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 = "argfileOutputFiles")
 109   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 110           String[] filenames) 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   @DataProvider(name = "argfileOutputFiles")
 137   public Object[][] argfileOutputFiles()
 138   {
 139     return new Object[][] {
 140         //
 141         { "--argfile=" + testfiles + "/**/*.txt", new String[]
 142         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 143             testfiles + "/dir3/subdir/test0.png" } },
 144         { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
 145         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 146         { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 147         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 148         { "--initsubstitutions --append examples/uniref50.fa --image "
 149                 + testfiles + "/{basename}.png",
 150             new String[]
 151             { testfiles + "/uniref50.png" } },
 152         { "--append examples/uniref50.fa --nosubstitutions --image "
 153                 + testfiles + "/{basename}.png",
 154             new String[]
 155             { testfiles + "/{basename}.png" } }
 156         //
 157     };
 158
 159   }
 160
 161   @DataProvider(name = "cmdLines")
 162   public Object[][] cmdLines()
 163   {
 164     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 165         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 166     String[] t1 = new String[] { "TEST1" };
 167     String[] t2 = new String[] { "TEST2" };
 168     String[] t3 = new String[] { "TEST3" };
 169     return new Object[][] {
 170         /*
 171         */
 172         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 173         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 174         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 175         // NOTE we cannot use shell expansion in tests, so list all files!
 176         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 177             someUniref50Seqs },
 178         { "--append=[new]examples/uniref50*.fa", true, 2,
 179             someUniref50Seqs },
 180         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 181         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 182         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 183             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 184         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 185         { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
 186             ArrayUtils.concatArrays(t1, t3) },
 187         { "--argfile=" + testfiles + "/argfile*.txt", true, 5,
 188             ArrayUtils.concatArrays(t1, t2, t3) },
 189         { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
 190             ArrayUtils.concatArrays(t1, t2) } };
 191
 192   }
 193
 194   public static boolean lookForSequenceName(String sequenceName)
 195   {
 196     AlignFrame[] afs = Desktop.getAlignFrames();
 197     for (AlignFrame af : afs)
 198     {
 199       for (String name : af.getViewport().getAlignment().getSequenceNames())
 200       {
 201         if (sequenceName.equals(name))
 202         {
 203           return true;
 204         }
 205       }
 206     }
 207     return false;
 208   }
 209
 210   public static void cleanupFiles(String[] filenames)
 211   {
 212     for (String filename : filenames)
 213     {
 214       File file = new File(filename);
 215       if (file.exists())
 216       {
 217         file.delete();
 218       }
 219     }
 220   }
 221
 222   @Test(
 223     groups = "Functional",
 224     dataProvider = "allLinkedIdsData",
 225     singleThreaded = true)
 226   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 227           String[] nonfilenames)
 228   {
 229     String[] args = cmdLine.split("\\s+");
 230     Jalview.main(args);
 231     Commands cmds = Jalview.getInstance().getCommands();
 232     Assert.assertNotNull(cmds);
 233     for (String filename : filenames)
 234     {
 235       Assert.assertTrue(new File(filename).exists(),
 236               "File '" + filename + "' was not created");
 237     }
 238     cleanupFiles(filenames);
 239     if (nonfilenames != null)
 240     {
 241       for (String nonfilename : nonfilenames)
 242       {
 243         File nonfile = new File(nonfilename);
 244         Assert.assertFalse(nonfile.exists(),
 245                 "File " + nonfilename + " exists when it shouldn't!");
 246       }
 247     }
 248   }
 249
 250   @DataProvider(name = "allLinkedIdsData")
 251   public Object[][] allLinkedIdsData()
 252   {
 253     return new Object[][] {
 254         //
 255         /*
 256          */
 257         { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 258             new String[]
 259             { "test/jalview/bin/argparser/testfiles/test1.stk",
 260                 "test/jalview/bin/argparser/testfiles/test2.stk",
 261                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 262             null },
 263         { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 264             new String[]
 265             { "test/jalview/bin/argparser/testfiles/test1.png",
 266                 "test/jalview/bin/argparser/testfiles/test2.png",
 267                 "test/jalview/bin/argparser/testfiles/test3.png", },
 268             null },
 269         { "--open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 270             new String[]
 271             { "test/jalview/bin/argparser/testfiles/test1.stk",
 272                 "test/jalview/bin/argparser/testfiles/test2.stk",
 273                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 274             new String[]
 275             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 276                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 277                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 278                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 279                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 280                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 281                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 282                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 283                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 284         { "--open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 285             new String[]
 286             { "test/jalview/bin/argparser/testfiles/test1.stk",
 287                 "test/jalview/bin/argparser/testfiles/test2.stk",
 288                 "test/jalview/bin/argparser/testfiles/test3.stk",
 289                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 290                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 291                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 292                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 293                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 294                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 295                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 296                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 297                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 298             null },
 299         { "--open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
 300             new String[]
 301             { "test/jalview/bin/argparser/testfiles/test1.stk",
 302                 "test/jalview/bin/argparser/testfiles/test2.stk",
 303                 "test/jalview/bin/argparser/testfiles/test3.stk",
 304                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 305                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 306                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 307                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 308                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 309                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 310                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 311                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 312                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 313             null },
 314         { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
 315             new String[]
 316             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 317                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 318                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 319                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 320                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 321             new String[]
 322             { "test/jalview/bin/argparser/testfiles/test1.stk",
 323                 "test/jalview/bin/argparser/testfiles/test2.stk",
 324                 "test/jalview/bin/argparser/testfiles/test3.stk",
 325                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 326                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 327                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 328                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 329         { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
 330             new String[]
 331             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 332                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 333                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 334             new String[]
 335             { "test/jalview/bin/argparser/testfiles/test1.stk",
 336                 "test/jalview/bin/argparser/testfiles/test2.stk",
 337                 "test/jalview/bin/argparser/testfiles/test3.stk",
 338                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 339                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 340                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 341                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 342                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 343                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 344         { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
 345             new String[]
 346             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 347                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 348                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 349             new String[]
 350             { "test/jalview/bin/argparser/testfiles/test1.stk",
 351                 "test/jalview/bin/argparser/testfiles/test2.stk",
 352                 "test/jalview/bin/argparser/testfiles/test3.stk",
 353                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 354                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 355                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 356                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 357                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 358                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 359         { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
 360             new String[]
 361             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 362                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 363                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 364                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 365                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 366             new String[]
 367             { "test/jalview/bin/argparser/testfiles/test1.stk",
 368                 "test/jalview/bin/argparser/testfiles/test2.stk",
 369                 "test/jalview/bin/argparser/testfiles/test3.stk",
 370                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 371                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 372                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 373                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 374                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 375                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 376                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 377                 "test/jalview/bin/argparser/testfiles/test1.aln",
 378                 "test/jalview/bin/argparser/testfiles/test2.aln",
 379                 "test/jalview/bin/argparser/testfiles/test3.aln",
 380                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 381                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 382                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 383                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 384                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 385                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 386         //
 387     };
 388   }
 389
 390 }