sdk/cwl/arvados_cwl/arvtool.py

   1 from cwltool.draft2tool import CommandLineTool
   2 from .arvjob import ArvadosJob
   3 from .arvcontainer import ArvadosContainer
   4 from .pathmapper import ArvPathMapper
   5
   6 class ArvadosCommandTool(CommandLineTool):
   7     """Wrap cwltool CommandLineTool to override selected methods."""
   8
   9     def __init__(self, arvrunner, toolpath_object, **kwargs):
  10         super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
  11         self.arvrunner = arvrunner
  12         self.work_api = kwargs["work_api"]
  13
  14     def makeJobRunner(self):
  15         if self.work_api == "containers":
  16             return ArvadosContainer(self.arvrunner)
  17         elif self.work_api == "jobs":
  18             return ArvadosJob(self.arvrunner)
  19
  20     def makePathMapper(self, reffiles, stagedir, **kwargs):
  21         # type: (List[Any], unicode, **Any) -> PathMapper
  22         if self.work_api == "containers":
  23             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
  24                                  "/keep/%s",
  25                                  "/keep/%s/%s",
  26                                  **kwargs)
  27         elif self.work_api == "jobs":
  28             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
  29                                  "$(task.keep)/%s",
  30                                  "$(task.keep)/%s/%s",
  31                                  **kwargs)
  32
  33     def job(self, joborder, output_callback, **kwargs):
  34         if self.work_api == "containers":
  35             kwargs["outdir"] = "/var/spool/cwl"
  36             kwargs["docker_outdir"] = "/var/spool/cwl"
  37         elif self.work_api == "jobs":
  38             kwargs["outdir"] = "$(task.outdir)"
  39             kwargs["docker_outdir"] = "$(task.outdir)"
  40             kwargs["tmpdir"] = "$(task.tmpdir)"
  41             kwargs["docker_tmpdir"] = "$(task.tmpdir)"
  42         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)