from . import done
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: \$\(task\.outdir\)=(.*)")
}
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:
+ 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"
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"],
filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
try:
- with Perf(logger, "create %s" % self.name):
+ with Perf(metrics, "create %s" % self.name):
response = self.arvrunner.api.jobs().create(
body={
"owner_uuid": self.arvrunner.project_uuid,
logger.info("Job %s (%s) is %s", self.name, response["uuid"], response["state"])
if response["state"] in ("Complete", "Failed", "Cancelled"):
- with Perf(logger, "done %s" % self.name):
+ with Perf(metrics, "done %s" % self.name):
self.done(response)
except Exception as e:
logger.error("Got error %s" % str(e))
def update_pipeline_component(self, record):
if self.arvrunner.pipeline:
self.arvrunner.pipeline["components"][self.name] = {"job": record}
- with Perf(logger, "update_pipeline_component %s" % self.name):
+ with Perf(metrics, "update_pipeline_component %s" % self.name):
self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
body={
"components": self.arvrunner.pipeline["components"]
outputs = {}
try:
if record["output"]:
- with Perf(logger, "inspect log %s" % self.name):
- logc = arvados.collection.Collection(record["log"])
+ with Perf(metrics, "inspect log %s" % self.name):
+ 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])
tmpdir = None
outdir = None
if g:
keepdir = g.group(1)
- with Perf(logger, "output collection %s" % self.name):
+ with Perf(metrics, "output collection %s" % self.name):
outputs = done.done(self, record, tmpdir, outdir, keepdir)
except WorkflowException as e:
logger.error("Error while collecting job outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
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
return {
"script": "cwl-runner",
"script_version": "master",
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.
projects / arvados.git / blobdiff