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