From 72336a5876ddffba15aede5e02546e7dbf7a19f5 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 2 Sep 2022 17:28:26 +0300 Subject: 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. --- wqflask/utility/authentication_tools.py | 13 +++++++------ wqflask/utility/helper_functions.py | 27 +++++++++++++++------------ 2 files changed, 22 insertions(+), 18 deletions(-) (limited to 'wqflask/utility') 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())] -- cgit v1.2.3