X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/bc6b243539b5480493c7aa758a1272a1a42b58f1..b9d2799dfebae724dda3b3e28641116ca5daf5c7:/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 1256260598..7ebb13f1bb 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -9,40 +9,46 @@ import os import sys import threading import hashlib +import copy +import json from functools import partial 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 from .arvcontainer import ArvadosContainer, RunnerContainer from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate +from. runner import Runner, upload_instance from .arvtool import ArvadosCommandTool -from .arvworkflow import ArvadosWorkflow +from .arvworkflow import ArvadosWorkflow, upload_workflow from .fsaccess import CollectionFsAccess -from .arvworkflow import upload_workflow from .perf import Perf -from cwltool.pack import pack +from .pathmapper import FinalOutputPathMapper -from cwltool.process import shortname, UnsupportedRequirement -from cwltool.pathmapper import adjustFileObjs +from cwltool.pack import pack +from cwltool.process import shortname, UnsupportedRequirement, getListing +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs 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. """ - def __init__(self, api_client, work_api=None): + def __init__(self, api_client, work_api=None, keep_client=None, output_name=None): self.api = api_client self.processes = {} self.lock = threading.Lock() @@ -55,6 +61,15 @@ class ArvCwlRunner(object): self.work_api = work_api self.stop_polling = threading.Event() self.poll_api = None + self.pipeline = None + self.final_output_collection = None + self.output_name = output_name + self.project_uuid = None + + if keep_client is not None: + self.keep_client = keep_client + else: + self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries) if self.work_api is None: # todo: autodetect API to use. @@ -102,7 +117,7 @@ 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"]) - with Perf(logger, "done %s" % j.name): + with Perf(metrics, "done %s" % j.name): j.done(event["properties"]["new_attributes"]) self.cond.notify() finally: @@ -159,6 +174,59 @@ class ArvCwlRunner(object): for v in obj: self.check_writable(v) + def make_output_collection(self, name, outputObj): + outputObj = copy.deepcopy(outputObj) + + files = [] + def capture(fileobj): + files.append(fileobj) + + adjustDirObjs(outputObj, capture) + adjustFileObjs(outputObj, capture) + + generatemapper = FinalOutputPathMapper(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(): + 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) + reader = srccollections[srccollection] + try: + srcpath = "/".join(sp[1:]) if len(sp) > 1 else "." + final.copy(srcpath, v.target, source_collection=reader, overwrite=False) + except IOError as e: + logger.warn("While preparing output collection: %s", e) + + def rewrite(fileobj): + fileobj["location"] = generatemapper.mapper(fileobj["location"]).target + for k in ("basename", "size", "listing"): + if k in fileobj: + del fileobj[k] + + adjustDirObjs(outputObj, rewrite) + adjustFileObjs(outputObj, rewrite) + + with final.open("cwl.output.json", "w") as f: + json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': ')) + + final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True) + + logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(), + final.api_response()["name"], + final.manifest_locator()) + + self.final_output_collection = final + def arv_executor(self, tool, job_order, **kwargs): self.debug = kwargs.get("debug") @@ -167,7 +235,9 @@ class ArvCwlRunner(object): useruuid = self.api.users().current().execute()["uuid"] self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid self.pipeline = None - make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api) + 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"): @@ -198,6 +268,8 @@ 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"): if self.work_api == "containers": @@ -206,9 +278,9 @@ class ArvCwlRunner(object): self.output_callback, **kwargs).next() else: - runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse")) + runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name) else: - runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse")) + runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name) if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers": # Create pipeline for local run @@ -221,7 +293,7 @@ class ArvCwlRunner(object): logger.info("Pipeline instance %s", self.pipeline["uuid"]) if runnerjob and not kwargs.get("wait"): - runnerjob.run() + runnerjob.run(wait=kwargs.get("wait")) return runnerjob.uuid self.poll_api = arvados.api('v1') @@ -243,9 +315,12 @@ 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: - with Perf(logger, "run"): + with Perf(metrics, "run"): runnable.run(**kwargs) else: if self.processes: @@ -253,6 +328,8 @@ class ArvCwlRunner(object): 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) @@ -284,7 +361,15 @@ class ArvCwlRunner(object): if self.final_output is None: raise WorkflowException("Workflow did not return a result.") + if kwargs.get("submit") and isinstance(runnerjob, Runner): + logger.info("Final output collection %s", runnerjob.final_output) + 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 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 @@ -321,6 +406,8 @@ 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() @@ -332,6 +419,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser help="") 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("--ignore-docker-for-reuse", action="store_true", help="Ignore Docker image version when deciding whether to reuse past jobs.", default=False) @@ -364,8 +452,19 @@ def arg_parser(): # type: () -> argparse.ArgumentParser return parser - -def main(args, stdout, stderr, api_client=None): +def add_arv_hints(): + cache = {} + res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml') + cache["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] = {} + +def main(args, stdout, stderr, api_client=None, keep_client=None): parser = arg_parser() job_order_object = None @@ -373,10 +472,12 @@ 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()) - runner = ArvCwlRunner(api_client, work_api=arvargs.work_api) + runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name) except Exception as e: logger.error(e) return 1 @@ -388,6 +489,10 @@ def main(args, stdout, stderr, api_client=None): 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