Details
-
Type: Bug
-
Status: Closed (View Workflow)
-
Priority: Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 8.4.0 Major Release
-
Labels:None
-
Epic Link:
-
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]
Attachments
Activity
Field | Original Value | New Value |
---|---|---|
Epic Link | IGBF-632 [ 15706 ] |
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. 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$1.doIntersectionPrivilege(Unknown Source) [na:1.8.0_40] at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_40] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_40] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_40] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_40] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_40] at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_40] |
It seems that re-enabling Quickload after DAS has been initialized generates a null pointer exception (see below).
To reproduce: 1) Before selecting a genome, disable the IGB Quickload under the Data Sources tab in Preferences. 2) Select Homo Sapien genome to initizialize the UCSC (DAS) server. 3) Restart IGB and select the Homo Sapien genome. 4) Re-enable the IGB Quickload server under the Data Sources tab in Preferences. *Observe: a null pointer exception has been generated 12:49:01.011 ERROR c.l.quickload.util.QuickloadUtils - Missing required annots.xml file for genome version hg38, skipping this genome version for quickload site http://igbquickload.org/quickload/hg38/ java.io.IOException: null at com.affymetrix.genometry.util.UriUtils.checkIsValidRequest(UriUtils.java:86) ~[genometry-8.4.0.jar:na] at com.affymetrix.genometry.util.UriUtils.getInputStream(UriUtils.java:58) ~[genometry-8.4.0.jar:na] at com.lorainelab.quickload.util.QuickloadUtils.getGenomeVersionData(QuickloadUtils.java:124) ~[quickload-8.4.0.jar:na] at com.lorainelab.quickload.QuickloadDataProvider.getAvailableDataSets(QuickloadDataProvider.java:138) [quickload-8.4.0.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils.initializeDataContainer(GeneralLoadUtils.java:303) [igb-8.4.0.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils.lambda$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] |
Status | Open [ 1 ] | In Progress [ 3 ] |
Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
Resolution | Done [ 10000 ] | |
Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
Workflow | Loraine Lab Workflow [ 15993 ] | Fall 2019 Workflow Update [ 19515 ] |
Workflow | Fall 2019 Workflow Update [ 19515 ] | Revised Fall 2019 Workflow Update [ 21632 ] |