Protege desktop 5.5.0 SPARQL

classic Classic list List threaded Threaded
20 messages Options
Reply | Threaded
Open this post in threaded view
|

Protege desktop 5.5.0 SPARQL

Grove, Christian A. (Chris)
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Michael DeBellis-2
I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Csongor Nyulas
Administrator
In reply to this post by Grove, Christian A. (Chris)
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Csongor Nyulas
Administrator
In reply to this post by Michael DeBellis-2
Hi Michael,

Can you please file an issue for this here:
https://github.com/protegeproject/sparql-query-plugin/issues

It would be great if you could generate a (non-confidential) ontology that exhibits the behavior, and attach it to the issue. Otherwise we may not be able to reproduce it and fix it.

Thanks,
Csongor


On 7/9/19 12:57 PM, Michael DeBellis wrote:
I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Michael DeBellis-2
Sounds good.  

Michael

On Tue, Jul 9, 2019 at 1:07 PM Csongor Nyulas <[hidden email]> wrote:
Hi Michael,

Can you please file an issue for this here:
https://github.com/protegeproject/sparql-query-plugin/issues

It would be great if you could generate a (non-confidential) ontology that exhibits the behavior, and attach it to the issue. Otherwise we may not be able to reproduce it and fix it.

Thanks,
Csongor


On 7/9/19 12:57 PM, Michael DeBellis wrote:
I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Grove, Christian A. (Chris)
In reply to this post by Csongor Nyulas
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user <[hidden email]> on behalf of Csongor Nyulas <[hidden email]>
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Michael DeBellis-2
Chris, it might be a good idea for you to create the ticket if you have time. I'm still waiting to hear back from my colleague on whether we can share the ontology and we are in a crunch time now anyway to finish a paper for a deadline so I may not have time to create the ticket for a while. 

Michael

On Tue, Jul 9, 2019 at 2:09 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user <[hidden email]> on behalf of Csongor Nyulas <[hidden email]>
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Csongor Nyulas
Administrator
In reply to this post by Grove, Christian A. (Chris)
Hi Chris,
This may be different issue from what Michael described.

Can you try something for me:
- Download the platform independent version of Protege 5.5 (follow the link called "Download platform independent version (requires a Java Runtime Environment)" below the Download button on this page: https://protege.stanford.edu/products.php#desktop-protege).
- unpack the zip file, and copy the rdf-library-3.0.0.jar and sparql-query-plugin-3.0.0.jar files from the plugins directory to your Protege installation's plugins directory, and remove the older (2.0.3 and 2.0.2) versions of those plugins.
- see if you still get the error after restarting and trying to use the SPARQL Query tab.

Thanks,
Csongor


On 7/9/19 2:09 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Lorenz Buehmann
In reply to this post by Grove, Christian A. (Chris)
That is a dependency conflict where you have multiple versions of OWL API in the classpath
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Lorenz Buehmann
In reply to this post by Michael DeBellis-2
I checked the code, it looks very inefficient.

The ontology is converted to triples for RDF4J API, but the confusing thing is that for each single axiom a very expensive method RDFTranslator::translate() is called

        RDFTranslator translator = null;
       
        try {
            OWLOntology ontology = createOntology(manager, axiom);
            translator = new RDFTranslator(repository, manager, ontology);
            ValueFactory rdfFactory = repository.getValueFactory();
            RepositoryConnection connection = translator.getConnection();
            axiom.accept(translator);
            for (OWLEntity entity : axiom.getSignature()) {  // why aren't these getting included?
                connection.add(rdfFactory.createURI(entity.getIRI().toString()),
                               rdfFactory.createURI(OWLRDFVocabulary.RDF_TYPE.getIRI().toString()),
                               rdfFactory.createURI(entity.getEntityType().getVocabulary().getIRI().toString()),
                               translator.axiomResource);
            }

            org.openrdf.model.Literal hashCodeValue = rdfFactory.createLiteral(axiom.hashCode());
            connection.add(translator.axiomResource, hashCodeProperty, hashCodeValue);
            connection.add(translator.axiomResource, sourceOntologyProperty, ontologyRepresentative);
            success = true;
        }
so for each axiom, several objects like OWLOntology are created, a connection is opened, etc.

Wondering why this isn't just done as batch with something like translate(Set<OWLAxiom> axioms) instead? Would be much more efficient from my point of view.

