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| author | Frederick Muriuki Muriithi | 2024-11-22 12:16:28 -0600 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-11-22 12:16:28 -0600 |
| commit | 8a84c4d6762446e5fdf9f9121f539c89419ae6a0 (patch) | |
| tree | 0c4d175767bdfb24d83a7f0c15e0ab677e00ebba /uploader/genotypes | |
| parent | 82fb92db448f1985b821193bcfdee72d512e27bb (diff) | |
| download | gn-uploader-8a84c4d6762446e5fdf9f9121f539c89419ae6a0.tar.gz | |
Use gn-libs code for db connection.
Use the code in gn-libs to connect to the database, rather than a
local module.
Diffstat (limited to 'uploader/genotypes')
| -rw-r--r-- | uploader/genotypes/models.py | 7 | ||||
| -rw-r--r-- | uploader/genotypes/views.py | 2 |
2 files changed, 5 insertions, 4 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py index 44c98b1..4c3e634 100644 --- a/uploader/genotypes/models.py +++ b/uploader/genotypes/models.py @@ -4,8 +4,9 @@ from datetime import datetime import MySQLdb as mdb from MySQLdb.cursors import Cursor, DictCursor +from flask import current_app as app -from uploader.db_utils import debug_query +from gn_libs.mysqldb import debug_query def genocode_by_population( conn: mdb.Connection, population_id: int) -> tuple[dict, ...]: @@ -38,7 +39,7 @@ def genotype_markers( with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute(_query, (species_id,)) - debug_query(cursor) + debug_query(cursor, app.logger) return tuple(dict(row) for row in cursor.fetchall()) @@ -64,7 +65,7 @@ def genotype_dataset( with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute(_query, _params) - debug_query(cursor) + debug_query(cursor, app.logger) result = cursor.fetchone() if bool(result): return dict(result) diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 0821eca..e6b1ba7 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,5 +1,6 @@ """Views for the genotypes.""" from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection from flask import (flash, request, url_for, @@ -11,7 +12,6 @@ from flask import (flash, from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login -from uploader.db_utils import database_connection from uploader.species.models import all_species, species_by_id from uploader.monadic_requests import make_either_error_handler from uploader.request_checks import with_species, with_population |