[bot] Fast-forward for 26.7.8

nbri_ehr/resources/data/death_type.tsv

@@ -1,14 +1,14 @@
-value	title	sort_order
-A	Experimental	1
+value	title	sort_order	date_disabled
+A	Experimental	1	2026-09-03
 D	Spontaneous/Normal	2
-F	Fetal	3
-FD	Fetal Death	4
-FL	Fetal Live	5
-FN	Fetal found at necropsy	6
-FX	Fetal experimental	7
+F	Fetal	3	2026-09-03
+FD	Fetal Death	4	2026-09-03
+FL	Fetal Live	5	2026-09-03
+FN	Fetal found at necropsy	6	2026-09-03
+FX	Fetal experimental	7	2026-09-03
 K	Cull (scheduled)	8
 M	Medical cull (non-scheduled)	9
-ND	Non-vaginal (C-section) dead	10
-NT	Not pregnant at assessment	11
+ND	Non-vaginal (C-section) dead	10	2026-09-03
+NT	Not pregnant at assessment	11	2026-09-03
 S	Cull	12
 X	Experimental	13

nbri_ehr/resources/data/editable_lookups.tsv

@@ -40,7 +40,6 @@ ehr_lookups	country	Colony Management	Country
 ehr_lookups	country_category	Colony Management	Country Category	
 ehr_lookups	daily_enrich_codes	Behavior	Daily enrichment codes.	
 ehr_lookups	data_category	Clinical	Data Categories	Used in datasets.
-ehr_lookups	death_reason	Colony Management	Death Reason
 ehr_lookups	death_type	Colony Management	Death Type	Death type codes.
 ehr_lookups	delivery_mode	Colony Management	Delivery Mode
 ehr_lookups	delivery_state	Colony Management	Delivery State

nbri_ehr/resources/data/lookup_sets.tsv

@@ -31,7 +31,6 @@ country	Country	value	title
 country_category	Country Category	value	title
 daily_enrich_codes	Daily Enrichment Codes	value
 data_category	Data Category Field Values	value
-death_reason	Death Reason	value
 death_type	Death Type	value	title
 delivery_mode	Delivery Mode	value	title
 delivery_state	Delivery State	value	title

nbri_ehr/resources/data/lookupsManifest.tsv

@@ -35,7 +35,6 @@ country
 country_category
 daily_enrich_codes
 data_category
-death_reason
 death_type
 delivery_mode
 delivery_state

nbri_ehr/resources/data/lookupsManifestTest.tsv

@@ -35,7 +35,6 @@ country
 country_category
 daily_enrich_codes
 data_category
-death_reason
 death_type
 delivery_mode
 delivery_state

nbri_ehr/resources/queries/nbri_ehr/Conception.js

@@ -1 +1,45 @@
-require("ehr/triggers").initScript(this);
+/*
+ * 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);
+
+// the shared trigger collects modified participants from row.Id, which this table does not have, so announce the dams
+// here or their cached activeConceptions keeps a stale Pregnant value
+var damsModified = [];
+
+function addDam(dam) {
+    if (dam && damsModified.indexOf(dam) === -1) {
+        damsModified.push(dam);
+    }
+}
+
+EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'nbri_ehr', 'Conception', function(event, helper){
+    // the script scope can outlive a single save, so never inherit dams from a prior one
+    damsModified = [];
+});
+
+EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'nbri_ehr', 'Conception', function(helper, scriptErrors, row, oldRow) {
+    if (helper.isValidateOnly())
+        return;
+
+    addDam(row.Dam);
+
+    // a re-pointed conception frees the dam it used to belong to
+    addDam(oldRow ? oldRow.Dam : null);
+});
+
+EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_DELETE, 'nbri_ehr', 'Conception', function(helper, scriptErrors, row) {
+    // the row LabKey passes for a delete can carry keys only, and the record is still readable at this point
+    addDam(row.Dam || triggerHelper.getConceptionDam(row.ConceptId));
+});
+
+EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'nbri_ehr', 'Conception', function(event, errors, helper){
+    if (damsModified.length) {
+        triggerHelper.reportDataChange('nbri_ehr', 'Conception', damsModified);
+        damsModified = [];
+    }
+});

nbri_ehr/resources/queries/nbri_ehr/Conception.query.xml

@@ -2,6 +2,7 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="Conception" tableDbType="TABLE" useColumnOrder="true">
+                <javaCustomizer class="org.labkey.nbri_ehr.table.NBRI_EHRCustomizer"/>
                 <tableTitle>Conception Records</tableTitle>
                 <columns>
                     <column columnName="rowId">

nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.sql

@@ -9,17 +9,19 @@ SELECT
     c.ConceptDate,
     c.Estimated,
     c.Sire,
+    c.isActive,
     CASE
+        WHEN c.isActive = true THEN 'Unknown'
         WHEN b.conceptId IS NOT NULL THEN 'Live Birth'
-        WHEN po.conceptId IS NOT NULL THEN COALESCE(po.result, 'Unknown')
-        ELSE 'Unknown'
+        ELSE COALESCE(po.result, 'Unknown')
     END AS conceptionOutcome,
     b.offspring,
     c.Remark,
     c.QCState AS qcstate
 FROM Conception c
--- a conception yields at most one birth; the aggregate only guards against duplicates the birth trigger warns about but does not block
-LEFT JOIN (SELECT b.conceptId, MAX(b.Id) AS offspring FROM study.birth b WHERE b.conceptId IS NOT NULL GROUP BY b.conceptId) b
+-- 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
-LEFT JOIN (SELECT p.conceptId, MAX(p.result.title) AS result FROM study.pregnancy p WHERE p.conceptId IS NOT NULL GROUP BY p.conceptId) po
+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

nbri_ehr/resources/queries/study/activeConceptions.sql

@@ -0,0 +1,11 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * 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

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

@@ -7,9 +7,11 @@
                     <column columnName="Id"/>
                     <column columnName="date">
                         <columnTitle>Date Added</columnTitle>
+                        <formatString>DateTime</formatString>
                     </column>
                     <column columnName="enddate">
                         <columnTitle>Date Removed</columnTitle>
+                        <formatString>DateTime</formatString>
                         <isHidden>false</isHidden>
                     </column>
                     <column columnName="groupId">

nbri_ehr/resources/queries/study/arrival.js

@@ -8,6 +8,11 @@ require("ehr/triggers").initScript(this);
 var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
 var idsToSync = [];
 
+// generation 0 is a real value, so emptiness cannot be tested by truthiness the way the other demographics fields test it
+function isBlankGeneration(value) {
+    return value === null || value === undefined || value === '';
+}
+
 // opens one assignment record against the animal being entered; each dataset carries the assignment under its own field
 function createAssignment(scriptErrors, dataset, fieldName, value, row) {
     if (!value)
@@ -46,6 +51,11 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
         EHR.Server.Utils.addError(scriptErrors, 'Id', 'Animal Id ' + row.Id + ' is already in use. Please use a different Id.', 'ERROR');
     }
 
+    // only a form entry can be held to a generation: the form seeds it to 0, while a study import has no such column to carry
+    if (!row.rearrival && !helper.isETL() && helper.isEHRDataEntry() && helper.getEvent() == 'insert' && isBlankGeneration(row['Id/demographics/generation'])) {
+        EHR.Server.Utils.addError(scriptErrors, 'Id/demographics/generation', 'Generation is required', 'ERROR');
+    }
+
     if (row.eventDate) {
         row.date = row.eventDate;
     }
@@ -69,6 +79,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
         row.gender = row['Id/demographics/gender'] || null;
         row.geographic_origin = row['Id/demographics/geographic_origin'] || null;
         row.socialCode = row['Id/demographics/socialCode'] || null;
+        row.generation = isBlankGeneration(row['Id/demographics/generation']) ? null : parseInt(row['Id/demographics/generation'], 10);
 
         if (row.QCStateLabel) {
             row.qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId();
@@ -152,6 +163,12 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
                 hasUpdates = true;
             }
 
+            if (!isBlankGeneration(row.generation) && row.generation !== data.generation)
+            {
+                obj.generation = row.generation;
+                hasUpdates = true;
+            }
+
             if (row.sire && row.sire !== data.sire)
             {
                 obj.sire = row.sire;

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

@@ -11,6 +11,7 @@
                     <column columnName="Id"/>
                     <column columnName="date">
                         <columnTitle>Arrival Date</columnTitle>
+                        <formatString>DateTime</formatString>
                     </column>
                     <column columnName="arrivalType">
                         <columnTitle>Arrival Type</columnTitle>

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

@@ -7,7 +7,9 @@
                     <column columnName="date">
                         <formatString>DateTime</formatString>
                     </column>
-                    <column columnName="endDate"/>
+                    <column columnName="endDate">
+                        <formatString>DateTime</formatString>
+                    </column>
                     <column columnName="project">
                         <fk>
                             <fkDbSchema>ehr</fkDbSchema>

nbri_ehr/resources/queries/study/birth.js

@@ -9,10 +9,19 @@ EHR.Server.Utils = require("ehr/utils").EHR.Server.Utils;
 var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
 var idsToSync = [];
 
+// dams whose conception this save closes.  The birth row announces the newborn, so the dam's cached Pregnant value
+// would otherwise keep listing a conception that is no longer open.
+var damsToSync = [];
+
 // conception ids claimed by the rows of this save that have already been validated.  Rows entered together are not in
 // study.birth yet when each one is checked, so this is the only way the one-birth-per-conception rule can see them.
 var conceptIdsInSave = [];
 
+// generation 0 is a real value, so emptiness cannot be tested by truthiness the way the other demographics fields test it
+function isBlankGeneration(value) {
+    return value === null || value === undefined || value === '';
+}
+
 // opens one assignment record against the animal being entered; each dataset carries the assignment under its own field
 function createAssignment(scriptErrors, dataset, fieldName, value, row) {
     if (!value)
@@ -34,6 +43,17 @@ function createAssignment(scriptErrors, dataset, fieldName, value, row) {
     }
 }
 
