Merge pull request #3125 from mvdbeek/fix_invalid_section_key

Fix tools placed outside of panel section

lib/galaxy/queue_worker.py

@@ -40,6 +40,15 @@ def send_control_task(app, task, noop_self=False, kwargs={}):
 # just an example method.  Ideally this gets pushed into atomic tasks, whether
 # where they're currently invoked, or elsewhere.  (potentially using a dispatch
 # decorator).
+
+def create_panel_section(app, **kwargs):
+    """
+    Updates in memory toolbox dictionary.
+    """
+    log.debug("Updating in-memory tool panel")
+    app.toolbox.create_section(kwargs)
+
+
 def reload_tool(app, **kwargs):
     params = util.Params(kwargs)
     tool_id = params.get('tool_id', None)
@@ -117,7 +126,8 @@ def admin_job_lock(app, **kwargs):
     log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch."
              % (job_lock, "not" if job_lock else "now"))
 
-control_message_to_task = { 'reload_tool': reload_tool,
+control_message_to_task = { 'create_panel_section': create_panel_section,
+                            'reload_tool': reload_tool,
                             'reload_toolbox': reload_toolbox,
                             'reload_data_managers': reload_data_managers,
                             'reload_display_application': reload_display_application,

lib/galaxy/tools/__init__.py

@@ -9,6 +9,7 @@
 import re
 import tarfile
 import tempfile
+import time
 import threading
 import urllib
 from datetime import datetime
@@ -24,7 +25,10 @@
 from galaxy.managers import histories
 from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
 from galaxy import exceptions
-from galaxy.queue_worker import reload_toolbox
+from galaxy.queue_worker import (
+    reload_toolbox,
+    send_control_task
+)
 from galaxy.tools.actions import DefaultToolAction
 from galaxy.tools.actions.upload import UploadToolAction
 from galaxy.tools.actions.data_source import DataSourceToolAction
@@ -115,6 +119,14 @@ def __init__( self, config_filenames, tool_root_dir, app, tool_conf_watcher=None
     def handle_reload_toolbox(self):
         reload_toolbox(self.app)
 
+    def handle_panel_update(self, section_dict):
+        send_control_task(self.app, 'create_panel_section', noop_self=False, kwargs=section_dict)
+        max_wait = 10
+        i = 0
+        while not section_dict['id'] in self._tool_panel and i < max_wait:
+            i += 1
+            time.sleep(1)
+
     def has_reloaded(self, other_toolbox):
         return self._reload_count != other_toolbox._reload_count
 

lib/galaxy/tools/toolbox/base.py

@@ -95,6 +95,13 @@ def handle_reload_toolbox(self):
         interacting with the rest of the Galaxy app or message queues, etc....
         """
 
+    def handle_panel_update(self, section_dict):
+        """Extension-point for Galaxy-app specific reload logic.
+
+        This abstract representation of the toolbox shouldn't have details about
+        interacting with the rest of the Galaxy app or message queues, etc....
+        """
+
     def create_tool( self, config_file, repository_id=None, guid=None, **kwds ):
         raise NotImplementedError()
 
@@ -236,14 +243,19 @@ def get_section( self, section_id, new_label=None, create_if_needed=False ):
                 'id': section_id,
                 'version': '',
             }
-            tool_section = ToolSection( section_dict )
-            self._tool_panel.append_section( tool_panel_section_key, tool_section )
-            log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) )
+            self.handle_panel_update(section_dict)
+            tool_section = self._tool_panel[ tool_panel_section_key ]
             self._save_integrated_tool_panel()
         else:
             tool_section = None
         return tool_panel_section_key, tool_section
 
+    def create_section(self, section_dict):
+        tool_section = ToolSection(section_dict)
+        self._tool_panel.append_section(tool_section.id, tool_section)
+        log.debug("Loading new tool panel section: %s" % str(tool_section.name))
+        return tool_section
+
     def get_integrated_section_for_tool( self, tool ):
         tool_id = tool.id
 

test/unit/tools/test_toolbox.py

@@ -443,6 +443,9 @@ def __init__( self, test_case ):
         )
         self._tool_conf_watcher = get_tool_conf_watcher(dummy_callback)
 
+    def handle_panel_update(self, section_dict):
+        self.create_section(section_dict)
+
 
 def dummy_callback():
     pass