tripal/tripal_pub/theme/tripal_pub_admin.tpl.php

<br /><h3>Tripal Publication Quick Links</h3>
<ul>
  <li><?php print l('Search for Publications', 'find/publications') ?></li>
  <li><?php print l('Configuration', 'admin/tripal/tripal_pub/configuration') ?></li>
  <li><?php print l('Sync Publications', 'admin/tripal/tripal_pub/sync') ?></li>
  <li><?php print l('List of Importers', 'admin/tripal/tripal_pub/import_list') ?></li>
  <li><?php print l('Add a New Importer', 'admin/tripal/tripal_pub/import/new') ?></li>
</ul>

<h3>Module Description:</h3>
<p>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.
 </p>
<h3>Setup Instructions:</h3>
<ol>
  <li><p><b>Set Permissions</b>: 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 <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
    <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
    <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> 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.</p></li>
  <li><p><b>Sync Publications</b>:  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 <?php print l('sync publications', 'admin/tripal/tripal_pub/sync') ?>
    page to sync all publications.</p></li>
  <li><p><b>Configure the Search Behavior</b>: Before allowing site visitors to search for publications 
    visit the <?php print l('configuration page', 'admin/tripal/tripal_pub/configuration') ?> 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.</p></li>
  <li><p><b>AGL Importer</b>: 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:
    <ol>
      <li>Install the YAZ libraries: sudo apt-get install yaz libyaz4-dev</li>
      <li>Install the PHP YAZ extension: sudo pecl install yaz</li>
      <li>Add the text 'extesion=yaz.so' to the appropriate php.ini file (e.g. /etc/php5/apache2filter/php.ini)</li>
      <li>Restart the webserver</li>
    </ol>
    </p></li>
  <li><p><b>Automate Importers:</b> Site administrators can <?php print l('create publication importers', 'admin/tripal/tripal_pub/import/new') ?> 
    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 <?php print l('Drush', "http://drupal.org/project/drush")?> 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):  <br>
    <pre>0 9 * * 5  su - [web user] -c 'cd [drupal install path]; drush -l http://[site url] tpubs-import --report=[email]'
    </pre>
    Where:<br>
     [web user] is the name of the user on the system under which the web server runs</br>
     [drupal install path] is the location where drupal is installed</br>
     [site url] is the URL path for the site </br>
     [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).</br>
     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.
    </p></li>
</ol>
<h3>Features of this Module:</h3>
<ul>
     
  <li><p><b>Add/Edit/Delete Publications</b>: Publications can be maually added <?php  l('here', 'node/add/chado-pub') ?>. 
    Once added, publications can be modified or deleted by clicking the Edit tab at the top of a publication page.</p></li>
  
  <li><p><b>Publication Search Tool</b>: A <?php print l('search tool','find/publications') ?> is provided for 
    finding publications. Unlike most default search tools for Tripal, this tool does not rely on Drupal Views</p></li>
    
  <li><p><b>Bulk Import of Publications</b>: Site administrators can  <?php print l('add a new publication importer', 'admin/tripal/tripal_pub/import/new') ?> 
    which provides a set of search terms for querying a remote publication database (e.g. PubMed). Publications
    that matche the search terms can be imported when the publication import cron command is executed.  The
    cron command can be executed using the Drush command: drush tpubs-import.  This drush command can be added
    as a system-wide cron (in the same way the Tripal jobs cron is implemented) to be executed on a periodic basis.
    This will allow the site to import publications which have been newly added to remote databases and which 
    are relative to the site.  Site administrators can <?php print l('see the list of importers', 'admin/tripal/tripal_pub/import_list') ?> 
    and edit, disable or delete the importers.</p></li>
    
  

</ul>