Create case-only difference check for Postgres, supporting dashboard link

Author: labkey-jeckels

mGAP/resources/queries/mGAP/sampleSummary.query.xml

@@ -2,6 +2,7 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="" tableDbType="TABLE">
+                <javaCustomizer class="org.labkey.mgap.query.SampleSummaryCustomizer"/>
                 <pkColumnName>subjectName</pkColumnName>
                 <tableTitle>mGAP Subject/gVCF Summary</tableTitle>
                 <columns>

mGAP/resources/queries/mGAP/sampleSummary.sql

@@ -27,4 +27,5 @@ FROM (SELECT
 ) t
 
 LEFT JOIN mgap.subjectsSource ss on (t.subjectId = ss.originalId)
-LEFT JOIN mgap.animalMapping am on (t.subjectId = am.subjectname)
+-- Matched case-insensitively so an id whose alias-table spelling differs only in case still resolves; SampleSummaryCustomizer surfaces those as subjectCaseMismatch
+LEFT JOIN mgap.animalMapping am on (LOWER(t.subjectId) = LOWER(am.subjectname))

mGAP/src/org/labkey/mgap/query/SampleSummaryCustomizer.java

@@ -0,0 +1,38 @@
+package org.labkey.mgap.query;
+
+import org.labkey.api.data.AbstractTableInfo;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.gwt.client.FacetingBehaviorType;
+import org.labkey.api.ldk.table.AbstractTableCustomizer;
+import org.labkey.api.query.ExprColumn;
+
+public class SampleSummaryCustomizer extends AbstractTableCustomizer
+{
+    @Override
+    public void customize(TableInfo ti)
+    {
+        if (ti instanceof AbstractTableInfo ati)
+        {
+            customizeTable(ati);
+        }
+    }
+
+    private void customizeTable(AbstractTableInfo ti)
+    {
+        String fieldName = "subjectCaseMismatch";
+        if (ti.getColumn(fieldName) != null)
+        {
+            return;
+        }
+
+        // Pairs up with the case-insensitive join in sampleSummary.sql: that supplies aliasSubjectName for ids differing only in case, and this case-sensitive comparison is what spots them
+        SQLFragment sql = new SQLFragment("CASE WHEN " + ExprColumn.STR_TABLE_ALIAS + ".subjectId = " + ExprColumn.STR_TABLE_ALIAS + ".aliasSubjectName THEN NULL ELSE " + ExprColumn.STR_TABLE_ALIAS + ".aliasSubjectName END");
+        ExprColumn col = new ExprColumn(ti, fieldName, sql, JdbcType.VARCHAR, ti.getColumn("subjectId"), ti.getColumn("aliasSubjectName"));
+        col.setLabel("Id Case Mismatch?");
+        col.setFacetingBehaviorType(FacetingBehaviorType.ALWAYS_OFF);
+        col.setDescription("If the case of the subjectId differs from the alias table, the updated case is shown");
+        ti.addColumn(col);
+    }
+}