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