X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=ee03e7755a0df6445f864a12052c1249247099b3;hb=5b14c48157e617dd00342429090bb0be5193d9a5;hp=1761261175398814251b8086568ee5fba0f439e6;hpb=b4938d8d3018957d5c5fd4443278083e8b5e0864;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 1761261..ee03e77 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -29,6 +29,8 @@ 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;
@@ -52,7 +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
@@ -127,6 +129,8 @@ public class CommandLineOperations
 
   private static String modules = null;
 
+  private static String java_exe = null;
+
   public synchronized static String getClassPath()
   {
     if (scanner == null)
@@ -139,6 +143,9 @@ public class CommandLineOperations
       {
         modules.concat(mr.getName());
       }
+      java_exe = System.getProperty("java.home") + File.separator + "bin"
+              + File.separator + "java";
+
     }
     while (classpath == null)
     {
@@ -159,7 +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 + "\""
                     : "")
@@ -194,6 +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()
   {
@@ -204,7 +226,7 @@ public class CommandLineOperations
   public void setUpForHeadlessCommandLineInputOperations()
           throws IOException
   {
-    String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
+    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";
     Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
@@ -224,18 +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=30;
+    
+    // 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();
@@ -253,7 +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,
@@ -288,7 +345,7 @@ public class CommandLineOperations
         // headless mode input operations
         { "CMD [-color zappo] executed successfully!",
             "Failed command : -color zappo" },
-        { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
+        { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
             "Failed command : -props File" },
         { "CMD [-sortbytree] executed successfully!",
             "Failed command : -sortbytree" },
@@ -314,53 +371,58 @@ public class CommandLineOperations
   @DataProvider(name = "headlessModeOutputOperationsData")
   public static Object[][] getHeadlessModeOutputParams()
   {
+    // JBPNote: I'm not clear why need to specify full path for output file
+    // when running tests on build server, but we will keep this patch for now
+    // 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", "test/jalview/bin/test_uniref50_out.eps", true,
+        " -eps", workingDir + "test_uniref50_out.eps", true,
         MINFILESIZE_BIG, TEST_TIMEOUT },
         { "nodisplay -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", false,
+            workingDir + "test_uniref50_out.eps", false,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", false,
+            workingDir + "test_uniref50_out.eps", false,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -svg",
-            "test/jalview/bin/test_uniref50_out.svg", false,
+            workingDir + "test_uniref50_out.svg", false,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -png",
-            "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
+            workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -html",
-            "test/jalview/bin/test_uniref50_out.html", true,
+            workingDir + "test_uniref50_out.html", true,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -fasta",
-            "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -clustal",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -msf",
-            "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pileup",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pir",
-            "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pfam",
-            "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -blc",
-            "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -jalview",
-            "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT }, };
   }
 }