[kepler-users] semantic actor suggestion

Chris Weed chrisweed at gmail.com
Mon Jul 13 08:03:29 PDT 2009 

Is there a way to get actors into the local library until this is fixed?
Chris

On Fri, Jul 10, 2009 at 2:57 PM, Shawn Bowers<sbowers at ucdavis.edu> wrote:
> Yeah, this is the same one I was getting too --
>
> Aaron?
>
> Shawn
>
> On Fri, Jul 10, 2009 at 11:49 AM, Chris Weed<chrisweed at gmail.com> wrote:
>> After updating from SVN,
>> I just tried "Save in Library", and I am getting:
>> Exception occurred during event dispatching:
>> java.lang.NullPointerException
>>        at org.kepler.kar.gui.SaveInLibraryDialog.determineKarFile(SaveInLibraryDialog.java:255)
>>        at org.kepler.kar.gui.SaveInLibraryDialog._saveCommand(SaveInLibraryDialog.java:371)
>>        at org.kepler.kar.gui.SaveInLibraryDialog.access$0(SaveInLibraryDialog.java:290)
>>        at org.kepler.kar.gui.SaveInLibraryDialog$1.actionPerformed(SaveInLibraryDialog.java:646)
>>        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
>>        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
>>        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
>>        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
>>        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
>>        at java.awt.Component.processMouseEvent(Component.java:6216)
>>        at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
>>        at java.awt.Component.processEvent(Component.java:5981)
>>        at java.awt.Container.processEvent(Container.java:2041)
>>        at java.awt.Component.dispatchEventImpl(Component.java:4583)
>>        at java.awt.Container.dispatchEventImpl(Container.java:2099)
>>        at java.awt.Component.dispatchEvent(Component.java:4413)
>>        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4556)
>>        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4220)
>>        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4150)
>>        at java.awt.Container.dispatchEventImpl(Container.java:2085)
>>        at java.awt.Window.dispatchEventImpl(Window.java:2475)
>>        at java.awt.Component.dispatchEvent(Component.java:4413)
>>        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
>>        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>>        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>>        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:178)
>>        at java.awt.Dialog$1.run(Dialog.java:1051)
>>        at java.awt.Dialog$3.run(Dialog.java:1103)
>>        at java.security.AccessController.doPrivileged(Native Method)
>>        at java.awt.Dialog.show(Dialog.java:1101)
>>        at java.awt.Component.show(Component.java:1516)
>>        at java.awt.Component.setVisible(Component.java:1468)
>>        at java.awt.Window.setVisible(Window.java:841)
>>        at java.awt.Dialog.setVisible(Dialog.java:991)
>>        at org.kepler.kar.gui.SaveInLibraryAction.actionPerformed(SaveInLibraryAction.java:83)
>>        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
>>        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
>>        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
>>        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
>>        at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
>>        at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1225)
>>        at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1266)
>>        at java.awt.Component.processMouseEvent(Component.java:6216)
>>        at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
>>        at java.awt.Component.processEvent(Component.java:5981)
>>        at java.awt.Container.processEvent(Container.java:2041)
>>        at java.awt.Component.dispatchEventImpl(Component.java:4583)
>>        at java.awt.Container.dispatchEventImpl(Container.java:2099)
>>        at java.awt.Component.dispatchEvent(Component.java:4413)
>>        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4556)
>>        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4220)
>>        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4150)
>>        at java.awt.Container.dispatchEventImpl(Container.java:2085)
>>        at java.awt.Window.dispatchEventImpl(Window.java:2475)
>>        at java.awt.Component.dispatchEvent(Component.java:4413)
>>        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
>>        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>>        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>>        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>>        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>>        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>>        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>>
>> Is this working for you?
>> Chris
>>
>> On Fri, Jul 10, 2009 at 2:02 PM, Aaron Schultz<aschultz at nceas.ucsb.edu> wrote:
>>>
>>> Sure, Shawn, I've reenabled "Save in Library" until Save Archive is fully
>>> operational.
>>>
>>> Just remember that if you use Save in Library, then clean-cache, whatever
>>> you "Saved In Library" is lost forever.
>>>
>>> Aaron
>>>
>>> Shawn Bowers wrote:
>>>>
>>>> OK -- anyway you can resurrect the "Save in Library" and get it
>>>> working as it did w/ the new changes made to KARs/KAR handling, etc.,
>>>> until the "Save Archive (KAR)" is functional?
>>>>
>>>> Shawn
>>>>
>>>> On Fri, Jul 10, 2009 at 10:04 AM, Aaron Schultz<aschultz at nceas.ucsb.edu>
>>>> wrote:
>>>>
>>>>>
>>>>> Shawn, sounds good, if it is not working now as you have described then
>>>>> there are still bugs in the code somewhere.
>>>>>
>>>>> I have done very limited testing on the new code so bugs are quite
>>>>> likely...
>>>>>
>>>>> Aaron
>>>>>
>>>>>
>>>>> Shawn Bowers wrote:
>>>>>
>>>>>>
>>>>>> Hi Aaron,
>>>>>>
>>>>>> Just to clarify what I'm trying to do (which used to work with the
>>>>>> Save in Library feature):
>>>>>>
>>>>>> 1. Drag an actor from the library onto the canvas
>>>>>> 2. Right-click on the actor, select "Semantic Type Annotation..."
>>>>>> 3. Annotate an input port of the actor using the "Semantic Type
>>>>>> Annotation" widget
>>>>>> 4. Right-click on the actor, select "Save Archive (KAR)" (before: Save
>>>>>> in Library)
>>>>>> 5. Drag the actor back onto the canvas to see that its port annotations
>>>>>> survived
>>>>>> 6. Search the library for actors with a matching input annotation type
>>>>>>
>>>>>> When I now do step 4, I only seem to be able to save to the
>>>>>> "Workflows" directory using the Save Archive (KAR) action. When I do
>>>>>> this, I run into the following problems:
>>>>>>
>>>>>> A. The actor shows up under "Workflows", but it appears to be a
>>>>>> workflow (a can icon?).
>>>>>> B. I am not able to do anything with this component, e.g., I cannot
>>>>>> open it (in the tree view), I cannot drag it onto the canvas,
>>>>>> double-clicking it does nothing, right-clicking it does nothing, etc.
>>>>>> C. I am able to search for it by name, but not by its original
>>>>>> semantic type annotations (on actors or ports).
>>>>>>
>>>>>> In general, I like the idea of being able to save to local folders
>>>>>> (assuming one can do the above at a minimum), although it would also
>>>>>> be nice to be able to save to the library as well (and then as an
>>>>>> additional feature, "save the library" ...).  However, if we are going
>>>>>> to have "Save Archive (KAR)" replace the prior "Save in Library"
>>>>>> feature, it should at least support the above features.
>>>>>>
>>>>>> Shawn
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Jul 10, 2009 at 8:46 AM, Aaron Schultz<aschultz at nceas.ucsb.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> It should query the user if no sem types are found.  However it is no
>>>>>>> longer
>>>>>>> required to add sem types before saving since the ability to display
>>>>>>> non
>>>>>>> sem
>>>>>>> typed objs in the library now exists (folders).
>>>>>>>
>>>>>>> -Aaron
>>>>>>>
>>>>>>> On Jul 10, 2009, at 8:35 AM, Matt Jones <jones at nceas.ucsb.edu> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> Aaron,
>>>>>>>>
>>>>>>>> When you do 'Save Archive', it creates a kar file on disk.  Does it
>>>>>>>> also add it to the Library, and does it check that semantic types have
>>>>>>>> been assigned as the old 'Save in Library...' function did?
