X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/91b824a77fe19242de50e838f9f8c4fb30907fa3..60d986b8908487c086eb4e402ac69669cb26108b:/sdk/cwl/arvados_cwl/__init__.py?ds=sidebyside diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index d4af0f9129..02eca644d3 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -28,7 +28,7 @@ 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 from .arvtool import ArvadosCommandTool from .arvworkflow import ArvadosWorkflow, upload_workflow from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver @@ -46,6 +46,9 @@ 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 @@ -127,7 +130,7 @@ 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"): @@ -135,14 +138,16 @@ 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. @@ -172,7 +177,7 @@ class ArvCwlRunner(object): for p in proc_states["items"]: self.on_message({ - "object_uuid": p["uuid"], + "object_uuid": p["uuid"], "event_type": "update", "properties": { "new_attributes": p @@ -329,23 +334,44 @@ class ArvCwlRunner(object): keep_client=self.keep_client) 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") @@ -353,12 +379,8 @@ 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" @@ -369,26 +391,39 @@ 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={ @@ -400,7 +435,7 @@ 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) @@ -478,14 +513,11 @@ 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)) adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access)) - return self.final_output + return (self.final_output, self.final_status) def versionstring(): @@ -554,6 +586,12 @@ 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'.") @@ -566,10 +604,18 @@ 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.") @@ -638,6 +684,13 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): 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 @@ -656,4 +709,5 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): fetcher_constructor=partial(CollectionFetcher, api_client=api_client, keep_client=keep_client), - resolver=partial(collectionResolver, api_client)) + resolver=partial(collectionResolver, api_client), + logger_handler=arvados.log_handler)