Tripal CV Browser

This module can be used to display and browse a hierarchical tree representation
of any controlled vocabulary (CV) stored into Chado (cvterm table). The
vocabulary to browse must have relationships stored into the cvterm_relationship
table where the children term is the subject (subject_id) and the parent term is
the object (object_id). Circular relationships and network relationships are not
an issue since the tree is not generated nor loaded when the CV browser page is
accessed; Only root elements are displayed and each first level of a subtree is
loaded (ajax) when the used click on the parent node.

A generic CV browser page can be used to browse any CV from CV root term(s) or
from user-selected terms. The URL of the page can be constructed this way:
'tripal/cvbrowser/' + identifiers provided after> + by "+" signs if more than on value is provided)>.
Examples:
- tripal/cvbrowser/cv/biological_process+molecular_function+cellular_component
- tripal/cvbrowser/cvterm/1234

Requirements

• Tripal 7.x-2.x (not tested under 3.x) (http://www.drupal.org/project/tripal)
• jQuery >= 1.7 (use jQuery update module)

Installation

• Install as you would normally install a contributed Drupal module.
  See: https://drupal.org/documentation/install/modules-themes/modules-7
  for further information.
• Enable the module in "Admin menu > Site building > Modules" (/admin/modules).

Configuration

• Configure the CV browser in "Administration > Tripal > Extensions >
  Tripal CV Browser > Settings" (/admin/tripal/extension/tripal_cvb).
• Configure user permissions in "Administration > People > Permissions"
  (/admin/people/permissions):
  • "Use tripal cv browser page": allows users to access to the generic CV
    browser page. With this permission, any CV or CV term can be browsed as the
    user only needs to know the CV name or CV cv_id or CV term name or CV term
    cvterm_id in order to use it in the browser page URL. If you want to
    restrict CV browsing, then do not give this permission to your users.
  • "Administer Tripal CV Browser": allows users to access to the
    CV browser administration pages and see the administration help page.
• After creating custom CV browser(s), place them on your site using the block
  configuration page in "Administration > Structure > Blocks"
  (admin/structure/block). You can also configure access permission and block
  visibility for each block using their "configuration" link.
  If you prefer to have your browsers displayed as a page instead of a block,
  you can use the Drupal path 'tripal/cvbrowser/browser/' + the CV browser
  machine name. In this case, access are managed using the "Use tripal cv
  browser page" permission.