Yeah, this is the same one I was getting too -- Aaron?
Shawn On Fri, Jul 10, 2009 at 11:49 AM, Chris Weed<chrisweed at gmail.com> wrote: > After updating from SVN, > I just tried "Save in Library", and I am getting: > Exception occurred during event dispatching: > java.lang.NullPointerException > ? ? ? ?at > org.kepler.kar.gui.SaveInLibraryDialog.determineKarFile(SaveInLibraryDialog.java:255) > ? ? ? ?at > org.kepler.kar.gui.SaveInLibraryDialog._saveCommand(SaveInLibraryDialog.java:371) > ? ? ? ?at > org.kepler.kar.gui.SaveInLibraryDialog.access$0(SaveInLibraryDialog.java:290) > ? ? ? ?at > org.kepler.kar.gui.SaveInLibraryDialog$1.actionPerformed(SaveInLibraryDialog.java:646) > ? ? ? ?at > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) > ? ? ? ?at > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) > ? ? ? ?at > javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) > ? ? ? ?at > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) > ? ? ? ?at > javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) > ? ? ? ?at java.awt.Component.processMouseEvent(Component.java:6216) > ? ? ? ?at javax.swing.JComponent.processMouseEvent(JComponent.java:3265) > ? ? ? ?at java.awt.Component.processEvent(Component.java:5981) > ? ? ? ?at java.awt.Container.processEvent(Container.java:2041) > ? ? ? ?at java.awt.Component.dispatchEventImpl(Component.java:4583) > ? ? ? ?at java.awt.Container.dispatchEventImpl(Container.java:2099) > ? ? ? ?at java.awt.Component.dispatchEvent(Component.java:4413) > ? ? ? ?at > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4556) > ? ? ? ?at > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4220) > ? ? ? ?at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4150) > ? ? ? ?at java.awt.Container.dispatchEventImpl(Container.java:2085) > ? ? ? ?at java.awt.Window.dispatchEventImpl(Window.java:2475) > ? ? ? ?at java.awt.Component.dispatchEvent(Component.java:4413) > ? ? ? ?at java.awt.EventQueue.dispatchEvent(EventQueue.java:599) > ? ? ? ?at > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) > ? ? ? ?at > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) > ? ? ? ?at > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:178) > ? ? ? ?at java.awt.Dialog$1.run(Dialog.java:1051) > ? ? ? ?at java.awt.Dialog$3.run(Dialog.java:1103) > ? ? ? ?at java.security.AccessController.doPrivileged(Native Method) > ? ? ? ?at java.awt.Dialog.show(Dialog.java:1101) > ? ? ? ?at java.awt.Component.show(Component.java:1516) > ? ? ? ?at java.awt.Component.setVisible(Component.java:1468) > ? ? ? ?at java.awt.Window.setVisible(Window.java:841) > ? ? ? ?at java.awt.Dialog.setVisible(Dialog.java:991) > ? ? ? ?at > org.kepler.kar.gui.SaveInLibraryAction.actionPerformed(SaveInLibraryAction.java:83) > ? ? ? ?at > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) > ? ? ? ?at > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) > ? ? ? ?at > javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) > ? ? ? ?at > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) > ? ? ? ?at javax.swing.AbstractButton.doClick(AbstractButton.java:357) > ? ? ? ?at > javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1225) > ? ? ? ?at > javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1266) > ? ? ? ?at java.awt.Component.processMouseEvent(Component.java:6216) > ? ? ? ?at javax.swing.JComponent.processMouseEvent(JComponent.java:3265) > ? ? ? ?at java.awt.Component.processEvent(Component.java:5981) > ? ? ? ?at java.awt.Container.processEvent(Container.java:2041) > ? ? ? ?at java.awt.Component.dispatchEventImpl(Component.java:4583) > ? ? ? ?at java.awt.Container.dispatchEventImpl(Container.java:2099) > ? ? ? ?at java.awt.Component.dispatchEvent(Component.java:4413) > ? ? ? ?at > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4556) > ? ? ? ?at > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4220) > ? ? ? ?at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4150) > ? ? ? ?at java.awt.Container.dispatchEventImpl(Container.java:2085) > ? ? ? ?at java.awt.Window.dispatchEventImpl(Window.java:2475) > ? ? ? ?at java.awt.Component.dispatchEvent(Component.java:4413) > ? ? ? ?at java.awt.EventQueue.dispatchEvent(EventQueue.java:599) > ? ? ? ?at > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) > ? ? ? ?at > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) > ? ? ? ?at > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) > ? ? ? ?at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) > ? ? ? ?at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) > ? ? ? ?at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) > > Is this working for you? > Chris > > On Fri, Jul 10, 2009 at 2:02 PM, Aaron Schultz<aschultz at nceas.ucsb.edu> > wrote: >> >> 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 >>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>>>> >>>>>>> >>>>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> _______________________________________________ >> Kepler-users mailing list >> Kepler-users at kepler-project.org >> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users >> >
