def test_completion_cluster_error(self):
content = ERROR_MESSAGE
self.mock_log(
os.path.join(self.temp_output, MOCK_GENOME + '_diseased_genome',
SUBCOMMAND.CLUSTER), content)
result = checker.check_completion(self.temp_output)
self.assertEqual(False, result)
def test_completion_validate_error(self):
content = ERROR_MESSAGE
self.mock_log(
os.path.join(self.temp_output, MOCK_GENOME + '_diseased_genome',
SUBCOMMAND.VALIDATE, 'batch-mock-1'), content)
result = checker.check_completion(self.temp_output)
self.assertEqual(False, result)
def test_completion_rerun_dir(self):
content = "IndexError: list index out of range"
log = 'batch-mock-1.log2'
with open(
os.path.join(
os.path.join(self.temp_output,
MOCK_GENOME + '_diseased_genome',
SUBCOMMAND.ANNOTATE, 'batch-mock-1', log)),
'w') as f:
f.write(content)
print(
os.path.join(self.temp_output, MOCK_GENOME + '_diseased_genome',
SUBCOMMAND.ANNOTATE, 'batch-mock-1'))
result = checker.check_completion(self.temp_output)
self.assertEqual(True, result)
def test_completion_empty_dir(self):
temp_output = tempfile.mkdtemp()
result = checker.check_completion(temp_output)
self.assertEqual(False, result)
shutil.rmtree(temp_output)
def test_completion_pairing_error(self):
content = ERROR_MESSAGE
self.mock_log(os.path.join(self.temp_output, SUBCOMMAND.PAIR), content)
result = checker.check_completion(self.temp_output)
self.assertEqual(False, result)
def test_completion_incomplete_dir(self):
shutil.rmtree(os.path.join(self.temp_output, SUBCOMMAND.SUMMARY))
mkdirs(os.path.join(self.temp_output, SUBCOMMAND.SUMMARY))
result = checker.check_completion(self.temp_output)
self.assertEqual(False, result)
def test_completion_invalid_dir(self):
result = checker.check_completion('')
self.assertEqual(False, result)
def test_completion_valid_dir(self):
result = checker.check_completion(self.temp_output)
self.assertEqual(True, result)
