Bio::Chado::Schema
use lib qw(t/lib); use Bio::Chado::Schema::Test; use Test::More; my $schema = Bio::Chado::Schema::Test->init_schema();
use Bio::Chado::Schema; my $chado = Bio::Chado::Schema->connect( $dsn, $user, $password ); print "number of rows in feature table: ", $chado->resultset('Sequence::Feature')->count, "\n";
This module provides the basic utilities to write tests against Bio::Chado::Schema.
This is a standard object-relational mapping layer for use with the GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of the very fine DBIx::Class::Schema::Loader module.
Chado is an open-source modular database schema for biological data. It is divided into several notional "modules", which are reflected in the namespace organization of this package. Note that modules in the Chado context refers to sets of tables, they are not modules in the Perl sense.
To learn how to use this DBIx::Class ORM layer, a good starting point is the DBIx::Class::Manual.
Bio::Chado::Schema - A standard DBIx::Class layer for the Chado database schema.
Bio::Chado::Schema::CellLine
Bio::Chado::Schema::Companalysis
Bio::Chado::Schema::Composite
Bio::Chado::Schema::Contact
Bio::Chado::Schema::Cv
Bio::Chado::Schema::Expression
Bio::Chado::Schema::General
Bio::Chado::Schema::Genetic
Bio::Chado::Schema::Library
Bio::Chado::Schema::Mage
Bio::Chado::Schema::Map
Bio::Chado::Schema::NaturalDiversity
Bio::Chado::Schema::Organism
Bio::Chado::Schema::Phenotype
Bio::Chado::Schema::Phylogeny
Bio::Chado::Schema::Project
Bio::Chado::Schema::Pub
Bio::Chado::Schema::Sequence
Bio::Chado::Schema::Stock
Aureliano Bombarely, <ab782@cornell.edu>
Naama Menda, <nm249@cornell.edu>
Jonathan "Duke" Leto, <jonathan@leto.net>
Robert Buels, <rmb32@cornell.edu>
Copyright 2009 Boyce Thompson Institute for Plant Research
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
Bio::Chado::Schema::Test - Library to be used by Bio::Chado::Schema test scripts.
my $schema = Bio::Chado::Schema::Test->init_schema( deploy => 1, populate => 1, storage_type => '::DBI::Replicated', storage_type_args => { balancer_type=>'DBIx::Class::Storage::DBI::Replicated::Balancer::Random' }, );
This method removes the test SQLite database in t/var/BCS.db and then creates a new, empty database.
This method will call deploy_schema() by default, unless the deploy flag is set to 0.
This method will call populate_schema() if the populate argument is set to a true value.
Bio::Chado::Schema::Test->deploy_schema( $schema );
This method does one of two things to the schema. It can either call the experimental $schema->deploy() if the BCSTEST_SQLT_DEPLOY environment variable is set, otherwise the default is to read in the t/lib/sqlite.sql file and execute the SQL within. Either way you end up with a fresh set of tables for testing.
Bio::Chado::Schema::Test->populate_schema( $schema );
After you deploy your schema you can use this method to populate the tables with test data.
Robert Buels <rbuels@cpan.org>
This software is copyright (c) 2009 by Robert Buels.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install Bio::Chado::Schema, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Chado::Schema
CPAN shell
perl -MCPAN -e shell install Bio::Chado::Schema
For more information on module installation, please visit the detailed CPAN module installation guide.