[kepler-users] semantic actor suggestion

Aaron Schultz aschultz at nceas.ucsb.edu
Fri Jul 10 10:04:50 PDT 2009 

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
>>>>>>>>
>>>>>>>>                 
>>>> _______________________________________________
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>>>>
>>>>         
>>>
>>> --
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> 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
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>>       
>
>

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