def test_update_mlwh_filtered_positive_fields_batched_raises_with_error_updating_mlwh(
config, mlwh_connection, mongo_samples_with_filtered_positive_fields):
version = "v2"
update_timestamp = datetime.now()
with patch(
"migrations.helpers.update_legacy_filtered_positives_helper.run_mysql_execute_formatted_query",
side_effect=Exception("Boom!"),
):
with pytest.raises(Exception):
update_mlwh_filtered_positive_fields_batched(
config, mongo_samples_with_filtered_positive_fields, version,
update_timestamp)
def update_mlwh_filtered_positive_fields_batched_batched_return_false_with_no_connection(
config):
with patch(
"migrations.helpers.update_legacy_filtered_positives_helper.create_mysql_connection"
) as mock_connection:
version = "v2"
update_timestamp = datetime.now()
mock_connection().is_connected.return_value = False
result = update_mlwh_filtered_positive_fields_batched(
config, [], version, update_timestamp)
assert result is False
def test_update_mlwh_filtered_positive_fields_batched_calls_to_update_samples(
config, mlwh_connection, mongo_samples_with_filtered_positive_fields,
mlwh_samples_with_filtered_positive_fields):
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_with_filtered_positive_fields)
cursor.close()
mlwh_connection.commit()
# call to update the database with newly filtered positive entries
update_timestamp = datetime(2020, 6, 23, 14, 40, 8)
version = "v2"
result = update_mlwh_filtered_positive_fields_batched(
config, mongo_samples_with_filtered_positive_fields, version,
update_timestamp)
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"
assert filtered_positive_sample[2] == update_timestamp
assert not filtered_negative_sample[0]
assert filtered_negative_sample[1] == "v2"
assert filtered_negative_sample[2] == update_timestamp
def run(settings_module: str = "",
s_start_datetime: str = "",
s_end_datetime: str = "") -> None:
"""Migrate the existing samples to have the filtered positive values.
Arguments:
settings_module {str} -- settings module from which to generate the app config
"""
if not valid_datetime_string(s_start_datetime):
logger.error(
"Aborting run: Expected format of Start datetime is YYMMDD_HHmm")
return
if not valid_datetime_string(s_end_datetime):
logger.error(
"Aborting run: Expected format of End datetime is YYMMDD_HHmm")
return
start_datetime = datetime.strptime(s_start_datetime, MONGO_DATETIME_FORMAT)
end_datetime = datetime.strptime(s_end_datetime, MONGO_DATETIME_FORMAT)
fields_set_datetime = datetime.strptime(FILTERED_POSITIVE_FIELDS_SET_DATE,
"%Y-%m-%d")
if start_datetime > end_datetime:
logger.error(
"Aborting run: End datetime must be greater than Start datetime")
return
if end_datetime > fields_set_datetime:
logger.error(
"Aborting run: Date range must be prior to the 17th December")
return
config, settings_module = get_config(settings_module)
logging.config.dictConfig(config.LOGGING)
logger.info("-" * 80)
logger.info("STARTING FILTERED POSITIVES LEGACY UPDATE")
logger.info(f"Time start: {datetime.now()}")
start_time = time.time()
updated_key = "Updated"
time_key = "Time taken"
mongo_versions_updated = {
FILTERED_POSITIVE_VERSION_0: {
updated_key: False,
time_key: 0.0
},
FILTERED_POSITIVE_VERSION_1: {
updated_key: False,
time_key: 0.0
},
FILTERED_POSITIVE_VERSION_2: {
updated_key: False,
time_key: 0.0
},
}
mlwh_versions_updated = {
FILTERED_POSITIVE_VERSION_0: {
updated_key: False,
time_key: 0.0
},
FILTERED_POSITIVE_VERSION_1: {
updated_key: False,
time_key: 0.0
},
FILTERED_POSITIVE_VERSION_2: {
updated_key: False,
time_key: 0.0
},
}
try:
continue_migration = pre_migration_filtered_positive_check(
config, start_datetime, end_datetime)
if continue_migration:
logger.info(
f"Selecting legacy samples from Mongo between {start_datetime} and {end_datetime}..."
