# 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 subprocess import time import urllib from cwltool.errors import WorkflowException import cwltool.workflow from schema_salad.sourceline import SourceLine, cmap import schema_salad.validate as validate from schema_salad.ref_resolver import file_uri, uri_file_path import arvados import arvados.config from arvados.keep import KeepClient from arvados.errors import ApiError import arvados_cwl.util from .arvcontainer import RunnerContainer, cleanup_name_for_collection from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder, update_from_merged_map, print_keep_deps, ArvSecretStore from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool from .arvworkflow import ArvadosWorkflow, upload_workflow, make_workflow_record from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size from .perf import Perf from .pathmapper import NoFollowPathMapper from cwltool.task_queue import TaskQueue from .context import ArvLoadingContext, ArvRuntimeContext from ._version import __version__ from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class, aslist from cwltool.command_line_tool import compute_checksums from cwltool.load_tool import load_tool 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 self.updatingRuntimeStatus = False def emit(self, record): kind = None if record.levelno >= logging.ERROR: kind = 'error' elif record.levelno >= logging.WARNING: kind = 'warning' if kind == 'warning' and record.name in ("salad", "crunchstat_summary"): # Don't send validation warnings to runtime status, # they're noisy and unhelpful. return if kind is not None and self.updatingRuntimeStatus is not True: self.updatingRuntimeStatus = True try: 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()) ) finally: self.updatingRuntimeStatus = False class ArvCwlExecutor(object): """Execute a CWL tool or workflow, submit work (using 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, stdout=sys.stdout): if arvargs is None: arvargs = argparse.Namespace() arvargs.work_api = None arvargs.output_name = None arvargs.output_tags = None arvargs.thread_count = 1 arvargs.collection_cache_size = None arvargs.git_info = True arvargs.submit = False arvargs.defer_downloads = False 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 self.should_estimate_cache_size = True self.fs_access = None self.secret_store = None self.stdout = stdout self.fast_submit = False self.git_info = arvargs.git_info self.debug = False 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) if arvargs.collection_cache_size: collection_cache_size = arvargs.collection_cache_size*1024*1024 self.should_estimate_cache_size = False else: collection_cache_size = 256*1024*1024 self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries, cap=collection_cache_size) 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 = ["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.error(""" ******************************* The 'jobs' API is no longer supported. *******************************""") exit(1) 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('') # Remove existing RuntimeStatusLoggingHandlers if they exist handlers = [h for h in root_logger.handlers if not isinstance(h, RuntimeStatusLoggingHandler)] root_logger.handlers = handlers handler = RuntimeStatusLoggingHandler(self.runtime_status_update) root_logger.addHandler(handler) self.toplevel_runtimeContext = ArvRuntimeContext(vars(arvargs)) self.toplevel_runtimeContext.make_fs_access = partial(CollectionFsAccess, collection_cache=self.collection_cache) self.toplevel_runtimeContext.secret_store = ArvSecretStore() self.defer_downloads = arvargs.submit and arvargs.defer_downloads validate_cluster_target(self, self.toplevel_runtimeContext) 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) elif "class" in toolpath_object and toolpath_object["class"] == "ExpressionTool": return ArvadosExpressionTool(self, toolpath_object, loadingContext) else: raise Exception("Unknown tool %s" % toolpath_object.get("class")) 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), self.workflow_eval_lock, self.stop_polling) 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), self.workflow_eval_lock, self.stop_polling) 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. """ if kind not in ('error', 'warning', 'activity'): # Ignore any other status kind return with self.workflow_eval_lock: current = None try: current = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger) except Exception as e: logger.info("Couldn't get current container: %s", e) if current is None: return runtime_status = current.get('runtime_status', {}) original_updatemessage = updatemessage = runtime_status.get(kind, "") if kind == "activity" or not updatemessage: updatemessage = message # Subsequent messages tacked on in detail original_updatedetail = updatedetail = runtime_status.get(kind+'Detail', "") maxlines = 40 if updatedetail.count("\n") < maxlines: if updatedetail: updatedetail += "\n" updatedetail += message + "\n" if detail: updatedetail += detail + "\n" if updatedetail.count("\n") >= maxlines: updatedetail += "\nSome messages may have been omitted. Check the full log." if updatemessage == original_updatemessage and updatedetail == original_updatedetail: # don't waste time doing an update if nothing changed # (usually because we exceeded the max lines) return runtime_status.update({ kind: updatemessage, kind+'Detail': updatedetail, }) 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 