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+<?php
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+//
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+// Copyright 2009 Clemson University
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+//
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+/*******************************************************************************
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+ * Tripal Search initiation
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+ ******************************************************************************/
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+function tripal_search_init(){
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+ // Add javascript
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+ drupal_add_js(drupal_get_path('theme', 'tripal').
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+ '/js/tripal_search.js');
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+}
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+/*******************************************************************************
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+ * Tripal Search adds advanced search functions to Drupal's Search module
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+ */
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+function tripal_search_menu() {
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+ $items = array();
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+ foreach (module_list() as $name) {
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+ if (module_hook($name, 'search') && $title = module_invoke($name, 'search', 'name')) {
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+ $items['tripal_search/'. $name] = array(
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+ 'title' => $title,
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+ 'page callback' => 'tripal_search_view',
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+ 'access arguments' => array('search content'),
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+ 'type' => MENU_LOCAL_TASK
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+ );
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+ }
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+ }
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+ return $items;
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+}
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+
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+/*******************************************************************************
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+ * Implementation of hook_form_alter
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+ */
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+function tripal_search_form_alter(&$form, $form_state, $form_id) {
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+ if ($form_id == 'search_form' && arg(2)) {
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+ // for pagination etc.
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+ $get = drupal_query_string_encode($_GET, array('q'));
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+ if(preg_match("/node/",arg(1))){
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+ $form['basic']['inline']['fasta'] = array('#type' => 'markup',
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+ '#value' => "<br><br><a id=\"tripal_search_link\" href=\"".
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+ url('tripal_search/'. arg(1) .'/'. urlencode(search_get_keys()),
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+ array('query' => trim($get)?$get:NULL)).
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+ "\">Download features (multi-FASTA format)</a><br><br>");
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+
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+ }
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+ }
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+}
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+
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+/*******************************************************************************
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+ * Menu callback; presents an tripal_search results page.
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+ */
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+function tripal_search_view() {
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+ $type = arg(1);
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+ $keys = search_get_keys();
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+
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+ // Only perform search if there is non-whitespace search term:
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+ if (!module_hook($type, 'search')) {
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+ return drupal_not_found();
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+ }
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+
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+ if (trim($keys)) {
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+ $results = tripal_do_search($keys,$type); //var_dump($pager_total['0']);
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+ return tripal_search_file($type, $keys, $results);
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+ }
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+}
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+
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+/*******************************************************************************
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+ * Return an open search results file.
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+ */
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+function tripal_search_file($type, $keys, $results) {
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+
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+ drupal_set_header('Content-Type: text');
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+ drupal_set_header('Content-Disposition: attachment; filename="searchresults.fasta"');
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+
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+ foreach ($results as $result) {
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+ // Get feature id from drupal database
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+ $sqld = "SELECT * FROM {chado_feature} CF INNER JOIN {node} N on N.nid = CF.nid WHERE CF.nid = %d";
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+ if($f_objd = db_fetch_object(db_query($sqld, $result->sid))){
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+
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+ // Get sequence from chado database
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+ $previous_db = db_set_active('chado'); // use chado database
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+ $sqlc = "SELECT * FROM {feature} WHERE feature_id = '%s'";
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+ $f_objc = db_fetch_object(db_query($sqlc,$f_objd->feature_id));
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+ db_set_active($previous_db); // now use drupal database
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+ print tripal_feature_return_fasta($f_objc, $desc);
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+ }
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+ }
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+}
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+
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+/*******************************************************************************
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+ * This code is a duplicate of the do_search function but with the paging
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+ * call replaced by a simle db_query call.
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+ */
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+function tripal_do_search($keywords, $type, $join1 = '', $where1 = '1 = 1', $arguments1 = array(), $columns2 = 'i.relevance AS score', $join2 = '', $arguments2 = array(), $sort_parameters = 'ORDER BY score DESC') {
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+ $query = search_parse_query($keywords);
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+
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+ if ($query[2] == '') {
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+ form_set_error('keys', t('You must include at least one positive keyword with @count characters or more.', array('@count' => variable_get('minimum_word_size', 3))));
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+ }
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+ if ($query[6]) {
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+ if ($query[6] == 'or') {
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+ drupal_set_message(t('Search for either of the two terms with uppercase <strong>OR</strong>. For example, <strong>cats OR dogs</strong>.'));
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+ }
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+ }
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+ if ($query === NULL || $query[0] == '' || $query[2] == '') {
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+ return array();
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+ }
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+
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+ // Build query for keyword normalization.
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+ $conditions = "$where1 AND ($query[2]) AND i.type = '%s'";
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+ $arguments1 = array_merge($arguments1, $query[3], array($type));
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+ $join = "INNER JOIN {search_total} t ON i.word = t.word $join1";
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+ if (!$query[5]) {
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+ $conditions .= " AND ($query[0])";
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+ $arguments1 = array_merge($arguments1, $query[1]);
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+ $join .= " INNER JOIN {search_dataset} d ON i.sid = d.sid AND i.type = d.type";
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+ }
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+
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+ // Calculate maximum keyword relevance, to normalize it.
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+ $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";
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+ $arguments = array_merge($arguments1, array($query[4]));
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+ $normalize = db_result(db_query_range($select, $arguments, 0, 1));
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+ if (!$normalize) {
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+ return array();
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+ }
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+ $columns2 = str_replace('i.relevance', '('. (1.0 / $normalize) .' * SUM(i.score * t.count))', $columns2);
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+
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+ // Build query to retrieve results.
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+ $select = "SELECT i.type, i.sid, $columns2 FROM {search_index} i $join $join2 WHERE $conditions GROUP BY i.type, i.sid HAVING COUNT(*) >= %d";
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+ $count_select = "SELECT COUNT(*) FROM ($select) n1";
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+ $arguments = array_merge($arguments2, $arguments1, array($query[4]));
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+
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+ // Do actual search query
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+// $result = pager_query("$select $sort_parameters", 10, 0, $count_select, $arguments);
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+ $result = db_query("$select $sort_parameters",$arguments);
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+ $results = array();
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+ while ($item = db_fetch_object($result)) {
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+ $results[] = $item;
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+ }
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+ return $results;
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+}
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