Bio::DB::BioSQL::BasePersistenceAdaptor - DESCRIPTION of Object
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::DB::BioSQL::BasePersistenceAdaptor->new(); Function: Builds a new Bio::DB::BioSQL::BasePersistenceAdaptor object Returns : an instance of Bio::DB::BioSQL::BasePersistenceAdaptor Args :
This comprises of creating an object in the database (equivalent to an insert), storing an object in the database (equivalent to an update), removing an object from the database (equivalent to a delete), and adding and removing associations between objects when the underlying schema supports such associations.
Title : create Usage : $objectstoreadp->create($obj, @params) Function: Creates the object as a persistent object in the datastore. This is equivalent to an insert. Example : Returns : A Bio::DB::PersistentObjectI implementing object wrapping the inserted object. Args : The object to be inserted, and optionally additional (named) parameters. A common parameter will be -fkobjs, with a reference to an array of foreign key objects that are not retrievable from the persistent object itself.
Title : store Usage : $objectstoreadp->store($persistent_obj,@params) Function: Updates the given persistent object in the datastore. Example : Returns : TRUE on success and FALSE otherwise Args : The object to be updated, and optionally additional (named) parameters. A common parameter will be -fkobjs, with a reference to an array of foreign key objects that are not retrievable from the persistent 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.
Title : add_assocation Usage : Function: Stores the association between given objects in the datastore. Example : Returns : TRUE on success and FALSE otherwise Args : Named parameters. At least the following must be recognized: -objs a reference to an array of objects to be associated with each other -values a reference to a hash the keys of which are abstract column names and the values are values of those columns. These columns are generally those other than the ones for foreign keys to the entities to be associated -contexts optional; if given it denotes a reference to an array of context keys (strings), which allow the foreign key name to be determined through the slot-to-column map rather than through foreign_key_name(). This may be necessary if more than one object of the same type takes part in the association. The array must be in the same order as -objs, and have the same number of elements. Put undef for objects for which there are no multiple contexts. Caveats: Make sure you *always* give the objects to be associated in the same order.
Title : remove_assocation Usage : Function: Removes the association between the given objects in the datastore. Example : Returns : TRUE on success and FALSE otherwise Args : Named parameters. At least the following must be recognized: -objs a reference to an array of objects the association between which is to be removed -values a reference to a hash the keys of which are abstract column names and the values are values of those columns. These columns are generally those other than the ones for foreign keys to the entities to be associated. Supplying this is only necessary if those columns participate in a unique key by which to find those associations to be removed. -contexts optional; if given it denotes a reference to an array of context keys (strings), which allow the foreign key name to be determined through the slot-to-column map rather than through foreign_key_name(). This may be necessary if more than one object of the same type takes part in the association. The array must be in the same order as -objs, and have the same number of elements. Put undef for objects for which there are no multiple contexts. Caveats: Make sure you *always* give the objects to be associated in the same order.
The DBAdaptorI factory mandates this operation, but it will in most cases conduct the operation by first finding the appropriate persistence adaptor and then asking the adaptor to do the operation. Hence, here is where the real stuff happens.
Title : create_persistent Usage : Function: Takes the given object and turns it onto a 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 (the class will be suitable for this adaptor). Optionally, the class which actually implements wrapping the object to become a PersistentObjectI.
Title : _create_persistent Usage : Function: Calling this method recursively replaces all eligible children of the object, i.e., all slots that are objects themselves and for which an adaptor exists, with instances of Bio::DB::PersistentObjectI. This is an internal method. Do not call from outside. Example : Returns : The first argument. Args : - A Bio::DB::PersistentObjectI implementing object, the class of which is suitable for this adaptor (unless on a recursive call). - Optionally, the class which actually implements wrapping the object to become a PersistentObjectI.
This comprises of finding by primary key, finding by unique key (alternative key), finding by association, and finding by query.
Title : find_by_primary_key Usage : $objectstoreadp->find_by_primary_key($pk) Function: Locates the entry associated with the given primary key and initializes a persistent object with that entry. By default this implementation caches all objects by primary key if caching is enabled. Note that by default caching is disabled. Provide -cache_objects => 1 to the constructor in order to enable it. 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. Optionally, the Bio::Factory::ObjectFactoryI compliant object factory to be used for instantiating the proper class. If the object does not implement Bio::Factory::ObjectFactoryI, it is assumed to be the object to be populated with the query results.