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) if not keys: remain_wait = self.poll_interval continue begin_poll = time.time() if self.work_api == "containers": table = self.poll_api.container_requests() pageSize = self.poll_api._rootDesc.get('maxItemsPerResponse', 1000) while keys: page = keys[:pageSize] try: proc_states = table.list(filters=[["uuid", "in", page]], select=["uuid", "container_uuid", "state", "log_uuid", "output_uuid", "modified_at", "properties", "runtime_constraints"]).execute(num_retries=self.num_retries) except Exception as e: logger.warning("Temporary 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 } }) keys = keys[pageSize:] 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 Exception: logger.warning("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) except (KeyboardInterrupt, SystemExit): break def check_features(self, obj, parentfield=""): if isinstance(obj, dict): if obj.get("class") == "DockerRequirement": if obj.get("dockerOutputDirectory"): if not obj.get("dockerOutputDirectory").startswith('/'): raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError( "Option 'dockerOutputDirectory' must be an absolute path.") if obj.get("class") == "InplaceUpdateRequirement": if obj["inplaceUpdate"] and parentfield == "requirements": raise SourceLine(obj, "class", UnsupportedRequirement).makeError("InplaceUpdateRequirement not supported for keep collections.") for k,v in obj.items(): self.check_features(v, parentfield=k) elif isinstance(obj, list): for i,v in enumerate(obj): with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)): self.check_features(v, parentfield=parentfield) def make_output_collection(self, name, storage_classes, tagsString, output_properties, outputObj): outputObj = copy.deepcopy(outputObj) files = [] def captureFile(fileobj): files.append(fileobj) def captureDir(dirobj): if dirobj["location"].startswith("keep:") and 'listing' in dirobj: del dirobj['listing'] files.append(dirobj) adjustDirObjs(outputObj, captureDir) adjustFileObjs(outputObj, captureFile) 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 v.type == "Directory" and v.resolved.startswith("_:"): continue if v.type == "CreateFile" and (k.startswith("_:") or v.resolved.startswith("_:")): with final.open(v.target, "wb") as f: f.write(v.resolved.encode("utf-8")) continue if not v.resolved.startswith("keep:"): raise Exception("Output source is not in keep or a literal") sp = v.resolved.split("/") srccollection = sp[0][5:] try: reader = self.collection_cache.get(srccollection) srcpath = urllib.parse.unquote("/".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.error("While preparing output collection: %s", e) raise 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: res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False)) f.write(res) final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True, properties=output_properties) 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(), 'output_properties': self.final_output_collection.get_properties(), }).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: logger.exception("Setting container output") raise def apply_reqs(self, job_order_object, tool): if "https://w3id.org/cwl/cwl#requirements" in job_order_object: if tool.metadata.get("http://commonwl.org/cwltool#original_cwlVersion") == 'v1.0': raise WorkflowException( "`cwl:requirements` in the input object is not part of CWL " "v1.0. You can adjust to use `cwltool:overrides` instead; or you " "can set the cwlVersion to v1.1 or greater and re-run with " "--enable-dev.") job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"] for req in job_reqs: tool.requirements.append(req) @staticmethod def get_git_info(tool): in_a_git_repo = False cwd = None filepath = None if tool.tool["id"].startswith("file://"): # check if git is installed try: filepath = uri_file_path(tool.tool["id"]) cwd = os.path.dirname(filepath) subprocess.run( ["git", "log", "--format=%H", "-n1", "HEAD"], cwd=cwd, check=True, stdout=subprocess.DEVNULL, ) in_a_git_repo = True except Exception as e: pass gitproperties = {} if in_a_git_repo: def git_output(cmd): return subprocess.run( cmd, cwd=cwd, stdout=subprocess.PIPE, universal_newlines=True, ).stdout.strip() git_commit = git_output(["git", "log", "--format=%H", "-n1", "HEAD"]) git_date = git_output(["git", "log", "--format=%cD", "-n1", "HEAD"]) git_committer = git_output(["git", "log", "--format=%cn <%ce>", "-n1", "HEAD"]) git_branch = git_output(["git", "rev-parse", "--abbrev-ref", "HEAD"]) git_origin = git_output(["git", "remote", "get-url", "origin"]) git_status = git_output(["git", "status", "--untracked-files=no", "--porcelain"]) git_describe = git_output(["git", "describe", "--always", "--tags"]) git_toplevel = git_output(["git", "rev-parse", "--show-toplevel"]) git_path = filepath[len(git_toplevel):] gitproperties = { "http://arvados.org/cwl#gitCommit": git_commit, "http://arvados.org/cwl#gitDate": git_date, "http://arvados.org/cwl#gitCommitter": git_committer, "http://arvados.org/cwl#gitBranch": git_branch, "http://arvados.org/cwl#gitOrigin": git_origin, "http://arvados.org/cwl#gitStatus": git_status, "http://arvados.org/cwl#gitDescribe": git_describe, "http://arvados.org/cwl#gitPath": git_path, } else: for g in ("http://arvados.org/cwl#gitCommit", "http://arvados.org/cwl#gitDate", "http://arvados.org/cwl#gitCommitter", "http://arvados.org/cwl#gitBranch", "http://arvados.org/cwl#gitOrigin", "http://arvados.org/cwl#gitStatus", "http://arvados.org/cwl#gitDescribe", "http://arvados.org/cwl#gitPath"): if