X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=de6185c40b2e181dffd4616f4beebc3f68ae8c82;hb=2d44b9594da6c691eca72697060c166d0389affd;hp=36522c43836e5ab4ec5677f66e3eaec8ae199a48;hpb=871535152992c147f2175c3006b6bec4615fead4;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 36522c4..de6185c 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -2,11 +2,14 @@ package jalview.bin;
 
 import java.io.File;
 import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
 import java.nio.file.Files;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.Set;
 
+import javax.swing.SwingUtilities;
+
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.AfterMethod;
@@ -46,9 +49,26 @@ public class CommandsTest
   }
 
   @AfterMethod(alwaysRun = true)
-  public void tearDown()
+  public void tearDown() 
   {
-    Desktop.closeDesktop();
+    try
+    {
+      // occasionally we are blocked by Jmol redraws
+      SwingUtilities.invokeAndWait(new Runnable()
+      {
+
+        @Override
+        public void run()
+        {
+          Desktop.closeDesktop();
+        }
+      });
+    } catch (Exception foo)
+    {
+      System.err.println("Failed during teardown with exception");
+      foo.printStackTrace();
+    }
+
   }
 
   public static void callJalviewMain(String[] args)
@@ -76,7 +96,7 @@ public class CommandsTest
   }
   */
 
-  @Test(groups = "Functional", dataProvider = "cmdLines")
+  @Test(groups = {"Functional","testTask3"}, dataProvider = "cmdLines")
   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
           int numFrames, String[] sequences)
   {
@@ -91,13 +111,13 @@ public class CommandsTest
       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
               "Overall command parse and operation is false");
 
-      Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
               "Wrong number of AlignFrames");
 
       if (sequences != null)
       {
         Set<String> openedSequenceNames = new HashSet<>();
-        AlignFrame[] afs = Desktop.getAlignFrames();
+        AlignFrame[] afs = Desktop.getDesktopAlignFrames();
         for (AlignFrame af : afs)
         {
           openedSequenceNames.addAll(
@@ -127,7 +147,7 @@ public class CommandsTest
 
   @Test(
     groups =
-    { "Functional", "testTask1" },
+    { "Functional", "testTask3" },
     dataProvider = "structureImageOutputFiles")
   public void structureImageOutputTest(String cmdLine, String[] filenames)
           throws IOException
@@ -214,11 +234,11 @@ public class CommandsTest
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage2.png --structureimagescale=1.5"
+                + "/structureimage2.png --scale=1.5 "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage3.png --structureimagescale=2.0",
+                + "/structureimage3.png --scale=2.0 ",
             new String[]
             { testfiles + "/structureimage1.png",
                 testfiles + "/structureimage2.png",
@@ -229,11 +249,11 @@ public class CommandsTest
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage2.png --structureimagescale=1.5"
+                + "/structureimage2.png --scale=1.5 "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage3.png --structureimagescale=2.0",
+                + "/structureimage3.png --scale=2.0 ",
             new String[]
             { testfiles + "/structureimage1.png",
                 testfiles + "/structureimage2.png",
@@ -305,7 +325,7 @@ public class CommandsTest
 
   public static boolean lookForSequenceName(String sequenceName)
   {
-    AlignFrame[] afs = Desktop.getAlignFrames();
+    AlignFrame[] afs = Desktop.getDesktopAlignFrames();
     for (AlignFrame af : afs)
     {
       for (String name : af.getViewport().getAlignment().getSequenceNames())
@@ -331,6 +351,8 @@ public class CommandsTest
     }
   }
 
+  private final String deleteDir = "test/deleteAfter";
+
   @Test(
     groups = "Functional",
     dataProvider = "allLinkedIdsData",
@@ -357,6 +379,12 @@ public class CommandsTest
                 "File " + nonfilename + " exists when it shouldn't!");
       }
     }
+
+    File deleteDirF = new File(deleteDir);
+    if (deleteDirF.exists())
+    {
+      deleteDirF.delete();
+    }
   }
 
   @DataProvider(name = "allLinkedIdsData")
@@ -506,6 +534,81 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
+        // --mkdirs
+        { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
+                + deleteDir
+                + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
+                + deleteDir
+                + "/{dirname}/{basename}.aln --close --all --mkdirs",
+            new String[]
+            { deleteDir
+                    + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
+                deleteDir
+                        + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/test1.stk",
+                "test/jalview/bin/argparser/testfiles/test2.stk",
+                "test/jalview/bin/argparser/testfiles/test3.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+                "test/jalview/bin/argparser/testfiles/test1.aln",
+                "test/jalview/bin/argparser/testfiles/test2.aln",
+                "test/jalview/bin/argparser/testfiles/test3.aln",
+                "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+                "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+                "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test1.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test2.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test3.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test1.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test2.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/test3.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+                deleteDir
+                        + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
         //
     };
   }