By the way, it's part of the rdf-library project





I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Michael DeBellis-2
In reply to this post by Csongor Nyulas
Csongor, I received permission to send the ontology and I created the issue. However, when I tried to attach the problem ontology by dragging and dropping it into the issue report (as the issue tracking software suggests) I received the message "We don't support that file type, try JPEG, ..." I hope you don't mind but I will send the problem ontology directly to you. Feel free to share it with anyone who might help resolve the issue, it's just I would rather not submit it to the entire list.   Thanks for your help.

Michael



On Tue, Jul 9, 2019 at 1:07 PM Csongor Nyulas <[hidden email]> wrote:
Hi Michael,

Can you please file an issue for this here:
https://github.com/protegeproject/sparql-query-plugin/issues

It would be great if you could generate a (non-confidential) ontology that exhibits the behavior, and attach it to the issue. Otherwise we may not be able to reproduce it and fix it.

Thanks,
Csongor


On 7/9/19 12:57 PM, Michael DeBellis wrote:
I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Csongor Nyulas
Administrator
Hi Michael,

That's fine. I got the ontology. I will share it with my colleagues, as I may not have time to look at this issue in the upcoming days.
Thanks for submitting the issue, BTW!

Csongor

On 7/12/19 10:42 AM, Michael DeBellis wrote:
Csongor, I received permission to send the ontology and I created the issue. However, when I tried to attach the problem ontology by dragging and dropping it into the issue report (as the issue tracking software suggests) I received the message "We don't support that file type, try JPEG, ..." I hope you don't mind but I will send the problem ontology directly to you. Feel free to share it with anyone who might help resolve the issue, it's just I would rather not submit it to the entire list.   Thanks for your help.

Michael



On Tue, Jul 9, 2019 at 1:07 PM Csongor Nyulas <[hidden email]> wrote:
Hi Michael,

Can you please file an issue for this here:
https://github.com/protegeproject/sparql-query-plugin/issues

It would be great if you could generate a (non-confidential) ontology that exhibits the behavior, and attach it to the issue. Otherwise we may not be able to reproduce it and fix it.

Thanks,
Csongor


On 7/9/19 12:57 PM, Michael DeBellis wrote:
I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Grove, Christian A. (Chris)
In reply to this post by Csongor Nyulas
Hi Csongor,

OK, I've tried your suggestion, but now instead of throwing an error message to the log, as soon as I click on the "SPARQL Query" tab (with a non-trivial ontology) Protege completely freezes up and becomes totally unresponsive.

Also, I have a question about plugins and the paths where they should be stored/installed. I have a iMac and am running OS X (10.14.5) and I can find the default location for the 'rdf-library-3.0.0.jar' and 'sparql-query-plugin-3.0.0.jar' files in this location:

/Applications/Protege-5.5.0/Protégé.app/Contents/Java/plugins

I think it was working the other day where I could delete those .jar files from that directory, restart Protege, run "File > Check for plugins..." and then see the respective plugins appear with the 2.0.x versions allowing me to install those. Now, for some reason, if I repeat this process (after, say, reinstalling Protege-5.5.0 and deleting the jar files, or just deleting the rdf-library and sparql .jar files again), I don't get any suggested plugins after checking for plugins.

I'm wondering how I trigger Protege to suggest the 2.0.x versions of those plugins once I've deleted them (or where to download them manually and then where to install them).

Thanks,

Chris



From: protege-user <[hidden email]> on behalf of Csongor Nyulas <[hidden email]>
Sent: Tuesday, July 9, 2019 4:52 PM
To: [hidden email]
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,
This may be different issue from what Michael described.

Can you try something for me:
- Download the platform independent version of Protege 5.5 (follow the link called "Download platform independent version (requires a Java Runtime Environment)" below the Download button on this page: https://protege.stanford.edu/products.php#desktop-protege).
- unpack the zip file, and copy the rdf-library-3.0.0.jar and sparql-query-plugin-3.0.0.jar files from the plugins directory to your Protege installation's plugins directory, and remove the older (2.0.3 and 2.0.2) versions of those plugins.
- see if you still get the error after restarting and trying to use the SPARQL Query tab.

Thanks,
Csongor


On 7/9/19 2:09 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Grove, Christian A. (Chris)
In reply to this post by Michael DeBellis-2
Hi Michael,

Once I've exhausted the reasonable options with Csongor et al., I will surely make a ticket.

