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