test/jalview/bin/CommandsTest.java

   1 package jalview.bin;
   2
   3 import java.io.File;
   4 import java.io.IOException;
   5 import java.nio.file.Files;
   6 import java.util.Date;
   7 import java.util.HashSet;
   8 import java.util.Set;
   9
  10 import org.testng.Assert;
  11 import org.testng.annotations.AfterClass;
  12 import org.testng.annotations.AfterMethod;
  13 import org.testng.annotations.BeforeClass;
  14 import org.testng.annotations.DataProvider;
  15 import org.testng.annotations.Test;
  16
  17 import jalview.gui.AlignFrame;
  18 import jalview.gui.Desktop;
  19 import jalview.gui.JvOptionPane;
  20 import jalview.util.ArrayUtils;
  21
  22 @Test
  23 public class CommandsTest
  24 {
  25   private static final String testfiles = "test/jalview/bin/argparser/testfiles";
  26
  27   @BeforeClass(alwaysRun = true)
  28   public static void setUpBeforeClass() throws Exception
  29   {
  30     Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
  31     Date oneHourFromNow = new Date(
  32             System.currentTimeMillis() + 3600 * 1000);
  33     Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
  34   }
  35
  36   @AfterClass(alwaysRun = true)
  37   public static void resetProps()
  38   {
  39     Cache.loadProperties("test/jalview/testProps.jvprops");
  40   }
  41
  42   @BeforeClass(alwaysRun = true)
  43   public void setUpJvOptionPane()
  44   {
  45     JvOptionPane.setInteractiveMode(false);
  46     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  47   }
  48
  49   @AfterMethod(alwaysRun = true)
  50   public void tearDown()
  51   {
  52     Desktop.closeDesktop();
  53   }
  54
  55   public static void callJalviewMain(String[] args) {
  56     if (Jalview.getInstance()!=null) {
  57       Jalview.getInstance().doMain(args);
  58     } else {
  59       Jalview.main(args);
  60     }
  61   }
  62
  63   /* --setprops is currently disabled so this test won't work
  64   @Test(groups = "Functional")
  65   public void setpropsTest()
  66   {
  67     final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
  68     String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
  69     String[] args = cmdLine.split("\\s+");
  70     Jalview.main(args);
  71     Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
  72             "Earth");
  73   }
  74   */
  75
  76   @Test(groups = "Functional", dataProvider = "cmdLines")
  77   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
  78           int numFrames, String[] sequences)
  79   {
  80     String[] args = (cmdLine + " --gui").split("\\s+");
  81     callJalviewMain(args);
  82     Commands cmds = Jalview.getInstance().getCommands();
  83     Assert.assertNotNull(cmds);
  84     Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
  85             "Commands were not provided in the args");
  86     Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
  87             "Overall command parse and operation is false");
  88
  89     Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
  90             "Wrong number of AlignFrames");
  91
  92     if (sequences != null)
  93     {
  94       Set<String> openedSequenceNames = new HashSet<>();
  95       AlignFrame[] afs = Desktop.getAlignFrames();
  96       for (AlignFrame af : afs)
  97       {
  98         openedSequenceNames
  99                 .addAll(af.getViewport().getAlignment().getSequenceNames());
 100       }
 101       for (String sequence : sequences)
 102       {
 103         Assert.assertTrue(openedSequenceNames.contains(sequence),
 104                 "Sequence '" + sequence
 105                         + "' was not found in opened alignment files: "
 106                         + cmdLine + ".\nOpened sequence names are:\n"
 107                         + String.join("\n", openedSequenceNames));
 108       }
 109     }
 110
 111     Assert.assertFalse(
 112             lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
 113   }
 114
 115   @Test(groups = "Functional", dataProvider = "structureImageOutputFiles")
 116   public void structureImageOutputTest(String cmdLine, String[] filenames)
 117           throws IOException
 118   {
 119     cleanupFiles(filenames);
 120     String[] args = (cmdLine + " --gui").split("\\s+");
 121     callJalviewMain(args);
 122     Commands cmds = Jalview.getInstance().getCommands();
 123     Assert.assertNotNull(cmds);
 124     File lastFile = null;
 125     for (String filename : filenames)
 126     {
 127       File file = new File(filename);
 128       Assert.assertTrue(file.exists(), "File '" + filename
 129               + "' was not created by '" + cmdLine + "'");
 130       Assert.assertTrue(file.isFile(), "File '" + filename
 131               + "' is not a file from '" + cmdLine + "'");
 132       Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 133               + "' has no content from '" + cmdLine + "'");
 134       // make sure the successive output files get bigger!
