X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4bccbaed84c6b398f4cb4dbc7a9bc345e79d6550..15aca78766bda903480e327340d67d3d882ee69f:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index b3d47dd8d0..9cabedf7f7 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -139,34 +139,43 @@ class ArvCwlRunner(object): Runs in a separate thread. """ - 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 + 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.containers() - elif self.work_api == "jobs": - table = self.poll_api.jobs() + if self.work_api == "containers": + table = self.poll_api.containers() + 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 - } - }) + 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() @@ -287,22 +296,26 @@ class ArvCwlRunner(object): tool.visit(self.check_writable) - 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, api_client=self.api, keep_client=self.keep_client) self.fs_access = make_fs_access(kwargs["basedir"]) - 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 - - if kwargs.get("create_workflow") or kwargs.get("update_workflow"): - return upload_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow")) + existing_uuid = kwargs.get("update_workflow") + if existing_uuid or kwargs.get("create_workflow"): + if self.work_api == "jobs": + tmpl = RunnerTemplate(self, tool, job_order, + kwargs.get("enable_reuse"), + uuid=existing_uuid) + 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) self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") @@ -374,6 +387,10 @@ class ArvCwlRunner(object): loopperf.__enter__() for runnable in jobiter: loopperf.__exit__() + + if self.stop_polling.is_set(): + break + if runnable: with Perf(metrics, "run"): runnable.run(**kwargs) @@ -395,7 +412,7 @@ class ArvCwlRunner(object): 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()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) + 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) @@ -488,9 +505,10 @@ 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-workflow", action="store_true", help="Create an Arvados workflow.") - exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update existing Arvados workflow with uuid.") + 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.", @@ -528,7 +546,21 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): job_order_object = None arvargs = parser.parse_args(args) - if (arvargs.create_template or arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order: + + 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() @@ -554,6 +586,7 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): arvargs.conformance_test = None arvargs.use_container = True + arvargs.relax_path_checks = True return cwltool.main.main(args=arvargs, stdout=stdout,