def test_check_sfdb_comparison_sfdb_new_longer(self):
entries1 = [['1', '2'], ['1', '2'], ['1', '3']]
entries2 = [['1', '2'], ['1', '2']]
sfdb1 = create_test_sfdbcontainer(entries=entries1)
sfdb2 = create_test_sfdbcontainer(entries=entries2)
with self.assertRaises(sc.ComparisonError):
sc.check_sfdb_comparison(sfdb1, sfdb2)
def test_check_sfdb_comparison_sfdb_old_longer_insufficient_excluded_lines(
self):
entries1 = [['1', '2'], ['1', '2']]
entries2 = [['1', '2'], ['1', '2'], ['1', '3'], ['1', '4']]
sfdb1 = create_test_sfdbcontainer(entries=entries1)
sfdb2 = create_test_sfdbcontainer(entries=entries2)
excluded_lines2 = [2 + sc.INDEX_SHIFT]
with self.assertRaises(sc.ComparisonError):
sc.check_sfdb_comparison(sfdb1,
sfdb2,
excluded_lines_old=excluded_lines2)
def test_check_sfdb_comparison_identical_sfdb(self):
sfdb1 = create_test_sfdbcontainer()
sfdb2 = create_test_sfdbcontainer()
diverging_lines = sc.check_sfdb_comparison(sfdb1, sfdb2)
expected_output = []
self.assertEqual(expected_output, diverging_lines)
def test_check_sfdb_comparison_multiple_column_difference_excluded(self):
columns = ['COLUMN1', 'COLUMN2', 'COLUMN3']
entries1 = [['1', '2'], ['1', '2'], ['1', '2']]
entries2 = [['1', '2'], ['1', '3'], ['1', '4']]
sfdb1 = create_test_sfdbcontainer(entries=entries1, columns=columns)
sfdb2 = create_test_sfdbcontainer(entries=entries2, columns=columns)
excluded_columns = ['COLUMN2', 'COLUMN3']
diverging_lines = sc.check_sfdb_comparison(
sfdb1, sfdb2, excluded_columns=excluded_columns)
expected_output = []
self.assertEqual(expected_output, diverging_lines)
def test_check_sfdb_comparison_sfdb_new_longer_sufficient_excluded_lines(
self):
entries1 = [['1', '2'], ['1', '2'], ['1', '3'], ['1', '4']]
entries2 = [['1', '2'], ['1', '2']]
sfdb1 = create_test_sfdbcontainer(entries=entries1)
sfdb2 = create_test_sfdbcontainer(entries=entries2)
excluded_lines1 = [2 + sc.INDEX_SHIFT, 3 + sc.INDEX_SHIFT]
diverging_lines = sc.check_sfdb_comparison(
sfdb1, sfdb2, excluded_lines_new=excluded_lines1)
expected_output = []
self.assertEqual(expected_output, diverging_lines)
def test_check_sfdb_comparison_identical_sfdb_1_line_difference(self):
entries1 = [['1', '2'], ['1', '2']]
entries2 = [['1', '2'], ['1', '3']]
sfdb1 = create_test_sfdbcontainer(entries=entries1)
sfdb2 = create_test_sfdbcontainer(entries=entries2)
diverging_entries = sc.check_sfdb_comparison(sfdb1, sfdb2)
expected_output = [(1, np.array(['1', '2']), 1, np.array(['1', '3']))]
self.assertEqual(expected_output[0][0], diverging_entries[0][0])
np.testing.assert_array_equal(expected_output[0][1],
diverging_entries[0][1])
self.assertEqual(expected_output[0][2], diverging_entries[0][2])
np.testing.assert_array_equal(expected_output[0][3],
diverging_entries[0][3])
def test_check_sfdb_comparison_identical_sfdb_1_line_difference_excluded(
self):
entries1 = [['1', '2'], ['1', '2']]
entries2 = [['1', '2'], ['1', '3']]
sfdb1 = create_test_sfdbcontainer(entries=entries1)
sfdb2 = create_test_sfdbcontainer(entries=entries2)
excluded_lines1 = [1 + sc.INDEX_SHIFT]
excluded_lines2 = [1 + sc.INDEX_SHIFT]
diverging_lines = sc.check_sfdb_comparison(
