def test__admin__is_admin__is_accessible(client, faker):
user = faker.get_test_user(is_admin=True)
login(client, faker, user)
out = AdminCustomView(User, db.session)
assert out.is_accessible()
def test__ui_demographics_define_columns_post__not_owner(client, faker):
user = login(client, faker)
headers = faker.column_headers(10)
dr = do_create_request(client, faker, user, headers=headers)
logout(client)
user2 = login(client, faker)
response = client.post(
url_for('ui.demographics_define_columns', id=dr.id, _external=True),
data={
'uhl_system_number_column_id': 0,
'nhs_number_column_id': 0,
'family_name_column_id': 0,
'given_name_column_id': 0,
'gender_column_id': 0,
'dob_column_id': 0,
'postcode_column_id': 0,
},
)
assert response.status_code == 403
_remove_files(dr)
def test__get_value_from_all_arguments__get(client, faker):
login(client, faker)
field_name = 'hello'
value = 'jim'
resp = client.get(
url_for('json_requests', field_name=field_name, hello=value))
assert resp.get_json()['result'] == value
def test__get_value_from_all_arguments__post_json(client, faker):
login(client, faker)
field_name = 'bread'
value = 'cheese'
resp = client.post_json(url_for('json_requests', field_name=field_name),
data={field_name: value})
assert resp.get_json()['result'] == value
def test__ui_demographics_submit_post__not_owner(client, faker):
user = login(client, faker)
dr = do_create_request(client, faker, user)
do_define_columns_post(client, dr.id, dr.columns[0], dr.columns[1],
dr.columns[2], dr.columns[3], dr.columns[4],
dr.columns[5], dr.columns[6])
logout(client)
user2 = login(client, faker)
response = do_submit(client, dr.id)
assert response.status_code == 403
_remove_files(dr)
def test__ui_demographics_define_columns_get__not_owner(client, faker):
user = login(client, faker)
headers = faker.column_headers(10)
dr = do_create_request(client, faker, user, headers=headers)
logout(client)
user2 = login(client, faker)
response = client.get(
url_for('ui.demographics_define_columns', id=dr.id, _external=True))
assert response.status_code == 403
_remove_files(dr)
def test__boilerplate__pages(client, faker, item_count):
user = login(client, faker)
the_fields = [faker.get_test_field() for _ in range(item_count)]
assert__page_navigation(client, url_for('pages_of_fields',
_external=False), item_count)
def test__extract_data__normal(client, faker, extension, row_count, mock_schedule_lookup_tasks, mock_log_exception):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u, row_count=row_count, extension=extension)
dr = dth.get_demographics_request__data_extraction()
extract_data(dr.id)
actual = DemographicsRequest.query.get(dr.id)
mock_schedule_lookup_tasks.assert_called_once_with(dr.id)
mock_log_exception.assert_not_called()
assert len(actual.data) == row_count
assert actual.data_extracted == True
assert actual.data_extracted_datetime is not None
for e, a in zip(dth._person_details, actual.data):
assert e['uhl_system_number'] == a.uhl_system_number
assert e['nhs_number'] == a.nhs_number
assert e['family_name'] == a.family_name
assert e['given_name'] == a.given_name
assert e['gender'] == a.gender
assert parse_date(e['date_of_birth']) == parse_date(a.dob)
assert e['postcode'] == a.postcode
_remove_files(dr)
def test__extract_pre_pmi_details__next_processed(client, faker,
mock_pmi_details,
mock_schedule_lookup_tasks):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u, row_count=2)
dr = dth.get_demographics_request__pre_pmi_lookup()
dr.data[0].pmi_pre_processed_datetime = datetime.datetime.utcnow()
db.session.add(dr.data[0])
db.session.commit()
expected = PmiData(**faker.pmi_details(1))
mock_pmi_details.return_value = expected
extract_pre_pmi_details(dr.id)
actual = DemographicsRequest.query.get(dr.id)
assert actual.pmi_data_pre_completed_datetime is None
