From b6a473a783414d8c3a248af465af402071109e0a Mon Sep 17 00:00:00 2001
From: proost <proost@mpimp-golm.mpg.de>
Date: Fri, 8 Jan 2016 11:56:35 +0100
Subject: [PATCH] optimized XGMML export (json intermediate no longer
 necessary)

---
 planet/static/js/planet_graph.js      | 13 +------------
 planet/static/js/planet_svg_legend.js |  1 -
 planet/static/js/planet_xgmml.js      | 28 +++++++++++++--------------
 3 files changed, 15 insertions(+), 27 deletions(-)

diff --git a/planet/static/js/planet_graph.js b/planet/static/js/planet_graph.js
index 62a252f..ca09741 100644
--- a/planet/static/js/planet_graph.js
+++ b/planet/static/js/planet_graph.js
@@ -297,19 +297,8 @@ $('#cy-download-jsoncy').click(function(ev) {
 
 $('#cy-download-xgmml').click(function(ev) {
   ev.preventDefault();
-  var eles = cy.elements();
-
-  eles.each( function(i, ele) {
-    if (ele.isNode()) {
-      ele.data('current_color', ele.renderedStyle('background-color'));
-      ele.data('current_shape', ele.renderedStyle('shape'));
-    } else if (ele.isEdge()) {
-      ele.data('current_color', ele.renderedStyle('line-color'));
-      ele.data('current_width', ele.renderedStyle('width'));
-    }
-  });
 
-  xgmml = writeXGMML(cy.json());
+  xgmml = writeXGMML(cy);
 
   var element = document.createElement('a');
   element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(xgmml));
diff --git a/planet/static/js/planet_svg_legend.js b/planet/static/js/planet_svg_legend.js
index bf2f188..ef2af26 100644
--- a/planet/static/js/planet_svg_legend.js
+++ b/planet/static/js/planet_svg_legend.js
@@ -117,7 +117,6 @@ function generate_legend(label_set, attribute) {
     var document_height = parseInt(svg_legend.attr('height').replace('px',''));
     if (total_height > document_height) {
         var viewbox = svg_legend.attr('viewBox');
-        console.log(viewbox);
         svg_legend.attr('viewBox', '0 0 750 ' + total_height);
         svg_legend.attr('height', total_height + 'px');
     }
diff --git a/planet/static/js/planet_xgmml.js b/planet/static/js/planet_xgmml.js
index 8f16590..a9430b5 100644
--- a/planet/static/js/planet_xgmml.js
+++ b/planet/static/js/planet_xgmml.js
@@ -63,30 +63,30 @@ function writeXGMML(data) {
         xw.writeAttributeString( 'value', '#ffffff');
         xw.writeEndElement();
 
-        data.elements.nodes.forEach( function(node) {
+        data.nodes.forEach( function(node) {
               if (!node.data.compound)
               {
                   xw.writeStartElement( 'node' );
-                  xw.writeAttributeString( 'id', node.data.id );
-                  xw.writeAttributeString( 'label', node.data.name );
+                  xw.writeAttributeString( 'id', node.data('id') );
+                  xw.writeAttributeString( 'label', node.data('name') );
                   xw.writeAttributeString( 'name', 'base' );
 
                         xw.writeStartElement( 'att' );
                         xw.writeAttributeString( 'label', 'gene_name' );
                         xw.writeAttributeString( 'name', 'gene_name' );
-                        xw.writeAttributeString( 'value', node.data.gene_name );
+                        xw.writeAttributeString( 'value', node.data('gene_name') );
                         xw.writeAttributeString( 'type', 'string');
                         xw.writeEndElement();
 
                         xw.writeStartElement( 'graphics' );
                         xw.writeAttributeString( 'width', '1' );
-                        xw.writeAttributeString( 'fill', __convertColor(node.data.current_color) );
+                        xw.writeAttributeString( 'fill', __convertColor(node.renderedStyle('background-color')) );
                         xw.writeAttributeString( 'outline', "#000000" );
                         xw.writeAttributeString( 'x', node.position.x);
                         xw.writeAttributeString( 'y', node.position.y);
                         xw.writeAttributeString( 'h', '30.0');
                         xw.writeAttributeString( 'w', '30.0');
-                        xw.writeAttributeString( 'type', __convertShape(node.data.current_shape) );
+                        xw.writeAttributeString( 'type', __convertShape(node.renderedStyle('shape')) );
 
                             xw.writeStartElement( 'att' );
                             xw.writeAttributeString( 'name', 'cytoscapeNodeGraphicsAttributes' );
@@ -112,17 +112,17 @@ function writeXGMML(data) {
               }
         });
 
-        data.elements.edges.forEach( function(edge) {
+        data.edges.forEach( function(edge) {
             xw.writeStartElement( 'edge' );
-            xw.writeAttributeString( 'id', edge.data.id );
-            xw.writeAttributeString( 'label', edge.data.id );
-            xw.writeAttributeString( 'source', edge.data.source );
-            xw.writeAttributeString( 'target', edge.data.target );
+            xw.writeAttributeString( 'id', edge.data('id') );
+            xw.writeAttributeString( 'label', edge.data('id') );
+            xw.writeAttributeString( 'source', edge.data('source') );
+            xw.writeAttributeString( 'target', edge.data('target') );
 
                 xw.writeStartElement( 'graphics' );
-                xw.writeAttributeString( 'width', edge.data.current_width.replace('px', '') );
-                xw.writeAttributeString( 'fill', __convertColor(edge.data.current_color) );
-                if (edge.data.homology) {
+                xw.writeAttributeString( 'width', edge.renderedStyle('width').replace('px', '') );
+                xw.writeAttributeString( 'fill', __convertColor(edge.renderedStyle('line-color')) );
+                if (edge.data('homology')) {
                     xw.writeAttributeString( 'EDGE_LINE_TYPE', 'LONG_DASH' );
                 }
                 xw.writeEndElement();