diff options
Diffstat (limited to 'wqflask/db')
-rw-r--r-- | wqflask/db/__init__.py | 0 | ||||
-rw-r--r-- | wqflask/db/call.py | 62 | ||||
-rw-r--r-- | wqflask/db/gn_server.py | 9 | ||||
-rw-r--r-- | wqflask/db/webqtlDatabaseFunction.py | 54 |
4 files changed, 125 insertions, 0 deletions
diff --git a/wqflask/db/__init__.py b/wqflask/db/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/db/__init__.py diff --git a/wqflask/db/call.py b/wqflask/db/call.py new file mode 100644 index 00000000..194a7650 --- /dev/null +++ b/wqflask/db/call.py @@ -0,0 +1,62 @@ +# Module for calling the backend + +from flask import g + +import string +import urllib2 +import json +from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL +from utility.benchmark import Bench + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +# from inspect import stack + +def fetch1(query, path=None, func=None): + """Fetch one result using either a SQL query or the URI path to +GN_SERVER (when USE_GN_SERVER is True). Apply func to GN_SERVER result +when set. + + """ + if USE_GN_SERVER and path: + result = gn_server(path) + if func != None: + return [func(result)] + else: + return [result] + else: + return fetchone(query) + +def fetchone(query): + """Return tuple containing one row by calling SQL directly (the +original fetchone, but with logging) + + """ + with Bench("SQL",LOG_SQL): + def helper(query): + res = g.db.execute(query) + return res.fetchone() + return logger.sql(query, helper) + +def fetchall(query): + """Return row iterator by calling SQL directly (the +original fetchall, but with logging) + + """ + with Bench("SQL",LOG_SQL): + def helper(query): + res = g.db.execute(query) + return res.fetchall() + return logger.sql(query, helper) + +def gn_server(path): + """Return JSON record by calling GN_SERVER + + """ + with Bench("GN_SERVER",LOG_SQL): + res = urllib2.urlopen(GN_SERVER_URL+path) + rest = res.read() + res2 = json.loads(rest) + logger.debug(res2) + return res2 diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py new file mode 100644 index 00000000..da224112 --- /dev/null +++ b/wqflask/db/gn_server.py @@ -0,0 +1,9 @@ +# Backend query functions (logic) + +from db.call import gn_server + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +def menu_main(): + return gn_server("/int/menu/main.json") diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py new file mode 100644 index 00000000..7fc096a9 --- /dev/null +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -0,0 +1,54 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) + +from db.call import fetch1 + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +########################################################################### +#output: cursor instance +#function: connect to database and return cursor instance +########################################################################### +def getCursor(): + try: + logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)") + 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 retrieve_species(group): + """Get the species of a group (e.g. returns string "mouse" on "BXD" + + """ + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: r["species"])[0] + logger.debug("retrieve_species result:",result) + return result + + +def retrieve_species_id(group): + + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: r["species_id"])[0] + logger.debug("retrieve_species_id result:",result) + return result |