test/jalview/bin/argparser/ArgParserTest.java

   1 package jalview.bin.argparser;
   2
   3 import java.io.File;
   4 import java.io.IOException;
   5 import java.util.List;
   6 import java.util.Properties;
   7
   8 import org.testng.Assert;
   9 import org.testng.annotations.AfterClass;
  10 import org.testng.annotations.AfterMethod;
  11 import org.testng.annotations.DataProvider;
  12 import org.testng.annotations.Test;
  13
  14 import jalview.bin.Cache;
  15 import jalview.gui.Desktop;
  16
  17 @Test(singleThreaded = true)
  18 public class ArgParserTest
  19 {
  20   @AfterClass(alwaysRun = true)
  21   public static void resetProps()
  22   {
  23     Cache.loadProperties("test/jalview/testProps.jvprops");
  24   }
  25
  26   @AfterMethod(alwaysRun = true)
  27   public void tearDown()
  28   {
  29     if (Desktop.instance != null)
  30       Desktop.instance.closeAll_actionPerformed(null);
  31   }
  32
  33   @Test(groups = "Functional", dataProvider = "argLines")
  34   public void parseArgsTest(String commandLineArgs, Arg a, String other)
  35   {
  36     String[] args = commandLineArgs.split("\\s+");
  37     ArgParser argparser = new ArgParser(args);
  38   }
  39
  40   @Test(groups = "Functional", dataProvider = "argSubValsAndLinkedIds")
  41   public void parseSubValsAndLinkedIdsTest(String commandLineArgs,
  42           String linkedId, Arg a, String subvalKey, String value,
  43           boolean trueOrFalse)
  44   {
  45     String[] args = commandLineArgs.split("\\s+");
  46     ArgParser argparser = new ArgParser(args);
  47     ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
  48     ArgValue av = avm.getArgValue(a);
  49     SubVals sv = av.getSubVals();
  50     String testString = null;
  51     if (subvalKey.equals("GETINDEX"))
  52     {
  53       testString = String.valueOf(sv.getIndex());
  54     }
  55     else
  56     {
  57       testString = sv.get(subvalKey);
  58     }
  59     if (trueOrFalse)
  60     {
  61       Assert.assertEquals(testString, value);
  62     }
  63     else
  64     {
  65       Assert.assertNotEquals(testString, value);
  66     }
  67   }
  68
  69   @Test(
  70     groups = "Functional",
  71     dataProvider = "argAutoIndexAndSubstitutions")
  72   public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
  73           String linkedId, Arg a, String filename)
  74   {
  75     // { "--append=filename0 --new --append=filename1", "JALVIEW:1",
  76     // Arg.OPEN, "filename1" },
  77     String[] args = commandLineArgs.split("\\s+");
  78     ArgParser argparser = new ArgParser(args);
  79     ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
  80     ArgValue av = avm.getArgValue(a);
  81     Assert.assertEquals(av.getValue(), filename);
  82   }
  83
  84   @Test(groups = "Functional", dataProvider = "argLines")
  85   public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
  86   {
  87     String[] args = commandLineArgs.split("\\s+");
  88     BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
  89
  90     Assert.assertTrue(b.contains(a));
  91     if (a == Arg.PROPS)
  92     {
  93       Properties bP = Cache.bootstrapProperties(b.getValue(Arg.PROPS));
  94       Assert.assertNotNull(bP);
  95       Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
  96       Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
  97     }
  98     else if (a == Arg.ARGFILE)
  99     {
 100       List<String> filenames = b.getValueList(a);
 101       boolean found = false;
 102       for (String s : filenames)
 103       {
 104         File f = new File(s);
 105         File fo = new File(other);
 106         try
 107         {
 108           if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
 109           {
 110             found = true;
 111             break;
 112           }
 113         } catch (IOException e)
 114         {
 115         }
 116       }
 117       Assert.assertTrue(found,
 118               "File '" + other + "' not found in shell expanded glob '"
 119                       + commandLineArgs + "'");
 120     }
 121   }
 122
 123   @Test(groups = "Functional", dataProvider = "argFiles")
 124   public void argFilesTest(String commandLineArgs, Arg a, String other)
 125   {
 126     String[] args = commandLineArgs.split("\\s+");
 127     BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
 128
 129     Assert.assertTrue(b.contains(a));
