5 from cwltool.pack import pack
6 from cwltool.load_tool import fetch_document
7 from cwltool.process import shortname
9 import ruamel.yaml as yaml
11 from .runner import upload_docker, upload_dependencies
13 def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
14 upload_docker(arvRunner, tool)
16 document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
18 packed = pack(document_loader, workflowobj, uri, tool.metadata)
20 main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
21 for inp in main["inputs"]:
22 sn = shortname(inp["id"])
24 inp["default"] = job_order[sn]
26 name = os.path.basename(tool.tool["id"])
27 upload_dependencies(arvRunner, name, document_loader,
32 "owner_uuid": project_uuid,
33 "name": tool.tool.get("label", name),
34 "description": tool.tool.get("doc", ""),
35 "definition":yaml.safe_dump(packed)
39 return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
41 return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]