From 3e4089526e7d5f1c04dceb0418bcc58c681e64fd Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 15 Nov 2023 14:12:07 -0500
Subject: [PATCH] Fix duplicated tools in tool panel view section copying.

---
 lib/galaxy/tool_util/toolbox/panel.py        | 28 ++++++++++++++++++--
 lib/galaxy/tool_util/toolbox/views/static.py |  5 ++--
 2 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 8375d39441d..0c98a28d3f2 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -63,14 +63,38 @@ class ToolSection(Dictifiable, HasPanelItems):
         self.links = item.get("links") or None
         self.elems = ToolPanelElements()
 
-    def copy(self):
+    def copy(self, merge_tools=False):
         copy = ToolSection()
         copy.name = self.name
         copy.id = self.id
         copy.version = self.version
         copy.description = self.description
         copy.links = self.links
-        copy.elems.update(self.elems)
+
+        for key, panel_type, value in self.panel_items_iter():
+            if panel_type == panel_item_types.TOOL and merge_tools:
+                tool = value
+                tool_lineage = tool.lineage
+
+                tool_copied = False
+                if tool_lineage is not None:
+                    version_ids = tool_lineage.get_version_ids(reverse=True)
+
+                    for version_id in version_ids:
+                        if copy.elems.has_tool_with_id(version_id):
+                            tool_copied = True
+                            break
+
+                        if self.elems.has_tool_with_id(version_id):
+                            copy.elems.append_tool(self.elems.get_tool_with_id(version_id))
+                            tool_copied = True
+                            break
+
+                if not tool_copied:
+                    copy.elems[key] = value
+            else:
+                copy.elems[key] = value
+
         return copy
 
     def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None):
diff --git a/lib/galaxy/tool_util/toolbox/views/static.py b/lib/galaxy/tool_util/toolbox/views/static.py
index 750426e8908..2eba8eef3f4 100644
--- a/lib/galaxy/tool_util/toolbox/views/static.py
+++ b/lib/galaxy/tool_util/toolbox/views/static.py
@@ -120,7 +120,7 @@ class StaticToolPanelView(ToolPanelView):
                             f"Failed to find matching section for (id, name) = ({element.section}, {element.section})"
                         )
                         continue
-                    section = closest_section.copy()
+                    section = closest_section.copy(merge_tools=True)
                     apply_filter(element, section.elems)
                     new_panel.append_section(section.id, section)
                 elif element.content_type == "label":
@@ -151,7 +151,8 @@ class StaticToolPanelView(ToolPanelView):
                     if closest_section is None:
                         log.warning(f"Failed to find matching section for (id, name) = ({element.items_from}, None)")
                         continue
-                    elems = closest_section.elems.copy()
+                    section = closest_section.copy(merge_tools=True)
+                    elems = section.elems
                     apply_filter(element, elems)
                     for key, item in elems.items():
                         new_panel[key] = item