X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b8e3dea8979a7dbbdb62b8ecd47f7094a7f0863c..8c81e6c09228a9d7a3e8036624c60367615ddfc6:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 31272c825e..c0e919c6ce 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -1,4 +1,7 @@ #!/usr/bin/env python +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 # Implement cwl-runner interface for submitting and running work on Arvados, using # either the Crunch jobs API or Crunch containers API. @@ -11,38 +14,49 @@ import threading import hashlib import copy import json +import re from functools import partial import pkg_resources # part of setuptools +import Queue +import time from cwltool.errors import WorkflowException import cwltool.main import cwltool.workflow -import schema_salad +import cwltool.process +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 from .arvcontainer import ArvadosContainer, RunnerContainer from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate -from. runner import Runner, upload_instance +from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, upload_dependencies from .arvtool import ArvadosCommandTool from .arvworkflow import ArvadosWorkflow, upload_workflow -from .fsaccess import CollectionFsAccess +from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache from .perf import Perf -from .pathmapper import FinalOutputPathMapper +from .pathmapper import NoFollowPathMapper from ._version import __version__ from cwltool.pack import pack -from cwltool.process import shortname, UnsupportedRequirement, getListing -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs -from cwltool.draft2tool import compute_checksums +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 from arvados.api import OrderedJsonModel logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') logger.setLevel(logging.INFO) +arvados.log_handler.setFormatter(logging.Formatter( + '%(asctime)s %(name)s %(levelname)s: %(message)s', + '%Y-%m-%d %H:%M:%S')) + +DEFAULT_PRIORITY = 500 class ArvCwlRunner(object): """Execute a CWL tool or workflow, submit work (using either jobs or @@ -50,15 +64,17 @@ class ArvCwlRunner(object): """ - def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None): + def __init__(self, api_client, work_api=None, keep_client=None, + output_name=None, output_tags=None, num_retries=4, + parallel_submit_count=4): self.api = api_client self.processes = {} - self.lock = threading.Lock() - self.cond = threading.Condition(self.lock) + self.in_flight = 0 + self.workflow_eval_lock = threading.Condition(threading.RLock()) self.final_output = None self.final_status = None self.uploaded = {} - self.num_retries = 4 + self.num_retries = num_retries self.uuid = None self.stop_polling = threading.Event() self.poll_api = None @@ -67,12 +83,21 @@ class ArvCwlRunner(object): self.output_name = output_name self.output_tags = output_tags self.project_uuid = None + self.intermediate_output_ttl = 0 + self.intermediate_output_collections = [] + self.trash_intermediate = False + self.runnable_queue = Queue.Queue() + self.runnable_queue_threads = [] + self.parallel_submit_count = parallel_submit_count + self.poll_interval = 12 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.work_api = None expected_api = ["jobs", "containers"] for api in expected_api: @@ -93,6 +118,11 @@ class ArvCwlRunner(object): def arv_make_tool(self, toolpath_object, **kwargs): kwargs["work_api"] = self.work_api + kwargs["fetcher_constructor"] = partial(CollectionFetcher, + api_client=self.api, + fs_access=CollectionFsAccess("", collection_cache=self.collection_cache), + num_retries=self.num_retries) + kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries) if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool": return ArvadosCommandTool(self, toolpath_object, **kwargs) elif "class" in toolpath_object and toolpath_object["class"] == "Workflow": @@ -101,41 +131,73 @@ class ArvCwlRunner(object): return cwltool.workflow.defaultMakeTool(toolpath_object, **kwargs) def output_callback(self, out, processStatus): - if processStatus == "success": - logger.info("Overall process status is %s", processStatus) - if self.pipeline: - self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], - body={"state": "Complete"}).execute(num_retries=self.num_retries) - else: - logger.warn("Overall process status is %s", processStatus) - if self.pipeline: - self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], - body={"state": "Failed"}).execute(num_retries=self.num_retries) - self.final_status = processStatus - self.final_output = out + with self.workflow_eval_lock: + if processStatus == "success": + logger.info("Overall process status is %s", processStatus) + if self.pipeline: + self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], + body={"state": "Complete"}).execute(num_retries=self.num_retries) + else: + logger.warn("Overall process status is %s", processStatus) + if self.pipeline: + self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], + body={"state": "Failed"}).execute(num_retries=self.num_retries) + self.final_status = processStatus + self.final_output = out + + def runnable_queue_func(self): + while True: + task = self.runnable_queue.get() + if task is None: + return + task() + + def start_run(self, runnable, kwargs): + with self.workflow_eval_lock: + self.in_flight += 1 + self.runnable_queue.put(partial(runnable.run, **kwargs)) + + def process_submitted(self, container): + with self.workflow_eval_lock: + self.processes[container.uuid] = container + self.in_flight -= 1 + + def process_done(self, uuid): + with self.workflow_eval_lock: + if uuid in self.processes: + del self.processes[uuid] + + def wrapped_callback(self, cb, obj, st): + with self.workflow_eval_lock: + cb(obj, st) + + def get_wrapped_callback(self, cb): + return partial(self.wrapped_callback, cb) def on_message(self, event): if "object_uuid" in event: if event["object_uuid"] in self.processes and event["event_type"] == "update": if event["properties"]["new_attributes"]["state"] == "Running" and self.processes[event["object_uuid"]].running is False: uuid = event["object_uuid"] - with self.lock: + with self.workflow_eval_lock: j = self.processes[uuid] - logger.info("Job %s (%s) is Running", j.name, uuid) + logger.info("%s %s is Running", self.label(j), uuid) j.running = True j.update_pipeline_component(event["properties"]["new_attributes"]) elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"): uuid = event["object_uuid"] - try: - self.cond.acquire() + with self.workflow_eval_lock: j = self.processes[uuid] - txt = self.work_api[0].upper() + self.work_api[1:-1] - logger.info("%s %s (%s) is %s", txt, j.name, uuid, event["properties"]["new_attributes"]["state"]) - with Perf(metrics, "done %s" % j.name): - j.done(event["properties"]["new_attributes"]) - self.cond.notify() - finally: - self.cond.release() + logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"]) + def done_cb(): + j.done(event["properties"]["new_attributes"]) + with self.workflow_eval_lock: + self.workflow_eval_lock.notify() + self.runnable_queue.put(done_cb) + + + 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. @@ -144,15 +206,19 @@ class ArvCwlRunner(object): """ try: + remain_wait = self.poll_interval while True: - self.stop_polling.wait(15) + if remain_wait > 0: + self.stop_polling.wait(remain_wait) if self.stop_polling.is_set(): break - with self.lock: - keys = self.processes.keys() + 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": @@ -162,6 +228,7 @@ class ArvCwlRunner(object): proc_states = table.list(filters=[["uuid", "in", keys]]).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"]: @@ -172,12 +239,13 @@ class ArvCwlRunner(object): "new_attributes": p } }) + finish_poll = time.time() + remain_wait = self.poll_interval - (finish_poll - begin_poll) except: - logger.error("Fatal error in state polling thread.", exc_info=(sys.exc_info()[1] if self.debug else False)) - self.cond.acquire() - self.processes.clear() - self.cond.notify() - self.cond.release() + logger.exception("Fatal error in state polling thread.") + with self.workflow_eval_lock: + self.processes.clear() + self.workflow_eval_lock.notify() finally: self.stop_polling.set() @@ -187,15 +255,40 @@ class ArvCwlRunner(object): def add_uploaded(self, src, pair): self.uploaded[src] = pair - def check_writable(self, obj): + 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: + break + + def check_features(self, obj): if isinstance(obj, dict): - if obj.get("writable"): - raise UnsupportedRequirement("InitialWorkDir feature 'writable: true' not supported") + 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_writable(v) - if isinstance(obj, list): - for v in obj: - self.check_writable(v) + 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, tagsString, outputObj): outputObj = copy.deepcopy(outputObj) @@ -207,13 +300,12 @@ class ArvCwlRunner(object): adjustDirObjs(outputObj, capture) adjustFileObjs(outputObj, capture) - generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False) + generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False) final = arvados.collection.Collection(api_client=self.api, keep_client=self.keep_client, num_retries=self.num_retries) - srccollections = {} for k,v in generatemapper.items(): if k.startswith("_:"): if v.type == "Directory": @@ -227,26 +319,19 @@ class ArvCwlRunner(object): raise Exception("Output source is not in keep or a literal") sp = k.split("/") srccollection = sp[0][5:] - if srccollection not in srccollections: - try: - srccollections[srccollection] = arvados.collection.CollectionReader( - srccollection, - api_client=self.api, - keep_client=self.keep_client, - num_retries=self.num_retries) - except arvados.errors.ArgumentError as e: - logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e) - raise - reader = srccollections[srccollection] 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 ("basename", "listing", "contents"): + for k in ("listing", "contents", "nameext", "nameroot", "dirname"): if k in fileobj: del fileobj[k] @@ -291,6 +376,10 @@ class ArvCwlRunner(object): 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: @@ -304,71 +393,125 @@ class