Update calls to `database_connection` function

Pass in the database URI at call time.

4 files changed, 8 insertions, 53 deletions

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 9f4b670d..01b2fc15 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -37,7 +37,7 @@ sys.path.insert(0, './')
 # NEW: import app to avoid a circular dependency on utility.tools
 from wqflask import app
 
-from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
+from utility.tools import get_setting
 
 import simplejson as json
 import urllib.parse
@@ -48,21 +48,6 @@ from pprint import pformat as pf
 from wqflask.database import database_connection
 
 
-def parse_db_uri():
-    """Converts a database URI to the db name, host name, user name, and password"""
-
-    parsed_uri = urllib.parse.urlparse(SQL_URI)
-
-    db_conn_info = dict(
-        db=parsed_uri.path[1:],
-        host=parsed_uri.hostname,
-        user=parsed_uri.username,
-        passwd=parsed_uri.password)
-
-    print(db_conn_info)
-    return db_conn_info
-
-
 def get_species(cursor):
     """Build species list"""
     #cursor.execute("select Name, MenuName from Species where Species.Name != 'macaque monkey' order by OrderId")
@@ -268,8 +253,6 @@ def build_datasets(species, group, type_name):
 def main(cursor):
     """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
 
-    parse_db_uri()
-
     species = get_species(cursor)
     groups = get_groups(cursor, species)
     types = get_types(groups)
@@ -308,6 +291,6 @@ def _test_it():
 
 
 if __name__ == '__main__':
-    with database_connection() as conn:
+    with database_connection(get_setting("SQL_URI")) as conn:
         with conn.cursor() as cursor:
             main(cursor)
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index f43f952b..2f917c71 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -12,6 +12,7 @@ from base import webqtlConfig
 
 from pprint import pformat as pf
 
+from utility.tools import get_setting
 from wqflask.database import database_connection
 
 
@@ -107,7 +108,7 @@ def main():
         "(Oct08)_RankInv_Beta.txt")
     dataset_name = "Eye_AXBXA_1008_RankInv"
 
-    with database_connection as conn:
+    with database_connection(get_setting("SQL_URI")) as conn:
         with conn.cursor() as cursor:
             strains = get_strains(cursor)
             print("Getting probset_vals")
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 90ec72de..36049a82 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -9,21 +9,7 @@ from flask import Flask, g, request
 
 from wqflask import app
 from wqflask.database import database_connection
-
-
-def parse_db_uri():
-    """Converts a database URI to the db name, host name, user name, and password"""
-
-    parsed_uri = urllib.parse.urlparse(SQL_URI)
-
-    db_conn_info = dict(
-        db=parsed_uri.path[1:],
-        host=parsed_uri.hostname,
-        user=parsed_uri.username,
-        passwd=parsed_uri.password)
-
-    print(db_conn_info)
-    return db_conn_info
+from utility.tools import get_setting
 
 
 def create_dataframe(input_file):
@@ -99,7 +85,7 @@ def set_data(cursor, dataset_name):
 
 
 if __name__ == '__main__':
-    with database_connection as conn:
+    with database_connection(get_setting("SQL_URI")) as conn:
         with conn.cursor() as cursor:
             success, _ = bulk(es, set_data(cursor, sys.argv[1]))
 
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 0d9372ff..cebe33c0 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -26,7 +26,7 @@ sys.path.insert(0, './')
 from wqflask import app
 
 from utility import hmac
-from utility.tools import SQL_URI
+from utility.tools import get_setting
 from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info
 Redis = get_redis_conn()
 
@@ -35,21 +35,6 @@ import urllib.parse
 from wqflask.database import database_connection
 
 
-def parse_db_uri():
-    """Converts a database URI to the db name, host name, user name, and password"""
-
-    parsed_uri = urllib.parse.urlparse(SQL_URI)
-
-    db_conn_info = dict(
-        db=parsed_uri.path[1:],
-        host=parsed_uri.hostname,
-        user=parsed_uri.username,
-        passwd=parsed_uri.password)
-
-    print(db_conn_info)
-    return db_conn_info
-
-
 def insert_probeset_resources(cursor, default_owner_id):
     current_resources = Redis.hgetall("resources")
     cursor.execute("""  SELECT
@@ -163,6 +148,6 @@ def main(cursor):
 
 
 if __name__ == '__main__':
-    with database_connection() as conn:
+    with database_connection(get_setting("SQL_URI")) as conn:
         with conn.cursor() as cursor:
             main(cursor)