Thanks!

Chris

From: protege-user <[hidden email]> on behalf of Michael DeBellis <[hidden email]>
Sent: Tuesday, July 9, 2019 3:17 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Chris, it might be a good idea for you to create the ticket if you have time. I'm still waiting to hear back from my colleague on whether we can share the ontology and we are in a crunch time now anyway to finish a paper for a deadline so I may not have time to create the ticket for a while. 

Michael

On Tue, Jul 9, 2019 at 2:09 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user <[hidden email]> on behalf of Csongor Nyulas <[hidden email]>
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Grove, Christian A. (Chris)
In reply to this post by Lorenz Buehmann
Hi Lorenz,

OK, thanks! Can you suggest a fix for this? I'm still struggling a bit to understand all of the paths I should be checking and maintaining.

Chris

From: protege-user <[hidden email]> on behalf of Lorenz B. <[hidden email]>
Sent: Tuesday, July 9, 2019 11:44 PM
To: [hidden email]
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
That is a dependency conflict where you have multiple versions of OWL API in the classpath
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Csongor Nyulas
Administrator
In reply to this post by Grove, Christian A. (Chris)
Hi Chris,

The best would be to use the version 3.0.0 of both plug-ins. The previous 2.0.x versions may be incompatible with Protege 5.5. I think that is what Lorenz suggested also.

When Protege becomes unresponsive, will you get an OutOfMemory error after some time?
Can you confirm that you have the same problem described by Michael DeBellis in this issue:
    https://github.com/protegeproject/sparql-query-plugin/issues/21 ?
If yes, can you increase your maximum heap size (say double the current amount)?

Csongor


On 7/12/19 1:01 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

OK, I've tried your suggestion, but now instead of throwing an error message to the log, as soon as I click on the "SPARQL Query" tab (with a non-trivial ontology) Protege completely freezes up and becomes totally unresponsive.

Also, I have a question about plugins and the paths where they should be stored/installed. I have a iMac and am running OS X (10.14.5) and I can find the default location for the 'rdf-library-3.0.0.jar' and 'sparql-query-plugin-3.0.0.jar' files in this location:

/Applications/Protege-5.5.0/Protégé.app/Contents/Java/plugins

I think it was working the other day where I could delete those .jar files from that directory, restart Protege, run "File > Check for plugins..." and then see the respective plugins appear with the 2.0.x versions allowing me to install those. Now, for some reason, if I repeat this process (after, say, reinstalling Protege-5.5.0 and deleting the jar files, or just deleting the rdf-library and sparql .jar files again), I don't get any suggested plugins after checking for plugins.

I'm wondering how I trigger Protege to suggest the 2.0.x versions of those plugins once I've deleted them (or where to download them manually and then where to install them).

Thanks,

Chris



From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 4:52 PM
To: [hidden email]
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,
This may be different issue from what Michael described.

Can you try something for me:
- Download the platform independent version of Protege 5.5 (follow the link called "Download platform independent version (requires a Java Runtime Environment)" below the Download button on this page: https://protege.stanford.edu/products.php#desktop-protege).
- unpack the zip file, and copy the rdf-library-3.0.0.jar and sparql-query-plugin-3.0.0.jar files from the plugins directory to your Protege installation's plugins directory, and remove the older (2.0.3 and 2.0.2) versions of those plugins.
- see if you still get the error after restarting and trying to use the SPARQL Query tab.

Thanks,
Csongor


On 7/9/19 2:09 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

samsontu
In reply to this post by Michael DeBellis-2
Michael,

I loaded your ontology and opened SPARQL Query Tab. After a few minutes of being unresponsive, Protege came back normally with the standard subClassOf query (which worked fine). 

I am using a MacBook Pro, with
  INFO  14:00:05  ------------------------------------ Protege -----------------------------------
   INFO  14:00:05  Protege Desktop
   INFO  14:00:05  Version 5.5.0, Build 
   INFO  14:00:05  
   INFO  14:00:05  
   INFO  14:00:05  ----------------------------------- Platform -----------------------------------
   INFO  14:00:05  Java: JVM 1.8.0_121-b13  Memory: 5592M
   INFO  14:00:05  Language: en, Country: US
   INFO  14:00:05  Framework: Apache Software Foundation (1.8) 
   INFO  14:00:05  OS: macosx (10.14.5)
   INFO  14:00:05  Processor: x86-64

   INFO  14:00:05  
   INFO  14:00:05  ------------------------------------ Plugins -----------------------------------
   INFO  14:00:05  Plugin: OWLAPI RDF Library (3.0.0)
   INFO  14:00:05  Plugin: SPARQL Query Plugin (3.0.0)


There is no error message in the log file.

How much memory was allocated to Protege in your work? That may be the problem.

With best regards,
Samson


On Jul 9, 2019, at 12:57 PM, Michael DeBellis <[hidden email]> wrote:

I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Grove, Christian A. (Chris)
In reply to this post by Csongor Nyulas
Hi Csongor,

OK, so I let Protege run after hanging and the SPARQL Query tab eventually shows up without error but takes >15 minutes. I think my default heap/memory allocation was set to 1/4 of my physical memory, so 16GB (I have 64GB total). I upped the allocated memory by editing the "Info.plist" file in my directory:

/Applications/Protege-5.5.0/Protégé.app/Contents/

by editing the VMOptions from:

        <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>

to:

        <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xmn30G</string>
            <string>-Xms30G</string>
            <string>-Xmx30G</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>

The Protege log then reads, upon restarting:

   INFO  11:08:37  ------------------------------------ Protege -----------------------------------
   INFO  11:08:37  Protege Desktop
   INFO  11:08:37  Version 5.5.0, Build
   INFO  11:08:37  
   INFO  11:08:37  
   INFO  11:08:37  ----------------------------------- Platform -----------------------------------
   INFO  11:08:37  Java: JVM 1.8.0_121-b13  Memory: 28186M
   INFO  11:08:37  Language: en, Country: US
   INFO  11:08:37  Framework: Apache Software Foundation (1.8)
   INFO  11:08:37  OS: macosx (10.14.5)
   INFO  11:08:37  Processor: x86-64

so it seems the allocated memory is now about 28GB. I retried opening my ontology and then clicking on the SPARQL Query tab and it eventually loaded but took more than 25 minutes to do so. Should I really be expecting to wait that long for the tab to load?

Thanks,

Chris

PS. I'm pretty much hacking my way through adjusting the heap size, so please let me know if there's a better way.


From: protege-user <[hidden email]> on behalf of Csongor Nyulas <[hidden email]>
Sent: Friday, July 12, 2019 2:02 PM
To: [hidden email]
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

The best would be to use the version 3.0.0 of both plug-ins. The previous 2.0.x versions may be incompatible with Protege 5.5. I think that is what Lorenz suggested also.

When Protege becomes unresponsive, will you get an OutOfMemory error after some time?
Can you confirm that you have the same problem described by Michael DeBellis in this issue:
    https://github.com/protegeproject/sparql-query-plugin/issues/21 ?
If yes, can you increase your maximum heap size (say double the current amount)?

Csongor


On 7/12/19 1:01 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

OK, I've tried your suggestion, but now instead of throwing an error message to the log, as soon as I click on the "SPARQL Query" tab (with a non-trivial ontology) Protege completely freezes up and becomes totally unresponsive.

Also, I have a question about plugins and the paths where they should be stored/installed. I have a iMac and am running OS X (10.14.5) and I can find the default location for the 'rdf-library-3.0.0.jar' and 'sparql-query-plugin-3.0.0.jar' files in this location:

/Applications/Protege-5.5.0/Protégé.app/Contents/Java/plugins

I think it was working the other day where I could delete those .jar files from that directory, restart Protege, run "File > Check for plugins..." and then see the respective plugins appear with the 2.0.x versions allowing me to install those. Now, for some reason, if I repeat this process (after, say, reinstalling Protege-5.5.0 and deleting the jar files, or just deleting the rdf-library and sparql .jar files again), I don't get any suggested plugins after checking for plugins.

I'm wondering how I trigger Protege to suggest the 2.0.x versions of those plugins once I've deleted them (or where to download them manually and then where to install them).

Thanks,

Chris



From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 4:52 PM
To: [hidden email]
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,
This may be different issue from what Michael described.