 135       if (lastFile != null)
 136         Assert.assertTrue(
 137                 Files.size(file.toPath()) > Files.size(lastFile.toPath()));
 138     }
 139     cleanupFiles(filenames);
 140     tearDown();
 141   }
 142
 143   @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
 144   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 145           String[] filenames) throws IOException
 146   {
 147     cleanupFiles(filenames);
 148     String[] args = (cmdLine + " --gui").split("\\s+");
 149     callJalviewMain(args);
 150     Commands cmds = Jalview.getInstance().getCommands();
 151     Assert.assertNotNull(cmds);
 152     File lastFile = null;
 153     for (String filename : filenames)
 154     {
 155       File file = new File(filename);
 156       Assert.assertTrue(file.exists(), "File '" + filename
 157               + "' was not created by '" + cmdLine + "'");
 158       Assert.assertTrue(file.isFile(), "File '" + filename
 159               + "' is not a file from '" + cmdLine + "'");
 160       Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 161               + "' has no content from '" + cmdLine + "'");
 162       // make sure the successive output files get bigger!
 163       if (lastFile != null)
 164         Assert.assertTrue(
 165                 Files.size(file.toPath()) > Files.size(lastFile.toPath()));
 166     }
 167     cleanupFiles(filenames);
 168     tearDown();
 169   }
 170
 171   @DataProvider(name = "structureImageOutputFiles")
 172   public Object[][] structureImageOutputFiles()
 173   {
 174     return new Object[][] {
 175         //
 176         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 177                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 178                 + "--structureimage=" + testfiles + "/structureimage1.png "
 179                 + "--open=./examples/test_fab41.result/sample.a2m "
 180                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 181                 + "--structureimage=" + testfiles
 182                 + "/structureimage2.png --structureimagescale=1.5"
 183                 + "--open=./examples/test_fab41.result/sample.a2m "
 184                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 185                 + "--structureimage=" + testfiles
 186                 + "/structureimage3.png --structureimagescale=2.0",
 187             new String[]
 188             { testfiles + "/structureimage1.png",
 189                 testfiles + "/structureimage2.png",
 190                 testfiles + "/structureimage3.png" } },
 191         /*
 192         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 193                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 194                 + "--structureimage=" + testfiles + "/structureimage1.png "
 195                 + "--open=./examples/test_fab41.result/sample.a2m "
 196                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 197                 + "--structureimage=" + testfiles
 198                 + "/structureimage2.png --structureimagescale=1.5"
 199                 + "--open=./examples/test_fab41.result/sample.a2m "
 200                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 201                 + "--structureimage=" + testfiles
 202                 + "/structureimage3.png --structureimagescale=2.0",
 203             new String[]
 204             { testfiles + "/structureimage1.png",
 205                 testfiles + "/structureimage2.png",
 206                 testfiles + "/structureimage3.png" } },
 207                 */
 208         //
 209     };
 210
 211   }
 212
 213   @DataProvider(name = "argfileOutputFiles")
 214   public Object[][] argfileOutputFiles()
 215   {
 216     return new Object[][] {
 217         //
 218         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 219         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 220             testfiles + "/dir3/subdir/test0.png" } },
 221         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 222         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 223         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 224         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 225         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 226                 + testfiles + "/{basename}.png",
 227             new String[]
 228             { testfiles + "/uniref50.png" } },
 229         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 230                 + testfiles + "/{basename}.png",
 231             new String[]
 232             { testfiles + "/{basename}.png" } }
 233         //
 234     };
 235
 236   }
 237
 238   @DataProvider(name = "cmdLines")
 239   public Object[][] cmdLines()
 240   {
 241     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 242         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 243     String[] t1 = new String[] { "TEST1" };
 244     String[] t2 = new String[] { "TEST2" };
 245     String[] t3 = new String[] { "TEST3" };
 246     return new Object[][] {
 247         /*
 248         */
 249         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 250         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 251         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 252         // NOTE we cannot use shell expansion in tests, so list all files!
