def _load_lsg_credentials():
"""Read Life Science Grid Portal credentials from file and store in os.environ variables."""
#Get path to credential file
from divergence import resource_filename
lsgp_credentials_file = resource_filename(__name__, 'credentials/lsg-portal.cfg')
# Copy template config file to actual search path when file can not be found
if not os.path.exists(lsgp_credentials_file):
shutil.copy(lsgp_credentials_file + '.sample', lsgp_credentials_file)
logging.info('Copied .sample file to %s', lsgp_credentials_file)
logging.info('Credentials not found on path: Reading credentials from %s', lsgp_credentials_file)
#Parse credential file
from ConfigParser import SafeConfigParser
parser = SafeConfigParser()
parser.read(lsgp_credentials_file)
os.environ['lsg_username'] = parser.defaults()['lsg_username']
os.environ['lsg_password'] = parser.defaults()['lsg_password']
def _load_lsg_credentials():
"""Read Life Science Grid Portal credentials from file and store in os.environ variables."""
#Get path to credential file
from divergence import resource_filename
lsgp_credentials_file = resource_filename(__name__,
'credentials/lsg-portal.cfg')
# Copy template config file to actual search path when file can not be found
if not os.path.exists(lsgp_credentials_file):
shutil.copy(lsgp_credentials_file + '.sample', lsgp_credentials_file)
logging.info('Copied .sample file to %s', lsgp_credentials_file)
logging.info('Credentials not found on path: Reading credentials from %s',
lsgp_credentials_file)
#Parse credential file
from ConfigParser import SafeConfigParser
parser = SafeConfigParser()
parser.read(lsgp_credentials_file)
os.environ['lsg_username'] = parser.defaults()['lsg_username']
os.environ['lsg_password'] = parser.defaults()['lsg_password']
def _get_root_credentials():
"""Retrieve MySQL credentials from orthomcl.config to an account that is allowed to create new databases."""
orthomcl_credentials_file = resource_filename(__name__, 'credentials/orthomcl.cfg')
# Copy template config file to actual search path when file can not be found
if not os.path.exists(orthomcl_credentials_file):
shutil.copy(orthomcl_credentials_file + '.sample', orthomcl_credentials_file)
log.info('Copied .sample file to %s', orthomcl_credentials_file)
# Parse configuration file
config = SafeConfigParser()
config.read(orthomcl_credentials_file)
host = config.get('mysql', 'host')
port = config.getint('mysql', 'port')
user = config.get('mysql', 'user')
passwd = config.get('mysql', 'pass')
# Fall back to environment value for password when available
if passwd == 'pass' and 'mysql_password' in os.environ:
passwd = os.environ['mysql_password']
return host, port, user, passwd