// This is need by blast tests.
public Formatdb runInTempDir() throws ExecuteException {
Formatdb formatdb = new Formatdb();
formatdb.setTitle("My_Awesome_Database");
URL url =
Thread.currentThread().getContextClassLoader().getResource("formatdbTest/someSequences.fa");
formatdb.setInputFile(url.getPath());
formatdb.setBaseName("MADDB");
formatdb.setWorkingDirectory(System.getProperty("java.io.tmpdir"));
formatdb.run();
return formatdb;
}
@Test
public void testRun() throws ExecuteException {
Formatdb formatdb = runInTempDir();
if (formatdb.getLastExitValue() != 0) {
String errorMessage =
"Command: "
+ formatdb.getExecutedCommand()
+ "\n"
+ "Return: "
+ formatdb.getLastExitValue()
+ "\n"
+ "Output: "
+ formatdb.getLastRunOutput()
+ "\n"
+ "Error: "
+ formatdb.getLastRunError()
+ "\n"
+ "Formatdb test should return 0. Returned "
+ formatdb.getLastExitValue();
assertTrue(errorMessage, false);
}
}
