def run(self):
install.run(self)
from biomaj.schema_version import SchemaVersion
SchemaVersion.migrate_pendings()
SchemaVersion.add_property(prop='desc', cfg='db.fullname')
SchemaVersion.set_version()
def run(self):
install.run(self)
from biomaj.schema_version import SchemaVersion
SchemaVersion.migrate_pendings()
SchemaVersion.add_property(prop='desc', cfg='db.fullname')
SchemaVersion.set_version()
def run(self):
install.run(self)
from biomaj.schema_version import SchemaVersion
SchemaVersion.migrate_pendings()
action="store",
dest="cfg",
default=None,
help="Bank configuration key to retrieve prop value")
parser.add_argument('-p',
'--property',
action="store",
dest="prop",
required=True,
help="Property name")
parser.add_argument('-v',
'--value',
action="store",
dest="value",
help="Property value")
args = parser.parse_args()
if sys.argv == 1:
parser.print_help()
sys.exit(0)
if args.value and args.cfg:
logging.error("-v and -c are not compatible")
sys.exit(1)
logging.warn(
"Needs global.properties in local directory or env variable BIOMAJ_CONF")
SchemaVersion.add_property(bank=args.bank,
prop=args.prop,
value=args.value,
cfg=args.cfg)
logging.info("Insertion done")
sys.exit(0)
from biomaj.schema_version import SchemaVersion
import logging
logging.warn('Migrate BioMAJ database...')
logging.warn('Needs global.properties in local directory or env variable BIOMAJ_CONF')
SchemaVersion.migrate_pendings()
logging.warn('Migration done')
if not os.path.exists(process_dir):
os.makedirs(process_dir)
cache_dir = BiomajConfig.global_config.get('GENERAL', 'cache.dir')
if not os.path.exists(cache_dir):
os.makedirs(cache_dir)
lock_dir = BiomajConfig.global_config.get('GENERAL', 'lock.dir')
if not os.path.exists(lock_dir):
os.makedirs(lock_dir)
redis_client = redis.StrictRedis(host=config['redis']['host'],
port=config['redis']['port'],
db=config['redis']['db'],
decode_responses=True)
logging.info("Check database schema and upgrade if necessary")
SchemaVersion.migrate_pendings()
SchemaVersion.set_version()
app = Flask(__name__)
CORS(app)
biomaj_metric = Counter("biomaj_daemon_total", "Bank total update execution.",
['bank', 'action', 'updated'])
biomaj_error_metric = Counter("biomaj_daemon_errors",
"Bank total update errors.", ['bank', 'action'])
biomaj_time_metric = Gauge("biomaj_daemon_time",
"Bank update execution time in seconds.",
['bank', 'action', 'updated'],
multiprocess_mode='all')