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 from schema_salad.sourceline import SourceLine
  11 from cwltool.errors import WorkflowException
  12
  13 def check_cluster_target(self, builder, runtimeContext):
  14     cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget")
  15     if cluster_target_req and runtimeContext.cluster_target_id != id(cluster_target_req):
  16         with SourceLine(cluster_target_req, None, WorkflowException, runtimeContext.debug):
  17             runtimeContext.cluster_target_id = id(cluster_target_req)
  18             runtimeContext.submit_runner_cluster = builder.do_eval(cluster_target_req.get("cluster_id")) or runtimeContext.submit_runner_cluster
  19             runtimeContext.project_uuid = builder.do_eval(cluster_target_req.get("project_uuid")) or runtimeContext.project_uuid
  20             if runtimeContext.submit_runner_cluster and runtimeContext.submit_runner_cluster not in self.arvrunner.api._rootDesc["remoteHosts"]:
  21                 raise WorkflowException("Unknown or invalid cluster id '%s' known clusters are %s" % (runtimeContext.submit_runner_cluster,
  22                                                                                                       ", ".join(self.arvrunner.api._rootDesc["remoteHosts"].keys())))
  23
  24 class ArvadosCommandTool(CommandLineTool):
  25     """Wrap cwltool CommandLineTool to override selected methods."""
  26
  27     def __init__(self, arvrunner, toolpath_object, loadingContext):
  28         super(ArvadosCommandTool, self).__init__(toolpath_object, loadingContext)
  29         self.arvrunner = arvrunner
  30
  31     def make_job_runner(self, runtimeContext):
  32         if runtimeContext.work_api == "containers":
  33             return partial(ArvadosContainer, self.arvrunner, runtimeContext)
  34         elif runtimeContext.work_api == "jobs":
  35             return partial(ArvadosJob, self.arvrunner)
  36         else:
  37             raise Exception("Unsupported work_api %s", runtimeContext.work_api)
  38
  39     def make_path_mapper(self, reffiles, stagedir, runtimeContext, separateDirs):
  40         if runtimeContext.work_api == "containers":
  41             return ArvPathMapper(self.arvrunner, reffiles+runtimeContext.extra_reffiles, runtimeContext.basedir,
  42                                  "/keep/%s",
  43                                  "/keep/%s/%s")
  44         elif runtimeContext.work_api == "jobs":
  45             return ArvPathMapper(self.arvrunner, reffiles, runtimeContext.basedir,
  46                                  "$(task.keep)/%s",
  47                                  "$(task.keep)/%s/%s")
  48
  49     def job(self, joborder, output_callback, runtimeContext):
  50
  51         # Workaround for #13365
  52         builderargs = runtimeContext.copy()
  53         builderargs.toplevel = True
  54         builderargs.tmp_outdir_prefix = ""
  55         builder = self._init_job(joborder, builderargs)
  56         joborder = builder.job
  57
  58         runtimeContext = runtimeContext.copy()
  59
  60         check_cluster_target(self, builder, runtimeContext)
  61
  62         if runtimeContext.work_api == "containers":
  63             dockerReq, is_req = self.get_requirement("DockerRequirement")
  64             if dockerReq and dockerReq.get("dockerOutputDirectory"):
  65                 runtimeContext.outdir = dockerReq.get("dockerOutputDirectory")
  66                 runtimeContext.docker_outdir = dockerReq.get("dockerOutputDirectory")
  67             else:
  68                 runtimeContext.outdir = "/var/spool/cwl"
  69                 runtimeContext.docker_outdir = "/var/spool/cwl"
  70         elif runtimeContext.work_api == "jobs":
  71             runtimeContext.outdir = "$(task.outdir)"
  72             runtimeContext.docker_outdir = "$(task.outdir)"
  73             runtimeContext.tmpdir = "$(task.tmpdir)"
  74             runtimeContext.docker_tmpdir = "$(task.tmpdir)"
  75         return super(ArvadosCommandTool, self).job(joborder, output_callback, runtimeContext)