def test_post_event_no_plate_map_data(
app,
client,
biosero_auth_headers,
clear_events,
mocked_rabbit_channel,
run_id,
mocked_responses,
cherrytrack_mock_run_info,
):
with app.app_context():
with patch("lighthouse.hooks.events.uuid4",
return_value=int_to_uuid(1)):
with patch("lighthouse.classes.messages.warehouse_messages.uuid4",
side_effect=[int_to_uuid(2)]):
with patch(
"lighthouse.classes.events.PlateEvent.message_timestamp",
"mytime",
):
response = client.post(
"/events",
data={
"automation_system_run_id": 3,
"barcode": "plate_123",
"event_type":
Biosero.EVENT_SOURCE_NO_PLATE_MAP_DATA,
},
headers=biosero_auth_headers,
)
# Test creates the event
assert response.status_code == HTTPStatus.CREATED
mocked_rabbit_channel.basic_publish.assert_called_with(
exchange="lighthouse.test.examples",
routing_key=
f"test.event.{ Biosero.EVENT_SOURCE_NO_PLATE_MAP_DATA }",
body='{"event": {"uuid": "' + int_to_uuid(1) +
('", "event_type": "' +
Biosero.EVENT_SOURCE_NO_PLATE_MAP_DATA + '", '
'"occured_at": "mytime", "user_identifier": "user1", "subjects": '
'[{"role_type": "robot", "subject_type": "robot", "friendly_name": "CPA", '
'"uuid": "e465f4c6-aa4e-461b-95d6-c2eaab15e63f"}, '
'{"role_type": "run", "subject_type": "run", "friendly_name": 3, '
'"uuid": "' + int_to_uuid(2) + '"}], '
'"metadata": {"source_plate_barcode": "plate_123"}}, "lims": "LH_TEST"}'
),
)
# The record is there
event = get_event_with_uuid(int_to_uuid(1))
assert event is not None
# And it does not have errors
assert event[FIELD_EVENT_ERRORS] is None
def test_post_event_partially_completed_with_error_accessing_cherrytrack_for_samples_info(
app,
client,
biosero_auth_headers,
source_plates,
run_id,
clear_events,
source_barcode,
destination_barcode,
mocked_rabbit_channel,
mocked_responses,
cherrytrack_mock_source_plates,
):
with app.app_context():
with patch(
"lighthouse.hooks.events.uuid4",
side_effect=[
int_to_uuid(1),
int_to_uuid(2),
int_to_uuid(3),
int_to_uuid(4)
],
):
with patch(
"lighthouse.classes.events.PlateEvent.message_timestamp",
return_value="mytime",
):
response = client.post(
"/events",
data={
"automation_system_run_id": run_id,
"barcode": source_barcode,
"event_type": Biosero.EVENT_SOURCE_COMPLETED,
},
headers=biosero_auth_headers,
)
# Test creates the event
assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR
# However the message is not published
mocked_rabbit_channel.basic_publish.assert_not_called()
# But the record is there
event = get_event_with_uuid(int_to_uuid(1))
assert event is not None
# And it has errors
assert event[FIELD_EVENT_ERRORS] == {
"base": [
"Response from Cherrytrack is not OK: One error,Another error"
]
}
def test_set_errors_event_updates_correctly(app, plate_events):
with app.app_context():
plate_events, _ = plate_events
errorObj = {
FIELD_EVENT_USER_ID:
["The user does not exist", "The user id format is wrong"]
}
result = set_errors_to_event(plate_events[0][FIELD_EVENT_UUID],
errorObj)
assert result is True
assert get_event_with_uuid(
plate_events[0][FIELD_EVENT_UUID])[FIELD_EVENT_ERRORS] == errorObj
def test_post_event_partially_completed_with_validation_error_after_storing_in_mongo(
app, client, biosero_auth_headers, clear_events,
mocked_rabbit_channel):
with app.app_context():
with patch(
"lighthouse.hooks.events.uuid4",
side_effect=[
int_to_uuid(1),
int_to_uuid(2),
int_to_uuid(3),
int_to_uuid(4)
],
):
with patch(
"lighthouse.classes.events.PlateEvent.message_timestamp",
return_value="mytime",
):
response = client.post(
"/events",
data={
"automation_system_run_id": 3,
"barcode": "a Barcode",
"event_type": Biosero.EVENT_SOURCE_COMPLETED,
},
headers=biosero_auth_headers,
)
# Test creates the event
assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR
# However the message is not published
mocked_rabbit_channel.basic_publish.assert_not_called()
# But the record is there
event = get_event_with_uuid(int_to_uuid(1))
assert event is not None
# And it has errors
assert event[FIELD_EVENT_ERRORS] == {
"plate_barcode":
["'barcode' should not contain any whitespaces"],
"source_plate_uuid":
["'barcode' should not contain any whitespaces"],
"samples_picked_from_source":
["'barcode' should not contain any whitespaces"],
}
def test_post_event_partially_completed(
app,
client,
biosero_auth_headers,
clear_events,
mocked_rabbit_channel,
source_plates,
run_id,
mocked_responses,
cherrytrack_mock_run_info,
samples_from_cherrytrack_into_mongo,
centres,
destination_barcode,
mlwh_samples_in_cherrytrack,
cherrytrack_mock_destination_plate,
cherrytrack_destination_plate_response,
baracoda_mock_barcodes_group,
baracoda_mock_responses,
):
with app.app_context():
with patch(
"lighthouse.hooks.events.uuid4",
side_effect=[int_to_uuid(1)],
):
with patch(
"lighthouse.classes.messages.warehouse_messages.uuid4",
side_effect=[
int_to_uuid(2),
int_to_uuid(3),
int_to_uuid(4),
int_to_uuid(5)
],
):
with patch(
"lighthouse.classes.events.PlateEvent.message_timestamp",
"mytime",
):
mock_response_send_ss = MagicMock()
mock_response_send_ss.ok = True
with patch(
"lighthouse.classes.messages.sequencescape_messages.SequencescapeMessage._send_to_ss",
return_value=mock_response_send_ss,
) as send_to_ss:
response = client.post(
"/events",
data={
"automation_system_run_id":
3,
"barcode":
"HT-1234",
"event_type":
Biosero.
EVENT_ERROR_RECOVERED_DESTINATION_COMPLETED,
},
headers=biosero_auth_headers,
)
# Test creates the event
assert response.status_code == HTTPStatus.CREATED
event_message = ('{"event": {"uuid": "' + int_to_uuid(
1
) + (
'", "event_type": "' +
Biosero.EVENT_ERROR_RECOVERED_DESTINATION_COMPLETED
+ '", '
'"occured_at": "mytime", "user_identifier": "user1", "subjects": '
'[{"role_type": "sample", "subject_type": "sample", "friendly_name": '
'"aRootSampleId1__plate_123_A01__centre_1__Positive", "uuid": "aLighthouseUUID1"}, '
'{"role_type": "sample", "subject_type": "sample", "friendly_name": '
'"aRootSampleId3__plate_123_A03__centre_1__Positive", "uuid": "aLighthouseUUID3"}, '
'{"role_type": "control", "subject_type": "sample", "friendly_name": '
'"positive control: DN1234_A1", '
'"uuid": "' + int_to_uuid(2) + '"}, '
'{"role_type": "control", "subject_type": "sample", "friendly_name": '
'"negative control: DN1234_A1", '
'"uuid": "' + int_to_uuid(3) + '"}, '
'{"role_type": "cherrypicking_source_labware", "subject_type": "plate", '
'"friendly_name": "plate_123", "uuid": "a17c38cd-b2df-43a7-9896-582e7855b4cc"}, '
'{"role_type": "cherrypicking_destination_labware", "subject_type": "plate", '
'"friendly_name": "HT-1234", "uuid": "' +
int_to_uuid(4) + '"}, '
'{"role_type": "robot", "subject_type": "robot", "friendly_name": "CPA", '
'"uuid": "e465f4c6-aa4e-461b-95d6-c2eaab15e63f"}, '
'{"role_type": "run", "subject_type": "run", "friendly_name": 3, '
'"uuid": "' + int_to_uuid(5) + '"}'
'], "metadata": {}}, "lims": "LH_TEST"}'))
mocked_rabbit_channel.basic_publish.assert_called_with(
