from cwltool.draft2tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
from cwltool.draft2tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
import arvados.collection
from .arvdocker import arv_docker_get_image
from .runner import Runner
import arvados.collection
from .arvdocker import arv_docker_get_image
from .runner import Runner
if self.generatefiles["listing"]:
vwd = arvados.collection.Collection()
script_parameters["task.vwd"] = {}
if self.generatefiles["listing"]:
vwd = arvados.collection.Collection()
script_parameters["task.vwd"] = {}
- generatemapper = PathMapper([self.generatefiles], self.outdir,
- ".", separateDirs=False)
+ generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
for f, p in generatemapper.items():
if p.type == "CreateFile":
with vwd.open(p.target, "w") as n:
for f, p in generatemapper.items():
if p.type == "CreateFile":
with vwd.open(p.target, "w") as n:
if p.type == "CreateFile":
script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
if p.type == "CreateFile":
script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
"owner_uuid": self.arvrunner.project_uuid,
"script": "crunchrunner",
"repository": "arvados",
"owner_uuid": self.arvrunner.project_uuid,
"script": "crunchrunner",
"repository": "arvados",
"minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
"script_parameters": {"tasks": [script_parameters]},
"runtime_constraints": runtime_constraints
"minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
"script_parameters": {"tasks": [script_parameters]},
"runtime_constraints": runtime_constraints
body={
"owner_uuid": self.arvrunner.project_uuid,
"name": shortname(self.tool.tool["id"]),
body={
"owner_uuid": self.arvrunner.project_uuid,
"name": shortname(self.tool.tool["id"]),
# Title and description...
title = param.pop('label', '')
# Title and description...
title = param.pop('label', '')
spec['script_parameters'][param_id] = param
spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
spec['script_parameters'][param_id] = param
spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']