def test_import_network_source(self):
"""
Tests if the IoConnection uses the source dict.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(('banana', 2, 5))
nx.write_graphml(g, path="test.graphml")
import_networks("test.graphml", sources={"test": "banana"})
os.remove("test.graphml")
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT networkID " "FROM networks " "LIMIT 1;")
result = cur.fetchall()
cur.close()
conn.close()
conn_object.delete_tables()
self.assertEqual(result[0][0], 'test')
def test_import_networks(self):
"""
Tests if the import_networks function reads the correct database file,
and imports the network file, by querying the networks table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(('test', 2, 5))
nx.write_graphml(g, path="test.graphml")
import_networks("test.graphml")
os.remove("test.graphml")
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT studyID " "FROM networks " "LIMIT 1;")
result = cur.fetchall()
cur.close()
conn.close()
conn_object.delete_tables()
self.assertEqual(result[0][0], 'test')
def test_import_network_edge(self):
"""
Tests if the import_network function reads the correct database file,
and imports the network file, by querying the edges table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(('test', 2, 5))
nx.write_graphml(g, path="test.graphml")
import_networks("test.graphml")
os.remove("test.graphml")
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT source, target " "FROM edges " "LIMIT 2;")
result = cur.fetchall()
cur.close()
conn.close()
conn_object.delete_tables()
self.assertCountEqual(result, [("GG_OTU_1", "GG_OTU_2"),
("GG_OTU_2", "GG_OTU_5")])
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_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()
def test_add_taxon_missingvalues(self):
"""
Tests whether a row is added to the taxonomy table,
even when some assignments are unknown.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(values=('banana', 1, 2))
conn_object.add_taxon(values=('Listeria', 'banana', 'Bacteria',
'Firmicutes', 'Bacilli', None, None,
None, None))
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT * from taxonomy;")
result = cur.fetchall()
# long format table of 5 * 6 observations
self.assertEqual(result[0],
('Listeria', 'banana', 'Bacteria', 'Firmicutes',
'Bacilli', None, None, None, None))
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_summary(self):
"""
Tests whether a row is added to the bioms table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_summary(values=('potato', 5, 20))
conn = psycopg2.connect(
**{
"host": "localhost",
"database": "test",
"user": "******",
"password": "******"
})
cur = conn.cursor()
cur.execute("SELECT * from bioms;")
result = cur.fetchall()
# long format table of 5 * 6 observations
self.assertEqual(result[0], ('potato', 5, 20))
cur.close()
conn.close()
conn_object.delete_tables()