X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;fp=test%2Fjalview%2Fbin%2FCommandsTest.java;h=de6185c40b2e181dffd4616f4beebc3f68ae8c82;hp=73a024177dafeb40d008f41cf50d8ab17b6d7780;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hpb=e91b3bef83f320e13c59ad5d21d69f0abf3d7507 diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java index 73a0241..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; @@ -46,15 +49,36 @@ 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) { - if (Jalview.getInstance()!=null) { + + public static void callJalviewMain(String[] args) + { + if (Jalview.getInstance() != null) + { Jalview.getInstance().doMain(args); - } else { + } + else + { Jalview.main(args); } } @@ -72,7 +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) { @@ -87,13 +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 openedSequenceNames = new HashSet<>(); - AlignFrame[] afs = Desktop.getAlignFrames(); + AlignFrame[] afs = Desktop.getDesktopAlignFrames(); for (AlignFrame af : afs) { openedSequenceNames.addAll( @@ -121,7 +145,10 @@ public class CommandsTest } } - @Test(groups = {"Functional","testTask1"}, dataProvider = "structureImageOutputFiles") + @Test( + groups = + { "Functional", "testTask3" }, + dataProvider = "structureImageOutputFiles") public void structureImageOutputTest(String cmdLine, String[] filenames) throws IOException { @@ -164,28 +191,30 @@ public class CommandsTest { 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) + 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", + Assert.fail( + "Unexpected exception during argFilesGlobAndSubstitutions", x); } finally { @@ -205,31 +234,31 @@ 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", 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" + + "/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", testfiles + "/structureimage3.png" } }, + /* */ // }; @@ -296,7 +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()) @@ -322,6 +351,8 @@ public class CommandsTest } } + private final String deleteDir = "test/deleteAfter"; + @Test( groups = "Functional", dataProvider = "allLinkedIdsData", @@ -348,6 +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") @@ -355,8 +392,6 @@ public class CommandsTest { return new Object[][] { // - /* - */ { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", @@ -399,7 +434,7 @@ public class CommandsTest "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, null }, - { "--gui --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", @@ -414,7 +449,7 @@ public class CommandsTest "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, null }, - { "--gui --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", @@ -429,7 +464,20 @@ 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", }, }, - { "--gui --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", @@ -444,7 +492,7 @@ 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", }, }, - { "--gui --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", @@ -459,7 +507,7 @@ 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", }, }, - { "--gui --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", @@ -486,6 +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", }, }, // }; }