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# $Id$
#
# BioPerl module for Bio::DB::PersistenceAdaptorI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::PersistenceAdaptorI - DESCRIPTION of Interface
=head1 SYNOPSIS
Give standard usage here
=head1 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()).
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 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/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::PersistenceAdaptorI;
use vars qw(@ISA);
use strict;
use Carp;
use Bio::Root::RootI;
@ISA = qw( Bio::Root::RootI );
=head1 Methods for managing persistent objects
Create (insert), store (update), remove (delete)
=cut
=head2 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.
=cut
sub create{
shift->throw_not_implemented();
}
=head2 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.
=cut
sub create_persistent{
shift->throw_not_implemented();
}
=head2 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.
=cut
sub store{
shift->throw_not_implemented();
}
=head2 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.
=cut
sub remove{
shift->throw_not_implemented();
}
=head1 Methods for locating objects
Find by primary key, by unique key, by association, and by query.
=cut
=head2 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
=cut
sub find_by_primary_key{
shift->throw_not_implemented();
}
=head2 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.
=cut
sub find_by_unique_key{
shift->throw_not_implemented();
}
=head2 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.
=cut
sub find_by_association{
shift->throw_not_implemented();
}
=head2 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
=cut
sub find_by_query{
shift->throw_not_implemented();
}
=head1 Methods for transactional control
Rollback and commit
=cut
=head2 commit
Title : commit
Usage :
Function: Commits the current transaction, if the underlying driver
supports transactions.
Example :
Returns : TRUE
Args : none
=cut
sub commit{
shift->throw_not_implemented();
}
=head2 rollback
Title : rollback
Usage :
Function: Triggers a rollback of the current transaction, if the
underlying driver supports transactions.
Example :
Returns : TRUE
Args : none
=cut
sub rollback{
shift->throw_not_implemented();
}
1;
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