X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/efb3422f119be36e133ffbd14519c5d6c74addc8..31d31c010bb6b5170e3962fdd50c6d393cfe6076:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 25bddc002f..3c7de77ebf 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -11,13 +11,16 @@ import threading 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 import arvados import arvados.config @@ -26,17 +29,17 @@ 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, CollectionFetcher, collectionResolver +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.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 @@ -44,6 +47,9 @@ 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')) class ArvCwlRunner(object): """Execute a CWL tool or workflow, submit work (using either jobs or @@ -74,6 +80,8 @@ class ArvCwlRunner(object): 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: @@ -96,7 +104,8 @@ class ArvCwlRunner(object): kwargs["work_api"] = self.work_api kwargs["fetcher_constructor"] = partial(CollectionFetcher, api_client=self.api, - keep_client=self.keep_client) + fs_access=CollectionFsAccess("", collection_cache=self.collection_cache), + 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": @@ -125,7 +134,7 @@ class ArvCwlRunner(object): uuid = event["object_uuid"] with self.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"): @@ -133,14 +142,16 @@ class ArvCwlRunner(object): try: self.cond.acquire() 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"]) + 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. @@ -191,15 +202,21 @@ class ArvCwlRunner(object): def add_uploaded(self, src, pair): self.uploaded[src] = pair - def check_writable(self, obj): + def check_features(self, obj): if isinstance(obj, dict): if obj.get("writable"): - raise UnsupportedRequirement("InitialWorkDir feature 'writable: true' not supported") + 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_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): + self.check_features(v) def make_output_collection(self, name, tagsString, outputObj): outputObj = copy.deepcopy(outputObj) @@ -211,13 +228,12 @@ 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": @@ -231,20 +247,13 @@ 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) @@ -295,6 +304,10 @@ 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: @@ -308,32 +321,52 @@ 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"]) + 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. + upload_workflow_deps(self, tool) + + # 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) + + # 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"]) 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"]), + "success") self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") @@ -341,12 +374,8 @@ class ArvCwlRunner(object): 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 not kwargs["name"]: - del kwargs["name"] - if self.work_api == "containers": kwargs["outdir"] = "/var/spool/cwl" kwargs["docker_outdir"] = "/var/spool/cwl" @@ -357,26 +386,39 @@ class ArvCwlRunner(object): kwargs["docker_outdir"] = "$(task.outdir)" kwargs["tmpdir"] = "$(task.tmpdir)" - upload_instance(self, shortname(tool.tool["id"]), tool, job_order) - 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": kwargs["runnerjob"] = tool.tool["id"] + upload_dependencies(self, + kwargs["name"], + tool.doc_loader, + tool.tool, + tool.tool["id"], + False) 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")) + 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")) + 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")) - if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers": + if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and self.work_api == "jobs": # Create pipeline for local run self.pipeline = self.api.pipeline_instances().create( body={ @@ -388,7 +430,7 @@ 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) @@ -466,14 +508,11 @@ 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 + return (self.final_output, self.final_status) def versionstring(): @@ -542,6 +581,12 @@ 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'.") @@ -554,26 +599,37 @@ 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("--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("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 add_arv_hints(): - cache = {} + 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') - 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" + ]) def main(args, stdout, stderr, api_client=None, keep_client=None): parser = arg_parser() @@ -617,18 +673,31 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): 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 + + make_fs_access = partial(CollectionFsAccess, + collection_cache=runner.collection_cache) return cwltool.main.main(args=arvargs, stdout=stdout, @@ -637,10 +706,11 @@ 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, - keep_client=keep_client), + make_fs_access=make_fs_access, fetcher_constructor=partial(CollectionFetcher, api_client=api_client, - keep_client=keep_client), - resolver=partial(collectionResolver, 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)