X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/cb781d9b5e61c5494d29d53a0a12c678c839eecd..e2598332f9ecd40ab0dfd025bd1e5eba02ad8673:/sdk/cwl/arvados_cwl/arvjob.py diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py index 5250410086..1afb9afc0e 100644 --- a/sdk/cwl/arvados_cwl/arvjob.py +++ b/sdk/cwl/arvados_cwl/arvjob.py @@ -13,17 +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.""" @@ -86,9 +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: @@ -138,7 +139,7 @@ class ArvadosJob(object): with Perf(metrics, "done %s" % self.name): self.done(response) except Exception as e: - logger.error("Got error %s" % str(e)) + logger.exception("Job %s error" % (self.name)) self.output_callback({}, "permanentFail") def update_pipeline_component(self, record): @@ -183,6 +184,7 @@ class ArvadosJob(object): 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 @@ -194,27 +196,26 @@ 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) + g = crunchrunner_re.match(l) if g: - outdir = g.group(1) - g = keepre.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)) + logger.error("Error while collecting output for job %s:\n%s", self.name, e, exc_info=(e if self.arvrunner.debug else False)) processStatus = "permanentFail" - outputs = None except Exception as e: - logger.exception("Got unknown exception while collecting job outputs:") + logger.exception("Got unknown exception while collecting output for job %s:", self.name) + processStatus = "permanentFail" + + # Note: Currently, on error output_callback is expecting an empty dict, + # anything else will fail. + if not isinstance(outputs, dict): + logger.error("Unexpected output type %s '%s'", type(outputs), outputs) + outputs = {} processStatus = "permanentFail" - outputs = None self.output_callback(outputs, processStatus) finally: @@ -241,21 +242,41 @@ class RunnerJob(Runner): 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 + + if self.output_tags: + self.job_order["arv:output_tags"] = self.output_tags + + 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) + + job = self.arvrunner.api.jobs().create( + body=job_spec, + find_or_create=self.enable_reuse + ).execute(num_retries=self.arvrunner.num_retries) + + 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, @@ -268,14 +289,6 @@ class RunnerJob(Runner): self.uuid = self.arvrunner.pipeline["uuid"] return - job = None - while not job: - time.sleep(2) - self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().get( - uuid=self.arvrunner.pipeline["uuid"]).execute( - num_retries=self.arvrunner.num_retries) - job = self.arvrunner.pipeline["components"]["cwl-runner"].get("job") - self.uuid = job["uuid"] self.arvrunner.processes[self.uuid] = self @@ -295,7 +308,7 @@ class RunnerTemplate(object): 'string': 'text', } - def __init__(self, runner, tool, job_order, enable_reuse): + def __init__(self, runner, tool, job_order, enable_reuse, uuid): self.runner = runner self.tool = tool self.job = RunnerJob( @@ -303,7 +316,9 @@ class RunnerTemplate(object): tool=tool, job_order=job_order, enable_reuse=enable_reuse, - output_name=None) + output_name=None, + output_tags=None) + self.uuid = uuid def pipeline_component_spec(self): """Return a component that Workbench and a-r-p-i will understand. @@ -311,6 +326,7 @@ 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 @@ -365,13 +381,21 @@ class RunnerTemplate(object): return spec def save(self): - job_spec = self.pipeline_component_spec() - response = self.runner.api.pipeline_templates().create(body={ + body = { "components": { - self.job.name: job_spec, + self.job.name: self.pipeline_component_spec(), }, "name": self.job.name, - "owner_uuid": self.runner.project_uuid, - }, ensure_unique_name=True).execute(num_retries=self.runner.num_retries) - self.uuid = response["uuid"] - logger.info("Created template %s", self.uuid) + } + if self.runner.project_uuid: + body["owner_uuid"] = self.runner.project_uuid + if self.uuid: + self.runner.api.pipeline_templates().update( + uuid=self.uuid, body=body).execute( + num_retries=self.runner.num_retries) + logger.info("Updated template %s", self.uuid) + else: + self.uuid = self.runner.api.pipeline_templates().create( + body=body, ensure_unique_name=True).execute( + num_retries=self.runner.num_retries)['uuid'] + logger.info("Created template %s", self.uuid)