | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+), 4 deletions(-) create mode 100644 bento_wes/service_registry.py diff --git a/bento_wes/runs.py b/bento_wes/runs.py index 078c6f0c..6506fdb2 100644 --- a/bento_wes/runs.py +++ b/bento_wes/runs.py @@ -9,7 +9,7 @@ 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 +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, @@ -35,6 +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 ( @@ -186,8 +187,9 @@ def _create_run(db: sqlite3.Connection, c: sqlite3.Cursor) -> Response: 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: - # TODO: service input + 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: @@ -195,8 +197,19 @@ def _create_run(db: sqlite3.Connection, c: sqlite3.Cursor) -> Response: 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[namespaced_input(run_req.tags.workflow_id, run_input.id)] = config_value + 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(""" diff --git a/bento_wes/service_registry.py b/bento_wes/service_registry.py new file mode 100644 index 00000000..cf6d05b0 --- /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 From 90bc4055846d11c25916b6f833530e0c22d4aa5e Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 14 Nov 2023 12:05:21 -0500 Subject: [PATCH 11/13] chore: update base docker image --- Dockerfile | 2 +- dev.Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8d029a0b..5365bb7d 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/dev.Dockerfile b/dev.Dockerfile index 23d60d11..2fb72c9a 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='[{ \ From 6e745049184cab74a508aa8f90f76c965e679b79 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 14 Nov 2023 12:42:05 -0500 Subject: [PATCH 12/13] chore: bump version to 0.12.0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 16e04f0d..c6ad6a96 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 ", From d10cd58e7005a776cf8e6d74688f190a8fddab30 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 14 Nov 2023 12:43:26 -0500 Subject: [PATCH 13/13] lint --- bento_wes/runs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bento_wes/runs.py b/bento_wes/runs.py index 6506fdb2..900752bb 100644 --- a/bento_wes/runs.py +++ b/bento_wes/runs.py @@ -293,7 +293,7 @@ def run_list(): 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(f"Value error") + return flask_bad_request_error("Value error") # GET # Bento Extension: Include run public details with /runs request