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authorFrederick Muriuki Muriithi2022-03-10 08:55:26 +0300
committerFrederick Muriuki Muriithi2022-03-10 08:55:26 +0300
commit4a7e2c1602ed82aabd7d04953067ba49cb1cebff (patch)
treeea8c0cf11f1629d79844b2a4e9bb49a69e0bba33 /scripts/maintenance
parent80b02d37f60d172be01bf8cd62bd84b406b1e0dd (diff)
downloadgenenetwork2-4a7e2c1602ed82aabd7d04953067ba49cb1cebff.tar.gz
Use context manager with database connection
Use the `with` context manager with database connections and cursors to ensure that they are closed once they are no longer needed. Where it was not feasible to use the `with` context manager without a huge refactor/rewrite, the cursors and connections are closed manually.
Diffstat (limited to 'scripts/maintenance')
-rwxr-xr-xscripts/maintenance/QTL_Reaper_v6.py3
-rw-r--r--scripts/maintenance/Update_Case_Attributes_MySQL_tab.py23
-rwxr-xr-xscripts/maintenance/readProbeSetMean_v7.py1
-rwxr-xr-xscripts/maintenance/readProbeSetSE_v7.py1
-rw-r--r--scripts/maintenance/utilities.py10
5 files changed, 14 insertions, 24 deletions
diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py
index 35f2d1a1..20fd8e3b 100755
--- a/scripts/maintenance/QTL_Reaper_v6.py
+++ b/scripts/maintenance/QTL_Reaper_v6.py
@@ -106,3 +106,6 @@ for ProbeSetFreezeId in ProbeSetFreezeIds:
print(ProbeSetFreezeIds)
+
+cursor.close()
+con.close()
diff --git a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py
index bf796df4..a3cd1c35 100644
--- a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py
+++ b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py
@@ -10,18 +10,13 @@ import time
import csv
########################################################################
-mydb = MySQLdb.connect(host='localhost',
- user='username',
- passwd='',
- db='db_webqtl')
-cursor = mydb.cursor()
+with MySQLdb.connect(
+ host='localhost', user='username', passwd='', db='db_webqtl') as mydb:
+ with mydb.cursor() as cursor:
-csv_data = csv.reader(file('GN711_pvalues.txt'), delimiter ="\t")
-for row in csv_data:
-
- cursor.execute("""UPDATE ProbeSetXRef SET pValue = %s WHERE ProbeSetFreezeId = %s AND ProbeSetId = %s """,
- (row))
-#close the connection to the database.
-mydb.commit()
-cursor.close()
-print("Done") \ No newline at end of file
+ csv_data = csv.reader(file('GN711_pvalues.txt'), delimiter ="\t")
+ for row in csv_data:
+ cursor.execute(
+ """UPDATE ProbeSetXRef SET pValue = %s WHERE ProbeSetFreezeId = %s AND ProbeSetId = %s """,
+ (row))
+print("Done")
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index 43f084f4..56adcdfd 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -269,4 +269,5 @@ if len(values1) > 0:
cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
db.execute(cmd)
+db.close()
con.close()
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 2cfe2e07..88a347bf 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -251,4 +251,5 @@ if len(DataValues) > 0:
cmd = 'insert ProbeSetSE values %s' % DataValues
db.execute(cmd)
+db.close()
con.close()
diff --git a/scripts/maintenance/utilities.py b/scripts/maintenance/utilities.py
index 886410c2..1fe14809 100644
--- a/scripts/maintenance/utilities.py
+++ b/scripts/maintenance/utilities.py
@@ -1,16 +1,6 @@
-import MySQLdb
import re
import configparser
-def get_cursor():
- host = 'tux.uthsc.edu'
- user = 'webqtlout'
- passwd = 'webqtlout'
- db = 'db_webqtl'
- con = MySQLdb.Connect(db=db, host=host, user=user, passwd=passwd)
- cursor = con.cursor()
- return cursor, con
-
def clearspaces(s, default=None):
if s:
s = re.sub('\s+', ' ', s)