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  1. IGBfx
  2. IGBFX-81

PatternSyntaxException generated when selecting "Manage Custom Genomes"

          Details

          • Type: Bug
          • Status: To-Do (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Affects Version/s: None
          • Fix Version/s: IGBfx
          • Labels:
            None
          • Story Points:
            0.25
          • Sprint:
            Sprint 38

            Description

            Getting a PatternSyntaxException when I select "Manage Custom Genomes" from Genome menu.

            The "Manage Custom Genomes" feature is not yet fully implemented so maybe this is the reason the exception is occurring.

            2016-10-18 08:40:48,319 | INFO | ool-131-thread-1 | FeaturesServiceImpl | 9 - org.apache.karaf.features.core - 4.0.5 | Done.
            Exception in thread "JavaFX Application Thread" java.util.regex.PatternSyntaxException: Unexpected internal error near index 1
            \
            ^
            at java.util.regex.Pattern.error(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.util.regex.Pattern.<init>(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:270)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:267)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableCell.updateItem(Unknown Source)
            at javafx.scene.control.TableCell.indexChanged(Unknown Source)
            at javafx.scene.control.IndexedCell.updateIndex(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableViewSkin.resizeColumnToFitContent(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableViewSkin.resizeColumnToFitContent(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableColumnHeader.doColumnAutoSize(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableColumnHeader.updateScene(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableColumnHeader.handlePropertyChanged(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableColumnHeader.lambda$new$49(Unknown Source)
            at com.sun.javafx.scene.control.MultiplePropertyChangeListenerHandler$1.changed(Unknown Source)
            at javafx.beans.value.WeakChangeListener.changed(Unknown Source)
            at com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(Unknown Source)
            at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
            at javafx.beans.property.ReadOnlyObjectPropertyBase.fireValueChangedEvent(Unknown Source)
            at javafx.beans.property.ReadOnlyObjectWrapper.fireValueChangedEvent(Unknown Source)
            at javafx.scene.Node$ReadOnlyObjectWrapperManualFire.fireSuperValueChangedEvent(Unknown Source)
            at javafx.scene.Node.invalidatedScenes(Unknown Source)
            at javafx.scene.Node.setScenes(Unknown Source)
            at javafx.scene.Parent$1.onChanged(Unknown Source)
            at com.sun.javafx.collections.TrackableObservableList.lambda$new$19(Unknown Source)
            at com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
            at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(Unknown Source)
            at javafx.collections.ObservableListBase.fireChange(Unknown Source)
            at javafx.collections.ListChangeBuilder.commit(Unknown Source)
            at javafx.collections.ListChangeBuilder.endChange(Unknown Source)
            at javafx.collections.ObservableListBase.endChange(Unknown Source)
            at javafx.collections.ModifiableObservableListBase.setAll(Unknown Source)
            at com.sun.javafx.collections.VetoableListDecorator.setAll(Unknown Source)
            at com.sun.javafx.scene.control.skin.NestedTableColumnHeader.updateContent(Unknown Source)
            at com.sun.javafx.scene.control.skin.NestedTableColumnHeader.updateTableColumnHeaders(Unknown Source)
            at com.sun.javafx.scene.control.skin.NestedTableColumnHeader.checkState(Unknown Source)
            at com.sun.javafx.scene.control.skin.NestedTableColumnHeader.computePrefHeight(Unknown Source)
            at javafx.scene.Parent.prefHeight(Unknown Source)
            at javafx.scene.layout.Region.prefHeight(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableHeaderRow.computePrefHeight(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableHeaderRow.computeMinHeight(Unknown Source)
            at javafx.scene.Parent.minHeight(Unknown Source)
            at javafx.scene.layout.Region.minHeight(Unknown Source)
            at javafx.scene.control.SkinBase.computeMinHeight(Unknown Source)
            at javafx.scene.control.Control.computeMinHeight(Unknown Source)
            at javafx.scene.Parent.minHeight(Unknown Source)
            at javafx.scene.layout.Region.minHeight(Unknown Source)
            at org.tbee.javafx.scene.layout.MigPane$FX2ComponentWrapper.getMinimumHeight(Unknown Source)
            at net.miginfocom.layout.Grid$CompWrap.getSize(Unknown Source)
            at net.miginfocom.layout.Grid$CompWrap.validateSize(Unknown Source)
            at net.miginfocom.layout.Grid$CompWrap.getSizes(Unknown Source)
            at net.miginfocom.layout.Grid$CompWrap.getSize(Unknown Source)
            at net.miginfocom.layout.Grid$CompWrap.getSizeInclGaps(Unknown Source)
            at net.miginfocom.layout.Grid$CompWrap.access$5300(Unknown Source)
            at net.miginfocom.layout.Grid.getTotalSizeParallel(Unknown Source)
            at net.miginfocom.layout.Grid.access$4400(Unknown Source)
            at net.miginfocom.layout.Grid$LinkedDimGroup.getMinPrefMax(Unknown Source)
            at net.miginfocom.layout.Grid$LinkedDimGroup.access$3300(Unknown Source)
            at net.miginfocom.layout.Grid.getTotalGroupsSizeParallel(Unknown Source)
            at net.miginfocom.layout.Grid.calcRowsOrColsSizes(Unknown Source)
            at net.miginfocom.layout.Grid.calcGridSizes(Unknown Source)
            at net.miginfocom.layout.Grid.checkSizeCalcs(Unknown Source)
            at net.miginfocom.layout.Grid.getWidth(Unknown Source)
            at org.tbee.javafx.scene.layout.MigPane.computeWidth(Unknown Source)
            at org.tbee.javafx.scene.layout.MigPane.computePrefWidth(Unknown Source)
            at javafx.scene.Parent.prefWidth(Unknown Source)
            at javafx.scene.layout.Region.prefWidth(Unknown Source)
            at javafx.scene.Scene.getPreferredWidth(Unknown Source)
            at javafx.scene.Scene.resizeRootToPreferredSize(Unknown Source)
            at javafx.scene.Scene.preferredSize(Unknown Source)
            at javafx.scene.Scene.impl_preferredSize(Unknown Source)
            at javafx.stage.Window$9.invalidated(Unknown Source)
            at javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
            at javafx.beans.property.BooleanPropertyBase.set(Unknown Source)
            at javafx.stage.Window.setShowing(Unknown Source)
            at javafx.stage.Window.show(Unknown Source)
            at javafx.stage.Stage.show(Unknown Source)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes.lambda$null$13(EditCustomGenomes.java:126)
            at com.sun.javafx.application.PlatformImpl.lambda$null$173(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(Unknown Source)
            at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
            at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
            at com.sun.glass.ui.win.WinApplication.lambda$null$148(Unknown Source)
            at java.lang.Thread.run(Unknown Source)
            Exception in thread "JavaFX Application Thread" java.util.regex.PatternSyntaxException: Unexpected internal error near index 1
            \
            ^
            at java.util.regex.Pattern.error(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.util.regex.Pattern.<init>(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:270)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:267)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableCell.updateItem(Unknown Source)
            at javafx.scene.control.TableCell.indexChanged(Unknown Source)
            at javafx.scene.control.IndexedCell.updateIndex(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkinBase.updateCells(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkinBase.init(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkin.<init>(Unknown Source)
            at javafx.scene.control.TableRow.createDefaultSkin(Unknown Source)
            at javafx.scene.control.Control.impl_processCSS(Unknown Source)
            at javafx.scene.Node.processCSS(Unknown Source)
            at javafx.scene.Node.applyCss(Unknown Source)
            at com.sun.javafx.scene.control.skin.VirtualFlow.setCellIndex(Unknown Source)
            at com.sun.javafx.scene.control.skin.VirtualFlow.getCell(Unknown Source)
            at com.sun.javafx.scene.control.skin.VirtualFlow.getCellLength(Unknown Source)
            at com.sun.javafx.scene.control.skin.VirtualFlow.computeViewportOffset(Unknown Source)
            at com.sun.javafx.scene.control.skin.VirtualFlow.layoutChildren(Unknown Source)
            at javafx.scene.Parent.layout(Unknown Source)
            at javafx.scene.Parent.layout(Unknown Source)
            at javafx.scene.Parent.layout(Unknown Source)
            at javafx.scene.Scene.doLayoutPass(Unknown Source)
            at javafx.scene.Scene.preferredSize(Unknown Source)
            at javafx.scene.Scene.impl_preferredSize(Unknown Source)
            at javafx.stage.Window$9.invalidated(Unknown Source)
            at javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
            at javafx.beans.property.BooleanPropertyBase.set(Unknown Source)
            at javafx.stage.Window.setShowing(Unknown Source)
            at javafx.stage.Window.show(Unknown Source)
            at javafx.stage.Stage.show(Unknown Source)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes.lambda$null$13(EditCustomGenomes.java:126)
            at com.sun.javafx.application.PlatformImpl.lambda$null$173(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(Unknown Source)
            at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
            at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
            at com.sun.glass.ui.win.WinApplication.lambda$null$148(Unknown Source)
            at java.lang.Thread.run(Unknown Source)
            Exception in thread "JavaFX Application Thread" java.util.regex.PatternSyntaxException: Unexpected internal error near index 1
            \
            ^
            at java.util.regex.Pattern.error(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.util.regex.Pattern.<init>(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:270)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:267)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableCell.updateItem(Unknown Source)
            at javafx.scene.control.TableCell.indexChanged(Unknown Source)
            at javafx.scene.control.IndexedCell.updateIndex(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkinBase.updateCells(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkinBase.init(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkin.<init>(Unknown Source)
            at javafx.scene.control.TableRow.createDefaultSkin(Unknown Source)
            at javafx.scene.control.Control.impl_processCSS(Unknown Source)
            at javafx.scene.Parent.impl_processCSS(Unknown Source)
            at javafx.scene.Parent.impl_processCSS(Unknown Source)
            at javafx.scene.Parent.impl_processCSS(Unknown Source)
            at javafx.scene.control.Control.impl_processCSS(Unknown Source)
            at javafx.scene.Node.processCSS(Unknown Source)
            at javafx.scene.Node.processCSS(Unknown Source)
            at javafx.scene.Scene.doCSSPass(Unknown Source)
            at javafx.scene.Scene.access$3600(Unknown Source)
            at javafx.scene.Scene$ScenePulseListener.pulse(Unknown Source)
            at com.sun.javafx.tk.Toolkit.lambda$runPulse$30(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at com.sun.javafx.tk.Toolkit.runPulse(Unknown Source)
            at com.sun.javafx.tk.Toolkit.firePulse(Unknown Source)
            at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
            at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
            at com.sun.javafx.tk.quantum.QuantumToolkit.lambda$runToolkit$404(Unknown Source)
            at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
            at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
            at com.sun.glass.ui.win.WinApplication.lambda$null$148(Unknown Source)
            at java.lang.Thread.run(Unknown Source)
            Exception in thread "JavaFX Application Thread" java.util.regex.PatternSyntaxException: Unexpected internal error near index 1
            \
            ^
            at java.util.regex.Pattern.error(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.util.regex.Pattern.<init>(Unknown Source)
            at java.util.regex.Pattern.compile(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at java.lang.String.split(Unknown Source)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:270)
            at org.lorainelab.igb.menu.customgenome.EditCustomGenomes$4.call(EditCustomGenomes.java:267)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableColumn.getCellObservableValue(Unknown Source)
            at javafx.scene.control.TableCell.updateItem(Unknown Source)
            at javafx.scene.control.TableCell.indexChanged(Unknown Source)
            at javafx.scene.control.IndexedCell.updateIndex(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkinBase.updateCells(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkinBase.init(Unknown Source)
            at com.sun.javafx.scene.control.skin.TableRowSkin.<init>(Unknown Source)
            at javafx.scene.control.TableRow.createDefaultSkin(Unknown Source)
            at javafx.scene.control.Control.impl_processCSS(Unknown Source)
            at javafx.scene.Parent.impl_processCSS(Unknown Source)
            at javafx.scene.Parent.impl_processCSS(Unknown Source)
            at javafx.scene.Parent.impl_processCSS(Unknown Source)
            at javafx.scene.control.Control.impl_processCSS(Unknown Source)
            at javafx.scene.Node.processCSS(Unknown Source)
            at javafx.scene.Node.processCSS(Unknown Source)
            at javafx.scene.Scene.doCSSPass(Unknown Source)
            at javafx.scene.Scene.access$3600(Unknown Source)
            at javafx.scene.Scene$ScenePulseListener.pulse(Unknown Source)
            at com.sun.javafx.tk.Toolkit.lambda$runPulse$30(Unknown Source)
            at java.security.AccessController.doPrivileged(Native Method)
            at com.sun.javafx.tk.Toolkit.runPulse(Unknown Source)
            at com.sun.javafx.tk.Toolkit.firePulse(Unknown Source)
            at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
            at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
            at com.sun.javafx.tk.quantum.QuantumToolkit.lambda$runToolkit$404(Unknown Source)
            at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
            at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
            at com.sun.glass.ui.win.WinApplication.lambda$null$148(Unknown Source)
            at java.lang.Thread.run(Unknown Source)

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                  • Assignee:
                    Unassigned
                    Reporter:
                    mason Mason Meyer (Inactive)
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                    • Created:
                      Updated:
                      Resolved: