sdk/cwl/arvados_cwl/arvworkflow.py

   1 import os
   2 import json
   3 import copy
   4
   5 from cwltool.pack import pack
   6 from cwltool.load_tool import fetch_document
   7 from cwltool.process import shortname
   8
   9 import ruamel.yaml as yaml
  10
  11 from .runner import upload_docker, upload_dependencies
  12
  13 def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
  14     upload_docker(arvRunner, tool)
  15
  16     document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
  17
  18     packed = pack(document_loader, workflowobj, uri, tool.metadata)
  19
  20     main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
  21     for inp in main["inputs"]:
  22         sn = shortname(inp["id"])
  23         if sn in job_order:
  24             inp["default"] = job_order[sn]
  25
  26     name = os.path.basename(tool.tool["id"])
  27     upload_dependencies(arvRunner, name, document_loader,
  28                         packed, uri, False)
  29
  30     body = {
  31         "workflow": {
  32             "owner_uuid": project_uuid,
  33             "name": tool.tool.get("label", name),
  34             "description": tool.tool.get("doc", ""),
  35             "definition":yaml.safe_dump(packed)
  36         }}
  37
  38     if update_uuid:
  39         return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
  40     else:
  41         return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]