+// resolves the dam of a conception so the birth can announce her; the conception carries the dam, the birth row does not
+function addConceptionDam(conceptId) {
+    if (!conceptId)
+        return;
+
+    var dam = triggerHelper.getConceptionDam(conceptId);
+    if (dam && damsToSync.indexOf(dam) === -1) {
+        damsToSync.push(dam);
+    }
+}
+
 function onInit(event, helper){
     helper.setScriptOptions({
         allowAnyId: true,
@@ -43,13 +63,13 @@ function onInit(event, helper){
         skipHousingCheck: true,
         announceAllModifiedParticipants: true,
         allowDatesInDistantPast: true,
-        removeTimeFromDate: true,
         skipAssignmentCheck: true,
     });
 
     // the script scope can outlive a single save, so never inherit ids from a prior one
     idsToSync = [];
     conceptIdsInSave = [];
+    damsToSync = [];
 
     helper.decodeExtraContextProperty('birthsInTransaction');
 }
@@ -65,6 +85,16 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
         }
         idsToSync = [];
     }
+
+    if (damsToSync.length) {
+        triggerHelper.reportDataChange('nbri_ehr', 'Conception', damsToSync);
+        damsToSync = [];
+    }
+});
+
+EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_DELETE, 'study', 'birth', function(helper, scriptErrors, row) {
+    // deleting the birth reopens its conception
+    addConceptionDam(row.conceptId);
 });
 
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'birth', function(helper, scriptErrors, row, oldRow) {
@@ -96,6 +126,13 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
         }
     }
 
+    if (!helper.isETL() && !helper.isValidateOnly()) {
+        addConceptionDam(row.conceptId);
+
+        // a re-pointed birth reopens the conception it used to claim
+        addConceptionDam(oldRow ? oldRow.conceptId : null);
+    }
+
     if (!helper.isETL()) {
 
         if (row.QCStateLabel) {
@@ -146,6 +183,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
                 birth: row.date || null,
                 gender: row['Id/demographics/gender'] || null,
                 socialCode: row['Id/demographics/socialCode'] || null,
+                generation: isBlankGeneration(row['Id/demographics/generation']) ? null : parseInt(row['Id/demographics/generation'], 10),
                 taskid: row.taskid,
                 remark: row.remark,
                 QCStateLabel: row.QCStateLabel,
@@ -161,6 +199,19 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
                 obj.species = helper.getJavaHelper().getSpecies(obj.dam);
             }
 
+            // the conception window fills this in, so a blank one means a save that bypassed the form
+            if (isBlankGeneration(obj.generation)) {
+                var damGeneration = obj.dam ? triggerHelper.getGeneration(obj.dam) : null;
+                if (damGeneration === null) {
+                    var generationWarning = obj.dam
+                            ? 'No generation is recorded for dam ' + obj.dam + ', so this birth was recorded as generation 1'
+                            : 'This birth record has no dam, so it was recorded as generation 1';
+                    EHR.Server.Utils.addError(scriptErrors, 'Id/demographics/generation', generationWarning, 'WARN');
+                }
+
+                obj.generation = (damGeneration === null ? 0 : damGeneration) + 1;
+            }
+
             if (!oldRow) {
                 //if not already present, we insert into demographics
                 helper.getJavaHelper().createDemographicsRecord(row.Id, obj, extraDemographicsFieldMappings);
@@ -198,6 +249,11 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
                     hasUpdates = true;
                 }
 
+                if (!isBlankGeneration(obj.generation) && obj.generation !== data.generation) {
+                    record.generation = obj.generation;
+                    hasUpdates = true;
+                }
+
                 if (obj.performedby && obj.performedby !== data.performedby) {
                     record.performedby = obj.performedby;
                     hasUpdates = true;

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

@@ -11,6 +11,7 @@
                     <column columnName="Id" />
                     <column columnName="date">
                         <columnTitle>Birth Date</columnTitle>
+                        <formatString>DateTime</formatString>
                     </column>
                     <column columnName="conceptId">
                         <columnTitle>Conception Id</columnTitle>

nbri_ehr/resources/queries/study/clinical_observations.js

@@ -45,6 +45,13 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
             EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Yes' for " + row.category + ", please explain in the Remark", "WARN");
         }
 
+        // Always derive the type from the observation type's category rather than trusting the incoming value.
+        // The Observations form leaves it blank because it offers every type; the other forms set it explicitly,
+        // but their type pickers are filtered to the categories that agree with the value they set, so deriving
+        // here gives them the same answer. Deriving unconditionally also re-derives when a re-opened draft or a
+        // saved template carries a type left over from a different category.
+        row.type = triggerHelper.getObservationTypeCategory(row.category) === 'Behavior' ? 'Behavior' : 'Clinical';
+
         // Handle scheduled observations
         if (!helper.isValidateOnly() && row.scheduledDate) {
             var qc;

nbri_ehr/resources/queries/study/deathNotification.sql

@@ -8,6 +8,5 @@ SELECT
     Id,
     date,
     taskid,
-    performedBy.DisplayName AS performedBy,
-    reason.title AS reason
+    performedBy.DisplayName AS performedBy
 FROM study.deaths