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)