Bio::DB::BioSQL::BaseDriver - DESCRIPTION of Object
Give standard usage here
Describe the object here
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
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.
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://redmine.open-bio.org/projects/bioperl/
Email hlapp at gmx.net
Additional contributors names and emails here
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::BaseDriver->new(); Function: Builds a new Bio::DB::BioSQL::BaseDriver object Returns : an instance of Bio::DB::BioSQL::BaseDriver Args :
Title : prepare_delete_sth Usage : Function: Creates a prepared statement with one placeholder variable suitable to delete one row from the respective table the given class maps to. The method may throw an exception, or the database handle methods involved may throw an exception. Example : Returns : A DBI statement handle for a prepared statement with one placeholder Args : The calling adaptor (basically, it needs to implement dbh()). Optionally, additional arguments.
Title : prepare_findbypk_sth Usage : Function: Prepares and returns a DBI statement handle with one placeholder for the primary key. The statement is expected to return the primary key as the first and then as many columns as $adp->get_persistent_slots() returns, and in that order. Example : Returns : A DBI prepared statement handle with one placeholder Args : The Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh() and get_persistent_slots()). A reference to an array of foreign key slots (class names).
Title : prepare_findbyuk_sth Usage : Function: Prepares and returns a DBI SELECT statement handle with as many placeholders as necessary for the given unique key. The statement is expected to return the primary key as the first and then as many columns as $adp->get_persistent_slots() returns, and in that order. Example : Returns : A DBI prepared statement handle with as many placeholders as necessary for the given unique key Args : The calling Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh() and get_persistent_slots()). A reference to a hash with the names of the object''s slots in the unique key as keys and their values as values. A reference to an array of foreign key objects or slots (class names if slot).
Title : prepare_insert_association_sth Usage : Function: Prepares a DBI statement handle suitable for inserting the association between the two entities that correspond to the given objects. Example : Returns : the DBI statement handle Args : The calling adaptor. Named parameters. Currently recognized are: -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 column names and the values are values of columns 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 association 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 : prepare_delete_association_sth Usage : Function: Prepares a DBI statement handle suitable for deleting the association between the two entities that correspond to the given objects. Example : Returns : the DBI statement handle Args : The calling adaptor. Named parameters. Currently recognized are: -objs a reference to an array of objects the association between which is to be deleted -values a reference to a hash the keys of which are column names and the values are values of columns 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 association 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 : prepare_delete_query_sth Usage : Function: Prepares a DBI statement handle suitable for deleting rows from a table that match a number of attributes. Example : Returns : the DBI statement handle Args : The calling adaptor. Named parameters. Currently recognized are: -fkobjs optional; a reference to an array of foreign key objects by which to constrain; this is complementary to -values -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 association map rather than through foreign_key_name(). This may be necessary if an entity has more than one foreign key to the same entity. The array must be in the same order as -fkobjs, and have the same number of elements. Put undef for objects for which there are no multiple contexts. -values optional; a reference to a hash the keys of which are attribute names by which to constrain the query
Title : prepare_insert_sth Usage : Function: Prepares a DBI statement handles suitable for inserting a row (as values of the slots of an object) into a table. Example : Returns : the DBI statement handle Args : the calling adaptor (a Bio::DB::PersistenceAdaptorI object) a reference to an array of object slot names a reference to an array of foreign key objects (optional)
Title : prepare_update_sth Usage : Function: Prepares a DBI statement handle suitable for updating a row in a table where the row is identified by its primary key. Example : Returns : the DBI statement handle Args : the calling adaptor (a Bio::DB::PersistenceAdaptorI object) a reference to an array of object slot names a reference to an array of foreign key objects (optional)
Title : cascade_delete Usage : Function: Removes all persistent objects dependent from the given persistent object from the database (foreign key integrity). This implementation assumes that the underlying schema and RDBMS support cascading deletes, and hence does nothing other than returning TRUE. Example : Returns : TRUE on success, and FALSE otherwise Args : The DBContextI implementing object for the database. The object for which the dependent rows shall be deleted. Optionally, additional (named) arguments.
