Better cDNA import validation

Author: bbimber

singlecell/resources/queries/singlecell/sorts.js

@@ -35,10 +35,24 @@ function beforeUpsert(row, oldRow, errors){
     else if (['perLN', 'PerLN'].indexOf(row.population) !== -1){
         row.population = 'pLN';
     }
+    else if (['mesLN'].indexOf(row.population) !== -1){
+        row.population = 'MesLN';
+    }
+    else if (['Bone Marrow', 'BoneMarrow'].indexOf(row.population) !== -1){
+        row.population = 'Bone marrow';
+    }
+
 
+    //Tissue:
     if (['perLN', 'PerLN'].indexOf(row.tissue) !== -1){
         row.tissue = 'pLN';
     }
+    else if (['mesLN'].indexOf(row.tissue) !== -1){
+        row.tissue = 'MesLN';
+    }
+    else if (['Bone Marrow', 'BoneMarrow'].indexOf(row.tissue) !== -1){
+        row.tissue = 'Bone marrow';
+    }
 
     //Naive cells
     if (row.population && row.population.match(/ï/)){

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

@@ -46,6 +46,7 @@
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.RequiresPermission;
+import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.InsertPermission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
@@ -200,6 +201,7 @@ public Object execute(SimpleApiJsonForm form, BindException errors) throws Excep
             try (DbScope.Transaction transaction = DbScope.getLabKeyScope().ensureTransaction())
             {
                 BatchValidationException bve = new BatchValidationException();
+                validateBarcodes(readsetRows, getContainer(), getUser());
 
                 Map<String, Integer> sampleMap = new HashMap<>();
                 final List<Map<String, Object>> sampleRowsToInsert = new ArrayList<>();
@@ -308,12 +310,36 @@ public Object execute(SimpleApiJsonForm form, BindException errors) throws Excep
             {
                 _log.error(e);
 
+                errors.reject(ERROR_MSG, e.getMessage());
+                return null;
             }
 
             return new ApiSimpleResponse("success", true);
         }
     }
 
+    private static void validateBarcodes(List<Map<String, Object>> readsetRows, Container c, User u)
+    {
+        Set<String> uniqueBarcodeNames = new HashSet<>();
+        readsetRows.forEach(rs -> {
+            if (rs.get("barcode5") != null) {
+                uniqueBarcodeNames.add((String.valueOf(rs.get("barcode5"))));
+            }
+        });
+
+        if (!uniqueBarcodeNames.isEmpty())
+        {
+            TableInfo barcodes = QueryService.get().getUserSchema(u, c, SingleCellSchema.SEQUENCE_SCHEMA_NAME).getTable("barcodes");
+            Set<String> foundTags = new HashSet<>(new TableSelector(barcodes, PageFlowUtil.set("tag_name"), new SimpleFilter(FieldKey.fromString("tag_name"), uniqueBarcodeNames, CompareType.IN), null).getArrayList(String.class));
+            if (foundTags.size() != uniqueBarcodeNames.size())
+            {
+                uniqueBarcodeNames.removeAll(foundTags);
+
+                throw new ApiUsageException("The following barcodes were not found: " + StringUtils.join(uniqueBarcodeNames, ","));
+            }
+        }
+    }
+
     private static List<Map<String, Object>> parseRows(SimpleApiJsonForm form, String propName, Container container) throws ApiUsageException
     {
         if (!form.getJsonObject().containsKey(propName))