import os
import json
+import copy
+import logging
from cwltool.pack import pack
from cwltool.load_tool import fetch_document
from cwltool.process import shortname
+from cwltool.workflow import Workflow
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+
+import ruamel.yaml as yaml
from .runner import upload_docker, upload_dependencies
+from .arvtool import ArvadosCommandTool
+
+logger = logging.getLogger('arvados.cwl-runner')
-def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
+def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
upload_docker(arvRunner, tool)
document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
- for inp in workflowobj["inputs"]:
+
+ packed = pack(document_loader, workflowobj, uri, tool.metadata)
+
+ main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
+ for inp in main["inputs"]:
sn = shortname(inp["id"])
if sn in job_order:
inp["default"] = job_order[sn]
- packed = pack(document_loader, workflowobj, uri, tool.metadata)
-
name = os.path.basename(tool.tool["id"])
upload_dependencies(arvRunner, name, document_loader,
- packed, uri, "keep:", False)
+ packed, uri, False)
body = {
"workflow": {
"owner_uuid": project_uuid,
"name": tool.tool.get("label", name),
"description": tool.tool.get("doc", ""),
- "workflow":json.dumps(packed, sort_keys=True, indent=4)
+ "definition":yaml.safe_dump(packed)
}}
if update_uuid:
return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
else:
return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
+
+class ArvadosWorkflow(Workflow):
+ """Wrap cwltool Workflow to override selected methods."""
+
+ def __init__(self, arvrunner, toolpath_object, **kwargs):
+ super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs)
+ self.arvrunner = arvrunner
+ self.work_api = kwargs["work_api"]
+
+ def job(self, joborder, output_callback, **kwargs):
+ kwargs["work_api"] = self.work_api
+ req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
+ if req:
+ document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
+
+ workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
+ workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
+ packed = pack(document_loader, workflowobj, uri, self.metadata)
+
+ upload_dependencies(self.arvrunner,
+ kwargs.get("name", ""),
+ document_loader,
+ packed,
+ uri,
+ False)
+
+ upload_dependencies(self.arvrunner,
+ os.path.basename(joborder.get("id", "#")),
+ document_loader,
+ joborder,
+ joborder.get("id", "#"),
+ False)
+
+ joborder_keepmount = copy.deepcopy(joborder)
+
+ def keepmount(obj):
+ if obj["location"].startswith("keep:"):
+ obj["location"] = "/keep/" + obj["location"][5:]
+ else:
+ raise Exception("Uh oh %s" % obj["location"])
+ if "listing" in obj:
+ del obj["listing"]
+ adjustFileObjs(joborder_keepmount, keepmount)
+ adjustDirObjs(joborder_keepmount, keepmount)
+ adjustFileObjs(packed, keepmount)
+ adjustDirObjs(packed, keepmount)
+
+ wf_runner = {
+ "class": "CommandLineTool",
+ "baseCommand": "cwltool",
+ "inputs": self.tool["inputs"],
+ "outputs": self.tool["outputs"],
+ "stdout": "cwl.output.json",
+ "requirements": workflowobj["requirements"]+[
+ {"class": "InlineJavascriptRequirement"},
+ {
+ "class": "InitialWorkDirRequirement",
+ "listing": [{
+ "entryname": "workflow.cwl",
+ "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+ }, {
+ "entryname": "cwl.input.json",
+ "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+ }]
+ }],
+ "hints": workflowobj["hints"],
+ "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.json"]
+ }
+ kwargs["loader"] = self.doc_loader
+ kwargs["avsc_names"] = self.doc_schema
+ return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
+ else:
+ return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)