from cwltool.load_tool import fetch_document
from cwltool.process import shortname
from cwltool.workflow import Workflow
-from cwltool.pathmapper import adjustDirObjs
+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.hints + workflowobj.get("hints", [])
packed = pack(document_loader, workflowobj, uri, self.metadata)
- def prune_directories(obj):
- if obj["location"].startswith("keep:") and "listing" in obj:
+ 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"]
- adjustDirObjs(joborder, prune_directories)
+ adjustFileObjs(joborder_keepmount, keepmount)
+ adjustDirObjs(joborder_keepmount, keepmount)
+ adjustFileObjs(packed, keepmount)
+ adjustDirObjs(packed, keepmount)
wf_runner = {
"class": "CommandLineTool",
"entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}, {
"entryname": "cwl.input.json",
- "entry": yaml.safe_dump(joborder).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+ "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
"hints": workflowobj["hints"],
- "arguments": ["--no-container", "--move-outputs", "workflow.cwl", "cwl.input.json"]
+ "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.json"]
}
kwargs["loader"] = self.doc_loader
kwargs["avsc_names"] = self.doc_schema