Update to fix #1330

Author: manabuishii

cwltool/workflow.py

@@ -443,9 +443,9 @@ def job(
         for inp in job_order:
             field = shortname(inp)
             step_input[field] = job_order[inp]
-            # if not inp.get("not_connected"):
-            #    step_input[field] = job_order[field]
-
+            if hasattr(inp, "get"):
+                if not inp.get("not_connected"):
+                    step_input[field] = job_order[field]
         try:
             yield from self.embedded_tool.job(
                 step_input,

cwltool/workflow_job.py

@@ -387,7 +387,8 @@ def object_from_state(
 ) -> Optional[CWLObjectType]:
     inputobj = {}  # type: CWLObjectType
     for s in state.keys():
-        inputobj[s] = state[s].value
+        if hasattr(state[s], "value"):
+            inputobj[s] = state[s].value
     for inp in parms:
         iid = original_id = cast(str, inp["id"])
         if frag_only:
@@ -553,6 +554,23 @@ def do_output_callback(self, final_output_callback: OutputCallbackType) -> None:
             _logger.debug("[%s] outputs %s", self.name, json_dumps(wo, indent=4))
 
         self.did_callback = True
+        paramskey=[]
+        paramskeys=[]
+
+        if self.tool["outputs"] is not None:
+            for inp in self.tool["outputs"]:
+                for k,v in inp.items():
+                    if k == 'id':
+                        paramskey.append(v)
+                        paramskeys.append(shortname(v))
+
+        newwo={}
+        for k,v in wo.items():
+            if k in paramskey:
+                newwo[k]=v
+            elif k in paramskeys:
+                newwo[k]=v
+        wo = newwo
 
         final_output_callback(wo, self.processStatus)