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  1. Jalview
  2. JAL-3524

Backup system doesn't report error messages via console in headless mode



    • Type: Bug
    • Status: Open
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.11.0, 2.11.1
    • Fix Version/s: None
    • Component/s: Command Line Interface
    • Labels:
    • Environment:
      Java version: 12
      x86_64 Mac OS X 10.13.6
      Jalview Version: DEVELOPMENT (Source git-commit:325d9af46 [develop])


      after a gradle shadowJar build, the following command:
      java -jar build/libs/jalview-all-DEVELOPMENT-j11.jar -props ~/Documents/Jalview/ReleaseTests/ -headless -open examples/uniref50.fa - png ~/Documents/Jalview/ReleaseTests/

      Yielded a stack trace (below) from the output file backup system (JAL-3141). It looks like the backup system isn't honouring the 'nogui' flag and trying to pop open a dialog. It also isn't clear from the log why it "Could not get canonical path for file 'png'" !

      Running jalview.bin.Jalview with -Xmx15461882266
      Java version: 12
      x86_64 Mac OS X 10.13.6
      Jalview Version: DEVELOPMENT (Source git-commit:325d9af46 [develop])
      CMD [-props /Users/jprocter/Documents/Jalview/ReleaseTests/] executed successfully!
      DEBUG - Jalview Debugging Output Follows.
      Quaqua LaF not available on this plaform. Using VAqua(4).
      See https://issues.jalview.org/browse/JAL-2976
      Ignoring SO:0001957 as obsolete and duplicated by SO:0001979
      Ignoring SO:0000437 as obsolete and duplicated by SO:0000800
      Ignoring SO:0000554 as obsolete and duplicated by SO:0000801
      Ignoring SO:0000767 as obsolete and duplicated by SO:0000179
      Ignoring SO:0000058 as obsolete and duplicated by SO:0000803
      Ignoring SO:0001052 as obsolete and duplicated by SO:0001649
      Ignoring SO:0000052 as obsolete and duplicated by SO:0000802
      Ignoring SO:0001053 as obsolete and duplicated by SO:0001648
      Loaded Sequence Ontology from so-xp-simple.obo.zip (212ms)
      CMD [-open examples/uniref50.fa] executed successfully!
      File format identified as Fasta
      Feb 11, 2020 9:36:13 AM jalview.util.MessageManager <clinit>
      INFO: Getting messages for lang: en_GB
      Could not get canonical path for file 'png'
      Exception in thread "main" java.awt.HeadlessException
      at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:197)
      at java.desktop/java.awt.Window.<init>(Window.java:538)
      at java.desktop/java.awt.Frame.<init>(Frame.java:423)
      at java.desktop/java.awt.Frame.<init>(Frame.java:388)
      at java.desktop/javax.swing.SwingUtilities$SharedOwnerFrame.<init>(SwingUtilities.java:1919)
      at java.desktop/javax.swing.SwingUtilities.getSharedOwnerFrame(SwingUtilities.java:1995)
      at java.desktop/javax.swing.JOptionPane.getRootFrame(JOptionPane.java:1689)
      at java.desktop/javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:868)
      at java.desktop/javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:799)
      at java.desktop/javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:761)
      at jalview.gui.JvOptionPane.showConfirmDialog(JvOptionPane.java:64)
      at jalview.io.BackupFiles.rollBackupsAndRenameTempFile(BackupFiles.java:664)
      at jalview.gui.AlignFrame.saveAlignment(AlignFrame.java:1221)
      at jalview.bin.Jalview.doMain(Jalview.java:655)
      at jalview.bin.Jalview.main(Jalview.java:191)




            jprocter James Procter
            jprocter James Procter
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