[kepler-users] semantic actor suggestion

Aaron Schultz aschultz at nceas.ucsb.edu
Fri Jul 10 11:02:51 PDT 2009 

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
>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>
>>>>>
>>>>>           
>>>       
>>     
>
>

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