tripal/tripal_stock/theme/tripal_organism/tripal_organism_stocks.tpl.php

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

// expand the featuremap object to include the records from the featurepos table
// specify the number of features to show by default and the unique pager ID
$num_results_per_page = 25; 
$pager_id = 3;

// get the features aligned on this map
$options = array(  
  'return_array' => 1,
  'order_by' => array('name' => 'ASC'),
  'pager' => array(
    'limit' => $num_results_per_page, 
    'element' => $pager_id
  ),
  'include_fk' => array(
    'type_id' => 1    
  ),
);

$organism = tripal_core_expand_chado_vars($organism, 'table', 'stock', $options);
$stocks = $organism->stock;

// create the pager.  
// the total number of records for the paged query is stored in a session variable
$total_records = $_SESSION['chado_pager'][$pager_id]['total_records'];

 
if (count($stocks) > 0) { ?>
  <div id="tripal_organism-stocks-box" class="tripal_organism-info-box tripal-info-box">
    <div class="tripal_organism-info-box-title tripal-info-box-title">Stocks</div>
    <div class="tripal_organism-info-box-desc tripal-info-box-desc">This organism is associated with <?php print number_format($total_records) ?> stock(s):</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('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 ($stocks as $stock){
      $name = $stock->name;
      if (!$name) {
        $name = $stock->uniquename;
      }
      if ($stock->nid) {    
        $name = l($name, "node/$stock->nid", array('attributes' => array('target' => '_blank')));
      }

      $rows[] = array(
        $name,
        $stock->type_id->name
      );
    }
    // 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' => $rows,
      'attributes' => array(
        'id' => 'tripal_organism-table-stocks',
      ),
      'sticky' => FALSE,
      'caption' => '',
      'colgroups' => array(),
      'empty' => '',
    );
    // once we have our table array structure defined, we call Drupal's theme_table()
    // function to generate the table.
    print theme_table($table);
    
    // the $pager array values that control the behavior of the pager.  For
    // documentation on the values allows in this array see:
    // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
    // here we add the paramter 'block' => 'features'. This is because
    // the pager is not on the default block that appears. When the user clicks a
    // page number we want the browser to re-appear with the page is loaded.
    $pager = array(
      'tags' => array(),
      'element' => $pager_id,
      'parameters' => array(
        'block' => 'stocks'
      ),
      'quantity' => $num_results_per_page,
    );
    print theme_pager($pager);  ?>
  </div> <?php
}