[protege-discussion] Multi-threading problem (and solution) in Protege-3.2.1 with Jambalaya

[Micheal Hewett]

I am experiencing random deadlocks while
trying to create a knowledge base
from a program running in a tab widget.

Environment:
  Protege 3.2.1 full (all plugins installed), frame mode
  Java JDK 1.5.0_09
  Windows XP Pro
  Dell dual-core Intel hardware

Protege setup:
  tabs enabled: defaults + Algernon + my own

Overview:
  My plugin reads an XML file and imports the data into
  Protege by creating classes, slots and slot values.

Symptoms:
  The plugin randomly hangs in the middle of the import,
    at different places. 
  The more debugging output I generate, the less likely
    it is to hang (I presume because it is updating
    the knowledge base at a slower rate).
  My import program never hangs if I run it standalone
    rather than inside Protege.
  Using a remote debugger I find that the thread doing
    the import is running but not doing anything,
    which implies a deadlock condition.
    My own code is not using synchronization so the problem
    is somewhere else.
  I keep getting a mysterious "jambalaya.properties" file
    in my directory even though I'm not running the Jambalaya
    tab.
  The stack dump of a hung thread is interesting:

Thread [Thread-3] (Suspended)   
    MyJTabbedPane(Container).getComponents_NoClientCode() line: 298   
    MyJTabbedPane(Container).getComponents() line: 291   
    ProjectView.getTabByClassName(String) line: not available   
    JambalayaProjectPlugin.getJambalayaTab() line: 247   
    JambalayaProjectPlugin.knowledgeBaseChanged() line: 164   
    JambalayaProjectPlugin.access$0(JambalayaProjectPlugin) line: 160   
    JambalayaProjectPlugin$1.ownSlotValueChanged(FrameEvent) line: 49   
    EventDispatchFrameStore.dispatchFrameEvent(FrameEvent) line: not 
available   
    EventDispatchFrameStore.dispatchEvent(EventObject) line: not 
available   
    EventDispatchFrameStore.dispatchEvents(Collection, boolean) line: 
not available   
    EventDispatchFrameStore.dispatchEvents(boolean) line: not available   
    EventDispatchFrameStore.dispatchEvents() line: not available   
    EventDispatchFrameStore.setDirectOwnSlotValues(Frame, Slot, 
Collection) line: not available   
    SetDirectOwnSlotValuesCommand.doIt() line: not available   
    UndoFrameStore.simpleCommandExecute(Command) line: not available   
    UndoFrameStore.execute(Command) line: not available   
    UndoFrameStore.setDirectOwnSlotValues(Frame, Slot, Collection) line: 
not available   
    ArgumentCheckingFrameStore.setDirectOwnSlotValues(Frame, Slot, 
Collection) line: not available   
    ChangeMonitorFrameStore.setDirectOwnSlotValues(Frame, Slot, 
Collection) line: not available   
    DefaultDispatch.setDirectOwnSlotValues(FrameStore, Frame, Slot, 
Collection) line: not available   
    CleanDispatchFrameStore.setDirectOwnSlotValues(Frame, Slot, 
Collection) line: not available   
    
DeleteSimplificationFrameStore(FrameStoreAdapter).setDirectOwnSlotValues(Frame, 
Slot, Collection) line: not available   
    DefaultKnowledgeBase.setDirectOwnSlotValues(Frame, Slot, Collection) 
line: not available   
    DefaultKnowledgeBase.addOwnSlotValue(Frame, Slot, Object) line: not 
available   
    DefaultCls(DefaultFrame).addOwnSlotValue(Slot, Object) line: not 
available   
    ZProtegeClass.addSlotValue(Instance, Slot, Object) line: 226   
    ZProtegeClass.findOrCreateProtegeClass(Node, KnowledgeBase, Cls, 
Cls, ZParameters, List<String>) line: 156   
    Z.toProtegeTerm(Node, Cls, Cls, KnowledgeBase, ZParameters, 
List<String>) line: 384   
    Z.processComplexRelation(Node, Cls, Cls, KnowledgeBase, ZParameters, 
List<String>) line: 519   
    Z.toProtegeTerm(Node, Cls, Cls, KnowledgeBase, ZParameters, 
List<String>) line: 412   
    ImportTask.executeOne() line: 107   
    ImportTask(StandardManagedTask).run() line: 388   
    Thread.run() line: 595   

The Jambalaya plugin is apparently attaching a listener to
Protege even though it is not activated.  The listener code
is somehow accidentally causing a deadlock.  Jambalaya is
also unnecessarily using processing time.

Solution:
  I removed the Jambalaya plugin from the Protege folder.
  My import tab doesn't hang now.

Comments:
  Either Jambalaya is ill-behaved because it adds a listener
  in a static initializer or in setup() rather than in the initialize()
  method, or Protege is ill-behaved because it creates an instance
  of each plugin even if it isn't activated by the user.  A non-activated
  plugin shouldn't be consuming processor time.


Thanks,
Mike Hewett
System Architect
Evincii, Inc.