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-rw-r--r--wqflask/db/call.py17
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py17
2 files changed, 22 insertions, 12 deletions
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 6b15abb3..ba6eb149 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -15,6 +15,21 @@ logger = getLogger(__name__ )
from inspect import stack
+def fetch1(query, path=None, func=None):
+ """Fetch one result using either a SQL query or the URI path to
+GN_SERVER (when USE_GN_SERVER is True). Apply func to GN_SERVER result
+when set.
+
+ """
+ if USE_GN_SERVER and path:
+ result = gn_server(path)
+ if func != None:
+ return [func(result)]
+ else:
+ return [result]
+ else:
+ return fetchone(query)
+
def fetchone(query):
"""Return tuple containing one row by calling SQL directly
@@ -23,7 +38,7 @@ def fetchone(query):
def helper(query):
res = g.db.execute(query)
return res.fetchone()
- callername = stack()[1][3]
+ callername = stack()[2][3]
return logger.sql(callername, query, helper)
def gn_server(path):
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index bdc3eeb2..2bc4745b 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -30,7 +30,7 @@ from base import webqtlConfig
from utility.tools import USE_GN_SERVER, LOG_SQL
from utility.benchmark import Bench
-from db.call import fetchone, gn_server
+from db.call import fetch1
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -52,18 +52,13 @@ def retrieve_species(group):
"""Get the species of a group (e.g. returns string "mouse" on "BXD"
"""
- if USE_GN_SERVER:
- result = gn_server("/cross/"+group+".json")
- return result["species"]
- else:
- result = fetchone("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group))
- return result[0]
+ 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 getMappingMethod(cursor=None, groupName=None):
- if USE_GN_SERVER:
- return gn_server("/cross/"+group+".json")["mapping_method_id"]
- else:
- return fetchone("select MappingMethodId from InbredSet where Name= '%s'" % groupName)
+ return fetch1("select MappingMethodId from InbredSet where Name= '%s'" % groupName, "/cross/"+group+".json", lambda r: r["mapping_method_id"])[0]
###########################################################################
#input: cursor, inbredSetId (int), strainId (int)