tripal/tripal_feature/theme/tripal_feature/tripal_feature_references.tpl.php

<?php
$feature = $variables['node']->feature;
$references = array();

// First, get the dbxref record from feature record itself if one exists
if ($feature->dbxref_id) {
  $feature->dbxref_id->is_primary = 1;  // add this new property so we know it's the primary reference
  $references[] = $feature->dbxref_id;
}

// Second, expand the feature object to include the records from the feature_dbxref table
$options = array('return_array' => 1);
$feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_dbxref', $options);
$feature_dbxrefs = $feature->feature_dbxref;
if (count($feature_dbxrefs) > 0 ) {
  foreach ($feature_dbxrefs as $feature_dbxref) {    
    if($feature_dbxref->dbxref_id->db_id->name == 'GFF_source'){
      // check to see if the reference 'GFF_source' is there.  This reference is
      // used to if the Chado Perl GFF loader was used to load the features   
    }
    else {
      $references[] = $feature_dbxref->dbxref_id;
    }
  }
}


if(count($references) > 0){ ?>
  <div id="tripal_feature-references-box" class="tripal_feature-info-box tripal-info-box">
    <div class="tripal_feature-info-box-title tripal-info-box-title">Cross References</div>
    <div class="tripal_feature-info-box-desc tripal-info-box-desc">External references for this <?php print $feature->type_id->name ?></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('Dababase', '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){
    
      // skip the GFF_source entry as this is just needed for the GBrowse chado adapter 
      if ($dbxref->db_id->name == 'GFF_source'){
         continue;  
      } 
      $dbname = $dbxref->db_id->name; 
      if ($dbxref->db_id->url) { 
        $dbname = l($dbname, $dbxref->db_id->url, array('attributes' => array('target' => '_blank')));
      } 
      
      $accession = $dbxref->accession; 
      if ($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(
        $dbname,
        $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_feature-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 
}?>