import java.io.File;
import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
import java.nio.file.Files;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
+import javax.swing.SwingUtilities;
+
import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.AfterMethod;
}
@AfterMethod(alwaysRun = true)
- public void tearDown()
+ public void tearDown()
{
- Desktop.closeDesktop();
+ try
+ {
+ // occasionally we are blocked by Jmol redraws
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ Desktop.closeDesktop();
+ }
+ });
+ } catch (Exception foo)
+ {
+ System.err.println("Failed during teardown with exception");
+ foo.printStackTrace();
+ }
+
}
-
- public static void callJalviewMain(String[] args) {
- if (Jalview.getInstance()!=null) {
+
+ public static void callJalviewMain(String[] args)
+ {
+ if (Jalview.getInstance() != null)
+ {
Jalview.getInstance().doMain(args);
- } else {
+ }
+ else
+ {
Jalview.main(args);
}
}
}
*/
- @Test(groups = "Functional", dataProvider = "cmdLines")
+ @Test(groups = {"Functional","testTask3"}, dataProvider = "cmdLines")
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
{
}
}
- @Test(groups = {"Functional","testTask1"}, dataProvider = "structureImageOutputFiles")
+ @Test(
+ groups =
+ { "Functional", "testTask3" },
+ 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)
+ 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",
+ Assert.fail(
+ "Unexpected exception during argFilesGlobAndSubstitutions",
x);
} finally
{
+ "--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"
+ + "/structureimage2.png --scale=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",
+ + "/structureimage3.png --scale=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"
+ + "/structureimage2.png --scale=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",
+ + "/structureimage3.png --scale=2.0 ",
new String[]
{ testfiles + "/structureimage1.png",
testfiles + "/structureimage2.png",
testfiles + "/structureimage3.png" } },
+ /*
*/
//
};
}
}
+ private final String deleteDir = "test/deleteAfter";
+
@Test(
groups = "Functional",
dataProvider = "allLinkedIdsData",
"File " + nonfilename + " exists when it shouldn't!");
}
}
+
+ File deleteDirF = new File(deleteDir);
+ if (deleteDirF.exists())
+ {
+ deleteDirF.delete();
+ }
}
@DataProvider(name = "allLinkedIdsData")
{
return new Object[][] {
//
- /*
- */
{ "--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/dir3/subdir/test2.stk",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
null },
- { "--gui --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 },
- { "--gui --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", }, },
- { "--gui --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", }, },
- { "--gui --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", }, },
- { "--gui --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",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
+ // --mkdirs
+ { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
+ + deleteDir
+ + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
+ + deleteDir
+ + "/{dirname}/{basename}.aln --close --all --mkdirs",
+ new String[]
+ { deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
+ 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/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/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",
+ "test/jalview/bin/argparser/testfiles/test1.aln",
+ "test/jalview/bin/argparser/testfiles/test2.aln",
+ "test/jalview/bin/argparser/testfiles/test3.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test3.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
//
};
}