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.

1 files changed, 7 insertions, 7 deletions

diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index f303aabb..0a13315c 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -2,7 +2,7 @@ from collections import OrderedDict
 from dataclasses import dataclass
 from dataclasses import InitVar
 from typing import Optional, Dict
-from flask import g
+from wqflask.database import database_connection
 
 
 @dataclass
@@ -46,20 +46,20 @@ class Chromosomes:
         """Lazily fetch the chromosomes"""
         chromosomes = OrderedDict()
         if self.species is not None:
-            query = (
+            cursor.execute(
                 "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
                 "FROM Chr_Length, Species WHERE "
                 "Chr_Length.SpeciesId = Species.SpeciesId AND "
-                "Species.Name = "
-                "'%s' ORDER BY OrderId" % self.species.capitalize())
+                "Species.Name = %s "
+                "ORDER BY OrderId", (self.species.capitalize(),))
         else:
-            query = (
+            cursor.execute(
                 "SELECT Chr_Length.Name, Chr_Length.OrderId, "
                 "Length FROM Chr_Length, InbredSet WHERE "
                 "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
                 "InbredSet.Name = "
-                "'%s' ORDER BY OrderId" % self.dataset.group.name)
-        results = g.db.execute(query).fetchall()
+                "%s ORDER BY OrderId", (self.dataset.group.name,))
+        results = cursor.fetchall()
         for item in results:
             chromosomes[item.OrderId] = IndChromosome(
                 item.Name, item.Length)