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-rw-r--r--wqflask/dbFunction/webqtlDatabaseFunction.py26
-rw-r--r--wqflask/runserver.py4
-rw-r--r--wqflask/utility/logger.py16
-rw-r--r--wqflask/utility/tools.py1
4 files changed, 37 insertions, 10 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]
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 9339acf8..12ec904e 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -16,9 +16,11 @@ GREEN = '\033[92m'
BOLD = '\033[1m'
ENDC = '\033[0m'
-
logger.info("GN2 is running. Visit %shttp://localhost:5003/%s" % (BLUE,ENDC))
+import os
+app.config['SECRET_KEY'] = os.urandom(24)
+
from utility.tools import WEBSERVER_MODE
werkzeug_logger = logging.getLogger('werkzeug')
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index bc0578c9..0d374f1a 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -62,14 +62,24 @@ class GNLogger:
"""Call logging.error for multiple args"""
self.collect(self.logger.error,*args)
+ def infof(self,*args):
+ """Call logging.info for multiple args lazily"""
+ # only evaluate function when logging
+ if self.logger.getEffectiveLevel() < 30:
+ self.collectf(self.logger.debug,*args)
+
def debugf(self,*args):
"""Call logging.debug for multiple args lazily"""
- if self.logger.getEffectiveLevel() <= 10:
- self.debug("Calling debug function!")
+ # only evaluate function when logging
+ if self.logger.getEffectiveLevel() < 20:
self.collectf(self.logger.debug,*args)
- def sql(self, sqlcommand, fun = None):
+ def sql(self, description, sqlcommand, fun = None):
"""Log SQL command, optionally invoking a timed fun"""
+ self.info(description,sqlcommand)
+ if fun:
+ self.info("Invoking function")
+ return fun(sqlcommand)
def collect(self,fun,*args):
"""Collect arguments and use fun to output one by one"""
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 2affd130..fca5917e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -172,6 +172,7 @@ LOG_LEVEL = get_setting('LOG_LEVEL')
LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG')
LOG_SQL = get_setting_bool('LOG_SQL')
USE_REDIS = get_setting_bool('USE_REDIS')
+USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
PYLMM_COMMAND = pylmm_command()
GEMMA_COMMAND = gemma_command()