/ 
bioperl-db-1.5.2_100
/ Bio::DB::PersistenceAdaptorI

NAME

Bio::DB::PersistenceAdaptorI - DESCRIPTION of Interface

SYNOPSIS

Give standard usage here

DESCRIPTION

This interface gives the base methods to be implemented by modules that bridge persistent objects to and from their datastores.

The design choice mixes the strategy pattern with the factory pattern (find_by_XXXX()).

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Methods for managing persistent objects

Create (insert), store (update), remove (delete)

create

Title   : create
Usage   : $objectstoreadp->create($obj)
Function: Creates the object as a persistent object in the datastore. This
          is equivalent to an insert.

          If the object already implements this interface, it will be
          populated with values, and the primary key will be set.

Example :
Returns : A Bio::DB::PersistentObjectI implementing object wrapping
          the inserted object.
Args    : The object to be inserted.

          Optionally, additional named parameters. A common parameter
          will be -fkobjs, with a reference to an array of foreign
          key objects if these cannot be obtained from the object
          itself.

create_persistent

Title   : create_persistent
Usage   :
Function: Takes the given object and turns it onto a
          L<Bio::DB::PersistentObjectI> implementing object. Returns
          the result. Does not actually create the object in a
          database.

          Calling this method is expected to have a recursive effect
          such that all children of the object, i.e., all slots that
          are objects themselves, are made persistent objects, too.

Example :
Returns : A Bio::DB::PersistentObjectI implementing object wrapping the
          passed object.
Args    : An object to be made into a PersistentObjectI object, and the class
          of which is suitable for this adaptor.

          Optionally, the class which actually implements wrapping
          the object to become a PersistentObjectI.

store

Title   : store
Usage   : $objectstoreadp->store($persistent_obj)
Function: Updates the given persistent object in the datastore.

          Implementations should be flexible and delegate to create()
          if the primary_key() method of the object returns undef.

Example :
Returns : TRUE on success and FALSE otherwise
Args    : The object to be updated, which must implement
          Bio::DB:PersistentObjectI.

          Optionally, additional named parameters. A common parameter
          will be -fkobjs, with a reference to an array of foreign
          key objects if these cannot be obtained from the object
          itself.

remove

Title   : remove
Usage   : $objectstoreadp->remove($persistent_obj, @params)
Function: Removes the persistent object from the datastore.
Example :
Returns : TRUE on success and FALSE otherwise
Args    : The object to be removed, and optionally additional (named) 
          parameters.

Methods for locating objects

Find by primary key, by unique key, by association, and by query.

find_by_primary_key

Title   : find_by_primary_key
Usage   : $popj = $objectstoreadp->find_by_primary_key($pk)
Function: Locates the entry associated with the given primary key and
          initializes a persistent object with that entry.
Example :
Returns : An instance of the class this adaptor adapts, represented by an
          object implementing Bio::DB::PersistentObjectI, or undef if no
          matching entry was found.
Args    : The primary key

find_by_unique_key

Title   : find_by_unique_key
Usage   :
Function: Locates the entry matching the unique key attributes as set in the
          passed object, and populates a persistent object with this entry.
Example :
Returns : A Bio::DB::PersistentObjectI implementing object, with the
          attributes populated with values provided by the entry in
          the datastore, or undef if no matching entry was found. If
          one was found, the object returned will be the first
          argument if that implemented Bio::DB::PersistentObjectI
          already.

Args    : The object with those attributes set that constitute the
          chosen unique key (note that the class of the object must
          be suitable for the adaptor).

          Additional attributes and values if required, passed as a
          reference to a hash map.

find_by_association

Title   : find_by_association
Usage   :
Function: Locates those records associated between a number of
          objects. The focus object (the type to be instantiated)
          depends on the adaptor class that inherited from this
          class.

Example :
Returns : A Bio::DB::Query::QueryResultI implementing object 
Args    : Named parameters. At least the following must be recognized:
              -objs   a reference to an array of objects to be associated with
                      each other
              -obj_factory the factory to use for instantiating objects from
                      the found rows
 Caveats: Make sure you *always* give the objects to be associated in the
          same order.

find_by_query

Title   : find_by_query
Usage   :
Function: Locates entries that match a particular query and returns the
          result as an array of peristent objects.

          The query is represented by an instance of
          Bio::DB::Query::BioQuery or a derived class. Note that
          SELECT fields will be ignored and auto-determined. Give
          tables in the query as objects, class names, or adaptor
          names, and columns as slot names or foreign key class names
          in order to be maximally independent of the exact
          underlying schema. The driver of this adaptor will
          translate the query into tables and column names.

Example :
Returns : A Bio::DB::Query::QueryResultI implementing object
Args    : The query as a Bio::DB::Query::BioQuery or derived instance.
          Note that the SELECT fields of that query object will inadvertantly
          be overwritten.
          Optionally additional (named) parameters. Recognized parameters
          at this time are
             -fkobjs    a reference to an array of foreign key objects that
                        are not retrievable from the persistent object itself
             -obj_factory  the object factory to use for creating objects for
                        resulting rows
             -name      a unique name for the query, which will make the
                        the statement be a cached prepared statement, which
                        in subsequent invocations will only be re-bound with
                        parameters values, but not recreated
             -values    a reference to an array holding the values to be
                        bound, if the query is a named query

Methods for transactional control

Rollback and commit

commit

Title   : commit
Usage   :
Function: Commits the current transaction, if the underlying driver
          supports transactions.
Example :
Returns : TRUE
Args    : none

rollback

Title   : rollback
Usage   :
Function: Triggers a rollback of the current transaction, if the
          underlying driver supports transactions.
Example :
Returns : TRUE
Args    : none