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 def set_cluster_target(tool, arvrunner, builder, runtimeContext):
  20     cluster_target_req = None
  21     for field in ("hints", "requirements"):
  22         if field not in tool:
  23             continue
  24         for item in tool[field]:
  25             if item["class"] == "http://arvados.org/cwl#ClusterTarget":
  26                 cluster_target_req = item
  27
  28     if cluster_target_req is None:
  29         return runtimeContext
  30
  31     with SourceLine(cluster_target_req, None, WorkflowException, runtimeContext.debug):
  32         runtimeContext = runtimeContext.copy()
  33         runtimeContext.submit_runner_cluster = builder.do_eval(cluster_target_req.get("cluster_id")) or runtimeContext.submit_runner_cluster
  34         runtimeContext.project_uuid = builder.do_eval(cluster_target_req.get("project_uuid")) or runtimeContext.project_uuid
  35         validate_cluster_target(arvrunner, runtimeContext)
  36
  37     return runtimeContext
  38
  39
  40 class ArvadosCommandTool(CommandLineTool):
  41     """Wrap cwltool CommandLineTool to override selected methods."""
  42
  43     def __init__(self, arvrunner, toolpath_object, loadingContext):
  44         super(ArvadosCommandTool, self).__init__(toolpath_object, loadingContext)
  45         self.arvrunner = arvrunner
  46
  47     def make_job_runner(self, runtimeContext):
  48         if runtimeContext.work_api == "containers":
  49             return partial(ArvadosContainer, self.arvrunner, runtimeContext)
  50         else:
  51             raise Exception("Unsupported work_api %s", runtimeContext.work_api)
  52
  53     def make_path_mapper(self, reffiles, stagedir, runtimeContext, separateDirs):
  54         if runtimeContext.work_api == "containers":
  55             return ArvPathMapper(self.arvrunner, reffiles+runtimeContext.extra_reffiles, runtimeContext.basedir,
  56                                  "/keep/%s",
  57                                  "/keep/%s/%s")
  58
  59     def job(self, joborder, output_callback, runtimeContext):
  60         builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
  61         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
  62
  63         if runtimeContext.work_api == "containers":
  64             dockerReq, is_req = self.get_requirement("DockerRequirement")
  65             if dockerReq and dockerReq.get("dockerOutputDirectory"):
  66                 runtimeContext.outdir = dockerReq.get("dockerOutputDirectory")
  67                 runtimeContext.docker_outdir = dockerReq.get("dockerOutputDirectory")
  68             else:
  69                 runtimeContext.outdir = "/var/spool/cwl"
  70                 runtimeContext.docker_outdir = "/var/spool/cwl"
  71         return super(ArvadosCommandTool, self).job(joborder, output_callback, runtimeContext)
  72
  73 class ArvadosExpressionTool(ExpressionTool):
  74     def __init__(self, arvrunner, toolpath_object, loadingContext):
  75         super(ArvadosExpressionTool, self).__init__(toolpath_object, loadingContext)
  76         self.arvrunner = arvrunner
  77
  78     def job(self,
  79             job_order,         # type: Mapping[Text, Text]
  80             output_callback,  # type: Callable[[Any, Any], Any]
  81             runtimeContext     # type: RuntimeContext
  82            ):
  83         return super(ArvadosExpressionTool, self).job(job_order, self.arvrunner.get_wrapped_callback(output_callback), runtimeContext)