sdk/cwl/arvados_cwl/arvworkflow.py

   1 import os
   2 import json
   3
   4 from cwltool.pack import pack
   5 from cwltool.load_tool import fetch_document
   6 from cwltool.process import shortname
   7
   8 from .runner import upload_docker, upload_dependencies
   9
  10 def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
  11     upload_docker(arvRunner, tool)
  12
  13     document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
  14     print workflowobj["steps"]
  15     for inp in workflowobj["inputs"]:
  16         sn = shortname(inp["id"])
  17         if sn in job_order:
  18             inp["default"] = job_order[sn]
  19
  20     packed = pack(document_loader, workflowobj, uri, tool.metadata)
  21
  22     name = os.path.basename(tool.tool["id"])
  23     upload_dependencies(arvRunner, name, document_loader,
  24                         packed, uri, "keep:", False)
  25
  26     body = {
  27         "workflow": {
  28             "owner_uuid": project_uuid,
  29             "name": tool.tool.get("label", name),
  30             "description": tool.tool.get("doc", ""),
  31             "workflow":json.dumps(packed, sort_keys=True, indent=4)
  32         }}
  33
  34     if update_uuid:
  35         return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
  36     else:
  37         return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]