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-rw-r--r--wqflask/dbFunction/webqtlDatabaseFunction.py34
-rw-r--r--wqflask/utility/logger.py15
-rw-r--r--wqflask/wqflask/search_results.py1
-rw-r--r--wqflask/wqflask/views.py3
4 files changed, 27 insertions, 26 deletions
diff --git a/wqflask/dbFunction/webqtlDatabaseFunction.py b/wqflask/dbFunction/webqtlDatabaseFunction.py
index 299114b4..1bc67992 100644
--- a/wqflask/dbFunction/webqtlDatabaseFunction.py
+++ b/wqflask/dbFunction/webqtlDatabaseFunction.py
@@ -20,13 +20,15 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-
from flask import Flask, g
import MySQLdb
import string
from base import webqtlConfig
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
###########################################################################
#output: cursor instance
#function: connect to database and return cursor instance
@@ -76,33 +78,23 @@ def getAllSpecies(cursor=None):
allSpecies = cursor.fetchall()
return allSpecies
-###########################################################################
-#input: cursor, RISet (string)
-#output: specie's name (string), value will be None or else
-#function: retrieve specie's name info based on RISet
-###########################################################################
-
def retrieve_species(group):
- return g.db.execute("""select Species.Name
- from Species, InbredSet
- where InbredSet.Name = %s and
- InbredSet.SpeciesId = Species.Id""", (group)).fetchone()[0]
+ 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]
-###########################################################################
-# input: cursor
-# output: tissProbeSetFreezeIdList (list),
-# nameList (list),
-# fullNameList (list)
-# function: retrieve all TissueProbeSetFreezeId,Name,FullName info
-# from TissueProbeSetFreeze table.
-# These data will listed in the dropdown menu in the first page of Tissue Correlation
-###########################################################################
-
def getTissueDataSet(cursor=None):
+ """Retrieve all TissueProbeSetFreezeId,Name,FullName info from
+TissueProbeSetFreeze table. These data will listed in the dropdown
+menu in the first page of Tissue Correlation
+
+ """
tissProbeSetFreezeIdList=[]
nameList =[]
fullNameList = []
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 81202b05..bc0578c9 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -28,6 +28,7 @@
import logging
import string
+from inspect import isfunction
from utility.tools import LOG_LEVEL
class GNLogger:
@@ -62,8 +63,10 @@ class GNLogger:
self.collect(self.logger.error,*args)
def debugf(self,*args):
- """Call logging.debug for multiple args"""
- self.collect(self.logger.debug,*args)
+ """Call logging.debug for multiple args lazily"""
+ if self.logger.getEffectiveLevel() <= 10:
+ self.debug("Calling debug function!")
+ self.collectf(self.logger.debug,*args)
def sql(self, sqlcommand, fun = None):
"""Log SQL command, optionally invoking a timed fun"""
@@ -73,6 +76,14 @@ class GNLogger:
for a in args:
fun(a)
+ def collectf(self,fun,*args):
+ """Collect arguments and use fun to output one by one"""
+ for a in args:
+ if isfunction(a):
+ fun(a())
+ else:
+ fun(a)
+
# Get the module logger. You can override log levels at the
# module level
def getLogger(name, level = None):
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 30b65e80..494e1047 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -100,7 +100,6 @@ class SearchResultPage(object):
self.trait_list = []
species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name)
-
# result_set represents the results for each search term; a search of
# "shh grin2b" would have two sets of results, one for each term
logger.debug("self.results is:", pf(self.results))
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 88cce263..f486a8b5 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -119,11 +119,11 @@ def search_page():
else:
return render_template("data_sharing.html", **template_vars.__dict__)
else:
- logger.debug("key is:", pf(key))
result = None
if USE_REDIS:
with Bench("Trying Redis cache"):
key = "search_results:v1:" + json.dumps(request.args, sort_keys=True)
+ logger.debug("key is:", pf(key))
result = Redis.get(key)
if result:
logger.info("Redis cache hit on search results!")
@@ -131,7 +131,6 @@ def search_page():
else:
logger.info("Skipping Redis cache (USE_REDIS=False)")
- logger.info("calling search_results.SearchResultPage")
logger.info("request.args is", request.args)
the_search = search_results.SearchResultPage(request.args)
result = the_search.__dict__