Add natural sorting to file/readset name on import panel

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/Utils.js

@@ -137,7 +137,7 @@ SequenceAnalysis.Utils = new function(){
                     exonPosition = nt_position - startNT + exon[0];
                     nt_positions.push(exonPosition);
                     exons.push(idx);
-                    if(nt_positions.length == 3)
+                    if(nt_positions.length === 3)
                         return false;  //jump to next exon
 
                     nt_position++;
@@ -152,6 +152,22 @@ SequenceAnalysis.Utils = new function(){
                 nt_positions: nt_positions,
                 exons: exons
             };
+        },
+
+        // https://github.com/overset/javascript-natural-sort/blob/master/naturalSort.js
+        naturalSortFn: function(o1, o2){
+            o1 = SequenceAnalysis.Utils.getNaturalSortValue(o1);
+            o2 = SequenceAnalysis.Utils.getNaturalSortValue(o2);
+
+            if (o1 === o2) {
+                return 0;
+            }
+
+            return o1 < o2 ? -1 : 1;
+        },
+
+        getNaturalSortValue: function(value) {
+            return value ? value.replace(/(\d+)/g, "0000000000$1").replace(/0*(\d{10,})/g, "$1") : value;
         }
     }
 }

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceImportPanel.js

@@ -33,8 +33,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                 sequenceImportPanel: this,
                 extend: 'Ext.data.Model',
                 fields: [
-                    {name: 'fileGroupId', allowBlank: false},
-                    {name: 'readset', allowBlank: false},
+                    {name: 'fileGroupId', allowBlank: false, sortType: SequenceAnalysis.Utils.getNaturalSortValue},
+                    {name: 'readset', allowBlank: false, sortType: SequenceAnalysis.Utils.getNaturalSortValue},
                     {name: 'readsetname', useNull: true},
                     {name: 'importType', useNull: true},
                     {name: 'barcode5', useNull: true},
@@ -128,8 +128,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
             model: Ext4.define('SequenceAnalysis.model.ReadsetDataModel', {
                 extend: 'Ext.data.Model',
                 fields: [
-                    {name: 'id'},
-                    {name: 'fileGroupId', allowBlank: false},
+                    {name: 'id', sortType: SequenceAnalysis.Utils.getNaturalSortValue},
+                    {name: 'fileGroupId', allowBlank: false, sortType: SequenceAnalysis.Utils.getNaturalSortValue},
                     {name: 'fileRecord1'},
                     {name: 'fileRecord2'},
                     {name: 'platformUnit'},
@@ -332,7 +332,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                 distinctGroups.push(r.get('fileGroupId'));
             }
         }, this);
-        distinctGroups = Ext4.unique(distinctGroups);
+        distinctGroups = Ext4.unique(distinctGroups).sort(SequenceAnalysis.Utils.naturalSortFn);
 
         var found = [];
         Ext4.Array.forEach(this.fileGroupStore.getRange(), function(fg){
@@ -424,7 +424,13 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
     TENX_REGEX: /^(.+?)(_[0-9]+){0,1}_S(.+)_L(.+)_(R){0,1}([0-9])(_[0-9]+){0,1}(\.f(ast){0,1}q)(\.gz)?$/i,
 
     populateSamples: function(orderType, isPaired){
-        this.fileNameStore.sort('displayName', 'ASC');
+        this.fileNameStore.sort([{
+            sorterFn: function(o1, o2){
+                o1 = o1.get('displayName');
+                o2 = o2.get('displayName');
+                return o1 = SequenceAnalysis.Utils.naturalSortFn(o1, o2);
+            }
+        }]);
         this.readDataStore.removeAll();
         var errorMsgs = [];
 
@@ -483,9 +489,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                 }
             }, this);
 