ArvCwlRunner(object): def arv_executor(self, tool, job_order, **kwargs): self.debug = kwargs.get("debug") - tool.visit(self.check_writable) + tool.visit(self.check_features) self.project_uuid = kwargs.get("project_uuid") self.pipeline = None make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, - api_client=self.api, - keep_client=self.keep_client) + collection_cache=self.collection_cache) self.fs_access = make_fs_access(kwargs["basedir"]) + self.secret_store = kwargs.get("secret_store") + + self.trash_intermediate = kwargs["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 = kwargs["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 not kwargs.get("name"): + kwargs["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. + tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]], + makeTool=self.arv_make_tool, + loader=tool.doc_loader, + avsc_names=tool.doc_schema, + metadata=tool.metadata, + do_validate=False) + + # Upload local file references in the job order. + job_order = upload_job_order(self, "%s input" % kwargs["name"], + tool, job_order) existing_uuid = kwargs.get("update_workflow") if existing_uuid or kwargs.get("create_workflow"): + # Create a pipeline template or workflow record and exit. if self.work_api == "jobs": tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse"), uuid=existing_uuid, submit_runner_ram=kwargs.get("submit_runner_ram"), - name=kwargs.get("name")) + name=kwargs["name"], + merged_map=merged_map) tmpl.save() # cwltool.main will write our return value to stdout. - return tmpl.uuid - else: - return upload_workflow(self, tool, job_order, - self.project_uuid, - uuid=existing_uuid, - submit_runner_ram=kwargs.get("submit_runner_ram"), - name=kwargs.get("name")) + 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=kwargs.get("submit_runner_ram"), + name=kwargs["name"], + merged_map=merged_map), + "success") self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") + self.eval_timeout = kwargs.get("eval_timeout") kwargs["make_fs_access"] = make_fs_access kwargs["enable_reuse"] = kwargs.get("enable_reuse") kwargs["use_container"] = True kwargs["tmpdir_prefix"] = "tmp" - kwargs["on_error"] = "continue" kwargs["compute_checksum"] = kwargs.get("compute_checksum") if self.work_api == "containers": + if self.ignore_docker_for_reuse: + raise Exception("--ignore-docker-for-reuse not supported with containers API.") kwargs["outdir"] = "/var/spool/cwl" kwargs["docker_outdir"] = "/var/spool/cwl" kwargs["tmpdir"] = "/tmp" kwargs["docker_tmpdir"] = "/tmp" elif self.work_api == "jobs": + if kwargs["priority"] != DEFAULT_PRIORITY: + raise Exception("--priority not implemented for jobs API.") kwargs["outdir"] = "$(task.outdir)" kwargs["docker_outdir"] = "$(task.outdir)" kwargs["tmpdir"] = "$(task.tmpdir)" - upload_instance(self, shortname(tool.tool["id"]), tool, job_order) + if kwargs["priority"] < 1 or kwargs["priority"] > 1000: + raise Exception("--priority must be in the range 1..1000.") runnerjob = None if kwargs.get("submit"): + # Submit a runner job to run the workflow for us. if self.work_api == "containers": - if tool.tool["class"] == "CommandLineTool": + if tool.tool["class"] == "CommandLineTool" and kwargs.get("wait"): + kwargs["runnerjob"] = tool.tool["id"] runnerjob = tool.job(job_order, self.output_callback, **kwargs).next() else: - runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, - self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"), - name=kwargs.get("name")) - else: - runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, - self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"), - name=kwargs.get("name")) - - if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers": + runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), + self.output_name, + self.output_tags, + submit_runner_ram=kwargs.get("submit_runner_ram"), + name=kwargs.get("name"), + on_error=kwargs.get("on_error"), + submit_runner_image=kwargs.get("submit_runner_image"), + intermediate_output_ttl=kwargs.get("intermediate_output_ttl"), + merged_map=merged_map, + priority=kwargs.get("priority"), + secret_store=self.secret_store) + elif self.work_api == "jobs": + runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), + self.output_name, + self.output_tags, + submit_runner_ram=kwargs.get("submit_runner_ram"), + name=kwargs.get("name"), + on_error=kwargs.get("on_error"), + submit_runner_image=kwargs.get("submit_runner_image"), + merged_map=merged_map) + elif "cwl_runner_job" not in kwargs and self.work_api == "jobs": # Create pipeline for local run self.pipeline = self.api.pipeline_instances().create( body={ @@ -380,12 +523,17 @@ class ArvCwlRunner(object): if runnerjob and not kwargs.get("wait"): runnerjob.run(wait=kwargs.get("wait")) - return runnerjob.uuid + return (runnerjob.uuid, "success") self.poll_api = arvados.api('v1') self.polling_thread = threading.Thread(target=self.poll_states) self.polling_thread.start() + for r in xrange(0, self.parallel_submit_count): + t = threading.Thread(target=self.runnable_queue_func) + self.runnable_queue_threads.append(t) + t.start() + if runnerjob: