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 from functools import partial
  10
  11 class ArvadosCommandTool(CommandLineTool):
  12     """Wrap cwltool CommandLineTool to override selected methods."""
  13
  14     def __init__(self, arvrunner, toolpath_object, loadingContext):
  15         super(ArvadosCommandTool, self).__init__(toolpath_object, loadingContext)
  16         self.arvrunner = arvrunner
  17
  18     def make_job_runner(self, runtimeContext):
  19         if runtimeContext.work_api == "containers":
  20             return partial(ArvadosContainer, self.arvrunner)
  21         elif runtimeContext.work_api == "jobs":
  22             return partial(ArvadosJob, self.arvrunner)
  23         else:
  24             raise Exception("Unsupported work_api %s", runtimeContext.work_api)
  25
  26     def make_path_mapper(self, reffiles, stagedir, runtimeContext, separateDirs):
  27         if runtimeContext.work_api == "containers":
  28             return ArvPathMapper(self.arvrunner, reffiles+runtimeContext.extra_reffiles, runtimeContext.basedir,
  29                                  "/keep/%s",
  30                                  "/keep/%s/%s")
  31         elif runtimeContext.work_api == "jobs":
  32             return ArvPathMapper(self.arvrunner, reffiles, runtimeContext.basedir,
  33                                  "$(task.keep)/%s",
  34                                  "$(task.keep)/%s/%s")
  35
  36     def job(self, joborder, output_callback, runtimeContext):
  37
  38         # Workaround for #13365
  39         builderargs = runtimeContext.copy()
  40         builderargs.toplevel = True
  41         builderargs.tmp_outdir_prefix = ""
  42         builder = self._init_job(joborder, builderargs)
  43         joborder = builder.job
  44
  45         runtimeContext = runtimeContext.copy()
  46
  47         if runtimeContext.work_api == "containers":
  48             dockerReq, is_req = self.get_requirement("DockerRequirement")
  49             if dockerReq and dockerReq.get("dockerOutputDirectory"):
  50                 runtimeContext.outdir = dockerReq.get("dockerOutputDirectory")
  51                 runtimeContext.docker_outdir = dockerReq.get("dockerOutputDirectory")
  52             else:
  53                 runtimeContext.outdir = "/var/spool/cwl"
  54                 runtimeContext.docker_outdir = "/var/spool/cwl"
  55         elif runtimeContext.work_api == "jobs":
  56             runtimeContext.outdir = "$(task.outdir)"
  57             runtimeContext.docker_outdir = "$(task.outdir)"
  58             runtimeContext.tmpdir = "$(task.tmpdir)"
  59             runtimeContext.docker_tmpdir = "$(task.tmpdir)"
  60         return super(ArvadosCommandTool, self).job(joborder, output_callback, runtimeContext)