def test_missmatched_checksum_should_log_error(self, mock: MagicMock):
# Given
secure_key = 'uuid'
entity_type = 'run_experiment'
index = f'{entity_type}1'
file_name = 'file_name.extension1.ex2'
expected_checksum = 'checksum'
wrong_checksum = 'not-checksum'
mock.return_value = f"{file_name},{expected_checksum}"
# When
validator = UploadValidator(secure_key)
attributes = {
'uploaded_file_1': file_name,
'uploaded_file_1_checksum': wrong_checksum
}
entity = Entity(entity_type, index, attributes)
validator.validate_entity(entity)
# Then
expected_errors = {
'uploaded_file_1_checksum': [
f'The checksum found on drag-and-drop {expected_checksum} does not match: {wrong_checksum}'
]
}
self.assertDictEqual(expected_errors, entity.get_errors())
def map(self, entity_type: str, index: str, attributes: dict) -> Entity:
if entity_type in self.__map and index in self.__map[entity_type]:
entity = self.__handle_collision(entity_type, index, attributes)
else:
entity = Entity(entity_type, index, attributes)
self.__map.setdefault(entity_type, {})[index] = entity
return entity
def test_valid_sample_name_should_not_return_error(self):
# Given
sample_attributes = {
'scientific_name': 'Severe acute respiratory syndrome coronavirus 2'
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value=self.valid_sarscov2)
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertFalse(sample.has_errors())
self.assertDictEqual({}, sample.get_errors())
def test_valid_sample_tax_id_should_not_return_error(self):
# Given
sample_attributes = {
'tax_id': '2697049'
}
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value=self.valid_sarscov2)
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertFalse(sample.has_errors())
self.assertDictEqual({}, sample.get_errors())
def test_invalid_name_should_return_error(self):
sample_attributes = {'scientific_name': 'Lorem Ipsum'}
error = 'Not valid scientific_name: Lorem Ipsum.'
expected_error = {
'scientific_name': [error]
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value={'error': error})
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_error, sample.get_errors())
def test_invalid_tax_id_should_return_error(self):
# Given
sample_attributes = {'tax_id': '999999999999'}
error = 'Not valid tax_id: 999999999999.'
expected_error = {
'tax_id': [error]
}
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value={'error': error})
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_error, sample.get_errors())
def test_missing_file_should_log_error(self, mock: MagicMock):
# Given
entity_type = 'run_experiment'
index = f'{entity_type}1'
mock.return_value = f"file_name.extension1.ex2,checksum"
validator = UploadValidator('uuid')
entity = Entity(entity_type, index,
{'uploaded_file_1': 'missing.file'})
expected_errors = {
'uploaded_file_1':
['File has not been uploaded to drag-and-drop: missing.file']
}
# When
validator.validate_entity(entity)
# Then
self.assertDictEqual(expected_errors, entity.get_errors())
def test_validation_with_second_file_present(self, mock: MagicMock):
# Given
secure_key = 'uuid'
entity_type = 'run_experiment'
index = f'{entity_type}1'
mock.return_value = f"first-file,first-checksum\n" \
f"second-file,second-checksum"
# When
validator = UploadValidator(secure_key)
attributes = {
'uploaded_file_1': 'first-file',
'uploaded_file_1_checksum': 'first-checksum',
'uploaded_file_2': 'second-file',
'uploaded_file_2_checksum': 'second-checksum',
}
entity = Entity(entity_type, index, attributes)
validator.validate_entity(entity)
# Then
self.assertDictEqual({}, entity.get_errors())
def test_validation_should_edit_file_attributes(self, mock: MagicMock):
# Given
secure_key = 'uuid'
entity_type = 'run_experiment'
index = f'{entity_type}1'
file_name = 'file_name.extension1.ex2'
checksum = 'checksum'
mock.return_value = f"{file_name},{checksum}"
# When
validator = UploadValidator(secure_key)
attributes = {'uploaded_file_1': file_name}
entity = Entity(entity_type, index, attributes)
validator.validate_entity(entity)
# Then
expected_attributes = {
'uploaded_file_1': file_name,
'uploaded_file_1_checksum': checksum,
}
self.assertDictEqual(expected_attributes, entity.attributes)
def test_passed_bio_study_entity_returns_correct_json_representative(self):
bio_study_attributes = {
"study_accession": "PRJEB12345",
"study_alias": "SARS-CoV-2 genomes 123ABC alias",
"email_address": "*****@*****.**",
"center_name": "EBI",
'study_name': 'SARS-CoV-2 genomes 123ABC name',
"short_description": "test short description",
"abstract": "test abstract",
"release_date": "2020-08-21"
}
bio_study_entity = Entity(entity_type="study",
index=bio_study_attributes["study_alias"],
attributes=bio_study_attributes)
expected_payload = self.__get_expected_payload(bio_study_entity)
bio_study_json_payload = BioStudyConverter.convert_study(
bio_study_entity)
self.assertDictEqual(expected_payload, bio_study_json_payload)
def test_inconsistent_sample_should_return_error(self):
# Given
sample_attributes = {
'scientific_name': 'Severe acute respiratory syndrome coronavirus 2',
'tax_id': '9606'
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value=self.valid_sarscov2)
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value=self.valid_human)
consistent_error = 'Information is not consistent between taxId: 9606 and scientificName: Severe acute respiratory syndrome coronavirus 2'
expected_errors = {
'scientific_name': [consistent_error],
'tax_id': [consistent_error]
}
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_errors, sample.get_errors())
def test_validation_with_second_file_missing(self, mock: MagicMock):
# Given
secure_key = 'uuid'
entity_type = 'run_experiment'
index = f'{entity_type}1'
mock.return_value = f"first-file,first-checksum"
# When
validator = UploadValidator(secure_key)
attributes = {
'uploaded_file_1': 'first-file',
'uploaded_file_2': 'second-file'
}
entity = Entity(entity_type, index, attributes)
validator.validate_entity(entity)
# Then
expected_errors = {
'uploaded_file_2':
['File has not been uploaded to drag-and-drop: second-file']
}
self.assertDictEqual(expected_errors, entity.get_errors())
def test_invalid_sample_name_should_return_error(self):
# Given
sample_attributes = {
'scientific_name': 'Lorem Ipsum',
'tax_id': '2697049'
}
error = 'Not valid scientific_name: Lorem Ipsum.'
consistent_error = 'Information is not consistent between taxId: 2697049 and scientificName: Lorem Ipsum'
expected_errors = {
'scientific_name': [error, consistent_error],
'tax_id': [consistent_error]
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value={'error': error})
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value=self.valid_sarscov2)
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_errors, sample.get_errors())
