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  1. IGB
  2. IGBF-3417

Investigate: Update mi-Bundle to work with main-JDK8-r6

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          issue: When mi-bundle app is installed after any of the genomes is selected and when the home button is clicked, it is unresponsive and the following error appears in log:

          Exception

          INFO: Species: Homo sapiens / 9606
          Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
          at it.iit.genomics.cru.igb.bundles.mi.view.SearchPanel$18.groupSelectionChanged(SearchPanel.java:685)
          at com.affymetrix.genometry.GenometryModel.fireGroupSelectionEvent(GenometryModel.java:161)
          at com.affymetrix.genometry.GenometryModel.setSelectedGenomeVersion(GenometryModel.java:147)
          at com.affymetrix.igb.action.HomeAction.actionPerformed(HomeAction.java:27)
          at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
          at com.affymetrix.igb.view.IGBToolBar$JRPButtonTLP.fireActionPerformed(IGBToolBar.java:314)
          at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
          at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
          at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
          at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
          at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
          at java.awt.Component.processMouseEvent(Component.java:6539)
          at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
          at java.awt.Component.processEvent(Component.java:6304)
          at java.awt.Container.processEvent(Container.java:2239)
          at java.awt.Component.dispatchEventImpl(Component.java:4889)
          at java.awt.Container.dispatchEventImpl(Container.java:2297)
          at java.awt.Component.dispatchEvent(Component.java:4711)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
          at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
          at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
          at java.awt.Container.dispatchEventImpl(Container.java:2283)
          at java.awt.Window.dispatchEventImpl(Window.java:2746)
          at java.awt.Component.dispatchEvent(Component.java:4711)
          at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
          at java.awt.EventQueue.access$500(EventQueue.java:97)
          at java.awt.EventQueue$3.run(EventQueue.java:709)
          at java.awt.EventQueue$3.run(EventQueue.java:703)
          at java.security.AccessController.doPrivileged(Native Method)
          at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
          at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
          at java.awt.EventQueue$4.run(EventQueue.java:733)
          at java.awt.EventQueue$4.run(EventQueue.java:731)
          at java.security.AccessController.doPrivileged(Native Method)
          at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
          at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
          at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
          at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
          at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3379 Edit SCR annotations to use R6 instead of R5 syntax and observe the effects

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
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                kgopu Kaushik Gopu added a comment - - edited

                After cloning the repo of the mi-bundle plugin and setting it up locally, I encountered the following issues:

                • Some of the dependencies don't even exist in the Maven repository. Therefore, Maven is throwing unresolved dependency errors.
                • A few other dependencies, such as it.iit.genomics.cru.bridges cannot get downloaded due to unauthorized access ( authentication failure).
                • Finally, around 100-150 (overall) dependencies are unresolved. This might be due to the need to specify the version number. Check this article for more information about unresolved dependencies.
                  it can be challenging to set up this project locally, and we might need support from plugin developers to sort out these dependency issues (at least for authentication issues).
                Show
                kgopu Kaushik Gopu added a comment - - edited After cloning the repo of the mi-bundle plugin and setting it up locally, I encountered the following issues: Some of the dependencies don't even exist in the Maven repository. Therefore, Maven is throwing unresolved dependency errors. A few other dependencies, such as it.iit.genomics.cru.bridges cannot get downloaded due to unauthorized access ( authentication failure). Finally, around 100-150 (overall) dependencies are unresolved. This might be due to the need to specify the version number. Check this article for more information about unresolved dependencies. it can be challenging to set up this project locally, and we might need support from plugin developers to sort out these dependency issues (at least for authentication issues).
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Investigation is complete. Moving to Closed.

                Show
                ann.loraine Ann Loraine added a comment - Investigation is complete. Moving to Closed.

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    kgopu Kaushik Gopu
                  • Votes:
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                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: