X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1a87c77a5cfe200921a9d09e995383bc675e7370..224f384d411bb1b4cccc7165c55bb64fd5c695ad:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index b11ca54817..5262cb4971 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -15,6 +15,7 @@ import pkg_resources # part of setuptools from cwltool.errors import WorkflowException import cwltool.main import cwltool.workflow +import schema_salad import arvados import arvados.config @@ -22,8 +23,10 @@ import arvados.config from .arvcontainer import ArvadosContainer, RunnerContainer from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate from .arvtool import ArvadosCommandTool +from .arvworkflow import ArvadosWorkflow, upload_workflow from .fsaccess import CollectionFsAccess -from .arvworkflow import make_workflow +from .perf import Perf +from cwltool.pack import pack from cwltool.process import shortname, UnsupportedRequirement from cwltool.pathmapper import adjustFileObjs @@ -31,8 +34,10 @@ 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) + class ArvCwlRunner(object): """Execute a CWL tool or workflow, submit work (using either jobs or containers API), wait for them to complete, and report output. @@ -52,6 +57,7 @@ class ArvCwlRunner(object): self.work_api = work_api self.stop_polling = threading.Event() self.poll_api = None + self.pipeline = None if self.work_api is None: # todo: autodetect API to use. @@ -60,10 +66,12 @@ class ArvCwlRunner(object): if self.work_api not in ("containers", "jobs"): raise Exception("Unsupported API '%s'" % self.work_api) - def arvMakeTool(self, toolpath_object, **kwargs): + def arv_make_tool(self, toolpath_object, **kwargs): + kwargs["work_api"] = self.work_api if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool": - kwargs["work_api"] = self.work_api 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) @@ -97,7 +105,8 @@ class ArvCwlRunner(object): self.cond.acquire() j = self.processes[uuid] logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"]) - j.done(event["properties"]["new_attributes"]) + with Perf(metrics, "done %s" % j.name): + j.done(event["properties"]["new_attributes"]) self.cond.notify() finally: self.cond.release() @@ -153,15 +162,11 @@ class ArvCwlRunner(object): for v in obj: self.check_writable(v) - def arvExecutor(self, tool, job_order, **kwargs): + def arv_executor(self, tool, job_order, **kwargs): self.debug = kwargs.get("debug") tool.visit(self.check_writable) - if kwargs.get("quiet"): - logger.setLevel(logging.WARN) - logging.getLogger('arvados.arv-run').setLevel(logging.WARN) - useruuid = self.api.users().current().execute()["uuid"] self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid self.pipeline = None @@ -175,9 +180,8 @@ class ArvCwlRunner(object): return tmpl.uuid if kwargs.get("create_workflow") or kwargs.get("update_workflow"): - return make_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow")) + return upload_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow")) - self.debug = kwargs.get("debug") self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") kwargs["make_fs_access"] = make_fs_access @@ -242,15 +246,21 @@ class ArvCwlRunner(object): # except when in cond.wait(), at which point on_message can update # job state and process output callbacks. + loopperf = Perf(metrics, "jobiter") + loopperf.__enter__() for runnable in jobiter: + loopperf.__exit__() if runnable: - runnable.run(**kwargs) + with Perf(metrics, "run"): + runnable.run(**kwargs) else: if self.processes: self.cond.wait(1) else: logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.") break + loopperf.__enter__() + loopperf.__exit__() while self.processes: self.cond.wait(1) @@ -319,6 +329,8 @@ def arg_parser(): # type: () -> argparse.ArgumentParser 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() @@ -329,7 +341,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser default=True, dest="enable_reuse", help="") - 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("--ignore-docker-for-reuse", action="store_true", help="Ignore Docker image version when deciding whether to reuse past jobs.", default=False) @@ -341,7 +353,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser 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, help="Update Arvados workflow.") + exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update existing Arvados workflow with uuid.") exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.", @@ -362,6 +374,16 @@ def arg_parser(): # type: () -> argparse.ArgumentParser return parser +def add_arv_hints(): + cache = {} + res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml') + cache["http://arvados.org/cwl"] = res.read() + res.close() + _, 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, "")) def main(args, stdout, stderr, api_client=None): parser = arg_parser() @@ -371,6 +393,8 @@ def main(args, stdout, stderr, api_client=None): if (arvargs.create_template or 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()) @@ -379,14 +403,25 @@ def main(args, stdout, stderr, api_client=None): logger.error(e) return 1 + if arvargs.debug: + logger.setLevel(logging.DEBUG) + + if arvargs.quiet: + logger.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) + arvargs.conformance_test = None arvargs.use_container = True 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, make_fs_access=partial(CollectionFsAccess, api_client=api_client))