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, ExpressionTool
   6 from .arvcontainer import ArvadosContainer
   7 from .pathmapper import ArvPathMapper
   8 from .runner import make_builder
   9 from functools import partial
  10 from schema_salad.sourceline import SourceLine
  11 from cwltool.errors import WorkflowException
  12
  13 def validate_cluster_target(arvrunner, runtimeContext):
  14     if (runtimeContext.submit_runner_cluster and
  15         runtimeContext.submit_runner_cluster not in arvrunner.api._rootDesc["remoteHosts"] and
  16         runtimeContext.submit_runner_cluster != arvrunner.api._rootDesc["uuidPrefix"]):
  17         raise WorkflowException("Unknown or invalid cluster id '%s' known remote clusters are %s" % (runtimeContext.submit_runner_cluster,
  18                                                                                                      ", ".join(list(arvrunner.api._rootDesc["remoteHosts"].keys()))))
  19     if runtimeContext.project_uuid:
  20         cluster_target = runtimeContext.submit_runner_cluster or arvrunner.api._rootDesc["uuidPrefix"]
  21         if not runtimeContext.project_uuid.startswith(cluster_target):
  22             raise WorkflowException("Project uuid '%s' must be for target cluster '%s'" % (runtimeContext.project_uuid, cluster_target))
  23         try:
  24             arvrunner.api.groups().get(uuid=runtimeContext.project_uuid).execute()
  25         except Exception as e:
  26             raise WorkflowException("Invalid project uuid '%s': %s" % (runtimeContext.project_uuid, e))
  27
  28 def set_cluster_target(tool, arvrunner, builder, runtimeContext):
  29     cluster_target_req = None
  30     for field in ("hints", "requirements"):
  31         if field not in tool:
  32             continue
  33         for item in tool[field]:
  34             if item["class"] == "http://arvados.org/cwl#ClusterTarget":
  35                 cluster_target_req = item
  36
  37     if cluster_target_req is None:
  38         return runtimeContext
  39
  40     with SourceLine(cluster_target_req, None, WorkflowException, runtimeContext.debug):
  41         runtimeContext = runtimeContext.copy()
  42         runtimeContext.submit_runner_cluster = builder.do_eval(cluster_target_req.get("cluster_id")) or runtimeContext.submit_runner_cluster
  43         runtimeContext.project_uuid = builder.do_eval(cluster_target_req.get("project_uuid")) or runtimeContext.project_uuid
  44         validate_cluster_target(arvrunner, runtimeContext)
  45
  46     return runtimeContext
  47
  48
  49 class ArvadosCommandTool(CommandLineTool):
  50     """Wrap cwltool CommandLineTool to override selected methods."""
  51
  52     def __init__(self, arvrunner, toolpath_object, loadingContext):
  53         super(ArvadosCommandTool, self).__init__(toolpath_object, loadingContext)
  54         self.arvrunner = arvrunner
  55
  56     def make_job_runner(self, runtimeContext):
  57         if runtimeContext.work_api == "containers":
  58             return partial(ArvadosContainer, self.arvrunner, runtimeContext)
  59         else:
  60             raise Exception("Unsupported work_api %s", runtimeContext.work_api)
  61
  62     def make_path_mapper(self, reffiles, stagedir, runtimeContext, separateDirs):
  63         if runtimeContext.work_api == "containers":
  64             return ArvPathMapper(self.arvrunner, reffiles+runtimeContext.extra_reffiles, runtimeContext.basedir,
  65                                  "/keep/%s",
  66                                  "/keep/%s/%s")
  67
  68     def job(self, joborder, output_callback, runtimeContext):
  69         builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
  70         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
  71
  72         if runtimeContext.work_api == "containers":
  73             dockerReq, is_req = self.get_requirement("DockerRequirement")
  74             if dockerReq and dockerReq.get("dockerOutputDirectory"):
  75                 runtimeContext.outdir = dockerReq.get("dockerOutputDirectory")
  76                 runtimeContext.docker_outdir = dockerReq.get("dockerOutputDirectory")
  77             else:
  78                 runtimeContext.outdir = "/var/spool/cwl"
  79                 runtimeContext.docker_outdir = "/var/spool/cwl"
  80         return super(ArvadosCommandTool, self).job(joborder, output_callback, runtimeContext)
  81
  82 class ArvadosExpressionTool(ExpressionTool):
  83     def __init__(self, arvrunner, toolpath_object, loadingContext):
  84         super(ArvadosExpressionTool, self).__init__(toolpath_object, loadingContext)
  85         self.arvrunner = arvrunner
  86
  87     def job(self,
  88             job_order,         # type: Mapping[Text, Text]
  89             output_callback,  # type: Callable[[Any, Any], Any]
  90             runtimeContext     # type: RuntimeContext
  91            ):
  92         return super(ArvadosExpressionTool, self).job(job_order, self.arvrunner.get_wrapped_callback(output_callback), runtimeContext)