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Merge branch 'develop' into Jalview-JS/develop
[jalview.git] / test / jalview / bin / CommandLineOperations.java
diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 0424acc..c7b1d53 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -20,6 +20,9 @@
  */
 package jalview.bin;
 
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
 import jalview.gui.JvOptionPane;
 
 import java.io.BufferedReader;
@@ -140,7 +143,8 @@ public class CommandLineOperations
     }
     return classpath;
   }
-  private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
+
+  private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
           int timeout)
   {
     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
@@ -154,7 +158,7 @@ public class CommandLineOperations
     try
     {
       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
-    } catch (IOException e1)
+    } catch (Throwable e1)
     {
       e1.printStackTrace();
     }
@@ -171,7 +175,7 @@ public class CommandLineOperations
         worker.join(timeout);
       } catch (InterruptedException e)
       {
-        // e.printStackTrace();
+        System.err.println("Thread interrupted");
       }
       worker.setOutputReader(outputReader);
       worker.setErrorReader(errorReader);
@@ -189,23 +193,27 @@ 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 = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
+    Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
     String ln = null;
     while ((ln = worker.getOutputReader().readLine()) != null)
     {
       System.out.println(ln);
       successfulCMDs.add(ln);
     }
+    while ((ln = worker.getErrorReader().readLine()) != null)
+    {
+      System.err.println(ln);
+    }
   }
 
   @BeforeTest(alwaysRun = true)
   public void setUpForCommandLineInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
-    Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
+    Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
     String ln = null;
     int count = 0;
     while ((ln = worker.getErrorReader().readLine()) != null)
@@ -225,7 +233,7 @@ public class CommandLineOperations
     }
   }
 
-  @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
+  @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
   public void testAllInputOperations(String expectedString,
           String failureMsg)
   {
@@ -242,11 +250,13 @@ public class CommandLineOperations
     String cmd = harg + type + " " + fileName;
     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
     File file = new File(fileName);
-    Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
-
-    FileAssert.assertFile(file, "Didn't create an output" + type
-            + " file.[" + harg + "]");
-    FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
+    file.deleteOnExit();
+    Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
+    assertNotNull(worker, "worker is null");
+    String msg = "Didn't create an output" + type + " file.[" + harg + "]";
+    assertTrue(file.exists(), msg);
+    FileAssert.assertFile(file, msg);
+    FileAssert.assertMinLength(file, expectedMinFileSize);
     if (worker != null && worker.exit == null)
     {
       worker.interrupt();
@@ -258,42 +268,37 @@ public class CommandLineOperations
               + SETUP_TIMEOUT + "ms). ["
               + harg + "]");
     }
-    new File(fileName).delete();
+    file.delete();
   }
 
-  @DataProvider(name = "allInputOpearationsData")
+  @DataProvider(name = "allInputOperationsData")
   public Object[][] getHeadlessModeInputParams()
   {
     return new Object[][] {
         // 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")
@@ -301,36 +306,52 @@ 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 }, };
   }
 }