sdk/cwl/arvados_cwl/arvtool.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from cwltool.command_line_tool import CommandLineTool
   6 from .arvjob import ArvadosJob
   7 from .arvcontainer import ArvadosContainer
   8 from .pathmapper import ArvPathMapper
   9
  10 class ArvadosCommandTool(CommandLineTool):
  11     """Wrap cwltool CommandLineTool to override selected methods."""
  12
  13     def __init__(self, arvrunner, toolpath_object, **kwargs):
  14         super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
  15         self.arvrunner = arvrunner
  16         self.work_api = kwargs["work_api"]
  17
  18     def makeJobRunner(self, **kwargs):
  19         if self.work_api == "containers":
  20             return ArvadosContainer(self.arvrunner)
  21         elif self.work_api == "jobs":
  22             return ArvadosJob(self.arvrunner)
  23
  24     def makePathMapper(self, reffiles, stagedir, **kwargs):
  25         # type: (List[Any], unicode, **Any) -> PathMapper
  26         if self.work_api == "containers":
  27             return ArvPathMapper(self.arvrunner, reffiles+kwargs.get("extra_reffiles", []), kwargs["basedir"],
  28                                  "/keep/%s",
  29                                  "/keep/%s/%s",
  30                                  **kwargs)
  31         elif self.work_api == "jobs":
  32             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
  33                                  "$(task.keep)/%s",
  34                                  "$(task.keep)/%s/%s",
  35                                  **kwargs)
  36
  37     def job(self, joborder, output_callback, **kwargs):
  38
  39         # Workaround for #13365
  40         builderargs = kwargs.copy()
  41         builderargs["toplevel"] = True
  42         builderargs["tmp_outdir_prefix"] = ""
  43         builder = self._init_job(joborder, **builderargs)
  44         joborder = builder.job
  45
  46         if self.work_api == "containers":
  47             dockerReq, is_req = self.get_requirement("DockerRequirement")
  48             if dockerReq and dockerReq.get("dockerOutputDirectory"):
  49                 kwargs["outdir"] = dockerReq.get("dockerOutputDirectory")
  50                 kwargs["docker_outdir"] = dockerReq.get("dockerOutputDirectory")
  51             else:
  52                 kwargs["outdir"] = "/var/spool/cwl"
  53                 kwargs["docker_outdir"] = "/var/spool/cwl"
  54         elif self.work_api == "jobs":
  55             kwargs["outdir"] = "$(task.outdir)"
  56             kwargs["docker_outdir"] = "$(task.outdir)"
  57             kwargs["tmpdir"] = "$(task.tmpdir)"
  58             kwargs["docker_tmpdir"] = "$(task.tmpdir)"
  59         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)