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

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

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

$element = 3;        // an index to specify the pager this must be unique amongst all pub templates
$num_per_page = 25;  // the number of libraries to show per page$num_results_per_page = 25;

// get the libraries from the library_pub table
$options = [
  'return_array' => 1,
  'pager' => [
    'limit' => $num_per_page,
    'element' => $element,
  ],
];

$pub = chado_expand_var($pub, 'table', 'library_pub', $options);
$library_pubs = $pub->library_pub;
if (count($library_pubs) > 0) {
  foreach ($library_pubs as $library_pub) {
    $libraries[] = $library_pub->library_id;
  }
}

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

if (count($libraries) > 0) { ?>
    <div class="tripal_pub-data-block-desc tripal-data-block-desc">This
        publication contains information
        about <?php print number_format($total_records) ?> libraries:
    </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 = ['Library Name', 'Unique Name', 'Organism'];

  // 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 = [];

  foreach ($libraries as $library) {
    $library_name = $library->name;
    if (property_exists($library, 'nid')) {
      $library_name = l($library_name, 'node/' . $library->nid, ['attributes' => ['target' => '_blank']]);
    }
    $organism = '<i>' . $library->organism_id->genus . ' ' . $library->organism_id->species . '</i>';
    if (property_exists($library->organism_id, 'nid')) {
      $organism = l($organism, 'node/' . $library->organism_id->nid, ['attributes' => ['target' => '_blank']]);
    }
    $rows[] = [
      $library_name,
      $library->uniquename,
      $organism,
    ];
  }
  // 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 = [
    'header' => $headers,
    'rows' => $rows,
    'attributes' => [
      'id' => 'tripal_pub-table-libraries',
      'class' => 'tripal-data-table',
    ],
    'sticky' => FALSE,
    'caption' => '',
    'colgroups' => [],
    'empty' => '',
  ];
  // once we have our table array structure defined, we call Drupal's theme_table()
  // function to generate the table.
  print theme_table($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' => 'libraries'. 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 = [
    'tags' => [],
    'element' => $element,
    'parameters' => [
      'pane' => 'libraries',
    ],
    'quantity' => $num_per_page,
  ];
  print theme_pager($pager);
  $_GET = $get;
}