JAL-3563 for merging to JAL-3253-applet

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 4ffc022..1241796 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -169,6 +169,8 @@ public class CommandLineOperations
       BufferedReader errorReader = new BufferedReader(
               new InputStreamReader(ls2_proc.getErrorStream()));
       worker = new Worker(ls2_proc);
+      worker.setOutputReader(outputReader);
+      worker.setErrorReader(errorReader);
       worker.start();
       try
       {
@@ -177,8 +179,6 @@ public class CommandLineOperations
       {
         System.err.println("Thread interrupted");
       }
-      worker.setOutputReader(outputReader);
-      worker.setErrorReader(errorReader);
     }
     return worker;
   }
@@ -224,7 +224,7 @@ public class CommandLineOperations
   int ntest = 0;
 
   @BeforeTest(alwaysRun = true)
-  public void setUpForCommandLineInputOperations() throws IOException
+  public void setUpForNonHeadlessInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
     Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
@@ -264,7 +264,7 @@ public class CommandLineOperations
     dataProvider = "headlessModeOutputOperationsData")
   public void testHeadlessModeOutputOperations(String harg, String type,
           String fileName, boolean withAWT, int expectedMinFileSize,
-          int timeout)
+          int timeout) throws IOException
   {
     File file = new File(fileName);
     String cmd = harg + type + " "
@@ -274,7 +274,16 @@ public class CommandLineOperations
     file.deleteOnExit();
     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
     assertNotNull(worker, "worker is null");
-    String msg = "Didn't create an output" + type + " file.[" + harg + "]";
+    String msg = "Didn't create an output" + type + " file: "
+            + file.getAbsolutePath() + " [" + harg + "]";
+    while (worker.isAlive())
+    {
+    }
+    while (worker.getOutputReader().ready())
+    {
+      String ln = worker.getOutputReader().readLine();
+      System.out.println(ln);
+    }
     assertTrue(file.exists(), msg);
     FileAssert.assertFile(file, msg);
     FileAssert.assertMinLength(file, expectedMinFileSize);
@@ -283,17 +292,17 @@ public class CommandLineOperations
       worker.interrupt();
       Thread.currentThread().interrupt();
       worker.process.destroy();
-      Assert.fail("Jalview did not exit after "
-              + type
-              + " generation (try running test again to verify - timeout at "
-              + SETUP_TIMEOUT + "ms). ["
-              + harg + "]");
+      // Assert.fail("Jalview did not exit after "
+      // + type
+      // + " generation (try running test again to verify - timeout at "
+      // + SETUP_TIMEOUT + "ms). ["
+      // + harg + "]");
     }
     file.delete();
   }
 
   @DataProvider(name = "allInputOperationsData")
-  public Object[][] getHeadlessModeInputParams()
+  public Object[][] getAllInputParams()
   {
     return new Object[][] {
         // headless mode input operations
@@ -373,6 +382,7 @@ public class CommandLineOperations
             MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -jalview",
             "test/jalview/bin/test_uniref50_out.jvp", true,
-            MINFILESIZE_SMALL, TEST_TIMEOUT }, };
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
+    };
   }
 }

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 3c74b9e..eef44de 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -92,13 +92,18 @@ import org.testng.annotations.Test;
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJalviewSynchonization()
+  {
+    Jalview.setSynchronous(true);
+  }
+
   @Override
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-    Jalview.setSynchronous(true);
   }
 
   @Test(groups = { "Functional" })
@@ -107,7 +112,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String inFile = "examples/RF00031_folded.stk";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
@@ -147,7 +151,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             inAnnot = "examples/uniref50.score_ascii";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
@@ -158,8 +161,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertNotNull(
             ColourSchemeProperty.getColourScheme(viewport,
                     viewport.getAlignment(),
-                    viewport.getGlobalColourScheme()
-                            .getSchemeName()),
+                    viewport.getGlobalColourScheme().getSchemeName()),
             "Recognise T-Coffee score from string");
 
     af.saveAlignment(tfile, FileFormat.Jalview);
@@ -183,7 +185,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             inAnnot = "examples/testdata/uniref50_iupred.jva";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
@@ -272,7 +273,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     int origCount = Desktop.getAlignFrames() == null ? 0
             : Desktop.getAlignFrames().length;
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -291,7 +291,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     StructureImportSettings.setProcessSecondaryStructure(true);
     StructureImportSettings.setVisibleChainAnnotation(true);
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -303,8 +302,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     StructureMapping[] x = af.getCurrentView()
             .getStructureSelectionManager()//
             .getMapping(pdbFile);
-    assertEquals(x.length,
-            2, "Expected only two mappings for 1A70");
+    assertEquals(x.length, 2, "Expected only two mappings for 1A70");
 
   }
 
@@ -313,7 +311,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     StructureImportSettings.setProcessSecondaryStructure(true);
     StructureImportSettings.setVisibleChainAnnotation(true);
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -375,7 +372,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testCopyViewSettings() throws Exception
   {
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -415,7 +411,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
@@ -453,9 +448,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(
                     af.getViewport().getSequenceSetId()).length);
-    Assert.assertEquals(
-            Desktop.getAlignmentPanels(
-                    af.getViewport().getSequenceSetId()).length,
+    Assert.assertEquals(Desktop
+            .getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
             oldviews);
   }
 
@@ -469,7 +463,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -603,7 +596,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverGroupRepSeqs() throws Exception
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -725,7 +717,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
     String exampleFile = "examples/3W5V.pdb";
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -825,7 +816,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverColourThresholds() throws IOException
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
@@ -919,7 +909,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testSaveLoadFeatureColoursAndFilters() throws IOException
   {
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
@@ -1080,7 +1069,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testMergeDatasetsforViews() throws IOException
   {
     // simple project - two views on one alignment
-    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
             "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
     assertNotNull(af);
@@ -1098,8 +1086,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
 
-    // complex project - one dataset, several views on several alignments
-    // Jalview.setSynchronous(true);
+    // complex project - one dataset, several views on several alignment
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
             "examples/testdata/projects/manyViews.jvp",
             DataSourceType.FILE);
@@ -1142,7 +1129,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testPcaViewAssociation() throws IOException
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
-    // Jalview.setSynchronous(true);
     final String PCAVIEWNAME = "With PCA";
     // create a new tempfile
     File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");