diff options
Diffstat (limited to 'wqflask/base/data_set/mrnaassaydataset.py')
| -rw-r--r-- | wqflask/base/data_set/mrnaassaydataset.py | 7 |
1 files changed, 4 insertions, 3 deletions
diff --git a/wqflask/base/data_set/mrnaassaydataset.py b/wqflask/base/data_set/mrnaassaydataset.py index b76c5a74..4eb998b5 100644 --- a/wqflask/base/data_set/mrnaassaydataset.py +++ b/wqflask/base/data_set/mrnaassaydataset.py @@ -6,6 +6,7 @@ import codecs from .dataset import DataSet from .utils import geno_mrna_confidentiality from wqflask.database import database_connection +from utility.tools import get_setting class MrnaAssayDataSet(DataSet): ''' @@ -73,7 +74,7 @@ ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = %s""" # Note: setting trait_list to [] is probably not a great idea. if not trait_list: trait_list = [] - with database_connection() as conn, conn.cursor() as cursor: + with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: for this_trait in trait_list: if not this_trait.haveinfo: @@ -144,7 +145,7 @@ ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = %s""" return trait_list def retrieve_sample_data(self, trait): - with database_connection() as conn, conn.cursor() as cursor: + with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: cursor.execute( "SELECT Strain.Name, ProbeSetData.value, " "ProbeSetSE.error, NStrain.count, " @@ -168,7 +169,7 @@ ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = %s""" return cursor.fetchall() def retrieve_genes(self, column_name): - with database_connection() as conn, conn.cursor() as cursor: + with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: cursor.execute( f"SELECT ProbeSet.Name, ProbeSet.{column_name} " "FROM ProbeSet,ProbeSetXRef WHERE " |