def update_distro_conf_file(path, distro, d):
logger.debug('Updating distro %s' % path)
desc = ""
with open(path, 'r') as f:
for line in f:
if line.startswith('#@NAME:'):
desc = line[7:].strip()
if line.startswith('#@DESCRIPTION:'):
desc = line[14:].strip()
desc = re.sub(
r'Distribution configuration for( running)*( an)*( the)*',
'', desc)
break
distro_name = ''
try:
d = utils.parse_conf(path, d)
distro_name = d.getVar('DISTRO_NAME', True)
except Exception as e:
logger.warn('Error parsing distro configuration file %s: %s' %
(path, str(e)))
if distro_name:
distro.description = distro_name
else:
distro.description = desc
def args(self, p):
path = "cfgs/args"
if not isfile(path): return
d = parse_conf(path)
for k, v in d.items():
kwargs = v
try:
if kwargs["type"] == "int":
kwargs["type"] = int
elif kwargs["type"] == "float":
kwargs["type"] = float
except:
pass
p.add_argument("--" + self.__class__.__name__.lower() + "-" + k,
**kwargs)
#!/usr/bin/python
# This script queries the publication table and produces several statistics
import MySQLdb;
from utils import parse_conf;
#parse conf.php file
conf = open("../conf.php");
credentials = parse_conf(conf);
conf.close()
host = credentials['host']
user = credentials['user']
passwd = credentials['passwd']
db = credentials['db']
mysql = MySQLdb.connect(unix_socket="/tmp/mysql.sock", host=host, user=user, passwd=passwd, db=db);
cursor = mysql.cursor()
# Number of accessions in table publications:
cursor.execute("SELECT distinct accession FROM publications WHERE accession is not null and accession !='' and accession != 'null'");
result = cursor.fetchall()
accessions_pub = [];
for item in result:
accessions_pub.append(item[0]);
# Number of accessions in table sequences:
cursor.execute("SELECT distinct accession FROM sequences WHERE accession is not null and accession !='' and accession != 'null'");
result = cursor.fetchall()
accessions_seq = [];
for item in result:
def service(config):
"""Jaguar service operations."""
try:
parse_conf(config)
except:
config.server['port'] = '8080'
def policy(config):
"""Jaguar policy operations."""
parse_conf(config)