sfdb1,
sfdb2,
excluded_lines_new=excluded_lines1,
excluded_lines_old=excluded_lines2)
expected_output = []
self.assertEqual(expected_output, diverging_lines)
def run():
if len(sys.argv) == 1:
ap._build_parser().print_help()
sys.exit(1)
# Initialize logging
sfdb_path = os.path.abspath(sys.argv[1])
log_filepath = create_log_filepath(sfdb_path)
configurate_logger(log_filepath)
logging.log(LOGFILE_LEVEL, f'LOG FILE FOR SFDB FILE : {sfdb_path}')
logging.log(LOGFILE_LEVEL, 'Indices in this log start from 1\n')
warning_counter = 0
# Receive Arguments
args = ap.parse_args(sys.argv[1:])
if args.request:
args = ap.request_missing_args(args)
# Perform Tests on SFDB file
logging.log(LOGFILE_LEVEL, 'STARTING CONTENT FORMAT TEST')
wrong_format_entries = sc.check_content_format(args.sfdb_new)
sc.log_sfdb_content_format_check(len(args.sfdb_new.columns),
wrong_format_entries)
logging.log(LOGFILE_LEVEL, 'FINISHED CONTENT FORMAT TEST\n')
# Run tests that crash if SFDB file has format issues
if not wrong_format_entries:
logging.log(LOGFILE_LEVEL, 'STARTING EXCEL AUTOFORMATTING TEST')
formatted_cells_list = sc.check_excel_autoformatting(args.sfdb_new)
sc.log_excel_autoformatting_check(formatted_cells_list)
warning_counter += len(formatted_cells_list)
logging.log(LOGFILE_LEVEL, 'FINISHED EXCEL AUTOFORMATTING TEST\n')
logging.log(LOGFILE_LEVEL, 'STARTING DUPLICATE TEST')
duplicates = args.sfdb_new.get_duplicates()
sc.log_duplicates_check(duplicates)
warning_counter += len(args.sfdb_new._get_duplicate_index_list())
logging.log(LOGFILE_LEVEL, 'FINISHED DUPLICATE TEST\n')
logging.log(LOGFILE_LEVEL, 'STARTING DATATYPE TEST')
non_conform_entries = sc.check_datatype_conformity(args.sfdb_new)
sc.log_datatype_check(non_conform_entries)
warning_counter += 0 if non_conform_entries is None else len(
non_conform_entries)
logging.log(LOGFILE_LEVEL, 'FINISHED DATATYPE TEST\n')
if args.column_patterns:
logging.log(LOGFILE_LEVEL, 'STARTING REGEX TEST')
non_compliant_entries = sc.check_content_against_regex(
args.sfdb_new, args.column_patterns)
sc.log_regex_check(non_compliant_entries)
warning_counter += len(non_compliant_entries)
logging.log(LOGFILE_LEVEL, 'FINISHED REGEX TEST\n')
if args.sfdb_old:
logging.log(LOGFILE_LEVEL, 'STARTING COMPARISON TEST')
diverging_entries = sc.check_sfdb_comparison(
args.sfdb_new, args.sfdb_old, args.excluded_lines1,
args.excluded_lines2, args.excluded_columns)
sc.log_sfdb_comparison(diverging_entries)
warning_counter += len(diverging_entries)
logging.log(LOGFILE_LEVEL, 'FINISHED COMPARISON TEST\n')
if args.write:
no_dupl_sfdb_file = args.SFDBFile[:-5] + '_no_duplicates.sfdb'
logging.log(
LOGFILE_LEVEL,
'Writing SFDB file without duplicates to {no_dupl_sfdb_file}')
args.sfdb_new.write(no_dupl_sfdb_file,
sort=args.sorted,
remove_duplicates=True)
else:
logging.info(
'Only format tests were carried out due to the format issues.\n'
'Please run this software again after fixing them.')
# Finish logging
logging.log(LOGFILE_LEVEL, 'Done')
logging.info(f'The file caused {warning_counter} warning-messages.')
logging.info(f'Logfile written to {log_filepath}.\nDone')