>>>>>>>>
>>>>>>>> Matt
>>>>>>>>
>>>>>>>> On Fri, Jul 10, 2009 at 7:31 AM, Aaron
>>>>>>>> Schultz<aschultz at nceas.ucsb.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> It has been replaced by save archive
>>>>>>>>>
>>>>>>>>> -Aaron
>>>>>>>>>
>>>>>>>>> On Jul 10, 2009, at 8:05 AM, Shawn Bowers <sbowers at ucdavis.edu>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hi Chris,
>>>>>>>>>>
>>>>>>>>>> It looks like this is happening (possibly) because of changes to the
>>>>>>>>>> StringParameter hierarchy, which now throw NPEs if no named object
>>>>>>>>>> and
>>>>>>>>>> name is given to the constructor.  The semantic search functionality
>>>>>>>>>> was written a while back (circa 2005), and not really used other
>>>>>>>>>> than
>>>>>>>>>> a prototype/demonstration. It could use revamping.
>>>>>>>>>>
>>>>>>>>>> I think I might have fixed it though. However, I cannot easily test
>>>>>>>>>> this since the "Save in Library" functionality was removed, which
>>>>>>>>>> would allow modified actors to be saved in the library, and then
>>>>>>>>>> easily searched.  Typically, I would add sem types to ports and then
>>>>>>>>>> save them to the library. This would then allow me to search for
>>>>>>>>>> actors using this dialog or using the "suggest compatible
>>>>>>>>>> components"
>>>>>>>>>> dialog.
>>>>>>>>>>
>>>>>>>>>> I've CC'd Aaron Schultz (a Kepler developer at NCEAS) who might know
>>>>>>>>>> why this was removed, and whether similar functionality was added (I
>>>>>>>>>> can't find it if it was).  When I bring back the "Save in Library"
>>>>>>>>>> (via uiContextMappings configs) I get exceptions for building KAR
>>>>>>>>>> files ...
>>>>>>>>>>
>>>>>>>>>>  [run] Exception in thread "AWT-EventQueue-0"
>>>>>>>>>> java.lang.NullPointerException
>>>>>>>>>>  [run]    at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.kepler.kar.gui.SaveInLibraryDialog.determineKarFile(SaveInLibraryDialog.java:255)
>>>>>>>>>>  [run]    at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.kepler.kar.gui.SaveInLibraryDialog._saveCommand(SaveInLibraryDialog.java:371)
>>>>>>>>>>  [run]    at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.kepler.kar.gui.SaveInLibraryDialog.access$100(SaveInLibraryDialog.java:98)
>>>>>>>>>>  [run]    at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.kepler.kar.gui.SaveInLibraryDialog$1.actionPerformed(SaveInLibraryDialog.java:646)
>>>>>>>>>>  [run]    at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Shawn
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Tue, Jul 7, 2009 at 11:47 AM, Chris Weed<chrisweed at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> What about the Semantic Search functionality?
>>>>>>>>>>> This looks similar to what I am interested in, but when I try to do
>>>>>>>>>>> a
>>>>>>>>>>> search I get "No search criteria specified"
>>>>>>>>>>> I really expect that this would return a result for the search I
>>>>>>>>>>> specified.
>>>>>>>>>>> Chris
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Jul 1, 2009 at 1:48 PM, Shawn Bowers<sbowers at ucdavis.edu>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Hi Chris,
>>>>>>>>>>>>
>>>>>>>>>>>> Most of the semantic annotation code is now a bit old (3-4 yrs),
>>>>>>>>>>>> and
>>>>>>>>>>>> was a prototype. Prior to this version we actually had an approach
>>>>>>>>>>>> based on a SPARQL implementation, however, it was decided that
>>>>>>>>>>>> Kepler
>>>>>>>>>>>> should adopt an "object manager" approach, which stores actors and
>>>>>>>>>>>> actor metadata (including semantic annotations of actors) using
>>>>>>>>>>>> MoML
>>>>>>>>>>>> and within a relational (in-memory) db. So, SPARQL wouldn't work
>>>>>>>>>>>> for
>>>>>>>>>>>> this, unless we went to an RDF approach for representing
>>>>>>>>>>>> annotations,
>>>>>>>>>>>> metadata, etc. Another problem with SPARQL (I think this is what
>>>>>>>>>>>> you
>>>>>>>>>>>> meant) at least from my experience is that it is more focussed on
>>>>>>>>>>>> querying resources and their properties, and less useful for
>>>>>>>>>>>> querying
>>>>>>>>>>>> over class definitions. The latter requires a reasoner (like
>>>>>>>>>>>> Pellet,
>>>>>>>>>>>> Fact++, etc.). Finding actors based on their semantic types is all
>>>>>>>>>>>> about matching class definitions, and not about searching for
>>>>>>>>>>>> class
>>>>>>>>>>>> instances.
