From 4838b150a02f55669002430b865e5d285eb1bd30 Mon Sep 17 00:00:00 2001
From: preecej <preecej@localhost>
Date: Wed, 18 Jul 2012 02:52:09 +0000
Subject: [PATCH] Added TO (Trait Ontology) web service and db access, fixed
 Annotation form bug on listing Publications (no more tilde wildcards.)

svn path=/; revision=364
---
 planteome/paw/forms/Annotation.wiki                |  4 ++--
 planteome/paw/local_settings/dev.LocalSettings.php |  1 -
 planteome/paw/services/TermSearch_JSON.php         | 11 ++++++++++-
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/planteome/paw/forms/Annotation.wiki b/planteome/paw/forms/Annotation.wiki
index 7d7ac0b..69db501 100644
--- a/planteome/paw/forms/Annotation.wiki
+++ b/planteome/paw/forms/Annotation.wiki
@@ -184,8 +184,8 @@ __NOTOC__
 Need to add a reference to a publication without a PubMed ID or DOI (Digital Object Identifier)?<br>
 {{#formlink:form=Publication|link text=Add a new publication reference|link type=|query string=Publication[New Annotation Reference]={{PAGENAME}} }}
     
-    {{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }}
-      | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]]
+    {{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::{{PAGENAME}} ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::{{PAGENAME}} ]] }}
+      | {{#ask:[[Category:Publications]][[Is Associated With Annotations::{{PAGENAME}} ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::{{PAGENAME}} ]]
           |? has First Author
           |? has Publication Title
           |? has Journal Name
diff --git a/planteome/paw/local_settings/dev.LocalSettings.php b/planteome/paw/local_settings/dev.LocalSettings.php
index 3b264e1..1b0dff4 100644
--- a/planteome/paw/local_settings/dev.LocalSettings.php
+++ b/planteome/paw/local_settings/dev.LocalSettings.php
@@ -167,7 +167,6 @@ $wgCachePages       = false;
         *      */
 $wgCacheEpoch = 'date +%Y%m%d%H%M%S';
 
-
 # When you make changes to this configuration file, this will make
 # sure that cached pages are cleared.
 $wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
diff --git a/planteome/paw/services/TermSearch_JSON.php b/planteome/paw/services/TermSearch_JSON.php
index d127a66..277a5d2 100644
--- a/planteome/paw/services/TermSearch_JSON.php
+++ b/planteome/paw/services/TermSearch_JSON.php
@@ -5,7 +5,7 @@
 if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
 
         $arr_field_names = array('name','acc');
-        $arr_ontologies = array('go','po');
+        $arr_ontologies = array('go','po','to');
         
         /* read the params and/or set our own */
         $type = isset($_GET['type']) ? $_GET['type'] : autocomplete; // autocomplete is the default
@@ -48,6 +48,13 @@ if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
                 $term_types = "'biological_process','cellular_component','molecular_function'"; 
                 break;
 
+            case 'to':
+                $link = mysql_connect($_SERVER['to_host'], $_SERVER['to_user'], $_SERVER['to_pw']) or die('Cannot connect to the DB');
+                mysql_select_db($_SERVER['to_db'],$link) or die('Cannot select the DB');
+
+                $term_types = "'plant_trait_ontology'"; 
+                break;
+
             default:
                 die('Sorry, this ontology type is not available.');
         }
@@ -111,6 +118,8 @@ if(isset($_GET['user']) && ($_GET['user']) == 'paw') {
                                 $term_type_formal = "Cellular Component"; break;
                             case 'molecular_function':
                                 $term_type_formal = "Molecular Function"; break;
+                            case 'plant_trait_ontology':
+                                $term_type_formal = "Plant Trait Ontology"; break;
                         }
                         $terms[] = array(
                             'name'=>$term['name'],
-- 
2.34.1