)
samples = mongo_samples_by_date(config, start_datetime,
end_datetime)
legacy_samples_num = len(samples)
logger.info(f"{legacy_samples_num} samples found from Mongo")
root_sample_ids, plate_barcodes = extract_required_cp_info(samples)
logger.info("Querying for v0 cherrypicked samples from MLWH")
# Get v0 cherrypicked samples
v0_cp_samples_df = get_cherrypicked_samples_by_date(
config,
list(root_sample_ids),
list(plate_barcodes),
"1970-01-01 00:00:01",
V0_V1_CUTOFF_TIMESTAMP,
)
logger.debug(
f"Found {len(v0_cp_samples_df.index)} v0 cherrypicked samples"
) # type: ignore
logger.info("Querying for cherrypicked samples from MLWH")
# Get v1 cherrypicked samples
v1_cp_samples_df = get_cherrypicked_samples_by_date(
config,
list(root_sample_ids),
list(plate_barcodes),
V0_V1_CUTOFF_TIMESTAMP,
V1_V2_CUTOFF_TIMESTAMP,
)
logger.debug(
f"Found {len(v1_cp_samples_df.index)} v1 cherrypicked samples"
) # type: ignore
logger.info("Splitting samples by version...")
samples_by_version = split_mongo_samples_by_version(
samples, v0_cp_samples_df, v1_cp_samples_df)
update_timestamp = datetime.now()
for version, version_samples in samples_by_version.items():
filtered_positive_identifier = filtered_positive_identifier_by_version(
version)
logger.info(f"Updating {version} filtered positives...")
update_filtered_positive_fields(
filtered_positive_identifier,
version_samples,
version,
update_timestamp,
)
logger.info("Updated filtered positives")
logger.info("Updating Mongo")
for version, version_samples in samples_by_version.items():
logger.info(
f"Updating {version} filtered positives in Mongo, total {len(version_samples)} records..."
)
mongo_update_start_time = time.time()
mongo_updated = update_mongo_filtered_positive_fields(
config,
version_samples,
version,
update_timestamp,
)
if mongo_updated:
logger.info(
f"Finished updating {version} filtered positives in Mongo"
)
mongo_update_end_time = time.time()
mongo_versions_updated[version][updated_key] = True
mongo_versions_updated[version][time_key] = round(
mongo_update_end_time - mongo_update_start_time, 2)
logger.info(
f"Updating {version} filtered positives in MLWH...")
mlwh_update_start_time = time.time()
mlwh_updated = update_mlwh_filtered_positive_fields_batched(
config, version_samples, version, update_timestamp)
if mlwh_updated:
logger.info(
f"Finished updating {version} filtered positives in MLWH"
)
mlwh_update_end_time = time.time()
mlwh_versions_updated[version][updated_key] = True
mlwh_versions_updated[version][time_key] = round(
mlwh_update_end_time - mlwh_update_start_time, 2)
logger.info("Finished updating databases")
else:
logger.info("Now exiting migration")
except Exception as e:
logger.error("---------- Process aborted: ----------")
logger.error(f"An exception occurred, at {datetime.now()}")
logger.exception(e)
raise
finally:
end_time = time.time()
logger.info(f"""
---------- Processing status of filtered positive field migration: ----------
-- Mongo updated with v0 filtered positives: \
{mongo_versions_updated[FILTERED_POSITIVE_VERSION_0][updated_key]}, \
time taken: \
{mongo_versions_updated[FILTERED_POSITIVE_VERSION_0][time_key]}s
-- Mongo updated with v1 filtered positives: \
{mongo_versions_updated[FILTERED_POSITIVE_VERSION_1][updated_key]}, \
time taken: \
{mongo_versions_updated[FILTERED_POSITIVE_VERSION_1][time_key]}s
-- Mongo updated with v2 filtered positives: \
{mongo_versions_updated[FILTERED_POSITIVE_VERSION_2][updated_key]}, \
time taken: \
{mongo_versions_updated[FILTERED_POSITIVE_VERSION_2][time_key]}s
-- MLWH updated with v0 filtered positives: \
{mlwh_versions_updated[FILTERED_POSITIVE_VERSION_0][updated_key]}, \
time taken: \
{mlwh_versions_updated[FILTERED_POSITIVE_VERSION_0][time_key]}s
-- MLWH updated with v1 filtered positives: \
{mlwh_versions_updated[FILTERED_POSITIVE_VERSION_1][updated_key]}, \
time taken: \
{mlwh_versions_updated[FILTERED_POSITIVE_VERSION_1][time_key]}s
-- MLWH updated with v2 filtered positives: \
{mlwh_versions_updated[FILTERED_POSITIVE_VERSION_2][updated_key]}, \
time taken: \
{mlwh_versions_updated[FILTERED_POSITIVE_VERSION_2][time_key]}s
""")
logger.info(f"Time finished: {datetime.now()}")
logger.info(f"Migration complete in {round(end_time - start_time, 2)}s")
logger.info("=" * 80)