Bugfix to CalculateGeneComponentScores when selecting multiple components

Author: bbimber

jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java

@@ -105,7 +105,7 @@ private String tryUrlDecode(String input) {
             //special case for urls containing +; this isn't necessary for strings sent from the client-side, but URLs
             //sent via unit tests autodecode, and strings containing + rather than the URL-encoded symbol are unsafe
             //to pass through URLDecoded.decode
-            if(input.contains("+")) {
+            if (input.contains("+")) {
                 return input;
             }
 
@@ -202,7 +202,7 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
                 {
                     query = queryParser.parse(queryString);
                 }
-                else if(numericQueryParserFields.contains(fieldName))
+                else if (numericQueryParserFields.contains(fieldName))
                 {
                     try
                     {
@@ -212,7 +212,8 @@ else if(numericQueryParserFields.contains(fieldName))
                     {
                         e.printStackTrace();
                     }
-                } else
+                }
+                else
                 {
                     throw new IllegalArgumentException("No such field(s), or malformed query.");
                 }

singlecell/resources/chunks/CalculateGeneComponentScores.R

@@ -2,7 +2,9 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::ScoreUsingSavedComponent(seuratObj, componentOrName = savedComponent, fieldName = savedComponent)
+    for (sc in savedComponent) {
+        seuratObj <- RIRA::ScoreUsingSavedComponent(seuratObj, componentOrName = sc, fieldName = sc)
+    }
 
     saveData(seuratObj, datasetId)