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  1. INFO 23:38:13 ------------------------ Saving Workspace and Ontologies -----------------------
  2. INFO 23:38:13 Will prompt 'Save As' for the active ontology because it was not loaded from a local file
  3. INFO 23:38:13 Will prompt 'Save As' for the class ontology because it was not loaded from a local file but has been modified
  4. INFO 23:38:20 Saving class
  5. INFO 23:38:20 Saving ontology to temp file: /var/folders/9b/454rtm0976n68mf3n7jhtl900000gn/T/temp-ontology2933449547752795224
  6. INFO 23:38:20 Copying ontology from temp file (/var/folders/9b/454rtm0976n68mf3n7jhtl900000gn/T/temp-ontology2933449547752795224) to actual destination (/Users/danielbakas/test/Test.owl)
  7. INFO 23:38:20 Removing temp file: /var/folders/9b/454rtm0976n68mf3n7jhtl900000gn/T/temp-ontology2933449547752795224
  8. INFO 23:38:20 Saved ontology OntologyID(OntologyIRI(<http://archive.semantyk.com/class/>) VersionIRI(<null>)) to file:/Users/danielbakas/test/Test.owl in Turtle Syntax format
  9. INFO 23:38:21 [GitRepo] Git repository detected: /Users/danielbakas/.git
  10. INFO 23:38:21 [GitRepo] On branch: master
  11. WARN 23:39:48 Exception thrown by listener: org.protege.editor.owl.model.git.GitRepoStatusPresenter$$Lambda$87/677136608. Detatching bad listener.
  12. INFO 23:39:48 Saved tab state for 'Individual Hierarchy Tab' tab
  13. INFO 23:39:48 Saved tab state for 'Entities' tab
  14. INFO 23:39:48 Saved tab state for 'Individuals by class' tab
  15. INFO 23:39:48 Saved tab state for 'DL Query' tab
  16. INFO 23:39:48 Saved tab state for 'Active ontology' tab
  17. INFO 23:39:48 Saved workspace
  18. INFO 23:39:48
  19. INFO 23:39:48 [GitRepo] Git repository detected: /Users/danielbakas/.git
  20. INFO 23:39:48 [GitRepo] On branch: master
  21. ERROR 23:42:15 Uncaught Exception in thread 'AWT-EventQueue-0'
  22. java.lang.OutOfMemoryError: GC overhead limit exceeded
  23. at sun.nio.fs.UnixPath.encode(UnixPath.java:132) ~[na:1.8.0_121]
  24. at sun.nio.fs.UnixPath.<init>(UnixPath.java:71) ~[na:1.8.0_121]
  25. at sun.nio.fs.UnixFileSystem.getPath(UnixFileSystem.java:281) ~[na:1.8.0_121]
  26. at java.io.File.toPath(File.java:2234) ~[na:1.8.0_121]
  27. at org.eclipse.jgit.util.FileUtils.getFileAttributesPosix(FileUtils.java:772) ~[na:na]
  28. at org.eclipse.jgit.util.FS_POSIX.getAttributes(FS_POSIX.java:270) ~[na:na]
  29. at org.eclipse.jgit.treewalk.FileTreeIterator$FileEntry.<init>(FileTreeIterator.java:365) ~[na:na]
  30. at org.eclipse.jgit.treewalk.FileTreeIterator.entries(FileTreeIterator.java:242) ~[na:na]
  31. at org.eclipse.jgit.treewalk.FileTreeIterator.<init>(FileTreeIterator.java:227) ~[na:na]
  32. at org.eclipse.jgit.treewalk.FileTreeIterator.createSubtreeIterator(FileTreeIterator.java:233) ~[na:na]
  33. at org.eclipse.jgit.treewalk.AbstractTreeIterator.createSubtreeIterator(AbstractTreeIterator.java:572) ~[na:na]
  34. at org.eclipse.jgit.treewalk.TreeWalk.enterSubtree(TreeWalk.java:1271) ~[na:na]
  35. at org.eclipse.jgit.treewalk.TreeWalk.next(TreeWalk.java:835) ~[na:na]
  36. at org.eclipse.jgit.lib.IndexDiff.diff(IndexDiff.java:440) ~[na:na]
  37. at org.eclipse.jgit.lib.IndexDiff.diff(IndexDiff.java:380) ~[na:na]
  38. at org.eclipse.jgit.api.StatusCommand.call(StatusCommand.java:149) ~[na:na]
  39. at org.protege.editor.owl.model.git.GitRepositoryManager.getModifiedOntologyDocumentPaths(GitRepositoryManager.java:168) ~[na:na]
  40. at org.protege.editor.owl.model.git.GitRepositoryManager.isAnyOntologyDocumentModified(GitRepositoryManager.java:153) ~[na:na]
  41. at org.protege.editor.owl.model.git.GitRepoStatusPresenter.updateStatusView(GitRepoStatusPresenter.java:76) ~[na:na]
  42. at org.protege.editor.owl.model.git.GitRepoStatusPresenter.update(GitRepoStatusPresenter.java:63) ~[na:na]
  43. at org.protege.editor.owl.model.OWLWorkspace.handleActivated(OWLWorkspace.java:248) ~[na:na]
  44. at org.protege.editor.core.ui.workspace.WorkspaceFrame$1.windowActivated(WorkspaceFrame.java:71) ~[na:na]
  45. at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:389) ~[na:1.8.0_121]
  46. at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:389) ~[na:1.8.0_121]
  47. at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:389) ~[na:1.8.0_121]
  48. at java.awt.Window.processWindowEvent(Window.java:2066) ~[na:1.8.0_121]
  49. at javax.swing.JFrame.processWindowEvent(JFrame.java:305) ~[na:1.8.0_121]
  50. at java.awt.Window.processEvent(Window.java:2013) ~[na:1.8.0_121]
  51. at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
  52. at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
  53. at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
  54. at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
  55. INFO 23:44:32 [GitRepo] Git repository detected: /Users/danielbakas/.git
  56. INFO 23:44:32 [GitRepo] On branch: master
  57. ERROR 23:46:23 Uncaught Exception in thread 'AWT-EventQueue-0'
  58. java.lang.OutOfMemoryError: GC overhead limit exceeded
  59. at java.util.Arrays.copyOf(Arrays.java:3236) ~[na:1.8.0_121]
  60. at sun.nio.fs.UnixPath.encode(UnixPath.java:154) ~[na:1.8.0_121]
  61. at sun.nio.fs.UnixPath.<init>(UnixPath.java:71) ~[na:1.8.0_121]
  62. at sun.nio.fs.UnixFileSystem.getPath(UnixFileSystem.java:281) ~[na:1.8.0_121]
  63. at java.io.File.toPath(File.java:2234) ~[na:1.8.0_121]
  64. at org.eclipse.jgit.util.FileUtils.getFileAttributesPosix(FileUtils.java:772) ~[na:na]
  65. at org.eclipse.jgit.util.FS_POSIX.getAttributes(FS_POSIX.java:270) ~[na:na]
  66. at org.eclipse.jgit.treewalk.FileTreeIterator$FileEntry.<init>(FileTreeIterator.java:365) ~[na:na]
  67. at org.eclipse.jgit.treewalk.FileTreeIterator.entries(FileTreeIterator.java:242) ~[na:na]
  68. at org.eclipse.jgit.treewalk.FileTreeIterator.<init>(FileTreeIterator.java:227) ~[na:na]
  69. at org.eclipse.jgit.treewalk.FileTreeIterator.createSubtreeIterator(FileTreeIterator.java:233) ~[na:na]
  70. at org.eclipse.jgit.treewalk.AbstractTreeIterator.createSubtreeIterator(AbstractTreeIterator.java:572) ~[na:na]
  71. at org.eclipse.jgit.treewalk.TreeWalk.enterSubtree(TreeWalk.java:1271) ~[na:na]
  72. at org.eclipse.jgit.treewalk.TreeWalk.next(TreeWalk.java:835) ~[na:na]
  73. at org.eclipse.jgit.lib.IndexDiff.diff(IndexDiff.java:440) ~[na:na]
  74. at org.eclipse.jgit.lib.IndexDiff.diff(IndexDiff.java:380) ~[na:na]
  75. at org.eclipse.jgit.api.StatusCommand.call(StatusCommand.java:149) ~[na:na]
  76. at org.protege.editor.owl.model.git.GitRepositoryManager.getModifiedOntologyDocumentPaths(GitRepositoryManager.java:168) ~[na:na]
  77. at org.protege.editor.owl.model.git.GitRepositoryManager.isAnyOntologyDocumentModified(GitRepositoryManager.java:153) ~[na:na]
  78. at org.protege.editor.owl.model.git.GitRepoStatusPresenter.updateStatusView(GitRepoStatusPresenter.java:76) ~[na:na]
  79. at org.protege.editor.owl.model.git.GitRepoStatusPresenter.update(GitRepoStatusPresenter.java:63) ~[na:na]
  80. at org.protege.editor.owl.model.OWLWorkspace.handleActivated(OWLWorkspace.java:248) ~[na:na]
  81. at org.protege.editor.core.ui.workspace.WorkspaceFrame$1.windowActivated(WorkspaceFrame.java:71) ~[na:na]
  82. at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:389) ~[na:1.8.0_121]
  83. at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:389) ~[na:1.8.0_121]
  84. at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:389) ~[na:1.8.0_121]
  85. at java.awt.Window.processWindowEvent(Window.java:2066) ~[na:1.8.0_121]
  86. at javax.swing.JFrame.processWindowEvent(JFrame.java:305) ~[na:1.8.0_121]
  87. at java.awt.Window.processEvent(Window.java:2013) ~[na:1.8.0_121]
  88. at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
  89. at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
  90. at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
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