diff options
Diffstat (limited to 'wqflask/db')
| -rw-r--r-- | wqflask/db/call.py | 14 | ||||
| -rw-r--r-- | wqflask/db/gn_server.py | 3 | ||||
| -rw-r--r-- | wqflask/db/webqtlDatabaseFunction.py | 17 |
3 files changed, 16 insertions, 18 deletions
diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 0971d2a2..1fe0772b 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -4,7 +4,9 @@ from flask import g import string try: # Python2 support - import urllib.request, urllib.error, urllib.parse + import urllib.request + import urllib.error + import urllib.parse except: import urllib2 import json @@ -12,10 +14,11 @@ 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__ ) +logger = getLogger(__name__) # from inspect import stack + def fetch1(query, path=None, func=None): """Fetch one result as a Tuple using either a SQL query or the URI path to GN_SERVER (when USE_GN_SERVER is True). Apply func to @@ -35,6 +38,7 @@ GN_SERVER result when set (which should return a Tuple) else: return fetchone(query) + def fetchone(query): """Return tuple containing one row by calling SQL directly (the original fetchone, but with logging) @@ -46,6 +50,7 @@ original fetchone, but with logging) return res.fetchone() return logger.sql(query, helper) + def fetchall(query): """Return row iterator by calling SQL directly (the original fetchall, but with logging) @@ -57,6 +62,7 @@ original fetchall, but with logging) return res.fetchall() return logger.sql(query, helper) + def gn_server(path): """Return JSON record by calling GN_SERVER @@ -64,9 +70,9 @@ def gn_server(path): with Bench("GN_SERVER", LOG_SQL): res = () try: - res = urllib.request.urlopen(GN_SERVER_URL+path) + res = urllib.request.urlopen(GN_SERVER_URL + path) except: - res = urllib2.urlopen(GN_SERVER_URL+path) + res = urllib2.urlopen(GN_SERVER_URL + path) rest = res.read() res2 = json.loads(rest) logger.debug(res2) diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py index da224112..f9b01658 100644 --- a/wqflask/db/gn_server.py +++ b/wqflask/db/gn_server.py @@ -3,7 +3,8 @@ from db.call import gn_server from utility.logger import getLogger -logger = getLogger(__name__ ) +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 index 2805febd..9ec650a4 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -21,27 +21,18 @@ # This module is used by GeneNetwork project (www.genenetwork.org) from db.call import fetch1 -from utility.tools import USE_GN_SERVER -from utility.logger import getLogger -logger = getLogger(__name__ ) - -########################################################################### -#output: cursor instance -#function: connect to database and return cursor instance -########################################################################### 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) + 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] 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) + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % ( + group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0] return result |