bbcflib::genrep_cache Namespace Reference

Classes
class	Assembly
class	Store
class	Ass
Functions
def	dec
def	cached_ass
def	cached
def	init
def	configuration
def	get_session
Variables
tuple	home_dir = os.getenv('HOME')
string	conf_file = '.genrepcache.conf'
tuple	conf_path = os.path.join(home_dir, conf_file)
dictionary	default_conf
string	section = 'GenRep cache'
tuple	Base = declarative_base()
tuple	metadata = MetaData()
tuple	grc
tuple	ass
tuple	config = ConfigParser.ConfigParser()
tuple	nb = config.getint(section, 'time_limit')
tuple	connector = json.loads(config.get(section, 'connector'))
tuple	assembly_cache = json.loads(config.get(section, 'assembly_cache'))
tuple	unique_ids = json.loads(config.get(section, 'unique_ids'))
tuple	timedelta = datetime.timedelta(days=nb)
tuple	DBSession = init(connector, metadata, [grc, ass], echo=False)
tuple	session = get_session()
tuple	a = Assembly('mm9')

---

Detailed Description

Build a local database that store queries to GenRep. Once stored, result are fetched from it
instead of from GenRep web-service.

Use it :
from bbcflib import genrep_cache as genrep
print genrep.Assembly('mm9').chrnames

Warning :
You can only call Assembly and all methods belonging to it.
Direct calls to GenRep() or GenRepObject() are not supported

Functioning :
On import it create the configuration file `.genrepcache.conf` in your home directory with 
parameters :
    db_name = Database name.
    time_limit = Time limit when a cached response must be reloaded (in days).
    assembly_cache = List of methods you want to cache.
    unique_ids = Important attributes in your class that will determine the uniqueness of the child object
    connector = Default connector : change it to what you want and supported by sqlalchemy 
(see http://docs.sqlalchemy.org/en/latest/core/engines.html#supported-databases).

Then on method call, if the method is not in `assembly_cache` parameter, your call is redirected
to the original GenRep library, else the response is fetched from the local database (if query already logged
and not outdated)

---

Function Documentation

def bbcflib::genrep_cache::cached	(		obj,
			func,
			uid,
			args,
			kw,
			_property
	)

Look if the method is already cached and not outdated
then return the response

def bbcflib::genrep_cache::cached_ass	(		args,
			kw
	)

Cache assembly

def bbcflib::genrep_cache::dec	(		obj,
			func,
			_property = False
	)

Hook to fetch response from cache if there is one.

def bbcflib::genrep_cache::init	(		connector,
			metadata,
			tables,
			echo = False
	)

Initialization of the engine.

---

Variable Documentation

tuple bbcflib::genrep_cache::ass

Initial value:

Table('ass', metadata,
    Column('args', Text, primary_key=True),
    Column('kw', Text, primary_key=True),
    Column('assembly', PickleType),
    Column('date', DateTime))

dictionary bbcflib::genrep_cache::default_conf

Initial value:

{'db_name' : 'genrepcache.sqlite',
                'time_limit' : 14,
                'assembly_cache' : ['chrnames', 'fasta_path', 'get_sqlite_url', 'sqlite_path'],
                'unique_ids' : ['intype', 'nr_assembly_id', 'source_id'],
                }

tuple bbcflib::genrep_cache::grc

Initial value:

Table('grc', metadata,
     Column('uid', Text, primary_key=True),
     Column('args', Text, primary_key=True),
     Column('kw', Text, primary_key=True),
     Column('response', Text),
     Column('date', DateTime))