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, 10 insertions, 5 deletions

diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index d7e747aa..b371e39f 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -1,6 +1,6 @@
 import collections
 
-from flask import g
+from wqflask.database import database_connection
 
 from utility import db_tools
 from utility import Bunch
@@ -49,7 +49,11 @@ class MrnaAssayTissueData:
             # lower_symbols[gene_symbol.lower()] = True
             if gene_symbol != None:
                 lower_symbols[gene_symbol.lower()] = True
-        results = list(g.db.execute(query).fetchall())
+
+        results = None
+        with database_connection() as conn, conn.cursor() as cursor:
+            cursor.execute(query)
+            results = cursor.fetchall()
         for result in results:
             symbol = result[0]
             if symbol  is not None and lower_symbols.get(symbol.lower()):
@@ -81,9 +85,10 @@ class MrnaAssayTissueData:
                        FROM TissueProbeSetXRef, TissueProbeSetData
                        WHERE TissueProbeSetData.Id IN {} and
                              TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
-
-
-            results = g.db.execute(query).fetchall()
+            results = []
+            with database_connection() as conn, conn.cursor() as cursor:
+                cursor.execute(query)
+                results = cursor.fetchall()
             for result in results:
                 if result.Symbol.lower() not in symbol_values_dict:
                     symbol_values_dict[result.Symbol.lower()] = [result.value]