def test_update(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.")
update_vv_db.update()
db = update_vv_db.connect()
for table in [
'refSeqGene_loci', 'LRG_transcripts', 'LRG_proteins',
'LRG_RSG_lookup'
]:
print(table)
count = self.count_rows(db, table)
self.assertGreater(count, 0)
def test_connection(self):
db_conn = update_vv_db.connect()
self.assertIsInstance(db_conn, Database)
conn = db_conn.get_conn()
try:
self.assertTrue(conn.is_connected())
except AttributeError:
pass
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)
def test_connection(self):
db_conn = update_vv_db.connect()
self.assertIsInstance(db_conn, Database)
self.assertTrue(db_conn.conn.is_connected())
