#
# SPDX-License-Identifier: Apache-2.0
-from cwltool.draft2tool import CommandLineTool
+from cwltool.command_line_tool import CommandLineTool
from .arvjob import ArvadosJob
from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
def makePathMapper(self, reffiles, stagedir, **kwargs):
# type: (List[Any], unicode, **Any) -> PathMapper
if self.work_api == "containers":
- return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+ return ArvPathMapper(self.arvrunner, reffiles+kwargs.get("extra_reffiles", []), kwargs["basedir"],
"/keep/%s",
"/keep/%s/%s",
**kwargs)
**kwargs)
def job(self, joborder, output_callback, **kwargs):
+
+ # Workaround for #13365
+ builderargs = kwargs.copy()
+ builderargs["toplevel"] = True
+ builderargs["tmp_outdir_prefix"] = ""
+ builder = self._init_job(joborder, **builderargs)
+ joborder = builder.job
+
if self.work_api == "containers":
dockerReq, is_req = self.get_requirement("DockerRequirement")
if dockerReq and dockerReq.get("dockerOutputDirectory"):