WIP fix #1330

common-workflow-language · Nov 11, 2021 · fbed7db · fbed7db
1 parent 0209b0b
commit fbed7db
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Showing 3 changed files with 11 additions and 4 deletions.
diff --git a/cwltool/process.py b/cwltool/process.py
@@ -775,6 +775,10 @@ def _init_job(
             )
 
         job = copy.deepcopy(joborder)
+        if len(job.keys()) > 0:
+            for jo in joborder:
+                field = shortname(jo)
+                job[field] = joborder[jo]
 
         make_fs_access = getdefault(runtime_context.make_fs_access, StdFsAccess)
         fs_access = make_fs_access(runtime_context.basedir)

diff --git a/cwltool/workflow.py b/cwltool/workflow.py
@@ -440,10 +440,11 @@ def job(
             )
 
         step_input = {}
-        for inp in self.tool["inputs"]:
-            field = shortname(inp["id"])
-            if not inp.get("not_connected"):
-                step_input[field] = job_order[inp["id"]]
+        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]
 
         try:
             yield from self.embedded_tool.job(

diff --git a/cwltool/workflow_job.py b/cwltool/workflow_job.py
@@ -386,6 +386,8 @@ def object_from_state(
     incomplete: bool = False,
 ) -> Optional[CWLObjectType]:
     inputobj = {}  # type: CWLObjectType
+    for s in state.keys():
+        inputobj[s] = state[s].value
     for inp in parms:
         iid = original_id = cast(str, inp["id"])
         if frag_only: