Official development copies of internal web services used by the wiki

svn path=/; revision=159

diff --git a/preecej/semantic_wiki/services/NCBI_eDocSummary.php b/preecej/semantic_wiki/services/NCBI_eDocSummary.php
new file mode 100644 (file)
index 0000000..7e38a66
--- /dev/null
+++ b/preecej/semantic_wiki/services/NCBI_eDocSummary.php
@@ -0,0 +1,49 @@
+<?php
+$pub_id = $_GET["pub_id"];
+$url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi/?db=pubmed&id=" . $pub_id;
+$response = file_get_contents($url);
+
+$NCBI_doc = new SimpleXMLElement($response); // inst. NCBI eDocSummary as xml
+$xml_out = new SimpleXMLElement("<eSummaryResult/>"); // inst. new xml doc for output
+
+// build xml doc with NCBI data
+$DocSum = $xml_out->addChild("DocSum");
+$DocSum->addChild("Id",$NCBI_doc->DocSum->Id);
+
+foreach ($NCBI_doc->xpath("//Item") as $item) {
+    switch((string) $item["Name"]) { // Get attributes as element indices
+    case "PubDate":
+        $DocSum->addChild("PubDate",$item);
+        break;
+    case "Author":
+        $authorList[] = $item;
+        break;
+    case "LastAuthor":
+        $DocSum->addChild("LastAuthor",$item);
+        break;
+    case "Title":
+        $DocSum->addChild("Title",$item);
+        break;
+    case "Volume":
+        $DocSum->addChild("Volume",$item);
+        break;
+    case "Pages":
+        $DocSum->addChild("Pages",$item);
+        break;
+    case "FullJournalName":
+        $DocSum->addChild("FullJournalName",$item);
+        break;
+    }
+}
+
+$author_list = "";
+foreach ($authorList as $author) {
+    $author_list = $author_list . $author . ", ";
+}
+$DocSum->addChild("AuthorList",rtrim($author_list,", "));
+
+
+header('Content-Type: text/xml'); // output xml doctype in your response
+echo $xml_out->asXML(); 
+?>
+

diff --git a/preecej/semantic_wiki/services/TermSearch_JSON.php b/preecej/semantic_wiki/services/TermSearch_JSON.php
new file mode 100644 (file)
index 0000000..89c1033
--- /dev/null
+++ b/preecej/semantic_wiki/services/TermSearch_JSON.php
@@ -0,0 +1,106 @@
+<?php
+// JSON web service for PO terms: autocomplete and search methods
+
+/* require the user as the parameter */
+if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
+
+        $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; } 
+
+        $qval = $_GET['qval'];
+        
+        $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 
+            ? strtolower($_GET['qval'])
+            : die('Please provide a searchable value');
+
+        $format = strtolower($_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'],$link) or die('Cannot select the DB');
+
+        switch ($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)) {
+                        $terms[] = array('title'=>$term[$field]);
+                    }
+                }
+
+                /* output in necessary format */
+                if($format == 'json') {
+                    header('Content-type: application/json');
+                    echo json_encode(array('sfautocomplete'=>$terms));
+                }
+                else {
+                    die('Sorry, this request cannot be fulfilled in '.$format.' format.');
+                }
+                break;
+
+            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)) {
+                        $terms[] = array(
+                            'id'=>$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_result'=>$terms));
+                }
+                else {
+                    die('Sorry, this request cannot be fulfilled in '.$format.' format.');
+                }
+                break;
+            default:
+                die('Sorry, this web service method is not available.');
+        }
+        /* disconnect from the db */
+        @mysql_close($link);
+}
+else { die('Not authorized.'); }
+?>
+