Merge branch 'develop' into releases/Release_2_11_2_Branch

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

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index c340927..d829aae 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -54,7 +54,7 @@ public class CommandLineOperations
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
+  private static final int TEST_TIMEOUT = 12500; // Note longer timeout needed
                                                 // on
                                                 // full test run than on
                                                 // individual tests
@@ -129,6 +129,8 @@ public class CommandLineOperations
 
   private static String modules = null;
 
+  private static String java_exe = null;
+
   public synchronized static String getClassPath()
   {
     if (scanner == null)
@@ -141,6 +143,9 @@ public class CommandLineOperations
       {
         modules.concat(mr.getName());
       }
+      java_exe = System.getProperty("java.home") + File.separator + "bin"
+              + File.separator + "java";
+
     }
     while (classpath == null)
     {
@@ -161,7 +166,8 @@ public class CommandLineOperations
     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
     // not expanded by the shell
     String classpath = getClassPath();
-    String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
+    String _cmd = java_exe + " "
+            + (withAwt ? "-Djava.awt.headless=true" : "")
             + " -classpath " + classpath
             + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
                     : "")
@@ -195,17 +201,21 @@ public class CommandLineOperations
     }
     return worker;
   }
-  @Test(alwaysRun=true)
+
+  @Test(groups = { "Functional" })
   public void reportCurrentWorkingDirectory()
   {
-      try {
-          Path currentRelativePath = Paths.get("");
-          String s = currentRelativePath.toAbsolutePath().toString();
-          System.out.println("Test CWD is "+s);
-      } catch (Exception q) {
-          q.printStackTrace();
-      }
+    try
+    {
+      Path currentRelativePath = Paths.get("");
+      String s = currentRelativePath.toAbsolutePath().toString();
+      System.out.println("Test CWD is " + s);
+    } catch (Exception q)
+    {
+      q.printStackTrace();
+    }
   }
+
   @BeforeTest(alwaysRun = true)
   public void initialize()
   {
@@ -236,18 +246,53 @@ public class CommandLineOperations
   public void setUpForCommandLineInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
-    Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
-    String ln = null;
-    int count = 0;
-    while ((ln = worker.getErrorReader().readLine()) != null)
+    final Worker worker = getJalviewDesktopRunner(false, cmds,
+            SETUP_TIMEOUT);
+    
+    
+    // number of lines expected on STDERR when Jalview starts up normally
+    // may need to adjust this if Jalview is excessively noisy ?
+    final int STDERR_SETUPLINES=50;
+    
+    // thread monitors stderr - bails after SETUP_TIMEOUT or when
+    // STDERR_SETUPLINES have been read
+    Thread runner = new Thread(new Runnable()
     {
-      System.out.println(ln);
-      successfulCMDs.add(ln);
-      if (++count > 5)
+      public void run()
+      {
+        String ln = null;
+        int count = 0;
+        try
+        {
+          while ((ln = worker.getErrorReader().readLine()) != null)
+          {
+            System.out.println(ln);
+            successfulCMDs.add(ln);
+            if (++count > STDERR_SETUPLINES)
+            {
+              break;
+            }
+          }
+        } catch (Exception e)
+        {
+          System.err.println(
+                  "Unexpected Exception reading stderr from the Jalview process");
+          e.printStackTrace();
+        }
+      }
+    });
+    long t = System.currentTimeMillis() + SETUP_TIMEOUT;
+    runner.start();
+    while (!runner.isInterrupted() && System.currentTimeMillis() < t)
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
       {
-        break;
       }
     }
+    runner.interrupt();
     if (worker != null && worker.exit == null)
     {
       worker.interrupt();
@@ -265,7 +310,7 @@ public class CommandLineOperations
 
   @Test(
     groups =
-    { "Functional", "testben" },
+    { "Functional" },
     dataProvider = "headlessModeOutputOperationsData")
   public void testHeadlessModeOutputOperations(String harg, String type,
           String fileName, boolean withAWT, int expectedMinFileSize,