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#########################################################################
# MacSyFinder - Detection of macromolecular systems in protein dataset #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2024 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# This file is part of MacSyFinder package. #
# #
# MacSyFinder is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# MacSyFinder is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details . #
# #
# You should have received a copy of the GNU General Public License #
# along with MacSyFinder (COPYING). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
import tempfile
import shutil
import os
import argparse
import sys
import colorlog
import glob
import unittest
import platform
from tests import MacsyTest
from macsypy.scripts import macsy_gembase_split
class TestSplit(MacsyTest):
def setUp(self):
self.tmpdir = tempfile.mkdtemp()
self.test_dir = os.path.join(self.tmpdir, 'macsyfinder_test_split')
os.mkdir(self.test_dir)
self.args = argparse.Namespace()
def tearDown(self):
try:
shutil.rmtree(self.tmpdir)
except Exception:
pass
# some function in macsydata script suppress the traceback
# but without traceback it's hard to debug test :-(
sys.tracebacklimit = 1000 # the default value
logger = colorlog.getLogger('macsypy')
for h in logger.handlers[:]:
logger.removeHandler(h)
def test_functional_split(self):
gembase = self.find_data('base', 'gembase_short.fa')
seq_dir = os.path.join(self.test_dir, 'base')
cmd = f"macsy_gembase_split -o {seq_dir} --mute -qqq {gembase}"
with self.catch_io(out=True):
macsy_gembase_split.main(cmd.split()[1:])
seq_files = sys.stdout.getvalue().strip().split()
expected_dir = self.find_data('gembase_split')
expected_out_files = glob.glob(os.path.join(expected_dir, '*.fasta'))
self.assertSetEqual(set([os.path.basename(f) for f in expected_out_files]),
set([os.path.basename(f) for f in seq_files])
)
for file in [os.path.basename(f) for f in expected_out_files]:
with self.subTest(file):
expected_seq = os.path.join(expected_dir, file)
split_seq = os.path.join(seq_dir, file)
self.assertFileEqual(expected_seq, split_seq)
def test_functional_split_out_error(self):
gembase = self.find_data('base', 'gembase_short.fa')
seq_dir = os.path.join(self.test_dir, 'base')
###########################
# the -o option is a file
###########################
open(seq_dir, 'w').close()
cmd = f"macsy_gembase_split -o {seq_dir} {gembase}"
with self.catch_io(out=True):
# we cannot test the log message here
# because the logger are init when main is called
# after that the context is establish
# so when the wrapper is called the handler cannot be substitute by the fake
# but we can catch stdout
with self.assertRaises(IOError):
macsy_gembase_split.main(args=cmd.split()[1:], log_level='WARNING')
stdout = sys.stdout.getvalue().strip()
self.assertEqual(self.remove_red_ansi_color(stdout),
f'{seq_dir} is not a directory')
os.unlink(seq_dir)
@unittest.skipIf(platform.system() == 'Windows' or os.getuid() == 0, 'Skip test on Windows or if run as root')
def test_functional_split_out_not_writable(self):
gembase = self.find_data('base', 'gembase_short.fa')
seq_dir = os.path.join(self.test_dir, 'base')
######################################
# the -o option is a dir NOT writable
#####################################
os.mkdir(seq_dir, mode=0o444)
cmd = f"macsy_gembase_split -o {seq_dir} {gembase}"
try:
with self.catch_io(out=True):
with self.assertRaises(IOError):
macsy_gembase_split.main(args=cmd.split()[1:], log_level='WARNING')
stdout = sys.stdout.getvalue().strip()
self.assertEqual(self.remove_red_ansi_color(stdout),
f'{seq_dir} is not writable')
finally:
shutil.rmtree(seq_dir)
######################################
# the -o option parent is NOT writable
######################################
os.chmod(self.test_dir, mode=0o444)
with self.catch_io(out=True):
with self.assertRaises(IOError):
macsy_gembase_split.main(args=cmd.split()[1:], log_level='WARNING')
stdout = sys.stdout.getvalue().strip()
self.assertEqual(self.remove_red_ansi_color(stdout),
f"Cannot create {seq_dir} : [Errno 13] Permission denied: '{seq_dir}'")
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