-            var keys = Ext4.Object.getKeys(map);
-            keys.sort();
-
+            var keys = Ext4.Object.getKeys(map).sort(SequenceAnalysis.Utils.naturalSortFn);
             Ext4.Array.forEach(keys, function(key){
                 if (Ext4.isArray(map[key])){
                     Ext4.Array.forEach(map[key], function(r){
@@ -563,14 +567,15 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
             }
         }
 
+        this.readDataStore.sort('fileGroupId');
         this.down('#readDataGrid').getView().refresh();
 
         //populate readsets
         var distinctNames = [];
         this.readDataStore.each(function(r){
             distinctNames.push(r.get('fileGroupId'));
         }, this);
-        distinctNames = Ext4.unique(distinctNames);
+        distinctNames = Ext4.unique(distinctNames).sort(SequenceAnalysis.Utils.naturalSortFn);
 
         //update fileGroupIds
         Ext4.Array.forEach(distinctNames, function(name){
@@ -947,7 +952,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
             model: this.fileNameStore.model
         });
 
-        this.fileNames.sort();
+        this.fileNames.sort(SequenceAnalysis.Utils.naturalSortFn);
         Ext4.Msg.wait('Loading...');
         var multi = new LABKEY.MultiRequest();
         multi.add(LABKEY.Ajax.request, {
@@ -1073,8 +1078,20 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
             }
         }, this);
 
-        this.fileNameStore.sort('displayName');
-        this.fileNameStoreCopy.sort('displayName');
+        this.fileNameStore.sort([{
+            sorterFn: function(o1, o2){
+                o1 = o1.get('displayName');
+                o2 = o2.get('displayName');
+                return SequenceAnalysis.Utils.naturalSortFn(o1, o2);
+            }
+        }]);
+        this.fileNameStoreCopy.sort([{
+            sorterFn: function(o1, o2){
+                o1 = o1.get('displayName');
+                o2 = o2.get('displayName');
+                return SequenceAnalysis.Utils.naturalSortFn(o1, o2);
+            }
+        }]);
 
         this.down('#fileListView').refresh();
         this.down('#totalFiles').update('Total files: ' + this.fileNameStore.getCount());

singlecell/resources/web/singlecell/panel/LibraryExportPanel.js

@@ -874,17 +874,17 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
 
                                 }
                                 rows.push(data.join(delim));
-
-                                runMap[r.laneAssignment || 'Not Assigned'] = (runMap[r.laneAssignment || 'Not Assigned'] || 0) + (totalData || 0);
                             }, this);
+
+                            runMap[r.laneAssignment || 'Not Assigned'] = (runMap[r.laneAssignment || 'Not Assigned'] || 0) + (totalData || 0);
                         }
                     };
 
                     var delim = instrument.startsWith('Novogene') ? '\t' : ',';
                     Ext4.Array.forEach(sortedRows, function (r) {
                         var totalCells = totalCellsByReadset[r.plateId];
                         console.log(totalCells);
-                        var gexData = totalCells > 15000 ? 70 : 50;
+                        var gexData = totalCells > 15000 ? 70 : 40;
                         var tcrData = totalCells > 15000 ? 45 : 25;
                         processType(readsetIds, rows, r, 'readsetId', 'GEX', 500, 0.01, 'G', null, false, gexData, runMap, totalCells);
                         processType(readsetIds, rows, r, 'tcrReadsetId', 'TCR', 700, 0.01, 'T', null, false, tcrData, runMap, totalCells);
@@ -919,7 +919,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
 
                 duplicates = Ext4.unique(duplicates);
                 if (!allowDuplicates && duplicates.length){
-                    Ext4.Msg.alert('Error', 'Duplicate barcodes: ' + duplicates.join(', '));
+                    Ext4.Msg.alert('Error', 'Duplicate barcodes:<br>' + duplicates.join('<br>'));
                     btn.up('singlecell-libraryexportpanel').down('#outputArea').setValue(null);
                     btn.up('singlecell-libraryexportpanel').down('#downloadData').setDisabled(true);
                 }