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authorPjotr Prins2016-06-19 16:03:26 +0000
committerPjotr Prins2016-06-19 16:03:26 +0000
commitaae827674cdbe46c7f1ce5d2246bf485a24dbbb3 (patch)
treef6a106c6544c8d68aae29b8a2e3e1ceb3de648b3 /wqflask/dbFunction/webqtlDatabaseFunction.py
parent2214650621ee57b4c427bf8b5cab1128eb06db93 (diff)
downloadgenenetwork2-aae827674cdbe46c7f1ce5d2246bf485a24dbbb3.tar.gz
gn_server: SQL handling
Diffstat (limited to 'wqflask/dbFunction/webqtlDatabaseFunction.py')
-rw-r--r--wqflask/dbFunction/webqtlDatabaseFunction.py26
1 files changed, 20 insertions, 6 deletions
diff --git a/wqflask/dbFunction/webqtlDatabaseFunction.py b/wqflask/dbFunction/webqtlDatabaseFunction.py
index 1bc67992..5b968d7e 100644
--- a/wqflask/dbFunction/webqtlDatabaseFunction.py
+++ b/wqflask/dbFunction/webqtlDatabaseFunction.py
@@ -20,11 +20,13 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
+from inspect import stack
from flask import Flask, g
import MySQLdb
import string
from base import webqtlConfig
+from utility.tools import USE_GN_SERVER
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -35,13 +37,31 @@ logger = getLogger(__name__ )
###########################################################################
def getCursor():
try:
+ logger.warning("Creating new MySQLdb cursor")
con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
cursor = con.cursor()
return cursor
except:
return None
+def fetchone(cursor,query):
+ result = g.db.execute("""select Species.Name from Species, InbredSet where InbredSet.Name = %s and InbredSet.SpeciesId = Species.Id""", (group)).fetchone()[0]
+ return cursor.execute(query)
+def retrieve_species(group):
+ """Get the species of a group (e.g. returns string "mouse" on "BXD"
+
+ """
+ if USE_GN_SERVER:
+ raise Exception("NYI")
+ else:
+ res = logger.sql(stack()[0][3],"select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), g.db.execute)
+ result = res.fetchone()[0]
+
+ # result = g.db.execute("""select Species.Name from Species, InbredSet where InbredSet.Name = %s and InbredSet.SpeciesId = Species.Id""", (group)).fetchone()[0]
+
+ logger.info(result,type(result))
+ return result
###########################################################################
#input: cursor, groupName (string)
@@ -78,12 +98,6 @@ def getAllSpecies(cursor=None):
allSpecies = cursor.fetchall()
return allSpecies
-def retrieve_species(group):
- logger.debug("retrieve_species",group)
- logger.sql(""""select Species.Name from Species, InbredSet where InbredSet.Name = %s and InbredSet.SpeciesId = Species.Id""", (group))
-
- return g.db.execute("""select Species.Name from Species, InbredSet where InbredSet.Name =
-%s and InbredSet.SpeciesId = Species.Id""", (group)).fetchone()[0]
def retrieve_species_id(group):
return g.db.execute("select SpeciesId from InbredSet where Name = %s", (group)).fetchone()[0]