tripal/tripal_library/theme/tripal_organism/tripal_organism.libraries.tpl.php

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

// expand the organism object to include the libraries from the library
// table in chado.
$options = array('return_array' => 1);
$organism = tripal_core_expand_chado_vars($organism, 'table', 'library', $options);
$libraries = $organism->library;


if (count($libraries) > 0) {?>
  <div id="tripal_organism-library_list-box" class="tripal_organism-info-box tripal-info-box">
    <div class="tripal_organism-info-box-title tripal-info-box-title">Libraries</div>
    <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following libraries are associated with this organism.</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
    // This table for the analysis has a vertical header (down the first column)
    // so we do not provide headers here, but specify them in the $rows array below.
    $headers = array('Library Name', 'Type');
    
    // 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 
    $rows = array();
    foreach ($libraries as $library){ 
      
      $libname = $library->name;
      if ($library->nid) {
        $libname = l($libname, "node/".$library->nid, array('attributes' => array('target' => '_blank')));
      }
      
      $typename = $library->type_id->name;
      if ($typename == 'cdna_library') {
        $typename = 'cDNA';
      }
      else if ($typename == 'bac_library') {
        $typename = 'BAC';
      }
      
      $rows[] = array(
        $libname,
        $typename
      );      
    }
    
    // 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_organism-table-libraries',
      ),
      '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
}