Initial import of version 0.2

tripal_search/tripal_search.info

@@ -0,0 +1,10 @@
+; $Id:
+name = Tripal Search
+description = A module that adds advanced search functions to Drupal, including feature fasta file export from the search result.
+core = 6.x
+project = tripal_search
+package = Tripal
+version = 6.x-0.2b-m0.1
+dependencies[] = search
+dependencies[] = tripal_core
+dependencies[] = tripal_feature

tripal_search/tripal_search.module

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+<?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 = db_set_active('chado');  // use chado database
+       $sqlc = "SELECT * FROM {feature} WHERE feature_id = '%s'";
+       $f_objc = db_fetch_object(db_query($sqlc,$f_objd->feature_id));
+       db_set_active($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;
+}