예제 #1
0
    def test_get_uploadable_files(self):
        temp_dir = tempfile.mkdtemp()
        try:
            params = D3RParameters()
            task = MakeBlastDBTask(temp_dir, params)
            task.create_dir()

            # test on empty dir
            self.assertEqual(task.get_uploadable_files(), [])

            # test with stderr/stdout files
            stdout = os.path.join(task.get_dir(), 'makeblastdb.stdout')
            open(stdout, 'a').close()
            stderr = os.path.join(task.get_dir(), 'makeblastdb.stderr')
            open(stderr, 'a').close()
            flist = task.get_uploadable_files()
            self.assertEqual(len(flist), 2)
            flist.index(stdout)
            flist.index(stderr)

            # test with pdb_seqres.txt.gz file
            open(task.get_pdb_seqres_txt_gz(), 'a').close()
            flist = task.get_uploadable_files()
            self.assertEqual(len(flist), 3)
            flist.index(stdout)
            flist.index(stderr)
            flist.index(task.get_pdb_seqres_txt_gz())

            os.unlink(task.get_pdb_seqres_txt_gz())

            # test where pdb_seqres.txt is a dir unlikely but why not check
            os.makedirs(task.get_pdb_seqres_txt_gz())
            flist = task.get_uploadable_files()
            self.assertEqual(len(flist), 2)
            flist.index(stdout)
            flist.index(stderr)
        finally:
            shutil.rmtree(temp_dir)
예제 #2
0
 def test_get_pdbseqres_txt_gz(self):
     params = D3RParameters()
     task = MakeBlastDBTask('/foo', params)
     self.assertEqual(
         task.get_pdb_seqres_txt_gz(),
         os.path.join('/foo', task.get_dir_name(), 'pdb_seqres.txt.gz'))