[BUG-278] Activating ENSEMBL while a species on IGB quickload is selected throws an error - JIRA UNCC

Details

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

Description

Loading a species that has IGB Quickload as a data source THEN activating 'Ensemble' (Pref> Data Source) throws the exception below.

Data sources > configure > Activate ENSEMBL, load Vitis vinifera, no errors. Deselect ENSEMBL. Reselect ENSEMBL, get the following error.
All other species without IGB Quickload do not have this error

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31)
at javax.swing.SwingWorker$5.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
at sun.swing.AccumulativeRunnable.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source)
at javax.swing.Timer.fireActionPerformed(Unknown Source)
at javax.swing.Timer$DoPostEvent.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

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BUG-647 Server bugs

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Katharine Kubiak (Inactive) created issue - 31/Jan/12 9:38 AM

Katharine Kubiak (Inactive) made changes - 31/Jan/12 9:39 AM

Field	Original Value	New Value
Description	Prior to loading a species activating 'Ensembl' has no issue. Loading species that has IGB Quickload as a data source throws the exception. IGB acts as if it is loading, but never does.When inactivating Ensembl the load bar continues to look as if it is loading. Also, all data in 'Data Sources...' and "Data Manage..." disappear. All other species without IGB Quickload have no error Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)	Prior to loading a species activating 'Ensembl' has no issue. Loading species that has IGB Quickload as a data source throws the exception. IGB acts as if it is loading, but never does.When inactivating Ensembl the load bar continues to look as if it is loading. Also, all data in 'Data Sources...' and "Data Manage..." disappear. All other species without IGB Quickload do not have this error Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Katharine Kubiak (Inactive) made changes - 31/Jan/12 9:40 AM

Description

Prior to loading a species activating 'Ensembl' has no issue.

Loading species that has IGB Quickload as a data source throws the exception. IGB acts as if it is loading, but never does.When inactivating Ensembl the load bar continues to look as if it is loading. Also, all data in 'Data Sources...' and "Data Manage..." disappear.
*All other species without IGB Quickload do not have this error*

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31)
at javax.swing.SwingWorker$5.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
at sun.swing.AccumulativeRunnable.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source)
at javax.swing.Timer.fireActionPerformed(Unknown Source)
at javax.swing.Timer$DoPostEvent.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

Prior to loading a species activating 'Ensembl' has no issue.

Loading a species that has IGB Quickload as a data source THEN activating 'Ensemble' (Pref> Data Source) throws the exception below. IGB will then act as if it is loading, but never does. When inactivating Ensembl the load bar continues to look as if it is still loading. Also, all data in 'Data Sources...' and "Data Manage..." disappear.
*All other species without IGB Quickload do not have this error*

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31)
at javax.swing.SwingWorker$5.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
at sun.swing.AccumulativeRunnable.run(Unknown Source)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source)
at javax.swing.Timer.fireActionPerformed(Unknown Source)
at javax.swing.Timer$DoPostEvent.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

Katharine Kubiak (Inactive) made changes - 31/Jan/12 9:41 AM

Assignee

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 31/Jan/12 10:28 AM - edited

Mac also. Console Error is:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31)
at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
at javax.swing.Timer.fireActionPerformed(Timer.java:291)
at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
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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Alyssa Gulledge (Inactive) added a comment - 31/Jan/12 10:28 AM - edited Mac also. Console Error is: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(SwingWorker.java:717) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814) at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824) at javax.swing.Timer.fireActionPerformed(Timer.java:291) at javax.swing.Timer$DoPostEvent.run(Timer.java:221) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:647) 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)

Alyssa Gulledge (Inactive) made changes - 31/Jan/12 10:28 AM

Assignee

Alyssa Gulledge [ alyssa ]

Hiral Vora [ hiralv ]

Alyssa Gulledge (Inactive) made changes - 31/Jan/12 10:35 AM

Summary	Species with IGB quickload throws exception when activating Ensembl AND does not stop loading	Activating ENSEMBL while a species on IGB quickload is selected throws an error
Description	Prior to loading a species activating 'Ensembl' has no issue. Loading a species that has IGB Quickload as a data source THEN activating 'Ensemble' (Pref> Data Source) throws the exception below. IGB will then act as if it is loading, but never does. When inactivating Ensembl the load bar continues to look as if it is still loading. Also, all data in 'Data Sources...' and "Data Manage..." disappear. All other species without IGB Quickload do not have this error Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)	Loading a species that has IGB Quickload as a data source THEN activating 'Ensemble' (Pref> Data Source) throws the exception below. Data sources > configure > Activate ENSEMBL, load Vitis vinifera, no errors. Deselect ENSEMBL. Reselect ENSEMBL, get the following error. All other species without IGB Quickload do not have this error Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.GeneralLoadUtils$1.finished(GeneralLoadUtils.java:800) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:31) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Hiral Vora (Inactive) made changes - 31/Jan/12 10:58 AM

Assignee

Hiral Vora [ hiralv ]

David Norris [ david ]

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David Norris (Inactive) added a comment - 01/Feb/12 6:54 AM

Fixed in r10090

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David Norris (Inactive) added a comment - 01/Feb/12 6:54 AM Fixed in r10090

David Norris (Inactive) made changes - 01/Feb/12 6:54 AM

Assignee

David Norris [ david ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 01/Feb/12 10:04 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 01/Feb/12 10:04 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 01/Feb/12 10:05 AM

Project	IGB 6.7 [ 10040 ]	Bug Repository [ 10030 ]
Key	~~IGBB-314~~	~~BUG-278~~

darius made changes - 07/Jun/12 6:33 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Darius Bost [ darius ]

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darius added a comment - 07/Jun/12 6:35 AM

Passed 7.0 (11861)

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darius added a comment - 07/Jun/12 6:35 AM Passed 7.0 (11861)

darius made changes - 07/Jun/12 6:35 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Darius Bost [ darius ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 9:53 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 9:13 AM

Link

This issue is blocked by ~~BUG-647~~ [ ~~BUG-647~~ ]

Alyssa Gulledge (Inactive) made changes - 18/Dec/12 7:44 AM

Link

This issue relates to ~~BUG-647~~ [ ~~BUG-647~~ ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/12 6:15 AM

Link

This issue is blocked by ~~BUG-647~~ [ ~~BUG-647~~ ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/12 6:15 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Resolution		Fixed [ 1 ]

People

Assignee:

Unassigned

Reporter:

Katharine Kubiak (Inactive)

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Dates

Created:

31/Jan/12 9:38 AM

Updated:

19/Dec/12 6:15 AM

Resolved:

19/Dec/12 6:15 AM