 130     Assert.assertFalse(b.contains(Arg.APPEND));
 131     if (a == Arg.PROPS)
 132     {
 133       Properties bP = Cache.bootstrapProperties(b.getValue(Arg.PROPS));
 134       Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
 135     }
 136   }
 137
 138   @DataProvider(name = "argLinesNotworking")
 139   public Object[][] argLinesTest()
 140   {
 141     return new Object[][] {
 142         // can't use this one yet as it doesn't get shell glob expanded by the
 143         // test
 144         { "--argfile test/jalview/bin/argparser/testfiles/argfile*.txt",
 145             Arg.ARGFILE,
 146             "test/jalview/bin/argparser/testfiles/argfile0.txt" }, };
 147   }
 148
 149   @DataProvider(name = "argLines")
 150   public Object[][] argLines()
 151   {
 152     return new Object[][] { {
 153         "--append=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
 154         Arg.PROPS, "true" },
 155         { "--debug --append=test/jalview/bin/argparser/testfiles/test1.fa",
 156             Arg.DEBUG, null },
 157         { "--append=test/jalview/bin/argparser/testfiles/test1.fa --headless",
 158             Arg.HEADLESS, null },
 159
 160         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
 161             Arg.ARGFILE,
 162             "test/jalview/bin/argparser/testfiles/argfile0.txt" },
 163         // these next three are what a shell glob expansion would look like
 164         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
 165             Arg.ARGFILE,
 166             "test/jalview/bin/argparser/testfiles/argfile0.txt" },
 167         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
 168             Arg.ARGFILE,
 169             "test/jalview/bin/argparser/testfiles/argfile1.txt" },
 170         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
 171             Arg.ARGFILE,
 172             "test/jalview/bin/argparser/testfiles/argfile2.txt" },
 173         { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
 174             Arg.ARGFILE,
 175             "test/jalview/bin/argparser/testfiles/argfile0.txt" },
 176         { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
 177             Arg.ARGFILE,
 178             "test/jalview/bin/argparser/testfiles/argfile1.txt" },
 179         { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
 180             Arg.ARGFILE,
 181             "test/jalview/bin/argparser/testfiles/argfile2.txt" } };
 182   }
 183
 184   @DataProvider(name = "argSubValsAndLinkedIds")
 185   public Object[][] argSubValsAndLinkedIds()
 186   {
 187     return new Object[][] {
 188         //
 189         /*
 190          */
 191         { "--debug --append=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
 192             "JALVIEW:0", Arg.APPEND, "hi", "true", true },
 193         { "--append[linkedId1]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 194             "linkedId1", Arg.APPEND, "new", "true", true },
 195         { "--append[linkedId2]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 196             "linkedId2", Arg.APPEND, "hello", "world", true },
 197         { "--append[linkedId3]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 198             "linkedId3", Arg.APPEND, "GETINDEX", "1", true },
 199         { "--append[linkedId4]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 200             "linkedId5", Arg.APPEND, "new", "true", false },
 201         { "--append[linkedId5]=[new,hello=worlddomination,1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 202             "linkedId5", Arg.APPEND, "hello", "world", false },
 203         { "--append[linkedId6]=[new,hello=world,0]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 204             "linkedId7", Arg.APPEND, "GETINDEX", "0", false },
 205         /*
 206          */
 207         //
 208     };
 209   }
 210
 211   @DataProvider(name = "argAutoIndexAndSubstitutions")
 212   public Object[][] argAutoIndexAndSubstitutions()
 213   {
 214     return new Object[][] {
 215         //
 216         /*
 217          */
 218         { "--append=filename0 --append=filename1", "JALVIEW:0", Arg.APPEND,
 219             "filename0" },
 220         { "--append=filename0 --new --append=filename1", "JALVIEW:1",
 221             Arg.APPEND, "filename1" },
 222         { "--append=filename0 --new --new --append=filename2", "JALVIEW:0",
 223             Arg.APPEND, "filename0" },
 224         { "--append=filename0 --new --new --append=filename2", "JALVIEW:2",
