X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d10c79192b333191796d949841ec792e61a6006c..33f91bb5a4ed93e9cadf21920526daa53351dbea:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 371dd4fb8c..7f4b5c7549 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -1,760 +1,551 @@ #!/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 jobs on Arvados. +# Implement cwl-runner interface for submitting and running work on Arvados, using +# either the Crunch jobs API or Crunch containers API. import argparse -import arvados -import arvados.collection -import arvados.commands.keepdocker -import arvados.commands.run -import arvados.events -import arvados.util -import copy -import cwltool.docker -from cwltool.draft2tool import revmap_file, remove_hostfs, CommandLineTool -from cwltool.errors import WorkflowException -import cwltool.main -import cwltool.workflow -import fnmatch -from functools import partial -import json import logging import os -import pkg_resources # part of setuptools -import re import sys import threading -from cwltool.load_tool import fetch_document -from cwltool.builder import Builder -import urlparse +import hashlib +import copy +import json +import re +from functools import partial +import pkg_resources # part of setuptools + +from cwltool.errors import WorkflowException +import cwltool.main +import cwltool.workflow +import cwltool.process +import schema_salad +from schema_salad.sourceline import SourceLine -from cwltool.process import shortname, get_feature, adjustFiles, adjustFileObjs, scandeps +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_docker, upload_job_order, upload_workflow_deps, upload_dependencies +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 ._version import __version__ + +from cwltool.pack import pack +from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing +from cwltool.draft2tool 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) -tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)") -outdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)") -keepre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)") - - -def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid): - """Check if a Docker image is available in Keep, if not, upload it using arv-keepdocker.""" - - if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement: - dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"] - - sp = dockerRequirement["dockerImageId"].split(":") - image_name = sp[0] - image_tag = sp[1] if len(sp) > 1 else None - - images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3, - image_name=image_name, - image_tag=image_tag) - - if not images: - imageId = cwltool.docker.get_image(dockerRequirement, pull_image) - args = ["--project-uuid="+project_uuid, image_name] - if image_tag: - args.append(image_tag) - logger.info("Uploading Docker image %s", ":".join(args[1:])) - arvados.commands.keepdocker.main(args, stdout=sys.stderr) - - return dockerRequirement["dockerImageId"] - - -class CollectionFsAccess(cwltool.process.StdFsAccess): - """Implement the cwltool FsAccess interface for Arvados Collections.""" - - def __init__(self, basedir): - super(CollectionFsAccess, self).__init__(basedir) - self.collections = {} - - def get_collection(self, path): - p = path.split("/") - if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]): - pdh = p[0][5:] - if pdh not in self.collections: - self.collections[pdh] = arvados.collection.CollectionReader(pdh) - return (self.collections[pdh], "/".join(p[1:])) - else: - return (None, path) - - def _match(self, collection, patternsegments, parent): - if not patternsegments: - return [] - - if not isinstance(collection, arvados.collection.RichCollectionBase): - return [] - - ret = [] - # iterate over the files and subcollections in 'collection' - for filename in collection: - if patternsegments[0] == '.': - # Pattern contains something like "./foo" so just shift - # past the "./" - ret.extend(self._match(collection, patternsegments[1:], parent)) - elif fnmatch.fnmatch(filename, patternsegments[0]): - cur = os.path.join(parent, filename) - if len(patternsegments) == 1: - ret.append(cur) - else: - ret.extend(self._match(collection[filename], patternsegments[1:], cur)) - return ret - - def glob(self, pattern): - collection, rest = self.get_collection(pattern) - patternsegments = rest.split("/") - return self._match(collection, patternsegments, "keep:" + collection.manifest_locator()) - - def