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authorArthur Centeno2021-06-15 15:33:59 +0000
committerArthur Centeno2021-06-15 15:33:59 +0000
commitc1a6ca69f7c48d99b6c5d62e56a445583fd4c08b (patch)
treef98fccc44829e3f52e585d6b41a1942aa52bd8b7 /wqflask/db
parent7e49c006af9c4f7453c3578a7d4f1fc4d7bdf3ed (diff)
parent9e9e0e4d440383f617542e810a1115833eafd7bf (diff)
downloadgenenetwork2-c1a6ca69f7c48d99b6c5d62e56a445583fd4c08b.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acenteno
Diffstat (limited to 'wqflask/db')
-rw-r--r--wqflask/db/call.py14
-rw-r--r--wqflask/db/gn_server.py3
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py17
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