def test_add_network(self):
"""
Tests if the network file is added
to the database.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'banana')
conn_object = IoConnection()
conn_object.add_network(g, 'banana', 'banana')
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT * from edges;")
result = cur.fetchall()
# 3 edges in g
cur.close()
conn.close()
conn_object.delete_tables()
self.assertEqual(len(result), 3)
def test_add_observations(self):
"""
Tests whether multiple rows are added to the counts table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(values=('banana', 1, 2))
conn_object.add_sample(values=('Sample1', 'banana'))
conn_object.add_taxon(values=[('Listeria', 'banana', 'Bacteria',
'Firmicutes', 'Bacilli', 'Bacillales',
'Listeriaceae', 'Listeria',
'monocytogenes'),
('Listeria2', 'banana', 'Bacteria',
'Firmicutes', 'Bacilli', 'Bacillales',
'Listeriaceae', 'Listeria',
'monocytogenes')])
conn_object.add_observation(
values=[('banana', 'Listeria', 'Sample1',
0.5), ('banana', 'Listeria2', 'Sample1', 0.75)])
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT count from counts;")
result = cur.fetchall()
self.assertEqual(len(result), 2)
cur.close()
conn.close()
conn_object.delete_tables()
def test_observation_error(self):
"""
Tests if the query correctly reports an error
when a taxon is not present in the taxonomy table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(values=('banana', 1, 2))
conn_object.add_sample(values=('Sample1', 'banana'))
conn_object.add_taxon(values=('Listeria', 'banana', 'Bacteria',
'Firmicutes', 'Bacilli', 'Bacillales',
'Listeriaceae', 'Listeria',
'monocytogenes'))
self.assertRaises(
psycopg2.Error,
conn_object.add_observation(values=('banana', 'Streptococcus',
'Sample1', 0.5)),
)
# long format table of 5 * 6 observations
conn_object.delete_tables()
def test_add_meta(self):
"""
Tests whether a row is added to the meta table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(values=('banana', 1, 2))
conn_object.add_sample(values=('Sample1', 'banana'))
conn_object.add_meta(values=('Sample1', 'banana', 'colour', 'yellow',
None))
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT property from meta;")
result = cur.fetchall()
# long format table of 5 * 6 observations
self.assertEqual(result[0][0], 'colour')
cur.close()
conn.close()
conn_object.delete_tables()