 225             Arg.APPEND, "filename2" },
 226         { "--append[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
 227             "linkA-0", Arg.APPEND, "filenameA0" },
 228         { "--append[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
 229             "linkB-1", Arg.APPEND, "filenameB1" },
 230         { "--append[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
 231             "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
 232         { "--append[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
 233             "linkD-0", Arg.IMAGE, "outputD0.txt" },
 234         { "--append[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
 235             "linkE-0", Arg.IMAGE, "output-E0.txt" },
 236         { "--append[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
 237             "linkF-1", Arg.IMAGE, "outputF1.txt" },
 238         { "--append[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
 239             "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
 240         { "--append[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
 241             "linkH-0", Arg.IMAGE, "output-H0.txt" },
 242         { "--open=filename0 --append=filename1", "JALVIEW:0", Arg.OPEN,
 243             "filename0" },
 244         { "--open=filename0 --new --append=filename1", "JALVIEW:1",
 245             Arg.APPEND, "filename1" },
 246         { "--open=filename0 --new --new --append=filename2", "JALVIEW:0",
 247             Arg.OPEN, "filename0" },
 248         { "--open=filename0 --new --new --append=filename2", "JALVIEW:2",
 249             Arg.APPEND, "filename2" },
 250         { "--open[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
 251             "linkA-0", Arg.OPEN, "filenameA0" },
 252         { "--open[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
 253             "linkB-1", Arg.APPEND, "filenameB1" },
 254         { "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
 255             "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
 256         { "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
 257             "linkD-0", Arg.IMAGE, "outputD0.txt" },
 258         { "--open[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
 259             "linkE-0", Arg.IMAGE, "output-E0.txt" },
 260         { "--open[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
 261             "linkF-1", Arg.IMAGE, "outputF1.txt" },
 262         { "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
 263             "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
 264         { "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
 265             "linkH-0", Arg.IMAGE, "output-H0.txt" },
 266         /*
 267          */
 268
 269         //
 270     };
 271   }
 272
 273   @DataProvider(name = "argFiles")
 274   public Object[][] argFiles()
 275   {
 276     return new Object[][] { {
 277         "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
 278         Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
 279   }
 280
 281   @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
 282   public void allLinkedIdsTest(String commandLineArgs, Arg a,
 283           String[] values, String[] nonvalues)
 284   {
 285     String[] args = commandLineArgs.split("\\s+");
 286     ArgParser argparser = new ArgParser(args);
 287
 288     int num = values.length;
 289     List<String> linkedIds = argparser.getLinkedIds();
 290     Assert.assertEquals(linkedIds.size(), num,
 291             "Wrong number of linkedIds: " + linkedIds.toString());
 292     for (int i = 0; i < num; i++)
 293     {
 294       String value = values[i];
 295       String linkedId = linkedIds.get(i);
 296       ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
 297       if (value == null)
 298       {
 299         Assert.assertTrue(avm.containsArg(a),
 300                 "Arg value for " + a.argString()
 301                         + " not applied correctly to linkedId '" + linkedId
 302                         + "'");
 303       }
 304       else
 305       {
 306         ArgValues avs = avm.getArgValues(a);
 307         ArgValue av = avs.getArgValue();
 308         String v = av.getValue();
 309         value = new File(value).getAbsolutePath();
 310         Assert.assertEquals(v, value, "Arg value for " + a.argString()
 311                 + " not applied correctly to linkedId '" + linkedId + "'");
 312       }
 313     }
 314
 315   }
 316
 317   @DataProvider(name = "allLinkedIdsData")
 318   public Object[][] allLinkedIdsData()
 319   {
 320     return new Object[][] {
 321         //
 322         /*
 323         */
 324         { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 325             Arg.CLOSE, new String[]
 326             { null, null, null },
 327             null },
 328         { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 329             Arg.OUTPUT, new String[]
 330             { "test/jalview/bin/argparser/testfiles/test1.stk",
 331                 "test/jalview/bin/argparser/testfiles/test2.stk",
 332                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 333             null },
 334         { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 335             Arg.IMAGE, new String[]
 336             { "test/jalview/bin/argparser/testfiles/test1.png",
 337                 "test/jalview/bin/argparser/testfiles/test2.png",
 338                 "test/jalview/bin/argparser/testfiles/test3.png", },
 339             null },
 340         //
 341     };
 342   }
 343
 344   @Test(groups = "Functional", dataProvider = "bootstrapArgsData")
 345   public void bootstrapArgsValuesAndHeadlessModeTest(String commandLineArgs,
 346           Arg a, String valS, boolean valB, boolean headlessValue)
 347   {
 348     String[] args = commandLineArgs.split("\\s+");
 349     BootstrapArgs bsa = BootstrapArgs.getBootstrapArgs(args);
 350     if (a != null)
 351     {
 352       if (valS != null)
 353       {
 354         Assert.assertEquals(bsa.getValue(a), valS,
 355                 "BootstrapArg " + a.argString()
 356                         + " value does not match expected '" + valS + "'");
 357       }
 358       else
 359       {
 360         Assert.assertEquals(bsa.getBoolean(a), valB,
 361                 "Boolean/Unary value of BootstrapArg " + a.argString()
 362                         + "' is not the expected '" + valB + "'");
 363       }
 364     }
 365
 366     boolean isHeadless = bsa.isHeadless();
 367     Assert.assertEquals(isHeadless, headlessValue,
 368             "Assumed headless setting '" + isHeadless + "' is wrong.");
 369   }
 370
 371   @DataProvider(name = "bootstrapArgsData")
 372   public Object[][] bootstrapArgsData()
 373   {
 374     return new Object[][] {
 375         /*
 376          * cmdline args
 377          * Arg (null if only testing headless)
 378          * String value if there is one (null otherwise)
 379          * boolean value if String value is null
 380          * expected value of isHeadless()
 381          */
 382         /*
 383         */
 384         { "--open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
 385             Arg.JABAWS, "https://forwardsandbackwards.com/", false, true },
 386         { "--help-all --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
 387             Arg.HELP, null, true, true },
 388         { "--help-all --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
 389             Arg.NEWS, null, false, true },
 390         { "--help --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
 391             Arg.NEWS, null, false, true },
 392         { "--help-opening --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
 393             Arg.NEWS, null, false, true },
 394         { "--nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
 395             Arg.NEWS, null, false, true },
 396         { "--open thisway.fa --image thatway.png", null, null, false,
 397             true },
 398         { "--open thisway.fa --output thatway.png", null, null, false,
 399             true },
 400         { "--open thisway.fa --image thatway.png --noheadless", null, null,
 401             false, false },
 402         { "--open thisway.fa --output thatway.png --noheadless", null, null,
 403             false, false },
 404         { "--open thisway.fa --image thatway.png --gui", null, null, false,
 405             false },
 406         { "--open thisway.fa --output thatway.png --gui", null, null, false,
 407             false },
 408         // --gui takes precedence
 409         { "--open thisway.fa --image thatway.png --gui --headless", null,
 410             null, false, false },
 411         { "--open thisway.fa --output thatway.png --gui --headless", null,
 412             null, false, false },
 413         //
 414     };
 415   }
 416
 417 }