test/jalview/bin/CommandsTest.java

   1 package jalview.bin;
   2
   3 import java.util.Date;
   4 import java.util.HashSet;
   5 import java.util.Set;
   6
   7 import org.testng.Assert;
   8 import org.testng.annotations.AfterClass;
   9 import org.testng.annotations.AfterMethod;
  10 import org.testng.annotations.BeforeClass;
  11 import org.testng.annotations.DataProvider;
  12 import org.testng.annotations.Test;
  13
  14 import jalview.gui.AlignFrame;
  15 import jalview.gui.Desktop;
  16 import jalview.gui.JvOptionPane;
  17 import jalview.util.ArrayUtils;
  18
  19 @Test(singleThreaded = true)
  20 public class CommandsTest
  21 {
  22   @BeforeClass(alwaysRun = true)
  23   public static void setUpBeforeClass() throws Exception
  24   {
  25     Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
  26     Date oneHourFromNow = new Date(
  27             System.currentTimeMillis() + 3600 * 1000);
  28     Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
  29   }
  30
  31   @AfterClass(alwaysRun = true)
  32   public static void resetProps()
  33   {
  34     Cache.loadProperties("test/jalview/testProps.jvprops");
  35   }
  36
  37   @BeforeClass(alwaysRun = true)
  38   public void setUpJvOptionPane()
  39   {
  40     JvOptionPane.setInteractiveMode(false);
  41     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  42   }
  43
  44   @AfterMethod(alwaysRun = true)
  45   public void tearDown()
  46   {
  47     if (Desktop.instance != null)
  48       Desktop.instance.closeAll_actionPerformed(null);
  49   }
  50
  51   @Test(groups = "Functional", dataProvider = "cmdLines")
  52   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
  53           int numFrames, String[] sequences)
  54   {
  55     String[] args = cmdLine.split("\\s+");
  56     Jalview.main(args);
  57     Commands cmds = Jalview.getInstance().getCommands();
  58     Assert.assertNotNull(cmds);
  59     Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
  60             "Commands were not provided in the args");
  61     Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
  62             "Overall command parse and operation is false");
  63
  64     Assert.assertEquals(Desktop.getAlignFrames().length, numFrames);
  65
  66     if (sequences != null)
  67     {
  68       Set<String> openedSequenceNames = new HashSet<>();
  69       AlignFrame[] afs = Desktop.getAlignFrames();
  70       for (AlignFrame af : afs)
  71       {
  72         openedSequenceNames
  73                 .addAll(af.getViewport().getAlignment().getSequenceNames());
  74       }
  75       for (String sequence : sequences)
  76       {
  77         Assert.assertTrue(openedSequenceNames.contains(sequence),
  78                 "Sequence '" + sequence
  79                         + "' was not found in opened alignment files: "
  80                         + cmdLine + ".\nOpened sequence names are:\n"
  81                         + String.join("\n", openedSequenceNames));
  82       }
  83     }
  84
  85     Assert.assertFalse(
  86             lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
  87   }
  88
  89   @DataProvider(name = "cmdLines")
  90   public Object[][] cmdLines()
  91   {
  92     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
  93         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
  94     String[] t1 = new String[] { "TEST1" };
  95     String[] t2 = new String[] { "TEST2" };
  96     String[] t3 = new String[] { "TEST3" };
  97     return new Object[][] {
  98         { "--open=examples/uniref50.fa", true, 1, someUniref50Seqs },
  99         { "--open examples/uniref50.fa", true, 1, someUniref50Seqs },
 100         { "--open=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 101         // NOTE we cannot use shell expansion in tests, so list all files!
 102         { "--open examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 103             someUniref50Seqs },
 104         { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
 105         { "--opennew=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 106         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 107         { "examples/uniref50.fa test/jalview/bin/argparser/testfiles/test1.fa",
 108             true, 2, ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 109         { "examples/uniref50.fa test/jalview/bin/argparser/testfiles/test1.fa",
 110             true, 2, t1 },
 111         { "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt",
 112             true, 1, ArrayUtils.concatArrays(t1, t3) },
 113         { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
 114             true, 4, ArrayUtils.concatArrays(t1, t2, t3) },
 115         { "--argfile=test/jalview/bin/argparser/testfiles/argfile.autocounter",
 116             true, 3, ArrayUtils.concatArrays(t1, t2) } };
 117   }
 118
 119   public static boolean lookForSequenceName(String sequenceName)
 120   {
 121     AlignFrame[] afs = Desktop.getAlignFrames();
 122     for (AlignFrame af : afs)
 123     {
 124       for (String name : af.getViewport().getAlignment().getSequenceNames())
 125       {
 126         if (sequenceName.equals(name))
 127         {
 128           return true;
 129         }
 130       }
 131     }
 132     return false;
 133   }
 134
 135 }