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  1. IGB
  2. IGBF-1061

clearing data set fails when refreshing QL server

    Details

    • 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

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          dcnorris David Norris (Inactive) added a comment -

          fixed on master branch

          Show
          dcnorris David Norris (Inactive) added a comment - fixed on master branch
          Hide
          mason Mason Meyer (Inactive) added a comment -

          Testing confirms that this issue has now been resolved. Now, the status message indicates that IGB is removing the features from blueberrry genes, but the message only lasts a short time.

          Since this story is resolved it will now be closed.

          Show
          mason Mason Meyer (Inactive) added a comment - Testing confirms that this issue has now been resolved. Now, the status message indicates that IGB is removing the features from blueberrry genes, but the message only lasts a short time. Since this story is resolved it will now be closed.

            People

            • Assignee:
              mason Mason Meyer (Inactive)
              Reporter:
              ann.loraine Ann Loraine
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              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: