sdk/cwl/arvados_cwl/arvworkflow.py

   1 import os
   2 import json
   3 import copy
   4 import logging
   5
   6 from schema_salad.sourceline import SourceLine, cmap
   7
   8 from cwltool.pack import pack
   9 from cwltool.load_tool import fetch_document
  10 from cwltool.process import shortname
  11 from cwltool.workflow import Workflow, WorkflowException
  12 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
  13
  14 import ruamel.yaml as yaml
  15
  16 from .runner import upload_dependencies, trim_listing, packed_workflow
  17 from .arvtool import ArvadosCommandTool
  18 from .perf import Perf
  19
  20 logger = logging.getLogger('arvados.cwl-runner')
  21 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  22
  23 def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
  24                     submit_runner_ram=0, name=None):
  25
  26     packed = packed_workflow(arvRunner, tool)
  27
  28     adjustDirObjs(job_order, trim_listing)
  29
  30     main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
  31     for inp in main["inputs"]:
  32         sn = shortname(inp["id"])
  33         if sn in job_order:
  34             inp["default"] = job_order[sn]
  35
  36     if not name:
  37         name = tool.tool.get("label", os.path.basename(tool.tool["id"]))
  38
  39     upload_dependencies(arvRunner, name, tool.doc_loader,
  40                         packed, tool.tool["id"], False)
  41
  42     # TODO nowhere for submit_runner_ram to go.
  43
  44     body = {
  45         "workflow": {
  46             "name": name,
  47             "description": tool.tool.get("doc", ""),
  48             "definition":yaml.round_trip_dump(packed)
  49         }}
  50     if project_uuid:
  51         body["workflow"]["owner_uuid"] = project_uuid
  52
  53     if uuid:
  54         call = arvRunner.api.workflows().update(uuid=uuid, body=body)
  55     else:
  56         call = arvRunner.api.workflows().create(body=body)
  57     return call.execute(num_retries=arvRunner.num_retries)["uuid"]
  58
  59 class ArvadosWorkflow(Workflow):
  60     """Wrap cwltool Workflow to override selected methods."""
  61
  62     def __init__(self, arvrunner, toolpath_object, **kwargs):
  63         super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs)
  64         self.arvrunner = arvrunner
  65         self.work_api = kwargs["work_api"]
  66
  67     def job(self, joborder, output_callback, **kwargs):
  68         kwargs["work_api"] = self.work_api
  69         req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
  70         if req:
  71             with SourceLine(self.tool, None, WorkflowException):
  72                 if "id" not in self.tool:
  73                     raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
  74             document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
  75
  76             with Perf(metrics, "subworkflow upload_deps"):
  77                 workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
  78                 workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
  79                 packed = pack(document_loader, workflowobj, uri, self.metadata)
  80
  81                 upload_dependencies(self.arvrunner,
  82                                     kwargs.get("name", ""),
  83                                     document_loader,
  84                                     packed,
  85                                     uri,
  86                                     False)
  87
  88                 upload_dependencies(self.arvrunner,
  89                                     os.path.basename(joborder.get("id", "#")),
  90                                     document_loader,
  91                                     joborder,
  92                                     joborder.get("id", "#"),
  93                                     False)
  94
  95             with Perf(metrics, "subworkflow adjust"):
  96                 joborder_keepmount = copy.deepcopy(joborder)
  97
  98                 def keepmount(obj):
  99                     with SourceLine(obj, None, WorkflowException):
 100                         if "location" not in obj:
 101                             raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
 102                     with SourceLine(obj, "location", WorkflowException):
 103                         if obj["location"].startswith("keep:"):
 104                             obj["location"] = "/keep/" + obj["location"][5:]
 105                             if "listing" in obj:
 106                                 del obj["listing"]
 107                         elif obj["location"].startswith("_:"):
 108                             del obj["location"]
 109                         else:
 110                             raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
 111
 112                 adjustFileObjs(joborder_keepmount, keepmount)
 113                 adjustDirObjs(joborder_keepmount, keepmount)
 114                 adjustFileObjs(packed, keepmount)
 115                 adjustDirObjs(packed, keepmount)
 116
 117             wf_runner = cmap({
 118                 "class": "CommandLineTool",
 119                 "baseCommand": "cwltool",
 120                 "inputs": self.tool["inputs"],
 121                 "outputs": self.tool["outputs"],
 122                 "stdout": "cwl.output.json",
 123                 "requirements": workflowobj["requirements"]+[
 124                     {
 125                     "class": "InitialWorkDirRequirement",
 126                     "listing": [{
 127                             "entryname": "workflow.cwl",
 128                             "entry": yaml.round_trip_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
 129                         }, {
 130                             "entryname": "cwl.input.yml",
 131                             "entry": yaml.round_trip_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
 132                         }]
 133                 }],
 134                 "hints": workflowobj["hints"],
 135                 "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
 136             })
 137             kwargs["loader"] = self.doc_loader
 138             kwargs["avsc_names"] = self.doc_schema
 139             return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
 140         else:
 141             return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)