def test_integrate(self):
scripts_dir = tempfile.mkdtemp(dir=self.tmp_dir)
self._dirs_to_clean_up = [scripts_dir]
copyfile(self.script1, path.join(scripts_dir, 'script1.py'))
copyfile(self.script2, path.join(scripts_dir, 'script2.py'))
copyfile(self.script3, path.join(scripts_dir, 'script3.py'))
galaxy_dir = tempfile.mkdtemp(dir=self.tmp_dir)
self._dirs_to_clean_up.append(galaxy_dir)
galaxy_tool_conf_fp = path.join(galaxy_dir, 'tool_conf.xml')
f = open(galaxy_tool_conf_fp, 'w')
f.close()
galaxy_tools_dir = path.join(galaxy_dir, 'tools')
mkdir(galaxy_tools_dir)
integrate(scripts_dir, galaxy_dir, self.config_file, False, None)
self.assertTrue(path.exists(path.join(scripts_dir, 'integration.log')),
"The log file was not created in the appropriate location")
log_d, log_fp = tempfile.mkstemp(dir=self.tmp_dir)
self._paths_to_clean_up = [log_fp]
integrate(scripts_dir, galaxy_dir, self.config_file, True, log_fp)
self.assertTrue(path.exists(log_fp),
"The log file was not created in the appropriate location")
"%prog -i scripts_dir -g galaxy_dist_dir -c config_file.txt")]
script_info['output_description'] = ""
script_info['required_options'] = [
make_option('-i', '--input_dir', type="existing_dirpath",
help='directory containing the scripts to integrate'),
make_option('-g', '--galaxy_dist_dir', type="existing_dirpath",
help='The Galaxy installation directory'),
make_option('-c', '--config_file', type="existing_filepath",
help='Configuration file which contains the section structure' +
' of the scripts')
]
script_info['optional_options'] = [
make_option('--update_tool_conf', action='store_true',
help='By default, the Galaxy tool_conf file is overwritten.' +
' Use this option to update it instead of overwrite it.'),
make_option('-l', '--log_file', type='new_filepath',
help='File path where to store the log file.' +
' [Default: input_dir/integration.log]')
]
script_info['version'] = __version__
if __name__ == '__main__':
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_dir = opts.input_dir
galaxy_dir = opts.galaxy_dist_dir
config_file_fp = opts.config_file
update = opts.update_tool_conf
log_fp = opts.log_file
integrate(input_dir, galaxy_dir, config_file_fp, update, log_fp)