# Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 import argparse import logging import os import sys import threading import copy import json import re from functools import partial import time from cwltool.errors import WorkflowException import cwltool.workflow from schema_salad.sourceline import SourceLine import schema_salad.validate as validate import arvados import arvados.config from arvados.keep import KeepClient from arvados.errors import ApiError import arvados_cwl.util from .arvcontainer import RunnerContainer from .arvjob import RunnerJob, RunnerTemplate from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps from .arvtool import ArvadosCommandTool from .arvworkflow import ArvadosWorkflow, upload_workflow from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache from .perf import Perf from .pathmapper import NoFollowPathMapper from .task_queue import TaskQueue from .context import ArvLoadingContext, ArvRuntimeContext from ._version import __version__ from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing from cwltool.command_line_tool import compute_checksums logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') DEFAULT_PRIORITY = 500 class RuntimeStatusLoggingHandler(logging.Handler): """ Intercepts logging calls and report them as runtime statuses on runner containers. """ def __init__(self, runtime_status_update_func): super(RuntimeStatusLoggingHandler, self).__init__() self.runtime_status_update = runtime_status_update_func def emit(self, record): kind = None if record.levelno >= logging.ERROR: kind = 'error' elif record.levelno >= logging.WARNING: kind = 'warning' if kind is not None: log_msg = record.getMessage() if '\n' in log_msg: # If the logged message is multi-line, use its first line as status # and the rest as detail. status, detail = log_msg.split('\n', 1) self.runtime_status_update( kind, "%s: %s" % (record.name, status), detail ) else: self.runtime_status_update( kind, "%s: %s" % (record.name, record.getMessage()) ) class ArvCwlExecutor(object): """Execute a CWL tool or workflow, submit work (using either jobs or containers API), wait for them to complete, and report output. """ def __init__(self, api_client, arvargs=None, keep_client=None, num_retries=4, thread_count=4): if arvargs is None: arvargs = argparse.Namespace() arvargs.work_api = None arvargs.output_name = None arvargs.output_tags = None arvargs.thread_count = 1 self.api = api_client self.processes = {} self.workflow_eval_lock = threading.Condition(threading.RLock()) self.final_output = None self.final_status = None self.num_retries = num_retries self.uuid = None self.stop_polling = threading.Event() self.poll_api = None self.pipeline = None self.final_output_collection = None self.output_name = arvargs.output_name self.output_tags = arvargs.output_tags self.project_uuid = None self.intermediate_output_ttl = 0 self.intermediate_output_collections = [] self.trash_intermediate = False self.thread_count = arvargs.thread_count self.poll_interval = 12 self.loadingContext = None if keep_client is not None: self.keep_client = keep_client else: self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries) self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries) self.fetcher_constructor = partial(CollectionFetcher, api_client=self.api, fs_access=CollectionFsAccess("", collection_cache=self.collection_cache), num_retries=self.num_retries) self.work_api = None expected_api = ["jobs", "containers"] for api in expected_api: try: methods = self.api._rootDesc.get('resources')[api]['methods'] if ('httpMethod' in methods['create'] and (arvargs.work_api == api or arvargs.work_api is None)): self.work_api = api break except KeyError: pass if not self.work_api: if arvargs.work_api is None: raise Exception("No supported APIs") else: raise Exception("Unsupported API '%s', expected one of %s" % (arvargs.work_api, expected_api)) if self.work_api == "jobs": logger.warn(""" ******************************* Using the deprecated 'jobs' API. To get rid of this warning: Users: read about migrating at http://doc.arvados.org/user/cwl/cwl-style.html#migrate and use the option --api=containers Admins: configure the cluster to disable the 'jobs' API as described at: http://doc.arvados.org/install/install-api-server.html#disable_api_methods *******************************""") self.loadingContext = ArvLoadingContext(vars(arvargs)) self.loadingContext.fetcher_constructor = self.fetcher_constructor self.loadingContext.resolver = partial(collectionResolver, self.api, num_retries=self.num_retries) self.loadingContext.construct_tool_object = self.arv_make_tool # Add a custom logging handler to the root logger for runtime status reporting # if running inside a container if arvados_cwl.util.get_current_container(self.api, self.num_retries, logger): root_logger = logging.getLogger('') handler = RuntimeStatusLoggingHandler(self.runtime_status_update) root_logger.addHandler(handler) self.runtimeContext = ArvRuntimeContext(vars(arvargs)) self.runtimeContext.make_fs_access = partial(CollectionFsAccess, collection_cache=self.collection_cache) def arv_make_tool(self, toolpath_object, loadingContext): if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool": return ArvadosCommandTool(self, toolpath_object, loadingContext) elif "class" in toolpath_object and toolpath_object["class"] == "Workflow": return ArvadosWorkflow(self, toolpath_object, loadingContext) else: return cwltool.workflow.default_make_tool(toolpath_object, loadingContext) def output_callback(self, out, processStatus): with self.workflow_eval_lock: if processStatus == "success": logger.info("Overall process status is %s", processStatus) state = "Complete" else: logger.error("Overall process status is %s", processStatus) state = "Failed" if self.pipeline: self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], body={"state": state}).execute(num_retries=self.num_retries) self.final_status = processStatus self.final_output = out self.workflow_eval_lock.notifyAll() def start_run(self, runnable, runtimeContext): self.task_queue.add(partial(runnable.run, runtimeContext)) def process_submitted(self, container): with self.workflow_eval_lock: self.processes[container.uuid] = container def process_done(self, uuid, record): with self.workflow_eval_lock: j = self.processes[uuid] logger.info("%s %s is %s", self.label(j), uuid, record["state"]) self.task_queue.add(partial(j.done, record)) del self.processes[uuid] def runtime_status_update(self, kind, message, detail=None): """ Updates the runtime_status field on the runner container. Called when there's a need to report errors, warnings or just activity statuses, for example in the RuntimeStatusLoggingHandler. """ with self.workflow_eval_lock: current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger) if current is None: return runtime_status = current.get('runtime_status', {}) # In case of status being an error, only report the first one. if kind == 'error': if not runtime_status.get('error'): runtime_status.update({ 'error': message }) if detail is not None: runtime_status.update({ 'errorDetail': detail }) # Further errors are only mentioned as a count. else: # Get anything before an optional 'and N more' string. try: error_msg = re.match( r'^(.*?)(?=\s*\(and \d+ more\)|$)', runtime_status.get('error')).groups()[0] more_failures = re.match( r'.*\(and (\d+) more\)', runtime_status.get('error')) except TypeError: # Ignore tests stubbing errors return if more_failures: failure_qty = int(more_failures.groups()[0]) runtime_status.update({ 'error': "%s (and %d more)" % (error_msg, failure_qty+1) }) else: runtime_status.update({ 'error': "%s (and 1 more)" % error_msg }) elif kind in ['warning', 'activity']: # Record the last warning/activity status without regard of # previous occurences. runtime_status.update({ kind: message }) if detail is not None: runtime_status.update({ kind+"Detail": detail }) else: # Ignore any other status kind return try: self.api.containers().update(uuid=current['uuid'], body={ 'runtime_status': runtime_status, }).execute(num_retries=self.num_retries) except Exception as e: logger.info("Couldn't update runtime_status: %s", e) def wrapped_callback(self, cb, obj, st): with self.workflow_eval_lock: cb(obj, st) self.workflow_eval_lock.notifyAll() def get_wrapped_callback(self, cb): return partial(self.wrapped_callback, cb) def on_message(self, event): if event.get("object_uuid") in self.processes and event["event_type"] == "update": uuid = event["object_uuid"] if event["properties"]["new_attributes"]["state"] == "Running": with self.workflow_eval_lock: j = self.processes[uuid] if j.running is False: j.running = True j.update_pipeline_component(event["properties"]["new_attributes"]) logger.info("%s %s is Running", self.label(j), uuid) elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"): self.process_done(uuid, event["properties"]["new_attributes"]) def label(self, obj): return "[%s %s]" % (self.work_api[0:-1], obj.name) def poll_states(self): """Poll status of jobs or containers listed in the processes dict. Runs in a separate thread. """ try: remain_wait = self.poll_interval while True: if remain_wait > 0: