Add more metadata normalization

Author: bbimber

singlecell/resources/chunks/SubsetSeurat.R

@@ -2,12 +2,6 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- seuratObjects[[datasetId]]
     seuratObjects[[datasetId]] <- NULL
 
-    #TODO: remove
-    if (!'HTO.Classification' %in% names(seuratObj@meta.data) && 'consensuscall.global' %in% names(seuratObj@meta.data)) {
-        seuratObj$HTO.Classification <- seuratObj$consensuscall.global
-    }
-
-
     <SUBSETS>
 
     newSeuratObjects[[datasetId]] <- seuratObj

singlecell/resources/queries/singlecell/sorts.js

@@ -20,18 +20,25 @@ function beforeUpsert(row, oldRow, errors){
         row.well = row.well.toUpperCase();
     }
 
-    if (['TNF+', 'TNF Pos', 'CD69/TNF', 'CD69+/TNF+', 'CD69-Pos/TNF-Pos', 'CD69/TNFa', 'TNF+/CD69+'].indexOf(row.population) !== -1){
+    if (['TNF+', 'TNF Pos', 'CD69/TNF', 'CD69+/TNF+', 'CD69-Pos/TNF-Pos', 'CD69/TNFa', 'TNF+/CD69+', 'CD69+/TNFa+'].indexOf(row.population) !== -1){
         row.population = 'TNF-Pos';
     }
     else if (['TNF-', 'CD69-/TNF-', 'TNF Neg', 'CD69-Neg/TNF-Neg'].indexOf(row.population) !== -1){
         row.population = 'TNF-Neg';
     }
-    else if (['Bulk CD8', 'Bulk CD8 T-cells', 'Bulk-CD8', 'CD8+', 'CD8', 'CD8s'].indexOf(row.population) !== -1){
+    else if (['Bulk CD8', 'Bulk CD8 T-cells', 'Bulk-CD8', 'CD8+', 'CD8', 'CD8s', 'BULK CD8'].indexOf(row.population) !== -1){
         row.population = 'Bulk CD8s';
     }
     else if (['CD8-CD69-Pos', 'CD69-Pos/TNF-Neg', 'TNF-/CD69+', 'CD69+', 'CD69+/TNF-'].indexOf(row.population) !== -1){
         row.population = 'CD69-Pos';
     }
+    else if (['perLN', 'PerLN'].indexOf(row.population) !== -1){
+        row.population = 'pLN';
+    }
+
+    if (['perLN', 'PerLN'].indexOf(row.tissue) !== -1){
+        row.tissue = 'pLN';
+    }
 
     //Naive cells
     if (row.population && row.population.match(/ï/)){

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

@@ -100,7 +100,8 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
     },{
         name: 'hto_library_conc',
         labels: ['HTO Library Conc', 'HTO Library Conc (ng/uL)', 'HTO (qubit) ng/uL', 'HTO (quibit) ng/uL', 'MultiSeq Library Conc', 'MultiSeq Library (qubit) ng/uL', 'MultiSeq Library Conc (qubit) ng/uL'],
-        allowRowSpan: true
+        allowRowSpan: true,
+        transform: 'citeSeqPanel'
     },{
         name: 'citeseqpanel',
         labels: ['Cite-Seq Panel', 'Cite-Seq Panel Name', 'CiteSeq Panel', 'citeseqpanel'],
@@ -213,6 +214,12 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
             return val;
         },
 
+        citeSeqPanel: function(val, panel) {
+            if (val && val.toLower() === 'no') {
+                return null;
+            }
+        },
+
         citeSeqTenXBarcode: function(val, panel){
             if (!val){
                 return;
@@ -858,7 +865,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
             }
 
             var requireTCR = this.down('#requireTCR').getValue();
-            rs = this.processReadsetForGroup(poolName, rowArr, ret.readsetRows, 'tcr', 'TCR', 'RNA-seq, Single Cell', '10x 5\' VDJ (Rhesus A/B/G)');
+            rs = this.processReadsetForGroup(poolName, rowArr, ret.readsetRows, 'tcr', 'TCR', 'RNA-seq, Single Cell', '10x 5\' VDJ (Rhesus A/B/D/G)');
             if (Ext4.isString(rs)) {
                 readsetGUIDs.tcrReadsetGUID = rs;
             }