Tripal Multi-Chado

Tripal Multi-Chado

Synopsis

When you use Tripal module, it only allows the use of one Chado instance to manage your biological data. By default, Drupal is installed in the "public" schema of the website PostgreSQL database and Tripal can install Chado in the "chado" schema. This module enables the use of several Chado schemata inside a same database used by Drupal/Tripal.

The Multi-Chado module is an extension for Tripal that can be used to install more than one Chado instance across different schemata of your choice and it also enables the use of different PostgreSQL database credentials allowing the administrator to do fine tuning of database accesses. For instance, with this module, you can host on a same Drupal instance (config, tools and users) both a public and one or more private Chado instances. You could also have different public instances for different release of a same genome sequencing or event different species. And you may even think of other kind of uses.

Requirements

• Tripal 7.x-2.1: https://www.drupal.org/project/tripal
• Entity API: https://www.drupal.org/project/entity
• Entity Reference: https://www.drupal.org/project/entityreference
• PostgreSQL Drupal user account "search_path" set to "public" without "chado"
  or with "chado" coming after "public".
  ex.:

  ALTER USER drupal_user SET search_path = public;
  -- or
  ALTER USER drupal_user SET search_path = public,chado;
  -- or
  ALTER USER drupal_user SET search_path = "$user",public,chado;
  ...

  To figure out your current "search_path", you can issue the PostgreSQL query:
  SHOW search_path;

Recommended modules

• Masquerade: for admins, it allows easily testing of Chado connections used by your users

Companion module

This module includes a companion sub-module "Tripal Multi-Chado Selector" (tripal_mc_selector) which provides a block "Chado schema" with a drop-down allowing users to switch from a Chado instance to another associated to their user accounts.

Roadmap

• Improve documentation with tutorials (feedback on the use of this module is appreciated)
• Check how this module could support Tripal materialized views
• Test this module with Tripal 3

Credits

Many thanks to Lacey Sanderson and Stephen Ficklin that made the release of this module possible. Without their will to integrate into Tripal what is needed by this module, it would have been really complicated to have this module work properly.

Other warm thanks to Alexis Andrieu who helped the development of this module during his internship.