self.stop_polling.wait(remain_wait) if self.stop_polling.is_set(): break with self.workflow_eval_lock: keys = list(self.processes.keys()) if not keys: remain_wait = self.poll_interval continue begin_poll = time.time() if self.work_api == "containers": table = self.poll_api.container_requests() elif self.work_api == "jobs": table = self.poll_api.jobs() pageSize = self.poll_api._rootDesc.get('maxItemsPerResponse', 1000) while keys: page = keys[:pageSize] keys = keys[pageSize:] try: proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries) except Exception as e: logger.warn("Error checking states on API server: %s", e) remain_wait = self.poll_interval continue for p in proc_states["items"]: self.on_message({ "object_uuid": p["uuid"], "event_type": "update", "properties": { "new_attributes": p } }) finish_poll = time.time() remain_wait = self.poll_interval - (finish_poll - begin_poll) except: logger.exception("Fatal error in state polling thread.") with self.workflow_eval_lock: self.processes.clear() self.workflow_eval_lock.notifyAll() finally: self.stop_polling.set() def add_intermediate_output(self, uuid): if uuid: self.intermediate_output_collections.append(uuid) def trash_intermediate_output(self): logger.info("Cleaning up intermediate output collections") for i in self.intermediate_output_collections: try: self.api.collections().delete(uuid=i).execute(num_retries=self.num_retries) except: logger.warn("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit: break def check_features(self, obj): if isinstance(obj, dict): if obj.get("writable") and self.work_api != "containers": raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported with --api=jobs") if obj.get("class") == "DockerRequirement": if obj.get("dockerOutputDirectory"): if self.work_api != "containers": raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError( "Option 'dockerOutputDirectory' of DockerRequirement not supported with --api=jobs.") if not obj.get("dockerOutputDirectory").startswith('/'): raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError( "Option 'dockerOutputDirectory' must be an absolute path.") if obj.get("class") == "http://commonwl.org/cwltool#Secrets" and self.work_api != "containers": raise SourceLine(obj, "class", UnsupportedRequirement).makeError("Secrets not supported with --api=jobs") for v in obj.itervalues(): self.check_features(v) elif isinstance(obj, list): for i,v in enumerate(obj): with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)): self.check_features(v) def make_output_collection(self, name, storage_classes, tagsString, outputObj): outputObj = copy.deepcopy(outputObj) files = [] def capture(fileobj): files.append(fileobj) adjustDirObjs(outputObj, capture) adjustFileObjs(outputObj, capture) generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False) final = arvados.collection.Collection(api_client=self.api, keep_client=self.keep_client, num_retries=self.num_retries) for k,v in generatemapper.items(): if k.startswith("_:"): if v.type == "Directory": continue if v.type == "CreateFile": with final.open(v.target, "wb") as f: f.write(v.resolved.encode("utf-8")) continue if not k.startswith("keep:"): raise Exception("Output source is not in keep or a literal") sp = k.split("/") srccollection = sp[0][5:] try: reader = self.collection_cache.get(srccollection) srcpath = "/".join(sp[1:]) if len(sp) > 1 else "." final.copy(srcpath, v.target, source_collection=reader, overwrite=False) except arvados.errors.ArgumentError as e: logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e) raise except IOError as e: logger.warn("While preparing output collection: %s", e) def rewrite(fileobj): fileobj["location"] = generatemapper.mapper(fileobj["location"]).target for k in ("listing", "contents", "nameext", "nameroot", "dirname"): if k in fileobj: del fileobj[k] adjustDirObjs(outputObj, rewrite) adjustFileObjs(outputObj, rewrite) with final.open("cwl.output.json", "w") as f: json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': ')) final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True) logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(), final.api_response()["name"], final.manifest_locator()) final_uuid = final.manifest_locator() tags = tagsString.split(',') for tag in tags: self.api.links().create(body={ "head_uuid": final_uuid, "link_class": "tag", "name": tag }).execute(num_retries=self.num_retries) def finalcollection(fileobj): fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"]) adjustDirObjs(outputObj, finalcollection) adjustFileObjs(outputObj, finalcollection) return (outputObj, final) def