X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/95f399d4fca0c4e36c6da4e98e4092106ebfdc6d..3af6db5dc4e2f08b2ebb49a82109c4325ad7fcc4:/sdk/cwl/arvados_cwl/arvjob.py diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py index 0818d5d62b..8a62204f8f 100644 --- a/sdk/cwl/arvados_cwl/arvjob.py +++ b/sdk/cwl/arvados_cwl/arvjob.py @@ -2,6 +2,7 @@ import logging import re import copy import json +import time from cwltool.process import get_feature, shortname from cwltool.errors import WorkflowException @@ -12,17 +13,16 @@ from cwltool.builder import Builder import arvados.collection from .arvdocker import arv_docker_get_image -from .runner import Runner +from .runner import Runner, arvados_jobs_image from .pathmapper import InitialWorkDirPathMapper from .perf import Perf from . import done +from ._version import __version__ logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') -tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)") -outdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)") -keepre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)") +crunchrunner_re = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)") class ArvadosJob(object): """Submit and manage a Crunch job for executing a CWL CommandLineTool.""" @@ -40,7 +40,9 @@ class ArvadosJob(object): with Perf(metrics, "generatefiles %s" % self.name): if self.generatefiles["listing"]: - vwd = arvados.collection.Collection() + vwd = arvados.collection.Collection(api_client=self.arvrunner.api, + keep_client=self.arvrunner.keep_client, + num_retries=self.arvrunner.num_retries) script_parameters["task.vwd"] = {} generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "", separateDirs=False) @@ -83,9 +85,11 @@ class ArvadosJob(object): with Perf(metrics, "arv_docker_get_image %s" % self.name): (docker_req, docker_is_req) = get_feature(self, "DockerRequirement") if docker_req and kwargs.get("use_container") is not False: + if docker_req.get("dockerOutputDirectory"): + raise UnsupportedRequirement("Option 'dockerOutputDirectory' of DockerRequirement not supported.") runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid) else: - runtime_constraints["docker_image"] = "arvados/jobs" + runtime_constraints["docker_image"] = arvados_jobs_image(self.arvrunner) resources = self.builder.resources if resources is not None: @@ -95,7 +99,13 @@ class ArvadosJob(object): runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints") if runtime_req: - runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"] + if "keep_cache" in runtime_req: + runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"] + if "outputDirType" in runtime_req: + if runtime_req["outputDirType"] == "local_output_dir": + script_parameters["task.keepTmpOutput"] = False + elif runtime_req["outputDirType"] == "keep_output_dir": + script_parameters["task.keepTmpOutput"] = True filters = [["repository", "=", "arvados"], ["script", "=", "crunchrunner"], @@ -169,8 +179,12 @@ class ArvadosJob(object): try: if record["output"]: with Perf(metrics, "inspect log %s" % self.name): - logc = arvados.collection.Collection(record["log"]) + logc = arvados.collection.CollectionReader(record["log"], + api_client=self.arvrunner.api, + keep_client=self.arvrunner.keep_client, + num_retries=self.arvrunner.num_retries) log = logc.open(logc.keys()[0]) + dirs = {} tmpdir = None outdir = None keepdir = None @@ -182,19 +196,13 @@ class ArvadosJob(object): # the job restarts on a different node these values # will different runs, and we need to know about the # final run that actually produced output. - - g = tmpdirre.match(l) - if g: - tmpdir = g.group(1) - g = outdirre.match(l) - if g: - outdir = g.group(1) - g = keepre.match(l) + g = crunchrunner_re.match(l) if g: - keepdir = g.group(1) + dirs[g.group(1)] = g.group(2) with Perf(metrics, "output collection %s" % self.name): - outputs = done.done(self, record, tmpdir, outdir, keepdir) + outputs = done.done(self, record, dirs["tmpdir"], + dirs["outdir"], dirs["keep"]) except WorkflowException as e: logger.error("Error while collecting job outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False)) processStatus = "permanentFail" @@ -222,41 +230,62 @@ class RunnerJob(Runner): workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs) + # Need to filter this out, gets added by cwltool when providing + # parameters on the command line, and arv-run-pipeline-instance doesn't + # like it. + if "job_order" in self.job_order: + del self.job_order["job_order"] + self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"]).target[5:] + + if self.output_name: + self.job_order["arv:output_name"] = self.output_name + + self.job_order["arv:enable_reuse"] = self.enable_reuse + return { "script": "cwl-runner", - "script_version": "master", + "script_version": __version__, "repository": "arvados", "script_parameters": self.job_order, "runtime_constraints": { - "docker_image": "arvados/jobs" + "docker_image": arvados_jobs_image(self.arvrunner) } } def run(self, *args, **kwargs): job_spec = self.arvados_job_spec(*args, **kwargs) + job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid) - response = self.arvrunner.api.jobs().create( + job = self.arvrunner.api.jobs().create( body=job_spec, find_or_create=self.enable_reuse ).execute(num_retries=self.arvrunner.num_retries) - self.uuid = response["uuid"] + for k,v in job_spec["script_parameters"].items(): + if v is False or v is None or isinstance(v, dict): + job_spec["script_parameters"][k] = {"value": v} + + del job_spec["owner_uuid"] + job_spec["job"] = job + self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create( + body={ + "owner_uuid": self.arvrunner.project_uuid, + "name": shortname(self.tool.tool["id"]), + "components": {"cwl-runner": job_spec }, + "state": "RunningOnServer"}).execute(num_retries=self.arvrunner.num_retries) + logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"]) + + if kwargs.get("wait") is False: + self.uuid = self.arvrunner.pipeline["uuid"] + return + + self.uuid = job["uuid"] self.arvrunner.processes[self.uuid] = self - logger.info("Submitted job %s", response["uuid"]) - - if kwargs.get("submit"): - self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create( - body={ - "owner_uuid": self.arvrunner.project_uuid, - "name": shortname(self.tool.tool["id"]), - "components": {"cwl-runner": {"job": {"uuid": self.uuid, "state": response["state"]} } }, - "state": "RunningOnClient"}).execute(num_retries=self.arvrunner.num_retries) - - if response["state"] in ("Complete", "Failed", "Cancelled"): - self.done(response) + if job["state"] in ("Complete", "Failed", "Cancelled"): + self.done(job) class RunnerTemplate(object): @@ -278,7 +307,8 @@ class RunnerTemplate(object): runner=runner, tool=tool, job_order=job_order, - enable_reuse=enable_reuse) + enable_reuse=enable_reuse, + output_name=None) def pipeline_component_spec(self): """Return a component that Workbench and a-r-p-i will understand. @@ -286,6 +316,7 @@ class RunnerTemplate(object): Specifically, translate CWL input specs to Arvados pipeline format, like {"dataclass":"File","value":"xyz"}. """ + spec = self.job.arvados_job_spec() # Most of the component spec is exactly the same as the job