[kepler-users] semantic actor suggestion

Shawn Bowers sbowers at ucdavis.edu
Fri Jul 10 10:06:55 PDT 2009 

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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