Merge branch 'patch/JAL-4062_sort_and_merge_contiguousregions' into develop

[jalview.git] / test / jalview / bin / CommandLineOperations.java

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 9b9adf8..77cbd92 100644 (file)
--- 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;
 
@@ -54,7 +53,7 @@ public class CommandLineOperations
   }
 
   // Note longer timeout needed on full test run than on individual tests
-  private static final int TEST_TIMEOUT = 23000;
+  private static final int TEST_TIMEOUT = 15000;
 
   private static final int SETUP_TIMEOUT = 9500;
 
@@ -213,13 +212,13 @@ 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
   {
@@ -230,16 +229,17 @@ public class CommandLineOperations
     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";
@@ -248,6 +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
@@ -258,14 +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;
             }