Title : insert_object Usage : Function: Example : Returns : The primary key of the newly inserted record. Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh(), sth($key, $sth), dbcontext(), and get_persistent_slots()). The object to be inserted. A reference to an array of foreign key objects; if any of those foreign key values is NULL (some foreign keys may be nullable), then give the class name.
Title : update_object Usage : Function: Example : Returns : The number of updated rows Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh(), sth($key, $sth), dbcontext(), and get_persistent_slots()). The object to be updated. A reference to an array of foreign key objects; if any of those foreign key values is NULL (some foreign keys may be nullable), then give the class name.
Title : get_sth Usage : Function: Retrieves the (prepared) statement handle to bind parameters for and to execute for the given operation. By default this will use the supplied key to retrieve the statement from the cache. This method is here to provide an opportunity for inheriting drivers to intercept the cached statement retrieval in order to on-the-fly redirect the statement execution to use a different statement than it would have used by default. This method may return undef if for instance there is no appropriate statement handle in the cache. Returning undef will trigger the calling method to construct a statement from scratch. Example : Returns : a prepared statement handle if one is exists for the query, and undef otherwise Args : - the calling adaptor (a Bio::DB::BioSQL::BasePersistenceAdaptor derived object - the object for the persistence operation - a reference to an array of foreign key objects; if any of those foreign key values is NULL then the class name - the key to the cache of the adaptor - the operation requesting a cache key (a scalar basically representing the name of the method)
Title : translate_query Usage : Function: Translates the given query as represented by the query object from objects and class names and slot names to tables and column names. Example : Returns : An object of the same class as the input query, but representing the translated query, and also with the SELECT fields properly set to facilitate object construction. Args : The calling adaptor. The query as a Bio::DB::Query::BioQuery or derived object. A reference to an array of foreign key objects.
Title : _build_select_list Usage : Function: Builds and returns the select list for an object query. The list contains those columns, in the right order, that are necessary to populate the object. Example : Returns : An array of strings (column names, not prefixed) Args : The calling persistence adaptor. A reference to an array of foreign key entities (objects, class names, or adaptors) the object must attach. A reference to a hash table mapping entity names to aliases (if omitted, aliases will not be used, and SELECT columns can only be from one table)
Title : table_name Usage : Function: Obtain the name of the table in the relational schema corresponding to the given class name, object, or persistence adaptor. This implementation uses a object-relational hash map keyed by class to obtain the table name. Example : Returns : the name of the table (a string), or undef if the table cannot be determined Args : The referenced object, class name, or the persistence adaptor for it.
Title : association_table_name Usage : Function: Obtain the name of the table in the relational schema corresponding to the association of entities as represented by their corresponding class names, objects, or persistence adaptors. This implementation will use table_name() and the map returned by association_entity_map(). This method will throw an exception if the association is not mapped (not to be confused with the association being unsupported). Example : Returns : the name of the table (a string, or undef if the association is not supported by the schema) Args : A reference to an array of objects, class names, or persistence adaptors. The array may freely mix types.
Title : primary_key_name Usage : Function: Obtain the name of the primary key attribute for the given table in the relational schema. This implementation just appends _id to the table name, which yields correct results for at least the MySQL version of the BioSQL schema. Override it for your own schema if necessary. Example : Returns : The name of the primary key (a string) Args : The name of the table (a string)
Title : foreign_key_name Usage : Function: Obtain the foreign key name for referencing an object, as represented by object, class name, or the persistence adaptor. Example : Returns : the name of the foreign key (a string) Args : The referenced object, class name, or the persistence adaptor for it.
Title : _build_foreign_key_name Usage : Function: Build the column name for a foreign key to the given table. The default implementation here retrieves the primary key for the given table. This is called by foreign_key_name() once it has determined the table name. If a particular driver wants to build the foreign key name in a specific or generally different way than the default implementation here, this is the method to override (unless you also want to change the way the table is determined; in that case you would override foreign_key_name()). Example : Returns : The name of the foreign key column as a string Args : The table name as a string
Title : sequence_name Usage : Function: Returns the name of the primary key generator (SQL sequence) for the given table. The value returned is passed as the second argument to the L<Bio::DB:DBI>::last_id_value as implemented by the driver. Because the parameter is not required irregardless of driver, it is perfectly legal for this method to return undef. If the L<Bio::DB::DBI> driver does need this parameter, this method should be overridden by the matching adaptor driver. The default we assume here is we dont need this value. Example : Returns : the name of the sequence (a string) Args : The name of the table.
Title : objrel_map Usage : Function: Get/set the object-relational map from classes to entities. Example : Returns : A reference to a hash map where object interfaces are the keys Args : Optional, on set a reference to the respective hash map
Title : slot_attribute_map Usage : Function: Get/set the mapping for each entity from object slot names to column names. Example : Returns : A reference to a hash map with entity names being the keys, if no key (entity name, object, or adaptor) was provided. Otherwise, a hash reference with the slot names being keys to their corresponding column names. Args : Optionally, the object, adaptor, or entity for which to obtain the map. Optionally, on set a reference to a hash map satisfying the features of the returned value.
Title : not_select_attrs Usage : $obj->not_select_attrs($newval) Function: Get/set a map of all columns that should not be included in SELECT lists. Example : Returns : value of not_select_attrs (a reference to a hash map) Args : new value (a reference to a hash map, optional)
Title : association_entity_map Usage : $obj->association_entity_map($newval) Function: Get/set the association entity map. The map is an anonymous hash with entities that participate in associations being keys. The values are hash refs themselves, with the other participating entity being the key, and the value being either the name of the respective association entity, or another hash ref with the same structure if more entities participate in the association. The hash map must be commutative. I.e., the association entity must be locatable irregardless with which of the participating entities one starts. Example : Returns : value of association_entity_map (a hash ref of hash refs) Args : new value (a hash ref of hash refs, optional)
These will usually delegate straightforward DBI calls on the supplied handle, but can also be used by an inheriting adaptor driver to intercept the call and add additional parameters, for example a hash reference with named parameters.
Title : commit Usage : Function: Commits the current transaction, if the underlying driver supports transactions. Example : Returns : TRUE Args : The database connection handle for which to commit.
Title : rollback Usage : Function: Triggers a rollback of the current transaction, if the underlying driver supports transactions. Example : Returns : TRUE Args : The database connection for which to rollback.
Title : bind_param Usage : Function: Binds a parameter value to a prepared statement. The reason this method is here is to give RDBMS-specific drivers a chance to intercept the parameter binding and perform additional actions, or add additional parameters to the call, like data type. Certain drivers need to be helped for certain types, for example DBD::Oracle for LOB parameters. Example : Returns : the return value of the DBI::bind_param() call Args : the DBI statement handle to bind to the index of the column the value to bind additional arguments to be passed to the sth->bind_param call
Title : prepare Usage : Function: Prepares a SQL statement and returns a statement handle. The reason this method is here is the same as for bind_param. Example : Returns : the return value of the DBI::prepare() call Args : the DBI database handle for preparing the statement the SQL statement to prepare (a scalar) additional arguments to be passed to the dbh->prepare call
Title : report_execute_failure Usage : Function: Report the failure to execute a SQL statement. The reporting by default uses warn() but may be requested to throw(). Example : Returns : Args : Named paramaters. Currently recognized are -sth the statement handle whose execution failed -adaptor the calling adaptor (a Bio::DB::PersistenceAdaptorI object) -op the type of operation that failed ('insert', 'update',...) -vals a reference to an array of values that were bound -fkobjs a reference to an array of foreign key objects that were bound (optional) -report_func the name of the method to call for reporting the message (optional, default is 'warn')
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.