<?php
-// JSON web service for PO terms: autocomplete and search methods
+/*
+JSON web service for Plant Ontology terms
-/* require the user as the parameter */
-if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
+Required parameters:
+ request_type
+ max
+Optional parameters:
+ app_key (for access to restricted methods)
+ format (JSON only for now)
- $arr_field_names = array('name','acc');
-
- /* read the params and/or set our own */
- $type = isset($_GET['type']) ? $_GET['type'] : autocomplete; // autocomplete is the default
-
- // security measures; helps to avoid SQL injection attacks
- $field = isset($_GET['field']) && in_array($_GET['field'],$arr_field_names)
- ? $_GET['field']
- : die('"field" is a required parameter and must match an available data field.');
-
- $number_of_terms = isset($_GET['max']) ? intval($_GET['max']) : 10; //10 is the default
- if ($number_of_terms > 50) { $number_of_terms = 50; }
+Public Request Types:
+ term_search(req str search_value, opt bool inc_synonyms,
+ opt bool inc_accessions, opt str branch_filter)
+ term_detail(req str accession_id)
- $qval = $_GET['qval'];
-
- $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0
- ? strtolower($_GET['qval'])
- : die('Please provide a searchable value');
+Restricted Request Types (requires user key):
+ wiki_autocomplete(req str search_value)
+ wiki_term_detail(req str accession_id || req str term_name)
+*/
- $format = strtolower($_GET['format']) != 'json'
- ? strtolower($_GET['format'])
- : 'json'; //json is the default
-
- /* connect to the db */
- $link = mysql_connect($_SERVER['mysql_host'], $_SERVER['mysql_user'], $_SERVER['mysql_pw']) or die('Cannot connect to the DB');
- mysql_select_db($_SERVER['mysql_db'],$link) or die('Cannot select the DB');
+/* read the params and/or set our own */
+$request_type = isset($_GET['request_type'])
+ ? $_GET['request_type']
+ : die('Please provide a request type.');
- switch ($type) {
- case 'autocomplete':
- /* grab the terms from the db */
- $query = "SELECT t.$field FROM term t"
- . " LEFT JOIN term_definition d ON d.term_id = t.id"
- . " WHERE t.$field LIKE '%$qval%'"
- . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')"
- . " AND t.is_obsolete = 0"
- . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
- . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
- . " ORDER BY name LIMIT $number_of_terms";
- $result = mysql_query($query,$link) or die('Errant query: '.$query);
-
- /* create one master array of the records */
- $terms = array();
- if(mysql_num_rows($result)) {
- while($term = mysql_fetch_assoc($result)) {
- $terms[] = array('term'=>$term[$field]);
- }
- }
+$number_of_terms = isset($_GET['max']) ? intval($_GET['max']) : 10; // default
+if ($number_of_terms > 50) { $number_of_terms = 50; } // ceiling
- /* output in necessary format */
- if($format == 'json') {
- header('Content-type: application/json');
- echo json_encode(array('PO_term_lookup_response'=>$terms));
- }
- else {
- die('Sorry, this request cannot be fulfilled in '.$format.' format.');
- }
- break;
+$format = isset($_GET['format']) && strtolower($_GET['format']) != 'json'
+ ? strtolower($_GET['format'])
+ : 'json'; //json is the default
- case 'term_detail':
- /* grab the ontology data from the db */
- $query = "SELECT DISTINCT t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'"
- . " FROM term t"
- . " LEFT JOIN term_definition d ON d.term_id = t.id"
- . " WHERE t.name = '$qval'"
- . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')"
- . " AND t.is_obsolete = 0"
- . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
- . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
- . " ORDER BY t.name LIMIT 1";
- $result = mysql_query($query,$link) or die('Errant query: '.$query);
-
- /* create one master array of the records */
- $terms = array();
- if(mysql_num_rows($result)) {
- while($term = mysql_fetch_assoc($result)) {
- $terms[] = array(
- 'accession_id'=>$term['acc'],
- 'aspect'=>$term['type'] == "plant_anatomy" ? "Plant Anatomy" : "Plant Growth and Development Stage",
- 'definition'=>$term['definition'],
- 'comment'=>$term['comment']);
- }
- }
- /* output in necessary format */
- if($format == 'json') {
- header('Content-type: application/json');
- echo json_encode(array('PO_term_detail_response'=>$terms));
- }
- else {
- die('Sorry, this request cannot be fulfilled in '.$format.' format.');
+$inc_synonyms = isset($_GET['inc_synonyms']) ? 1 : 0; // default
+
+/* connect to the db */
+$link = mysql_connect($_SERVER['dev_po_host'], $_SERVER['dev_po_user'],
+ $_SERVER['dev_po_pw']) or die(mysql_error() . 'Cannot connect to the DB');
+mysql_select_db($_SERVER['dev_po_db'],$link) or die('Cannot select the DB');
+
+switch ($request_type) {
+
+ case 'term_search':
+ $search_value = $_GET['search_value'];
+ $search_value = isset($_GET['search_value']) && strlen($_GET['search_value']) > 0
+ ? strtolower($_GET['search_value'])
+ : die('Please provide the "search_value" parameter.');
+
+ /* grab the terms from the db */
+ $query = "(SELECT t.name, 'term' as match_type, t.acc, null as parent_name"
+ . " FROM term t"
+ . " LEFT JOIN term_definition d ON d.term_id = t.id"
+ . " LEFT JOIN term_synonym s ON s.term_id = t.id"
+ . " WHERE t.name LIKE '%$search_value%'"
+ . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')"
+ . " AND t.is_obsolete = 0"
+ . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
+ . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
+ . " GROUP BY t.id)";
+ if ($inc_synonyms) {
+ $query .= " UNION"
+ . " (SELECT ts.term_synonym as name, 'synonym' as match_type, t2.acc, t2.name as parent_name"
+ . " FROM term_synonym ts"
+ . " LEFT JOIN term t2 ON ts.term_id = t2.id"
+ . " LEFT JOIN term_definition d2 ON d2.term_id = t2.id"
+ . " WHERE ts.term_synonym LIKE '%$search_value%'"
+ . " AND t2.term_type in ('plant_anatomy','plant_growth_and_development_stage')"
+ . " AND t2.is_obsolete = 0"
+ . " AND UCASE(t2.name) NOT LIKE 'OBSOLETE%'"
+ . " AND UCASE(d2.term_definition) NOT LIKE 'OBSOLETE%')";
+ }
+ $query .= " ORDER BY name LIMIT $number_of_terms";
+
+ $result = mysql_query($query,$link) or die('Errant query: '.$query);
+
+ /* create one master array of the records */
+ $term_matches = array();
+ if(mysql_num_rows($result)) {
+ while($term = mysql_fetch_assoc($result)) {
+ $ary_match = array(
+ 'match'=>$term['name'],
+ 'match_type'=>$term['match_type'],
+ 'accession_id'=>$term['acc']);
+ if ($term['match_type'] == 'synonym') {
+ $ary_match['has_parent_term_name'] = $term['parent_name'];
}
- break;
- default:
- die('Sorry, this web service method is not available.');
+ $term_matches[] = $ary_match;
+ }
+ }
+
+ /* output in necessary format */
+ if($format == 'json') {
+ header('Content-type: application/json');
+ echo json_encode(array('PO_term_search_response'=>$term_matches));
+ }
+ else {
+ die('Sorry, this request cannot be fulfilled in '.$format.' format.');
+ }
+ break;
+
+ case 'term_detail':
+ $accession_id = $_GET['accession_id'];
+ $accession_id = isset($_GET['accession_id']) && strlen($_GET['accession_id']) > 0
+ ? $_GET['accession_id']
+ : die('Please provide the "accession_id" parameter.');
+
+ /* grab the ontology data from the db */
+ $query = "SELECT DISTINCT t.name, t.acc as 'acc', t.term_type as 'type',"
+ . " d.term_definition as 'definition', d.term_comment as 'comment',"
+ . " group_concat(s.term_synonym separator ', ') as synonyms"
+ . " FROM term t"
+ . " LEFT JOIN term_definition d ON d.term_id = t.id"
+ . " LEFT JOIN term_synonym s ON s.term_id = t.id"
+ . " WHERE t.acc = '$accession_id'"
+ . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')"
+ . " AND t.is_obsolete = 0"
+ . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'"
+ . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'"
+ . " GROUP BY t.id"
+ . " ORDER BY t.name LIMIT 1";
+ $result = mysql_query($query,$link) or die('Errant query: '.$query);
+
+ /* create one master array of the records */
+ $term_details = array();
+ if(mysql_num_rows($result)) {
+ while($term = mysql_fetch_assoc($result)) {
+ $term_details[] = array(
+ 'accession_id'=>$term['acc'],
+ 'name'=>$term['name'],
+ 'aspect'=>$term['type'] == "plant_anatomy" ? "Plant Anatomy" : "Plant Growth and Development Stage",
+ 'definition'=>$term['definition'],
+ 'comment'=>$term['comment'],
+ 'synonyms'=>preg_split("/, /",$term['synonyms'])
+ );
+ }
+ }
+ /* output in necessary format */
+ if($format == 'json') {
+ header('Content-type: application/json');
+ echo json_encode(array('PO_term_detail_response'=>$term_details));
+ }
+ else {
+ die('Sorry, this request cannot be fulfilled in '.$format.' format.');
}
- /* disconnect from the db */
- @mysql_close($link);
+ break;
+ default:
+ die('Sorry, this web service method is not available.');
}
-else { die('Not authorized.'); }
+/* disconnect from the db */
+@mysql_close($link);
?>
projects / old-jaiswallab-svn / .git / commitdiff