tripal/tripal_pub/theme/tripal_pub/tripal_pub_references.tpl.php

<?php
$pub = $variables['node']->pub;


// expand the pub object to include the records from the pub_dbxref table
$options = array('return_array' => 1);
$pub = tripal_core_expand_chado_vars($pub, 'table', 'pub_dbxref', $options);
$pub_dbxrefs = $pub->pub_dbxref;

$references = array();
if (count($pub_dbxrefs) > 0 ) {
  foreach ($pub_dbxrefs as $pub_dbxref) {    
    $references[] = $pub_dbxref->dbxref_id;
  }
}

if(count($references) > 0){ ?>
  <div id="tripal_pub-references-box" class="tripal_pub-info-box tripal-info-box">
    <div class="tripal_pub-info-box-title tripal-info-box-title">Cross References</div>
    <div class="tripal_pub-info-box-desc tripal-info-box-desc">This publication is also available in the following databases:</div><?php 
    
    // the $headers array is an array of fields to use as the colum headers.
    // additional documentation can be found here
    // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
    $headers = array('Database', 'Accession');
    
    // the $rows array contains an array of rows where each row is an array
    // of values for each column of the table in that row.  Additional documentation
    // can be found here:
    // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
    $rows = array();
    
    foreach ($references as $dbxref){
      $database = $dbxref->db_id->name . ': ' . $dbxref->db_id->description;
      if ($dbxref->db_id->url) {
        $database = l($dbxref->db_id->name, $dbxref->db_id->url, array('attributes' => array('target' => '_blank'))) . ': ' . $dbxref->db_id->description; 
      }
      $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
      if ($dbxref->db_id->urlprefix) {
        $accession = l($accession, $dbxref->db_id->urlprefix . $dbxref->accession, array('attributes' => array('target' => '_blank')));
      }
      if (property_exists($dbxref, 'is_primary')) {
        $accession .= " <i>(primary cross-reference)</i>";
      }
      
      $rows[] = array(
        $database,
        $accession
      );
    }
    // the $table array contains the headers and rows array as well as other
    // options for controlling the display of the table.  Additional
    // documentation can be found here:
    // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
    $table = array(
      'header' => $headers,
      'rows' => $rows,
      'attributes' => array(
        'id' => 'tripal_pub-table-references',
      ),
      'sticky' => FALSE,
      'caption' => '',
      'colgroups' => array(),
      'empty' => '',
    );
    
    // once we have our table array structure defined, we call Drupal's theme_table()
    // function to generate the table.
    print theme_table($table);?>
  </div><?php 
}