def test_functional_merge_one_results_empty(self):
# res_1 has hits
# res_2 has no hits and no systems
res_1 = 'results_no_hits'
src_res_1 = self.find_data('data_set', res_1)
dest_res_1 = os.path.join(self.test_dir, res_1)
res_2 = 'results_2'
src_res_2 = self.find_data('data_set', res_2)
dest_res_2 = os.path.join(self.test_dir, res_2)
shutil.copytree(src_res_1, dest_res_1)
shutil.copytree(src_res_2, dest_res_2)
merge_dir = os.path.join(self.test_dir, 'merged_results')
os.mkdir(merge_dir)
cmd = f"macsymerge -o {merge_dir} --mute -qq {dest_res_1} {dest_res_2}"
macsy_merge_results.main(args=cmd.split()[1:])
results_files = ('best_solution.tsv', 'best_solution_summary.tsv',
'best_solution_loners.tsv',
'best_solution_multisystems.tsv',
'all_best_solutions.tsv', 'all_systems.tsv',
'all_systems.txt', 'rejected_clusters.txt')
for res in results_files:
with self.subTest(res):
expected = self.find_data('data_set',
'merged_results_one_res_no_hits',
f"merged_{res}")
recieved = os.path.join(merge_dir, f"merged_{res}")
self.assertFileEqual(expected, recieved, comment='#')
def test_functional_merge_out_error(self):
res_1 = 'results_1'
src_res_1 = self.find_data('data_set', res_1)
dest_res_1 = os.path.join(self.test_dir, res_1)
res_2 = 'results_no_hits'
src_res_2 = self.find_data('data_set', res_2)
dest_res_2 = os.path.join(self.test_dir, res_2)
merge_dir = os.path.join(self.test_dir, 'merged_results')
###########################
# the -o option is a file
###########################
open(merge_dir, 'w').close()
cmd = f"macsy_merge_results -o {merge_dir} {dest_res_1} {dest_res_2}"
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_merge_results.main(args=cmd.split()[1:],
log_level='WARNING')
stdout = sys.stdout.getvalue().strip()
self.assertEqual(self.remove_red_ansi_color(stdout),
f'{merge_dir} is not a directory')
os.unlink(merge_dir)
def test_functional_merge_out_not_writable(self):
res_1 = 'results_1'
src_res_1 = self.find_data('data_set', res_1)
dest_res_1 = os.path.join(self.test_dir, res_1)
res_2 = 'results_no_hits'
src_res_2 = self.find_data('data_set', res_2)
dest_res_2 = os.path.join(self.test_dir, res_2)
merge_dir = os.path.join(self.test_dir, 'merged_results')
######################################
# the -o option is a dir NOT writable
#####################################
os.mkdir(merge_dir, mode=0o444)
cmd = f"macsy_merge_results -o {merge_dir} {dest_res_1} {dest_res_2}"
try:
with self.catch_io(out=True):
with self.assertRaises(IOError):
macsy_merge_results.main(args=cmd.split()[1:],
log_level='WARNING')
stdout = sys.stdout.getvalue().strip()
self.assertEqual(self.remove_red_ansi_color(stdout),
f'{merge_dir} is not writable')
finally:
shutil.rmtree(merge_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_merge_results.main(args=cmd.split()[1:],
log_level='WARNING')
stdout = sys.stdout.getvalue().strip()
self.assertEqual(
self.remove_red_ansi_color(stdout),
f"Cannot create {merge_dir} : [Errno 13] Permission denied: '{merge_dir}'"
)