[kepler-users] semantic actor suggestion

Fri Jul 10 09:46:13 PDT 2009

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 It has been replaced by save archive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
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>