X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4b037a38dbe848a77224dd05dd035736b5d0c0c1..0e1522f8e0cbe5d1626a7f66dc4c28b7b1bf0efc:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 7a951e93ca..9cabedf7f7 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -49,7 +49,7 @@ class ArvCwlRunner(object): """ - def __init__(self, api_client, work_api=None, keep_client=None, output_name=None): + def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None): self.api = api_client self.processes = {} self.lock = threading.Lock() @@ -64,6 +64,7 @@ class ArvCwlRunner(object): self.pipeline = None self.final_output_collection = None self.output_name = output_name + self.output_tags = output_tags self.project_uuid = None if keep_client is not None: @@ -138,34 +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 - - 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: + 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() + + 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() @@ -183,7 +193,7 @@ class ArvCwlRunner(object): for v in obj: self.check_writable(v) - def make_output_collection(self, name, outputObj): + def make_output_collection(self, name, tagsString, outputObj): outputObj = copy.deepcopy(outputObj) files = [] @@ -201,14 +211,28 @@ class ArvCwlRunner(object): srccollections = {} 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:] if srccollection not in srccollections: - srccollections[srccollection] = arvados.collection.CollectionReader( - srccollection, - api_client=self.api, - keep_client=self.keep_client, - num_retries=self.num_retries) + 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: srcpath = "/".join(sp[1:]) if len(sp) > 1 else "." @@ -218,7 +242,7 @@ class ArvCwlRunner(object): def rewrite(fileobj): fileobj["location"] = generatemapper.mapper(fileobj["location"]).target - for k in ("basename", "size", "listing"): + for k in ("basename", "listing", "contents"): if k in fileobj: del fileobj[k] @@ -234,7 +258,20 @@ class ArvCwlRunner(object): final.api_response()["name"], final.manifest_locator()) - self.final_output_collection = final + 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": @@ -259,22 +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") @@ -305,9 +346,9 @@ class ArvCwlRunner(object): self.output_callback, **kwargs).next() else: - runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name) + runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, self.output_tags) else: - runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name) + runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, self.output_tags) if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers": # Create pipeline for local run @@ -346,6 +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) @@ -367,7 +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) @@ -390,7 +435,9 @@ class ArvCwlRunner(object): else: if self.output_name is None: self.output_name = "Output of %s" % (shortname(tool.tool["id"])) - self.make_output_collection(self.output_name, self.final_output) + 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 self.final_status != "success": @@ -448,6 +495,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser 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) @@ -457,9 +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.", @@ -469,7 +518,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser parser.add_argument("--api", type=str, default=None, dest="work_api", - help="Select work submission API, one of 'jobs' or 'containers'.") + help="Select work submission API, one of 'jobs' or 'containers'. 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", @@ -497,7 +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() @@ -505,7 +568,7 @@ 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) + runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name, output_tags=arvargs.output_tags) except Exception as e: logger.error(e) return 1 @@ -523,6 +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,