From 061d5a4b6258f7c5cfabd6b910f103af8f1d69f5 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Thu, 25 Apr 2024 15:29:05 +0200
Subject: [PATCH 1/3] copy comments when copying workflow

---
 lib/galaxy/model/__init__.py | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 3e78689a2a39..9de5be22593a 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7707,6 +7707,25 @@ def copy(self, user=None):
         for old_step, new_step in zip(self.steps, copied_steps):
             old_step.copy_to(new_step, step_mapping, user=user)
         copied_workflow.steps = copied_steps
+
+        copied_comments = []
+        for comment in self.comments:
+            copied_comments.append(comment.copy())
+
+        # copy comment relationships
+        for old_comment, new_comment in zip(self.comments, copied_comments):
+            for step_id in [step.order_index for step in old_comment.child_steps]:
+                child_step = copied_workflow.steps[step_id]
+                if child_step:
+                    child_step.parent_comment = new_comment
+
+            for comment_id in [comment.order_index for comment in old_comment.child_comments]:
+                child_comment = copied_workflow.comments[comment_id]
+                if child_comment:
+                    child_comment.parent_comment = new_comment
+
+        copied_workflow.comments = copied_comments
+
         return copied_workflow
 
     @property
@@ -8266,6 +8285,17 @@ def from_dict(dict):
         comment.data = dict.get("data", None)
         return comment
 
+    def copy(self):
+        comment = WorkflowComment()
+        comment.order_index = self.order_index
+        comment.type = self.type
+        comment.position = self.position
+        comment.size = self.size
+        comment.color = self.color
+        comment.data = self.data
+
+        return comment
+
 
 class StoredWorkflowUserShareAssociation(Base, UserShareAssociation):
     __tablename__ = "stored_workflow_user_share_connection"

From f9b2a68ce4c48fa48a35faf6020ac7bc83ebf846 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 26 Apr 2024 14:25:50 +0200
Subject: [PATCH 2/3] use dict instead of relying on list order

---
 lib/galaxy/model/__init__.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 9de5be22593a..d592f9308bfa 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7712,15 +7712,18 @@ def copy(self, user=None):
         for comment in self.comments:
             copied_comments.append(comment.copy())
 
+        steps_by_id = {s.order_index: s for s in copied_workflow.steps}
+        comments_by_id = {c.order_index: c for c in copied_workflow.comments}
+
         # copy comment relationships
         for old_comment, new_comment in zip(self.comments, copied_comments):
             for step_id in [step.order_index for step in old_comment.child_steps]:
-                child_step = copied_workflow.steps[step_id]
+                child_step = steps_by_id.get(step_id)
                 if child_step:
                     child_step.parent_comment = new_comment
 
             for comment_id in [comment.order_index for comment in old_comment.child_comments]:
-                child_comment = copied_workflow.comments[comment_id]
+                child_comment = comments_by_id.get(comment_id)
                 if child_comment:
                     child_comment.parent_comment = new_comment
 

From 69fb6cee1f3937a382ed63e847618a77ffb46add Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 26 Apr 2024 14:41:42 +0200
Subject: [PATCH 3/3] fix comments used before assigned

---
 lib/galaxy/model/__init__.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d592f9308bfa..40a8d414f8c9 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7708,12 +7708,9 @@ def copy(self, user=None):
             old_step.copy_to(new_step, step_mapping, user=user)
         copied_workflow.steps = copied_steps
 
-        copied_comments = []
-        for comment in self.comments:
-            copied_comments.append(comment.copy())
-
+        copied_comments = [comment.copy() for comment in self.comments]
         steps_by_id = {s.order_index: s for s in copied_workflow.steps}
-        comments_by_id = {c.order_index: c for c in copied_workflow.comments}
+        comments_by_id = {c.order_index: c for c in copied_comments}
 
         # copy comment relationships
         for old_comment, new_comment in zip(self.comments, copied_comments):