package jalview.bin;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
import org.testng.Assert;
+import org.testng.annotations.AfterClass;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+import jalview.util.ArrayUtils;
@Test(singleThreaded = true)
public class CommandsTest
{
+ private static final String testfiles = "test/jalview/bin/argparser/testfiles";
+
+ private static final String png1 = testfiles + "/dir1/test1.png";
+
+ private static final String png2 = testfiles + "/dir2/test1.png";
+
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
}
+ @AfterClass(alwaysRun = true)
+ public static void resetProps()
+ {
+ Cache.loadProperties("test/jalview/testProps.jvprops");
+ }
+
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
}
+ /* --setprop currently disabled
+ @Test(groups = "Functional")
+ public void setpropsTest()
+ {
+ String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
+ String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
+ String[] args = cmdLine.split("\\s+");
+ Jalview.main(args);
+ Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
+ "Earth");
+ }
+ */
+
@Test(groups = "Functional", dataProvider = "cmdLines")
- public void commandsOpenTest(String cmdLine, String sequence)
+ public void commandsOpenTest(String cmdLine, boolean cmdArgs,
+ int numFrames, String[] sequences)
{
String[] args = cmdLine.split("\\s+");
Jalview.main(args);
- ArgParser argparser = new ArgParser(args);
- boolean commandsSuccess = Commands.processArgs(argparser, false);
- Assert.assertTrue(commandsSuccess, "Overall commandsSuccess is false");
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
+ "Commands were not provided in the args");
+ Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
+ "Overall command parse and operation is false");
+
+ Assert.assertEquals(Desktop.getAlignFrames().length, numFrames);
- if (sequence != null)
+ if (sequences != null)
{
+ Set<String> openedSequenceNames = new HashSet<>();
AlignFrame[] afs = Desktop.getAlignFrames();
- boolean found = false;
- ALIGNFRAME: for (AlignFrame af : afs)
+ for (AlignFrame af : afs)
{
- for (String name : af.getViewport().getAlignment()
- .getSequenceNames())
- {
- if (sequence.equals(name))
- {
- found = true;
- break ALIGNFRAME;
- }
- }
+ openedSequenceNames
+ .addAll(af.getViewport().getAlignment().getSequenceNames());
+ }
+ for (String sequence : sequences)
+ {
+ Assert.assertTrue(openedSequenceNames.contains(sequence),
+ "Sequence '" + sequence
+ + "' was not found in opened alignment files: "
+ + cmdLine + ".\nOpened sequence names are:\n"
+ + String.join("\n", openedSequenceNames));
}
- Assert.assertTrue(found, "Sequence '" + sequence
- + "' was not found in opened alignment files: " + cmdLine);
}
+
+ Assert.assertFalse(
+ lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ }
+
+ @Test(groups = "Functional")
+ public void argFilesGlobAndSubstitutionsTest() throws IOException
+ {
+ cleanupArgfilesImages();
+ String cmdLine = "--argfile=" + testfiles + "/dir*/argfile.txt";
+ String[] args = cmdLine.split("\\s+");
+ Jalview.main(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ File file1 = new File(png1);
+ File file2 = new File(png2);
+ Assert.assertTrue(file1.exists(),
+ "Did not make file " + png1 + " from argfile");
+ Assert.assertTrue(file2.exists(),
+ "Did not make file " + png2 + " from argfile");
+ long size1 = Files.size(file1.toPath());
+ long size2 = Files.size(file2.toPath());
+ Assert.assertTrue(file1.isFile() && size1 > 0);
+ Assert.assertTrue(file2.isFile() && size2 > 0);
+ Assert.assertTrue(size2 > size1); // png2 has three sequences, png1 has 2
+ cleanupArgfilesImages();
}
@DataProvider(name = "cmdLines")
public Object[][] cmdLines()
{
- return new Object[][] { { "--open=examples/uniref50.fa", "FER1_SPIOL" },
- { "--argfile=test/jalview/bin/argparser/argfile0.txt", null } };
+ String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
+ "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
+ String[] t1 = new String[] { "TEST1" };
+ String[] t2 = new String[] { "TEST2" };
+ String[] t3 = new String[] { "TEST3" };
+ return new Object[][] {
+ { "--open=examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "--open examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "--open=examples/uniref50*.fa", true, 1, someUniref50Seqs },
+ // NOTE we cannot use shell expansion in tests, so list all files!
+ { "--open examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+ someUniref50Seqs },
+ { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
+ { "--opennew=examples/uniref50*.fa", true, 2, someUniref50Seqs },
+ { "examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
+ ArrayUtils.concatArrays(someUniref50Seqs, t1) },
+ { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
+ { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
+ ArrayUtils.concatArrays(t1, t3) },
+ { "--argfile=" + testfiles + "/argfile*.txt", true, 4,
+ ArrayUtils.concatArrays(t1, t2, t3) },
+ { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
+ ArrayUtils.concatArrays(t1, t2) } };
+ }
+
+ public static boolean lookForSequenceName(String sequenceName)
+ {
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ for (AlignFrame af : afs)
+ {
+ for (String name : af.getViewport().getAlignment().getSequenceNames())
+ {
+ if (sequenceName.equals(name))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public static void cleanupArgfilesImages()
+ {
+ File png1File = new File(png1);
+ File png2File = new File(png2);
+ if (png1File.exists())
+ {
+ png1File.delete();
+ }
+ if (png2File.exists())
+ {
+ png2File.delete();
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff