From 8edced26852bafdd8f1fd8aa3845403357d5cf5f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 29 Dec 2014 11:48:38 -0500
Subject: [PATCH] Bugfix: Apply tool panel filtering in workflow editor. Bug
 originally reported by Eric here -
 http://dev.list.galaxyproject.org/Bug-Toolbox-filters-not-applied-in-workflows-td4662879.html
 (though this only fixes the superficial bug of them showing up in the
 workflow editor - and does not yet implement "strong" toolbox filters as
 requested).

This is actually a broader change that centralizes logic for listing out tool panel contents when displaying components to the user and the added filtering comes about from that. It also eliminates the last places Galaxy was accessing toolbox.tool_panel directly (in those mako templates).
---
 lib/galaxy/tools/__init__.py                  | 24 +++++++++----------
 templates/admin/package_tool.mako             |  2 +-
 templates/admin/reload_tool.mako              |  2 +-
 templates/webapps/galaxy/workflow/editor.mako |  2 +-
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 19e05bf92f9..c026b8fe481 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1147,24 +1147,22 @@ class ToolBox( object, Dictifiable ):
         """
         return self.app.model.context
 
+    def tool_panel_contents( self, trans, **kwds ):
+        """ Filter tool_panel contents for displaying for user.
+        """
+        context = Bunch( toolbox=self, trans=trans )
+        filters = self.filter_factory.build_filters( trans )
+        for elt in self.tool_panel.itervalues():
+            elt = _filter_for_panel( elt, filters, context )
+            if elt:
+                yield elt
+
     def to_dict( self, trans, in_panel=True, **kwds ):
         """
         to_dict toolbox.
         """
-
-        context = Bunch( toolbox=self, trans=trans, **kwds )
         if in_panel:
-            panel_elts = [ val for val in self.tool_panel.itervalues() ]
-
-            filters = self.filter_factory.build_filters( trans, **kwds )
-
-            filtered_panel_elts = []
-            for index, elt in enumerate( panel_elts ):
-                elt = _filter_for_panel( elt, filters, context )
-                if elt:
-                    filtered_panel_elts.append( elt )
-            panel_elts = filtered_panel_elts
-
+            panel_elts = list( self.tool_panel_contents( trans, **kwds ) )
             # Produce panel.
             rval = []
             kwargs = dict(
diff --git a/templates/admin/package_tool.mako b/templates/admin/package_tool.mako
index fef8ac765d5..1557a5a8273 100644
--- a/templates/admin/package_tool.mako
+++ b/templates/admin/package_tool.mako
@@ -26,7 +26,7 @@ $().ready(function() {
                 Tool to bundle:
             </label>
             <select name="tool_id">
-                %for key, val in toolbox.tool_panel.items():
+                %for val in toolbox.tool_panel_contents( trans ):
                     %if isinstance( val, Tool ):
                         <option value="${val.id|h}">${val.name|h}</option>
                     %elif isinstance( val, ToolSection ):
diff --git a/templates/admin/reload_tool.mako b/templates/admin/reload_tool.mako
index df5dfd498c5..11d486f3b1e 100644
--- a/templates/admin/reload_tool.mako
+++ b/templates/admin/reload_tool.mako
@@ -26,7 +26,7 @@ $().ready(function() {
                 Tool to reload:
             </label>
             <select name="tool_id">
-                %for key, val in toolbox.tool_panel.items():
+                %for val in toolbox.tool_panel_contents( trans ):
                     %if isinstance( val, Tool ):
                         <option value="${val.id}">${val.name|h}</option>
                     %elif isinstance( val, ToolSection ):
diff --git a/templates/webapps/galaxy/workflow/editor.mako b/templates/webapps/galaxy/workflow/editor.mako
index d50d4a27b1e..e4de18ee64f 100644
--- a/templates/webapps/galaxy/workflow/editor.mako
+++ b/templates/webapps/galaxy/workflow/editor.mako
@@ -284,7 +284,7 @@
                 <img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" class="search-spinner" />
             </div>
             <div class="toolSectionList">
-                %for key, val in app.toolbox.tool_panel.items():
+                %for val in app.toolbox.tool_panel_contents( trans ):
                     <div class="toolSectionWrapper">
                     %if isinstance( val, Tool ):
                         ${render_tool( val, False )}