open(self, fn, mode): - collection, rest = self.get_collection(fn) - if collection: - return collection.open(rest, mode) - else: - return open(self._abs(fn), mode) - - def exists(self, fn): - collection, rest = self.get_collection(fn) - if collection: - return collection.exists(rest) - else: - return os.path.exists(self._abs(fn)) - -class ArvadosJob(object): - """Submit and manage a Crunch job for executing a CWL CommandLineTool.""" - - def __init__(self, runner): - self.arvrunner = runner - self.running = False - - def run(self, dry_run=False, pull_image=True, **kwargs): - script_parameters = { - "command": self.command_line - } - runtime_constraints = {} - - if self.generatefiles: - vwd = arvados.collection.Collection() - script_parameters["task.vwd"] = {} - for t in self.generatefiles: - if isinstance(self.generatefiles[t], dict): - src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"].replace("$(task.keep)/", "keep:")) - vwd.copy(rest, t, source_collection=src) - else: - with vwd.open(t, "w") as f: - f.write(self.generatefiles[t]) - vwd.save_new() - for t in self.generatefiles: - script_parameters["task.vwd"][t] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), t) - - script_parameters["task.env"] = {"TMPDIR": "$(task.tmpdir)"} - if self.environment: - script_parameters["task.env"].update(self.environment) - - if self.stdin: - script_parameters["task.stdin"] = self.pathmapper.mapper(self.stdin)[1] - - if self.stdout: - script_parameters["task.stdout"] = self.stdout - - (docker_req, docker_is_req) = get_feature(self, "DockerRequirement") - if docker_req and kwargs.get("use_container") is not False: - runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid) - else: - runtime_constraints["docker_image"] = "arvados/jobs" - - resources = self.builder.resources - if resources is not None: - runtime_constraints["min_cores_per_node"] = resources.get("cores", 1) - runtime_constraints["min_ram_mb_per_node"] = resources.get("ram") - runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0) - - filters = [["repository", "=", "arvados"], - ["script", "=", "crunchrunner"], - ["script_version", "in git", "9e5b98e8f5f4727856b53447191f9c06e3da2ba6"]] - if not self.arvrunner.ignore_docker_for_reuse: - filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]]) - - try: - response = self.arvrunner.api.jobs().create( - body={ - "owner_uuid": self.arvrunner.project_uuid, - "script": "crunchrunner", - "repository": "arvados", - "script_version": "master", - "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6", - "script_parameters": {"tasks": [script_parameters]}, - "runtime_constraints": runtime_constraints - }, - filters=filters, - find_or_create=kwargs.get("enable_reuse", True) - ).execute(num_retries=self.arvrunner.num_retries) - - self.arvrunner.jobs[response["uuid"]] = self - - self.update_pipeline_component(response) - - logger.info("Job %s (%s) is %s", self.name, response["uuid"], response["state"]) - - if response["state"] in ("Complete", "Failed", "Cancelled"): - self.done(response) - except Exception as e: - logger.error("Got error %s" % str(e)) - self.output_callback({}, "permanentFail") - - def update_pipeline_component(self, record): - if self.arvrunner.pipeline: - self.arvrunner.pipeline["components"][self.name] = {"job": record} - self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"], - body={ - "components": self.arvrunner.pipeline["components"] - }).execute(num_retries=self.arvrunner.num_retries) - if self.arvrunner.uuid: - try: - job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute() - if job: - components = job["components"] - components[self.name] = record["uuid"] - self.arvrunner.api.jobs().update(uuid=self.arvrunner.uuid, - body={ - "components": components - }).execute(num_retries=self.arvrunner.num_retries) - except Exception as e: - logger.info("Error adding to components: %s", e) - - def done(self, record): - try: - self.update_pipeline_component(record) - except: - pass - - try: - if record["state"] == "Complete": - processStatus = "success" - else: - processStatus = "permanentFail" - - try: - outputs = {} - if record["output"]: - logc = arvados.collection.Collection(record["log"]) - log = logc.open(logc.keys()[0]) - tmpdir = None - outdir = None - keepdir = None - for l in log: - # Determine the tmpdir, outdir and keepdir paths from - # the job run. Unfortunately, we can't take the first - # values we find (which are expected to be near the - # top) and stop scanning because if the node fails and - # the job restarts on a different node these values - # will different runs, and we need to know about the - # final run that actually produced output. - - g = tmpdirre.match(l) - if g: - tmpdir = g.group(1) - g = outdirre.match(l) - if g: - outdir = g.group(1) - g = keepre.match(l) - if g: - keepdir = g.group(1) - - colname = "Output %s of %s" % (record["output"][0:7], self.name) - - # check if collection already exists with same owner, name and content - collection_exists = self.arvrunner.api.collections().list( - filters=[["owner_uuid", "=", self.arvrunner.project_uuid], - ['portable_data_hash', '=', record["output"]], - ["name", "=", colname]] - ).execute(num_retries=self.arvrunner.num_retries) - - if not collection_exists["items"]: - # Create a collection located in the same project as the - # pipeline with the contents of the output. - # First, get output record. - collections = self.arvrunner.api.collections().list( - limit=1, - filters=[['portable_data_hash', '=', record["output"]]], - select=["manifest_text"] - ).execute(num_retries=self.arvrunner.num_retries) - - if not collections["items"]: - raise WorkflowException( - "Job output '%s' cannot be found on API server" % ( - record["output"])) - - # Create new collection in the parent project - # with the output contents. - self.arvrunner.api.collections().create(body={ - "owner_uuid": self.arvrunner.project_uuid, - "name": colname, - "portable_data_hash": record["output"], - "manifest_text": collections["items"][0]["manifest_text"] - }, ensure_unique_name=True).execute( - num_retries=self.arvrunner.num_retries) - - self.builder.outdir = outdir - self.builder.pathmapper.keepdir = keepdir - outputs = self.collect_outputs("keep:" + record["output"]) - except WorkflowException as e: - logger.error("Error while collecting job outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False)) - processStatus = "permanentFail" - except Exception as e: - logger.exception("Got unknown exception while collecting job outputs:") - processStatus = "permanentFail" - - self.output_callback(outputs, processStatus) - finally: - del self.arvrunner.jobs[record["uuid"]] - - -class RunnerJob(object): - """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner.""" - - def __init__(self, runner, tool, job_order, enable_reuse): - self.arvrunner = runner - self.tool = tool - self.job_order = job_order - self.running = False - self.enable_reuse = enable_reuse - - def update_pipeline_component(self, record): - pass - - def upload_docker(self, tool): - if isinstance(tool, CommandLineTool): - (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement") - if docker_req: - arv_docker_get_image(self.arvrunner.api, docker_req, True, self.arvrunner.project_uuid) - elif isinstance(tool, cwltool.workflow.Workflow): - for s in tool.steps: - self.upload_docker(s.embedded_tool) - - def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs): - """Create an Arvados job specification for this workflow. - - The returned dict can be used to create a job (i.e., passed as - the +body+ argument to jobs().create()), or as a component in - a pipeline template or pipeline instance. - """ - self.upload_docker(self.tool) - - workflowfiles = set() - jobfiles = set() - workflowfiles.add(self.tool.tool["id"]) - - self.name = os.path.basename(self.tool.tool["id"]) - - def visitFiles(files, path): - files.add(path) - return path - - document_loader, workflowobj, uri = fetch_document(self.tool.tool["id"]) - def loadref(b, u): - return document_loader.fetch(urlparse.urljoin(b, u)) - - sc = scandeps(uri, workflowobj, - set(("$import", "run")), - set(("$include", "$schemas", "path")), - loadref) - adjustFiles(sc, partial(visitFiles, workflowfiles)) - adjustFiles(self.job_order, partial(visitFiles, jobfiles)) - - workflowmapper = ArvPathMapper(self.arvrunner, workflowfiles, "", - "%s", - "%s/%s", - name=self.name, - **kwargs) - - jobmapper = ArvPathMapper(self.arvrunner, jobfiles, "", - "%s", - "%s/%s", - name=os.path.basename(self.job_order.get("id", "#")), - **kwargs) - - adjustFiles(self.job_order, lambda p: jobmapper.mapper(p)[1]) - - if "id" in self.job_order: - del self.job_order["id"] - - self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"])[1] - return { - "script": "cwl-runner", - "script_version": "master", - "repository": "arvados", - "script_parameters": self.job_order, - "runtime_constraints": { - "docker_image": "arvados/jobs" - } - } - - def run(self, *args, **kwargs): - job_spec = self.arvados_job_spec(*args, **kwargs) - job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid) - - response = self.arvrunner.api.jobs().create( - body=job_spec, - find_or_create=self.enable_reuse - ).execute(num_retries=self.arvrunner.num_retries) - - self.uuid = response["uuid"] - self.arvrunner.jobs[self.uuid] = self - - logger.info("Submitted job %s", response["uuid"]) - - if kwargs.get("submit"): - self.pipeline = self.arvrunner.api.pipeline_instances().create( - body={ - "owner_uuid": self.arvrunner.project_uuid, - "name": shortname(self.tool.tool["id"]), - "components": {"cwl-runner": {"job": {"uuid": self.uuid, "state": response["state"]} } }, - "state": "RunningOnClient"}).execute(num_retries=self.arvrunner.num_retries) - - if response["state"] in ("Complete", "Failed", "Cancelled"): - self.done(response) - - def done(self, record): - if record["state"] == "Complete": - processStatus = "success" - else: - processStatus = "permanentFail" - - outputs = None - try: - try: - outc = arvados.collection.Collection(record["output"]) - with outc.open("cwl.output.json") as f: - outputs = json.load(f) - def keepify(path): - if not path.startswith("keep:"): - return "keep:%s/%s" % (record["output"], path) - adjustFiles(outputs, keepify) - except Exception as e: - logger.error("While getting final output object: %s", e) - self.arvrunner.output_callback(outputs, processStatus) - finally: - del self.arvrunner.jobs[record["uuid"]] - - -class RunnerTemplate(object): - """An Arvados pipeline template that invokes a CWL workflow.""" - - type_to_dataclass = { - 'boolean': 'boolean', - 'File': 'File', - 'float': 'number', - 'int': 'number', - 'string': 'text', - } - - def __init__(self, runner, tool, job_order, enable_reuse): - self.runner = runner - self.tool = tool - self.job = RunnerJob( - runner=runner, - tool=tool, - job_order=job_order, - enable_reuse=enable_reuse) - - def pipeline_component_spec(self): - """Return a component that Workbench and a-r-p-i will understand. - - Specifically, translate CWL input specs to Arvados pipeline - format, like {"dataclass":"File","value":"xyz"}. - """ - spec = self.job.arvados_job_spec() - - # Most of the component spec is exactly the same as the job - # spec (script, script_version, etc.). - # spec['script_parameters'] isn't right, though. A component - # spec's script_parameters hash is a translation of - # self.tool.tool['inputs'] with defaults/overrides taken from - # the job order. So we move the job parameters out of the way - # and build a new spec['script_parameters']. - job_params = spec['script_parameters'] - spec['script_parameters'] = {} - - for param in self.tool.tool['inputs']: - param = copy.deepcopy(param) - - # Data type and "required" flag... - types = param['type'] - if not isinstance(types, list): - types = [types] - param['required'] = 'null' not in types - non_null_types = set(types) - set(['null']) - if len(non_null_types) == 1: - the_type = [c for c in non_null_types][0] - dataclass = self.type_to_dataclass.get(the_type) - if dataclass: - param['dataclass'] = dataclass - # Note: If we didn't figure out a single appropriate - # dataclass, we just left that attribute out. We leave - # the "type" attribute there in any case, which might help - # downstream. - - # Title and description... - title = param.pop('label', '') - descr = param.pop('description', '').rstrip('\n') - if title: - param['title'] = title - if descr: - param['description'] = descr - - # Fill in the value from the current job order, if any. - param_id = shortname(param.pop('id')) - value = job_params.get(param_id) - if value is None: - pass - elif not isinstance(value, dict): - param['value'] = value - elif param.get('dataclass') == 'File' and value.get('path'): - param['value'] = value['path'] - - spec['script_parameters'][param_id] = param - spec['script_parameters']['cwl:tool'] = job_params['cwl:tool'] - return spec - - def save(self): - job_spec = self.pipeline_component_spec() - response = self.runner.api.pipeline_templates().create(body={ - "components": { - self.job.name: job_spec, - }, - "name": self.job.name, - "owner_uuid": self.runner.project_uuid, - }, ensure_unique_name=True).execute(num_retries=self.runner.num_retries) - self.uuid = response["uuid"] - logger.info("Created template %s", self.uuid) - - -class ArvPathMapper(cwltool.pathmapper.PathMapper): - """Convert container-local paths to and from Keep collection ids.""" - - def __init__(self, arvrunner, referenced_files, input_basedir, - collection_pattern, file_pattern, name=None, **kwargs): - self._pathmap = arvrunner.get_uploaded() - uploadfiles = set() - - pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+') - - for src in referenced_files: - if isinstance(src, basestring) and pdh_path.match(src): - self._pathmap[src] = (src, collection_pattern % src[5:]) - if "#" in src: - src = src[:src.index("#")] - if src not in self._pathmap: - ab = cwltool.pathmapper.abspath(src, input_basedir) - st = arvados.commands.run.statfile("", ab, fnPattern=file_pattern) - if kwargs.get("conformance_test"): - self._pathmap[src] = (src, ab) - elif isinstance(st, arvados.commands.run.UploadFile): - uploadfiles.add((src, ab, st)) - elif isinstance(st, arvados.commands.run.ArvFile): - self._pathmap[src] = (ab, st.fn) - else: - raise cwltool.workflow.WorkflowException("Input file path '%s' is invalid" % st) - - if uploadfiles: - arvados.commands.run.uploadfiles([u[2] for u in uploadfiles], - arvrunner.api, - dry_run=kwargs.get("dry_run"), - num_retries=3, - fnPattern=file_pattern, - name=name, - project=arvrunner.project_uuid) - - for src, ab, st in uploadfiles: - arvrunner.add_uploaded(src, (ab, st.fn)) - self._pathmap[src] = (ab, st.fn) - - self.keepdir = None - - def reversemap(self, target): - if target.startswith("keep:"): - return (target, target) - elif self.keepdir and target.startswith(self.keepdir): - return (target, "keep:" + target[len(self.keepdir)+1:]) - else: - return super(ArvPathMapper, self).reversemap(target) - - -class ArvadosCommandTool(CommandLineTool): - """Wrap cwltool CommandLineTool to override selected methods.""" - - def __init__(self, arvrunner, toolpath_object, **kwargs): - super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs) - self.arvrunner = arvrunner - - def makeJobRunner(self): - return ArvadosJob(self.arvrunner) - - def makePathMapper(self, reffiles, **kwargs): - return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"], - "$(task.keep)/%s", - "$(task.keep)/%s/%s", - **kwargs) - +arvados.log_handler.setFormatter(logging.Formatter( + '%(asctime)s %(name)s %(levelname)s: %(message)s', + '%Y-%m-%d %H:%M:%S')) class ArvCwlRunner(object): - """Execute a CWL tool or workflow, submit crunch jobs, wait for them to - complete, and report output.""" + """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): + def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None, num_retries=4): self.api = api_client - self.jobs = {} + self.processes = {} self.lock = threading.Lock() self.cond = threading.Condition(self.lock) 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 + self.pipeline = None + self.final_output_collection = None + 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 + + 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) - def arvMakeTool(self, toolpath_object, **kwargs): + 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 + (work_api == api or work_api is None)): + self.work_api = api + break + except KeyError: + pass + + if not self.work_api: + if work_api is None: + raise Exception("No supported APIs") + else: + raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api)) + + 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, + overrides=kwargs.get("override_tools")) + 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": + return ArvadosWorkflow(self, toolpath_object, **kwargs) else: return cwltool.workflow.defaultMakeTool(toolpath_object, **kwargs) def output_callback(self, out, processStatus): if processStatus == "success": - logger.info("Overall job status is %s", processStatus) + 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 job status is %s", processStatus) + 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 on_message(self, event): if "object_uuid" in event: - if event["object_uuid"] in self.jobs and event["event_type"] == "update": - if event["properties"]["new_attributes"]["state"] == "Running" and self.jobs[event["object_uuid"]].running is False: + 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: - j = self.jobs[uuid] - logger.info("Job %s (%s) is Running", j.name, uuid) + j = self.processes[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"): + elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"): uuid = event["object_uuid"] try: self.cond.acquire() - j = self.jobs[uuid] - logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"]) - j.done(event["properties"]["new_attributes"]) + j = self.processes[uuid] + logger.info("%s %s is %s", self.label(j), 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() + 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: + while True: + self.stop_polling.wait(15) + if self.stop_polling.is_set(): + break + with self.lock: + keys = self.processes.keys() + if not keys: + continue + + if self.work_api == "containers": + table = self.poll_api.container_requests() + elif self.work_api == "jobs": + table = self.poll_api.jobs() + + try: + 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) + continue + + for p in proc_states["items"]: + self.on_message({ + "object_uuid": p["uuid"], + "event_type": "update", + "properties": { + "new_attributes": p + } + }) + 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() + finally: + self.stop_polling.set() + def get_uploaded(self): return self.uploaded.copy() def add_uploaded(self, src, pair): self.uploaded[src] = pair - def arvExecutor(self, tool, job_order, **kwargs): + 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 SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported") + if obj.get("class") == "DockerRequirement": + if obj.get("dockerOutputDirectory"): + # TODO: can be supported by containers API, but not jobs API. + raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError( + "Option 'dockerOutputDirectory' of DockerRequirement not supported.") + for v in obj.itervalues(): + self.check_features(v) + elif isinstance(obj, list): + for i,v in enumerate(obj): + with SourceLine(obj, i, UnsupportedRequirement): + self.check_features(v) + + def make_output_collection(self, name, 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 ("basename", "listing", "contents"): + 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, 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": + try: + current = self.api.containers().current().execute(num_retries=self.num_retries) + except ApiError as e: + # Status code 404 just means we're not running in a container. + if e.resp.status != 404: + logger.info("Getting current container: %s", e) + 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, **kwargs): self.debug = kwargs.get("debug") - if kwargs.get("quiet"): - logger.setLevel(logging.WARN) - logging.getLogger('arvados.arv-run').setLevel(logging.WARN) + tool.visit(self.check_features) - useruuid = self.api.users().current().execute()["uuid"] - self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid + self.project_uuid = kwargs.get("project_uuid") self.pipeline = None + make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, + collection_cache=self.collection_cache) + self.fs_access = make_fs_access(kwargs["basedir"]) + + + 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. + override_tools = {} + upload_workflow_deps(self, tool, override_tools) + + # Reload tool object which may have been updated by + # upload_workflow_deps + 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, + override_tools=override_tools) + + # 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["name"]) + 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=kwargs.get("submit_runner_ram"), + name=kwargs["name"]), + "success") - if kwargs.get("create_template"): - tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse")) - tmpl.save() - # cwltool.main will write our return value to stdout. - return tmpl.uuid + self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") + kwargs["make_fs_access"] = make_fs_access + kwargs["enable_reuse"] = kwargs.get("enable_reuse") + kwargs["use_container"] = True + kwargs["tmpdir_prefix"] = "tmp" + kwargs["compute_checksum"] = kwargs.get("compute_checksum") + + if self.work_api == "containers": + kwargs["outdir"] = "/var/spool/cwl" + kwargs["docker_outdir"] = "/var/spool/cwl" + kwargs["tmpdir"] = "/tmp" + kwargs["docker_tmpdir"] = "/tmp" + elif self.work_api == "jobs": + kwargs["outdir"] = "$(task.outdir)" + kwargs["docker_outdir"] = "$(task.outdir)" + kwargs["tmpdir"] = "$(task.tmpdir)" + + runnerjob = None if kwargs.get("submit"): - runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse")) - - if not kwargs.get("submit") and "cwl_runner_job" not in kwargs: + # Submit a runner job to run the workflow for us. + if self.work_api == "containers": + 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"), + on_error=kwargs.get("on_error"), + submit_runner_image=kwargs.get("submit_runner_image"), + intermediate_output_ttl=kwargs.get("intermediate_output_ttl")) + 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")) + 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={ "owner_uuid": self.project_uuid, - "name": shortname(tool.tool["id"]), + "name": kwargs["name"] if kwargs.get("name") else shortname(tool.tool["id"]), "components": {}, "state": "RunningOnClient"}).execute(num_retries=self.num_retries) logger.info("Pipeline instance %s", self.pipeline["uuid"]) - if kwargs.get("submit") and not kwargs.get("wait"): - runnerjob.run() - return runnerjob.uuid + if runnerjob and not kwargs.get("wait"): + runnerjob.run(wait=kwargs.get("wait")) + return (runnerjob.uuid, "success") - events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message) + self.poll_api = arvados.api('v1') + self.polling_thread = threading.Thread(target=self.poll_states) + self.polling_thread.start() - self.debug = kwargs.get("debug") - self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") - self.fs_access = CollectionFsAccess(kwargs["basedir"]) - - kwargs["fs_access"] = self.fs_access - kwargs["enable_reuse"] = kwargs.get("enable_reuse") + if runnerjob: + jobiter = iter((runnerjob,)) + else: + if "cwl_runner_job" in kwargs: + self.uuid = kwargs.get("cwl_runner_job").get('uuid') + jobiter = tool.job(job_order, + self.output_callback, + **kwargs) - kwargs["outdir"] = "$(task.outdir)" - kwargs["tmpdir"] = "$(task.tmpdir)" + try: + self.cond.acquire() + # Will continue to hold the lock for the duration of this code + # except when in cond.wait(), at which point on_message can update + # job state and process output callbacks. - if kwargs.get("conformance_test"): - return cwltool.main.single_job_executor(tool, job_order, **kwargs) - else: - if kwargs.get("submit"): - jobiter = iter((runnerjob,)) - else: - if "cwl_runner_job" in kwargs: - self.uuid = kwargs.get("cwl_runner_job").get('uuid') - jobiter = tool.job(job_order, - self.output_callback, - docker_outdir="$(task.outdir)", - **kwargs) + loopperf = Perf(metrics, "jobiter") + loopperf.__enter__() + for runnable in jobiter: + loopperf.__exit__() - 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. + if self.stop_polling.is_set(): + break - for runnable in jobiter: - if runnable: + if runnable: + with Perf(metrics, "run"): runnable.run(**kwargs) + else: + if self.processes: + self.cond.wait(1) else: - if self.jobs: - self.cond.wait(1) - else: - logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.") - break + logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.") + break + loopperf.__enter__() + loopperf.__exit__() - while self.jobs: - self.cond.wait(1) + while self.processes: + self.cond.wait(1) - events.close() - except: - if sys.exc_info()[0] is KeyboardInterrupt: - logger.error("Interrupted, marking pipeline as failed") - else: - logger.error("Caught unhandled exception, marking pipeline as failed. Error was: %s", sys.exc_info()[0], 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) - finally: - self.cond.release() + except UnsupportedRequirement: + raise + except: + if sys.exc_info()[0] is KeyboardInterrupt: + logger.error("Interrupted, marking pipeline as failed") + else: + logger.error("Execution failed: %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.cond.release() + self.stop_polling.set() + self.polling_thread.join() - if self.final_output is None: - raise cwltool.workflow.WorkflowException("Workflow did not return a result.") + 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 kwargs.get("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 = "" + 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 kwargs.get("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) - return self.final_output def versionstring(): """Print version string of key packages for provenance and debugging.""" @@ -763,14 +554,14 @@ def versionstring(): arvpkg = pkg_resources.require("arvados-python-client") cwlpkg = pkg_resources.require("cwltool") - return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version, + return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version, "arvados-python-client", arvpkg[0].version, "cwltool", cwlpkg[0].version) + def