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authorPjotr Prins2016-06-23 06:17:27 +0000
committerPjotr Prins2016-06-23 06:17:27 +0000
commit5e4c967ded2c4146af261914dc30c7e03d575c2b (patch)
treef207d5ca5a5f000f5e99126e7bbe2148327017bf /wqflask/db/webqtlDatabaseFunction.py
parent2e8351ee52a67bf7dfee7d323458b3fa80cacf41 (diff)
downloadgenenetwork2-5e4c967ded2c4146af261914dc30c7e03d575c2b.tar.gz
DB: created fetch1 function which can do both SQL and GN_SERVER
Diffstat (limited to 'wqflask/db/webqtlDatabaseFunction.py')
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py17
1 files changed, 6 insertions, 11 deletions
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)