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-rw-r--r--wqflask/db/call.py21
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py8
2 files changed, 18 insertions, 11 deletions
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 1a1b3adc..0971d2a2 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -3,7 +3,10 @@
from flask import g
import string
-import urllib2
+try: # Python2 support
+ import urllib.request, urllib.error, urllib.parse
+except:
+ import urllib2
import json
from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL
from utility.benchmark import Bench
@@ -26,8 +29,8 @@ GN_SERVER result when set (which should return a Tuple)
else:
res2 = result,
if LOG_SQL:
- logger.debug("Replaced SQL call",query)
- logger.debug(path,res2)
+ logger.debug("Replaced SQL call", query)
+ logger.debug(path, res2)
return res2
else:
return fetchone(query)
@@ -37,7 +40,7 @@ def fetchone(query):
original fetchone, but with logging)
"""
- with Bench("SQL",LOG_SQL):
+ with Bench("SQL", LOG_SQL):
def helper(query):
res = g.db.execute(query)
return res.fetchone()
@@ -48,7 +51,7 @@ def fetchall(query):
original fetchall, but with logging)
"""
- with Bench("SQL",LOG_SQL):
+ with Bench("SQL", LOG_SQL):
def helper(query):
res = g.db.execute(query)
return res.fetchall()
@@ -58,8 +61,12 @@ def gn_server(path):
"""Return JSON record by calling GN_SERVER
"""
- with Bench("GN_SERVER",LOG_SQL):
- res = urllib2.urlopen(GN_SERVER_URL+path)
+ with Bench("GN_SERVER", LOG_SQL):
+ res = ()
+ try:
+ res = urllib.request.urlopen(GN_SERVER_URL+path)
+ except:
+ res = urllib2.urlopen(GN_SERVER_URL+path)
rest = res.read()
res2 = json.loads(rest)
logger.debug(res2)
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 8a9dc79d..2805febd 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -35,13 +35,13 @@ 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]
+ 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)
+ 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