Codon tree viewer fix for #2361 (#971)

* Fix for CodonTree viewer. #2361
PATRIC3 · May 26, 2020 · 8a23791 · 8a23791
1 parent 81a9f18
commit 8a23791
Show file tree

Hide file tree

Showing 2 changed files with 17 additions and 13 deletions.
diff --git a/public/js/p3/widget/WorkspaceBrowser.js b/public/js/p3/widget/WorkspaceBrowser.js
@@ -583,22 +583,10 @@ define([
         });
       }, self.path.split('/').length < 3);
 
-      this.browserHeader.addAction('ViewCodonTree', 'fa icon-tree2 fa-2x', {
-        label: 'VIEW',
-        multiple: false,
-        validTypes: ['CodonTree'],
-        tooltip: 'View Codon Tree'
-      }, function (selection) {
-        var sel = selection[0],
-          path = sel.path + '.' + sel.name + '/codontree_treeWithGenomeIds.nwk';
-
-        Topic.publish('/navigate', { href: '/view/PhylogeneticTree/?&labelSearch=true&idType=genome_id&labelType=genome_name&wsTreeFile=' + encodePath(path) });
-      }, false);
-
       this.browserHeader.addAction('ViewTree', 'fa icon-tree2 fa-2x', {
         label: 'VIEW',
         multiple: false,
-        validTypes: ['PhylogeneticTree'],
+        validTypes: ['PhylogeneticTree', 'CodonTree'],
         tooltip: 'View Tree'
       }, function (selection) {
         var expPath = this.get('path');

diff --git a/public/js/p3/widget/viewer/PhylogeneticTree.js b/public/js/p3/widget/viewer/PhylogeneticTree.js
@@ -94,6 +94,8 @@ define([
       this.addChild(this.viewer);
       this.inherited(arguments);
       var dataFiles = [];
+      var nwkIds = null;
+      var nwkNames = null;
       var folderCheck = this.state.search.match(/wsTreeFolder=..+?(?=&|$)/);
       var fileCheck = this.state.search.match(/wsTreeFile=..+?(?=&|$)/);
       var idType = this.state.search.match(/idType=..+?(?=&|$)/);
@@ -127,6 +129,10 @@ define([
             Object.values(objs).forEach(function (obj) {
               if (obj.type == 'json') {
                 dataFiles.push(obj.path);
+              } else if (obj.type == 'nwk' && obj.path.endsWith('treeWithGenomeIds.nwk')) {
+                nwkIds = obj.path;
+              } else if (obj.type == 'nwk' && obj.path.endsWith('treeWithGenomeNames.nwk')) {
+                nwkNames = obj.path;
               }
             });
             if (dataFiles.length >= 1) {
@@ -139,6 +145,16 @@ define([
                   }
                   _self.prepareTree(treeDat, idType, labelType, labelSearch);
                 });
+            } else if (nwkIds || nwkNames) {
+              var objPath = nwkIds || nwkNames;
+              WorkspaceManager.getObjects([objPath]).then(lang.hitch(this, function (objs) {
+                var obj = objs[0];
+                var treeDat = {};
+                if (typeof obj.data == 'string') {
+                  treeDat.tree = obj.data.replace(/[^(,)]+_@_/g, ''); // get rid of ridiculously annoying, super dirty embedded labels
+                  _self.prepareTree(treeDat, idType, labelType, labelSearch);
+                }
+              }));
             }
           });
       }