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=fe40682d82111e81fcdd9491ef0fad08d1a5e9c0;hp=0000000000000000000000000000000000000000;hb=f680b9a507cc1643c9eead990e15026c1eca4e6e;hpb=265e81c0b3599a09c312f17188e3a892e9d96c4e diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java new file mode 100644 index 0000000..fe40682 --- /dev/null +++ b/test/jalview/bin/CommandsTest.java @@ -0,0 +1,502 @@ +package jalview.bin; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.Date; +import java.util.HashSet; +import java.util.Set; + +import org.testng.Assert; +import org.testng.annotations.AfterClass; +import org.testng.annotations.AfterMethod; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; +import jalview.util.ArrayUtils; + +public class CommandsTest +{ + private static final String testfiles = "test/jalview/bin/argparser/testfiles"; + + @BeforeClass(alwaysRun = true) + public static void setUpBeforeClass() throws Exception + { + Cache.loadProperties("test/jalview/gui/quitProps.jvprops"); + Date oneHourFromNow = new Date( + System.currentTimeMillis() + 3600 * 1000); + Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow); + } + + @AfterClass(alwaysRun = true) + public static void resetProps() + { + Cache.loadProperties("test/jalview/testProps.jvprops"); + } + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + @AfterMethod(alwaysRun = true) + public void tearDown() + { + 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 + @Test(groups = "Functional") + public void setpropsTest() + { + final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS"; + String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth"; + String[] args = cmdLine.split("\\s+"); + Jalview.main(args); + Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"), + "Earth"); + } + */ + + @Test(groups = "Functional", dataProvider = "cmdLines") + public void commandsOpenTest(String cmdLine, boolean cmdArgs, + int numFrames, String[] sequences) + { + 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"); + + if (sequences != null) + { + Set 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)); + } + } + + 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) + { + 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(); + } + } + + @Test(groups = "Functional", dataProvider = "argfileOutputFiles") + public void argFilesGlobAndSubstitutionsTest(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) + { + 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(); + } + } + + @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[][] { + // + { "--gui --argfile=" + testfiles + "/**/*.txt", new String[] + { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png", + testfiles + "/dir3/subdir/test0.png" } }, + { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[] + { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, + { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[] + { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, + { "--gui --initsubstitutions --append examples/uniref50.fa --image " + + testfiles + "/{basename}.png", + new String[] + { testfiles + "/uniref50.png" } }, + { "--gui --append examples/uniref50.fa --nosubstitutions --image " + + testfiles + "/{basename}.png", + new String[] + { testfiles + "/{basename}.png" } } + // + }; + + } + + @DataProvider(name = "cmdLines") + public Object[][] cmdLines() + { + String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN", + "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" }; + String[] t1 = new String[] { "TEST1" }; + String[] t2 = new String[] { "TEST2" }; + String[] t3 = new String[] { "TEST3" }; + return new Object[][] { + /* + */ + { "--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! + { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1, + 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 }, + { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1, + ArrayUtils.concatArrays(t1, t3) }, + { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5, + ArrayUtils.concatArrays(t1, t2, t3) }, + { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3, + ArrayUtils.concatArrays(t1, t2) } }; + + } + + public static boolean lookForSequenceName(String sequenceName) + { + AlignFrame[] afs = Desktop.getAlignFrames(); + for (AlignFrame af : afs) + { + for (String name : af.getViewport().getAlignment().getSequenceNames()) + { + if (sequenceName.equals(name)) + { + return true; + } + } + } + return false; + } + + public static void cleanupFiles(String[] filenames) + { + for (String filename : filenames) + { + File file = new File(filename); + if (file.exists()) + { + file.delete(); + } + } + } + + @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", }, }, + // + }; + } + +}