Tripal Publication Quick Links

Module Description:

The Tripal Publication Module provides the functionality for adding, editing, deleting viewing and bulk importing of publications. This module additionally provides a search tool for finding publications that have been added to Chado database.

Setup Instructions:

  1. Set Permissions: The publication module supports the Drupal user permissions interface for controlling access to publication content and functions. These permissions include viewing, creating, editing or administering of publications. The default is that only the original site administrator has these permissions. You can add roles for classifying users, assign users to roles and assign permissions for the publication content to those roles. For a simple setup, allow anonymous users access to view publication content and allow the site administrator all other permissions.

  2. Sync Publications: If you already have publications in your Chado database, or you loaded them through a means other than Tripal, and you want those publications to appear on your site then you will need to "sync" them with Drupal. Use the page to sync all publications.

  3. Configure the Search Behavior: Before allowing site visitors to search for publications visit the to disable or enable fields for searching. Tripal uses its own ontology for storing publication information in Chado, and all child terms of the "Publication Details" are made available for searching. However, some of these may not be desired for searching and can be disabled.

  4. AGL Importer: Initially, the Tripal publication module supports creating publication importers using PubMed and the USDA National Agricultural Library (AGL). The AGL database uses a Z39.50 protocol for querying and therefore Tripal requires the 'YAZ' library to connect. Before you can query AGL you must install the YAZ library and the PHP YAZ library. The following steps can be used on an Ubuntu 12.04 server to intall the necessary pre-requisites:

    1. Install the YAZ libraries: sudo apt-get install yaz libyaz4-dev
    2. Install the PHP YAZ extension: sudo pecl install yaz
    3. Add the text 'extension=yaz.so' to the appropriate php.ini file (e.g. /etc/php5/apache2filter/php.ini). On Ubuntu you may need to add it to the php.ini file specfic for the Apache webserver and also to the php.ini specific for the command-line.
    4. Restart the webserver

  5. Automate Importers: Site administrators can that can be used to query remote databases (e.g. PubMed) and import publications into this database. After creation of importers you can automate import of publications into the site by creating a cron job with a command. The cron job can be setup to run the importers periodically. The following is an example entry, added to the 'root' crontab, that would run importers on a weekly bases (Friday at 9am): 

    0 9 * * 5  su - [web user] -c 'cd [drupal install path]; drush -l http://[site url] tpubs-import --report=[email]'
    Where:

    [web user] is the name of the user on the system under which the web server runs
    [drupal install path] is the location where drupal is installed
    [site url] is the URL path for the site
    [email] is the email address of the person who should receive an HTML report of the publications added. Separate multiple emails with a comma (no spaces).
    The --report=Y option indicates that an HTML style report should be generated listing the publications that were added. If this options is not used then no report is generated.

Features of this Module: