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.DataProvider;
  11 import org.testng.annotations.Test;
  12
  13 import jalview.bin.Cache;
  14
  15 @Test(singleThreaded = true)
  16 public class ArgParserTest
  17 {
  18   @AfterClass(alwaysRun = true)
  19   public static void resetProps()
  20   {
  21     Cache.loadProperties("test/jalview/testProps.jvprops");
  22   }
  23
  24   @Test(groups = "Functional", dataProvider = "argLines")
  25   public void parseArgsTest(String commandLineArgs, Arg a, String other)
  26   {
  27     String[] args = commandLineArgs.split("\\s+");
  28     ArgParser argparser = new ArgParser(args);
  29   }
  30
  31   @Test(groups = "Functional", dataProvider = "argSubValsAndLinkedIds")
  32   public void parseSubValsAndLinkedIdsTest(String commandLineArgs,
  33           String linkedId, Arg a, String subvalKey, String value,
  34           boolean trueOrFalse)
  35   {
  36     String[] args = commandLineArgs.split("\\s+");
  37     ArgParser argparser = new ArgParser(args);
  38     ArgValuesMap avm = argparser.linkedArgs(linkedId);
  39     ArgValue av = avm.getArgValue(a);
  40     SubVals sv = av.getSubVals();
  41     String testString = null;
  42     if (subvalKey.equals("GETINDEX"))
  43     {
  44       testString = String.valueOf(sv.getIndex());
  45     }
  46     else
  47     {
  48       testString = sv.get(subvalKey);
  49     }
  50     if (trueOrFalse)
  51     {
  52       Assert.assertEquals(testString, value);
  53     }
  54     else
  55     {
  56       Assert.assertNotEquals(testString, value);
  57     }
  58   }
  59
  60   @Test(
  61     groups = "Functional",
  62     dataProvider = "argAutoIndexAndSubstitutions")
  63   public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
  64           String linkedId, Arg a, String filename)
  65   {
  66     // { "--append=filename0 --newframe --append=filename1", "JALVIEW:1",
  67     // Arg.OPEN, "filename1" },
  68     String[] args = commandLineArgs.split("\\s+");
  69     ArgParser argparser = new ArgParser(args);
  70     ArgValuesMap avm = argparser.linkedArgs(linkedId);
  71     ArgValue av = avm.getArgValue(a);
  72     Assert.assertEquals(av.getValue(), filename);
  73   }
  74
  75   @Test(groups = "Functional", dataProvider = "argLines")
  76   public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
  77   {
  78     String[] args = commandLineArgs.split("\\s+");
  79     BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
  80
  81     Assert.assertTrue(b.contains(a));
  82     if (a == Arg.PROPS)
  83     {
  84       Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
  85       Assert.assertNotNull(bP);
  86       Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
  87       Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
  88     }
  89     else if (a == Arg.ARGFILE)
  90     {
  91       List<String> filenames = b.getList(a);
  92       boolean found = false;
  93       for (String s : filenames)
  94       {
  95         File f = new File(s);
  96         File fo = new File(other);
  97         try
  98         {
  99           if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
 100           {
 101             found = true;
 102             break;
 103           }
 104         } catch (IOException e)
 105         {
 106         }
 107       }
 108       Assert.assertTrue(found,
 109               "File '" + other + "' not found in shell expanded glob '"
 110                       + commandLineArgs + "'");
 111     }
 112   }
 113
 114   @Test(groups = "Functional", dataProvider = "argFiles")
 115   public void argFilesTest(String commandLineArgs, Arg a, String other)
 116   {
 117     String[] args = commandLineArgs.split("\\s+");
 118     BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
 119
 120     Assert.assertTrue(b.contains(a));
 121     Assert.assertFalse(b.contains(Arg.APPEND));
 122     if (a == Arg.PROPS)
 123     {
 124       Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
 125       Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
 126     }
 127   }
 128
 129   @DataProvider(name = "argLinesNotworking")
 130   public Object[][] argLinesTest()
 131   {
 132     return new Object[][] {
 133         // can't use this one yet as it doesn't get shell glob expanded by the
 134         // test
 135         { "--argfile test/jalview/bin/argparser/testfiles/argfile*.txt",
 136             Arg.ARGFILE,
 137             "test/jalview/bin/argparser/testfiles/argfile0.txt" }, };
 138   }
 139
 140   @DataProvider(name = "argLines")
 141   public Object[][] argLines()
 142   {
 143     return new Object[][] { {
 144         "--append=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
 145         Arg.PROPS, "true" },
 146         { "--debug --append=test/jalview/bin/argparser/testfiles/test1.fa",
 147             Arg.DEBUG, null },
 148         { "--append=test/jalview/bin/argparser/testfiles/test1.fa --headless",
 149             Arg.HEADLESS, null },
 150
 151         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
 152             Arg.ARGFILE,
 153             "test/jalview/bin/argparser/testfiles/argfile0.txt" },
 154         // these next three are what a shell glob expansion would look like
 155         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
 156             Arg.ARGFILE,
 157             "test/jalview/bin/argparser/testfiles/argfile0.txt" },
 158         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
 159             Arg.ARGFILE,
 160             "test/jalview/bin/argparser/testfiles/argfile1.txt" },