assert sum(1 for d in actual.data
if d.pmi_pre_processed_datetime is not None) == 2
assert expected == actual.data[1].pmi_data
assert len(actual.data[0].messages) == 0
mock_schedule_lookup_tasks.assert_called_once_with(dr.id)
_remove_files(dr)
def test__extract_post_pmi_details__pmi_exception(client, faker,
mock_pmi_details,
mock_schedule_lookup_tasks):
ERROR_MESSAGE = 'An Exception'
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker,
user=u,
row_count=1,
find_pre_pmi_details=False)
dr = dth.get_demographics_request__post_pmi_lookup()
mock_pmi_details.side_effect = PmiException(ERROR_MESSAGE)
extract_post_pmi_details(dr.id)
actual = DemographicsRequest.query.get(dr.id)
assert actual.pmi_data_post_completed_datetime is None
assert sum(1 for d in actual.data
if d.pmi_post_processed_datetime is not None) == 1
assert actual.data[0].pmi_data is None
assert len(actual.data[0].messages) == 1
m = actual.data[0].messages[0]
assert m.type == 'error'
assert m.source == 'pmi_details'
assert m.scope == 'pmi_details'
assert m.message == ERROR_MESSAGE
mock_schedule_lookup_tasks.assert_called_once_with(dr.id)
_remove_files(dr)
def test__extract_post_pmi_details__invalid_uhl_system_number(
client, faker, mock_pmi_details, mock_schedule_lookup_tasks):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker,
user=u,
row_count=1,
find_pre_pmi_details=False)
dr = dth.get_demographics_request__post_pmi_lookup()
dr.data[0].uhl_system_number = faker.invalid_uhl_system_number()
db.session.add(dr.data[0])
db.session.commit()
expected = PmiData(**faker.pmi_details(1))
mock_pmi_details.return_value = expected
extract_post_pmi_details(dr.id)
actual = DemographicsRequest.query.get(dr.id)
assert actual.pmi_data_post_completed_datetime is None
assert sum(1 for d in actual.data
if d.pmi_post_processed_datetime is not None) == 1
assert expected == actual.data[0].pmi_data
assert len(actual.data[0].messages) == 1
m = actual.data[0].messages[0]
assert m.type == 'warning'
assert m.source == 'pmi_details'
assert m.scope == 'uhl_system_number'
assert m.message == f'Invalid format {faker.invalid_uhl_system_number()}'
mock_schedule_lookup_tasks.assert_called_once_with(dr.id)
_remove_files(dr)
def test__process_demographics_request_data__data_has_error(client, faker, mock_schedule_lookup_tasks, mock_spine_lookup, mock_log_exception):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u, row_count=1)
dr = dth.get_demographics_request__spine_lookup()
db.session.add(DemographicsRequestDataMessage(
demographics_request_data=dr.data[0],
type='error',
source='TEST',
scope='DATA',
message='A message',
))
db.session.commit()
process_demographics_request_data(dr.id)
mock_spine_lookup.assert_called_once_with(dr.data[0])
mock_schedule_lookup_tasks.assert_called_once_with(dr.id)
mock_log_exception.assert_not_called()
actual = DemographicsRequest.query.get(dr.id)
assert actual.lookup_completed_datetime is None
assert actual.data[0].processed_datetime is not None
_remove_files(dr)
def test__spine_lookup__spine_exception(client, faker,
mock_get_spine_parameters,
mock_get_demographics_from_nhs_number,
mock_get_demographics_from_search,
exception_class, message_type):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u)
dr = dth.get_demographics_request__spine_lookup()
drd = dr.data[0]
params = SpineParameters()
params.nhs_number = drd.nhs_number
params.dob = drd.dob
mock_get_spine_parameters.return_value = params
mock_get_demographics_from_nhs_number.side_effect = exception_class
spine_lookup(drd)
assert drd.response is None
assert len(drd.messages) == 1
assert drd.messages[0].type == message_type
assert drd.messages[0].source == 'spine'
assert drd.messages[0].scope == 'request'
_remove_files(dr)
def test__spine_lookup__no_parameters(client, faker, mock_get_spine_parameters,
