Package Bio :: Package config :: Module DBRegistry :: Class BioSQLDB

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Class BioSQLDB

Registry.RegisterableObject --+    
                              |    
                       DBObject --+
                                  |
                                 BioSQLDB

Represent a BioSQL-style database to retrieve SeqRecord objects.

This returns a SeqRecord-like object from _get() instead of a handle (since BioSQL is not going to give you a handle).

Instance Methods

__init__(self, name, doc='', db_host='localhost', db_port='', db_user='root', db_passwd='', sql_db='', namespace_db='', db_type='mysql')
Intialize with information for connecting to the BioSQL db. source code

_get_db_module(self, db_type)
Retrieve the appropriate module to use for connecting to a database

source code

data

_get(self, key)

source code

another data type

_convert_to(self, data, to_io)

source code

pickleable_obj

_make_pickleable(self, item)

source code

data

_unmake_pickleable(self, item)

source code

Inherited from DBObject: __getitem__, get, get_as, set

Inherited from DBObject (private): _set

Method Details

init(self, name, doc=`''`, db_host=`'localhost'`, db_port=`''`, db_user=`'root'`, db_passwd=`''`, sql_db=`''`, namespace_db=`''`, db_type=`'mysql'`)
(Constructor)

Intialize with information for connecting to the BioSQL db.

Overrides: Registry.RegisterableObject.__init__

_get_db_module(self, db_type)

Retrieve the appropriate module to use for connecting to a database

This parses a description of the database and tries to determine which module is appropriate for that database type.

_get(self, key)

Returns: data
Overrides: DBObject._get: (inherited documentation)

_convert_to(self, data, to_io)

Returns: another data type
Overrides: DBObject._convert_to: (inherited documentation)

_make_pickleable(self, item)

Returns: pickleable_obj
Overrides: DBObject._make_pickleable: (inherited documentation)

_unmake_pickleable(self, item)

Returns: data
Overrides: DBObject._unmake_pickleable: (inherited documentation)