tripal/tripal_project/theme/tripal_project/tripal_project.publications.tpl.php

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

// expand project to include pubs 
$options = array('return_array' => 1);
$project = tripal_core_expand_chado_vars($project, 'table', 'project_pub', $options);
$project_pubs = $project->project_pub; 


if (count($project_pubs) > 0) { ?>
  <div id="tripal_project_pub-pub-box" class="tripal_project_pub-info-box tripal-info-box">
    <div class="tripal_project_pub-info-box-title tripal-info-box-title">Publications</div>
    <div class="tripal_project_pub-info-box-desc tripal-info-box-desc"></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('Year', 'Publication');
    
    // 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 ($project_pubs as $project_pub) {
      $pub = $project_pub->pub_id;
      $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.title');
      $citation = $pub->title;  // use the title as the default citation
      
      // get the citation for this pub if it exists
      $values = array(
        'pub_id' => $pub->pub_id, 
        'type_id' => array(
          'name' => 'Citation',
        ),
      );
      $options = array('return_array' => 1);
      $citation_prop = tripal_core_generate_chado_var('pubprop', $values, $options); 
      if (count($citation_prop) == 1) {
        $citation_prop = tripal_core_expand_chado_vars($citation_prop, 'field', 'pubprop.value');
        $citation = $citation_prop[0]->value;
      }
      
      // if the publication is synced then link to it
      if ($pub->nid) {
        // replace the title with a link
        $link = l($pub->title, 'node/' . $pub->nid ,array('attributes' => array('target' => '_blank')));
        $patterns = array(
          '/(\()/', '/(\))/',
          '/(\])/', '/(\[)/',
          '/(\{)/', '/(\})/',
          '/(\+)/', '/(\.)/', '/(\?)/',
        );
        $fixed_title = preg_replace($patterns, "\\\\$1", $pub->title);
        $citation = preg_replace('/' . $fixed_title . '/', $link, $citation);
      }
      
      $rows[] = array(
        $pub->pyear,
        $citation,
      );
    }
    
    // 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_project-table-publications',
      ),
      '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 
}