g in tool.metadata: gitproperties[g] = tool.metadata[g] return gitproperties def set_container_request_properties(self, container, properties): resp = self.api.container_requests().list(filters=[["container_uuid", "=", container["uuid"]]], select=["uuid", "properties"]).execute(num_retries=self.num_retries) for cr in resp["items"]: cr["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in properties.items()}) self.api.container_requests().update(uuid=cr["uuid"], body={"container_request": {"properties": cr["properties"]}}).execute(num_retries=self.num_retries) def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None): self.debug = runtimeContext.debug self.runtime_status_update("activity", "initialization") git_info = self.get_git_info(updated_tool) if self.git_info else {} if git_info: logger.info("Git provenance") for g in git_info: if git_info[g]: logger.info(" %s: %s", g.split("#", 1)[1], git_info[g]) runtimeContext.git_info = git_info workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"] workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"] controller = self.api.config()["Services"]["Controller"]["ExternalURL"] logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller) if not self.fast_submit: updated_tool.visit(self.check_features) 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)) runtimeContext = runtimeContext.copy() default_storage_classes = ",".join([k for k,v in self.api.config().get("StorageClasses", {"default": {"Default": True}}).items() if v.get("Default") is True]) if runtimeContext.storage_classes == "default": runtimeContext.storage_classes = default_storage_classes if runtimeContext.intermediate_storage_classes == "default": runtimeContext.intermediate_storage_classes = default_storage_classes if not runtimeContext.name: self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"]) if git_info.get("http://arvados.org/cwl#gitDescribe"): self.name = "%s (%s)" % (self.name, git_info.get("http://arvados.org/cwl#gitDescribe")) runtimeContext.name = self.name if runtimeContext.copy_deps is None and (runtimeContext.create_workflow or runtimeContext.update_workflow): # When creating or updating workflow record, by default # always copy dependencies and ensure Docker images are up # to date. runtimeContext.copy_deps = True runtimeContext.match_local_docker = True if runtimeContext.print_keep_deps: runtimeContext.copy_deps = False runtimeContext.match_local_docker = False if runtimeContext.update_workflow and self.project_uuid is None: # If we are updating a workflow, make sure anything that # gets uploaded goes into the same parent project, unless # an alternate --project-uuid was provided. existing_wf = self.api.workflows().get(uuid=runtimeContext.update_workflow).execute() runtimeContext.project_uuid = existing_wf["owner_uuid"] self.project_uuid = runtimeContext.project_uuid self.runtime_status_update("activity", "data transfer") # Upload local file references in the job order. with Perf(metrics, "upload_job_order"): job_order, jobmapper = upload_job_order(self, "%s input" % runtimeContext.name, updated_tool, job_order, runtimeContext) # determine if we are submitting or directly executing the workflow. # # the last clause means: if it is a command line tool, and we # are going to wait for the result, and always_submit_runner # is false, then we don't submit a runner process. submitting = (runtimeContext.submit and not (updated_tool.tool["class"] == "CommandLineTool" and runtimeContext.wait and not runtimeContext.always_submit_runner)) loadingContext = self.loadingContext.copy() loadingContext.do_validate = False loadingContext.disable_js_validation = True tool = updated_tool # Upload direct dependencies of workflow steps, get back mapping of files to keep references. # Also uploads docker images. if not self.fast_submit: logger.info("Uploading workflow dependencies") with Perf(metrics, "upload_workflow_deps"): merged_map = upload_workflow_deps(self, tool, runtimeContext) else: # in the fast submit case, we are running a workflow that # has already been uploaded to Arvados, so we assume all # the dependencies have been pinned to keep references and # there is nothing to do. merged_map = {} loadingContext.loader = tool.doc_loader loadingContext.avsc_names = tool.doc_schema loadingContext.metadata = tool.metadata loadingContext.skip_resolve_all = True workflow_wrapper = None if (submitting and not self.fast_submit) or runtimeContext.update_workflow or runtimeContext.create_workflow or runtimeContext.print_keep_deps: # upload workflow and get back the workflow wrapper workflow_wrapper = upload_workflow(self, tool, job_order, runtimeContext.project_uuid, runtimeContext, uuid=runtimeContext.update_workflow, submit_runner_ram=runtimeContext.submit_runner_ram, name=runtimeContext.name, merged_map=merged_map, submit_runner_image=runtimeContext.submit_runner_image, git_info=git_info, set_defaults=(runtimeContext.update_workflow or runtimeContext.create_workflow), jobmapper=jobmapper) if runtimeContext.update_workflow or runtimeContext.create_workflow: # We're registering the workflow, so create or update # the workflow record and then exit. uuid = make_workflow_record(self, workflow_wrapper, runtimeContext.name, tool, runtimeContext.project_uuid, runtimeContext.update_workflow) self.stdout.write(uuid + "\n") return (None, "success") if runtimeContext.print_keep_deps: # Just find and print out all the collection dependencies and exit print_keep_deps(self, runtimeContext, merged_map, tool) return (None, "success") # Did not register a workflow, we're going to submit # it instead. loadingContext.loader.idx.clear() loadingContext.loader.idx["_:main"] = workflow_wrapper workflow_wrapper["id"] = "_:main" # Reload the minimal wrapper workflow. self.fast_submit = True tool = load_tool(workflow_wrapper, loadingContext) loadingContext.loader.idx["_:main"] = workflow_wrapper if not submitting: # If we are going to run the workflow now (rather than # submit it), we need to update the workflow document # replacing file references with keep references. If we # are just going to construct a run submission, we don't # need to do this. update_from_merged_map(tool, merged_map) self.apply_reqs(job_order, tool) self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse self.eval_timeout = runtimeContext.eval_timeout runtimeContext.use_container = True runtimeContext.tmpdir_prefix = "tmp" runtimeContext.work_api = self.work_api if not self.output_name: self.output_name = "Output from workflow %s" % runtimeContext.name self.output_name = cleanup_name_for_collection(self.output_name) 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" if runtimeContext.priority < 1 or runtimeContext.priority > 1000: raise Exception("--priority must be in the range 1..1000.") if self.should_estimate_cache_size: visited = set() estimated_size = [0] def estimate_collection_cache(obj): if obj.get("location", "").startswith("keep:"): m = pdh_size.match(obj["location"][5:]) if m and m.group(1) not in visited: visited.add(m.group(1)) estimated_size[0] += int(m.group(2)) visit_class(job_order, ("File", "Directory"), estimate_collection_cache) runtimeContext.collection_cache_size = max(((estimated_size[0]*192) // (1024*1024))+1, 256) self.collection_cache.set_cap(runtimeContext.collection_cache_size*1024*1024) logger.info("Using collection cache size %s MiB", runtimeContext.collection_cache_size) runnerjob = None if runtimeContext.submit: # We are submitting instead of running immediately. # # Create a "Runner job" that when run() is invoked, # creates the container request to run the workflow. if self.work_api == "containers": if submitting: loadingContext.metadata = updated_tool.metadata.copy() tool = RunnerContainer(self, tool, loadingContext, 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, collection_cache_size=runtimeContext.collection_cache_size, collection_cache_is_default=self.should_estimate_cache_size, git_info=git_info) else: runtimeContext.runnerjob = tool.tool["id"] 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) if runtimeContext.submit and not runtimeContext.wait: # User provided --no-wait so submit the container request, # get the container request uuid, print it out, and exit. runnerjob = next(jobiter) runnerjob.run(runtimeContext) self.stdout.write(runnerjob.uuid+"\n") return (None, "success") # We either running the workflow directly, or submitting it # and will wait for a final result. self.runtime_status_update("activity", "workflow execution") 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.set_container_request_properties(current_container, git_info) 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() # 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: if self.final_status is None: logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.") break if self.stop_polling.is_set(): 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") elif isinstance(sys.exc_info()[1], WorkflowException): logger.error("Workflow execution failed:\n%s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) else: logger.exception("Workflow execution failed") if self.pipeline: self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], body={"state": "Failed"}).execute(num_retries=self.num_retries) if self.work_api == "containers" and not current_container: # Not running in a crunch container, so cancel any outstanding processes. for p in self.processes: try: self.api.container_requests().update(uuid=p, body={"priority": "0"} ).execute(num_retries=self.num_retries) except Exception: pass 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.usage_report_notes: logger.info("Steps with low resource utilization (possible optimization opportunities):") for x in runtimeContext.usage_report_notes: logger.info(" %s", x) if runtimeContext.submit and isinstance(tool, Runner): logger.info("Final output collection %s", tool.final_output) if workbench2 or workbench1: logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output) else: if self.output_tags is None: self.output_tags = "" storage_classes = "" storage_class_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputStorageClass") if storage_class_req and storage_class_req.get("finalStorageClass"): storage_classes = aslist(storage_class_req["finalStorageClass"]) else: storage_classes = runtimeContext.storage_classes.strip().split(",") output_properties = {} output_properties_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputCollectionProperties") if output_properties_req: builder = make_builder(job_order, tool.hints, tool.requirements, runtimeContext, tool.metadata) for pr in output_properties_req["outputProperties"]: output_properties[pr["propertyName"]] = builder.do_eval(pr["propertyValue"]) self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, output_properties, 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) def blank_secrets(job_order_object, process): secrets_req, _ = process.get_requirement("http://commonwl.org/cwltool#Secrets") pass