Bio::MAGETAB::Util::DBLoader - A persistent storage class used to track Bio::MAGETAB object creation and insertion into a relational database.
require Bio::MAGETAB::Util::Reader; require Bio::MAGETAB::Util::Persistence; require Bio::MAGETAB::Util::DBLoader; my $reader = Bio::MAGETAB::Util::Reader->new({ idf => $idf }); my $db = Bio::MAGETAB::Util::Persistence->new({ dbparams => ["dbi:SQLite:$db_file"], }); # If this is a new database, deploy the schema. unless ( -e $db_file ) { $db->deploy(); } # Connect to the database. $db->connect(); my $builder = Bio::MAGETAB::Util::DBLoader->new({ database => $db, }); $reader->set_builder( $builder ); # Read objects into the database. $reader->parse();
DBLoader is a Builder subclass which uses a relational database backend to track object creation, rather than the simple hash reference mechanism used by Builder. See the Persistence class and the Tangram module documentation for more information on supported database engines.
See the Builder class for documentation on the superclass attributes.
The internal store to use for object lookups. This must be a Bio::MAGETAB::Util::Persistence object.
See the Builder class for documentation on the superclass methods.
Objects when modified are not automatically updated in the database. You should use the update method to do this (see METHODS in the Builder class). In particular, it is important to bear in mind that there are places in the Bio::MAGETAB model where relationships between objects are being maintained behind the scenes (this allows certain relationships to be navigable in both directions). When modifying these objects, you must also call update on their target objects to ensure the database is kept synchronized with the objects held in memory. For example:
update
# SDRFRow to Nodes is a reciprocal relationship: my $row = $loader->create_sdrf_row({ nodes => \@nodes, }); # @nodes now know about $row, but the database doesn't know this: $loader->update( @nodes ); # Similarly, with Edges and Nodes: my $edge = $loader->find_or_create_edge({ inputNode => $in, outputNode => $out, }); # Again, $in and $out know about $edge, but the database does not: $loader->update( $in, $out );
When used with SQLite or MySQL (and possibly others), the Tangram modules incorrectly modify any select statements containing the '%' character, so that this character is replaced with '%%'. This means that while values are correctly inserted into the database they are not retrieved correctly, and this may result in errors or duplicate entries when working with objects whose identifying fields contains a '%' character. See the Builder class for a discussion on object identity, and http://rt.cpan.org/Public/Bug/Display.html?id=29133 for a possible quick fix for this Tangram bug.
select
Bio::MAGETAB::Util::Reader Bio::MAGETAB::Util::Builder Bio::MAGETAB::Util::Persistence
Tim F. Rayner <tfrayner@gmail.com>
This library is released under version 2 of the GNU General Public License (GPL).
To install Bio::MAGETAB, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MAGETAB
CPAN shell
perl -MCPAN -e shell install Bio::MAGETAB
For more information on module installation, please visit the detailed CPAN module installation guide.