Replace g.db with database_connection() context manager

* wqflask/base/mrna_assay_tissue_data.py: Replace "flask.g" with database_connection.
(MrnaAssayTissueData.__init__): Use database_connection.
(MrnaAssayTissueData.get_symbol_values_pairs): Ditto.
* wqflask/base/species.py: Replace "Flask.g" imports with
"database_connection".
(Chromosomes.chromosomes): Use database_connection.
* wqflask/base/trait.py: Import database_connection.
(retrieve_trait_info): Use database_connection.
* wqflask/utility/authentication_tools.py: Replace "flask.g" with
database_connection.
(get_group_code): Use database_connection.
* wqflask/utility/helper_functions.py: Replace "flask.g" with
"database_connection".
(get_species_groups): Use database_connection.
* wqflask/wqflask/db_info.py: Replace "Flask" and "g" with
"database_connection".
(InfoPage.get_info): Use database_connection.
* wqflask/wqflask/do_search.py (DoSearch.execute): Use
database_connection().
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Replace
"Flask" and "g" import with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Replace
"Flask, g" imports with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/gsearch.py: Replace "Flask" and "g" import with
database_connection.
(GSearch.__init__): Use database_connection.
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes):
Use database_connection().
* wqflask/wqflask/show_trait/SampleList.py: Replace "flask.g import"
with database_connection.
(SampleList.get_attributes): Use database_connection.
(SampleList.get_extra_attribute_values): Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Replace "Flask" and "g"
import with database_connection.
(ShowTrait.__init__): Use database_connection.
(ShowTrait.get_external_links): Ditto.
(get_nearest_marker): Ditto.

2 files changed, 22 insertions, 18 deletions

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 96cc0b00..a8c03fe2 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -85,12 +85,13 @@ def add_new_resource(dataset, trait_id=None):
 
 
 def get_group_code(dataset):
-    results = g.db.execute(
-        "SELECT InbredSetCode from InbredSet where Name='{}'".format(
-            dataset.group.name)).fetchone()
-    if results[0]:
-        return results[0]
-    else:
+    with database_connection() as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT InbredSetCode FROM InbredSet WHERE Name=%s",
+            (dataset.group.name,)
+        )
+        if results := cursor.fetchone():
+            return results[0]
         return ""
 
 
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 4229a91f..0c0794dc 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -4,7 +4,7 @@ from base.species import TheSpecies
 
 from utility import hmac
 
-from flask import g
+from wqflask.database import database_connection
 
 
 def get_species_dataset_trait(self, start_vars):
@@ -50,16 +50,19 @@ def get_trait_db_obs(self, trait_db_list):
 def get_species_groups():
     """Group each species into a group"""
     _menu = {}
-
-    for species, group_name in g.db.execute(
+    species, group_name = None, None
+    with database_connection() as conn, conn.cursor() as cursor:
+        cursor.execute(
             "SELECT s.MenuName, i.InbredSetName FROM InbredSet i "
             "INNER JOIN Species s ON s.SpeciesId = i.SpeciesId "
-            "ORDER BY i.SpeciesId ASC, i.Name ASC").fetchall():
-        if species in _menu:
-            if _menu.get(species):
-                _menu = _menu[species].append(group_name)
-            else:
-                _menu[species] = [group_name]
-    return [{"species": key,
-             "groups": value} for key, value in
-            list(_menu.items())]
+            "ORDER BY i.SpeciesId ASC, i.Name ASC"
+        )
+        for species, group_name in cursor.fetchall():
+            if species in _menu:
+                if _menu.get(species):
+                    _menu = _menu[species].append(group_name)
+                else:
+                    _menu[species] = [group_name]
+        return [{"species": key,
+                 "groups": value} for key, value in
+                list(_menu.items())]