Add animal group assignment tracking and recode pairing formation types

nbri_ehr/resources/data/pairing_formation_types.tsv

@@ -1,7 +1,11 @@
-value
-Full Contact Pair
-Group Formation
-Introduction
-Limited Contact Pair
-Pair Formation
-Other
+value	title	date_disabled
+C	Compatible	2026-08-06
+CF	CF
+CP	Continuous pair
+F	Fought	2026-08-06
+FC	Full Contact
+IC	Intermittent Contact
+IG	Indoor Group Housing
+PC	Protected Contact
+S	Single Housing
+U	Unsuccessful

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

@@ -0,0 +1,15 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="animalGroupHousingSummary" tableDbType="TABLE">
+                <tableTitle>Animal Groups Housing Summary</tableTitle>
+                <columns>
+                    <column columnName="totalAnimals">
+                        <columnTitle>Total Animals</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=demographics&amp;query.id/curLocation/room~eq=${room}&amp;query.id/activeAnimalGroups/groups~contains=${groupId/title}</url>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/study/animalGroupHousingSummary.sql

@@ -0,0 +1,13 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+SELECT
+  m.groupId,
+  m.id.curLocation.room,
+  count(distinct m.id) as totalAnimals
+
+FROM study.animal_group_members m
+WHERE m.isActive = true
+GROUP BY m.groupId, m.id.curLocation.room

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

@@ -0,0 +1,22 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="animalGroupOverlapSummary" tableDbType="TABLE">
+                <tableTitle>Animal Group Member Summary</tableTitle>
+                <description>This query identifies the total distinct animals that were part of a group over the provided date range</description>
+                <columns>
+                    <column columnName="totalAnimals">
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=animalGroupOverlaps&amp;query.param.StartDate=${StartDate}&amp;query.param.EndDate=${EndDate}&amp;query.groupId/title~eq=${groupId/title}</url>
+                        <columnTitle>Total Animals</columnTitle>
+                    </column>
+                    <column columnName="startDate">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="endDate">
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/study/animalGroupOverlapSummary.sql

@@ -0,0 +1,15 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+SELECT
+  o.groupId,
+  count(distinct o.id) as totalAnimals,
+
+  max(o.StartDate) as StartDate,
+  max(o.EndDate) as EndDate
+
+FROM study.animalGroupOverlaps o
+
+GROUP BY o.groupId

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

@@ -0,0 +1,18 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="animalGroupOverlaps" tableDbType="TABLE">
+                <tableTitle>Animal Group Overlaps</tableTitle>
+                <description>This query identifies distinct animals that were part of a group over the provided date range</description>
+                <columns>
+                    <column columnName="startDate">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="endDate">
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/study/animalGroupOverlaps.sql

@@ -0,0 +1,34 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+/**
+  * This query is designed to find distinct animals that were part of a group at a given point in time
+  */
+PARAMETERS(StartDate TIMESTAMP, EndDate TIMESTAMP)
+
+SELECT
+  m.Id,
+  m.groupId,
+
+  max(StartDate) as StartDate,
+  max(EndDate) as EndDate
+FROM study.animal_group_members m
+
+WHERE (
+    /* entered startdate must be <= entered enddate */
+    coalesce( StartDate , cast('1900-01-01 00:00:00.0' as timestamp)) <= coalesce(EndDate, now())
+    AND
+
+    /* entered startdate must be less than record's enddate */
+    cast(coalesce( StartDate , cast('1900-01-01 00:00:00.0' as DATE)) AS DATE) <= m.enddateCoalesced
+
+    and
+
+    /* entered enddate must be greater than record's startdate */
+    cast(coalesce(EndDate, curdate()) AS DATE) >= m.dateOnly
+  )
+
+GROUP BY m.groupId, m.id

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

@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="animalGroupsPivoted" tableDbType="TABLE">
+                <tableTitle>Active Groups</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/study/animalGroupsPivoted.sql

@@ -0,0 +1,17 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+SELECT
+g.id,
+g.groupId.title as name,
+cast('yes' as varchar) as valueField
+
+FROM study.animal_group_members g
+
+WHERE (g.enddate IS NULL OR COALESCE(g.enddate, curdate()) >= curdate())
+
+GROUP BY g.id, g.groupId.title
+
+PIVOT valueField by name IN (select title FROM ehr_lookups.breeding_type)

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

@@ -0,0 +1,42 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="animal_group_members" tableDbType="TABLE" useColumnOrder="true">
+                <tableTitle>Animal Group Members</tableTitle>
+                <columns>
+                    <column columnName="Id"/>
+                    <column columnName="date">
+                        <columnTitle>Date Added</columnTitle>
+                    </column>
+                    <column columnName="enddate">
+                        <columnTitle>Date Removed</columnTitle>
+                        <isHidden>false</isHidden>
+                    </column>
+                    <column columnName="groupId">
+                        <columnTitle>Group</columnTitle>
+                        <fk>
+                            <fkDbSchema>ehr_lookups</fkDbSchema>
+                            <fkTable>breeding_type</fkTable>
+                            <fkColumnName>value</fkColumnName>
+                            <fkDisplayColumnName>title</fkDisplayColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="qcstate">
+                        <fk>
+                            <fkDbSchema>core</fkDbSchema>
+                            <fkTable>qcstate</fkTable>
+                            <fkColumnName>rowid</fkColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="project">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="performedBy">
+                        <shownInUpdateView>false</shownInUpdateView>
+                        <shownInInsertView>false</shownInInsertView>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

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

@@ -0,0 +1,19 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsActiveAnimalGroups" tableDbType="NOT_IN_DB">
+                <tableTitle>Active Animal Groups</tableTitle>
+                <columns>
+                    <column columnName="Id"/>
+                    <column columnName="totalGroups">
+                        <facetingBehavior>ALWAYS_OFF</facetingBehavior>
+                        <columnTitle>Total Groups</columnTitle>
+                    </column>
+                    <column columnName="groups">
+                        <columnTitle>Groups</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/study/demographicsActiveAnimalGroups.sql

@@ -0,0 +1,16 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+SELECT
+    m.Id,
+    count(distinct m.objectid) as totalGroups,
+    group_concat(distinct m.name, chr(10)) as groups
+
+FROM (SELECT Id,
+             objectid,
+             groupId.title as name
+      FROM study.animal_group_members
+      WHERE enddate is NULL AND qcstate.publicdata = true) m
+GROUP BY m.Id

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

@@ -45,6 +45,7 @@
                             <fkDbSchema>ehr_lookups</fkDbSchema>
                             <fkTable>pairing_formation_types</fkTable>
                             <fkColumnName>value</fkColumnName>
+                            <fkDisplayColumnName>title</fkDisplayColumnName>
                         </fk>
                     </column>
                     <column columnName="remark">

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

@@ -2,6 +2,7 @@
 <datasets metaDataFile="datasets_metadata.xml" xmlns="http://labkey.org/study/xml">
     <datasets>
         <dataset name="alias" id="1038" category="Colony Management" type="Standard"/>
+        <dataset name="animal_group_members" id="1042" category="Colony Management" type="Standard"/>
         <dataset name="arrival" id="1001" category="Colony Management" type="Standard"/>
         <dataset name="assignment" id="1002" category="Colony Management" type="Standard"/>
         <dataset name="blood" id="1005" category="Clinical" type="Standard"/>

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

@@ -58,6 +58,32 @@
             </column>
         </columns>
     </table>
+    <table tableName="animal_group_members" tableDbType="TABLE">
+        <tableTitle>Animal Group Members</tableTitle>
+        <description>Records membership of individual primates in named animal groups, with the date the animal joined and the date it was removed.</description>
+        <columns>
+            <column columnName="Id">
+                <datatype>varchar</datatype>
+                <propertyURI>http://cpas.labkey.com/Study#ParticipantId</propertyURI>
+                <importAliases>
+                    <importAlias>ptid</importAlias>
+                </importAliases>
+            </column>
+            <column columnName="date">
+                <datatype>timestamp</datatype>
+                <propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
+                <conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
+            </column>
+            <column columnName="enddate">
+                <datatype>timestamp</datatype>
+                <propertyURI>urn:ehr.labkey.org/#EndDate</propertyURI>
+            </column>
+            <column columnName="groupId">
+                <columnTitle>Group</columnTitle>
+                <datatype>varchar</datatype>
+            </column>
+        </columns>
+    </table>
     <table tableName="arrival" tableDbType="TABLE">
         <tableTitle>Arrival</tableTitle>
         <description>Tracks the arrival of primates into the research facility, including source, acquisition type, and associated documentation.</description>

nbri_ehr/resources/scripts/nbri_triggers.js

@@ -27,7 +27,7 @@ exports.init = function (EHR) {
         EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'cases', EHR.Server.TriggerManager.Events.AFTER_DELETE);
 
         helper.setScriptOptions({
-            datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags']
+            datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags', 'animal_group_members']
         });
     });
 
@@ -54,6 +54,14 @@ exports.init = function (EHR) {
         });
     });
 
+    EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'animal_group_members', function(event, helper) {
+        // group memberships are routinely backdated, so historical dates must not raise a warning
+        helper.setScriptOptions({
+            requiresStatusRecalc: false,
+            allowDatesInDistantPast: true
+        });
+    });
+
     EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'assignment', function(event, helper) {
         helper.setScriptOptions({
             allowAnyId: isAllowAnyIdRequested(helper),
@@ -136,7 +144,7 @@ exports.init = function (EHR) {
     EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'deaths', function(event, helper) {
 
         helper.setScriptOptions({
-            datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags'],
+            datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags', 'animal_group_members'],
             allowShippedIds: false,
             allowDeadIds: false,
             requiresStatusRecalc: true,

nbri_ehr/resources/web/nbri_ehr/data/AllowAnyIdClientStore.js

@@ -0,0 +1,16 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+Ext4.define('NBRI_EHR.data.AllowAnyIdClientStore', {
+    extend: 'EHR.data.DataEntryClientStore',
+
+    getExtraContext: function () {
+        var ret = this.callParent(arguments) || {};
+
+        // Tell the trigger scripts to allow any Id. Requires handling in trigger script to fully enable.
+        ret['allowAnyId'] = true;
+        return ret;
+    }
+});