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, **kwargs):
  21         if self.work_api == "containers":
  22             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
  23                                  "/keep/%s",
  24                                  "/keep/%s/%s",
  25                                  **kwargs)
  26         elif self.work_api == "jobs":
  27             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
  28                                  "$(task.keep)/%s",
  29                                  "$(task.keep)/%s/%s",
  30                                  **kwargs)