exchange="lighthouse.test.examples",
routing_key=
f"test.event.{ Biosero.EVENT_ERROR_RECOVERED_DESTINATION_COMPLETED }",
body=event_message,
)
ss_message = (
'{"data": {"type": "plates", "attributes": {"barcode": "HT-1234", '
'"purpose_uuid": "ss_uuid_plate_purpose", '
'"study_uuid": "ss_uuid_study", "wells": '
'{"H08": {"content": {"name": "plate_123_A01", "sample_description": "aRootSampleId1", '
'"supplier_name": "COGUK1", "phenotype": "positive", "uuid": "aLighthouseUUID1"}}, '
'"H12": {"content": {"name": "plate_123_A03", "sample_description": "aRootSampleId3", '
'"supplier_name": "COGUK2", '
'"phenotype": "positive", "uuid": "aLighthouseUUID3"}}, '
'"E10": {"content": {"supplier_name": "positive control: DN1234_A1", "control": true, '
'"control_type": "positive"}}, '
'"E11": {"content": {"supplier_name": "negative control: DN1234_A1", "control": true, '
'"control_type": "negative"}}}, '
'"events": []}}}')
send_to_ss.assert_called_once_with(
ss_url=
f"{app.config['SS_URL']}/api/v2/heron/plates",
headers={
"X-Sequencescape-Client-Id":
app.config["SS_API_KEY"],
"Content-type":
"application/json",
},
data=ss_message,
)
# The record is there
event = get_event_with_uuid(int_to_uuid(1))
assert event is not None
# And it does not have errors
assert event[FIELD_EVENT_ERRORS] is None
def test_post_event_partially_completed(
app,
client,
lighthouse_ui_auth_headers,
clear_events,
mocked_rabbit_channel,
source_plates,
run_id,
mocked_responses,
cherrytrack_mock_run_info,
samples_from_cherrytrack_into_mongo,
centres,
destination_barcode,
mlwh_samples_in_cherrytrack,
cherrytrack_mock_destination_plate,
cherrytrack_destination_plate_response,
baracoda_mock_barcodes_group,
baracoda_mock_responses,
):
with app.app_context():
with patch(
"lighthouse.hooks.events.uuid4",
side_effect=[int_to_uuid(1)],
):
with patch(
"lighthouse.classes.messages.warehouse_messages.uuid4",
side_effect=[
int_to_uuid(2),
int_to_uuid(3),
int_to_uuid(4),
int_to_uuid(5)
],
):
with patch(
"lighthouse.classes.events.PlateEvent.message_timestamp",
"mytime",
):
failure_type = Beckman.get_failure_types()[0].get("type")
assert failure_type is not None
response = client.post(
"/events",
data={
"barcode": "HT-1234",
"event_type": Biosero.EVENT_DESTINATION_FAILED,
"failure_type": failure_type,
"user_id": "user1",
},
headers=lighthouse_ui_auth_headers,
)
# Test creates the event
assert response.status_code == HTTPStatus.CREATED
event_message = ('{"event": {"uuid": "' + int_to_uuid(1) + (
'", "event_type": "' +
Biosero.EVENT_DESTINATION_FAILED + '", '
'"occured_at": "mytime", "user_identifier": "user1", "subjects": '
'[{"role_type": "sample", "subject_type": "sample", "friendly_name": '
'"aRootSampleId1__plate_123_A01__centre_1__Positive", "uuid": "aLighthouseUUID1"}, '
'{"role_type": "sample", "subject_type": "sample", "friendly_name": '
'"aRootSampleId3__plate_123_A03__centre_1__Positive", "uuid": "aLighthouseUUID3"}, '
'{"role_type": "control", "subject_type": "sample", "friendly_name": '
'"positive control: DN1234_A1", '
'"uuid": "' + int_to_uuid(2) + '"}, '
'{"role_type": "control", "subject_type": "sample", "friendly_name": '
'"negative control: DN1234_A1", '
'"uuid": "' + int_to_uuid(3) + '"}, '
'{"role_type": "cherrypicking_source_labware", "subject_type": "plate", '
'"friendly_name": "plate_123", "uuid": "a17c38cd-b2df-43a7-9896-582e7855b4cc"}, '
'{"role_type": "cherrypicking_destination_labware", "subject_type": "plate", '