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. This method will ask get_unique_key_query() for the actual alternative key(s) by which to search. It can handle multiple alternative keys returned by get_unique_key_query(). So the knowledge about which properties of an object constitute an alternative key, and how to retrieve the values for those properties, is with get_unique_key_query() which therefore must be overridden by every adaptor. Multiple keys will be semantically ORed with short-cut evaluation, meaning the method will loop over all alternative keys and terminate the loop as soon as a match is found. Thus, the order of multiple keys returned by get_unique_key_query() does matter. 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, and a new persistent object otherwise. 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 named parameters. Specifically noteworthy are -fkobjs a reference to an array holding foreign key objects if those can't be retrieved from the object itself (e.g., a Comment object will need the Seq object passed with this argument) -obj_factory the object factory to use to create new objects when a matching row is found. If not specified, the passed object will be populated rather than creating a new object. -flat_only do not retrieve and attach children (objects having a foreign key to the entity handled by this adaptor) if value evaluates to true (default: false)
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. This is the protected version of find_by_unique_key. Since it requires more upfront work to pass the right parameters in the right order, you should not call it from outside, but there may be situations where you want to call this method from a derived class. 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, and a new persistent object otherwise. 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). - The query as an anonymous hash with keys being properties in the unique key. See get_unique_key_query() for a more detailed description on what the expected structure is. - A reference to an array of foreign key objects if applicable (undef if the entity doesn't have any foreign keys). - The object factory to use to create a new object if a matching row is found. Optional; if not specified the passed object will be populated with the found values rather than a new object created. - A flag indicating whether not to retrieve and attach children (objects having a foreign key to the object to build). Defaults to false if omitted, meaning children will be attached.
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 -contexts optional; if given it denotes a reference to an array of context keys (strings), which allow the foreign key name to be determined through the slot-to-column map rather than through foreign_key_name(). This may be necessary if more than one object of the same type takes part in the association. The array must be in the same order as -objs, and have the same number of elements. Put undef for objects for which there are no multiple contexts. -obj_factory the factory to use for instantiating object from the found rows -constraints a reference to an array of additional L<Bio::DB::Query::QueryConstraint> objects -values the values to bind to the constraint clauses, as a hash reference keyed by the constraints 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::AbstractQuery 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::AbstractQuery 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 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 -flat_only do not retrieve and attach children (objects having a foreign key to the entity handled by this adaptor) if value evaluates to true (default: false)
Title : _build_object Usage : Function: Build and populate an object or populate a prepuilt object from a row from the database. This is a private method primarily to centralize the code for this task from the various find_by_XXXX methods. Don't call from outside unless you know what you're doing. Example : Returns : A persistent object (implements Bio::DB::PersistentObjectI) Args : Named parameters. Currently supported are: -obj A prebuilt object to be populated only (optional) -row a reference to an array of column values (mandatory) -pk the primary key to be associated with the new object (optional) -num_fks the number of foreign key instances which need to be associated with the object to be built (optional, defaults to 0) -obj_factory an object factory to be used for instantiating the object if it needs to be created -flat_only do not retrieve and attach children (objects having a foreign key to the object to build) if value evaluates to true (default: false)
This comprises of rollback and commit. The point to have those here even though they merely delegate to the driver is that the caller doesn't need to distinguish whether the RDBMS driver supports transactions or not. If the DBI driver doesn't then simply the adaptor driver won't do anything.
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
These are published attributes for convenient perusal by derived adaptors.
Title : dbcontext Usage : $obj->dbcontext($newval) Function: Get/set the DBContextI object representing the physical database. Example : Returns : A Bio::DB::DBContextI implementing object Args : on set, the new Bio::DB::DBContextI implementing object
Title : dbh Usage : $obj->dbh($newval) Function: Get/set the DBI connection handle. If you set this from outside, you should know exactly what you are doing. Example : Returns : value of dbh (a database handle) Args : on set, the new value (a database handle, optional)
Title : dbd Usage : $obj->dbd($newval) Function: Get/set the driver for this adaptor. The driver will usually be an instance of a class derived from L<Bio::DB::BioSQL::BaseDriver>. It will usually also have to implement L<Bio::DB::Persistent::ObjectRelMapperI>. If you set this from outside, you should know exactly what you are doing. If the value is requested in get-mode but no value has been set yet, the driver will be auto-loaded. Most if not all of the adaptors will in fact use this auto-loading feature. Example : Returns : value of dbd (a scalar) Args : new value (a scalar, optional)
Title : db Usage : $dbadaptor = $obj->db() Function: This is just shorthand for $obj->dbcontext()->dbadaptor(). Example : Returns : value of db (a Bio::DB::DBAdaptorI implementing object) Args : none
