From fb5288a2601d6b4d0b8c52b4293a8ccc745b4425 Mon Sep 17 00:00:00 2001
From: Manabu Ishii <manabu.ishii.rb@gmail.com>
Date: Thu, 11 Nov 2021 12:13:09 +0900
Subject: [PATCH] WIP fix #1330

---
 cwltool/process.py      | 4 ++++
 cwltool/workflow.py     | 9 +++++----
 cwltool/workflow_job.py | 2 ++
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/cwltool/process.py b/cwltool/process.py
index 9abbfd7048..4d9878abf8 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -774,6 +774,10 @@ 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
index 986db5b99a..e4c3cade42 100644
--- a/cwltool/workflow.py
+++ b/cwltool/workflow.py
@@ -448,10 +448,11 @@ 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
index 26af81f58f..11ddd5257c 100644
--- 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 params:
         iid = original_id = cast(str, inp["id"])
         if frag_only: