X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=20ccd110cd1e0155cb8f085a5a84c3203121f007;hb=b5fade85256c0fbcedd48b078a31e8c2ac86ba1e;hp=30c5e4e47caa2fae222bee6f0be61260bd51cfb3;hpb=404d5b51a7a7781ad6924df6a7ce63c754370f16;p=jalview.git diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java index 30c5e4e..20ccd11 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 { @@ -57,11 +53,11 @@ public class CommandsTest Desktop.instance.closeAll_actionPerformed(null); } - /* --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); @@ -83,7 +79,8 @@ 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) { @@ -140,6 +137,7 @@ public class CommandsTest public Object[][] argfileOutputFiles() { return new Object[][] { + // { "--argfile=" + testfiles + "/**/*.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png", testfiles + "/dir3/subdir/test0.png" } }, @@ -147,14 +145,17 @@ public class CommandsTest { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, - { "--initsubstitutions --open examples/uniref50.fa --image " + { "--initsubstitutions --append examples/uniref50.fa --image " + testfiles + "/{basename}.png", new String[] { testfiles + "/uniref50.png" } }, - { "--open examples/uniref50.fa --image " + testfiles - + "/{basename}.png", + { "--append examples/uniref50.fa --nosubstitutions --image " + + testfiles + "/{basename}.png", new String[] - { testfiles + "/{basename}.png" } } }; + { testfiles + "/{basename}.png" } } + // + }; + } @DataProvider(name = "cmdLines") @@ -166,24 +167,28 @@ 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 }, + { "--append=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs }, - { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs }, - { "--opennew=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, ArrayUtils.concatArrays(t1, t3) }, - { "--argfile=" + testfiles + "/argfile*.txt", true, 4, + { "--argfile=" + testfiles + "/argfile*.txt", true, 5, ArrayUtils.concatArrays(t1, t2, t3) }, { "--argfile=" + testfiles + "/argfile.autocounter", true, 3, ArrayUtils.concatArrays(t1, t2) } }; + } public static boolean lookForSequenceName(String sequenceName) @@ -214,4 +219,172 @@ public class CommandsTest } } + @Test( + groups = "Functional", + dataProvider = "allLinkedIdsData", + singleThreaded = true) + public void allLinkedIdsTest(String cmdLine, String[] filenames, + String[] nonfilenames) + { + String[] args = cmdLine.split("\\s+"); + Jalview.main(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[][] { + // + /* + */ + { "--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", + 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", + 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", }, }, + { "--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 }, + { "--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 }, + { "--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", }, }, + { "--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", }, }, + { "--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", }, }, + { "--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", }, }, + // + }; + } + }