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
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", [])
+ 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": [
+ "requirements": workflowobj["requirements"]+[
{"class": "InlineJavascriptRequirement"},
{
"class": "InitialWorkDirRequirement",
"listing": [{
- "entryname": "workflow.json",
- "entry": json.dumps(packed, sort_keys=True, indent=4)
+ "entryname": "workflow.cwl",
+ "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}, {
"entryname": "cwl.input.json",
- "entry": "$(JSON.stringify(inputs))"
+ "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
- "arguments": ["--debug", "workflow.json", "cwl.input.json"]
+ "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