1: <?php
 2: 
 3: namespace webservices\combisearch;
 4: 
 5: use \PDO as PDO;
 6: 
 7: /**
 8:  * WebService.
 9:  * Searches for features containing submitted GO or a child GO
10:  */
11: class Hasgo_or_children 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:         $query_get_parent_cvterm = <<<EOF
29: SELECT cvterm.cvterm_id
30:     FROM dbxref, cvterm, cvterm_relationship 
31:     WHERE db_id=(SELECT db_id FROM db WHERE name='GO') 
32:     AND trim(LEADING '0' FROM accession)=trim(LEADING '0' FROM :accession)
33:     AND dbxref.dbxref_id = cvterm.dbxref_id
34:     LIMIT 1
35: EOF;
36:         $stm_get_parent = $db->prepare($query_get_parent_cvterm);
37: 
38:         // selects all child GOs (actually containing the parent as well), join this with a pre-filtered feature table
39:         // get_cvterm_children can return duplicate rows, so it is grouped by cvterm_id, dbxref_id
40:         $query_get_features = <<<EOF
41: SELECT fd.feature_id 
42: FROM 
43:     feature_dbxref fd,
44:     (SELECT dbxref_id FROM get_cvterm_children(:parent) GROUP BY cvterm_id, dbxref_id
45:         ) AS dbxref,
46:     (SELECT feature_id FROM feature WHERE feature.type_id={$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
47: WHERE 
48: feature.feature_id = fd.feature_id
49: AND fd.dbxref_id = dbxref.dbxref_id
50: 
51: 
52: EOF;
53: 
54:         $stm_get_features = $db->prepare($query_get_features);
55: 
56: 
57:         $data = array('results' => array());
58: 
59:         $stm_get_parent->execute(array(
60:             'accession' => $term
61:         ));
62:         $parent = $stm_get_parent->fetchColumn();
63:         if ($parent == null)
64:             return $data;
65: 
66:         $stm_get_features->execute(array(
67:             'parent' => $parent,
68:             'species' => $species,
69:             'release' => $release
70:         ));
71:         while ($feature = $stm_get_features->fetch(PDO::FETCH_ASSOC)) {
72:             $data['results'][] = $feature['feature_id'];
73:         }
74: 
75:         return $data;
76:     }
77: 
78: }
79: 
80: ?>
81: