def test_add_network_node(self):
"""
Tests whether a row is added to the networks table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'potato')
conn_object = IoConnection()
conn_object.add_network_node(values=('potato', 'potato', 5, 20))
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT * from networks;")
result = cur.fetchall()
cur.close()
conn.close()
conn_object.delete_tables()
self.assertEqual(result[0], ('potato', 'potato', 5, 20))
def test_add_biom(self):
"""
Tests if the BIOM file is imported by
querying the count data.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'banana')
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT * from counts;")
result = cur.fetchall()
# long format table of 5 * 6 observations
self.assertEqual(len(result), 30)
cur.close()
conn.close()
conn_object.delete_tables()
def test_add_sample(self):
"""
Tests whether a row is added to the sample 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 = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT sampleid from samples;")
result = cur.fetchall()
# long format table of 5 * 6 observations
self.assertEqual(result[0][0], 'Sample1')
cur.close()
conn.close()
conn_object.delete_tables()
def test_import_biom_mapping(self):
"""
Tests if the BiomConnection uses the mapping dict.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
write_biom_table(testbiom, fmt='hdf5', filepath="test.biom")
import_biom("test.biom", mapping={'test': 'banana'})
os.remove("test.biom")
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT studyID " "FROM bioms " "LIMIT 1;")
result = cur.fetchall()
cur.close()
conn.close()
conn_object.delete_tables()
self.assertEqual(result[0][0], 'banana')