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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
from gn2.wqflask.database import database_connection
from gn2.utility.tools import get_setting
def retrieve_species(group):
"""Get the species of a group (e.g. returns string "mouse" on "BXD"
"""
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT Species.Name FROM Species, InbredSet WHERE InbredSet.Name = %s AND InbredSet.SpeciesId = Species.Id",
(group,))
results = cursor.fetchone()
if results and results[0]:
return results[0]
def retrieve_species_id(group):
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute("SELECT SpeciesId FROM InbredSet WHERE Name = %s",
(group,))
return cursor.fetchone()[0]
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