def test_all_functions_called(self, mock_get_parser, mock_validate_model,
mock_validate_file_size):
"""
Makes sure that all relevant functions are called so that it will parse and validate fully
:return:
"""
# add mock data (as strings) to the function calls that are essential
mock_parser_instance = unittest.mock.MagicMock()
mock_parser_instance.get_sample_sheet.side_effect = [
"mock_sample_sheet"
]
mock_parser_instance.get_sequencing_run.side_effect = [
"mock_sequencing_run"
]
mock_get_parser.side_effect = [mock_parser_instance]
mock_validation_result = unittest.mock.MagicMock()
mock_validation_result.is_valid.side_effect = [True, True]
mock_validate_model.side_effect = [mock_validation_result]
mock_validate_file_size.side_effect = [mock_validation_result]
res = parsing_handler.parse_and_validate("mock_directory")
# verify that the functions were called the mock data we set up
mock_parser_instance.get_sample_sheet.assert_called_once_with(
"mock_directory")
mock_parser_instance.get_sequencing_run.assert_called_once_with(
"mock_sample_sheet")
mock_validate_model.assert_called_once_with("mock_sequencing_run")
mock_validate_file_size.assert_called_once_with("mock_sequencing_run")
self.assertEqual(res, "mock_sequencing_run")
def run(self):
"""
This runs when the threads start call is done
:return:
"""
try:
status = parsing_handler.get_run_status(self._directory)
seq_run = parsing_handler.parse_and_validate(self._directory)
if self._parse_as_partial:
seq_run = upload_helpers.set_uploaded_samples_to_skip(
seq_run, status.get_sample_status_list())
self._run = seq_run
except exceptions.DirectoryError as e:
# Directory was not valid for some reason
full_error = "GUI: ERROR! An error occurred with directory '{}', with message: {}".format(
e.directory, e.message)
logging.error(full_error)
self._error = e.message
self._run = None
except exceptions.ValidationError as e:
# Sequencing Run / SampleSheet was not valid for some reason
error_msg = "GUI: ERROR! Errors occurred during validation with message: {}".format(
e.message)
logging.error(error_msg)
error_list_msg = "GUI: Error list: " + pformat(
e.validation_result.error_list)
logging.error(error_list_msg)
full_error = "Error: " + e.message + "\nError List:\n"
for err in e.validation_result.error_list:
full_error = full_error + str(err) + "\n"
self._error = full_error
self._run = None
except exceptions.SampleSheetError as e:
# SampleSheet was not valid for some reason
error_msg = "GUI: ERROR! Errors occurred during parsing with message: {}".format(
e.message)
logging.error(error_msg)
self._error = "Errors occurred during parsing `{}` with message: {}".format(
e.errors, e.message)
self._run = None
except exceptions.SequenceFileError as e:
# Sequence Files were invalid for some reason
full_error = "GUI: ERROR! An error occurred while parsing: {}".format(
e.message)
logging.error(full_error)
self._error = e.message
self._run = None
except Exception as e:
# Some other error occurred
full_error = "GUI: ERROR! An unknown error occurred while parsing: {}".format(
str(e))
logging.error(full_error)
self._error = "ERROR! An error occurred while parsing: {}".format(
str(e))
self._run = None
pass
def test_invalid_sequencing_run(self, mock_get_parser, mock_validate):
"""
Check that an exception is thrown when a given SequencingRun is given
:return:
"""
# add mock data (as strings) to the function calls that are essential
mock_parser_instance = unittest.mock.MagicMock()
mock_parser_instance.get_sample_sheet.side_effect = [
"mock_sample_sheet"
]
mock_parser_instance.get_sequencing_run.side_effect = [
"mock_sequencing_run"
]
mock_get_parser.side_effect = [mock_parser_instance]
mock_validation_result = unittest.mock.MagicMock()
mock_validation_result.is_valid.side_effect = [False]
mock_validate.side_effect = [mock_validation_result]
# make sure the invalid sequencing run raises a ValidationError
with self.assertRaises(parsers.exceptions.ValidationError):
parsing_handler.parse_and_validate("mock_directory")