From: preecej <preecej@localhost>
Date: Mon, 14 Nov 2011 20:22:05 +0000 (+0000)
Subject: Revised to make generically available via plantontology.org, also to add
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=b7bb98f9a69dfdf4f39c9eb2999181c5e94f2081;p=old-jaiswallab-svn%2F.git

Revised to make generically available via plantontology.org, also to add
synonym searching functionality

svn path=/; revision=214
---

diff --git a/Personnel/preecej/php_singletons/PO_web_service.php b/Personnel/preecej/php_singletons/PO_web_service.php
index 9ba7afe..1317b54 100644
--- a/Personnel/preecej/php_singletons/PO_web_service.php
+++ b/Personnel/preecej/php_singletons/PO_web_service.php
@@ -1,106 +1,152 @@
 <?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);
 ?>