Update calls to `database_connection` function

Pass in the database URI at call time.

9 files changed, 27 insertions, 21 deletions

diff --git a/wqflask/base/data_set/__init__.py b/wqflask/base/data_set/__init__.py
index e49c6a93..69eaab53 100644
--- a/wqflask/base/data_set/__init__.py
+++ b/wqflask/base/data_set/__init__.py
@@ -10,7 +10,7 @@ from redis import Redis
 # local imports
 from .dataset import DataSet
 from base import webqtlConfig
-from utility.tools import USE_REDIS
+from utility.tools import get_setting, USE_REDIS
 from .datasettype import DatasetType
 from .tempdataset import TempDataSet
 from .datasetgroup import DatasetGroup
@@ -54,7 +54,7 @@ def create_dataset(dataset_name, dataset_type=None,
 def datasets(group_name, this_group=None, redis_conn=Redis()):
     key = "group_dataset_menu:v2:" + group_name
     dataset_menu = []
-    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 '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
             FROM PublishFreeze,InbredSet
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)} "
diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py
index 72577f38..95dc976f 100644
--- a/wqflask/base/data_set/datasetgroup.py
+++ b/wqflask/base/data_set/datasetgroup.py
@@ -15,6 +15,7 @@ from utility.tools import (
     locate,
     USE_REDIS,
     flat_files,
+    get_setting,
     flat_file_exists,
     locate_ignore_error)
 
@@ -29,7 +30,7 @@ class DatasetGroup:
 
     def __init__(self, dataset, name=None):
         """This sets self.group and self.group_id"""
-        with database_connection() as conn, conn.cursor() as cursor:
+        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
             if not name:
                 cursor.execute(dataset.query_for_group,
                                (dataset.name,))
@@ -64,7 +65,7 @@ class DatasetGroup:
 
     def get_mapping_methods(self):
         mapping_id = ()
-        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 MappingMethodId FROM "
                 "InbredSet WHERE Name= %s",
diff --git a/wqflask/base/data_set/genotypedataset.py b/wqflask/base/data_set/genotypedataset.py
index 2381a42a..b903cd72 100644
--- a/wqflask/base/data_set/genotypedataset.py
+++ b/wqflask/base/data_set/genotypedataset.py
@@ -2,6 +2,7 @@
 
 from .dataset import DataSet
 from utility import webqtlUtil
+from utility.tools import get_setting
 from db import webqtlDatabaseFunction
 from .utils import geno_mrna_confidentiality
 from wqflask.database import database_connection
@@ -46,7 +47,7 @@ GenoFreeze.Name = %s"""
 
     def retrieve_sample_data(self, trait):
         results = []
-        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, GenoData.value, "
                 "GenoSE.error, 'N/A', Strain.Name2 "
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 "
diff --git a/wqflask/base/data_set/phenotypedataset.py b/wqflask/base/data_set/phenotypedataset.py
index bdf28a7a..5a39418a 100644
--- a/wqflask/base/data_set/phenotypedataset.py
+++ b/wqflask/base/data_set/phenotypedataset.py
@@ -2,6 +2,7 @@
 
 from .dataset import DataSet
 from base import webqtlConfig
+from utility.tools import get_setting
 from wqflask.database import database_connection
 
 class PhenotypeDataSet(DataSet):
@@ -96,7 +97,7 @@ SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetC
             this_trait.LRS_location_repr = "N/A"
 
             if this_trait.lrs:
-                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 Geno.Chr, Geno.Mb FROM "
                         "Geno, Species WHERE "
@@ -113,7 +114,7 @@ SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetC
                                 LRS_Chr, float(LRS_Mb))
 
     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, PublishData.value, "
                 "PublishSE.error, NStrain.count, "
diff --git a/wqflask/base/data_set/probably_unused.py b/wqflask/base/data_set/probably_unused.py
index 4e54bcff..abd3ad07 100644
--- a/wqflask/base/data_set/probably_unused.py
+++ b/wqflask/base/data_set/probably_unused.py
@@ -3,6 +3,7 @@
 import pickle as pickle
 
 from wqflask.database import database_connection
+from utility.tools import get_setting
 
 def create_datasets_list():
     if USE_REDIS:
@@ -19,7 +20,7 @@ def create_datasets_list():
                      'Geno': 'GenoFreeze'}
 
         for dataset_type in type_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 Name FROM %s",
                                (type_dict[dataset_type],))
                 results = cursor.fetchall(query)
diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
index 703fee04..d18180c4 100644
--- a/wqflask/base/data_set/utils.py
+++ b/wqflask/base/data_set/utils.py
@@ -7,12 +7,12 @@ import hashlib
 from typing import List
 
 
-from utility.tools import SQL_URI
+from utility.tools import get_setting, SQL_URI
 from base.webqtlConfig import TMPDIR
 from wqflask.database import parse_db_url, database_connection
 
 def geno_mrna_confidentiality(ob):
-    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 confidentiality, "
             f"AuthorisedUsers FROM {ob.type}Freeze WHERE Name = %s",
@@ -26,7 +26,7 @@ def query_table_timestamp(dataset_type: str):
     """function to query the update timestamp of a given dataset_type"""
 
     # computation data and actions
-    with database_connection() as conn, conn.cursor() as cursor:
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
         fetch_db_name = parse_db_url(SQL_URI)
         cursor.execute(
             "SELECT UPDATE_TIME FROM "
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 37085448..103ff0c0 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -7,7 +7,7 @@ from base import webqtlConfig
 from base.webqtlCaseData import webqtlCaseData
 from base.data_set import create_dataset
 from utility.authentication_tools import check_resource_availability
-from utility.tools import GN2_BASE_URL
+from utility.tools import get_setting, GN2_BASE_URL
 from utility.redis_tools import get_redis_conn, get_resource_id
 
 from flask import g, request, url_for
@@ -394,7 +394,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
     if not dataset:
         raise ValueError("Dataset doesn't exist")
 
-    with database_connection() as conn, conn.cursor() as cursor:
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
         trait_info = ()
         if dataset.type == 'Publish':
             cursor.execute(