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 jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+import jalview.util.ArrayUtils;
-@Test(singleThreaded = true)
+@Test
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
{
Desktop.instance.closeAll_actionPerformed(null);
}
+ /* --setprops is currently disabled so this test won't work
+ @Test(groups = "Functional")
+ public void setpropsTest()
+ {
+ final 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);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
- Assert.assertTrue(cmds.commandArgsProvided(),
+ Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
"Commands were not provided in the args");
- Assert.assertTrue(cmds.argsWereParsed(),
+ Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
"Overall command parse and operation is false");
- if (sequence != null)
+ Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+ "Wrong number of AlignFrames");
+
+ if (sequences != null)
{
- Assert.assertTrue(lookForSequenceName(sequence),
- "Sequence '" + sequence
- + "' was not found in opened alignment files: "
- + cmdLine);
+ Set<String> openedSequenceNames = new HashSet<>();
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ for (AlignFrame af : afs)
+ {
+ 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));
+ }
}
- System.out.println("##### GOT TO END");
+ Assert.assertFalse(
+ lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ }
+
+ @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
+ public void argFilesGlobAndSubstitutionsTest(String cmdLine,
+ String[] filenames) throws IOException
+ {
+ cleanupFiles(filenames);
+ String[] args = cmdLine.split("\\s+");
+ Jalview.main(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ File lastFile = null;
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ Assert.assertTrue(file.exists(), "File '" + filename
+ + "' was not created by '" + cmdLine + "'");
+ Assert.assertTrue(file.isFile(), "File '" + filename
+ + "' is not a file from '" + cmdLine + "'");
+ Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ + "' has no content from '" + cmdLine + "'");
+ // make sure the successive output files get bigger!
+ if (lastFile != null)
+ Assert.assertTrue(
+ Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+ }
+ cleanupFiles(filenames);
+ tearDown();
+ }
+
+ @DataProvider(name = "argfileOutputFiles")
+ public Object[][] argfileOutputFiles()
+ {
+ return new Object[][] {
+ { "--argfile=" + testfiles + "/**/*.txt", new String[]
+ { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
+ testfiles + "/dir3/subdir/test0.png" } },
+ { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
+ { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
+ { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
+ { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
+ { "--initsubstitutions --append examples/uniref50.fa --image "
+ + testfiles + "/{basename}.png",
+ new String[]
+ { testfiles + "/uniref50.png" } },
+ { "--append examples/uniref50.fa --image " + testfiles
+ + "/{basename}.png",
+ new String[]
+ { testfiles + "/{basename}.png" } } };
+ }
+
+ @DataProvider(name = "cmdLines")
+ public Object[][] cmdLines()
+ {
+ 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[][] {
+ /*
+ */
+ { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
+ { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
+ // NOTE we cannot use shell expansion in tests, so list all files!
+ { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+ someUniref50Seqs },
+ { "--append=[new]examples/uniref50*.fa", true, 2,
+ someUniref50Seqs },
+ { "--open=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, 5,
+ ArrayUtils.concatArrays(t1, t2, t3) },
+ { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
+ ArrayUtils.concatArrays(t1, t2) } };
+
}
public static boolean lookForSequenceName(String sequenceName)
return false;
}
- @DataProvider(name = "cmdLines")
- public Object[][] cmdLines()
+ public static void cleanupFiles(String[] filenames)
{
- return new Object[][] { { "--open=examples/uniref50.fa", "FER1_SPIOL" },
- { "--argfile=test/jalview/bin/argparser/argfile0.txt", null } };
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ if (file.exists())
+ {
+ file.delete();
+ }
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff