A DBIx::Class layer for Chado

Oxford, UK

August 6-7, 2009

What is DBIx::Class?

• Object-relational mapping framework for Perl
• is now the de-facto standard
• very powerful features for:

What is DBIx::Class?

• Object-relational mapping framework for Perl
• is now the de-facto standard
• very powerful features for:
• query building (the magic of chainable ResultSets)

What is DBIx::Class?

• Object-relational mapping framework for Perl
• is now the de-facto standard
• very powerful features for:
• query building (the magic of chainable ResultSets)
• cross-database deployment (using SQL::Translator in the backend)

What is DBIx::Class?

• Object-relational mapping framework for Perl
• is now the de-facto standard
• very powerful features for:
• query building (the magic of chainable ResultSets)
• cross-database deployment (using SQL::Translator in the backend)
• testing with Fixtures

see http://search.cpan.org/dist/DBIx-Class/lib/DBIx/Class/Manual.pod

Chado needs middleware

A layer of software between the application (e.g. website) and the relational database.

Chado needs middleware

Chado's design makes for:

• complex queries
• steep learning curve
• hard to get good performance

Chado needs middleware

Middleware can help by:

• complex queries

Chado needs middleware

Middleware can help by:

• complex queries
• storing and/or automating them

Chado needs middleware

Middleware can help by:

• complex queries
• storing and/or automating them
• steep learning curve

Chado needs middleware

Middleware can help by:

• complex queries
• storing and/or automating them
• steep learning curve
• codifying best practices
• unified, high-level documentation
• can help with database administration

Chado needs middleware

Middleware can help by:

• complex queries
• storing and/or automating them
• steep learning curve
• codifying best practices
• unified, high-level documentation
• can help with database administration
• hard to get good performance

Chado needs middleware

Middleware can help by:

• complex queries
• storing and/or automating them
• steep learning curve
• codifying best practices
• unified, high-level documentation
• can help with database administration
• hard to get good performance
• some performance optimizations can be put in middleware
• can assist in creating indexes and materialed views

Current State

Currently composed of:

• maintenance script to generate/synchronize DBIx::Class modules for every chado table
• the modules that are thus generated

http://github.com/rbuels/dbic_chado/tree/master

Further Work: fix relationships

Still need to add in some DBIx::Class relationships:

• many_to_many
• has_many and belongs_to for relationships across Chado module boundaries, e.g. feature.type_id -> cvterm.cvterm_id

Further Work: add more useful things

More useful things are needed:

• automate common querying and loading patterns
• compatibility with BioPerl objects
• the things that Modware does, and more

Rob proposes

• other people should start building features onto and into it
• and do some of the things on the previous slides
• make a new version of Modware based on it
• do you think somebody could get funding to work on it full time?

That's All

• The END