diff options
| -rw-r--r-- | wqflask/dbFunction/webqtlDatabaseFunction.py | 34 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 3 |
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__ |