Title : sth Usage : $obj->sth($key, $prepared_sth) Function: caches prepared statements Example : Returns : a DBI statement handle cached under the key, or all statement handles in the cache if no key is supplied Args : the key for the cached prepared statement handle, and optionally on set the new statement handle to be cached, or undef to remove the handle from the cache
Title : sql_generator Usage : $obj->sql_generator($newval) Function: Get/set the SQL generator object to use for turning query objects into SQL statements. Example : Returns : value of sql_generator (an instance of Bio::DB::Query::SqlGenerator or a derived object) Args : new value (an instance of Bio::DB::Query::SqlGenerator or a derived object, optional)
Title : caching_mode Usage : $obj->caching_mode($newval) Function: Get/set whether objects are cached for find_by_primary_key() and find_by_unique_key(). See obj_cache() for documentation on how to use the object cache. If you disable caching through this method, the entire cache will be flushed as a side effect. Example : Returns : TRUE if caching of objects is enabled and FALSE otherwise Args : new value (a scalar, optional)
Title : obj_cache Usage : Function: Implements a simple cache of objects by key. Often, this will be used by derived classes to cache singletons, if there is only a limited number of certain base objects, like Species, or Ontology_Term. A derived adaptor may want to override this method to cache only selectively. The constructor of this class turns off caching by default; supply -cache_objects => 1 in order to turn it on, or call $adp->caching_mode(1). Example : Returns : The object cached under the key, or undef if there is no such key Args : The key under which to cache the object. Optionally, on set the object to be cached. Pass undef to un-cache an object stored under the key.
Title : crc64 Usage : Function: Computes and returns the CRC64 checksum for a given string. This method may be called as a static method too as it doesn't not make any references to instance properties. However, it isn't really meant for outside consumption, but rather for derived classes as a utility method. At present, in fact this module itself doesn't use it. This is basically ripped out of the bioperl swissprot parser. Credits go to whoever contributed it there. Example : Returns : the CRC64 checksum as a string Args : the string as a scalar for which to obtain the CRC64
Title : finish Usage : $objectadp->finish() Function: Finishes the resources used by this object. Note that this will not disconnect the database handle, but it will remove the reference to it. This behaviour is needed because the connection handle may be shared between multiple objects. Note that given the implementation here you may continue to use the adaptor after calling this method, since a new db handle will be obtained automatically if needed, and objects removed from the cache will be rebuilt. Basically, this method will reset the object cache if any and finish all cached statement handles and reset the statement handle cache. Note that this method will not throw an exception even if finishing the resources causes an error. It will issue a warning though, and if verbose() >= 1 warnings become exceptions. Example : Returns : none Args : none
Title : DESTROY Usage : Function: We override this here to call finish(). Example : Returns : Args :
Almost all of the following methods MUST be overridden by a derived class. For some methods there is an implementation here that assumes "no action" is the right thing, but for many adaptors this won't be right. There is no way this base implementation can make any meaningful guesses at the correct values for those.
Title : get_persistent_slots Usage : Function: Get the slots of the object that map to attributes in its respective entity in the datastore. Slot name generally refers to a method name, but is not required to do so, since determining the values is under the control of get_persistent_slot_values(). This is a strictly abstract method. A derived class MUST override it to return something meaningful. Example : Returns : an array of method names constituting the serializable slots Args : the object about to be inserted or updated
Title : get_persistent_slot_values Usage : Function: Obtain the values for the slots returned by get_persistent_slots(), in exactly that order. The reason this method is here is that sometimes the actual slot values need to be post-processed to yield the value that gets actually stored in the database. E.g., slots holding arrays will need some kind of join function applied. Another example is if the method call needs additional arguments. Supposedly the adaptor for a specific interface knows exactly what to do here. Since there is also populate_from_row() the adaptor has full control over mapping values to a version that is actually stored. This is a strictly abstract method and it MUST be overridden by a derived class. Example : Returns : A reference to an array of values for the persistent slots of this object. Individual values may be undef. Args : The object about to be serialized. A reference to an array of foreign key objects if not retrievable from the object itself.
Title : get_foreign_key_objects Usage : Function: Gets the objects referenced by this object, and which therefore need to be referenced as foreign keys in the datastore. Note that the objects are expected to implement Bio::DB::PersistentObjectI. An implementation may obtain the values either through the object to be serialized, or through the additional arguments. An implementation should also make sure that the order of foreign key objects returned is always the same. Note also that in order to indicate a NULL value for a nullable foreign key, either put an object returning undef from primary_key(), or put the name of the class instead. DO NOT SIMPLY LEAVE IT OUT. This implementation assumes a default of no foreign keys and returns an empty array. Example : Returns : an array of Bio::DB::PersistentObjectI implementing objects Args : The object about to be inserted or updated, or undef if the call is for a SELECT query. In the latter case return class or interface names that are mapped to the foreign key tables. Optionally, additional named parameters. A common parameter will be -fkobjs, with a reference to an array of foreign key objects that are not retrievable from the persistent object itself.
