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  1. Jalview
  2. JAL-2455

JMol viewer test throws exceptions

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.10.1
    • Fix Version/s: None
    • Component/s: Test suite
    • Labels:
      None

      Description

      Running JMolViewerTest from Eclipse or the command line produces (different) exceptions. These appear to be related to tearDown rather than the test itself.

      In Eclipse (last section of output):
      ===============================================
      Default suite
      Total tests run: 1, Failures: 0, Skips: 0
      ===============================================

      [TestNG] Time taken by org.testng.reporters.EmailableReporter2@a9c6fd8: 12 ms
      [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 2 ms
      Squashed Jmol callback handler error:
      java.lang.NullPointerException
      at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1187)
      at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:952)
      at org.jmol.viewer.StatusManager.setFileLoadStatus(StatusManager.java:407)
      at org.jmol.viewer.Viewer.setFileLoadStatus(Viewer.java:4694)
      at org.jmol.viewer.Viewer.createModelSetAndReturnError(Viewer.java:2249)
      at org.jmol.viewer.Viewer.loadModelFromFile(Viewer.java:1737)
      at org.jmol.script.ScriptEval.cmdLoad(ScriptEval.java:4671)
      at org.jmol.script.ScriptEval.processCommand(ScriptEval.java:2380)
      at org.jmol.script.ScriptEval.commandLoop(ScriptEval.java:2248)
      at org.jmol.script.ScriptEval.dispatchCommands(ScriptEval.java:2111)
      at org.jmol.script.ScriptEval.executeCommands(ScriptEval.java:417)
      at org.jmol.script.ScriptEval.evaluateCompiledScript(ScriptEval.java:403)
      at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(ScriptManager.java:356)
      at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Viewer.java:3835)
      at org.jmol.script.ScriptQueueThread.runNextScript(ScriptQueueThread.java:111)
      at org.jmol.script.ScriptQueueThread.run1(ScriptQueueThread.java:78)
      at org.jmol.thread.JmolThread.run(JmolThread.java:105)
      Time for creating model: 860 ms
      OXIDOREDUCTASE/ELECTRON TRANSPORT 08-MAY-00 1GAQ
      1GAQ


      Adding embedded #jmolscript: select ({0:689});backbone only;select *;
      [TestNG] Time taken by org.testng.reporters.jq.Main@55f3bd93: 270 ms
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/junitreports/TEST-jalview.ext.jmol.JmolViewerTest.xml
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/junitreports exists: true
      [TestNG] Time taken by org.testng.reporters.JUnitReportReporter@4358cfda: 15 ms
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/toc.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/Default test.properties
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/index.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/main.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/groups.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/classes.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/reporter-output.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/methods-not-run.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/Default suite/testng.xml.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old/Default suite exists: true
      [Utils] Attempting to create /Users/kmourao/jalview/jalview/test-output/old/index.html
      [Utils] Directory /Users/kmourao/jalview/jalview/test-output/old exists: true
      [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter@15d05b0a: 110 ms
      [TestNG] Time taken by org.testng.reporters.XMLReporter@5f92e49f: 25 ms
      Exception in thread "Thread-18" java.lang.NullPointerException
      at jalview.gui.AppJmol.showFilesInViewer(AppJmol.java:414)
      at jalview.gui.AppJmol.run(AppJmol.java:345)
      at java.lang.Thread.run(Thread.java:745)


      From command line:
      [testng] java.lang.NullPointerException
         [testng] at jalview.gui.AppJmolBinding.releaseReferences(AppJmolBinding.java:202)
         [testng] at jalview.structure.StructureSelectionManager.removeStructureViewerListener(StructureSelectionManager.java:722)
         [testng] at jalview.gui.AlignmentPanel.closePanel(AlignmentPanel.java:1654)
         [testng] at jalview.gui.AlignFrame.closeMenuItem_actionPerformed(AlignFrame.java:1454)
         [testng] at jalview.gui.AlignFrame$6.internalFrameClosed(AlignFrame.java:821)
         [testng] at javax.swing.JInternalFrame.fireInternalFrameEvent(JInternalFrame.java:1573)
         [testng] at javax.swing.JInternalFrame.dispose(JInternalFrame.java:1802)
         [testng] at javax.swing.JInternalFrame.setClosed(JInternalFrame.java:831)
         [testng] at jalview.gui.Desktop.closeAll_actionPerformed(Desktop.java:1365)
         [testng] at jalview.ext.jmol.JmolViewerTest.tearDownAfterClass(JmolViewerTest.java:67)
         [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
         [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         [testng] at java.lang.reflect.Method.invoke(Method.java:498)
         [testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
         [testng] at org.testng.internal.Invoker.invokeConfigurationMethod(Invoker.java:515)
         [testng] at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:213)
         [testng] at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:140)
         [testng] at org.testng.internal.TestMethodWorker.invokeAfterClassMethods(TestMethodWorker.java:220)
         [testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:111)
         [testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
         [testng] at org.testng.TestRunner.run(TestRunner.java:621)
         [testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
         [testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
         [testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
         [testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
         [testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
         [testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
         [testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
         [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
         [testng] at org.testng.TestNG.run(TestNG.java:1009)
         [testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
         [testng] at org.testng.TestNG.main(TestNG.java:1285)

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            Assignee:
            jprocter Jim Procter
            Reporter:
            kmourao Kira MourĂ£o
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              Dates

              Created:
              Updated: