with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
self.check_features(v, parentfield=parentfield)
- def make_output_collection(self, name, storage_classes, tagsString, outputObj):
+ def make_output_collection(self, name, storage_classes, tagsString, output_properties, outputObj):
outputObj = copy.deepcopy(outputObj)
files = []
res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False))
f.write(res)
- final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)
+
+ final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes,
+ ensure_unique_name=True, properties=output_properties)
logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
final.api_response()["name"],
self.api.containers().update(uuid=current['uuid'],
body={
'output': self.final_output_collection.portable_data_hash(),
+ 'output_properties': self.final_output_collection.get_properties(),
}).execute(num_retries=self.num_retries)
self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
body={
updated_tool.visit(self.check_features)
- self.project_uuid = runtimeContext.project_uuid
self.pipeline = None
self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
self.secret_store = runtimeContext.secret_store
# gets uploaded goes into the same parent project, unless
# an alternate --project-uuid was provided.
existing_wf = self.api.workflows().get(uuid=runtimeContext.update_workflow).execute()
- self.project_uuid = existing_wf["owner_uuid"]
+ runtimeContext.project_uuid = existing_wf["owner_uuid"]
+
+ self.project_uuid = runtimeContext.project_uuid
# Upload local file references in the job order.
job_order = upload_job_order(self, "%s input" % runtimeContext.name,
# Create a pipeline template or workflow record and exit.
if self.work_api == "containers":
uuid = upload_workflow(self, tool, job_order,
- self.project_uuid,
+ runtimeContext.project_uuid,
runtimeContext,
uuid=runtimeContext.update_workflow,
submit_runner_ram=runtimeContext.submit_runner_ram,
else:
storage_classes = runtimeContext.storage_classes.strip().split(",")
- self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output)
+ output_properties = {}
+ output_properties_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
+ if output_properties_req:
+ for pr in output_properties_req["outputProperties"]:
+ output_properties[pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+
+ self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes,
+ self.output_tags, output_properties,
+ self.final_output)
self.set_crunch_output()
if runtimeContext.compute_checksum: