tripal/modules/base/tripal_search/tripal_search.module

<?php
//
// Copyright 2009 Clemson University
//
/*******************************************************************************
 * Tripal Search initiation
 ******************************************************************************/
function tripal_search_init(){
   // Add javascript
   drupal_add_js(drupal_get_path('theme', 'tripal').
                                  '/js/tripal_search.js');
}
/*******************************************************************************
 *  Tripal Search adds advanced search functions to Drupal's Search module
 */
function tripal_search_menu() {
  $items = array();
  foreach (module_list() as $name) {
    if (module_hook($name, 'search') && $title = module_invoke($name, 'search', 'name')) {
      $items['tripal_search/'. $name] = array(
        'title' => $title,
        'page callback' => 'tripal_search_view',
        'access arguments' => array('search content'),
        'type' => MENU_LOCAL_TASK
      );
    }
  }
  return $items;
}

/*******************************************************************************
 * Implementation of hook_form_alter
 */
function tripal_search_form_alter(&$form, $form_state, $form_id) {
  if ($form_id == 'search_form' && arg(2)) {
    // for pagination etc.
    $get = drupal_query_string_encode($_GET, array('q'));
    if(preg_match("/node/",arg(1))){
      $form['basic']['inline']['fasta'] = array('#type' => 'markup',
          '#value' => "<br><br><a id=\"tripal_search_link\" href=\"".
                      url('tripal_search/'. arg(1) .'/'. urlencode(search_get_keys()),
                      array('query' => trim($get)?$get:NULL)).
                      "\">Download features (multi-FASTA format)</a><br><br>");

    }
  }
}

/*******************************************************************************
 * Menu callback; presents an tripal_search results page.
 */
function tripal_search_view() {
  $type = arg(1);
  $keys = search_get_keys();

  // Only perform search if there is non-whitespace search term:
  if (!module_hook($type, 'search')) {
    return drupal_not_found();
  }

  if (trim($keys)) {  	
    $results = tripal_do_search($keys,$type);    //var_dump($pager_total['0']);
    return tripal_search_file($type, $keys, $results);
  }
}

/*******************************************************************************
 * Return an open search results file.
 */
function tripal_search_file($type, $keys, $results) {

  drupal_set_header('Content-Type: text');
  drupal_set_header('Content-Disposition: attachment; filename="searchresults.fasta"');
	
  foreach ($results as $result) {
    // Get feature id from drupal database
    $sqld = "SELECT * FROM {chado_feature} CF INNER JOIN {node} N on N.nid = CF.nid WHERE CF.nid = %d";
    if($f_objd = db_fetch_object(db_query($sqld, $result->sid))){

       // Get sequence from chado database
       $previous_db = tripal_db_set_active('chado');  // use chado database
       $sqlc = "SELECT * FROM {feature} WHERE feature_id = '%s'";
       $f_objc = db_fetch_object(db_query($sqlc,$f_objd->feature_id));
       tripal_db_set_active($previous_db);  // now use drupal database
       print tripal_feature_return_fasta($f_objc, $desc);
    } 
  }
}

/*******************************************************************************
 *  This code is a duplicate of the do_search function but with the paging 
 *  call replaced by a simle db_query call.
 */
function tripal_do_search($keywords, $type, $join1 = '', $where1 = '1 = 1', $arguments1 = array(), $columns2 = 'i.relevance AS score', $join2 = '', $arguments2 = array(), $sort_parameters = 'ORDER BY score DESC') {
  $query = search_parse_query($keywords);

  if ($query[2] == '') {
    form_set_error('keys', t('You must include at least one positive keyword with @count characters or more.', array('@count' => variable_get('minimum_word_size', 3))));
  }
  if ($query[6]) {
    if ($query[6] == 'or') {
      drupal_set_message(t('Search for either of the two terms with uppercase <strong>OR</strong>. For example, <strong>cats OR dogs</strong>.'));
    }
  }
  if ($query === NULL || $query[0] == '' || $query[2] == '') {
    return array();
  }

  // Build query for keyword normalization.
  $conditions = "$where1 AND ($query[2]) AND i.type = '%s'";
  $arguments1 = array_merge($arguments1, $query[3], array($type));
  $join = "INNER JOIN {search_total} t ON i.word = t.word $join1";
  if (!$query[5]) {
    $conditions .= " AND ($query[0])";
    $arguments1 = array_merge($arguments1, $query[1]);
    $join .= " INNER JOIN {search_dataset} d ON i.sid = d.sid AND i.type = d.type";
  }

  // Calculate maximum keyword relevance, to normalize it.
  $select = "SELECT SUM(i.score * t.count) AS score FROM {search_index} i $join WHERE $conditions GROUP BY i.type, i.sid HAVING COUNT(*) >= %d ORDER BY score DESC";
  $arguments = array_merge($arguments1, array($query[4]));
  $normalize = db_result(db_query_range($select, $arguments, 0, 1));
  if (!$normalize) {
    return array();
  }
  $columns2 = str_replace('i.relevance', '('. (1.0 / $normalize) .' * SUM(i.score * t.count))', $columns2);

  // Build query to retrieve results.
  $select = "SELECT i.type, i.sid, $columns2 FROM {search_index} i $join $join2 WHERE $conditions GROUP BY i.type, i.sid HAVING COUNT(*) >= %d";
  $count_select =  "SELECT COUNT(*) FROM ($select) n1";
  $arguments = array_merge($arguments2, $arguments1, array($query[4]));
 
  // Do actual search query
//  $result = pager_query("$select $sort_parameters", 10, 0, $count_select, $arguments);
  $result = db_query("$select $sort_parameters",$arguments);
  $results = array();
  while ($item = db_fetch_object($result)) {
    $results[] = $item;
  }
  return $results;
}