import copy
import logging
+from schema_salad.sourceline import SourceLine, cmap
+
from cwltool.pack import pack
from cwltool.load_tool import fetch_document
from cwltool.process import shortname
-from cwltool.workflow import Workflow
+from cwltool.workflow import Workflow, WorkflowException
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
import ruamel.yaml as yaml
-from .runner import upload_docker, upload_dependencies
+from .runner import upload_docker, upload_dependencies, trim_listing
from .arvtool import ArvadosCommandTool
+from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
+metrics = logging.getLogger('arvados.cwl-runner.metrics')
-def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
+def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
+ submit_runner_ram=0, name=None):
upload_docker(arvRunner, tool)
document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
packed = pack(document_loader, workflowobj, uri, tool.metadata)
+ adjustDirObjs(job_order, trim_listing)
+
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]
- name = os.path.basename(tool.tool["id"])
+ if not name:
+ name = tool.tool.get("label", os.path.basename(tool.tool["id"]))
+
upload_dependencies(arvRunner, name, document_loader,
packed, uri, False)
+ # TODO nowhere for submit_runner_ram to go.
+
body = {
"workflow": {
- "owner_uuid": project_uuid,
- "name": tool.tool.get("label", name),
+ "name": name,
"description": tool.tool.get("doc", ""),
- "definition":yaml.safe_dump(packed)
+ "definition":yaml.round_trip_dump(packed)
}}
+ if project_uuid:
+ body["workflow"]["owner_uuid"] = project_uuid
- if update_uuid:
- return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
+ if uuid:
+ call = arvRunner.api.workflows().update(uuid=uuid, body=body)
else:
- return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
+ call = arvRunner.api.workflows().create(body=body)
+ return call.execute(num_retries=arvRunner.num_retries)["uuid"]
class ArvadosWorkflow(Workflow):
"""Wrap cwltool Workflow to override selected methods."""
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.requirements + workflowobj.get("hints", [])
- packed = pack(document_loader, workflowobj, uri, self.metadata)
- wf_runner = {
+
+ with Perf(metrics, "subworkflow upload_deps"):
+ 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)
+
+ with Perf(metrics, "subworkflow adjust"):
+ joborder_keepmount = copy.deepcopy(joborder)
+
+ def keepmount(obj):
+ with SourceLine(obj, None, WorkflowException):
+ if "location" not in obj:
+ raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
+ with SourceLine(obj, "location", WorkflowException):
+ if obj["location"].startswith("keep:"):
+ obj["location"] = "/keep/" + obj["location"][5:]
+ if "listing" in obj:
+ del obj["listing"]
+ elif obj["location"].startswith("_:"):
+ del obj["location"]
+ else:
+ raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
+
+ adjustFileObjs(joborder_keepmount, keepmount)
+ adjustDirObjs(joborder_keepmount, keepmount)
+ adjustFileObjs(packed, keepmount)
+ adjustDirObjs(packed, keepmount)
+
+ wf_runner = cmap({
"class": "CommandLineTool",
"baseCommand": "cwltool",
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
- "requirements": [
- {"class": "InlineJavascriptRequirement"},
+ "requirements": workflowobj["requirements"]+[
{
"class": "InitialWorkDirRequirement",
"listing": [{
- "entryname": "workflow.json",
- "entry": json.dumps(packed, sort_keys=True, indent=4)
+ "entryname": "workflow.cwl",
+ "entry": yaml.round_trip_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}, {
- "entryname": "cwl.input.json",
- "entry": "$(JSON.stringify(inputs))"
+ "entryname": "cwl.input.yml",
+ "entry": yaml.round_trip_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
- "arguments": ["--debug", "workflow.json", "cwl.input.json"]
- }
+ "hints": workflowobj["hints"],
+ "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
+ })
kwargs["loader"] = self.doc_loader
kwargs["avsc_names"] = self.doc_schema
return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
projects / arvados.git / blobdiff