Move conception records to a study dataset and report the elapsed days

nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.sql → nbri_ehr/resources/queries/study/ConceptionsByDam.sql

@@ -4,24 +4,25 @@
  * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
  */
 SELECT
-    c.Dam AS Id,
-    c.ConceptId,
-    c.ConceptDate,
-    c.Estimated,
-    c.Sire,
+    c.Id,
+    c.conceptId,
+    c.date,
+    c.conceptionDays,
+    c.estimated,
+    c.sire,
     c.isActive,
     CASE
         WHEN c.isActive = true THEN 'Unknown'
         WHEN b.conceptId IS NOT NULL THEN 'Live Birth'
         ELSE COALESCE(po.result, 'Unknown')
     END AS conceptionOutcome,
     b.offspring,
-    c.Remark,
-    c.QCState AS qcstate
-FROM Conception c
+    c.remark,
+    c.qcstate
+FROM conception c
 -- Both joins match isActive: a record claims its conception unless its QC state is explicitly non-public, so a null state counts as public.
 -- The birth trigger blocks a duplicate conceptId, but ETL imports skip that check, so the aggregate guards against one.
 LEFT JOIN (SELECT b.conceptId, MAX(b.Id) AS offspring FROM study.birth b WHERE b.conceptId IS NOT NULL AND (b.qcstate IS NULL OR b.qcstate.publicdata = true) GROUP BY b.conceptId) b
-    ON b.conceptId = c.ConceptId
+    ON b.conceptId = c.conceptId
 LEFT JOIN (SELECT p.conceptId, MAX(p.result.title) AS result FROM study.pregnancy p WHERE p.conceptId IS NOT NULL AND (p.qcstate IS NULL OR p.qcstate.publicdata = true) GROUP BY p.conceptId) po
-    ON po.conceptId = c.ConceptId
+    ON po.conceptId = c.conceptId

nbri_ehr/resources/queries/study/activeConceptions.sql

@@ -4,8 +4,8 @@
  * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
  */
 SELECT
-    c.Dam AS Id,
-    c.ConceptId,
-    c.ConceptDate
-FROM nbri_ehr.Conception c
-WHERE c.isActive = true AND c.Dam IS NOT NULL
+    c.Id,
+    c.conceptId,
+    c.date
+FROM study.conception c
+WHERE c.isActive = true AND c.Id IS NOT NULL

nbri_ehr/resources/queries/study/birth.js

@@ -87,7 +87,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
     }
 
     if (damsToSync.length) {
-        triggerHelper.reportDataChange('nbri_ehr', 'Conception', damsToSync);
+        triggerHelper.reportDataChange('study', 'conception', damsToSync);
         damsToSync = [];
     }
 });
@@ -104,7 +104,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
     }
 
     if (!helper.isETL() && row.conceptId) {
-        if (triggerHelper.totalRecords('nbri_ehr', 'Conception', 'ConceptId', row.conceptId) === 0) {
+        if (triggerHelper.totalRecords('study', 'conception', 'conceptId', row.conceptId) === 0) {
             EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id does not match any conception record', 'WARN');
         }
 

nbri_ehr/resources/queries/study/birth.query.xml

@@ -16,9 +16,9 @@
                     <column columnName="conceptId">
                         <columnTitle>Conception Id</columnTitle>
                         <fk>
-                            <fkDbSchema>nbri_ehr</fkDbSchema>
-                            <fkTable>Conception</fkTable>
-                            <fkColumnName>ConceptId</fkColumnName>
+                            <fkDbSchema>study</fkDbSchema>
+                            <fkTable>conception</fkTable>
+                            <fkColumnName>conceptId</fkColumnName>
                         </fk>
                     </column>
                     <column columnName="cage">

nbri_ehr/resources/queries/study/conception.js

@@ -0,0 +1,47 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+require("ehr/triggers").initScript(this);
+
+var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
+
+// conception ids claimed by the rows of this save that have already been validated.  Rows entered together are not in
+// study.conception yet when each one is checked, so this is the only way the one-record-per-conception rule can see them.
+var conceptIdsInSave = [];
+
+EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'conception', function(event, helper){
+    helper.setScriptOptions({
+        // gestation puts the conception date months behind the entry date, so a distant past date is the normal case
+        allowDatesInDistantPast: true,
+        allowDeadIds: true,
+        skipHousingCheck: true,
+        skipAssignmentCheck: true
+    });
+
+    // the script scope can outlive a single save, so never inherit ids from a prior one
+    conceptIdsInSave = [];
+});
+
+// conceptId was a unique constraint before this became a dataset, and the birth and pregnancy triggers still resolve a
+// conception by that id alone, so the rule is enforced here now.  Unlike the sibling checks in birth.js and
+// pregnancy.js this one does not exempt ETL: getConceptionDam() reads the dam with getObject(), which throws on a
+// second match, so a duplicate from any write path breaks later birth and pregnancy saves.
+EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'conception', function(helper, scriptErrors, row, oldRow) {
+    if (!row.conceptId)
+        return;
+
+    //when updating a record that already carries this conception id, the existing row accounts for one match
+    var conceptIdThreshold = (oldRow && oldRow.conceptId === row.conceptId) ? 1 : 0;
+    var claimedBySavedRow = triggerHelper.totalRecords('study', 'conception', 'conceptId', row.conceptId) > conceptIdThreshold;
+
+    // rows are validated one at a time and collected below, so this list holds the earlier rows of this save only
+    var claimedByEarlierRow = conceptIdsInSave.indexOf(row.conceptId) > -1;
+
+    if (claimedBySavedRow || claimedByEarlierRow) {
+        EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id is already used by another conception record', 'ERROR');
+    }
+
+    conceptIdsInSave.push(row.conceptId);
+});

