Try to fix SingleR/ExperimentHub issue

Author: bbimber

singlecell/resources/chunks/RunSingleR.R

@@ -1,5 +1,12 @@
 # Added to avoid celldex/ExperimentHub/BiocFileCache write errors
-Sys.setenv('HOME', '/dockerHomeDir')
+cacheDir <- '/BiocFileCache/.cache'
+if (dir.exists(cacheDir)) {
+   unlink(cacheDir, recursive = TRUE)
+}
+
+dir.create(cacheDir, recursive=TRUE)
+ExperimentHub::setExperimentHubOption('cache', cacheDir)
+library(ExperimentHub)
 
  for (datasetId in names(seuratObjects)) {
     printName(datasetId)

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

@@ -58,6 +58,11 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
         allowRowSpan: false,
         allowBlank: false,
         transform: 'assaytype'
+    },{
+        name: 'treatment',
+        labels: ['Treatment'],
+        allowRowSpan: false,
+        allowBlank: false
     },{
         name: 'tube_num',
         labels: ['Tube #', 'Stim #'],
@@ -617,6 +622,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
                 stim: r.stim,
                 celltype: r.celltype,
                 assaytype: r.assaytype || 'None',
+                treatment: r.treatment,
                 tissue: r.tissue,
                 objectId: r.objectId,
                 population: r.population,
@@ -837,6 +843,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
                     celltype: row.celltype,
                     tissue: row.tissue,
                     assaytype: row.assaytype || 'None',
+                    treatment: row.treatment,
                     objectId: guid,
                     workbook: row.workbook
                 });
@@ -1120,7 +1127,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
     },
 
     getSampleKey: function(data){
-        return [data.sampleId, data.subjectId, data.stim, data.assaytype, data.tissue, (Ext4.isDate(data.sampleDate) ? Ext4.Date.format(data.sampleDate, 'Y-m-d') : data.sampleDate)].join('|');
+        return [data.sampleId, data.subjectId, data.stim, data.assaytype, data.treatment, data.tissue, (Ext4.isDate(data.sampleDate) ? Ext4.Date.format(data.sampleDate, 'Y-m-d') : data.sampleDate)].join('|');
     },
 
     getSortKey: function(data){

singlecell/src/org/labkey/singlecell/SingleCellController.java

@@ -378,7 +378,7 @@ private static List<Map<String, Object>> parseRows(SimpleApiJsonForm form, Strin
     @RequiresPermission(ReadPermission.class)
     public static class GetMatchingSamplesAction extends ReadOnlyApiAction<SimpleApiJsonForm>
     {
-        final List<String> FIELDS = Arrays.asList("subjectId", "sampledate", "subjectid", "celltype", "tissue", "assaytype", "stim");
+        final List<String> FIELDS = Arrays.asList("subjectId", "sampledate", "subjectid", "celltype", "tissue", "assaytype", "stim", "treatment");
 
         @Override
         public Object execute(SimpleApiJsonForm form, BindException errors) throws Exception