NAME

Test::Chado::Role::Helper::WithBcs

VERSION

version v4.1.1

DESCRIPTION

Bio::Chado::Schema base Moo role to manage various db, cv, cvterm and dbxref values. This is primarilly consumed by various flatfile based fixture loaders.

API

Attributes

Handling Bio::Chado::Schema::Result::Cv object

get_cvrow(term name)

Gets an cached instances of Bio::Chado::Schema::Result::Cv

set_cvrow(term name,Bio::Chado::Schema::Result::Cv)

Cache an Bio::Chado::Schema::Result::Cv object

exist_cvrow(term name)

Check for Bio::Chado::Schema::Result::Cv in the cache

Handling of Bio::Chado::Schema::Result::Cvterm

get_cvterm_row

set_cvterm_row

exist_cvterm_row

Handling of Bio::Chado::Schema::Result::Db

get_dbrow

set_dbrow

exist_dbrow

dbmanager

Instance of Test::Chado::Role::Role::HasDBManager

schema

Instance of Bio::Chado::Schema

Methods

find_cv_id(cv name)

Given a cv name returns cv_id column value from cv table.

find_or_create_cv_id(cv name)

Similar to previous, however creates a cv if absent in the database.

find_cvterm_id

Similar to find_cv_id method, however works on cvterm table to return the cvterm_id.

find_or_create_cvterm_id(cvterm,cv,db,dbxref)

Similar to previous find_or_create_cv_id method, however needs few more parameters to work.

search_cvterm_ids_by_namespace(cv name)

Given a cv name returns a list(arrayref) of cvterm_ids

find_db_id(db name)

Given a db name returns a db_id from db table

find_or_create_db_id(db name)

AUTHOR

Siddhartha Basu <biosidd@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Siddhartha Basu.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.