<br />
<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/storage/chado/pub-search-config') ?>
  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:</p>
  <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 '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.</li>
    <li>Restart the webserver</li>
  </ol>
  </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>
  </p>
  <pre>0 9 * * 5  su - [web user] -c 'cd [drupal install path]; drush -l http://[site url] tpubs-import --report=[email]'</pre>
  Where:<br>
  <p>[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>

