import jalview.gui.JvOptionPane;
import jalview.util.ArrayUtils;
-@Test
public class CommandsTest
{
private static final String testfiles = "test/jalview/bin/argparser/testfiles";
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- if (Desktop.instance != null)
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.closeDesktop();
+ }
+
+ public static void callJalviewMain(String[] args)
+ {
+ if (Jalview.getInstance() != null)
+ {
+ Jalview.getInstance().doMain(args);
+ }
+ else
+ {
+ Jalview.main(args);
+ }
}
/* --setprops is currently disabled so this test won't work
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.assertEquals(cmds.commandArgsProvided(), cmdArgs,
- "Commands were not provided in the args");
- Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
- "Overall command parse and operation is false");
+ try
+ {
+ String[] args = (cmdLine + " --gui").split("\\s+");
+ callJalviewMain(args);
+ 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,
- "Wrong number of AlignFrames");
+ Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+ "Wrong number of AlignFrames");
- if (sequences != null)
- {
- Set<String> openedSequenceNames = new HashSet<>();
- AlignFrame[] afs = Desktop.getAlignFrames();
- for (AlignFrame af : afs)
+ if (sequences != null)
{
- openedSequenceNames
- .addAll(af.getViewport().getAlignment().getSequenceNames());
+ 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));
+ }
}
- for (String sequence : sequences)
+
+ Assert.assertFalse(
+ lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during commandsOpenTest", x);
+ } finally
+ {
+ tearDown();
+
+ }
+ }
+
+ @Test(
+ groups =
+ { "Functional", "testTask1" },
+ dataProvider = "structureImageOutputFiles")
+ public void structureImageOutputTest(String cmdLine, String[] filenames)
+ throws IOException
+ {
+ cleanupFiles(filenames);
+ String[] args = (cmdLine + " --gui").split("\\s+");
+ try
+ {
+ callJalviewMain(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ File lastFile = null;
+ for (String filename : filenames)
{
- Assert.assertTrue(openedSequenceNames.contains(sequence),
- "Sequence '" + sequence
- + "' was not found in opened alignment files: "
- + cmdLine + ".\nOpened sequence names are:\n"
- + String.join("\n", openedSequenceNames));
+ 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()));
}
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during structureImageOutputTest",
+ x);
+ } finally
+ {
+ cleanupFiles(filenames);
+ tearDown();
}
-
- Assert.assertFalse(
- lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
}
@Test(groups = "Functional", dataProvider = "argfileOutputFiles")
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)
+ String[] args = (cmdLine + " --gui").split("\\s+");
+ try
{
- 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()));
+ callJalviewMain(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()));
+ }
+ } catch (Exception x)
+ {
+ Assert.fail(
+ "Unexpected exception during argFilesGlobAndSubstitutions",
+ x);
+ } finally
+ {
+ cleanupFiles(filenames);
+ tearDown();
}
- cleanupFiles(filenames);
- tearDown();
+ }
+
+ @DataProvider(name = "structureImageOutputFiles")
+ public Object[][] structureImageOutputFiles()
+ {
+ return new Object[][] {
+ //
+ { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
+ + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ + "--structureimage=" + testfiles + "/structureimage1.png "
+ + "--open=./examples/test_fab41.result/sample.a2m "
+ + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ + "--structureimage=" + testfiles
+ + "/structureimage2.png --structureimagescale=1.5"
+ + "--open=./examples/test_fab41.result/sample.a2m "
+ + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ + "--structureimage=" + testfiles
+ + "/structureimage3.png --structureimagescale=2.0",
+ new String[]
+ { testfiles + "/structureimage1.png",
+ testfiles + "/structureimage2.png",
+ testfiles + "/structureimage3.png" } },
+ { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
+ + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ + "--structureimage=" + testfiles + "/structureimage1.png "
+ + "--open=./examples/test_fab41.result/sample.a2m "
+ + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ + "--structureimage=" + testfiles
+ + "/structureimage2.png --structureimagescale=1.5"
+ + "--open=./examples/test_fab41.result/sample.a2m "
+ + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ + "--structureimage=" + testfiles
+ + "/structureimage3.png --structureimagescale=2.0",
+ new String[]
+ { testfiles + "/structureimage1.png",
+ testfiles + "/structureimage2.png",
+ testfiles + "/structureimage3.png" } },
+ /*
+ */
+ //
+ };
+
}
@DataProvider(name = "argfileOutputFiles")
{
return new Object[][] {
//
- { "--argfile=" + testfiles + "/**/*.txt", new String[]
+ { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
{ testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
testfiles + "/dir3/subdir/test0.png" } },
- { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
+ { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
{ testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
- { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
+ { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
{ testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
- { "--initsubstitutions --append examples/uniref50.fa --image "
+ { "--gui --initsubstitutions --append examples/uniref50.fa --image "
+ testfiles + "/{basename}.png",
new String[]
{ testfiles + "/uniref50.png" } },
- { "--append examples/uniref50.fa --nosubstitutions --image "
+ { "--gui --append examples/uniref50.fa --nosubstitutions --image "
+ testfiles + "/{basename}.png",
new String[]
{ testfiles + "/{basename}.png" } }
{ "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,
+ { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
ArrayUtils.concatArrays(t1, t3) },
- { "--argfile=" + testfiles + "/argfile*.txt", true, 5,
+ { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
ArrayUtils.concatArrays(t1, t2, t3) },
- { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
+ { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
ArrayUtils.concatArrays(t1, t2) } };
}
public void allLinkedIdsTest(String cmdLine, String[] filenames,
String[] nonfilenames)
{
- String[] args = cmdLine.split("\\s+");
- Jalview.main(args);
+ String[] args = (cmdLine + " --gui").split("\\s+");
+ callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
for (String filename : filenames)
{
return new Object[][] {
//
- /*
- */
- { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/test3.stk", },
null },
- { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.png",
"test/jalview/bin/argparser/testfiles/test2.png",
"test/jalview/bin/argparser/testfiles/test3.png", },
null },
- { "--open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
- { "--open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
null },
- { "--open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
null },
- { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
- { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
"test/jalview/bin/argparser/testfiles/dir2/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
- { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
"test/jalview/bin/argparser/testfiles/dir2/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
- { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.stk",
git://source.jalview.org / jalview.git / blobdiff