Improve PVL validation

Author: bbimber

SivStudies/resources/queries/study/viralloads.query.xml

@@ -10,6 +10,7 @@
                     </column>
                     <column columnName="sampleType">
                         <columnTitle>Sample Type</columnTitle>
+                        <nullable>false</nullable>
                         <fk>
                             <fkDbSchema>studies</fkDbSchema>
                             <fkTable>vl_sample_types</fkTable>
@@ -28,6 +29,7 @@
                     </column>
                     <column columnName="result">
                         <columnTitle>Result</columnTitle>
+                        <nullable>false</nullable>
                     </column>
                     <column columnName="units">
                         <columnTitle>Units</columnTitle>

SivStudies/src/org/labkey/sivstudies/query/ViralLoadsTriggerFactory.java

@@ -60,6 +60,23 @@ private void handlePVL(@Nullable Map<String, Object> row, Container c, Validatio
                 return;
             }
 
+            if ("Plasma".equalsIgnoreCase(String.valueOf(row.get("sampleType"))) & row.get("units") == null)
+            {
+                row.put("units", "Copies/mL");
+            }
+
+            // Enforce consistent case:
+            if ("Copies/mL".equalsIgnoreCase(String.valueOf(row.get("units"))))
+            {
+                row.put("units", "Copies/mL");
+            }
+
+            inspectResultValue(row, errors);
+
+        }
+
+        private void inspectResultValue(@NotNull Map<String, Object> row, ValidationException errors)
+        {
             if (row.get("result") == null || NumberUtils.isCreatable(row.get("result").toString()))
             {
                 return;
@@ -73,7 +90,7 @@ private void handlePVL(@Nullable Map<String, Object> row, Container c, Validatio
             }
             else if (val.toLowerCase().startsWith("below"))
             {
-                StringUtils.replaceIgnoreCase(val, "below ", "");
+                val = StringUtils.replaceIgnoreCase(val, "below ", "");
                 if (NumberUtils.isCreatable(val))
                 {
                     row.put("result", val);