Update the birth, arrival, death, and pregnancy data entry forms

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/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/birth.js

@@ -13,6 +13,11 @@ var idsToSync = [];
 // 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)
@@ -146,6 +151,7 @@ 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 +167,19 @@ 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 +217,11 @@ 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/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

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

@@ -16,15 +16,6 @@
                             <fkDisplayColumnName>title</fkDisplayColumnName>
                         </fk>
                     </column>
-                    <column columnName="reason">
-                        <columnTitle>Disposition</columnTitle>
-                        <fk>
-                            <fkDbSchema>ehr_lookups</fkDbSchema>
-                            <fkTable>death_reason</fkTable>
-                            <fkColumnName>value</fkColumnName>
-                            <fkDisplayColumnName>title</fkDisplayColumnName>
-                        </fk>
-                    </column>
                     <column columnName="deathWeight">
                         <columnTitle>Death Weight (kg)</columnTitle>
                     </column>

nbri_ehr/resources/queries/study/deaths/.qview.xml

@@ -7,7 +7,6 @@
         <column name="Id/Demographics/species"/>
         <column name="date"/>
         <column name="type"/>
-        <column name="reason"/>
         <column name="deathWeight"/>
         <column name="remark"/>
         <column name="performedBy"/>

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

@@ -100,6 +100,9 @@
                             <fkDisplayColumnName>title</fkDisplayColumnName>
                         </fk>
                     </column>
+                    <column columnName="generation">
+                        <columnTitle>Generation</columnTitle>
+                    </column>
                     <column columnName="cites">
                         <columnTitle>CITES</columnTitle>
                     </column>

nbri_ehr/resources/queries/study/demographics/.qview.xml

@@ -13,6 +13,7 @@
         <column name="dam"/>
         <column name="sire"/>
         <column name="socialCode"/>
+        <column name="generation"/>
         <column name="disposition"/>
         <column name="termination"/>
         <column name="implantNumber"/>

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

@@ -29,6 +29,16 @@
                             <fkColumnName>ConceptId</fkColumnName>
                         </fk>
                     </column>
+                    <column columnName="type">
+                        <columnTitle>Delivery Mode</columnTitle>
+                        <required>false</required>
+                        <fk>
+                            <fkDbSchema>ehr_lookups</fkDbSchema>
+                            <fkTable>delivery_mode</fkTable>
+                            <fkColumnName>value</fkColumnName>
+                            <fkDisplayColumnName>title</fkDisplayColumnName>
+                        </fk>
+                    </column>
                 </columns>
             </table>
         </tables>

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

@@ -509,6 +509,9 @@
             <column columnName="socialCode">
                 <datatype>varchar</datatype>
             </column>
+            <column columnName="generation">
+                <datatype>integer</datatype>
+            </column>
             <column columnName="CITES">
                 <datatype>varchar</datatype>
             </column>
@@ -561,9 +564,6 @@
                 <propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
                 <conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
             </column>
-            <column columnName="reason">
-                <datatype>varchar</datatype>
-            </column>
             <column columnName="deathWeight">
                 <datatype>double</datatype>
             </column>
@@ -1367,7 +1367,6 @@
                 <conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
             </column>
             <column columnName="type">
-                <columnTitle>Type</columnTitle>
                 <datatype>varchar</datatype>
             </column>
             <column columnName="result">

nbri_ehr/resources/views/necropsy.html

@@ -62,7 +62,7 @@
                 schemaName: 'study',
                 queryName: 'deaths',
                 filterArray: filterArray,
-                columns: 'Id,Id/demographics/species,Id/demographics/gender,date,reason,deathWeight,Id/lastProtocol/protocol,Id/lastProject/project',
+                columns: 'Id,Id/demographics/species,Id/demographics/gender,date,deathWeight,Id/lastProtocol/protocol,Id/lastProject/project',
             },
             title: 'Death',
             renderTo: 'animalDeath',

nbri_ehr/resources/web/nbri_ehr/model/sources/Arrival.js

@@ -20,7 +20,8 @@ EHR.model.DataModelManager.registerMetadata('Arrival', {
     byQuery: {
         'study.arrival': {
             'cage': {
-                // allowBlank: false,
+                allowBlank: false,
+                nullable: false,
                 columnConfig: {
                     fixed: true,
                     width: 200
@@ -55,6 +56,21 @@ EHR.model.DataModelManager.registerMetadata('Arrival', {
                     width: 200
                 }
             },
+            // an arriving animal establishes its own lineage, so it starts at generation 0
+            'Id/demographics/generation': {
+                allowBlank: false,
+                nullable: false,
+                getInitialValue: function(v) {
+                    return Ext4.isEmpty(v) ? 0 : v;
+                },
+                editorConfig: {
+                    minValue: 0
+                },
+                columnConfig: {
+                    fixed: true,
+                    width: 120
+                }
+            },
             // an animal joins the colony already assigned to a project, a protocol and a group; the trigger script
             // opens the matching assignment record for each one
             project: {

nbri_ehr/resources/web/nbri_ehr/model/sources/Birth.js

@@ -59,7 +59,8 @@ EHR.model.DataModelManager.registerMetadata('Birth', {
                 }
             },
             'cage': {
-                // allowBlank: false,
+                allowBlank: false,
+                nullable: false,
                 columnConfig: {
                     fixed: true,
                     width: 200
@@ -145,6 +146,17 @@ EHR.model.DataModelManager.registerMetadata('Birth', {
                 columnConfig: {
                     width: 200
                 }
+            },
+            // derived from the dam by the conception window, but left editable so it can be corrected by hand
+            'Id/demographics/generation': {
+                allowBlank: false,
+                nullable: false,
+                editorConfig: {
+                    minValue: 0
+                },
+                columnConfig: {
+                    width: 120
+                }
             }
         }
     }

nbri_ehr/resources/web/nbri_ehr/model/sources/Death.js

@@ -36,11 +36,9 @@ EHR.model.DataModelManager.registerMetadata('Death', {
                 nullable: false,
                 columnConfig: {
                     width: 160
-                }
-            },
-            reason: {
-                columnConfig: {
-                    width: 160
+                },
+                lookup: {
+                    filterArray: [LABKEY.Filter.create('date_disabled', null, LABKEY.Filter.Types.ISBLANK)]
                 }
             },
             remark: {

nbri_ehr/resources/web/nbri_ehr/model/sources/Pregnancy.js

@@ -12,9 +12,6 @@ EHR.model.DataModelManager.registerMetadata('Pregnancy', {
             project: {
                 hidden: true,
             },
-            type: {
-                hidden: true,
-            },
             diagnosis: {
                 hidden: true,
             },
@@ -26,9 +23,18 @@ EHR.model.DataModelManager.registerMetadata('Pregnancy', {
                 nullable: false,
             },
             conceptId: {
+                allowBlank: false,
+                nullable: false,
                 columnConfig: {
                     width: 150
                 }
+            },
+            // shares the delivery_mode lookup with study.birth, but is optional here: an outcome can be recorded
+            // before the delivery mode is known
+            type: {
+                columnConfig: {
+                    width: 200
+                }
             }
         },