from cwltool.draft2tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
-from cwltool.pathmapper import adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
from schema_salad.sourceline import SourceLine
import arvados.collection
from .arvdocker import arv_docker_get_image
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing, upload_workflow_collection
-from .pathmapper import InitialWorkDirPathMapper
+from .runner import Runner, arvados_jobs_image, packed_workflow, upload_workflow_collection, trim_anonymous_location
+from .pathmapper import VwdPathMapper, trim_listing
from .perf import Perf
from . import done
from ._version import __version__
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
script_parameters["task.vwd"] = {}
- generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
- separateDirs=False)
+ generatemapper = VwdPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
with Perf(metrics, "createfiles %s" % self.name):
for f, p in generatemapper.items():
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()
+ if vwd:
+ with Perf(metrics, "generatefiles.save_new %s" % self.name):
+ vwd.save_new()
for f, p in generatemapper.items():
if p.type == "File":
if runtime_req:
if "keep_cache" in runtime_req:
runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"]
+ runtime_constraints["min_ram_mb_per_node"] += runtime_req["keep_cache"]
if "outputDirType" in runtime_req:
if runtime_req["outputDirType"] == "local_output_dir":
script_parameters["task.keepTmpOutput"] = False
self.update_pipeline_component(response)
- if response["state"] in ("Complete", "Failed", "Cancelled"):
- logger.info("%s reuse job %s", self.arvrunner.label(self), response["uuid"])
+ if response["state"] == "Complete":
+ logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
with Perf(metrics, "done %s" % self.name):
self.done(response)
else:
self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
adjustDirObjs(self.job_order, trim_listing)
+ adjustFileObjs(self.job_order, trim_anonymous_location)
+ adjustDirObjs(self.job_order, trim_anonymous_location)
if self.output_name:
self.job_order["arv:output_name"] = self.output_name
find_or_create=self.enable_reuse
).execute(num_retries=self.arvrunner.num_retries)
+ if self.enable_reuse:
+ # When reusing jobs, copy its output/log collection to the desired project
+ reused_collections = [('Output', job.get('output', None)),
+ ('Log', job.get('log', None))]
+ for col_type, pdh in [(n, p) for n, p in reused_collections if p]:
+ c = arvados.collection.Collection(pdh,
+ api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
+ c.save_new(name="{} of {}".format(col_type, self.name),
+ owner_uuid=self.arvrunner.project_uuid,
+ ensure_unique_name=True,
+ num_retries=self.arvrunner.num_retries)
+ logger.info("Copied reused job's %s to collection %s",
+ col_type.lower(),
+ c.manifest_locator())
+ # Give read permission to the desired project on reused jobs
+ for job_name, job_uuid in job.get('components', {}).items():
+ self.arvrunner.api.links().create(body={
+ 'link_class': 'can_read',
+ 'tail_uuid': self.arvrunner.project_uuid,
+ 'head_uuid': job_uuid,
+ }).execute(num_retries=self.arvrunner.num_retries)
+
for k,v in job_spec["script_parameters"].items():
if v is False or v is None or isinstance(v, dict):
job_spec["script_parameters"][k] = {"value": v}