tripal/tripal_pub/theme/tripal_pub/tripal_pub_stocks.tpl.php

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

// get the stocks that are associated with this publication.  But we only
// want 25 and we want a pager to let the user cycle between pages of stocks.
// so we, use the tripal_core_chado_select API function to get the results and
// generate the pager.  The function is smart enough to know which page the user is
// on and retrieves the proper set of stocks

$element = 5;        // an index to specify the pager this must be unique amongst all pub templates
$num_per_page = 25;  // the number of stocks to show per page$num_results_per_page = 25; 

// get the stocks from the stock_pub table
$options = array(  
  'return_array' => 1,
  'pager' => array(
    'limit'   => $num_per_page, 
    'element' => $element
  ),
);

$pub = tripal_core_expand_chado_vars($pub, 'table', 'stock_pub', $options);
$stock_pubs = $pub->stock_pub;
if (count($stock_pubs) > 0 ) {
  foreach ($stock_pubs as $stock_pub) {    
    $stocks[] = $stock_pub->stock_id;
  }
}

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

if(count($stocks) > 0){ ?>
  <div id="tripal_pub-stocks-box" class="tripal_pub-info-box tripal-info-box">
    <div class="tripal_pub-info-box-title tripal-info-box-title">Stocks</div>
    <div class="tripal_pub-info-box-desc tripal-info-box-desc">This publication contains information about <?php print number_format($total_records) ?> stocks:</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('Stock Name', 'Uniquenaem', '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){
       $stock_name = $stock->name;
       if (property_exists($stock, 'nid')) {
         $stock_name = l($stock_name, 'node/' . $stock->nid, array('attributes' => array('target' => '_blank')));
       }
       
       $rows[] = array(
         $stock_name,
         $stock->uniquename,
         $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' => $rows,
      'attributes' => array(
        'id' => 'tripal_pub-table-stocks',
      ),
      'sticky' => FALSE,
      'caption' => '',
      'colgroups' => array(),
      'empty' => '',
    );
    // once we have our table array structure defined, we call Drupal's theme_table()
    // function to generate the table.
    print theme_table($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' => 'stocks'. 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' => $element,
      'parameters' => array(
        'block' => 'stocks'
      ),
      'quantity' => $num_per_page,
    );
    print theme_pager($pager); ?>
  </div><?php 
}?>