From 0687784c571ab3ed05a43a43af1abf5cb5b14013 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 17 Aug 2026 17:11:53 +0300
Subject: [PATCH 1/2] Revert "expression refactor: always set the ID for
 ExpressionTools"

This reverts commit 910f114cf812995c53c4efab138607dc0dc7e5c5.
---
 src/cwl_utils/cwl_v1_0_expression_refactor.py | 2 --
 src/cwl_utils/cwl_v1_1_expression_refactor.py | 3 ---
 src/cwl_utils/cwl_v1_2_expression_refactor.py | 3 ---
 3 files changed, 8 deletions(-)

diff --git a/src/cwl_utils/cwl_v1_0_expression_refactor.py b/src/cwl_utils/cwl_v1_0_expression_refactor.py
index d584224e..320dc7e7 100755
--- a/src/cwl_utils/cwl_v1_0_expression_refactor.py
+++ b/src/cwl_utils/cwl_v1_0_expression_refactor.py
@@ -409,7 +409,6 @@ def generate_etool_from_expr(
         else None
     )
     return cwl.ExpressionTool(
-        id="_:" + str(uuid.uuid4()),
         inputs=inputs,
         outputs=outputs,
         expression=expression,
@@ -1732,7 +1731,6 @@ def generate_etool_from_expr2(
  }"""
     )
     return cwl.ExpressionTool(
-        id="_:" + str(uuid.uuid4()),
         inputs=inputs,
         outputs=outputs,
         expression=expression,
diff --git a/src/cwl_utils/cwl_v1_1_expression_refactor.py b/src/cwl_utils/cwl_v1_1_expression_refactor.py
index 685520e7..c890bc46 100755
--- a/src/cwl_utils/cwl_v1_1_expression_refactor.py
+++ b/src/cwl_utils/cwl_v1_1_expression_refactor.py
@@ -5,7 +5,6 @@
 
 import copy
 import hashlib
-import uuid
 from collections.abc import MutableSequence, Sequence
 from contextlib import suppress
 from typing import Any, cast, Final
@@ -407,7 +406,6 @@ def generate_etool_from_expr(
         else None
     )
     return cwl.ExpressionTool(
-        id="_:" + str(uuid.uuid4()),
         inputs=inputs,
         outputs=outputs,
         expression=expression,
@@ -1738,7 +1736,6 @@ def generate_etool_from_expr2(
  }"""
     )
     return cwl.ExpressionTool(
-        id="_:" + str(uuid.uuid4()),
         inputs=inputs,
         outputs=outputs,
         expression=expression,
diff --git a/src/cwl_utils/cwl_v1_2_expression_refactor.py b/src/cwl_utils/cwl_v1_2_expression_refactor.py
index eca589a6..4087743b 100755
--- a/src/cwl_utils/cwl_v1_2_expression_refactor.py
+++ b/src/cwl_utils/cwl_v1_2_expression_refactor.py
@@ -5,7 +5,6 @@
 
 import copy
 import hashlib
-import uuid
 from collections.abc import Mapping, MutableSequence, Sequence
 from contextlib import suppress
 from typing import Any, cast, Final
@@ -408,7 +407,6 @@ def generate_etool_from_expr(
         else None
     )
     return cwl.ExpressionTool(
-        id="_:" + str(uuid.uuid4()),
         inputs=inputs,
         outputs=outputs,
         expression=expression,
@@ -1851,7 +1849,6 @@ def generate_etool_from_expr2(
  }"""
     )
     return cwl.ExpressionTool(
-        id="_:" + str(uuid.uuid4()),
         inputs=inputs,
         outputs=outputs,
         expression=expression,

From b00b1d20517e527911dea317a831484cade400f8 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 17 Aug 2026 18:24:31 +0300
Subject: [PATCH 2/2] expr refactor: set ID for created workflows

TODO: test using src/cwl_utils/testdata/wc3-tool_v1_0.cwl
---
 src/cwl_utils/cwl_v1_0_expression_refactor.py | 2 +-
 src/cwl_utils/cwl_v1_1_expression_refactor.py | 1 +
 src/cwl_utils/cwl_v1_2_expression_refactor.py | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/cwl_utils/cwl_v1_0_expression_refactor.py b/src/cwl_utils/cwl_v1_0_expression_refactor.py
index 320dc7e7..854a9f21 100755
--- a/src/cwl_utils/cwl_v1_0_expression_refactor.py
+++ b/src/cwl_utils/cwl_v1_0_expression_refactor.py
@@ -5,7 +5,6 @@
 
 import copy
 import hashlib
-import uuid
 from collections.abc import MutableSequence, Sequence
 from contextlib import suppress
 from typing import Any, cast, Final
@@ -294,6 +293,7 @@ def traverse(
                 run=copy.deepcopy(process),
             )
             workflow = cwl.Workflow(
+                id=process.id,
                 inputs=wf_inputs,
                 outputs=wf_outputs,
                 steps=[step],
diff --git a/src/cwl_utils/cwl_v1_1_expression_refactor.py b/src/cwl_utils/cwl_v1_1_expression_refactor.py
index c890bc46..fba3babe 100755
--- a/src/cwl_utils/cwl_v1_1_expression_refactor.py
+++ b/src/cwl_utils/cwl_v1_1_expression_refactor.py
@@ -293,6 +293,7 @@ def traverse(
                 run=copy.deepcopy(process),
             )
             workflow = cwl.Workflow(
+                id=process.id,
                 inputs=wf_inputs,
                 outputs=wf_outputs,
                 steps=[step],
diff --git a/src/cwl_utils/cwl_v1_2_expression_refactor.py b/src/cwl_utils/cwl_v1_2_expression_refactor.py
index 4087743b..2a4ca6da 100755
--- a/src/cwl_utils/cwl_v1_2_expression_refactor.py
+++ b/src/cwl_utils/cwl_v1_2_expression_refactor.py
@@ -294,6 +294,7 @@ def traverse(
                 run=copy.deepcopy(process),
             )
             workflow = cwl.Workflow(
+                id=process.id,
                 inputs=wf_inputs,
                 outputs=wf_outputs,
                 steps=[step],