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."""
}
runtime_constraints = {}
- if self.generatefiles["listing"]:
- vwd = arvados.collection.Collection()
- script_parameters["task.vwd"] = {}
- generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
- separateDirs=False)
- for f, p in generatemapper.items():
- if p.type == "CreateFile":
- with vwd.open(p.target, "w") as n:
- n.write(p.resolved.encode("utf-8"))
- vwd.save_new()
- for f, p in generatemapper.items():
- if p.type == "File":
- script_parameters["task.vwd"][p.target] = p.resolved
- if p.type == "CreateFile":
- script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
+ with Perf(metrics, "generatefiles %s" % self.name):
+ if self.generatefiles["listing"]:
+ vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
+ script_parameters["task.vwd"] = {}
+ generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
+
+ with Perf(metrics, "createfiles %s" % self.name):
+ for f, p in generatemapper.items():
+ if p.type == "CreateFile":
+ with vwd.open(p.target, "w") as n:
+ n.write(p.resolved.encode("utf-8"))
+
+ with Perf(metrics, "generatefiles.save_new %s" % self.name):
+ vwd.save_new()
+
+ for f, p in generatemapper.items():
+ if p.type == "File":
+ script_parameters["task.vwd"][p.target] = p.resolved
+ if p.type == "CreateFile":
+ script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
if self.environment:
if self.permanentFailCodes:
script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
- (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
- if docker_req and kwargs.get("use_container") is not False:
- 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"
+ 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_image(self.arvrunner)
resources = self.builder.resources
if resources is not None:
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"],
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
# 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"
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)
}
}
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):
runner=runner,
tool=tool,
job_order=job_order,
- enable_reuse=enable_reuse)
+ enable_reuse=enable_reuse,
+ output_name=None,
+ output_tags=None)
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
projects / arvados.git / blobdiff