Can you try something for me:
- Download the platform independent version of Protege 5.5 (follow the link called "Download platform independent version (requires a Java Runtime Environment)" below the Download button on this page: https://protege.stanford.edu/products.php#desktop-protege).
- unpack the zip file, and copy the rdf-library-3.0.0.jar and sparql-query-plugin-3.0.0.jar files from the plugins directory to your Protege installation's plugins directory, and remove the older (2.0.3 and 2.0.2) versions of those plugins.
- see if you still get the error after restarting and trying to use the SPARQL Query tab.

Thanks,
Csongor


On 7/9/19 2:09 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Michael DeBellis-2
In reply to this post by samsontu
Samson, I'm just catching up on my emails. I had a feeling this had to do with memory due to the error message I got. I haven't done anything special regarding setting up memory allocation for Protege so it just has whatever the out of the box memory configuration is for 5.5.0 on a Windows machine. I just went into Help>About and it says (underneath Version next to Memory Settings): Max memory set to 444MB via Java -Xmx setting Currently using 155MB (this is with no ontology loaded). 

I went into Java from the Start menu of applications on Windows and found a dialogue with tabs for General, Update, Security, and Advanced but didn't see anything that looked like the right parameter to edit. 

I'm sure for most people the way to add more memory would be obvious but can you or someone give me the "For Dummies" version of how one adds memory for Protege in Windows?  I'm guessing I have to edit a configuration file or something but am really ignorant when it comes to that kind of stuff. Thanks in advance for any guidance.

Michael

On Fri, Jul 12, 2019 at 2:16 PM Samson Tu <[hidden email]> wrote:
Michael,

I loaded your ontology and opened SPARQL Query Tab. After a few minutes of being unresponsive, Protege came back normally with the standard subClassOf query (which worked fine). 

I am using a MacBook Pro, with
  INFO  14:00:05  ------------------------------------ Protege -----------------------------------
   INFO  14:00:05  Protege Desktop
   INFO  14:00:05  Version 5.5.0, Build 
   INFO  14:00:05  
   INFO  14:00:05  
   INFO  14:00:05  ----------------------------------- Platform -----------------------------------
   INFO  14:00:05  Java: JVM 1.8.0_121-b13  Memory: 5592M
   INFO  14:00:05  Language: en, Country: US
   INFO  14:00:05  Framework: Apache Software Foundation (1.8) 
   INFO  14:00:05  OS: macosx (10.14.5)
   INFO  14:00:05  Processor: x86-64

   INFO  14:00:05  
   INFO  14:00:05  ------------------------------------ Plugins -----------------------------------
   INFO  14:00:05  Plugin: OWLAPI RDF Library (3.0.0)
   INFO  14:00:05  Plugin: SPARQL Query Plugin (3.0.0)


There is no error message in the log file.

How much memory was allocated to Protege in your work? That may be the problem.

With best regards,
Samson


On Jul 9, 2019, at 12:57 PM, Michael DeBellis <[hidden email]> wrote:

I'm not sure if it's the same problem but I've also been having trouble getting the SPARQL tab to work with non trivial ontologies. I'm able to open the tab when no ontology is loaded and when a small ontology (about 30 objects) is loaded but I have an ontology with over 1,000 individuals and when I try to open the SPARQL tab with that ontology in the SPARQL tab I see the error message below. I was waiting to report it because I'm working with another person and I don't want to share the ontology without his permission but since it seems someone else is having similar problems thought I would mention it. The SPARQL tab has the red error message: 

An error occurred whilst creating the view
BufferAllocationException:
Not enough memory to allocate buffers to grow from 0 -> 32 element. 

In the log I see the following error trace:

  ERROR  12:50:46  An error occurred whilst creating the view content for the 'SPARQL query' view: {}
com.carrotsearch.hppcrt.BufferAllocationException: Not enough memory to allocate buffers to grow from 0 -> 32 elements
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:513) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) [na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) [na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) [na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) [na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) [na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) [na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) [na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) [na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) [na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) [na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) [na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) [na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) [na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) [na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) [na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) [na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) [na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) [na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) [na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.allocateBuffers(ObjectObjectHashMap.java:491) ~[na:na]
at com.carrotsearch.hppcrt.maps.ObjectObjectHashMap.<init>(ObjectObjectHashMap.java:191) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.MapPointer.<init>(MapPointer.java:68) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.buildLazy(Internals.java:722) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.Internals.<init>(Internals.java:248) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLAxiomIndexImpl.<init>(OWLAxiomIndexImpl.java:71) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.<init>(OWLImmutableOntologyImpl.java:167) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.<init>(OWLOntologyImpl.java:58) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.NonConcurrentOWLOntologyBuilder.createOWLOntology(NonConcurrentOWLOntologyBuilder.java:19) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyBuilder.createOWLOntology(ConcurrentOWLOntologyBuilder.java:39) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.createOWLOntology(OWLOntologyFactoryImpl.java:74) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:955) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:923) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1004) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.createOntology(OWLOntologyManagerImpl.java:1014) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.createOntology(RDFTranslator.java:103) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:54) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:24) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) [protege-editor-core.jar:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) [protege-editor-core.jar:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) [na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) [na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) [na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) [na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) [na:1.8.0_121]


