JAL-1889 correct props param, remove dasserver, output file paths

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index cbc2391..e878e25 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -176,7 +176,6 @@ public class CommandLineOperations
       } catch (InterruptedException e)
       {
         System.err.println("Thread interrupted");
-        e.printStackTrace();
       }
       worker.setOutputReader(outputReader);
       worker.setErrorReader(errorReader);
@@ -194,8 +193,8 @@ public class CommandLineOperations
   public void setUpForHeadlessCommandLineInputOperations()
           throws IOException
   {
-    String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
-            + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
+    String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/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);
     String ln = null;
@@ -204,6 +203,10 @@ public class CommandLineOperations
       System.out.println(ln);
       successfulCMDs.add(ln);
     }
+    while ((ln = worker.getErrorReader().readLine()) != null)
+    {
+      System.err.println(ln);
+    }
   }
 
   @BeforeTest(alwaysRun = true)
@@ -248,11 +251,11 @@ public class CommandLineOperations
     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
     File file = new File(fileName);
     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
-    assertNotNull(worker);
+    assertNotNull(worker, "worker is null");
     String msg = "Didn't create an output" + type + " file.[" + harg + "]";
-    assertTrue(file.exists());
+    assertTrue(file.exists(), msg);
     FileAssert.assertFile(file, msg);
-    FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
+    FileAssert.assertMinLength(file, expectedMinFileSize);
     if (worker != null && worker.exit == null)
     {
       worker.interrupt();
@@ -264,7 +267,7 @@ public class CommandLineOperations
               + SETUP_TIMEOUT + "ms). ["
               + harg + "]");
     }
-    new File(fileName).delete();
+    file.delete();
   }
 
   @DataProvider(name = "allInputOperationsData")
@@ -274,32 +277,27 @@ public class CommandLineOperations
         // headless mode input operations
         { "CMD [-color zappo] executed successfully!",
             "Failed command : -color zappo" },
-        { "CMD [-props FILE] executed successfully!",
+        { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
             "Failed command : -props File" },
         { "CMD [-sortbytree] executed successfully!",
             "Failed command : -sortbytree" },
-        {
-            "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
+        { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
         { "CMD [-open examples/uniref50.fa] executed successfully!",
             "Failed command : -open examples/uniref50.fa" },
         { "CMD [-nosortbytree] executed successfully!",
             "Failed command : -nosortbytree" },
-        {
-            "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
+        { "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
             "Failed command : -features examples/testdata/plantfdx.features" },
-        {
-            "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
+        { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
-        {
-            "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
+        { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
             "Failed command : -tree examples/testdata/uniref50_test_tree" },
         // non headless mode input operations
         { "CMD [-nousagestats] executed successfully!",
             "Failed command : -nousagestats" },
         { "CMD [-noquestionnaire] executed successfully!",
             "Failed command : -noquestionnaire" } };
-
   }
 
   @DataProvider(name = "headlessModeOutputOperationsData")
@@ -307,36 +305,52 @@ public class CommandLineOperations
   {
     return new Object[][] {
         { "nodisplay -open examples/uniref50.fa", " -eps",
-            "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "nodisplay -open examples/uniref50.fa", " -eps",
-            "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.eps", false,
+            MINFILESIZE_BIG, TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.eps", false,
+            MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -eps",
-            "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -svg",
-            "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.svg", false,
+            MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -png",
-            "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -html",
-            "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.html", true,
+            MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -fasta",
-            "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.mfa", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -clustal",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.aln", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -msf",
-            "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.msf", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pileup",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.aln", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pir",
-            "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.pir", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pfam",
-            "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.pfam", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -blc",
-            "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "test/jalview/bin/test_uniref50_out.blc", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -jalview",
-            "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
+            "test/jalview/bin/test_uniref50_out.jvp", true,
+            MINFILESIZE_SMALL, TEST_TIMEOUT }, };
   }
 }