mock_get_demographics_from_nhs_number,
mock_get_demographics_from_search):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u)
dr = dth.get_demographics_request__spine_lookup()
drd = dr.data[0]
params = SpineParameters()
mock_get_spine_parameters.return_value = params
mock_get_demographics_from_search.return_value = spine_response_full
spine_lookup(drd)
mock_get_demographics_from_search.assert_not_called()
mock_get_demographics_from_nhs_number.assert_not_called()
assert drd.response is None
assert len(drd.messages) == 1
assert drd.messages[0].type == 'error'
assert drd.messages[0].source == 'validation'
assert drd.messages[0].scope == 'request'
assert drd.messages[
0].message == 'Not enough values to perform Spine lookup'
_remove_files(dr)
def test__spine_lookup__search_no_gender(client, faker,
mock_get_spine_parameters,
mock_get_demographics_from_nhs_number,
mock_get_demographics_from_search):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u)
dr = dth.get_demographics_request__spine_lookup()
drd = dr.data[0]
params = SpineParameters()
params.nhs_number = ''
params.dob = drd.dob
params.family_name = drd.family_name
params.given_name = drd.given_name
params.gender = None
params.postcode = drd.postcode
mock_get_spine_parameters.return_value = params
mock_get_demographics_from_search.return_value = spine_response_full
spine_lookup(drd)
mock_get_demographics_from_search.assert_not_called()
mock_get_demographics_from_nhs_number.assert_not_called()
_remove_files(dr)
def test__label_print__requires_id_entry(client, faker):
user = login(client, faker)
faker.add_all_studies(user)
pack = LabelPack.query.filter_by(type='GoDcmPack').one()
resp = client.get(
_url(
referrer='study',
study_id=pack.study_id,
pack_name=pack.type,
count=1,
))
assert__redirect(
resp,
'ui.label_print_definition',
referrer='study',
study_id=pack.study_id,
pack_name=pack.type,
count=1,
)
assert PseudoRandomId.query.join(PseudoRandomIdProvider).filter_by(
prefix=GO_DCM_ID_TYPE_PARTICIPANT).count() == 0
def test__extract_data__missing_columns(client, faker, column_headings, extension, mock_schedule_lookup_tasks, mock_log_exception):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u, extension=extension, column_headings=column_headings)
dr = dth.get_demographics_request__data_extraction()
extract_data(dr.id)
actual = DemographicsRequest.query.get(dr.id)
mock_schedule_lookup_tasks.assert_called_once_with(dr.id)
mock_log_exception.assert_not_called()
assert len(actual.data) == 1
assert actual.data_extracted == True
assert actual.data_extracted_datetime is not None
for e, a in zip(dth.get_input_details(), actual.data):
assert e.get('uhl_system_number', '') == a.uhl_system_number
assert e.get('nhs_number', '') == a.nhs_number
assert e.get('family_name', '') == a.family_name
assert e.get('given_name', '') == a.given_name
assert e.get('gender', '') == a.gender
assert parse_date(e.get('date_of_birth', '')) == parse_date(a.dob)
assert e.get('postcode', '') == a.postcode
_remove_files(dr)
def test__study_details_uploads_and_complete(client, faker, outstanding,
completed, deleted):
user = login(client, faker)
user2 = faker.get_test_user()
study = faker.get_test_study(owner=user)
# Cycle is used to alternately allocate
# the uploads to a different user
# thus we can test that we can see
# uploads by users other than ourselves
users = cycle([user, user2])
uploads = []
for _ in range(outstanding):
u = faker.get_test_upload(study=study, uploader=next(users))
uploads.append(u)
for _ in range(completed):
u = faker.get_test_upload(study=study,
completed=True,
uploader=next(users))
uploads.append(u)
for _ in range(deleted):
u = faker.get_test_upload(study=study,
deleted=True,
uploader=next(users))
resp = _get(client, _url(study_id=study.id, showCompleted='y'), user,
study)
