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: 8.5.2 MInor Release
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Labels:
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Sprint:Sprint 30
Description
Refreshing a Quickload site causes IGB to continually display rolling status message.
To repeat:
1) reset prefs to defaults
2) click the blueberry image on the start screen
3) select Data Access tab > configure
4) click "refresh" icon for QL server naemd "blueberry"
6) a dialog will appear notifying you that clicking refresh will force all the configuration files on the server to be re-read
7) click "ok"
Observe that the status bar on the lower left of IGB now displays the message "Removing feature Blueberry genes" and shows the rolling status bar thing. It never goes away.
Open the console and observe the following message:
0:57:31.599 ERROR c.a.genometry.thread.CThreadWorker - null
java.lang.NullPointerException: null
at com.affymetrix.genometry.general.DataSet.clear(DataSet.java:245) ~[na:na]
at com.affymetrix.igb.view.TrackView.deleteSymsOnSeq(TrackView.java:191) ~[na:na]
at com.affymetrix.igb.view.load.GeneralLoadView$6.runInBackground(GeneralLoadView.java:709) ~[na:na]
at com.affymetrix.igb.view.load.GeneralLoadView$6.runInBackground(GeneralLoadView.java:703) ~[na:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_66]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_66]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_66]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_66]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_66]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_66]
10:57:32.243 INFO c.l.quickload.QuickloadDataProvider - Initializing Quickload Server http://www.igbquickload.org/blueberry/
10:57:32.275 WARN c.l.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://www.igbquickload.org/blueberry/synonyms.txt
10:57:32.282 WARN c.l.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://www.igbquickload.org/blueberry/species.txt
10:57:32.383 INFO c.a.genometry.util.ServerUtils - STOPWATCH METRICS for createSymLoader 35.17 ms
10:57:41.470 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded Gene Predictions / Augustus in 9.086 s
10:57:46.872 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded Gene Predictions / Augustus in 5.402 s
fixed on master branch