tripal/legacy/tripal_pub/theme/templates/tripal_pub_help.tpl.php

<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>