_assert_response(study, uploads, resp)
def test__boilerplate__search(client, faker):
user = login(client, faker)
resp = get_and_assert_standards(client,
url_for('search'),
user,
has_form=True)
assert__search_html(resp.soup, clear_url=url_for('search'))
def test__get_spine_parameters__no_pmi__valid_except_names(
client, faker, mock_convert_name):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker,
user=u,
find_pre_pmi_details=False)
dr = dth.get_demographics_request__spine_lookup()
drd = dr.data[0]
error_message = 'ABCDEFG'
mock_convert_name.return_value = (error_message, '')
actual = get_spine_parameters(drd)
mock_convert_name.call_count = 2
assert parse_date(actual.dob) == parse_date(drd.dob)
assert actual.family_name == None
assert actual.gender == convert_gender(drd.gender)[1]
assert actual.given_name == None
assert actual.nhs_number == drd.nhs_number
assert actual.postcode == drd.postcode
assert len(actual.warnings) == 2
assert actual.warnings[0].scope == 'family_name'
assert actual.warnings[0].message == error_message
assert actual.warnings[1].scope == 'given_name'
assert actual.warnings[1].message == error_message
_remove_files(dr)
def test__get__requires_login(client, faker):
user = login(client, faker)
dr = do_create_request(client, faker, user)
logout(client)
assert__requires_login(client, _url(id=dr.id, external=False))
def test__get_spine_parameters__with_pmi__valid_except_pmi_postcode(
client, faker, mock_convert_postcode):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u)
dr = dth.get_demographics_request__spine_lookup()
drd = dr.data[0]
error_message = 'ABCDEFG'
mock_convert_postcode.side_effect = [
(None, drd.postcode),
(error_message, ''),
]
actual = get_spine_parameters(drd)
mock_convert_postcode.call_count == 2
assert parse_date(actual.dob) == parse_date(drd.dob)
assert actual.family_name == drd.family_name
assert actual.gender == convert_gender(drd.gender)[1]
assert actual.given_name == drd.given_name
assert actual.nhs_number == drd.nhs_number
assert actual.postcode == drd.postcode
assert len(actual.warnings) == 1
assert actual.warnings[0].scope == 'pmi_postcode'
assert actual.warnings[0].message == error_message
_remove_files(dr)
def test__schedule_lookup_tasks__got_post_pmi(
client,
faker,
mock_process_demographics_request_data,
mock_extract_data,
mock_produce_demographics_result,
mock_extract_pre_pmi_details,
mock_extract_post_pmi_details,
mock_log_exception,
):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u)
dr = dth.get_demographics_request__create_results()
do_lookup_tasks(dr.id)
mock_extract_data.delay.assert_not_called()
mock_extract_pre_pmi_details.delay.assert_not_called()
mock_process_demographics_request_data.delay.assert_not_called()
mock_extract_post_pmi_details.delay.assert_not_called()
mock_produce_demographics_result.delay.assert_called_once_with(dr.id)
mock_log_exception.assert_not_called()
_remove_files(dr)
def test__schedule_lookup_tasks__deleted(
client,
faker,
mock_process_demographics_request_data,
mock_extract_data,
mock_produce_demographics_result,
mock_extract_pre_pmi_details,
mock_extract_post_pmi_details,
mock_log_exception,
):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u)
dr = dth.get_demographics_request__uploaded()
dr.deleted_datetime = datetime.utcnow()
db.session.add(dr)
db.session.commit()
do_lookup_tasks(dr.id)
mock_extract_data.delay.assert_not_called()
mock_extract_pre_pmi_details.delay.assert_not_called()
mock_process_demographics_request_data.delay.assert_not_called()
mock_extract_post_pmi_details.delay.assert_not_called()
mock_produce_demographics_result.delay.assert_not_called()
mock_log_exception.assert_not_called()
_remove_files(dr)
def test__ui_demographics_define_columns_post_404(client, faker):
user = login(client, faker)
response = do_define_columns_post(client, 999, None, None, None, None,
