X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c7a461e97640697e390aff96bf25126972396b19..5fc627d22b47723289251e1e1d9dc45c0e1bd49e:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 7d5590b952..a22b075ce4 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -24,14 +24,16 @@ 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, upload_workflow from .fsaccess import CollectionFsAccess from .perf import Perf from .pathmapper import FinalOutputPathMapper +from ._version import __version__ from cwltool.pack import pack -from cwltool.process import shortname, UnsupportedRequirement +from cwltool.process import shortname, UnsupportedRequirement, getListing from cwltool.pathmapper import adjustFileObjs, adjustDirObjs from cwltool.draft2tool import compute_checksums from arvados.api import OrderedJsonModel @@ -47,7 +49,7 @@ class ArvCwlRunner(object): """ - def __init__(self, api_client, work_api=None, keep_client=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() @@ -57,22 +59,32 @@ class ArvCwlRunner(object): self.uploaded = {} self.num_retries = 4 self.uuid = None - 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. - self.work_api = "jobs" - - if self.work_api not in ("containers", "jobs"): - raise Exception("Unsupported API '%s'" % self.work_api) + for api in ["jobs", "containers"]: + try: + methods = self.api._rootDesc.get('resources')[api]['methods'] + if ('httpMethod' in methods['create'] and + (work_api == api or work_api is None)): + self.work_api = api + break + except KeyError: + pass + if not self.work_api: + if work_api is None: + raise Exception("No supported APIs") + else: + raise Exception("Unsupported API '%s'" % work_api) def arv_make_tool(self, toolpath_object, **kwargs): kwargs["work_api"] = self.work_api @@ -112,7 +124,8 @@ class ArvCwlRunner(object): try: self.cond.acquire() j = self.processes[uuid] - logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"]) + 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"]) with Perf(metrics, "done %s" % j.name): j.done(event["properties"]["new_attributes"]) self.cond.notify() @@ -170,7 +183,7 @@ class ArvCwlRunner(object): for v in obj: self.check_writable(v) - def make_output_collection(self, name, outputObj): + def make_output_collection(self, name, outputObj, tagsString): outputObj = copy.deepcopy(outputObj) files = [] @@ -217,10 +230,35 @@ class ArvCwlRunner(object): final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True) - logger.info("Final output collection %s (%s)", final.portable_data_hash(), final.manifest_locator()) + logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(), + final.api_response()["name"], + final.manifest_locator()) + + 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() self.final_output_collection = final + def set_crunch_output(self): + if self.work_api == "containers": + try: + current = self.api.containers().current().execute(num_retries=self.num_retries) + self.api.containers().update(uuid=current['uuid'], + body={ + 'output': self.final_output_collection.portable_data_hash(), + }).execute(num_retries=self.num_retries) + except Exception as e: + logger.info("Setting container output: %s", e) + elif self.work_api == "jobs" and "TASK_UUID" in os.environ: + self.api.job_tasks().update(uuid=os.environ["TASK_UUID"], + body={ + 'output': self.final_output_collection.portable_data_hash(), + 'success': self.final_status == "success", + 'progress':1.0 + }).execute(num_retries=self.num_retries) + def arv_executor(self, tool, job_order, **kwargs): self.debug = kwargs.get("debug") @@ -262,6 +300,8 @@ 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": @@ -270,9 +310,9 @@ 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 @@ -285,7 +325,7 @@ 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') @@ -347,19 +387,22 @@ class ArvCwlRunner(object): if self.final_status == "UnsupportedRequirement": raise UnsupportedRequirement("Check log for details.") - if self.final_status != "success": - raise WorkflowException("Workflow failed.") - if self.final_output is None: raise WorkflowException("Workflow did not return a result.") - if kwargs.get("submit"): + if kwargs.get("submit") and isinstance(runnerjob, Runner): logger.info("Final output collection %s", runnerjob.final_output) else: - self.make_output_collection("Output of %s" % (shortname(tool.tool["id"])), - self.final_output) + 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, kwargs.get("output_tags", "")) + 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 @@ -372,7 +415,7 @@ def versionstring(): arvpkg = pkg_resources.require("arvados-python-client") cwlpkg = pkg_resources.require("cwltool") - return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version, + return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version, "arvados-python-client", arvpkg[0].version, "cwltool", cwlpkg[0].version) @@ -409,6 +452,8 @@ 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("--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) @@ -430,7 +475,7 @@ 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", @@ -466,7 +511,7 @@ 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) + 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