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_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 masq(masq_args):
"""
Main function for running masq.
Accepts a dictionary of arguments from the argument parser
and calls the appropriate module function.
:param masq_args: Arguments.
:return:
"""
if masq_args['version']:
info = VersionInfo('anuran')
logger.info('Version ' + info.version_string())
sys.exit(0)
# unpack args
config = masq_args['config']
database = masq_args['config']
networks = masq_args['networks']
bioms = masq_args['bioms']
username = masq_args['username']
password = masq_args['password']
host = masq_args['host']
mapping = masq_args['mapping']
sources = masq_args['sources']
if masq_args['mapping']:
try:
with open(masq_args['mapping'], 'r') as file:
contents = file.read()
mapping = literal_eval(contents)
except (ValueError, TypeError):
logger.warning("Mapping file could not be imported,\n"
"and will be ignored. ")
if masq_args['sources']:
try:
with open(masq_args['sources'], 'r') as file:
contents = file.read()
mapping = literal_eval(contents)
except (ValueError, TypeError):
logger.warning("Source file could not be imported,\n"
"and will be ignored. ")
if masq_args['create']:
logger.info('Setting up tables in PostgreSQL database. ')
setup_database(config=config,
create=True,
host=host,
database=database,
username=username,
password=password)
elif masq_args['delete']:
setup_database(config=config,
create=False,
host=host,
database=database,
username=username,
password=password)
logger.info("Deleted tables in PostgreSQL database.")
if masq_args['bioms']:
logger.info('Importing BIOM files... ')
for biom in bioms:
import_biom(location=biom,
mapping=mapping,
config=config,
host=host,
database=database,
username=username,
password=password)
if masq_args['networks']:
logger.info('Importing network files...')
for network in networks:
import_networks(location=network,
mapping=mapping,
sources=sources,
config=config,
host=host,
database=database,
username=username,
password=password)
logger.info('Completed tasks! ')