nbri_ehr/resources/queries/study/conception.query.xml

@@ -0,0 +1,31 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="conception" tableDbType="TABLE" useColumnOrder="true">
+                <tableTitle>Conception Records</tableTitle>
+                <tableUrl>/query/recordDetails.view?schemaName=study&amp;query.queryName=conception&amp;keyField=conceptId&amp;key=${conceptId}</tableUrl>
+                <!-- Without this the lookup display falls back to the first string column, which is the dam -->
+                <titleColumn>conceptId</titleColumn>
+                <columns>
+                    <column columnName="Id">
+                        <columnTitle>Dam</columnTitle>
+                    </column>
+                    <column columnName="date">
+                        <columnTitle>Conception Date</columnTitle>
+                        <formatString>Date</formatString>
+                    </column>
+                    <column columnName="conceptId">
+                        <columnTitle>Conception Id</columnTitle>
+                        <required>true</required>
+                    </column>
+                    <column columnName="estimated">
+                        <columnTitle>Estimated</columnTitle>
+                        <description>Conception date is estimated rather than observed</description>
+                    </column>
+                    <column columnName="sire"/>
+                    <column columnName="remark"/>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/study/pregnancy.js

@@ -30,7 +30,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
 
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'pregnancy', function(helper, scriptErrors, row, oldRow) {
     if (!helper.isETL() && row.conceptId) {
-        if (triggerHelper.totalRecords('nbri_ehr', 'Conception', 'ConceptId', row.conceptId) === 0) {
+        if (triggerHelper.totalRecords('study', 'conception', 'conceptId', row.conceptId) === 0) {
             EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id does not match any conception record', 'WARN');
         }
 
@@ -61,7 +61,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
 
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'study', 'pregnancy', function(event, errors, helper){
     if (damsToSync.length) {
-        triggerHelper.reportDataChange('nbri_ehr', 'Conception', damsToSync);
+        triggerHelper.reportDataChange('study', 'conception', damsToSync);
         damsToSync = [];
     }
 });

nbri_ehr/resources/queries/study/pregnancy.query.xml

@@ -24,9 +24,9 @@
                     <column columnName="conceptId">
                         <columnTitle>Conception Id</columnTitle>
                         <fk>
-                            <fkDbSchema>nbri_ehr</fkDbSchema>
-                            <fkTable>Conception</fkTable>
-                            <fkColumnName>ConceptId</fkColumnName>
+                            <fkDbSchema>study</fkDbSchema>
+                            <fkTable>conception</fkTable>
+                            <fkColumnName>conceptId</fkColumnName>
                         </fk>
                     </column>
                     <column columnName="type">

nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml

@@ -13,6 +13,7 @@
         <dataset name="clinremarks" id="1009" category="Clinical" type="Standard"/>
         <dataset name="cases" id="1023" category="Clinical" type="Standard"/>
         <dataset name="chemistryResults" id="1024" category="ClinPath" type="Standard"/>
+        <dataset name="conception" id="1050" category="Reproductive Management" type="Standard"/>
         <dataset name="deaths" id="1011" category="Pathology" demographicData="true" type="Standard"/>
         <dataset name="demographics" id="1012" category="Colony Management" demographicData="true" type="Standard"/>
         <dataset name="departure" id="1013" category="Colony Management" type="Standard"/>

nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml

@@ -442,6 +442,42 @@
             </column>
         </columns>
     </table>
+    <table tableName="conception" tableDbType="TABLE">
+        <tableTitle>Conception Records</tableTitle>
+        <description>Records a conception, filed against the dam. The outcome is claimed later by a birth or pregnancy outcome record carrying the same conception Id.</description>
+        <columns>
+            <column columnName="Id">
+                <columnTitle>Dam</columnTitle>
+                <datatype>varchar</datatype>
+                <propertyURI>http://cpas.labkey.com/Study#ParticipantId</propertyURI>
+                <importAliases>
+                    <importAlias>ptid</importAlias>
+                    <importAlias>dam</importAlias>
+                </importAliases>
+            </column>
+            <column columnName="date">
+                <columnTitle>Conception Date</columnTitle>
+                <datatype>timestamp</datatype>
+                <propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
+                <conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
+                <importAliases>
+                    <importAlias>conceptDate</importAlias>
+                </importAliases>
+            </column>
+            <column columnName="conceptId">
+                <columnTitle>Conception Id</columnTitle>
+                <datatype>varchar</datatype>
+            </column>
+            <column columnName="estimated">
+                <columnTitle>Estimated</columnTitle>
+                <datatype>boolean</datatype>
+            </column>
+            <column columnName="sire">
+                <columnTitle>Sire</columnTitle>
+                <datatype>varchar</datatype>
+            </column>
+        </columns>
+    </table>
     <table tableName="demographics" tableDbType="TABLE">
         <tableTitle>Demographics</tableTitle>
         <description>Contains core demographic information for each primate, including species, sex, parentage, birth and death dates, and colony status.</description>