'"friendly_name": "HT-1234", "uuid": "' +
int_to_uuid(4) + '"}, '
'{"role_type": "robot", "subject_type": "robot", "friendly_name": "CPA", '
'"uuid": "e465f4c6-aa4e-461b-95d6-c2eaab15e63f"}, '
'{"role_type": "run", "subject_type": "run", "friendly_name": 3, '
'"uuid": "' + int_to_uuid(5) + '"}'
'], "metadata": {"failure_type": "' + failure_type +
'"}}, "lims": "LH_TEST"}'))
mocked_rabbit_channel.basic_publish.assert_called_with(
exchange="lighthouse.test.examples",
routing_key=
f"test.event.{ Biosero.EVENT_DESTINATION_FAILED }",
body=event_message,
)
# The record is there
event = get_event_with_uuid(int_to_uuid(1))
assert event is not None
# And it does not have errors
assert event[FIELD_EVENT_ERRORS] is None
def test_post_event_partially_completed(
app,
client,
biosero_auth_headers,
clear_events,
mocked_rabbit_channel,
source_plates,
run_id,
source_barcode,
destination_barcode,
mocked_responses,
cherrytrack_mock_run_info,
cherrytrack_mock_source_plates,
samples_from_cherrytrack_into_mongo,
):
with app.app_context():
with patch(
"lighthouse.hooks.events.uuid4",
side_effect=[int_to_uuid(1)],
):
with patch("lighthouse.classes.messages.warehouse_messages.uuid4",
side_effect=[int_to_uuid(2)]):
with patch(
"lighthouse.classes.events.PlateEvent.message_timestamp",
"mytime",
):
with patch(
"lighthouse.classes.services.labwhere.set_locations_in_labwhere"
) as mocked_labwhere:
response = client.post(
"/events",
data={
"automation_system_run_id": run_id,
"barcode": source_barcode,
"event_type": Biosero.EVENT_SOURCE_COMPLETED,
},
headers=biosero_auth_headers,
)
# Test creates the event
assert response.status_code == HTTPStatus.CREATED
mocked_rabbit_channel.basic_publish.assert_called_with(
exchange="lighthouse.test.examples",
routing_key=
f"test.event.{ Biosero.EVENT_SOURCE_COMPLETED }",
body='{"event": {"uuid": "' + int_to_uuid(1) +
('", "event_type": "' +
Biosero.EVENT_SOURCE_COMPLETED + '", '
'"occured_at": "mytime", "user_identifier": "user1", "subjects": '
'[{"role_type": "sample", "subject_type": "sample", "friendly_name": '
'"aRootSampleId1__plate_123_A01__centre_1__Positive", "uuid": "aLighthouseUUID1"}, '
'{"role_type": "sample", "subject_type": "sample", "friendly_name": '
'"aRootSampleId3__plate_123_A03__centre_1__Positive", "uuid": "aLighthouseUUID3"}, '
'{"role_type": "cherrypicking_source_labware", "subject_type": "plate", '
'"friendly_name": "plate_123", "uuid": "a17c38cd-b2df-43a7-9896-582e7855b4cc"}, '
'{"role_type": "robot", "subject_type": "robot", "friendly_name": "CPA", '
'"uuid": "e465f4c6-aa4e-461b-95d6-c2eaab15e63f"}, '
'{"role_type": "run", "subject_type": "run", "friendly_name": 3, '
'"uuid": "' + int_to_uuid(2) + '"}'
'], "metadata": {}}, "lims": "LH_TEST"}'),
)
mocked_labwhere.assert_called_once_with(
labware_barcodes=[source_barcode],
location_barcode=app.
config["LABWHERE_DESTROYED_BARCODE"],
user_barcode="CPA",
)
# The record is there
event = get_event_with_uuid(int_to_uuid(1))
assert event is not None
# And it does not have errors
assert event[FIELD_EVENT_ERRORS] is None
def get_event_wih_uuid_finds_none_event(app, plate_events):
with app.app_context():
plate_events, _ = plate_events
assert get_event_with_uuid("11111") is None
def get_event_with_uuid_finds_event(app, plate_events):
with app.app_context():
plate_events, _ = plate_events
assert get_event_with_uuid(
plate_events[0][FIELD_EVENT_UUID]) == plate_events[0]