Bio::DB PersistenceAdaptorI
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Summary
Bio::DB::PersistenceAdaptorI - DESCRIPTION of Interface
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Carp
Inherit
Bio::Root::RootI
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()).
Methods
createDescriptionCode
create_persistentDescriptionCode
storeDescriptionCode
removeDescriptionCode
find_by_primary_keyDescriptionCode
find_by_unique_keyDescriptionCode
find_by_associationDescriptionCode
find_by_queryDescriptionCode
commitDescriptionCode
rollbackDescriptionCode
Methods description
createcode    nextTop
 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_persistentcodeprevnextTop
 Title   : create_persistent
Usage :
Function: Takes the given object and turns it onto a
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.
storecodeprevnextTop
 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.
removecodeprevnextTop
 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.
find_by_primary_keycodeprevnextTop
 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_keycodeprevnextTop
 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_associationcodeprevnextTop
 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_querycodeprevnextTop
 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
commitcodeprevnextTop
 Title   : commit
Usage :
Function: Commits the current transaction, if the underlying driver
supports transactions.
Example :
Returns : TRUE
Args : none
rollbackcodeprevnextTop
 Title   : rollback
Usage :
Function: Triggers a rollback of the current transaction, if the
underlying driver supports transactions.
Example :
Returns : TRUE
Args : none
Methods code
createdescriptionprevnextTop
sub create {
    shift->throw_not_implemented();
}
create_persistentdescriptionprevnextTop
sub create_persistent {
    shift->throw_not_implemented();
}
storedescriptionprevnextTop
sub store {
    shift->throw_not_implemented();
}
removedescriptionprevnextTop
sub remove {
    shift->throw_not_implemented();
}
find_by_primary_keydescriptionprevnextTop
sub find_by_primary_key {
    shift->throw_not_implemented();
}
find_by_unique_keydescriptionprevnextTop
sub find_by_unique_key {
    shift->throw_not_implemented();
}
find_by_associationdescriptionprevnextTop
sub find_by_association {
    shift->throw_not_implemented();
}
find_by_querydescriptionprevnextTop
sub find_by_query {
    shift->throw_not_implemented();
}
commitdescriptionprevnextTop
sub commit {
    shift->throw_not_implemented();
}
rollbackdescriptionprevnextTop
sub rollback {
    shift->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
 
Please direct usage questions or support issues to the mailing list:

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.
Reporting BugsTop
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 LappTop
Email hlapp at gmx.net
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Methods for managing persistent objectsTop
   Create (insert), store (update), remove (delete)
Methods for locating objectsTop
    Find by primary key, by unique key, by association, and by query.
Methods for transactional controlTop
   Rollback and commit