diff options
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 13 |
1 files changed, 10 insertions, 3 deletions
diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index fdf711b..e6623fe 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -74,6 +74,14 @@ def save_phenotypes( if idx != 0)) +def __fetch_next_dataid__(conn: mysqldb.Connection) -> int: + """Fetch the next available DataId value from the database.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT MAX(DataId) AS CurrentMaxDataId FROM PublishXRef") + return int(cursor.fetchone()) + 1 + + def save_phenotypes_data(conn: mysqldb.Connection, dataidmap, samples, datafiles): """Read the `datafiles` and save the data in the database.""" pass @@ -107,13 +115,12 @@ def load_data(conn, job): logger.info("Saving basic phenotype data.") _phenos = save_phenotypes(cursor, _control_data) - _next_data_id = fetch_next_dataid(...) dataidmap = { row["phenotype_id"]: { "phenotype_id": row["phenotype_id"], - "data_id": _nextid + "data_id": dataid } - for _nextid, row in enumerate(_phenos, start=_next_data_id) + for dataid, row in enumerate(_phenos, start=__fetch_next_dataid__(conn)) } # 2. Save any new publications (in multi-file bundle): # -> return publication IDS |