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Parentage dam mismatch in Colony alert (#1643)
* Added a new report in the Colony alert: Parentage Dam mismatch records * Fixed a few comments and typos
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‎onprc_ehr/resources/queries/study/ParentageDamMismatch.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="ParentageDamMismatch" tableDbType="TABLE">
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<tableTitle>Mismatched Genetic and Observed Dams</tableTitle>
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</table>
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</tables>
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</metadata>
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</query>

‎onprc_ehr/resources/queries/study/ParentageDamMismatch.sql‎

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

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

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

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doHousingChecks(c, u, msg);
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transfersYesterday(c, u, msg);
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roomsWithMixedViralStatus(c, u, msg);
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/*Added by kollil, Jan, 2026
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Refer to tkt # 14114
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*/
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mismatchedObservedAndGeneticDam(c, u, msg);
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livingAnimalsWithoutWeight(c, u, msg);
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hospitalAnimalsWithoutCase(c, u, msg);
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