jobiter = iter((runnerjob,)) else: @@ -396,10 +544,11 @@ class ArvCwlRunner(object): **kwargs) try: - self.cond.acquire() - # Will continue to hold the lock for the duration of this code - # except when in cond.wait(), at which point on_message can update - # job state and process output callbacks. + 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__() @@ -411,10 +560,10 @@ class ArvCwlRunner(object): if runnable: with Perf(metrics, "run"): - runnable.run(**kwargs) + self.start_run(runnable, kwargs) else: - if self.processes: - self.cond.wait(1) + if (self.in_flight + len(self.processes)) > 0: + self.workflow_eval_lock.wait(3) else: logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.") break @@ -422,7 +571,7 @@ class ArvCwlRunner(object): loopperf.__exit__() while self.processes: - self.cond.wait(1) + self.workflow_eval_lock.wait(3) except UnsupportedRequirement: raise @@ -438,9 +587,19 @@ class ArvCwlRunner(object): self.api.container_requests().update(uuid=runnerjob.uuid, body={"priority": "0"}).execute(num_retries=self.num_retries) finally: - self.cond.release() + self.workflow_eval_lock.release() + try: + # Drain queue + while not self.runnable_queue.empty(): + self.runnable_queue.get() + except Queue.Empty: + pass self.stop_polling.set() self.polling_thread.join() + for t in self.runnable_queue_threads: + self.runnable_queue.put(None) + for t in self.runnable_queue_threads: + t.join() if self.final_status == "UnsupportedRequirement": raise UnsupportedRequirement("Check log for details.") @@ -458,14 +617,14 @@ class ArvCwlRunner(object): self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output) self.set_crunch_output() - if self.final_status != "success": - raise WorkflowException("Workflow failed.") - if kwargs.get("compute_checksum"): - adjustDirObjs(self.final_output, partial(getListing, self.fs_access)) + adjustDirObjs(self.final_output, partial(get_listing, self.fs_access)) adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access)) - return self.final_output + if self.trash_intermediate and self.final_status == "success": + self.trash_intermediate_output() + + return (self.final_output, self.final_status) def versionstring(): @@ -475,7 +634,7 @@ def versionstring(): arvpkg = pkg_resources.require("arvados-python-client") cwlpkg = pkg_resources.require("cwltool") - return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version, + return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version, "arvados-python-client", arvpkg[0].version, "cwltool", cwlpkg[0].version) @@ -492,7 +651,12 @@ def arg_parser(): # type: () -> argparse.ArgumentParser help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.", type=float, default=20) - parser.add_argument("--version", action="store_true", help="Print version and exit") + + exgroup = parser.add_mutually_exclusive_group() + exgroup.add_argument("--print-dot", action="store_true", + help="Print workflow visualization in graphviz format and exit") + exgroup.add_argument("--version", action="version", help="Print version and exit", version=versionstring()) + exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.") exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--verbose", action="store_true", help="Default logging") @@ -506,10 +670,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--enable-reuse", action="store_true", default=True, dest="enable_reuse", - help="") + help="Enable job or container reuse (default)") exgroup.add_argument("--disable-reuse", action="store_false", default=True, dest="enable_reuse", - help="") + help="Disable job or container reuse") parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.") parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None) @@ -534,9 +698,16 @@ def arg_parser(): # type: () -> argparse.ArgumentParser exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.", default=True, dest="wait") + exgroup = parser.add_mutually_exclusive_group() + exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp", + default=True, dest="log_timestamps") + exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines", + default=True, dest="log_timestamps") + parser.add_argument("--api", type=str, default=None, dest="work_api", - help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.") + choices=("jobs", "containers"), + help="Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.") parser.add_argument("--compute-checksum", action="store_true", default=False, help="Compute checksum of contents while collecting outputs", @@ -546,26 +717,70 @@ def arg_parser(): # type: () -> argparse.ArgumentParser help="RAM (in MiB) required for the workflow runner job (default 1024)", default=1024) + parser.add_argument("--submit-runner-image", type=str, + help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__, + default=None) + parser.add_argument("--name", type=str, help="Name to use for workflow execution instance.", default=None) - parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute") + parser.add_argument("--on-error", type=str, + help="Desired workflow behavior when a step fails. One of 