12416: Merge Put() into PutReader().

[arvados.git] / sdk / cwl / arvados_cwl / arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 13615798628b692c13d13755f5a3a25201d0d98d..fdf506effa68aeb8ab5b5267fef8f2ee937d51a9 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -13,11 +13,11 @@ from cwltool.pack import pack
 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 .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
 from .pathmapper import trim_listing
 from .arvtool import ArvadosCommandTool
 from .perf import Perf
@@ -83,7 +83,7 @@ class ArvadosWorkflow(Workflow):
         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"])
@@ -113,10 +113,11 @@ class ArvadosWorkflow(Workflow):
                 joborder_keepmount = copy.deepcopy(joborder)
 
                 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:]
                             if "listing" in obj:
@@ -126,8 +127,7 @@ class ArvadosWorkflow(Workflow):
                         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)
 
                 if self.wf_pdh is None:
                     adjustFileObjs(packed, keepmount)