tripal/legacy/tripal_pub/theme/templates/tripal_pub_features.tpl.php

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

// get the features that are associated with this publication.  But we only
// want 25 and we want a pager to let the user cycle between pages of features.
// so we, use the chado_select_record 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 features

$element = 2;        // an index to specify the pager this must be unique amongst all pub templates
$num_per_page = 25;  // the number of features to show per page$num_results_per_page = 25;

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

$pub = chado_expand_var($pub, 'table', 'feature_pub', $options);
$feature_pubs = $pub->feature_pub;
if (count($feature_pubs) > 0 ) {
  foreach ($feature_pubs as $feature_pub) {
    $features[] = $feature_pub->feature_id;
  }
}

// get the total number of records
$total_records = chado_pager_get_count($element);

if(count($features) > 0){ ?>
  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> features:</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('Feature Name', 'Uniquename', '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 ($features as $feature){
     $feature_name = $feature->name;
     if (property_exists($feature, 'nid')) {
       $feature_name = l($feature_name, 'node/' . $feature->nid, array('attributes' => array('target' => '_blank')));
     }

     $rows[] = array(
       $feature_name,
       $feature->uniquename,
       $feature->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' => $rows,
    'attributes' => array(
      'id' => 'tripal_pub-table-features',
      'class' => 'tripal-data-table'
    ),
    'sticky' => FALSE,
    'caption' => '',
    'colgroups' => array(),
    'empty' => '',
  );
  // once we have our table array structure defined, we call Drupal's theme_table()
  // function to generate the table.
  print theme_table($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.
  // We remove the 'pane' parameter from the original query parameters because
  // Drupal won't reset the parameter if it already exists.
  $get = $_GET;
  unset($_GET['pane']);
  $pager = array(
    'tags' => array(),
    'element' => $element,
    'parameters' => array(
      'pane' => 'features'
    ),
    'quantity' => $num_per_page,
  );
  print theme_pager($pager);
  $_GET = $get;
}