Details
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Type: Bug
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Status: Closed (View Workflow)
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Priority: Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 8.4.0 Major Release
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Labels:None
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Epic Link:
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Sprint:Sprint 21
Description
It seems that re-enabling Quickload after DAS has been initialized generates a null pointer exception (see below).
To reproduce:
1) Before selecting a genome, disable the IGB Quickload under the Data Sources tab in Preferences.
2) Select Homo Sapien genome to initizialize the UCSC (DAS) server.
3) Restart IGB and select the Homo Sapien genome.
4) Re-enable the IGB Quickload server under the Data Sources tab in Preferences.
*Observe: a null pointer exception has been generated
12:49:01.011 ERROR c.l.quickload.util.QuickloadUtils - Missing required annots.xml file for genome version hg38, skipping this genome version for quickload site http://igbquickload.org/quickload/hg38/
java.io.IOException: null
at com.affymetrix.genometry.util.UriUtils.checkIsValidRequest(UriUtils.java:86) ~[genometry-8.4.0.jar:na]
at com.affymetrix.genometry.util.UriUtils.getInputStream(UriUtils.java:58) ~[genometry-8.4.0.jar:na]
at com.lorainelab.quickload.util.QuickloadUtils.getGenomeVersionData(QuickloadUtils.java:124) ~[quickload-8.4.0.jar:na]
at com.lorainelab.quickload.QuickloadDataProvider.getAvailableDataSets(QuickloadDataProvider.java:138) [quickload-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.initializeDataContainer(GeneralLoadUtils.java:303) [igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.lambda$initVersionAndSeq$81(GeneralLoadUtils.java:326) [igb-8.4.0.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$$Lambda$259/1019567302.accept(Unknown Source) [igb-8.4.0.jar:na]
at java.lang.Iterable.forEach(Unknown Source) [na:1.8.0_40]
at com.affymetrix.igb.view.load.GeneralLoadUtils.initVersionAndSeq(GeneralLoadUtils.java:325) [igb-8.4.0.jar:na]
at com.affymetrix.igb.general.DataProviderManager.enableDataProvider(DataProviderManager.java:391) [igb-8.4.0.jar:na]
at com.affymetrix.igb.general.DataProviderTableModel.setColumnValue(DataProviderTableModel.java:214) [igb-8.4.0.jar:na]
at com.affymetrix.igb.general.DataProviderTableModel.setValueAt(DataProviderTableModel.java:190) [igb-8.4.0.jar:na]
at javax.swing.JTable.setValueAt(Unknown Source) [na:1.8.0_40]
at com.jidesoft.grid.JideTable.editingStopped(Unknown Source) [jide-ultimate-3.5.15.jar:na]
at javax.swing.AbstractCellEditor.fireEditingStopped(Unknown Source) [na:1.8.0_40]
at javax.swing.DefaultCellEditor$EditorDelegate.stopCellEditing(Unknown Source) [na:1.8.0_40]
at javax.swing.DefaultCellEditor.stopCellEditing(Unknown Source) [na:1.8.0_40]
at javax.swing.DefaultCellEditor$EditorDelegate.actionPerformed(Unknown Source) [na:1.8.0_40]
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_40]
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_40]
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_40]
at javax.swing.JToggleButton$ToggleButtonModel.setPressed(Unknown Source) [na:1.8.0_40]
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) [na:1.8.0_40]
at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(Unknown Source) [na:1.8.0_40]
at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_40]
at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) [na:1.8.0_40]
at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_40]
at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_40]
at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_40]
at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_40]
at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_40]
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_40]
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_40]
at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_40]
at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_40]
at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_40]
at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40]
at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40]
at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40]