X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=3855dc70192cea743d9320a9919ab24fd3786a29;hb=82eb22b5c4cc991fad95822c71ab3ed90da759a6;hp=67e2433774858ebc61f2e3ff4586e7192bd01585;hpb=bcc114c5106c3cee78db99955fee2392edece7df;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 67e2433..3855dc7 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -34,7 +34,6 @@ import java.util.ArrayList;
 import org.testng.Assert;
 import org.testng.FileAssert;
 import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeTest;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -53,10 +52,8 @@ public class CommandLineOperations
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  private static final int TEST_TIMEOUT = 13000; // Note longer timeout needed
-                                                 // on
-                                                 // full test run than on
-                                                 // individual tests
+  // Note longer timeout needed on full test run than on individual tests
+  private static final int TEST_TIMEOUT = 15000;
 
   private static final int SETUP_TIMEOUT = 9500;
 
@@ -74,7 +71,7 @@ public class CommandLineOperations
    * @author jimp
    * 
    */
-  private static class Worker extends Thread
+  public static class Worker extends Thread
   {
     private final Process process;
 
@@ -159,7 +156,7 @@ public class CommandLineOperations
     return classpath;
   }
 
-  private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+  public static Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
           int timeout)
   {
     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
@@ -186,7 +183,7 @@ public class CommandLineOperations
               new InputStreamReader(ls2_proc.getInputStream()));
       BufferedReader errorReader = new BufferedReader(
               new InputStreamReader(ls2_proc.getErrorStream()));
-      worker = new Worker(ls2_proc);
+      worker = new CommandLineOperations.Worker(ls2_proc);
       worker.start();
       try
       {
@@ -215,33 +212,34 @@ public class CommandLineOperations
     }
   }
 
-  @BeforeTest(alwaysRun = true)
+  @BeforeClass(alwaysRun = true)
   public void initialize()
   {
     new CommandLineOperations();
   }
 
-  @BeforeTest(alwaysRun = true)
+  @BeforeClass(alwaysRun = true)
   public void setUpForHeadlessCommandLineInputOperations()
           throws IOException
   {
     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
-            + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree --debug";
+            + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
     Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
     String ln = null;
     while ((ln = worker.getOutputReader().readLine()) != null)
     {
-      System.out.println(ln);
+      System.out.println("STDOUT: " + ln);
       successfulCMDs.add(ln);
     }
     while ((ln = worker.getErrorReader().readLine()) != null)
     {
-      System.err.println(ln);
+      System.err.println("STDERR: " + ln);
+      successfulCMDs.add(ln);
     }
   }
 
-  @BeforeTest(alwaysRun = true)
+  @BeforeClass(alwaysRun = true)
   public void setUpForCommandLineInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
@@ -250,6 +248,7 @@ public class CommandLineOperations
 
     // number of lines expected on STDERR when Jalview starts up normally
     // may need to adjust this if Jalview is excessively noisy ?
+    final int STDOUT_SETUPLINES = 50;
     final int STDERR_SETUPLINES = 50;
 
     // thread monitors stderr - bails after SETUP_TIMEOUT or when
@@ -260,14 +259,24 @@ public class CommandLineOperations
       public void run()
       {
         String ln = null;
-        int count = 0;
+        int stdoutcount = 0;
+        int stderrcount = 0;
         try
         {
-          while ((ln = worker.getErrorReader().readLine()) != null)
+          while ((ln = worker.getOutputReader().readLine()) != null)
           {
             System.out.println(ln);
             successfulCMDs.add(ln);
-            if (++count > STDERR_SETUPLINES)
+            if (++stdoutcount > STDOUT_SETUPLINES)
+            {
+              break;
+            }
+          }
+          while ((ln = worker.getErrorReader().readLine()) != null)
+          {
+            System.err.println(ln);
+            successfulCMDs.add(ln);
+            if (++stderrcount > STDERR_SETUPLINES)
             {
               break;
             }
@@ -342,8 +351,8 @@ public class CommandLineOperations
   {
     return new Object[][] {
         // headless mode input operations
-        { "CMD [-color zappo] executed successfully!",
-            "Failed command : -color zappo" },
+        { "CMD [-colour zappo] executed successfully!",
+            "Failed command : -colour zappo" },
         { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
             "Failed command : -props File" },
         { "CMD [-sortbytree] executed successfully!",
@@ -375,9 +384,11 @@ public class CommandLineOperations
     // since it works.
     // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
     String workingDir = "test/jalview/bin/";
-    return new Object[][] { { "nodisplay -open examples/uniref50.fa",
-        " -eps", workingDir + "test_uniref50_out.eps", true,
-        MINFILESIZE_BIG, TEST_TIMEOUT },
+    return new Object[][] {
+        //
+        { "nodisplay -open examples/uniref50.fa", " -eps",
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "nodisplay -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
             TEST_TIMEOUT },
@@ -422,6 +433,8 @@ public class CommandLineOperations
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -jalview",
             workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT }, };
+            TEST_TIMEOUT },
+        //
+    };
   }
 }