 253         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 254             someUniref50Seqs },
 255         { "--append=[new]examples/uniref50*.fa", true, 2,
 256             someUniref50Seqs },
 257         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 258         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 259         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 260             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 261         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 262         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 263             ArrayUtils.concatArrays(t1, t3) },
 264         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 265             ArrayUtils.concatArrays(t1, t2, t3) },
 266         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 267             ArrayUtils.concatArrays(t1, t2) } };
 268
 269   }
 270
 271   public static boolean lookForSequenceName(String sequenceName)
 272   {
 273     AlignFrame[] afs = Desktop.getAlignFrames();
 274     for (AlignFrame af : afs)
 275     {
 276       for (String name : af.getViewport().getAlignment().getSequenceNames())
 277       {
 278         if (sequenceName.equals(name))
 279         {
 280           return true;
 281         }
 282       }
 283     }
 284     return false;
 285   }
 286
 287   public static void cleanupFiles(String[] filenames)
 288   {
 289     for (String filename : filenames)
 290     {
 291       File file = new File(filename);
 292       if (file.exists())
 293       {
 294         file.delete();
 295       }
 296     }
 297   }
 298
 299   @Test(
 300     groups = "Functional",
 301     dataProvider = "allLinkedIdsData",
 302     singleThreaded = true)
 303   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 304           String[] nonfilenames)
 305   {
 306     String[] args = (cmdLine + " --gui").split("\\s+");
 307     callJalviewMain(args);
 308     Commands cmds = Jalview.getInstance().getCommands();
 309     Assert.assertNotNull(cmds);
 310     for (String filename : filenames)
 311     {
 312       Assert.assertTrue(new File(filename).exists(),
 313               "File '" + filename + "' was not created");
 314     }
 315     cleanupFiles(filenames);
 316     if (nonfilenames != null)
 317     {
 318       for (String nonfilename : nonfilenames)
 319       {
 320         File nonfile = new File(nonfilename);
 321         Assert.assertFalse(nonfile.exists(),
 322                 "File " + nonfilename + " exists when it shouldn't!");
 323       }
 324     }
 325   }
 326
 327   @DataProvider(name = "allLinkedIdsData")
 328   public Object[][] allLinkedIdsData()
 329   {
 330     return new Object[][] {
 331         //
 332         /*
 333          */
 334         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 335             new String[]
 336             { "test/jalview/bin/argparser/testfiles/test1.stk",
 337                 "test/jalview/bin/argparser/testfiles/test2.stk",
 338                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 339             null },
 340         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 341             new String[]
 342             { "test/jalview/bin/argparser/testfiles/test1.png",
 343                 "test/jalview/bin/argparser/testfiles/test2.png",
 344                 "test/jalview/bin/argparser/testfiles/test3.png", },
 345             null },
 346         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 347             new String[]
 348             { "test/jalview/bin/argparser/testfiles/test1.stk",
 349                 "test/jalview/bin/argparser/testfiles/test2.stk",
 350                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 351             new String[]
 352             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 353                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 354                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 355                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 356                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 357                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 358                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 359                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 360                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 361         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 362             new String[]
 363             { "test/jalview/bin/argparser/testfiles/test1.stk",
 364                 "test/jalview/bin/argparser/testfiles/test2.stk",
 365                 "test/jalview/bin/argparser/testfiles/test3.stk",
 366                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 367                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 368                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 369                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 370                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 371                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 372                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 373                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 374                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 375             null },
 376         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
 377             new String[]
 378             { "test/jalview/bin/argparser/testfiles/test1.stk",
 379                 "test/jalview/bin/argparser/testfiles/test2.stk",
 380                 "test/jalview/bin/argparser/testfiles/test3.stk",
 381                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 382                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 383                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 384                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 385                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 386                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 387                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 388                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 389                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 390             null },
 391         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
 392             new String[]
 393             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 394                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 395                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 396                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 397                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 398             new String[]
 399             { "test/jalview/bin/argparser/testfiles/test1.stk",
 400                 "test/jalview/bin/argparser/testfiles/test2.stk",
 401                 "test/jalview/bin/argparser/testfiles/test3.stk",
 402                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 403                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 404                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 405                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 406         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
 407             new String[]
 408             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 409                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 410                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 411             new String[]
 412             { "test/jalview/bin/argparser/testfiles/test1.stk",
 413                 "test/jalview/bin/argparser/testfiles/test2.stk",
 414                 "test/jalview/bin/argparser/testfiles/test3.stk",
 415                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 416                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 417                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 418                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 419                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 420                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 421         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
 422             new String[]
 423             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 424                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 425                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 426             new String[]
 427             { "test/jalview/bin/argparser/testfiles/test1.stk",
 428                 "test/jalview/bin/argparser/testfiles/test2.stk",
 429                 "test/jalview/bin/argparser/testfiles/test3.stk",
 430                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 431                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 432                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 433                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 434                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 435                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 436         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
 437             new String[]
 438             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 439                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 440                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 441                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 442                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 443             new String[]
 444             { "test/jalview/bin/argparser/testfiles/test1.stk",
 445                 "test/jalview/bin/argparser/testfiles/test2.stk",
 446                 "test/jalview/bin/argparser/testfiles/test3.stk",
 447                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 448                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 449                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 450                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 451                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 452                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 453                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 454                 "test/jalview/bin/argparser/testfiles/test1.aln",
 455                 "test/jalview/bin/argparser/testfiles/test2.aln",
 456                 "test/jalview/bin/argparser/testfiles/test3.aln",
 457                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 458                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 459                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 460                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 461                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 462                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 463         //
 464     };
 465   }
 466
 467 }