X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=61892dfbe8738cfdfa085d55849ad5ea3e3562c2;hb=e4c2a9483a41740a85c95ffbf014e23f9afe79f6;hp=30c5e4e47caa2fae222bee6f0be61260bd51cfb3;hpb=404d5b51a7a7781ad6924df6a7ce63c754370f16;p=jalview.git diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java index 30c5e4e..61892df 100644 --- a/test/jalview/bin/CommandsTest.java +++ b/test/jalview/bin/CommandsTest.java @@ -19,15 +19,11 @@ import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.util.ArrayUtils; -@Test(singleThreaded = true) +@Test public class CommandsTest { private static final String testfiles = "test/jalview/bin/argparser/testfiles"; - private static final String png1 = testfiles + "/dir1/test1.png"; - - private static final String png2 = testfiles + "/dir2/test1.png"; - @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { @@ -53,15 +49,22 @@ 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); + } } - /* --setprop currently disabled + /* --setprops is currently disabled so this test won't work @Test(groups = "Functional") public void setpropsTest() { - String MOSTLY_HARMLESS = "MOSTLY_HARMLESS"; + final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS"; String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth"; String[] args = cmdLine.split("\\s+"); Jalview.main(args); @@ -74,8 +77,8 @@ public class CommandsTest public void commandsOpenTest(String cmdLine, boolean cmdArgs, int numFrames, String[] sequences) { - String[] args = cmdLine.split("\\s+"); - Jalview.main(args); + String[] args = (cmdLine + " --gui").split("\\s+"); + callJalviewMain(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs, @@ -83,7 +86,8 @@ public class CommandsTest Assert.assertEquals(cmds.argsWereParsed(), cmdArgs, "Overall command parse and operation is false"); - Assert.assertEquals(Desktop.getAlignFrames().length, numFrames); + Assert.assertEquals(Desktop.getAlignFrames().length, numFrames, + "Wrong number of AlignFrames"); if (sequences != null) { @@ -108,13 +112,41 @@ public class CommandsTest lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST")); } + @Test(groups = "Functional", dataProvider = "structureImageOutputFiles") + public void structureImageOutputTest(String cmdLine, String[] filenames) + throws IOException + { + cleanupFiles(filenames); + String[] args = (cmdLine + " --gui").split("\\s+"); + 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())); + } + cleanupFiles(filenames); + tearDown(); + } + @Test(groups = "Functional", dataProvider = "argfileOutputFiles") public void argFilesGlobAndSubstitutionsTest(String cmdLine, String[] filenames) throws IOException { cleanupFiles(filenames); - String[] args = cmdLine.split("\\s+"); - Jalview.main(args); + String[] args = (cmdLine + " --gui").split("\\s+"); + callJalviewMain(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); File lastFile = null; @@ -136,25 +168,71 @@ public class CommandsTest 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") public Object[][] argfileOutputFiles() { 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 --open examples/uniref50.fa --image " + { "--gui --initsubstitutions --append examples/uniref50.fa --image " + testfiles + "/{basename}.png", new String[] { testfiles + "/uniref50.png" } }, - { "--open examples/uniref50.fa --image " + testfiles - + "/{basename}.png", + { "--gui --append examples/uniref50.fa --nosubstitutions --image " + + testfiles + "/{basename}.png", new String[] - { testfiles + "/{basename}.png" } } }; + { testfiles + "/{basename}.png" } } + // + }; + } @DataProvider(name = "cmdLines") @@ -166,24 +244,28 @@ public class CommandsTest String[] t2 = new String[] { "TEST2" }; String[] t3 = new String[] { "TEST3" }; return new Object[][] { - { "--open=examples/uniref50.fa", true, 1, someUniref50Seqs }, - { "--open examples/uniref50.fa", true, 1, someUniref50Seqs }, - { "--open=examples/uniref50*.fa", true, 1, someUniref50Seqs }, + /* + */ + { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs }, + { "--append examples/uniref50.fa", true, 1, someUniref50Seqs }, + { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs }, // NOTE we cannot use shell expansion in tests, so list all files! - { "--open examples/uniref50.fa examples/uniref50_mz.fa", true, 1, + { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1, someUniref50Seqs }, - { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs }, - { "--opennew=examples/uniref50*.fa", true, 2, someUniref50Seqs }, + { "--append=[new]examples/uniref50*.fa", true, 2, + someUniref50Seqs }, + { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs }, { "examples/uniref50.fa", true, 1, someUniref50Seqs }, { "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, 4, + { "--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) } }; + } public static boolean lookForSequenceName(String sequenceName) @@ -214,4 +296,172 @@ public class CommandsTest } } + @Test( + groups = "Functional", + dataProvider = "allLinkedIdsData", + singleThreaded = true) + public void allLinkedIdsTest(String cmdLine, String[] filenames, + String[] nonfilenames) + { + String[] args = (cmdLine + " --gui").split("\\s+"); + callJalviewMain(args); + Commands cmds = Jalview.getInstance().getCommands(); + Assert.assertNotNull(cmds); + for (String filename : filenames) + { + Assert.assertTrue(new File(filename).exists(), + "File '" + filename + "' was not created"); + } + cleanupFiles(filenames); + if (nonfilenames != null) + { + for (String nonfilename : nonfilenames) + { + File nonfile = new File(nonfilename); + Assert.assertFalse(nonfile.exists(), + "File " + nonfilename + " exists when it shouldn't!"); + } + } + } + + @DataProvider(name = "allLinkedIdsData") + public Object[][] allLinkedIdsData() + { + 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", + "test/jalview/bin/argparser/testfiles/test2.stk", + "test/jalview/bin/argparser/testfiles/test3.stk", }, + null }, + { "--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 }, + { "--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", + "test/jalview/bin/argparser/testfiles/test3.stk", }, + new String[] + { "test/jalview/bin/argparser/testfiles/dir1/test1.stk", + "test/jalview/bin/argparser/testfiles/dir1/test2.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", }, }, + { "--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", + "test/jalview/bin/argparser/testfiles/test3.stk", + "test/jalview/bin/argparser/testfiles/dir1/test1.stk", + "test/jalview/bin/argparser/testfiles/dir1/test2.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", }, + null }, + { "--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", + "test/jalview/bin/argparser/testfiles/test3.stk", + "test/jalview/bin/argparser/testfiles/dir1/test1.stk", + "test/jalview/bin/argparser/testfiles/dir1/test2.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", }, + null }, + { "--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/dir1/test1.stk", + "test/jalview/bin/argparser/testfiles/dir1/test2.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", }, + 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=open*.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/dir1/test1.stk", + "test/jalview/bin/argparser/testfiles/dir1/test2.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 --opened --output={dirname}/{basename}.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/dir1/test1.stk", + "test/jalview/bin/argparser/testfiles/dir1/test2.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 --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close", + new String[] + { "test/jalview/bin/argparser/testfiles/dir1/test1.stk", + "test/jalview/bin/argparser/testfiles/dir1/test2.stk", + "test/jalview/bin/argparser/testfiles/dir2/test1.aln", + "test/jalview/bin/argparser/testfiles/dir2/test2.aln", + "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", }, }, + // + }; + } + }