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         if "cwlVersion" not in self.metadata:
  16             raise Exception("missing")
  17         self.arvrunner = arvrunner
  18         self.work_api = kwargs["work_api"]
  19
  20     def makeJobRunner(self, **kwargs):
  21         if self.work_api == "containers":
  22             return ArvadosContainer(self.arvrunner)
  23         elif self.work_api == "jobs":
  24             return ArvadosJob(self.arvrunner)
  25
  26     def makePathMapper(self, reffiles, stagedir, **kwargs):
  27         # type: (List[Any], unicode, **Any) -> PathMapper
  28         if self.work_api == "containers":
  29             return ArvPathMapper(self.arvrunner, reffiles+kwargs.get("extra_reffiles", []), kwargs["basedir"],
  30                                  "/keep/%s",
  31                                  "/keep/%s/%s",
  32                                  **kwargs)
  33         elif self.work_api == "jobs":
  34             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
  35                                  "$(task.keep)/%s",
  36                                  "$(task.keep)/%s/%s",
  37                                  **kwargs)
  38
  39     def job(self, joborder, output_callback, **kwargs):
  40
  41         # Workaround for #13365
  42         builderargs = kwargs.copy()
  43         builderargs["toplevel"] = True
  44         builderargs["tmp_outdir_prefix"] = ""
  45         builder = self._init_job(joborder, **builderargs)
  46         joborder = builder.job
  47
  48         if self.work_api == "containers":
  49             dockerReq, is_req = self.get_requirement("DockerRequirement")
  50             if dockerReq and dockerReq.get("dockerOutputDirectory"):
  51                 kwargs["outdir"] = dockerReq.get("dockerOutputDirectory")
  52                 kwargs["docker_outdir"] = dockerReq.get("dockerOutputDirectory")
  53             else:
  54                 kwargs["outdir"] = "/var/spool/cwl"
  55                 kwargs["docker_outdir"] = "/var/spool/cwl"
  56         elif self.work_api == "jobs":
  57             kwargs["outdir"] = "$(task.outdir)"
  58             kwargs["docker_outdir"] = "$(task.outdir)"
  59             kwargs["tmpdir"] = "$(task.tmpdir)"
  60             kwargs["docker_tmpdir"] = "$(task.tmpdir)"
  61         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)