from .arvcontainer import ArvadosContainer, RunnerContainer
from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
+from. runner import Runner
from .arvtool import ArvadosCommandTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
from .fsaccess import CollectionFsAccess
"""
- def __init__(self, api_client, work_api=None, keep_client=None):
+ def __init__(self, api_client, work_api=None, keep_client=None, output_name=None):
self.api = api_client
self.processes = {}
self.lock = threading.Lock()
self.poll_api = None
self.pipeline = None
self.final_output_collection = None
+ self.output_name = output_name
if keep_client is not None:
self.keep_client = keep_client
else:
final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True)
- logger.info("Final output collection %s (%s)", final.portable_data_hash(), final.manifest_locator())
+ logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
+ final.api_response()["name"],
+ final.manifest_locator())
self.final_output_collection = final
self.output_callback,
**kwargs).next()
else:
- runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"))
+ runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name)
else:
- runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"))
+ runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name)
if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
# Create pipeline for local run
if self.final_output is None:
raise WorkflowException("Workflow did not return a result.")
- if kwargs.get("submit"):
+ if kwargs.get("submit") and isinstance(runnerjob, Runner):
logger.info("Final output collection %s", runnerjob.final_output)
else:
- self.make_output_collection("Output of %s" % (shortname(tool.tool["id"])),
- self.final_output)
+ if self.output_name is None:
+ self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
+ self.make_output_collection(self.output_name, self.final_output)
if kwargs.get("compute_checksum"):
adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
help="")
parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
+ parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
parser.add_argument("--ignore-docker-for-reuse", action="store_true",
help="Ignore Docker image version when deciding whether to reuse past jobs.",
default=False)
try:
if api_client is None:
api_client=arvados.api('v1', model=OrderedJsonModel())
- runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client)
+ runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name)
except Exception as e:
logger.error(e)
return 1