improve CheckExpectations criteria

Author: bbimber

singlecell/resources/chunks/CheckExpectations.R

@@ -1,3 +1,13 @@
+CheckField <- function(seuratObj, datasetId, fieldName) {
+  if (!fieldName %in% names(seuratObj@meta.data)) {
+    addErrorMessage(paste0(paste0('Missing ', fieldName, ' for dataset: ', datasetId)))
+  }
+
+  if (any(is.na(seuratObj@meta.data[[fieldName]]))) {
+    addErrorMessage(paste0(paste0('NA values found for ', fieldName, ' for dataset: ', datasetId)))
+  }
+}
+
 for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
@@ -28,16 +38,20 @@ for (datasetId in names(seuratObjects)) {
     }
   }
 
-  if (requireSaturation && !'Saturation.RNA' %in% names(seuratObj@meta.data)) {
-    addErrorMessage(paste0('Missing per-cell RNA saturation data for dataset: ', datasetId))
+  if (requireSaturation) {
+    CheckField(seuratObj, datasetId, 'Saturation.RNA')
+  }
+
+  if (requireSingleR) {
+    CheckField(seuratObj, datasetId, 'SingleRConsensus')
   }
 
-  if (requireSingleR && !'SingleRConsensus' %in% names(seuratObj@meta.data)) {
-    addErrorMessage(paste0('Missing SingleRConsensus label for dataset: ', datasetId))
+  if (requireScGate) {
+    CheckField(seuratObj, datasetId, 'scGateConsensus')
   }
 
-  if (requireScGate && !'scGateConsensus' %in% names(seuratObj@meta.data)) {
-    addErrorMessage(paste0('Missing scGateConsensus label for dataset: ', datasetId))
+  if (requireRiraImmune) {
+    CheckField(seuratObj, datasetId, 'RIRA_Immune_v2.cellclass')
   }
 
   if (length(errorMessages) > 0) {

singlecell/src/org/labkey/singlecell/pipeline/singlecell/CheckExpectations.java

@@ -33,7 +33,8 @@ public Provider()
                     SeuratToolParameter.create("requireCiteSeq", "Require Cite-Seq, If Used", "If this dataset uses CITE-seq, cite-seq data are required", "checkbox", null, true),
                     SeuratToolParameter.create("requireSaturation", "Require Per-Cell Saturation", "If this dataset uses TCR sequencing, these data are required", "checkbox", null, true),
                     SeuratToolParameter.create("requireSingleR", "Require SingleR", "If checked, SingleR calls, including singleRConsensus are required to pass", "checkbox", null, true),
-                    SeuratToolParameter.create("requireScGate", "Require scGate", "If checked, scGateConsensus calls are required to pass", "checkbox", null, true)
+                    SeuratToolParameter.create("requireScGate", "Require scGate", "If checked, scGateConsensus calls are required to pass", "checkbox", null, true),
+                    SeuratToolParameter.create("requireRiraImmune", "Require RIRA Immune V2", "If checked, RIRA_Immune_v2 calls (field RIRA_Immune_v2.cellclass) are required to pass", "checkbox", null, true)
             ), null, null);
         }