import re
import copy
import json
+import time
from cwltool.process import get_feature, shortname
from cwltool.errors import WorkflowException
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."""
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:
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):
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
# 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:
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
+
+ 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),
+ "min_ram_mb_per_node": self.submit_runner_ram
}
}
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):
'string': 'text',
}
- def __init__(self, runner, tool, job_order, enable_reuse):
+ def __init__(self, runner, tool, job_order, enable_reuse, uuid, submit_runner_ram=0):
self.runner = runner
self.tool = tool
self.job = RunnerJob(
tool=tool,
job_order=job_order,
enable_reuse=enable_reuse,
- output_name=None)
+ output_name=None,
+ output_tags=None,
+ submit_runner_ram=submit_runner_ram)
+ self.uuid = uuid
def pipeline_component_spec(self):
"""Return a component that Workbench and a-r-p-i will understand.
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
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)
projects / arvados.git / blobdiff