 161         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
 162             Arg.ARGFILE,
 163             "test/jalview/bin/argparser/testfiles/argfile2.txt" },
 164         { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
 165             Arg.ARGFILE,
 166             "test/jalview/bin/argparser/testfiles/argfile0.txt" },
 167         { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
 168             Arg.ARGFILE,
 169             "test/jalview/bin/argparser/testfiles/argfile1.txt" },
 170         { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
 171             Arg.ARGFILE,
 172             "test/jalview/bin/argparser/testfiles/argfile2.txt" } };
 173   }
 174
 175   @DataProvider(name = "argSubValsAndLinkedIds")
 176   public Object[][] argSubValsAndLinkedIds()
 177   {
 178     return new Object[][] { {
 179         "--debug --append=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
 180         "JALVIEW:0", Arg.APPEND, "hi", "true", true },
 181         { "--append[linkedId1]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 182             "linkedId1", Arg.APPEND, "new", "true", true },
 183         { "--append[linkedId2]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 184             "linkedId2", Arg.APPEND, "hello", "world", true },
 185         { "--append[linkedId3]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
 186             "linkedId3", Arg.APPEND, "GETINDEX", "1", true },
 187         { "--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",
 188             "linkedId5", Arg.APPEND, "new", "true", false },
 189         { "--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",
 190             "linkedId5", Arg.APPEND, "hello", "world", false },
 191         { "--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",
 192             "linkedId7", Arg.APPEND, "GETINDEX", "0", false }, };
 193   }
 194
 195   @DataProvider(name = "argAutoIndexAndSubstitutions")
 196   public Object[][] argAutoIndexAndSubstitutions()
 197   {
 198     return new Object[][] {
 199         //
 200         /*
 201          */
 202         { "--append=filename0 --append=filename1", "JALVIEW:0", Arg.APPEND,
 203             "filename0" },
 204         { "--append=filename0 --newframe --append=filename1", "JALVIEW:1",
 205             Arg.APPEND, "filename1" },
 206         { "--append=filename0 --newframe --newframe --append=filename2",
 207             "JALVIEW:0", Arg.APPEND, "filename0" },
 208         { "--append=filename0 --newframe --newframe --append=filename2",
 209             "JALVIEW:2", Arg.APPEND, "filename2" },
 210         { "--append[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
 211             "linkA-0", Arg.APPEND, "filenameA0" },
 212         { "--append[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
 213             "linkB-1", Arg.APPEND, "filenameB1" },
 214         { "--append[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
 215             "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
 216         { "--append[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
 217             "linkD-0", Arg.IMAGE, "outputD0.txt" },
 218         { "--append[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
 219             "linkE-0", Arg.IMAGE, "output-E0.txt" },
 220         { "--append[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
 221             "linkF-1", Arg.IMAGE, "outputF1.txt" },
 222         { "--append[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
 223             "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
 224         { "--append[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
 225             "linkH-0", Arg.IMAGE, "output-H0.txt" },
 226         { "--open=filename0 --append=filename1", "JALVIEW:1", Arg.OPEN,
 227             "filename0" },
 228         { "--open=filename0 --newframe --append=filename1", "JALVIEW:2",
 229             Arg.APPEND, "filename1" },
 230         { "--open=filename0 --newframe --newframe --append=filename2",
 231             "JALVIEW:1", Arg.OPEN, "filename0" },
 232         { "--open=filename0 --newframe --newframe --append=filename2",
 233             "JALVIEW:3", Arg.APPEND, "filename2" },
 234         { "--open[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
 235             "linkA-0", Arg.OPEN, "filenameA0" },
 236         { "--open[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
 237             "linkB-1", Arg.APPEND, "filenameB1" },
 238         { "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
 239             "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
 240         { "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
 241             "linkD-0", Arg.IMAGE, "outputD0.txt" },
 242         { "--open[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
 243             "linkE-0", Arg.IMAGE, "output-E0.txt" },
 244         { "--open[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
 245             "linkF-1", Arg.IMAGE, "outputF1.txt" },
 246         { "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
 247             "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
 248         { "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
 249             "linkH-0", Arg.IMAGE, "output-H0.txt" },
 250
 251         //
 252     };
 253   }
 254
 255   @DataProvider(name = "argFiles")
 256   public Object[][] argFiles()
 257   {
 258     return new Object[][] { {
 259         "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
 260         Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
 261   }
 262 }