arg_parser(): # type: () -> argparse.ArgumentParser parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language') - parser.add_argument("--conformance-test", action="store_true") parser.add_argument("--basedir", type=str, help="Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).") parser.add_argument("--outdir", type=str, default=os.path.abspath('.'), @@ -780,24 +571,33 @@ 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="store_true", help="Print version and exit") + 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") exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.") exgroup.add_argument("--debug", action="store_true", help="Print even more logging") + parser.add_argument("--metrics", action="store_true", help="Print timing metrics") + parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool") 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, help="Project that will own the workflow jobs, if not provided, will go to home project.") + 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) + parser.add_argument("--output-tags", type=str, help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None) parser.add_argument("--ignore-docker-for-reuse", action="store_true", help="Ignore Docker image version when deciding whether to reuse past jobs.", default=False) @@ -807,7 +607,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser default=True, dest="submit") exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).", default=True, dest="submit") - exgroup.add_argument("--create-template", action="store_true", help="Create an Arvados pipeline template.") + exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.", + dest="create_workflow") + exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.") + exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.") exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.", @@ -815,31 +618,156 @@ 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") - parser.add_argument("workflow", type=str, nargs="?", default=None) - parser.add_argument("job_order", nargs=argparse.REMAINDER) + 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", + 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", + dest="compute_checksum") + + parser.add_argument("--submit-runner-ram", type=int, + 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("--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) + + 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, nargs="?", 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 main(args, stdout, stderr, api_client=None): +def add_arv_hints(): + cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*") + cwltool.draft2tool.ACCEPTLIST_RE = cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE + res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml') + use_custom_schema("v1.0", "http://arvados.org/cwl", res.read()) + res.close() + 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() job_order_object = None arvargs = parser.parse_args(args) - if arvargs.create_template and not arvargs.job_order: + + if arvargs.version: + print versionstring() + return + + if arvargs.update_workflow: + if arvargs.update_workflow.find('-7fd4e-') == 5: + want_api = 'containers' + elif arvargs.update_workflow.find('-p5p6p-') == 5: + want_api = 'jobs' + else: + want_api = None + if want_api and arvargs.work_api and want_api != arvargs.work_api: + logger.error('--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'.format( + arvargs.update_workflow, want_api, arvargs.work_api)) + return 1 + arvargs.work_api = want_api + + if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order: job_order_object = ({}, "") + add_arv_hints() + try: if api_client is None: api_client=arvados.api('v1', model=OrderedJsonModel()) - runner = ArvCwlRunner(api_client) + 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.validate = None + arvargs.print_supported_versions = False + + make_fs_access = partial(CollectionFsAccess, + collection_cache=runner.collection_cache) + return cwltool.main.main(args=arvargs, stdout=stdout, stderr=stderr, - executor=runner.arvExecutor, - makeTool=runner.arvMakeTool, + executor=runner.arv_executor, + makeTool=runner.arv_make_tool, versionfunc=versionstring, - job_order_object=job_order_object) + job_order_object=job_order_object, + 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)