def test_update_mlwh_filtered_positive_fields_raises_with_error_updating_mlwh(config, mlwh_connection):
with patch(
"migrations.helpers.update_filtered_positives_helper.run_mysql_executemany_query",
side_effect=NotImplementedError("Boom!"),
):
with pytest.raises(NotImplementedError):
update_mlwh_filtered_positive_fields(config, [])
def test_update_mlwh_filtered_positive_fields_return_false_with_no_connection(
config):
with patch(
"migrations.helpers.update_filtered_positives_helper.create_mysql_connection"
) as mock_connection:
mock_connection().is_connected.return_value = False
result = update_mlwh_filtered_positive_fields(config, [])
assert result is False
filtered_positive_identifier,
non_cp_pos_pending_samples,
version,
update_timestamp,
)
logger.info("Updated filtered positives")
logger.info("Updating Mongo...")
mongo_updated = update_mongo_filtered_positive_fields(
config, non_cp_pos_pending_samples, version,
update_timestamp)
logger.info("Finished updating Mongo")
if mongo_updated:
logger.info("Updating MLWH...")
mlwh_updated = update_mlwh_filtered_positive_fields(
config, non_cp_pos_pending_samples)
logger.info("Finished updating MLWH")
if not omit_dart and mlwh_updated:
logger.info("Updating DART...")
dart_updated = update_dart_fields(
config, non_cp_pos_pending_samples)
logger.info("Finished updating DART")
else:
logger.warning(
"No non-cherrypicked matching positive samples found, not updating any database"
)
else:
logger.warning(
"No matching positive samples found in Mongo, not updating any database"
)
def test_update_mlwh_filtered_positive_fields_calls_to_update_samples(config, mlwh_connection):
# populate the mlwh database with existing entries
mlwh_samples = [
{
MLWH_MONGODB_ID: "1",
MLWH_COORDINATE: "A1",
MLWH_PLATE_BARCODE: "123",
MLWH_ROOT_SAMPLE_ID: "MCM001",
MLWH_RNA_ID: "AAA123",
MLWH_RESULT: RESULT_VALUE_POSITIVE,
MLWH_FILTERED_POSITIVE: None,
MLWH_FILTERED_POSITIVE_VERSION: None,
MLWH_FILTERED_POSITIVE_TIMESTAMP: None,
},
{
MLWH_MONGODB_ID: "2",
MLWH_COORDINATE: "B1",
MLWH_PLATE_BARCODE: "123",
MLWH_ROOT_SAMPLE_ID: "MCM002",
MLWH_RNA_ID: "BBB123",
MLWH_RESULT: RESULT_VALUE_POSITIVE,
MLWH_FILTERED_POSITIVE: True,
MLWH_FILTERED_POSITIVE_VERSION: "v1.0",
MLWH_FILTERED_POSITIVE_TIMESTAMP: datetime(2020, 4, 23, 14, 40, 8),
},
]
insert_sql = """\
INSERT INTO lighthouse_sample (mongodb_id, root_sample_id, rna_id, plate_barcode, coordinate,
result, filtered_positive, filtered_positive_version, filtered_positive_timestamp)
VALUES (%(mongodb_id)s, %(root_sample_id)s, %(rna_id)s, %(plate_barcode)s, %(coordinate)s,
%(result)s, %(filtered_positive)s, %(filtered_positive_version)s,
%(filtered_positive_timestamp)s)
"""
cursor = mlwh_connection.cursor()
cursor.executemany(insert_sql, mlwh_samples)
cursor.close()
mlwh_connection.commit()
# call to update the database with newly filtered positive entries
update_timestamp = datetime(2020, 6, 23, 14, 40, 8)
mongo_samples = [
{
FIELD_MONGODB_ID: "1",
FIELD_COORDINATE: "A01",
FIELD_PLATE_BARCODE: "123",
FIELD_ROOT_SAMPLE_ID: "MCM001",
FIELD_RNA_ID: "AAA123",
FIELD_FILTERED_POSITIVE: True,
FIELD_FILTERED_POSITIVE_VERSION: "v2.3",
FIELD_FILTERED_POSITIVE_TIMESTAMP: update_timestamp,
},
{
FIELD_MONGODB_ID: "2",
FIELD_COORDINATE: "B01",
FIELD_PLATE_BARCODE: "123",
FIELD_ROOT_SAMPLE_ID: "MCM002",
FIELD_RNA_ID: "BBB123",
FIELD_FILTERED_POSITIVE: False,
FIELD_FILTERED_POSITIVE_VERSION: "v2.3",
FIELD_FILTERED_POSITIVE_TIMESTAMP: update_timestamp,
},
]
result = update_mlwh_filtered_positive_fields(config, mongo_samples) # type: ignore
assert result is True
cursor = mlwh_connection.cursor()
cursor.execute("SELECT COUNT(*) FROM lighthouse_sample")
sample_count = cursor.fetchone()[0]
cursor.execute(
"SELECT filtered_positive, filtered_positive_version, filtered_positive_timestamp FROM "
"lighthouse_sample WHERE mongodb_id = '1'"
)
filtered_positive_sample = cursor.fetchone()
cursor.execute(
"SELECT filtered_positive, filtered_positive_version, filtered_positive_timestamp FROM "
"lighthouse_sample WHERE mongodb_id = '2'"
)
filtered_negative_sample = cursor.fetchone()
cursor.close()
assert sample_count == 2
assert filtered_positive_sample[0]
assert filtered_positive_sample[1] == "v2.3"
assert filtered_positive_sample[2] == update_timestamp
assert not filtered_negative_sample[0]
assert filtered_negative_sample[1] == "v2.3"
assert filtered_negative_sample[2] == update_timestamp