Parentage dam mismatch in Colony alert

onprc_ehr/resources/queries/study/ParentageDamMismatch.query.xml

@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="ParentageDamMismatch" tableDbType="TABLE">
+                <tableTitle>Mismatched Genetic and Observed Dams</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>

onprc_ehr/resources/queries/study/ParentageDamMismatch.sql

@@ -0,0 +1,61 @@
+/*
+ Added by Kolli, Feb 2026
+ Refer tkt# 14114 for details
+ Display 4 columns: Animal Id, Area, Genetic dam, Observed dam
+
+ Get genetic and observed dam mismatch data.
+ Use the following criteria,
+ * 1. One genetic dam per animal
+ * 2. Included Alive + Dead animals
+ * 3. Excludes animals that have a foster dam
+ * 4. Excludes rows where observedDam or geneticDam IS BLANK
+ * 5. Keeps only mismatches between observed and genetic dams
+ * 6. Excludes old parentage entries, enddate IS BLANK
+*/
+
+SELECT
+    d.Id,
+    d.Id.curLocation.area AS Area,
+    coalesce(p2.parent, '') as geneticDam,
+    coalesce(b.dam, '') as observedDam
+FROM study.demographics d
+
+    LEFT JOIN (
+    SELECT
+        p2.Id,
+        MAX(p2.parent) AS parent
+    FROM study.parentage p2
+    WHERE (p2.method = 'Genetic' OR p2.method = 'Provisional Genetic')
+      AND p2.relationship = 'Dam'
+      AND p2.enddate IS NULL
+    GROUP BY p2.Id
+) p2 ON d.Id = p2.Id
+
+    LEFT JOIN (
+    SELECT
+        p3.Id,
+        MAX(p3.parent) AS parent
+    FROM study.parentage p3
+    WHERE p3.relationship = 'Foster Dam'
+      AND p3.enddate IS NULL
+    GROUP BY p3.Id
+) p3 ON d.Id = p3.Id
+
+    LEFT JOIN study.birth b
+        ON b.Id = d.Id
+
+WHERE d.calculated_status.code IN ('Alive', 'Dead') AND d.qcstate = 18
+    /* exclude foster-dam cases (NULL or blank only) */
+  AND COALESCE(RTRIM(LTRIM(CAST(p3.parent AS VARCHAR(50)))), '') = ''
+
+    /* exclude blank observed dam */
+  AND COALESCE(RTRIM(LTRIM(CAST(b.dam AS VARCHAR(50)))), '') <> ''
+
+    /* exclude blank genetic dam */
+  AND COALESCE(RTRIM(LTRIM(CAST(p2.parent AS VARCHAR(50)))), '') <> ''
+
+    /* mismatch observed vs genetic */
+  AND COALESCE(RTRIM(LTRIM(CAST(b.dam AS VARCHAR(50)))), '') <>
+      COALESCE(RTRIM(LTRIM(CAST(p2.parent AS VARCHAR(50)))), '')
+
+

onprc_ehr/src/org/labkey/onprc_ehr/notification/ColonyAlertsNotification.java

@@ -312,6 +312,70 @@ protected void roomsReportingNegativeCagesAvailable(final Container c, User u, f
         }
     }
 
+    /**
+     * Kollil, Jan, 2026 :
+     * Refer tkt# 14114 for more details
+     * Alert title: WARNING: There are [x total] mismatches of observed and genetic dam data requiring review
+     * Format: Table
+     * 4 columns: Animal Id, Area, Genetic dam, Observed dam
+     * Alert criteria:
+     * 1. One genetic dam per animal
+     * 2. Included Alive + Dead animals
+     * 3. Excludes animals that have a foster dam
+     * 4. Excludes rows where observedDam or geneticDam IS BLANK
+     * 5. Keeps only mismatches between observed and genetic dams
+     * 6. Excludes old parentage entries, enddate IS BLANK
+     */
+    protected void mismatchedObservedAndGeneticDam(final Container c, User u, final StringBuilder msg)
+    {
+        if (QueryService.get().getUserSchema(u, c, "study") == null) {
+            msg.append("<b>Warning: The study schema has not been enabled in this folder, so the alert cannot run.<p><hr>");
+            return;
+        }
+
+        //Dam mismatch query
+        TableInfo ti = QueryService.get().getUserSchema(u, c, "study").getTable("ParentageDamMismatch", ContainerFilter.Type.AllFolders.create(c, u));
+        TableSelector ts = new TableSelector(ti, null, null);
+        long count = ts.getRowCount();
+
+        //Get num of rows
+        if (count > 0) {
+            msg.append("<b> WARNING: There are " + count + " mismatches of observed and genetic dam data requiring review.</b>");
+            msg.append("<a href='" + getExecuteQueryUrl(c, "study", "ParentageDamMismatch", null) + "&query.containerFilterName=AllFolders'> Click here to view them in a grid</a>\n");
+
+            //Display the report in the email
+            Set<FieldKey> columns = new HashSet<>();
+            columns.add(FieldKey.fromString("Id"));
+            columns.add(FieldKey.fromString("area"));
+            columns.add(FieldKey.fromString("geneticdam"));
+            columns.add(FieldKey.fromString("observeddam"));
+
+            final Map<FieldKey, ColumnInfo> colMap = QueryService.get().getColumns(ti, columns);
+            TableSelector ts2 = new TableSelector(ti, colMap.values(), null, null);
+
+            msg.append("<br><br>\n");
+            msg.append("<table border=1 style='border-collapse: collapse;'>");
+            msg.append("<tr bgcolor = " + '"' + "#FFFACD" + '"' + "style='font-weight: bold;'>");
+            msg.append("<td>Id </td><td>Area </td><td>Genetic Dam </td><td>Observed Dam </td></tr>");
+
+            ts2.forEach(object -> {
+                Results rs = new ResultsImpl(object, colMap);
+                String url = getParticipantURL(c, rs.getString("Id"));
+                msg.append("<tr><td><b> <a href='" + url + "'>" + PageFlowUtil.filter(rs.getString("Id")) + "</a> </b></td>\n");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("area")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("geneticdam")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("observeddam")) + "</td>");
+                msg.append("</tr>");
+            });
+        }
+        else {
+            msg.append("<b> There are NO mismatches of observed and genetic dam data. </b>");
+        }
+        msg.append("</table>");
+        msg.append("<hr>\n");
+    }
+    //End of Dam mismatch report
+
     /**
      * Finds all rooms with animals of mixed viral status
      * Modified by Kollil, 2/17/2023

onprc_ehr/src/org/labkey/onprc_ehr/notification/ColonyMgmtNotification.java

@@ -74,6 +74,10 @@ public String getMessageBodyHTML(Container c, User u)
         doHousingChecks(c, u, msg);
         transfersYesterday(c, u, msg);
         roomsWithMixedViralStatus(c, u, msg);
+         /*Added by kollil, Jan, 2026
+        Refer to tkt # 14114
+        */
+        mismatchedObservedAndGeneticDam(c, u, msg);
         livingAnimalsWithoutWeight(c, u, msg);
         hospitalAnimalsWithoutCase(c, u, msg);