X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=36522c43836e5ab4ec5677f66e3eaec8ae199a48;hb=871535152992c147f2175c3006b6bec4615fead4;hp=20ccd110cd1e0155cb8f085a5a84c3203121f007;hpb=fc07ec3706c45b21d90eadddd00f23d6318a7008;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 20ccd11..36522c4 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -19,7 +19,6 @@ import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.util.ArrayUtils;
 
-@Test
 public class CommandsTest
 {
   private static final String testfiles = "test/jalview/bin/argparser/testfiles";
@@ -49,8 +48,19 @@ public class CommandsTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    if (Desktop.instance != null)
-      Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.closeDesktop();
+  }
+
+  public static void callJalviewMain(String[] args)
+  {
+    if (Jalview.getInstance() != null)
+    {
+      Jalview.getInstance().doMain(args);
+    }
+    else
+    {
+      Jalview.main(args);
+    }
   }
 
   /* --setprops is currently disabled so this test won't work
@@ -70,39 +80,89 @@ public class CommandsTest
   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
           int numFrames, String[] sequences)
   {
-    String[] args = cmdLine.split("\\s+");
-    Jalview.main(args);
-    Commands cmds = Jalview.getInstance().getCommands();
-    Assert.assertNotNull(cmds);
-    Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
-            "Commands were not provided in the args");
-    Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
-            "Overall command parse and operation is false");
+    try
+    {
+      String[] args = (cmdLine + " --gui").split("\\s+");
+      callJalviewMain(args);
+      Commands cmds = Jalview.getInstance().getCommands();
+      Assert.assertNotNull(cmds);
+      Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
+              "Commands were not provided in the args");
+      Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
+              "Overall command parse and operation is false");
 
-    Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
-            "Wrong number of AlignFrames");
+      Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+              "Wrong number of AlignFrames");
 
-    if (sequences != null)
-    {
-      Set<String> openedSequenceNames = new HashSet<>();
-      AlignFrame[] afs = Desktop.getAlignFrames();
-      for (AlignFrame af : afs)
+      if (sequences != null)
       {
-        openedSequenceNames
-                .addAll(af.getViewport().getAlignment().getSequenceNames());
+        Set<String> openedSequenceNames = new HashSet<>();
+        AlignFrame[] afs = Desktop.getAlignFrames();
+        for (AlignFrame af : afs)
+        {
+          openedSequenceNames.addAll(
+                  af.getViewport().getAlignment().getSequenceNames());
+        }
+        for (String sequence : sequences)
+        {
+          Assert.assertTrue(openedSequenceNames.contains(sequence),
+                  "Sequence '" + sequence
+                          + "' was not found in opened alignment files: "
+                          + cmdLine + ".\nOpened sequence names are:\n"
+                          + String.join("\n", openedSequenceNames));
+        }
       }
-      for (String sequence : sequences)
+
+      Assert.assertFalse(
+              lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception during commandsOpenTest", x);
+    } finally
+    {
+      tearDown();
+
+    }
+  }
+
+  @Test(
+    groups =
+    { "Functional", "testTask1" },
+    dataProvider = "structureImageOutputFiles")
+  public void structureImageOutputTest(String cmdLine, String[] filenames)
+          throws IOException
+  {
+    cleanupFiles(filenames);
+    String[] args = (cmdLine + " --gui").split("\\s+");
+    try
+    {
+      callJalviewMain(args);
+      Commands cmds = Jalview.getInstance().getCommands();
+      Assert.assertNotNull(cmds);
+      File lastFile = null;
+      for (String filename : filenames)
       {
-        Assert.assertTrue(openedSequenceNames.contains(sequence),
-                "Sequence '" + sequence
-                        + "' was not found in opened alignment files: "
-                        + cmdLine + ".\nOpened sequence names are:\n"
-                        + String.join("\n", openedSequenceNames));
+        File file = new File(filename);
+        Assert.assertTrue(file.exists(), "File '" + filename
+                + "' was not created by '" + cmdLine + "'");
+        Assert.assertTrue(file.isFile(), "File '" + filename
+                + "' is not a file from '" + cmdLine + "'");
+        Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+                + "' has no content from '" + cmdLine + "'");
+        // make sure the successive output files get bigger!
+        if (lastFile != null)
+          Assert.assertTrue(Files.size(file.toPath()) > Files
+                  .size(lastFile.toPath()));
       }
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception during structureImageOutputTest",
+              x);
+    } finally
+    {
+      cleanupFiles(filenames);
+      tearDown();
     }
-
-    Assert.assertFalse(
-            lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
   }
 
   @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
@@ -110,27 +170,79 @@ public class CommandsTest
           String[] filenames) throws IOException
   {
     cleanupFiles(filenames);
-    String[] args = cmdLine.split("\\s+");
-    Jalview.main(args);
-    Commands cmds = Jalview.getInstance().getCommands();
-    Assert.assertNotNull(cmds);
-    File lastFile = null;
-    for (String filename : filenames)
+    String[] args = (cmdLine + " --gui").split("\\s+");
+    try
     {
-      File file = new File(filename);
-      Assert.assertTrue(file.exists(), "File '" + filename
-              + "' was not created by '" + cmdLine + "'");
-      Assert.assertTrue(file.isFile(), "File '" + filename
-              + "' is not a file from '" + cmdLine + "'");
-      Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
-              + "' has no content from '" + cmdLine + "'");
-      // make sure the successive output files get bigger!
-      if (lastFile != null)
-        Assert.assertTrue(
-                Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+      callJalviewMain(args);
+      Commands cmds = Jalview.getInstance().getCommands();
+      Assert.assertNotNull(cmds);
+      File lastFile = null;
+      for (String filename : filenames)
+      {
+        File file = new File(filename);
+        Assert.assertTrue(file.exists(), "File '" + filename
+                + "' was not created by '" + cmdLine + "'");
+        Assert.assertTrue(file.isFile(), "File '" + filename
+                + "' is not a file from '" + cmdLine + "'");
+        Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+                + "' has no content from '" + cmdLine + "'");
+        // make sure the successive output files get bigger!
+        if (lastFile != null)
+          Assert.assertTrue(Files.size(file.toPath()) > Files
+                  .size(lastFile.toPath()));
+      }
+    } catch (Exception x)
+    {
+      Assert.fail(
+              "Unexpected exception during argFilesGlobAndSubstitutions",
+              x);
+    } finally
+    {
+      cleanupFiles(filenames);
+      tearDown();
     }
-    cleanupFiles(filenames);
-    tearDown();
+  }
+
+  @DataProvider(name = "structureImageOutputFiles")
+  public Object[][] structureImageOutputFiles()
+  {
+    return new Object[][] {
+        //
+        { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--structureimage=" + testfiles + "/structureimage1.png "
+                + "--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"
+                + "--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",
+            new String[]
+            { testfiles + "/structureimage1.png",
+                testfiles + "/structureimage2.png",
+                testfiles + "/structureimage3.png" } },
+        { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--structureimage=" + testfiles + "/structureimage1.png "
+                + "--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"
+                + "--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",
+            new String[]
+            { testfiles + "/structureimage1.png",
+                testfiles + "/structureimage2.png",
+                testfiles + "/structureimage3.png" } },
+        /*
+                */
+        //
+    };
+
   }
 
   @DataProvider(name = "argfileOutputFiles")
@@ -138,18 +250,18 @@ public class CommandsTest
   {
     return new Object[][] {
         //
-        { "--argfile=" + testfiles + "/**/*.txt", new String[]
+        { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
             testfiles + "/dir3/subdir/test0.png" } },
-        { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
+        { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
-        { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
+        { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
-        { "--initsubstitutions --append examples/uniref50.fa --image "
+        { "--gui --initsubstitutions --append examples/uniref50.fa --image "
                 + testfiles + "/{basename}.png",
             new String[]
             { testfiles + "/uniref50.png" } },
-        { "--append examples/uniref50.fa --nosubstitutions --image "
+        { "--gui --append examples/uniref50.fa --nosubstitutions --image "
                 + testfiles + "/{basename}.png",
             new String[]
             { testfiles + "/{basename}.png" } }
@@ -182,11 +294,11 @@ public class CommandsTest
         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
-        { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
+        { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
             ArrayUtils.concatArrays(t1, t3) },
-        { "--argfile=" + testfiles + "/argfile*.txt", true, 5,
+        { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
             ArrayUtils.concatArrays(t1, t2, t3) },
-        { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
+        { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
             ArrayUtils.concatArrays(t1, t2) } };
 
   }
@@ -226,8 +338,8 @@ public class CommandsTest
   public void allLinkedIdsTest(String cmdLine, String[] filenames,
           String[] nonfilenames)
   {
-    String[] args = cmdLine.split("\\s+");
-    Jalview.main(args);
+    String[] args = (cmdLine + " --gui").split("\\s+");
+    callJalviewMain(args);
     Commands cmds = Jalview.getInstance().getCommands();
     Assert.assertNotNull(cmds);
     for (String filename : filenames)
@@ -252,21 +364,19 @@ public class CommandsTest
   {
     return new Object[][] {
         //
-        /*
-         */
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/test1.stk",
                 "test/jalview/bin/argparser/testfiles/test2.stk",
                 "test/jalview/bin/argparser/testfiles/test3.stk", },
             null },
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/test1.png",
                 "test/jalview/bin/argparser/testfiles/test2.png",
                 "test/jalview/bin/argparser/testfiles/test3.png", },
             null },
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/test1.stk",
                 "test/jalview/bin/argparser/testfiles/test2.stk",
@@ -281,7 +391,7 @@ public class CommandsTest
                 "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", }, },
-        { "--open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/test1.stk",
                 "test/jalview/bin/argparser/testfiles/test2.stk",
@@ -296,7 +406,7 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
             null },
-        { "--open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/test1.stk",
                 "test/jalview/bin/argparser/testfiles/test2.stk",
@@ -311,7 +421,7 @@ public class CommandsTest
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
             null },
-        { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
@@ -326,7 +436,20 @@ public class CommandsTest
                 "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", }, },
-        { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
+            new String[]
+            { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+                "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
+            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/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", }, },
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
@@ -341,7 +464,7 @@ public class CommandsTest
                 "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", }, },
-        { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
@@ -356,7 +479,7 @@ public class CommandsTest
                 "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", }, },
-        { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
+        { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
             new String[]
             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",