Bob Dionne bdionne
bdionne
/ manifest.mf
Created
November 11, 2016 16:04
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| Manifest-Version: 1.0 | |
| Bnd-LastModified: 1478876035268 | |
| Build-Jdk: 1.8.0_101 | |
| Built-By: bitdiddle | |
| Bundle-Description: Provides client functionality for Protege 5 to conne | |
| ct to a Protege Server, allowing end users to collaboratively edit coll | |
| ections of OWL ontologies. | |
| Bundle-DocURL: http://bmir.stanford.edu/ | |
| Bundle-License: http://www.gnu.org/copyleft/lesser.html | |
| Bundle-ManifestVersion: 2 |
bdionne
/ gist:c0bb93df41c51123b7f4e693750865cf
Created
October 18, 2016 10:49
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| Java-level deadlock detected | |
| This means that some threads are blocked waiting to enter a synchronization block or | |
| waiting to reenter a synchronization block after an Object.wait() call, where each thread | |
| owns one monitor while trying to obtain another monitor already held by another thread. | |
| Deadlock: | |
| AWT-EventQueue-0 is waiting to lock java.util.concurrent.locks.ReentrantReadWriteLock$NonfairSync@199666c5 which is held by Thread-4 | |
| Thread-4 is waiting to lock java.awt.Component$AWTTreeLock@60803f48 which is held by AWT-EventQueue-0 |
bdionne
/ Thesaurus-160919-Lint.txt
Created
September 21, 2016 16:53
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| ================================================================== | |
| OWL Lints found for ontology OntologyID(OntologyIRI(<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl>) VersionIRI(<null>)): | |
| [EquivalentAndSubclassAxiomPattern: A named concept appears in equivalent axiom(s) and on the left-hand side of a subclass axiom] | |
| <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Adenosine-A2A_Receptor> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Adenosine-A2B_Receptor> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Adenosine-A3_Receptor> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Apolipoprotein_A-I> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#BAF57> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#BTB-POZ_Domain-Containing_Adapter_For_CUL3-Mediated_RhoA_Degradation_Protein_2> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Barrett_s_Esophagus> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Beta_Adrenergic_Receptor_Kinase-2> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus. |
bdionne
/ gist:6c7f563b8f3e847f2c0772d90f8bd533
Created
July 27, 2016 15:59
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| { | |
| "host": { | |
| "uri": "http://localhost:8080" | |
| }, | |
| "root": "root/data", | |
| "metaproject": { | |
| "policy": { | |
| "root": { | |
| "all-projects": [ | |
| "mp-admin", |
bdionne
/ gist:4585350ba2c1d5b43e1b9f1a42060f6e
Created
July 27, 2016 15:45
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| http://ncicb.nci.nih.gov/xml/owl/EVS/owl2lexevs.owl#Preferred_Name | |
| org.protege.editor.owl.client.api.exception.ClientRequestException | |
| at org.protege.editor.owl.client.LocalHttpClient.getOperations(LocalHttpClient.java:776) | |
| at org.protege.editor.owl.client.LocalHttpClient.getActiveOperations(LocalHttpClient.java:953) | |
| at gov.nih.nci.ui.NCIEditTab.initProperties(NCIEditTab.java:927) | |
| at gov.nih.nci.ui.NCIEditTab.handleChange(NCIEditTab.java:839) | |
| at org.protege.editor.owl.client.ClientSession.fireChangeEvent(ClientSession.java:65) | |
| at org.protege.editor.owl.client.ClientSession.access$0(ClientSession.java:62) | |
| at org.protege.editor.owl.client.ClientSession$1.handleChange(ClientSession.java:47) | |
| at org.protege.editor.owl.model.OWLModelManagerImpl.lambda$fireEvent$224(OWLModelManagerImpl.java:776) |
bdionne
/ gist:04fdad87a25b3a424cca03d93540b30d
Created
July 23, 2016 09:47
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| [1;31mUncaught Exception in thread 'AWT-EventQueue-0'[0;39m | |
| java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 | |
| at java.util.ArrayList.rangeCheck(ArrayList.java:653) ~[na:1.8.0_31] | |
| at java.util.ArrayList.get(ArrayList.java:429) ~[na:1.8.0_31] | |
| at org.protege.editor.owl.client.diff.model.LogDiffManager.setSelectedCommitToLatest(LogDiffManager.java:143) ~[na:na] | |
| at org.protege.editor.owl.client.diff.ui.ReviewButtonsPanel.lambda$0(ReviewButtonsPanel.java:183) ~[na:na] | |
| at org.protege.editor.owl.client.diff.ui.ReviewButtonsPanel$$Lambda$141/357408260.actionPerformed(Unknown Source) ~[na:na] | |
| at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) ~[na:1.8.0_31] | |
| at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346) ~[na:1.8.0_31] | |
| at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) ~[na:1.8.0_31] |
bdionne
/ gist:dbcd74ad2f9555ca61d0e6e68b3c1ab6
Created
July 22, 2016 09:50
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| java.util.NoSuchElementException: No value present | |
| at java.util.Optional.get(Optional.java:135) | |
| at org.protege.editor.owl.client.diff.model.LogDiff.findBaselineMatches(LogDiff.java:374) | |
| at org.protege.editor.owl.client.diff.model.LogDiff.initDiff(LogDiff.java:68) | |
| at org.protege.editor.owl.client.diff.ui.ChangesPanel$1.statusChanged(ChangesPanel.java:73) | |
| at org.protege.editor.owl.client.diff.model.LogDiffManager.statusChanged(LogDiffManager.java:167) | |
| at org.protege.editor.owl.client.diff.ui.AuthorPanel.lambda$new$40(AuthorPanel.java:71) | |
| at org.protege.editor.owl.client.diff.ui.AuthorPanel$$Lambda$136/842515158.handleChange(Unknown Source) | |
| at org.protege.editor.owl.model.OWLModelManagerImpl.lambda$fireEvent$224(OWLModelManagerImpl.java:779) | |
| at org.protege.editor.owl.model.OWLModelManagerImpl$$Lambda$30/1959956575.run(Unknown Source) |
bdionne
/ gist:d9946b2336d1337ba7407a5d786496bd
Created
July 21, 2016 15:38
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| [31mAn error occurred whilst highlighting an unsatisfiable property: {}[0;39m | |
| java.lang.NullPointerException: null | |
| at org.protege.editor.owl.model.inference.NoOpReasoner.getBottomObjectPropertyNode(NoOpReasoner.java:195) ~[protege-editor-owl.jar:na] | |
| at org.protege.editor.owl.ui.renderer.OWLCellRenderer.lambda$highlightPropertyIfUnsatisfiable$7(OWLCellRenderer.java:913) [protege-editor-owl.jar:na] | |
| at org.protege.editor.owl.ui.renderer.OWLCellRenderer$$Lambda$84/1534823216.run(Unknown Source) ~[na:na] | |
| at org.protege.editor.owl.model.inference.DisplayedInferencePreferences.executeTask(DisplayedInferencePreferences.java:118) ~[protege-editor-owl.jar:na] | |
| at org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:182) ~[protege-editor-owl.jar:na] | |
| at org.protege.editor.owl.ui.renderer.OWLCellRenderer.highlightPropertyIfUnsatisfiable(OWLCellRenderer.java:908) [protege-editor-owl.jar:na] | |
| at org.protege.editor.owl.ui.renderer.OWLCellRenderer.renderToken(OWLCellRenderer.j |
bdionne
/ manifest.mf
Created
July 5, 2016 11:06
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| Manifest-Version: 1.0 | |
| Bnd-LastModified: 1467495296546 | |
| Build-Jdk: 1.8.0_31 | |
| Built-By: thor | |
| Bundle-Activator: org.protege.editor.owl.ProtegeOWL | |
| Bundle-ClassPath: .,lucene-core-5.4.1.jar,lucene-analyzers-common-5.4.1. | |
| jar,lucene-queryparser-5.4.1.jar,lucene-analyzers-phonetic-5.4.1.jar | |
| Bundle-Description: A plug-in for Protege that provides a high-performan | |
| ce search capability for very large ontologies. | |
| Bundle-DocURL: http://bmir.stanford.edu/ |
bdionne
/ gist:97b2db6e5f1343241fdb9a092e505588
Created
July 3, 2016 10:54
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| [34mCreating and setting up empty (default) editor kit[0;39m | |
| [34mOWL API Version: 4.2.5.20160517-0735[0;39m | |
| [1;31mAn error was thrown: java.lang.ClassCastException: org.protege.editor.owl.OWLEditorKit cannot be cast to org.protege.editor.owl.OWLEditorKit[0;39m | |
| java.lang.RuntimeException: java.lang.ClassCastException: org.protege.editor.owl.OWLEditorKit cannot be cast to org.protege.editor.owl.OWLEditorKit | |
| at org.protege.editor.core.editorkit.AbstractEditorKit.initialiseCompleted(AbstractEditorKit.java:48) ~[protege-editor-core.jar:na] | |
| at org.protege.editor.core.editorkit.AbstractEditorKit.<init>(AbstractEditorKit.java:34) ~[protege-editor-core.jar:na] | |
| at org.protege.editor.owl.OWLEditorKit.<init>(OWLEditorKit.java:80) ~[na:na] | |
| at org.protege.editor.owl.OWLEditorKitFactory.createEditorKit(OWLEditorKitFactory.java:40) ~[na:na] | |
| at org.protege.editor.core.ProtegeManager.createAndSetupNewEditorKit(ProtegeManager.java:136) ~[protege-editor-core.jar:na] | |
| at org.protege.editor.core.ProtegeManager.createA |