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  1. IGB
  2. IGBF-698

Reenabling Quickload after DAS has been initialized generates a null pointer exception

    Details

      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]

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          dcnorris David Norris (Inactive) added a comment -

          Fixed

          Show
          dcnorris David Norris (Inactive) added a comment - Fixed
          Hide
          mason Mason Meyer (Inactive) added a comment -

          My testing verifies that this issue has been resolved so it will now be closed.

          Show
          mason Mason Meyer (Inactive) added a comment - My testing verifies that this issue has been resolved so it will now be closed.

            People

            • Assignee:
              mason Mason Meyer (Inactive)
              Reporter:
              mason Mason Meyer (Inactive)
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              Dates

              • Created:
                Updated:
                Resolved: