def __init__(self, host, api_key=None, label=None, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
self.host = host
self.api_key = api_key
self.label = label
self.loglevel = loglevel
self.wms = self.build_wms()
def main():
app = App()
parser = app.make_parser()
args = parser.parse_args()
logger = a_logger('main', level=args.loglevel, filename=args.logfile)
args.func(logger, args) if hasattr(args, 'func') else parser.print_help()
def __init__(self, yaml_file, loglevel='INFO'):
self.logger = a_logger(self.__class__.__name__, level=loglevel)
if os.path.isfile(yaml_file):
self.conf = load_config(yaml_file)
else:
self.logger.critical('{} not exists'.format(yaml_file))
sys.exit()
def __init__(self, host, user, password, server_host, server_user, loglevel='INFO'):
self.host = host
self.username = user
self.password = password
self.server_host = server_host
self.server_user = server_user
self.log = a_logger(self.__class__.__name__, level=loglevel)
MC = import_from("vcfminerclient", "VCFMinerClient",
error_msg=NO_VCFMINER_CLIENT_MESSAGE)
if not host.startswith(('http://', 'https://')):
self.log.warning('Must be provided a wellformed url to the VCFMiner server')
self.client = MC(conf=dict(host=self.host,
username=self.username,
password=self.password,
server_host=self.server_host,
server_user=self.server_user),
logger=self.log)
self.is_connected = self.client and self.client.is_authenticate
if not self.is_connected:
self.log.warning("{} VCFMiner server connection failed".format(host))
else:
self.log.info("Connected to {} VCFMiner server".format(host))
def main():
app = App()
parser = app.make_parser()
args = parser.parse_args()
logger = a_logger('main', level=args.loglevel, filename=args.logfile)
args.func(logger, args) if hasattr(args, 'func') else parser.print_help()
def __init__(self, host, user, password, bims_label, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
self.host = host
self.user = user
self.password = password
self.bims_label = bims_label
self.loglevel = loglevel
self.bims = self._build_bims()
def __init__(self, host, user, password, bims_label, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
self.host = host
self.user = user
self.password = password
self.bims_label = bims_label
self.loglevel = loglevel
self.bims = self._build_bims()
def main():
app = App()
parser = app.make_parser()
args = parser.parse_args()
ensure_dir(os.path.dirname(args.logfile))
logger = a_logger('Main', level=args.loglevel, filename=args.logfile)
logger.info('{} started'.format(__appname__.capitalize()))
args.func(logger, args) if hasattr(args, 'func') else parser.print_help()
def __init__(self, url, user, password, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
BC = import_from("bikaclient", "BikaClient",
error_msg=NO_BIKALIMS_CLIENT_MESSAGE)
if not url.startswith(('http://', 'https://')):
self.log.warning('Must be provided a wellformed url to the Bika '
'server')
self.client = BC(host=url, username=user, password=password)
self.log.info("{}".format(self.client.version))
self.log.info("Connected to {} Bika server".format(url))
def __init__(self, args=None):
self.loglevel = args.loglevel
self.logfile = args.logfile
self.logger = a_logger(self.__class__.__name__,
level=self.loglevel,
filename=self.logfile)
path_from_cli = args.config_file if 'config_file' in vars(
args) else None
cm = ConfigurationManager(args=args, path_from_cli=path_from_cli)
self.conf = cm.get_pipelines_config
self.cache_dir = cache_dir
def __init__(self, url, user, password, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
BC = import_from("bikaclient",
"BikaClient",
error_msg=NO_BIKALIMS_CLIENT_MESSAGE)
if not url.startswith(('http://', 'https://')):
self.log.warning('Must be provided a wellformed url to the Bika '
'server')
self.client = BC(host=url, username=user, password=password)
self.log.info("{}".format(self.client.version))
self.log.info("Connected to {} Bika server".format(url))
def __init__(self, host, user='******', password='******', browsers_label='',
server_host=None, server_user=None,
loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
self.host = host
self.user = user
self.password = password
self.server_host = server_host
self.server_user = server_user
self.browsers_label = browsers_label
self.loglevel = loglevel
self.browsers = self._build_browsers()
def __init__(self, host, user, password, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
self.log.debug('Opening connection to {} OMERO server'.format(host))
KB = import_from("bl.vl.kb", "KnowledgeBase")
try:
self.kb = KB(driver='omero')(host, user, password)
except ImportError, e:
self.log.error("{}. Have you forgotten to load the OMERO's "
"libraries?".format(e))
sys.exit()
def __init__(self, host, user, password, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
self.log.debug('Opening connection to {} OMERO server'.format(
host))
KB = import_from("bl.vl.kb", "KnowledgeBase")
try:
self.kb = KB(driver='omero')(host, user, password)
except ImportError, e:
self.log.error("{}. Have you forgotten to load the OMERO's "
"libraries?".format(e))
sys.exit()
def main(argv):
parser = get_parser()
args = parser.parse_args(argv)
logger = a_logger('BikaService',
level='INFO',
host=args.log_host,
port=args.log_port)
bikaApi = BikaApiRestService(logger)
irodsApi = IrodsApiRestService(logger)
bikaService = BikaService(bikaApi=bikaApi, irodsApi=irodsApi)
logger.info("Starting Service")
bikaService.start_service(args.host, args.port, args.log_file,
args.pid_file, args.server)
def __init__(self,
host,
user='******',
password='******',
browsers_label='',
server_host=None,
server_user=None,
loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
self.host = host
self.user = user
self.password = password
self.server_host = server_host
self.server_user = server_user
self.browsers_label = browsers_label
self.loglevel = loglevel
self.browsers = self._build_browsers()
def __init__(self, args=None):
self.loglevel = args.loglevel
self.logfile = args.logfile
self.logger = a_logger(self.__class__.__name__,
level=self.loglevel,
filename=self.logfile)
path_from_cli = args.config_file if 'config_file' in vars(
args) else None
cm = ConfigurationManager(args=args, path_from_cli=path_from_cli)
self.conf = cm.get_pipelines_config
self.core_environment_file = cm.get_default_config[
'core_environment_file']
self.environment_file = cm.get_default_config[
'project_environment_file']
self.cache_dir = cache_dir
ensure_dir(self.cache_dir)
self.ask_before_to_refresh = args.ask if 'ask' in vars(args) else False
def __init__(self,
args=None,
path_from_cli=None,
path_from_package='config/config.yaml',
config_filename='config.yaml'):
def copy_config_file_from_package(appname, src, dst):
_from_package = resource_filename(appname, src)
copyfile(_from_package, dst)
self.loglevel = args.loglevel
self.logfile = args.logfile
logger = a_logger(self.__class__.__name__,
level=self.loglevel,
filename=self.logfile)
cfg_dir = os.path.join(config_dir)
config_file_path = os.path.join(cfg_dir, config_filename)
# Create configuration file from default if needed
if not path_exists(cfg_dir, logger, force=False):
logger.info('Creating config dir {}'.format(cfg_dir))
ensure_dir(cfg_dir)
if not path_exists(config_file_path, logger, force=False):
logger.info('Copying default config file from {} package '
'resource'.format(__appname__))
copy_config_file_from_package(__appname__, path_from_package,
config_file_path)
config_file_paths = []
if path_from_cli and path_exists(path_from_cli, logger, force=False):
config_file_paths.append(WeightedPath(path_from_cli, 0))
if path_exists(config_file_path, logger, force=False):
config_file_paths.append(WeightedPath(config_file_path, 1))
logger.debug("config file paths: {}".format(config_file_paths))
config_file_path = sorted(config_file_paths)[0].path
logger.info('Reading configuration from {}'.format(config_file_path))
c = load_config(config_file_path)
self.pipes_conf = c['pipelines'] if 'pipelines' in c else None
self.default_conf = c['default_vars'] if 'default_vars' in c else None
def __init__(self):
logger = a_logger('app')
conf = get_conf(logger, config_file_from_cli=None, profile='celery')
celery_conf = conf.get_section('celery')
self.broker_url = celery_conf.get('broker_url',
'amqp://*****:*****@localhost:5672')
self.result_backend = celery_conf.get('result_backend',
'amqp://*****:*****@localhost:5672')
self.task_serializer = celery_conf.get('task_serializer', 'json')
self.result_serializer = celery_conf.get('result_serializer', 'json')
self.enable_utc = celery_conf.get('enable_utc', False)
self.timezone = celery_conf.get('timezone', 'Europe/Rome')
self.task_publish_retry = celery_conf.get('task_publish_retry', True)
retry_policy = {
'max_retries': 10,
'interval_start': 5,
'interval_step': 5,
'interval_max': 5,
}
self.task_publish_retry_policy = celery_conf.get(
'task_publish_retry_policy', retry_policy)
def __init__(self):
logger = a_logger('app')
conf = get_conf(logger, config_file_from_cli=None, profile='celery')
celery_conf = conf.get_section('celery')
self.broker_url = celery_conf.get('broker_url',
'amqp://*****:*****@localhost:5672')
self.result_backend = celery_conf.get(
'result_backend', 'amqp://*****:*****@localhost:5672')
self.task_serializer = celery_conf.get('task_serializer', 'json')
self.result_serializer = celery_conf.get('result_serializer', 'json')
self.enable_utc = celery_conf.get('enable_utc', False)
self.timezone = celery_conf.get('timezone', 'Europe/Rome')
self.task_publish_retry = celery_conf.get('task_publish_retry', True)
retry_policy = {
'max_retries': 10,
'interval_start': 5,
'interval_step': 5,
'interval_max': 5,
}
self.task_publish_retry_policy = celery_conf.get(
'task_publish_retry_policy', retry_policy)
def __init__(self, galaxy_host, api_key, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
GI = import_from('bioblend.galaxy.objects', 'GalaxyInstance')
self.client = GI(galaxy_host, api_key)
self.log.info("Connected to {}".format(galaxy_host))
def __init__(self, loglevel='INFO'):
self.log = a_logger(self.__class__.__name__, level=loglevel)
def __init__(self, config, loglevel='INFO', logfile=sys.stdout):
self.config = config
self.logger = a_logger(self.__class__.__name__,
level=loglevel,
filename=logfile)