>>>>>>>>>>>>
>>>>>>>>>>>> Anyway, we are currently in the process of revamping the
>>>>>>>>>>>> annotation
>>>>>>>>>>>> interfaces to make it easier and hopefully more obvious to folks
>>>>>>>>>>>> that
>>>>>>>>>>>> actors (and their ports) can be tagged (e.g., a draft plan for
>>>>>>>>>>>> this
>>>>>>>>>>>> is
>>>>>>>>>>>> here:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> https://kepler-project.org/developers/incubation/GUI/kepler-tagging).
>>>>>>>>>>>> So far, zero Kepler actors have their ports annotated. But perhaps
>>>>>>>>>>>> with some UI changes more actors will be annotated, etc.  We are
>>>>>>>>>>>> also
>>>>>>>>>>>> making changes so that basic types of ontology creation and
>>>>>>>>>>>> editing
>>>>>>>>>>>> are exposed and available from within Kepler. Again, this might
>>>>>>>>>>>> make
>>>>>>>>>>>> the annotation capabilities more usable.
>>>>>>>>>>>>
>>>>>>>>>>>> If you would like to help with any of this (designing and/or
>>>>>>>>>>>> implement
>>>>>>>>>>>> ui's, designing apis, suggesting features, architecture,
>>>>>>>>>>>> technology's,
>>>>>>>>>>>> etc.) that would be awesome!
>>>>>>>>>>>>
>>>>>>>>>>>> Shawn
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Jul 1, 2009 at 10:18 AM, Chris Weed<chrisweed at gmail.com>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>> I have a few questions about the semantic annotation
>>>>>>>>>>>>> functionality.
>>>>>>>>>>>>> I noticed in the semantic search browser it displays the
>>>>>>>>>>>>> properties,
>>>>>>>>>>>>> but I wasn't sure if it used that for doing searches.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Also, I was looking through the code for performing the semantic
>>>>>>>>>>>>> actor
>>>>>>>>>>>>> suggestion,
>>>>>>>>>>>>> and it looks like it uses a hand-coded matching algorithm instead
>>>>>>>>>>>>> of
>>>>>>>>>>>>> a
>>>>>>>>>>>>> SQARQL
>>>>>>>>>>>>> based inference engine. Would it make sense to update this
>>>>>>>>>>>>> functionality
>>>>>>>>>>>>> which would allow more sophisticated searches with properties.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Chris
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Kepler-users mailing list
>>>>>>>>>>>>> Kepler-users at kepler-project.org
>>>>>>>>>>>>>
>>>>>>>>>>>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Kepler-users mailing list
>>>>>>>>> Kepler-users at kepler-project.org
>>>>>>>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>>>> Matthew B. Jones
>>>>>>>> Director of Informatics Research and Development
>>>>>>>> National Center for Ecological Analysis and Synthesis (NCEAS)
>>>>>>>> UC Santa Barbara
>>>>>>>> jones at nceas.ucsb.edu                       Ph: 1-907-523-1960
>>>>>>>> http://www.nceas.ucsb.edu/ecoinfo
>>>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Kepler-users mailing list
>>> Kepler-users at kepler-project.org
>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>
>>
>

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