$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))) {
$form['basic']['inline']['fasta'] = array('#type' => 'markup',
'#value' => "
trim($get)?$get:NULL)) .
"\">Download features (multi-FASTA format)
");
}
}
}
/*******************************************************************************
* 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 ($query[6] == 'or') {
drupal_set_message(t('Search for either of the two terms with uppercase OR. For example, cats OR dogs.'));
}
}
if ($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;
}