Add check for duplicated MCC parent aliases

Author: bbimber

mcc/resources/queries/mcc/duplicatedAggregatedDemographicsParents.sql

@@ -0,0 +1,25 @@
+SELECT
+
+    m.originalDam as Id,
+    GROUP_CONCAT(distinct m.dam, ',') as mccIds,
+    'Dam' as category,
+    GROUP_CONCAT(distinct m.colony, ',') as colonies
+
+FROM mcc.aggregatedDemographics m
+WHERE m.dam IS NOT NULL
+GROUP BY m.originalDam
+HAVING COUNT(distinct m.dam) > 1
+
+UNION ALL
+
+SELECT
+
+    m.originalSire as Id,
+    GROUP_CONCAT(distinct m.sire, ',') as mccIds,
+    'Sire' as category,
+    GROUP_CONCAT(distinct m.colony, ',') as colonies
+
+FROM mcc.aggregatedDemographics m
+WHERE m.sire IS NOT NULL
+GROUP BY m.originalSire
+HAVING COUNT(distinct m.sire) > 1

mcc/src/org/labkey/mcc/MccMaintenanceTask.java

@@ -58,6 +58,16 @@ private void checkForDuplicateAliases(Logger log)
             log.error("The LDK module property BackgroundAdminUser must be set for the MCC Maintenance code to function");
         }
 
+        Container animalData = MccManager.get().getMCCContainer(ContainerManager.getRoot());
+        if (animalData != null)
+        {
+            TableInfo ti = QueryService.get().getUserSchema(u, animalData, MccSchema.NAME).getTable("duplicatedAggregatedDemographicsParents");
+            if (new TableSelector(ti).exists())
+            {
+                log.error("Duplicate MCC aliases for parents found. Please load the query mcc/duplicatedAggregatedDemographicsParents for more detail");
+            }
+        }
+
         for (Study s : studies)
         {
             if (!s.getContainer().getActiveModules().contains(ModuleLoader.getInstance().getModule(MccModule.NAME)))