'stop' or 'continue'. " + "Default is 'continue'.", default="continue", choices=("stop", "continue")) + + parser.add_argument("--enable-dev", action="store_true", + help="Enable loading and running development versions " + "of CWL spec.", default=False) + + parser.add_argument("--intermediate-output-ttl", type=int, metavar="N", + help="If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).", + default=0) + + parser.add_argument("--priority", type=int, + help="Workflow priority (range 1..1000, higher has precedence over lower, containers api only)", + default=DEFAULT_PRIORITY) + + parser.add_argument("--disable-validate", dest="do_validate", + action="store_false", default=True, + help=argparse.SUPPRESS) + + parser.add_argument("--disable-js-validation", + action="store_true", default=False, + help=argparse.SUPPRESS) + + parser.add_argument("--parallel-submit-count", type=int, + default=4, help="Submit requests in parallel (default 4)") + + exgroup = parser.add_mutually_exclusive_group() + exgroup.add_argument("--trash-intermediate", action="store_true", + default=False, dest="trash_intermediate", + help="Immediately trash intermediate outputs on workflow success.") + exgroup.add_argument("--no-trash-intermediate", action="store_false", + default=False, dest="trash_intermediate", + help="Do not trash intermediate outputs (default).") + + parser.add_argument("workflow", type=str, default=None, help="The workflow to execute") parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.") return parser def add_arv_hints(): - cache = {} + cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*") + cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml') - cache["http://arvados.org/cwl"] = res.read() + use_custom_schema("v1.0", "http://arvados.org/cwl", res.read()) res.close() - document_loader, cwlnames, _, _ = cwltool.process.get_schema("v1.0") - _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", cache=cache) - for n in extnames.names: - if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""): - cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, "")) - document_loader.idx["http://arvados.org/cwl#"+n] = {} + cwltool.process.supportedProcessRequirements.extend([ + "http://arvados.org/cwl#RunInSingleContainer", + "http://arvados.org/cwl#OutputDirType", + "http://arvados.org/cwl#RuntimeConstraints", + "http://arvados.org/cwl#PartitionRequirement", + "http://arvados.org/cwl#APIRequirement", + "http://commonwl.org/cwltool#LoadListingRequirement", + "http://arvados.org/cwl#IntermediateOutput", + "http://arvados.org/cwl#ReuseRequirement" + ]) def main(args, stdout, stderr, api_client=None, keep_client=None): parser = arg_parser() @@ -573,10 +788,6 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): job_order_object = None arvargs = parser.parse_args(args) - if arvargs.version: - print versionstring() - return - if arvargs.update_workflow: if arvargs.update_workflow.find('-7fd4e-') == 5: want_api = 'containers' @@ -597,26 +808,44 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): try: if api_client is None: - api_client=arvados.api('v1', model=OrderedJsonModel()) - runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name, output_tags=arvargs.output_tags) + api_client = arvados.safeapi.ThreadSafeApiCache(api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}) + keep_client = api_client.keep + if keep_client is None: + keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4) + runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, + num_retries=4, output_name=arvargs.output_name, + output_tags=arvargs.output_tags) except Exception as e: logger.error(e) return 1 if arvargs.debug: logger.setLevel(logging.DEBUG) + logging.getLogger('arvados').setLevel(logging.DEBUG) if arvargs.quiet: logger.setLevel(logging.WARN) + logging.getLogger('arvados').setLevel(logging.WARN) logging.getLogger('arvados.arv-run').setLevel(logging.WARN) if arvargs.metrics: metrics.setLevel(logging.DEBUG) logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG) + if arvargs.log_timestamps: + arvados.log_handler.setFormatter(logging.Formatter( + '%(asctime)s %(name)s %(levelname)s: %(message)s', + '%Y-%m-%d %H:%M:%S')) + else: + arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s')) + arvargs.conformance_test = None arvargs.use_container = True arvargs.relax_path_checks = True + arvargs.print_supported_versions = False + + make_fs_access = partial(CollectionFsAccess, + collection_cache=runner.collection_cache) return cwltool.main.main(args=arvargs, stdout=stdout, @@ -625,4 +854,11 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): makeTool=runner.arv_make_tool, versionfunc=versionstring, job_order_object=job_order_object, - make_fs_access=partial(CollectionFsAccess, api_client=api_client)) + make_fs_access=make_fs_access, + fetcher_constructor=partial(CollectionFetcher, + api_client=api_client, + fs_access=make_fs_access(""), + num_retries=runner.num_retries), + resolver=partial(collectionResolver, api_client, num_retries=runner.num_retries), + logger_handler=arvados.log_handler, + custom_schema_callback=add_arv_hints)