Is there a way to get actors into the local library until this is fixed? Chris
On Fri, Jul 10, 2009 at 2:57 PM, Shawn Bowers<sbowers at ucdavis.edu> wrote: > 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 >>> >> >
