Allow toolbox reloading via app, UI, and API.

Introduce an app ToolCache to help ensure this operation remains speedy.

lib/galaxy/config.py

@@ -744,19 +744,26 @@ class ConfiguresGalaxyMixin:
     def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ):
         self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style )
 
-    def _configure_toolbox( self ):
+    def reload_toolbox(self):
         # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
+
         tool_configs = self.config.tool_configs
         if self.config.migrated_tools_config not in tool_configs:
             tool_configs.append( self.config.migrated_tools_config )
 
-        from galaxy.managers.citations import CitationsManager
-        self.citations_manager = CitationsManager( self )
-
         from galaxy import tools
         self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
         self.reindex_tool_search()
 
+    def _configure_toolbox( self ):
+        from galaxy.managers.citations import CitationsManager
+        self.citations_manager = CitationsManager( self )
+
+        from galaxy.tools.toolbox.cache import ToolCache
+        self.tool_cache = ToolCache()
+
+        self.reload_toolbox()
+
         from galaxy.tools.deps import containers
         galaxy_root_dir = os.path.abspath(self.config.root)
         file_path = os.path.abspath(getattr(self.config, "file_path"))

lib/galaxy/tools/toolbox/base.py

@@ -708,7 +708,12 @@ def quick_load( tool_file, async=True ):
     def load_tool( self, config_file, guid=None, repository_id=None, **kwds ):
         """Load a single tool from the file named by `config_file` and return an instance of `Tool`."""
         # Parse XML configuration file and get the root element
-        tool = self.create_tool( config_file=config_file, repository_id=repository_id, guid=guid, **kwds )
+        tool_cache = getattr( self.app, 'tool_cache', None )
+        tool = tool_cache and tool_cache.get_tool( config_file )
+        if tool is None:
+            tool = self.create_tool( config_file=config_file, repository_id=repository_id, guid=guid, **kwds )
+            if tool_cache:
+                self.app.tool_cache.cache_tool(config_file, tool)
         tool_id = tool.id
         if not tool_id.startswith("__"):
             # do not monitor special tools written to tmp directory - no reason

lib/galaxy/tools/toolbox/cache.py

@@ -0,0 +1,17 @@
+
+
+class ToolCache(object):
+    """ Cache tool defintions to allow quickly reloading the whole
+    toolbox.
+    """
+
+    def __init__(self):
+        self._tools_by_path = {}
+
+    def get_tool(self, config_filename):
+        """ Get the tool from the cache if the tool is up to date.
+        """
+        return self._tools_by_path.get(config_filename, None)
+
+    def cache_tool(self, config_filename, tool):
+        self._tools_by_path[config_filename] = tool

lib/galaxy/webapps/galaxy/api/configuration.py

@@ -82,6 +82,15 @@ def tool_lineages(self, trans):
             rval.append(entry)
         return rval
 
+    @expose_api
+    @require_admin
+    def reload_toolbox(self, trans):
+        """
+        PUT /api/configuration/toolbox
+        Reload the Galaxy toolbox (but not individual tools).
+        """
+        self.app.reload_toolbox()
+
 
 def _tool_conf_to_dict(conf):
     return dict(

lib/galaxy/webapps/galaxy/buildapp.py

@@ -277,6 +277,12 @@ def populate_api_routes( webapp, app ):
         controller="configuration",
         action="tool_lineages"
     )
+    webapp.mapper.connect(
+        '/api/configuration/toolbox',
+        controller="configuration",
+        action="reload_toolbox",
+        conditions=dict( method=["PUT"] )
+    )
     webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' )
     webapp.mapper.connect( "configuration_version",
                            "/api/version", controller="configuration",

lib/tool_shed/galaxy_install/tool_migration_manager.py

@@ -11,6 +11,7 @@
 
 from galaxy import util
 from galaxy.tools.toolbox import ToolSection
+from galaxy.tools.toolbox.parser import ensure_tool_conf_item
 from galaxy.util.odict import odict
 
 from tool_shed.galaxy_install import install_manager
@@ -272,7 +273,7 @@ def get_containing_tool_sections( self, tool_config ):
                         proprietary_tool_config = section_elem.get( 'file' )
                         if tool_config == proprietary_tool_config:
                             # The tool is loaded inside of the section_elem.
-                            tool_sections.append( ToolSection( proprietary_tool_panel_elem ) )
+                            tool_sections.append( ToolSection( ensure_tool_conf_item( proprietary_tool_panel_elem ) ) )
                             if not is_displayed:
                                 is_displayed = True
         return is_displayed, tool_sections

templates/admin/reload_tool.mako

@@ -14,6 +14,17 @@ $().ready(function() {
 %endif
     focus_el.focus();
 });
+$().ready(function() {
+    $("#reload_toolbox").click(function(){
+        $.ajax({
+            url: "${h.url_for(controller="/api/configuration", action="toolbox")}",
+            type: 'PUT',
+            success: function(result) {
+                alert("Toolbox reloaded.");
+            }
+        });
+    });
+});
 </script>
 
 %if message:
@@ -54,3 +65,18 @@ $().ready(function() {
     </form>
     </div>
 </div>
+<p>
+<div class="toolForm">
+    <div class="toolFormTitle">Reload Toolbox</div>
+    <div class="toolFormBody">
+    <form name="reload_toolbox_form" id="reload_toolbox_form" action="" method="" >
+        <div class="form-row">
+        Clicking <a href="#" id="reload_toolbox">here</a> will reload
+        the Galaxy toolbox. This will cause newly discovered tools
+        to be added, tools now missing from tool confs to be removed,
+        and items in the panel reordered. Individual tools, even ones
+        with modified tool descriptions willl not be reloaded.
+        </div>
+    </form>
+    </div>
+</div>