None, None, None)
assert response.status_code == 404
def test__ui_demographics_define_columns_get_404(client, faker):
user = login(client, faker)
response = client.get(
url_for('ui.demographics_define_columns', id=999, _external=True))
assert response.status_code == 404
def test__ui_demographics_define_columns_update(client, faker):
user = login(client, faker)
dr = do_create_request(client, faker, user)
response = do_define_columns_post(client, dr.id, dr.columns[0],
dr.columns[1], dr.columns[2],
dr.columns[3], dr.columns[4],
dr.columns[5], dr.columns[6])
assert response.status_code == 302
assert response.location == url_for('ui.demographics_submit',
id=dr.id,
_external=True)
response = client.get(
url_for('ui.demographics_define_columns', id=dr.id, _external=True))
for i, name in enumerate([
'uhl_system_number_column_id', 'nhs_number_column_id',
'family_name_column_id', 'given_name_column_id',
'gender_column_id', 'dob_column_id', 'postcode_column_id'
]):
select = response.soup.find('select', {'name': name})
assert select is not None
option = select.find('option', {"value": dr.columns[i].id})
assert option is not None
assert 'selected' in option.attrs
_assert_uploaded_file_on_index(client, dr.filename, dr.id,
AWAITING_SUBMISSION)
_remove_files(dr)
def test__spine_lookup__nhs_number(client, faker, mock_get_spine_parameters,
mock_get_demographics_from_nhs_number,
mock_get_demographics_from_search,
warning_count):
u = login(client, faker)
dth = DemographicsTestHelper(faker=faker, user=u)
dr = dth.get_demographics_request__spine_lookup()
drd = dr.data[0]
params = SpineParameters()
params.nhs_number = drd.nhs_number
params.dob = drd.dob
params.family_name = drd.family_name
params.given_name = drd.given_name
params.gender = drd.gender
params.postcode = drd.postcode
for i in range(warning_count):
params.add_warning(
scope=f'scope {i}',
message=f'message {i}',
)
mock_get_spine_parameters.return_value = params
mock_get_demographics_from_nhs_number.return_value = spine_response_full
spine_lookup(drd)
mock_get_demographics_from_nhs_number.assert_called_once_with(
nhs_number=params.nhs_number,
dob=params.dob,
)
mock_get_demographics_from_search.assert_not_called()
assert drd.response is not None
assert drd.response.nhs_number == spine_response_full.nhs_number
assert drd.response.title == spine_response_full.title
assert drd.response.forename == spine_response_full.forename
assert drd.response.middlenames == spine_response_full.middlenames
assert drd.response.lastname == spine_response_full.lastname
assert drd.response.sex == spine_response_full.sex
assert drd.response.postcode == spine_response_full.postcode
assert drd.response.address == spine_response_full.address
assert parse_date(drd.response.date_of_birth) == parse_date(
spine_response_full.date_of_birth)
assert parse_date(drd.response.date_of_death) == parse_date(
spine_response_full.date_of_death)
assert drd.response.is_deceased == spine_response_full.is_deceased
assert drd.response.current_gp_practice_code == spine_response_full.current_gp_practice_code
assert len(drd.messages) == warning_count
for i, w in enumerate(drd.messages):
assert w.type == 'warning'
assert w.source == 'validation'
assert w.scope == f'scope {i}'
assert w.message == f'message {i}'
_remove_files(dr)
def test__study_details_uploads__with_files(client, faker):
user = login(client, faker)
study = faker.get_test_study(owner=user)
uf = faker.get_test_upload_file(study=study)
resp = _get(client, _url(study_id=study.id), user, study)
_assert_response(study, [uf.upload], resp)
def _test_blinding(client, faker, study, expected_blinding_types):
u = login(client, faker)
ids = study.get_blind_ids('hello', u)
db.session.commit()
_assert_ids_created_correctly('hello', ids, expected_blinding_types)