set_crunch_output(self): if self.work_api == "containers": current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger) if current is None: return try: self.api.containers().update(uuid=current['uuid'], body={ 'output': self.final_output_collection.portable_data_hash(), }).execute(num_retries=self.num_retries) self.api.collections().update(uuid=self.final_output_collection.manifest_locator(), body={ 'is_trashed': True }).execute(num_retries=self.num_retries) except Exception as e: logger.info("Setting container output: %s", e) elif self.work_api == "jobs" and "TASK_UUID" in os.environ: self.api.job_tasks().update(uuid=os.environ["TASK_UUID"], body={ 'output': self.final_output_collection.portable_data_hash(), 'success': self.final_status == "success", 'progress':1.0 }).execute(num_retries=self.num_retries) def arv_executor(self, tool, job_order, runtimeContext, logger=None): self.debug = runtimeContext.debug tool.visit(self.check_features) self.project_uuid = runtimeContext.project_uuid self.pipeline = None self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir) self.secret_store = runtimeContext.secret_store self.trash_intermediate = runtimeContext.trash_intermediate if self.trash_intermediate and self.work_api != "containers": raise Exception("--trash-intermediate is only supported with --api=containers.") self.intermediate_output_ttl = runtimeContext.intermediate_output_ttl if self.intermediate_output_ttl and self.work_api != "containers": raise Exception("--intermediate-output-ttl is only supported with --api=containers.") if self.intermediate_output_ttl < 0: raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl) if runtimeContext.submit_request_uuid and self.work_api != "containers": raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api)) if not runtimeContext.name: runtimeContext.name = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"]) # Upload direct dependencies of workflow steps, get back mapping of files to keep references. # Also uploads docker images. merged_map = upload_workflow_deps(self, tool) # Reload tool object which may have been updated by # upload_workflow_deps # Don't validate this time because it will just print redundant errors. loadingContext = self.loadingContext.copy() loadingContext.loader = tool.doc_loader loadingContext.avsc_names = tool.doc_schema loadingContext.metadata = tool.metadata loadingContext.do_validate = False tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]], loadingContext) # Upload local file references in the job order. job_order = upload_job_order(self, "%s input" % runtimeContext.name, tool, job_order) existing_uuid = runtimeContext.update_workflow if existing_uuid or runtimeContext.create_workflow: # Create a pipeline template or workflow record and exit. if self.work_api == "jobs": tmpl = RunnerTemplate(self, tool, job_order, runtimeContext.enable_reuse, uuid=existing_uuid, submit_runner_ram=runtimeContext.submit_runner_ram, name=runtimeContext.name, merged_map=merged_map) tmpl.save() # cwltool.main will write our return value to stdout. return (tmpl.uuid, "success") elif self.work_api == "containers": return (upload_workflow(self, tool, job_order, self.project_uuid, uuid=existing_uuid, submit_runner_ram=runtimeContext.submit_runner_ram, name=runtimeContext.name, merged_map=merged_map), "success") self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse self.eval_timeout = runtimeContext.eval_timeout runtimeContext = runtimeContext.copy() runtimeContext.use_container = True runtimeContext.tmpdir_prefix = "tmp" runtimeContext.work_api = self.work_api if self.work_api == "containers": if self.ignore_docker_for_reuse: raise Exception("--ignore-docker-for-reuse not supported with containers API.") runtimeContext.outdir = "/var/spool/cwl" runtimeContext.docker_outdir = "/var/spool/cwl" runtimeContext.tmpdir = "/tmp" runtimeContext.docker_tmpdir = "/tmp" elif self.work_api == "jobs": if runtimeContext.priority != DEFAULT_PRIORITY: raise Exception("--priority not implemented for jobs API.") runtimeContext.outdir = "$(task.outdir)" runtimeContext.docker_outdir = "$(task.outdir)" runtimeContext.tmpdir = "$(task.tmpdir)" if runtimeContext.priority < 1 or runtimeContext.priority > 1000: raise Exception("--priority must be in the range 1..1000.") runnerjob = None if runtimeContext.submit: # Submit a runner job to run the workflow for us. if self.work_api == "containers": if tool.tool["class"] == "CommandLineTool" and runtimeContext.wait and (not runtimeContext.always_submit_runner): runtimeContext.runnerjob = tool.tool["id"] runnerjob = tool.job(job_order, self.output_callback, runtimeContext).next() else: runnerjob = RunnerContainer(self, tool, job_order, runtimeContext.enable_reuse, self.output_name, self.output_tags, submit_runner_ram=runtimeContext.submit_runner_ram, name=runtimeContext.name, on_error=runtimeContext.on_error, submit_runner_image=runtimeContext.submit_runner_image, intermediate_output_ttl=runtimeContext.intermediate_output_ttl, merged_map=merged_map, priority=runtimeContext.priority, secret_store=self.secret_store) elif self.work_api == "jobs": runnerjob = RunnerJob(self, tool, job_order, runtimeContext.enable_reuse, self.output_name, self.output_tags, submit_runner_ram=runtimeContext.submit_runner_ram, name=runtimeContext.name, on_error=runtimeContext.on_error, submit_runner_image=runtimeContext.submit_runner_image, merged_map=merged_map) elif runtimeContext.cwl_runner_job is None and self.work_api == "jobs": # Create pipeline for local run self.pipeline = self.api.pipeline_instances().create( body={ "owner_uuid": self.project_uuid, "name": runtimeContext.name if runtimeContext.name else shortname(tool.tool["id"]), "components": {}, "state": "RunningOnClient"}).execute(num_retries=self.num_retries) logger.info("Pipeline instance %s", self.pipeline["uuid"]) if runnerjob and not runtimeContext.wait: submitargs = runtimeContext.copy() submitargs.submit = False runnerjob.run(submitargs) return (runnerjob.uuid, "success") current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger) if current_container: logger.info("Running inside container %s", current_container.get("uuid")) self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout) self.polling_thread = threading.Thread(target=self.poll_states) self.polling_thread.start() self.task_queue = TaskQueue(self.workflow_eval_lock, self.thread_count) try: self.workflow_eval_lock.acquire() if runnerjob: jobiter = iter((runnerjob,)) else: if runtimeContext.cwl_runner_job is not None: self.uuid = runtimeContext.cwl_runner_job.get('uuid') jobiter = tool.job(job_order, self.output_callback, runtimeContext) # Holds the lock while this code runs and releases it when # it is safe to do so in self.workflow_eval_lock.wait(), # at which point on_message can update job state and # process output callbacks. loopperf = Perf(metrics, "jobiter") loopperf.__enter__() for runnable in jobiter: loopperf.__exit__() if self.stop_polling.is_set(): break if self.task_queue.error is not None: raise self.task_queue.error if runnable: with Perf(metrics, "run"): self.start_run(runnable, runtimeContext) else: if (self.task_queue.in_flight + len(self.processes)) > 0: self.workflow_eval_lock.wait(3) else: logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.") break loopperf.__enter__() loopperf.__exit__() while (self.task_queue.in_flight + len(self.processes)) > 0: if self.task_queue.error is not None: raise self.task_queue.error self.workflow_eval_lock.wait(3) except UnsupportedRequirement: raise except: if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit: logger.error("Interrupted, workflow will be cancelled") else: logger.error("Execution failed:\n%s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) if self.pipeline: self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], body={"state": "Failed"}).execute(num_retries=self.num_retries) if runnerjob and runnerjob.uuid and self.work_api == "containers": self.api.container_requests().update(uuid=runnerjob.uuid, body={"priority": "0"}).execute(num_retries=self.num_retries) finally: self.workflow_eval_lock.release() self.task_queue.drain() self.stop_polling.set() self.polling_thread.join() self.task_queue.join() if self.final_status == "UnsupportedRequirement": raise UnsupportedRequirement("Check log for details.") if self.final_output is None: raise WorkflowException("Workflow did not return a result.") if runtimeContext.submit and isinstance(runnerjob, Runner): logger.info("Final output collection %s", runnerjob.final_output) else: if self.output_name is None: self.output_name = "Output of %s" % (shortname(tool.tool["id"])) if self.output_tags is None: self.output_tags = "" storage_classes = runtimeContext.storage_classes.strip().split(",") self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output) self.set_crunch_output() if runtimeContext.compute_checksum: adjustDirObjs(self.final_output, partial(get_listing, self.fs_access)) adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access)) if self.trash_intermediate and self.final_status == "success": self.trash_intermediate_output() return (self.final_output, self.final_status)