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)