diff options
Diffstat (limited to 'wqflask/maintenance/quantile_normalize.py')
| -rw-r--r-- | wqflask/maintenance/quantile_normalize.py | 27 |
1 files changed, 13 insertions, 14 deletions
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 32780ca6..2e2b0ec3 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -1,6 +1,5 @@ import sys sys.path.insert(0, './') -import MySQLdb import urllib.parse import numpy as np @@ -9,6 +8,7 @@ import pandas as pd from flask import Flask, g, request from wqflask import app +from wqflask.database import database_connection def parse_db_uri(): @@ -52,7 +52,7 @@ def quantileNormalize(df_input): return df -def set_data(dataset_name): +def set_data(cursor, dataset_name): orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt" sample_list = [] @@ -80,8 +80,8 @@ def set_data(dataset_name): ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and ProbeSetXRef.ProbeSetId = ProbeSet.Id and ProbeSet.Name = '%s'""" % (dataset_name, line1.split('\t')[0]) - Cursor.execute(query) - result_info = Cursor.fetchone() + cursor.execute(query) + result_info = cursor.fetchone() yield { "_index": "traits", @@ -99,15 +99,14 @@ def set_data(dataset_name): if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri()) - Cursor = Conn.cursor() + with database_connection as conn: + with conn.cursor as cursor: + success, _ = bulk(es, set_data(cursor, sys.argv[1])) - success, _ = bulk(es, set_data(sys.argv[1])) - - response = es.search( - index="traits", doc_type="trait", body={ - "query": {"match": {"name": "ENSMUSG00000028982"}} - } - ) + response = es.search( + index="traits", doc_type="trait", body={ + "query": {"match": {"name": "ENSMUSG00000028982"}} + } + ) - print(response) + print(response) |