diff options
Diffstat (limited to 'wqflask/base/data_set/dataset.py')
| -rw-r--r-- | wqflask/base/data_set/dataset.py | 11 |
1 files changed, 6 insertions, 5 deletions
diff --git a/wqflask/base/data_set/dataset.py b/wqflask/base/data_set/dataset.py index feab2b23..435d74a9 100644 --- a/wqflask/base/data_set/dataset.py +++ b/wqflask/base/data_set/dataset.py @@ -7,6 +7,7 @@ from redis import Redis from base import species from utility import chunks +from utility.tools import get_setting from gn3.monads import MonadicDict, query_sql from pymonad.maybe import Maybe, Nothing from .datasetgroup import DatasetGroup @@ -64,7 +65,7 @@ class DataSet: """Get the accession_id of this dataset depending on the dataset type.""" __query = "" - with database_connection() as conn: + with database_connection(get_setting("SQL_URI")) as conn: if self.type == "Publish": __query = ( "SELECT InfoFiles.GN_AccesionId AS accession_id FROM " @@ -115,7 +116,7 @@ class DataSet: all is passed. """ - with database_connection() as conn, conn.cursor() as cursor: + with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: try: if self.type == "ProbeSet": cursor.execute( @@ -148,7 +149,7 @@ class DataSet: results = {} traits_name_dict = () - 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 ProbeSetXRef.DataId,ProbeSet.Name " "FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze " @@ -179,7 +180,7 @@ class DataSet: if self.group.parlist != None and self.group.f1list != None: if (self.group.parlist + self.group.f1list) in self.samplelist: self.samplelist += self.group.parlist + self.group.f1list - 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, Strain.Id FROM " "Strain, Species WHERE Strain.Name IN " @@ -219,7 +220,7 @@ class DataSet: if (self.group.parlist + self.group.f1list) in self.samplelist: self.samplelist += self.group.parlist + self.group.f1list - 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, Strain.Id FROM Strain, Species " f"WHERE Strain.Name IN {create_in_clause(self.samplelist)} " |