diff options
Diffstat (limited to 'wqflask/maintenance/generate_probesetfreeze_file.py')
| -rw-r--r-- | wqflask/maintenance/generate_probesetfreeze_file.py | 26 |
1 files changed, 9 insertions, 17 deletions
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index e964c8ed..f43f952b 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -8,20 +8,11 @@ import os import collections import csv -import MySQLdb - from base import webqtlConfig from pprint import pformat as pf - -def get_cursor(): - con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME, - host=webqtlConfig.MYSQL_UPDSERVER, - user=webqtlConfig.DB_UPDUSER, - passwd=webqtlConfig.DB_UPDPASSWD) - cursor = con.cursor() - return cursor +from wqflask.database import database_connection def show_progress(process, counter): @@ -116,13 +107,14 @@ def main(): "(Oct08)_RankInv_Beta.txt") dataset_name = "Eye_AXBXA_1008_RankInv" - cursor = get_cursor() - strains = get_strains(cursor) - print("Getting probset_vals") - probeset_vals = get_probeset_vals(cursor, dataset_name) - print("Finished getting probeset_vals") - trimmed_strains = trim_strains(strains, probeset_vals) - write_data_matrix_file(trimmed_strains, probeset_vals, filename) + with database_connection as conn: + with conn.cursor() as cursor: + strains = get_strains(cursor) + print("Getting probset_vals") + probeset_vals = get_probeset_vals(cursor, dataset_name) + print("Finished getting probeset_vals") + trimmed_strains = trim_strains(strains, probeset_vals) + write_data_matrix_file(trimmed_strains, probeset_vals, filename) if __name__ == '__main__': |