def test_single_other_query():
args = ['-q', 'linear', '-t', 'Topology', '-o', "%s/query_o.csv" % tmpdir] + base_args
opts = parse_args(args)
manage_pickle.run('query', opts)
assert filecmp.cmp("%s/query_o.csv" % tmpdir, 'test/data/query_o.exp')
cleanup()
def test_update():
args = ['-f', 'test/data/notes.txt', '-t', 'Notes'] + base_args
opts = parse_args(args)
manage_pickle.run('update', opts)
args = ['-f', "%s/updated.csv" % tmpdir] + base_args
opts = parse_args(args)
manage_pickle.run('save', opts)
assert filecmp.cmp("%s/updated.csv" % tmpdir, 'test/data/exp_updated.csv')
-f|file CSV output file
-d|database name of database
Example:
resistome.py save -f output_db.csv -d resistome1
avail: list available databases
Example:
resistome.py avail
help: Show this help menu
"""
# MAIN
args = sys.argv[1:]
try:
mode = args.pop(0)
except IndexError:
print_usage()
sys.exit()
if mode in ['add', 'query', 'update', 'save', 'avail', 'test']:
opts = parse_args(args)
manage_pickle.run(mode, opts)
elif mode == 'help':
print_usage()
else:
print "Please specify valid mode:"
print_usage()
def test_file_acc_query():
args = ['-f', 'test/data/q.txt', '-o', "%s/query_f.csv" % tmpdir] + base_args
opts = parse_args(args)
manage_pickle.run('query', opts)
assert filecmp.cmp("%s/query_f.csv" % tmpdir, 'test/data/query_f.exp')
def test_single_acc_query():
args = ['-q', 'CP000356', '-o', "%s/query_s.csv" % tmpdir] + base_args
opts = parse_args(args)
manage_pickle.run('query', opts)
assert filecmp.cmp("%s/query_s.csv" % tmpdir, 'test/data/query_s.exp')
def test_save():
args = ['-f', "%s/test.csv" % tmpdir] + base_args
opts = parse_args(args)
manage_pickle.run('save', opts)
assert filecmp.cmp("%s/test.csv" % tmpdir, 'test/data/exp.csv')
def test_add():
args = ['-f', 'test/data/small_db.txt'] + base_args
opts = parse_args(args)
manage_pickle.run('add', opts)
assert os.path.exists("%s/resistome_testing.db" % tmpdir)
