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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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          Activity

          ann.loraine Ann Loraine created issue -
          ann.loraine Ann Loraine made changes -
          Field Original Value New Value
          Rank Ranked higher
          ann.loraine Ann Loraine made changes -
          Sprint Sprint 30 [ 38 ]
          ann.loraine Ann Loraine made changes -
          Rank Ranked lower
          ann.loraine Ann Loraine made changes -
          Rank Ranked higher
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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
          dcnorris David Norris (Inactive) made changes -
          Status Open [ 1 ] Needs Testing [ 10002 ]
          dcnorris David Norris (Inactive) made changes -
          Fix Version/s 8.5.2 MInor Release [ 10200 ]
          dcnorris David Norris (Inactive) made changes -
          Assignee David Norris [ dcnorris ] Tarun Mall [ tmall ]
          mason Mason Meyer (Inactive) made changes -
          Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
          mason Mason Meyer (Inactive) made changes -
          Assignee Tarun Mall [ tmall ] Mason Meyer [ mason ]
          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.
          mason Mason Meyer (Inactive) made changes -
          Resolution Done [ 10000 ]
          Status Testing In Progress [ 10003 ] Closed [ 6 ]
          mason Mason Meyer (Inactive) made changes -
          Resolution Done [ 10000 ]
          Status Closed [ 6 ] Open [ 1 ]
          mason Mason Meyer (Inactive) made changes -
          Labels Data_Provider
          mason Mason Meyer (Inactive) made changes -
          Resolution Done [ 10000 ]
          Status Open [ 1 ] Closed [ 6 ]
          ann.loraine Ann Loraine made changes -
          Workflow Loraine Lab Workflow [ 16928 ] Fall 2019 Workflow Update [ 19744 ]
          ann.loraine Ann Loraine made changes -
          Workflow Fall 2019 Workflow Update [ 19744 ] Revised Fall 2019 Workflow Update [ 21863 ]

            People

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

              Dates

              • Created:
                Updated:
                Resolved: