from cwltool.draft2tool import CommandLineTool from .arvjob import ArvadosJob from .arvcontainer import ArvadosContainer from .pathmapper import ArvPathMapper class ArvadosCommandTool(CommandLineTool): """Wrap cwltool CommandLineTool to override selected methods.""" def __init__(self, arvrunner, toolpath_object, **kwargs): super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs) self.arvrunner = arvrunner self.work_api = kwargs["work_api"] def makeJobRunner(self): if self.work_api == "containers": return ArvadosContainer(self.arvrunner) elif self.work_api == "jobs": return ArvadosJob(self.arvrunner) def makePathMapper(self, reffiles, **kwargs): if self.work_api == "containers": return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"], "/keep/%s", "/keep/%s/%s", **kwargs) elif self.work_api == "jobs": return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"], "$(task.keep)/%s", "$(task.keep)/%s/%s", **kwargs)