15 Apr 2011 19:35:57 UTC
- Distribution: BioPerl-DB
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- License: perl_5
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- This version
- Latest versionCJFIELDS Christopher Fieldsand 1 contributors
- BioPerl Team
- AUTHOR - Hilmar Lapp
- Methods for managing persistent objects
- Methods for locating objects
- Methods for transactional control
Bio::DB::PersistenceAdaptorI - DESCRIPTION of Interface
Give standard usage here
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()).
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Email hlapp at gmx.net
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Create (insert), store (update), remove (delete)
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.
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.
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.
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 key, by unique key, by association, and by query.
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
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.
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.
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
Rollback and commit
Title : commit Usage : Function: Commits the current transaction, if the underlying driver supports transactions. Example : Returns : TRUE Args : none
Title : rollback Usage : Function: Triggers a rollback of the current transaction, if the underlying driver supports transactions. Example : Returns : TRUE Args : none
Module Install Instructions
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.