On Tue, Jul 9, 2019 at 12:03 PM Grove, Christian A. (Chris) <[hidden email]> wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Protege desktop 5.5.0 SPARQL

Grove, Christian A. (Chris)
In reply to this post by Grove, Christian A. (Chris)
Hi Csongor,

I just thought I'd follow up on this SPARQL Query tab issue: I believe I was able to increase my heap size to about 28GB (see below), and yet the SPARQL Query tab took about 25 minutes to load. Am I doing something wrong?

For reference, this is the ontology that I'm working with:


Any help would be greatly appreciated!

Thanks,

Chris

From: protege-user <[hidden email]> on behalf of Grove, Christian A. (Chris) <[hidden email]>
Sent: Monday, July 15, 2019 8:57 AM
To: [hidden email] <[hidden email]>
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Csongor,

OK, so I let Protege run after hanging and the SPARQL Query tab eventually shows up without error but takes >15 minutes. I think my default heap/memory allocation was set to 1/4 of my physical memory, so 16GB (I have 64GB total). I upped the allocated memory by editing the "Info.plist" file in my directory:

/Applications/Protege-5.5.0/Protégé.app/Contents/

by editing the VMOptions from:

        <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>

to:

        <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xmn30G</string>
            <string>-Xms30G</string>
            <string>-Xmx30G</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>

The Protege log then reads, upon restarting:

   INFO  11:08:37  ------------------------------------ Protege -----------------------------------
   INFO  11:08:37  Protege Desktop
   INFO  11:08:37  Version 5.5.0, Build
   INFO  11:08:37  
   INFO  11:08:37  
   INFO  11:08:37  ----------------------------------- Platform -----------------------------------
   INFO  11:08:37  Java: JVM 1.8.0_121-b13  Memory: 28186M
   INFO  11:08:37  Language: en, Country: US
   INFO  11:08:37  Framework: Apache Software Foundation (1.8)
   INFO  11:08:37  OS: macosx (10.14.5)
   INFO  11:08:37  Processor: x86-64

so it seems the allocated memory is now about 28GB. I retried opening my ontology and then clicking on the SPARQL Query tab and it eventually loaded but took more than 25 minutes to do so. Should I really be expecting to wait that long for the tab to load?

Thanks,

Chris

PS. I'm pretty much hacking my way through adjusting the heap size, so please let me know if there's a better way.


From: protege-user <[hidden email]> on behalf of Csongor Nyulas <[hidden email]>
Sent: Friday, July 12, 2019 2:02 PM
To: [hidden email]
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

The best would be to use the version 3.0.0 of both plug-ins. The previous 2.0.x versions may be incompatible with Protege 5.5. I think that is what Lorenz suggested also.

When Protege becomes unresponsive, will you get an OutOfMemory error after some time?
Can you confirm that you have the same problem described by Michael DeBellis in this issue:
    https://github.com/protegeproject/sparql-query-plugin/issues/21 ?
If yes, can you increase your maximum heap size (say double the current amount)?

Csongor


On 7/12/19 1:01 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

OK, I've tried your suggestion, but now instead of throwing an error message to the log, as soon as I click on the "SPARQL Query" tab (with a non-trivial ontology) Protege completely freezes up and becomes totally unresponsive.

Also, I have a question about plugins and the paths where they should be stored/installed. I have a iMac and am running OS X (10.14.5) and I can find the default location for the 'rdf-library-3.0.0.jar' and 'sparql-query-plugin-3.0.0.jar' files in this location:

/Applications/Protege-5.5.0/Protégé.app/Contents/Java/plugins

I think it was working the other day where I could delete those .jar files from that directory, restart Protege, run "File > Check for plugins..." and then see the respective plugins appear with the 2.0.x versions allowing me to install those. Now, for some reason, if I repeat this process (after, say, reinstalling Protege-5.5.0 and deleting the jar files, or just deleting the rdf-library and sparql .jar files again), I don't get any suggested plugins after checking for plugins.

