from cwltool.load_tool import fetch_document
from cwltool.process import shortname
from cwltool.workflow import Workflow, WorkflowException
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
import ruamel.yaml as yaml
-from .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location
-from .pathmapper import trim_listing
+from .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
+from .pathmapper import ArvPathMapper, trim_listing
from .arvtool import ArvadosCommandTool
from .perf import Perf
kwargs["work_api"] = self.work_api
req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
if req:
- with SourceLine(self.tool, None, WorkflowException):
+ with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "id" not in self.tool:
raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
False)
with Perf(metrics, "subworkflow adjust"):
+ joborder_resolved = copy.deepcopy(joborder)
joborder_keepmount = copy.deepcopy(joborder)
+ reffiles = []
+ visit_class(joborder_keepmount, ("File", "Directory"), lambda x: reffiles.append(x))
+
+ mapper = ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+ "/keep/%s",
+ "/keep/%s/%s",
+ **kwargs)
+
def keepmount(obj):
- with SourceLine(obj, None, WorkflowException):
+ remove_redundant_fields(obj)
+ with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "location" not in obj:
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
- with SourceLine(obj, "location", WorkflowException):
+ with SourceLine(obj, "location", WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
- obj["location"] = "/keep/" + obj["location"][5:]
+ obj["location"] = mapper.mapper(obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
else:
raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
- adjustFileObjs(joborder_keepmount, keepmount)
- adjustDirObjs(joborder_keepmount, keepmount)
+ visit_class(joborder_keepmount, ("File", "Directory"), keepmount)
+
+ def resolved(obj):
+ if obj["location"].startswith("keep:"):
+ obj["location"] = mapper.mapper(obj["location"]).resolved
+
+ visit_class(joborder_resolved, ("File", "Directory"), resolved)
if self.wf_pdh is None:
adjustFileObjs(packed, keepmount)
})
kwargs["loader"] = self.doc_loader
kwargs["avsc_names"] = self.doc_schema
- return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
+ return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder_resolved, output_callback, **kwargs)
else:
return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)