def test_deletion(self):
db = update_vv_db.connect()
initial_count = self.count_rows(db, 'LRG_transcripts')
if initial_count > 0:
pytest.skip(
"Already have data so not going to run this test here.")
db.insert_refseq_gene_data([
'id', 'chr', 'genome', '0', '1', '1', '10', '2', '2', '1', 'hgnc',
'False'
])
count = self.count_rows(db, 'refSeqGene_loci')
self.assertGreaterEqual(count, 1)
update_vv_db.delete()
db = update_vv_db.connect()
for table in [
'transcript_info', 'refSeqGene_loci', 'LRG_transcripts',
'LRG_proteins', 'LRG_RSG_lookup'
]:
print(table)
count = self.count_rows(db, table)
self.assertEqual(count, 0)
#! /usr/bin/env python
from VariantValidator import update_vv_db
import argparse
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--delete', '-d', action='store_true', help='Delete the contents of the current database '
'before updating')
args = parser.parse_args()
if args.delete:
print("Deleting current database contents")
update_vv_db.delete()
update_vv_db.update()
# <LICENSE>
# Copyright (C) 2019 VariantValidator Contributors
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License