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":
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