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  1. Bug Repository
  2. BUG-812

File not listed in DMT, cannot be loaded if IGB is "fresh"

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None

            Description

            Open a completely fresh IGB with no preferences. Drag in a file with a single gene (attached unknown.gff3). Notice that it does not show in DMT and Load Button is unavailable. Drag in the second file (all.gff3), now you can get it to load. Also if you load second file, you get the same bug when it first loads, but if you switch chromosomes it resolves.

            This bug does not happen if preferences etc are in place.

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                Issue Links

                relates to

                Task - A task that needs to be done. BUG-623 File management bugs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  no problem in v15424

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - no problem in v15424
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Cannot reproduce.

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                  hiralv Hiral Vora (Inactive) added a comment - Cannot reproduce.
                  Hide
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                  tkanapar Tarun Santosh (Inactive) added a comment -

                  The test passed however when we load the Unknown file provided in the attachment and right click on the track the following exception got generated
                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.tiers.SeqMapViewPopup.popupNotify(SeqMapViewPopup.java:283)
                  at com.affymetrix.igb.tiers.TierLabelManager.doPopup(TierLabelManager.java:592)
                  at com.affymetrix.igb.tiers.TierLabelManager$1.mousePressed(TierLabelManager.java:136)
                  at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1281)
                  at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540)
                  at com.affymetrix.genoviz.widget.NeoAbstractWidget.mousePressed(NeoAbstractWidget.java:814)
                  at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:934)
                  at com.affymetrix.genoviz.bioviews.View.mousePressed(View.java:850)
                  at java.awt.Component.processMouseEvent(Component.java:6411)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
                  at java.awt.Component.processEvent(Component.java:6179)
                  at java.awt.Container.processEvent(Container.java:2083)
                  at java.awt.Component.dispatchEventImpl(Component.java:4776)
                  at java.awt.Container.dispatchEventImpl(Container.java:2141)
                  at java.awt.Component.dispatchEvent(Component.java:4604)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4277)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
                  at java.awt.Container.dispatchEventImpl(Container.java:2127)
                  at java.awt.Window.dispatchEventImpl(Window.java:2489)
                  at java.awt.Component.dispatchEvent(Component.java:4604)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
                  at java.awt.EventQueue.access$400(EventQueue.java:82)
                  at java.awt.EventQueue$2.run(EventQueue.java:676)
                  at java.awt.EventQueue$2.run(EventQueue.java:674)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
                  at java.awt.EventQueue$3.run(EventQueue.java:690)
                  at java.awt.EventQueue$3.run(EventQueue.java:688)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

                  Show
                  tkanapar Tarun Santosh (Inactive) added a comment - The test passed however when we load the Unknown file provided in the attachment and right click on the track the following exception got generated Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.tiers.SeqMapViewPopup.popupNotify(SeqMapViewPopup.java:283) at com.affymetrix.igb.tiers.TierLabelManager.doPopup(TierLabelManager.java:592) at com.affymetrix.igb.tiers.TierLabelManager$1.mousePressed(TierLabelManager.java:136) at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1281) at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540) at com.affymetrix.genoviz.widget.NeoAbstractWidget.mousePressed(NeoAbstractWidget.java:814) at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:934) at com.affymetrix.genoviz.bioviews.View.mousePressed(View.java:850) at java.awt.Component.processMouseEvent(Component.java:6411) at javax.swing.JComponent.processMouseEvent(JComponent.java:3275) at java.awt.Component.processEvent(Component.java:6179) at java.awt.Container.processEvent(Container.java:2083) at java.awt.Component.dispatchEventImpl(Component.java:4776) at java.awt.Container.dispatchEventImpl(Container.java:2141) at java.awt.Component.dispatchEvent(Component.java:4604) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4277) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210) at java.awt.Container.dispatchEventImpl(Container.java:2127) at java.awt.Window.dispatchEventImpl(Window.java:2489) at java.awt.Component.dispatchEvent(Component.java:4604) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97) at java.awt.EventQueue$3.run(EventQueue.java:690) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:687) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r14959.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r14959.

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: