[BUG-812] File not listed in DMT, cannot be loaded if IGB is "fresh" - JIRA UNCC

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.

Attachments

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Attachments

all.gff3.zip
35 kB
15/Jul/13 11:39 AM
Unknown.gff3.zip
164 kB
15/Jul/13 11:39 AM

Issue Links

relates to

BUG-623 File management bugs

Closed

Activity

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Alyssa Gulledge (Inactive) created issue - 15/Jul/13 11:38 AM

Alyssa Gulledge (Inactive) made changes - 15/Jul/13 11:39 AM

Field	Original Value	New Value
Attachment		all.gff3.zip [ 12084 ]
Attachment		Unknown.gff3.zip [ 12085 ]

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Hiral Vora (Inactive) added a comment - 19/Jul/13 6:38 AM

Fixed in r14959.

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Hiral Vora (Inactive) added a comment - 19/Jul/13 6:38 AM Fixed in r14959.

Hiral Vora (Inactive) made changes - 19/Jul/13 6:38 AM

Assignee

Hiral Vora [ hiralv ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 22/Jul/13 6:27 AM

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

Alyssa Gulledge (Inactive) made changes - 22/Jul/13 6:27 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 01/Oct/13 7:19 AM

Project	IGB 7.1 [ 10240 ]	Bug Repository [ 10030 ]
Key	~~IGBD-267~~	~~BUG-812~~

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 5:55 AM

Link

This issue relates to ~~BUG-623~~ [ ~~BUG-623~~ ]

Alyssa Gulledge (Inactive) made changes - 02/Oct/13 10:23 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Tarun Santosh [ tkanapar ]

Tarun Santosh (Inactive) made changes - 04/Oct/13 12:33 PM

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

Tarun Santosh (Inactive) made changes - 04/Oct/13 12:39 PM

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

Tarun Santosh (Inactive) made changes - 04/Oct/13 12:40 PM

Comment

[ Passed in Mac IGB 7.0.4 (15398)
]

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Tarun Santosh (Inactive) added a comment - 04/Oct/13 12:42 PM

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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Tarun Santosh (Inactive) added a comment - 04/Oct/13 12:42 PM 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)

Tarun Santosh (Inactive) made changes - 04/Oct/13 12:42 PM

Assignee

Tarun Santosh [ tkanapar ]

Hiral Vora [ hiralv ]

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Hiral Vora (Inactive) added a comment - 08/Oct/13 5:08 AM

Cannot reproduce.

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Hiral Vora (Inactive) added a comment - 08/Oct/13 5:08 AM Cannot reproduce.

Hiral Vora (Inactive) made changes - 08/Oct/13 5:08 AM

Assignee

Hiral Vora [ hiralv ]

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 08/Oct/13 5:19 AM

no problem in v15424

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Alyssa Gulledge (Inactive) added a comment - 08/Oct/13 5:19 AM no problem in v15424

Alyssa Gulledge (Inactive) made changes - 08/Oct/13 5:19 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 08/Oct/13 5:19 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

People

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Reporter:

Alyssa Gulledge (Inactive)

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Dates

Created:

15/Jul/13 11:38 AM

Updated:

08/Oct/13 5:19 AM

Resolved:

08/Oct/13 5:19 AM