Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.25
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Epic Link:
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Sprint:Sprint 14
Description
*Found by Ivory in 8.3.0 (also happens on 8.4.0):
This bug was found when performing residue searches. If you consecutively use the advanced search feature it will fail on the 9th search and generate an exception (see below for exception, Ivory's comments, and a screenshot of the problem.)
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Attachment | Screen Shot 2015-02-16 at 1.29.08 PM.png [ 12974 ] |
13:28:53.358 INFO com.affymetrix.igb.Application - Copied 36 residues from selected region to clipboard
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 8
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at javax.swing.SwingWorker.get(SwingWorker.java:602)
at com.affymetrix.igb.search.SearchView$SearchAction$1.finished(SearchView.java:170)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:47)
at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
at javax.swing.Timer.fireActionPerformed(Timer.java:313)
at javax.swing.Timer$DoPostEvent.run(Timer.java:245)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:744)
at java.awt.EventQueue.access$400(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:697)
at java.awt.EventQueue$3.run(EventQueue.java:691)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:714)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 8
at com.affymetrix.igb.search.SearchModeResidue.search(SearchModeResidue.java:295)
at com.affymetrix.igb.search.SearchModeResidue.searchResidue(SearchModeResidue.java:251)
at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:135)
at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:130)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
| Rank | Ranked higher |
| Description |
*Found by Ivory in 8.3.0:
This bug was found when performing residue searches. If you consecutively use the advanced search feature it will fail on the 9th search and generate an exception (see below for exception, Ivory's comments, and a screenshot of the problem.) |
*Found by Ivory in 8.3.0 (also happens on 8.4.0):
This bug was found when performing residue searches. If you consecutively use the advanced search feature it will fail on the 9th search and generate an exception (see below for exception, Ivory's comments, and a screenshot of the problem.) |
| Story Points | 0.25 |
| Assignee | Tarun Mall [ tmall ] |
| Sprint | Sprint 14 [ 19 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Pull Request Submitted [ 10101 ] |
| Epic Link | IGBF-439 [ 15497 ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Assignee | Tarun Mall [ tmall ] | Mason Meyer [ mason ] |
Testing verifies that using the Advanced Search 9 times in a row no longer causes search to fail and no longer generates an exception. A user can now search as many times as they want and the 8 colors continue to cycle.
Since this story is resolved it will now be closed.
| Resolution | Done [ 10000 ] | |
| Status | Needs Testing [ 10002 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 15669 ] | Fall 2019 Workflow Update [ 19358 ] |
| Workflow | Fall 2019 Workflow Update [ 19358 ] | Revised Fall 2019 Workflow Update [ 21475 ] |
*From Ivory:
IGB hangs on advanced search of nucleotide sequences. I did several searches and they all worked until the peach color had been used (even if there were no peach results to show). After that, if tried a new residue search it just searched indefinitely until I restarted the program. Its like it doesn’t want to admit that it has run out of colors. Even if a search has no results, if you hit the search button several times, each one is a search and uses a color and after 9?, it will hang. I could avoid the hang by clearing search results when I got to peach.