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Enumerate Directory contents in output when --compute-checksum is
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvjob.py
diff --git
a/sdk/cwl/arvados_cwl/arvjob.py
b/sdk/cwl/arvados_cwl/arvjob.py
index 4ede88d7ca2b8cbb3c9c57a420ab39b28407d484..8b1a9346830b349e145fcb0fe5ec3f3cf1acf823 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvjob.py
+++ b/
sdk/cwl/arvados_cwl/arvjob.py
@@
-40,7
+40,9
@@
class ArvadosJob(object):
with Perf(metrics, "generatefiles %s" % self.name):
if self.generatefiles["listing"]:
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)
script_parameters["task.vwd"] = {}
generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
separateDirs=False)
@@
-175,7
+177,10
@@
class ArvadosJob(object):
try:
if record["output"]:
with Perf(metrics, "inspect log %s" % self.name):
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
log = logc.open(logc.keys()[0])
tmpdir = None
outdir = None
@@
-229,6
+234,8
@@
class RunnerJob(Runner):
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:]
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",
return {
"script": "cwl-runner",
"script_version": "master",
@@
-284,7
+291,8
@@
class RunnerTemplate(object):
runner=runner,
tool=tool,
job_order=job_order,
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.
def pipeline_component_spec(self):
"""Return a component that Workbench and a-r-p-i will understand.