Merge remote-tracking branch 'origin/develop' into fb_gradle_9.0.0

Author: labkey-susanh

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

@@ -603,8 +603,6 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
             this.fileNameStore.each(function(f){
                 msg += '[' + f.get('fileName') + ']\n';
             }, this);
-
-            LDK.Utils.logError(msg);
         }
 
         return errorMsgs;
@@ -630,7 +628,6 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                     msg += '[' + f.get('fileName') + ']\n';
                 }, this);
 
-                LDK.Utils.logError(msg);
                 errorMsgs.push('Possible error: Encountered reverse reads prior to forward reads for ' + setId + ', which can indicate files are out of alphabetical order, one file from a pair is missing, or a problem parsing the filenames.  Please check over the file groups carefully.');
 
                 var m = Ext4.create('SequenceAnalysis.model.ReadsetDataModel', {});

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -494,10 +494,7 @@ public Set<ExperimentRunType> getExperimentRunTypes(@Nullable Container containe
 
         ExperimentService.get().registerExperimentDataHandler(new HtmlExpDataHandler());
 
-        SearchService ss = SearchService.get();
-
-        if (null != ss)
-            ss.addDocumentParser(new SequenceNoOpDocumentParser());
+        SearchService.get().addDocumentParser(new SequenceNoOpDocumentParser());
     }
 
     @Override

singlecell/resources/web/singlecell/panel/PoolImportPanel.js

@@ -149,7 +149,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
         allowRowSpan: true
     },{
         name: 'kitType',
-        labels: ['Kit Type', 'V1.1/V2/HT', 'V1.1/HT', 'HT/V1.1/V2'],
+        labels: ['Kit Type', 'V1.1/V2/HT', 'V1.1/HT', 'HT/V1.1/V2', 'V2/HT'],
         transform: 'kitType'
     }],
 
@@ -819,7 +819,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
                 if (row[kitCol.dataIdx].toUpperCase() === 'V1.1') {
                     data.dualIndex10x = false;
                 }
-                else if (row[kitCol.dataIdx].toUpperCase() === 'V2' || row[kitCol.dataIdx].toUpperCase() === 'HT') {
+                else if (row[kitCol.dataIdx].toUpperCase() === 'V2' || row[kitCol.dataIdx].toUpperCase() === 'HT'  || row[kitCol.dataIdx].toUpperCase() === 'V3') {
                     data.dualIndex10x = true;
                 }
                 else {
@@ -828,7 +828,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
             }
 
             Ext4.Array.forEach(colArray, function(col, colIdx){
-                var cell = Ext4.isDefined(col.dataIdx) ? Ext4.String.trim(row[col.dataIdx]) : '';
+                var cell = Ext4.isDefined(col.dataIdx) && row[col.dataIdx] ? Ext4.String.trim(row[col.dataIdx]) : '';
                 if (cell){
                     if (col.transform && this.transforms[col.transform]){
                         cell = this.transforms[col.transform](cell, this, data);