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Merge branch 'develop' into task/JAL-3130_Java_11_investigations-getdown_src
[jalview.git] / test / jalview / bin / CommandLineOperations.java
diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index cbc2391..ace1868 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -51,7 +51,8 @@ public class CommandLineOperations
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on
+  private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
+                                                // on
                                                 // full test run than on
                                                 // individual tests
 
@@ -150,8 +151,7 @@ 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 " + (withAwt ? "-Djava.awt.headless=true" : "")
             + " -classpath " + classpath + " jalview.bin.Jalview ";
     Process ls2_proc = null;
     Worker worker = null;
@@ -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)
@@ -238,7 +241,8 @@ public class CommandLineOperations
   }
 
   @Test(
-    groups = { "Functional" },
+    groups =
+    { "Functional", "testben" },
     dataProvider = "headlessModeOutputOperationsData")
   public void testHeadlessModeOutputOperations(String harg, String type,
           String fileName, boolean withAWT, int expectedMinFileSize,
@@ -247,24 +251,23 @@ public class CommandLineOperations
     String cmd = harg + type + " " + fileName;
     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
     File file = new File(fileName);
+    file.deleteOnExit();
     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();
       Thread.currentThread().interrupt();
       worker.process.destroy();
-      Assert.fail("Jalview did not exit after "
-              + type
+      Assert.fail("Jalview did not exit after " + type
               + " generation (try running test again to verify - timeout at "
-              + SETUP_TIMEOUT + "ms). ["
-              + harg + "]");
+              + timeout + "ms). [" + harg + "]");
     }
-    new File(fileName).delete();
+    file.delete();
   }
 
   @DataProvider(name = "allInputOperationsData")
@@ -274,69 +277,79 @@ 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")
   public static Object[][] getHeadlessModeOutputParams()
   {
-    return new Object[][] {
-        { "nodisplay -open examples/uniref50.fa", " -eps",
-            "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+    return new Object[][] { { "nodisplay -open examples/uniref50.fa",
+        " -eps", "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_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -clustal",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "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_uniref50_out.msf", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pileup",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "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_uniref50_out.pir", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pfam",
-            "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+            "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_uniref50_out.blc", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -jalview",
-            "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
+            "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT }, };
   }
 }