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from unittest import TestCase
from collections import namedtuple
import os
import inspect
import contextlib
import shutil
import seqcluster.libs.parameters
import seqcluster.libs.logger as mylog
from seqcluster.libs.do import find_cmd
from seqcluster.libs.read import load_data
from seqcluster.db import make_database
from seqcluster.libs.logger import initialize_logger
from nose.plugins.attrib import attr
@contextlib.contextmanager
def make_workdir():
remove_old_dir = True
dirname = os.path.join(os.path.dirname(__file__), "test_automated_output")
if remove_old_dir:
if os.path.exists(dirname):
shutil.rmtree(dirname)
os.makedirs(dirname)
orig_dir = os.getcwd()
try:
os.chdir(dirname)
yield dirname
finally:
os.chdir(orig_dir)
class TestDatabase(TestCase):
@attr(database=True)
def test_database(self):
if find_cmd("sqlite3"):
with make_workdir() as workdir:
arg = namedtuple('args', 'debug print_debug json ')
args = arg(True, True, "../../data/examples/seqcluster.json")
initialize_logger(".", args.debug, args.print_debug)
logger = mylog.getLogger(__name__)
logger.info(args)
logger.info("Reading data")
data = load_data(args.json)
logger.info("Create database")
make_database(data)
# self.assertTrue()
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