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)
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])
tmpdir = None
outdir = None
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.