-from cwltool.draft2tool import CommandLineTool
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from cwltool.command_line_tool import CommandLineTool
from .arvjob import ArvadosJob
from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
def __init__(self, arvrunner, toolpath_object, **kwargs):
super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
self.arvrunner = arvrunner
- self.crunch2 = (kwargs["work_api"] == "containers")
+ self.work_api = kwargs["work_api"]
- def makeJobRunner(self):
- if self.crunch2:
+ def makeJobRunner(self, **kwargs):
+ if self.work_api == "containers":
return ArvadosContainer(self.arvrunner)
- else:
+ elif self.work_api == "jobs":
return ArvadosJob(self.arvrunner)
- def makePathMapper(self, reffiles, **kwargs):
- if self.crunch2:
+ def makePathMapper(self, reffiles, stagedir, **kwargs):
+ # type: (List[Any], unicode, **Any) -> PathMapper
+ if self.work_api == "containers":
return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
"/keep/%s",
"/keep/%s/%s",
**kwargs)
- else:
+ elif self.work_api == "jobs":
return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
"$(task.keep)/%s",
"$(task.keep)/%s/%s",
**kwargs)
+
+ def job(self, joborder, output_callback, **kwargs):
+ if self.work_api == "containers":
+ dockerReq, is_req = self.get_requirement("DockerRequirement")
+ if dockerReq and dockerReq.get("dockerOutputDirectory"):
+ kwargs["outdir"] = dockerReq.get("dockerOutputDirectory")
+ kwargs["docker_outdir"] = dockerReq.get("dockerOutputDirectory")
+ else:
+ kwargs["outdir"] = "/var/spool/cwl"
+ kwargs["docker_outdir"] = "/var/spool/cwl"
+ elif self.work_api == "jobs":
+ kwargs["outdir"] = "$(task.outdir)"
+ kwargs["docker_outdir"] = "$(task.outdir)"
+ kwargs["tmpdir"] = "$(task.tmpdir)"
+ kwargs["docker_tmpdir"] = "$(task.tmpdir)"
+ return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)