test_epiLION.py

# -*- coding: utf-8 -*-
#
# Copyright (C) 2016-2019  SysMedOs_team @ AG Bioanalytik, University of Leipzig:
# SysMedOs_team: Zhixu Ni, Georgia Angelidou, Mike Lange, Maria Fedorova
#
# For more info please contact:
#     Developer Zhixu Ni zhixu.ni@uni-leipzig.de
import os
import sys
import unittest

epiLION_Path = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, epiLION_Path + '/../')

import epiLION
from epilion.libLION.DefaultParams import logger


class epiLIONTestCase(unittest.TestCase):

    def setUp(self):
        logger.debug('SETUP TESTS...')

        in_file_lst = [
            r'../test/TestInput/test_names.txt',
            r'test/TestInput/test_names.txt',
            r'../TestInput/test_names.txt',
            r'TestInput/test_names.txt',
        ]
        in_file = ''
        for f in in_file_lst:
            if os.path.isfile(f):
                in_file = os.path.abspath(f)
                break
        logger.info(f'Input file is: {in_file}')

        bad_in_file = r'test/TestInput/test_names_x.txt'

        out_folder_lst = [
            r'../test/TestOutput/',
            r'test/TestOutput/',
            r'../TestOutput/',
            r'TestOutput/',
        ]
        out_folder = ''
        for p in out_folder_lst:
            if os.path.isdir(p):
                out_folder = os.path.abspath(p)
                break
        out_file = os.path.join(out_folder, 'test_names_sdf.sdf')
        logger.info(f'Out put file will be: {out_file}')

        self.pass_params = ['-i', in_file, '-o', out_file]
        self.fail_input_params = ['-i', bad_in_file, '-o', out_file]

    @staticmethod
    def test_epiLION_help():
        logger.debug('test help...')
        result = epiLION.main(['-h'])
        if result is False:
            logger.debug('test help... PASSED')
        else:
            raise Exception('test help... Failed')

    @staticmethod
    def test_epiLION_bad_params():
        logger.debug('test bad parameter...')
        result = epiLION.main(['-test'])
        if result is False:
            logger.debug('test bad parameter... PASSED')
        else:
            raise Exception('test bad parameter... Failed')

    def test_epiLION_bad_input(self):
        logger.debug('test bad input...')
        result = epiLION.main(self.fail_input_params)
        if result is False:
            logger.debug('test bad input... PASSED')
        else:
            raise Exception('test bad input... Failed')

    def test_epiLION_good_input(self):
        logger.debug('test sample data...')
        result = epiLION.main(self.pass_params)
        if result is True:
            logger.debug('test sample data... PASSED')
        else:
            raise Exception('test sample data... Failed')

    def tearDown(self):
        logger.debug('TEST END!')


if __name__ == '__main__':
    # python epiLION.py -i test/TestInput/test_names.txt -o test/TestOutput/test_names_sdf.sdf

    unittest.main()
    logger.info('TESTS FINISHED!')