diff options
| -rw-r--r-- | uploader/genotypes/models.py | 10 |
1 files changed, 7 insertions, 3 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py index 75afabd..40afb1e 100644 --- a/uploader/genotypes/models.py +++ b/uploader/genotypes/models.py @@ -1,14 +1,17 @@ """Functions for handling genotypes.""" +import logging from typing import Optional from functools import reduce from datetime import datetime import MySQLdb as mdb from MySQLdb.cursors import Cursor, DictCursor -from flask import current_app as app from gn_libs.mysqldb import debug_query +logger = logging.getLogger(__name__) + + def genocode_by_population( conn: mdb.Connection, population_id: int) -> tuple[dict, ...]: """Get the allele/genotype codes.""" @@ -68,7 +71,7 @@ def genotype_markers( if bool(limit) and limit >= 0 else "")), (species_id, population_id)) - debug_query(cursor, app.logger) + debug_query(cursor, logger) _records = tuple(dict(row) for row in cursor.fetchall()) return _records, _total_records @@ -112,6 +115,7 @@ def genotype_records( _query_template.replace( "%%PARAMS_STR%%", ",".join(["%s"] * len(_genoids))), _genoids) + debug_query(cursor, logger) _records: dict[str, dict] = reduce( __organise_geno_records__, cursor.fetchall(), {}) return ( @@ -146,7 +150,7 @@ def genotype_dataset( with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute(_query, _params) - debug_query(cursor, app.logger) + debug_query(cursor, logger) result = cursor.fetchone() if bool(result): return dict(result) |