Merge branch 'Issue-#1870' of https://github.com/mjshepherd/phenotips

phenotips · Sep 27, 2015 · a81720e · a81720e
2 parents c97bab6 + 5f85071
commit a81720e
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Showing 64 changed files with 21,911 additions and 21,532 deletions.
diff --git a/components/pedigree/resources/src/main/resources/pedigree/controller.js b/components/pedigree/resources/src/main/resources/pedigree/controller.js
diff --git a/components/pedigree/resources/src/main/resources/pedigree/disorder.js b/components/pedigree/resources/src/main/resources/pedigree/disorder.js
@@ -5,62 +5,67 @@
  * @param disorderID the id number for the disorder, taken from the OMIM database
  * @param name a string representing the name of the disorder e.g. "Down Syndrome"
  */
+define([
+        "pedigree/model/helpers"
+    ], function(
+        Helpers
+    ){
+    var Disorder = Class.create( {
 
-var Disorder = Class.create( {
+        initialize: function(disorderID, name, callWhenReady) {
+            // user-defined disorders
+            if (name == null && !Helpers.isInt(disorderID)) {
+                name = disorderID;
+            }
+
+            this._disorderID = disorderID;
+            this._name       = name ? name : "loading...";
 
-    initialize: function(disorderID, name, callWhenReady) {
-        // user-defined disorders
-        if (name == null && !isInt(disorderID)) {
-            name = disorderID;
-        }
-
-        this._disorderID = disorderID;
-        this._name       = name ? name : "loading...";
+            if (!name && callWhenReady)
+                this.load(callWhenReady);
+        },
 
-        if (!name && callWhenReady)
-            this.load(callWhenReady);
-    },
+        /*
+         * Returns the disorderID of the disorder
+         */
+        getDisorderID: function() {
+            return this._disorderID;
+        },
 
-    /*
-     * Returns the disorderID of the disorder
-     */
-    getDisorderID: function() {
-        return this._disorderID;
-    },
+        /*
+         * Returns the name of the disorder
+         */
+        getName: function() {
+            return this._name;
+        },
 
-    /*
-     * Returns the name of the disorder
-     */
-    getName: function() {
-        return this._name;
-    },
+        load: function(callWhenReady) {
+            var baseOMIMServiceURL = Disorder.getOMIMServiceURL();
+            var queryURL           = baseOMIMServiceURL + "&q=id:" + this._disorderID;
+            //console.log("queryURL: " + queryURL);
+            new Ajax.Request(queryURL, {
+                method: "GET",
+                onSuccess: this.onDataReady.bind(this),
+                //onComplete: complete.bind(this)
+                onComplete: callWhenReady ? callWhenReady : {}
+            });
+        },
 
-    load: function(callWhenReady) {
-        var baseOMIMServiceURL = Disorder.getOMIMServiceURL();
-        var queryURL           = baseOMIMServiceURL + "&q=id:" + this._disorderID;
-        //console.log("queryURL: " + queryURL);
-        new Ajax.Request(queryURL, {
-            method: "GET",
-            onSuccess: this.onDataReady.bind(this),
-            //onComplete: complete.bind(this)
-            onComplete: callWhenReady ? callWhenReady : {}
-        });
-    },
-
-    onDataReady : function(response) {
-        try {
-            var parsed = JSON.parse(response.responseText);
-            //console.log(stringifyObject(parsed));
-            console.log("LOADED DISORDER: disorder id = " + this._disorderID + ", name = " + parsed.rows[0].name);
-            this._name = parsed.rows[0].name;
-        } catch (err) {
-            console.log("[LOAD DISORDER] Error: " +  err);
+        onDataReady : function(response) {
+            try {
+                var parsed = JSON.parse(response.responseText);
+                //console.log(Helpers.stringifyObject(parsed));
+                console.log("LOADED DISORDER: disorder id = " + this._disorderID + ", name = " + parsed.rows[0].name);
+                this._name = parsed.rows[0].name;
+            } catch (err) {
+                console.log("[LOAD DISORDER] Error: " +  err);
+            }
         }
-    }
-});
-
+    });
 
+    Disorder.getOMIMServiceURL = function() {
+        return new XWiki.Document('OmimService', 'PhenoTips').getURL("get", "outputSyntax=plain");
+    };
 
-Disorder.getOMIMServiceURL = function() {
-    return new XWiki.Document('OmimService', 'PhenoTips').getURL("get", "outputSyntax=plain");
-}
+    return Disorder;
+});
diff --git a/components/pedigree/resources/src/main/resources/pedigree/editor.css b/components/pedigree/resources/src/main/resources/pedigree/editor.css
@@ -712,7 +712,7 @@
 }
 .node-type-options .person-type-option.square span {
   display: inline-block;
-  width: 12px;
+  width: 12px; 
   height: 12px;
   border: 1px solid black;
 }
@@ -721,7 +721,7 @@
 }
 .node-type-options .person-type-option.diamond span {
   display: inline-block;
-  width: 10px;
+  width: 10px; 
   height: 10px;
   border: 1px solid black;
   -webkit-transform: rotate(45deg);
@@ -733,7 +733,7 @@
 }
 .node-type-options .person-type-option.circle span {
   display: inline-block;
-  width: 12px;
+  width: 12px; 
   height: 12px;
   border-radius: 50%;
   border: 1px solid black;
@@ -745,7 +745,7 @@
   font-weight: bold;
   font-size: 8px;
   position: absolute;
-  top: 8px;
+  top: 8px; 
   left: 10px;
 }
 .expand-arrow {