Title : attach_foreign_key_objects Usage : Function: Attaches foreign key objects to the given object as far as necessary. This method is called after find_by_XXX() queries, not for INSERTs or UPDATEs. This implementation assumes there are no foreign keys that need to be retrieved and instantiated. You MUST override this method in order to have foreign key objects taken care of upon SELECTs. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object to which to attach foreign key objects. A reference to an array of foreign key values, in the order of foreign keys returned by get_foreign_key_objects().
Title : store_children Usage : Function: Inserts or updates the child entities of the given object in the datastore. Usually, those child objects will reference the given object as a foreign key. The implementation can assume that all of the child objects are already Bio::DB::PersistentObjectI. While obtaining and looping over all child objects could have been implemented as a generic business logic method, supplying the right foreign key objects is hard to accomplish in a generic fashion. The implementation here assumes there are no children and hence just returns TRUE. You MUST override it in order to have any children taken care of. Example : Returns : TRUE on success, and FALSE otherwise Args : The Bio::DB::PersistentObjectI implementing object for which the child objects shall be made persistent. A reference to an array of foreign key values, in the order of foreign keys returned by get_foreign_key_objects().
Title : attach_children Usage : Function: Possibly retrieve and attach child objects of the given object. This is needed when whole object trees are supposed to be built when a base object is queried for and returned. An example would be Bio::SeqI objects and all the annotation objects that hang off of it. This is called by the find_by_XXXX() methods once the base object has been built. This implementation will do nothing unless it is overridden. Whether to override it or not will depend on which of the children shall be loaded instantly instead of lazily. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object for which to find and to which to attach the child objects.
Title : remove_children Usage : Function: This method is to cascade deletes in maintained objects. Child records in the database will usually be cascaded by the RDBMS. In order to cascade removals to persistent child objects, you must override this method. Usually you will need to undefine the primary key of child objects, and possibly remove them from caches if they are cached. Because failure to do so may result in serious and often non-obvious bugs, there is no default provided here. You *must* override this method in a derived adaptor as evidence that you know what you are doing, even if all you do is just return TRUE. Example : Returns : TRUE on success and FALSE otherwise Args : The persistent object that was just removed from the database. Additional (named) parameter, as passed to remove().
Title : instantiate_from_row Usage : Function: Instantiates the class this object is an adaptor for, and populates it with values from columns of the row. Usually a derived class will instantiate the proper class and pass it on to populate_from_row(). This implementation assumes that the object factory is provided, uses it to instantiate a new object, and then passes on to populate_from_row(). If this is not appropriate the method must be overridden by a derived object. Example : Returns : An object, or undef, if the row contains no values Args : A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots(). Optionally, the object factory to be used for instantiating the proper class. The adaptor must be able to instantiate a default class if this value is undef.
Title : populate_from_row Usage : Function: Populates the given object with values from columns of the row. This method is strictly abstract and MUST be overridden by a derived object. Example : Returns : The object populated, or undef, if the row contains no values Args : The object to be populated. A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots().
Title : get_unique_key_query Usage : Function: Obtain the suitable unique key slots and values as determined by the attribute values of the given object and the additional foreign key objects, in case foreign keys participate in a UK. This method embodies the knowledge about which properties constitute the alternative keys for an object (entity) and how to obtain the values of those properties from the object. Therefore, unless there is no alternative key for an entity, the respective (derived) adaptor must override this method. If there are multiple alternative keys for an entity, the overriding implementation may choose to determine at runtime the best alternative key given the object and then return only a single alternative key, or it may choose to return an array of (supposedly equally suitable) alternative keys. Note that if every alternative key returned will be searched for until a match is found (short-cut evaluation), so returning partially populated alternative keys is usually not wise. This implementation assumes there are no unique keys defined for the entity adapted by this class and hence returns an empty hash ref. Instead of overriding this method a derived class may choose to override find_by_unique_key() instead, as that one calls this method. See the documentation of find_by_unique_key() for further information on what the return value is used for and what the implications are. Example : Returns : One or more references to hash(es) where each hash represents one unique key, and the keys of each hash represent the names of the object's slots that are part of the particular unique key and their values are the values of those slots as suitable for the key. Args : The object with those attributes set that constitute the chosen unique key (note that the class of the object will be suitable for the adaptor). A reference to an array of foreign key objects if not retrievable from the object itself.
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::BioEntry
CPAN shell
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.