sdk/cwl/arvados_cwl/arvworkflow.py

   1 import os
   2 import json
   3 import copy
   4 import logging
   5
   6 from cwltool.pack import pack
   7 from cwltool.load_tool import fetch_document
   8 from cwltool.process import shortname
   9 from cwltool.workflow import Workflow
  10
  11 import ruamel.yaml as yaml
  12
  13 from .runner import upload_docker, upload_dependencies
  14 from .arvtool import ArvadosCommandTool
  15
  16 logger = logging.getLogger('arvados.cwl-runner')
  17
  18 def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
  19     upload_docker(arvRunner, tool)
  20
  21     document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
  22
  23     packed = pack(document_loader, workflowobj, uri, tool.metadata)
  24
  25     main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
  26     for inp in main["inputs"]:
  27         sn = shortname(inp["id"])
  28         if sn in job_order:
  29             inp["default"] = job_order[sn]
  30
  31     name = os.path.basename(tool.tool["id"])
  32     upload_dependencies(arvRunner, name, document_loader,
  33                         packed, uri, False)
  34
  35     body = {
  36         "workflow": {
  37             "owner_uuid": project_uuid,
  38             "name": tool.tool.get("label", name),
  39             "description": tool.tool.get("doc", ""),
  40             "definition":yaml.safe_dump(packed)
  41         }}
  42
  43     if update_uuid:
  44         return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
  45     else:
  46         return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
  47
  48 class ArvadosWorkflow(Workflow):
  49     """Wrap cwltool Workflow to override selected methods."""
  50
  51     def __init__(self, arvrunner, toolpath_object, **kwargs):
  52         super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs)
  53         self.arvrunner = arvrunner
  54         self.work_api = kwargs["work_api"]
  55
  56     def job(self, joborder, output_callback, **kwargs):
  57         kwargs["work_api"] = self.work_api
  58         req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
  59         if req:
  60             document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
  61             workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
  62             workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
  63             packed = pack(document_loader, workflowobj, uri, self.metadata)
  64             wf_runner = {
  65                 "class": "CommandLineTool",
  66                 "baseCommand": "cwltool",
  67                 "inputs": self.tool["inputs"],
  68                 "outputs": self.tool["outputs"],
  69                 "stdout": "cwl.output.json",
  70                 "requirements": workflowobj["requirements"]+[
  71                     {"class": "InlineJavascriptRequirement"},
  72                     {
  73                     "class": "InitialWorkDirRequirement",
  74                     "listing": [{
  75                             "entryname": "workflow.json",
  76                             "entry": json.dumps(packed, sort_keys=True, indent=4).replace('$(', '\$(').replace('${', '\${')
  77                         }, {
  78                             "entryname": "cwl.input.json",
  79                             "entry": "$(JSON.stringify(inputs))"
  80                         }]
  81                 }],
  82                 "hints": workflowobj["hints"],
  83                 "arguments": ["--no-container", "--move-outputs", "workflow.json", "cwl.input.json"]
  84             }
  85             kwargs["loader"] = self.doc_loader
  86             kwargs["avsc_names"] = self.doc_schema
  87             return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
  88         else:
  89             return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)