X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=2ccb5dd751412ff1a04d34cfdbcda4fc3369ca40;hb=ef1d19d74a85425a99ed463d638545c46297ef0e;hp=98e4eb54297ca74f2197b2e938ee834870bf3296;hpb=05efc2ac3c6427a4dabce842ebbd6f2ae17f49b9;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 98e4eb5..2ccb5dd 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -20,12 +20,17 @@
  */
 package jalview.bin;
 
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
 import jalview.gui.JvOptionPane;
 
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 
 import org.testng.Assert;
@@ -49,7 +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 = 10500; // Note longer timeout needed
                                                 // on
                                                 // full test run than on
                                                 // individual tests
@@ -124,6 +129,8 @@ public class CommandLineOperations
 
   private static String modules = null;
 
+  private static String java_exe = null;
+
   public synchronized static String getClassPath()
   {
     if (scanner == null)
@@ -136,6 +143,9 @@ public class CommandLineOperations
       {
         modules.concat(mr.getName());
       }
+      java_exe = System.getProperty("java.home") + File.separator + "bin"
+              + File.separator + "java";
+
     }
     while (classpath == null)
     {
@@ -156,7 +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 + "\""
                     : "")
@@ -191,6 +202,20 @@ public class CommandLineOperations
     return worker;
   }
 
+  @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();
+    }
+  }
+
   @BeforeTest(alwaysRun = true)
   public void initialize()
   {
@@ -221,18 +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();
@@ -250,7 +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,
@@ -262,8 +322,7 @@ 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 at '"
-            + file.getAbsolutePath() + "'.[" + harg + "]";
+    String msg = "Didn't create an output" + type + " file.[" + harg + "]";
     assertTrue(file.exists(), msg);
     FileAssert.assertFile(file, msg);
     FileAssert.assertMinLength(file, expectedMinFileSize);