1: <?php
 2: 
 3: namespace webservices\combisearch;
 4: 
 5: use \PDO as PDO;
 6: 
 7: /**
 8:  * WebService.
 9:  * Searches for Features with specified GO.
10:  */
11: class Hasgo extends \WebService {
12: 
13:     /**
14:      * @param $querydata[species] organism id
15:      * @param $querydata[release] release name
16:      * @param $querydata[term] GO to search for
17:      * @returns array of feature ids
18:      */
19:     public function execute($querydata) {
20:         global $db;
21:         $constant = 'constant';
22: 
23:         $species = $querydata['species'];
24:         $release = $querydata['release'];
25: 
26:         $term = trim($querydata['term']);
27: 
28: // this query ignores leading zeroes in accession string
29:         $query_get_features = <<<EOF
30: SELECT fd.feature_id 
31: FROM 
32:     feature_dbxref fd,
33:     (SELECT dbxref_id FROM dbxref WHERE dbxref.db_id = (SELECT db_id FROM db WHERE db.name = 'GO' LIMIT 1) AND trim(LEADING '0' FROM dbxref.accession) = trim(LEADING '0' FROM :accession)) AS dbxref,
34:     (SELECT feature_id FROM feature WHERE feature.type_id={$constant('CV_ISOFORM')} AND feature.organism_id = :species AND feature.dbxref_id = (SELECT dbxref_id FROM dbxref WHERE db_id={$constant('DB_ID_IMPORTS')} AND accession=:release LIMIT 1)) as feature
35: WHERE 
36: feature.feature_id = fd.feature_id
37: AND fd.dbxref_id = dbxref.dbxref_id
38: EOF;
39: 
40:         $stm_get_features = $db->prepare($query_get_features);
41: 
42:         $data = array('results' => array());
43: 
44:         $stm_get_features->execute(array(
45:             'accession' => $term,
46:             'species' => $species,
47:             'release' => $release
48:         ));
49:         while ($feature = $stm_get_features->fetch(PDO::FETCH_ASSOC)) {
50:             $data['results'][] = $feature['feature_id'];
51:         }
52: 
53:         return $data;
54:     }
55: 
56: }
57: 
58: ?>
59: