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