I'm wondering how I trigger Protege to suggest the 2.0.x versions of those plugins once I've deleted them (or where to download them manually and then where to install them).

Thanks,

Chris



From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 4:52 PM
To: [hidden email]
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,
This may be different issue from what Michael described.

Can you try something for me:
- Download the platform independent version of Protege 5.5 (follow the link called "Download platform independent version (requires a Java Runtime Environment)" below the Download button on this page: https://protege.stanford.edu/products.php#desktop-protege).
- unpack the zip file, and copy the rdf-library-3.0.0.jar and sparql-query-plugin-3.0.0.jar files from the plugins directory to your Protege installation's plugins directory, and remove the older (2.0.3 and 2.0.2) versions of those plugins.
- see if you still get the error after restarting and trying to use the SPARQL Query tab.

Thanks,
Csongor


On 7/9/19 2:09 PM, Grove, Christian A. (Chris) wrote:
Hi Csongor,

Thanks! That did the trick to bring back the option to select the "SPARQL Query" tab (I had the rdf-library-3.0.0.jar file installed, removed it and replaced it with 2.0.3), but now I'm getting a problem that might be the same as what Michael pointed out. When I click on the tab, after adding it, I get a blank tab and the following error message shows up in the log:


ERROR  17:06:05  Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;Lorg/semanticweb/owlapi/util/AxiomAppearance;Ljava/util/concurrent/atomic/AtomicInteger;)V
at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:93) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:55) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:36) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:26) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6700) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6319) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.Component.createHierarchyEvents(Component.java:5549) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1445) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Container.createHierarchyEvents(Container.java:1441) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1639) ~[na:1.8.0_121]
at java.awt.Component.show(Component.java:1671) ~[na:1.8.0_121]
at java.awt.Component.setVisible(Component.java:1623) ~[na:1.8.0_121]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_121]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_121]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_121]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_121]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6530) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]

If this is a different from what Michael describes then I can create a new ticket.

Let me know.

Thanks!

Chris

From: protege-user [hidden email] on behalf of Csongor Nyulas [hidden email]
Sent: Tuesday, July 9, 2019 1:01 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege desktop 5.5.0 SPARQL
 
Hi Chris,

I'm afraid that the reason you don't see the SPARQL Query tab listed is that you have incompatible versions of the "SPARQL Query" and "OWLAPI RDF Library" plug-ins installed.
Can you check which versions of those two plug-ins do you have installed (go to Help -> About)?

Protege 5.5 comes with version 3.0.0 of both the "SPARQL Query" and "OWLAPI RDF Library" plugin-ins. However, those versions were not released independently, yet, and are not available through auto-update. So, if you have one of those at version 3.0.0 and the other one at 2.0.x, then the best thing to do is to delete the rdf-library-3.0.0.jar or sparql-query-plugin-3.0.0.jar file (whichever you have) from the plugins directory that is under your Protege 5.5 installation directory, and install the available versions of those plugins (2.0.2 for SPARQL Query, and 2.0.3 for OWLAPI RDF Library) through the File -> Check for plugins... menu.

Note: It may take some time for the "Automatic Update" window to show, because one of the plug-ins has a broken update link, so please be patient.

Csongor

PS: If the above didn't help, please let us know what OS do you have. Just asking to check if it is not related to this issue:
http://protege-project.136.n4.nabble.com/Protege-5-5-0-and-Fact-td4671904.html



On 7/9/19 12:03 PM, Grove, Christian A. (Chris) wrote:
Hello,

I ran into an issue in which Protege (5.5.0) was crashing whenever I tried to add the SPARQL Query tab to my viewport on any non-trivial ontology. After some fiddling, I decided to reinstall Protege 5.5.0 and have updated all plugins, but now I cannot see the "SPARQL Query" tab as an option to display in the "Windows > Tabs" menu. I recall having an issue earlier with understanding how to make sure plugins were properly installed (and needing to know the right directory to place .jar files, etc.).

Can someone help?

Thanks!

Chris Grove
WormBase
Alliance of Genome Resources

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user