Add conception tracking to birth and pregnancy outcomes

nbri_ehr/resources/queries/nbri_ehr/Conception.js

@@ -0,0 +1 @@
+require("ehr/triggers").initScript(this);

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

@@ -0,0 +1,39 @@
+<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>
+                <columns>
+                    <column columnName="rowId">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="ConceptId">
+                        <columnTitle>Conception Id</columnTitle>
+                        <required>true</required>
+                    </column>
+                    <column columnName="ConceptDate">
+                        <columnTitle>Conception Date</columnTitle>
+                    </column>
+                    <column columnName="ConceptDate">
+                        <columnTitle>Conception Date</columnTitle>
+                    </column>
+                    <column columnName="ConceptTermDate">
+                        <columnTitle>Conception Term Date</columnTitle>
+                    </column>
+                    <column columnName="Dam">
+                        <required>true</required>
+                    </column>
+                    <column columnName="Sire" />
+                    <column columnName="QCState">
+                        <columnTitle>Status</columnTitle>
+                        <fk>
+                            <fkDbSchema>core</fkDbSchema>
+                            <fkTable>qcstate</fkTable>
+                            <fkColumnName>rowid</fkColumnName>
+                        </fk>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.query.xml

@@ -0,0 +1,21 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="ConceptionsByDam" tableDbType="TABLE">
+                <javaCustomizer class="org.labkey.nbri_ehr.table.NBRI_EHRCustomizer"/>
+                <tableTitle>Conceptions by Dam</tableTitle>
+                <columns>
+                    <column columnName="Id">
+                        <columnTitle>Dam</columnTitle>
+                    </column>
+                    <column columnName="ConceptId">
+                        <columnTitle>Conception Id</columnTitle>
+                    </column>
+                    <column columnName="conceptionOutcome">
+                        <columnTitle>Conception Outcome</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

nbri_ehr/resources/queries/nbri_ehr/ConceptionsByDam.sql

@@ -0,0 +1,23 @@
+/*
+ * 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,
+    c.ConceptTermDate,
+    c.Sire,
+    CASE
+        WHEN b.conceptId IS NOT NULL THEN 'Live Birth'
+        WHEN po.conceptId IS NOT NULL THEN COALESCE(po.result, 'Unknown')
+        ELSE 'Unknown'
+    END AS conceptionOutcome,
+    c.Remark,
+    c.QCState AS qcstate
+FROM Conception c
+LEFT JOIN (SELECT DISTINCT b.conceptId FROM study.birth b WHERE b.conceptId IS NOT NULL) 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
+    ON po.conceptId = c.ConceptId

nbri_ehr/resources/queries/study/birth.js

@@ -30,6 +30,22 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
         EHR.Server.Utils.addError(scriptErrors, 'Id', 'Birth record already exists for this Id, update existing record to change birth information', 'ERROR');
     }
 
+    if (!helper.isETL() && row.conceptId) {
+        if (triggerHelper.totalRecords('nbri_ehr', 'Conception', 'ConceptId', row.conceptId) === 0) {
+            EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id does not match any conception record', 'WARN');
+        }
+
+        //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;
+        if (triggerHelper.totalRecords('study', 'birth', 'conceptId', row.conceptId) > conceptIdThreshold) {
+            EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id is already used by another birth record', 'INFO');
+        }
+
+        if (triggerHelper.totalRecords('study', 'pregnancy', 'conceptId', row.conceptId) > 0) {
+            EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id is already used by a pregnancy outcome record', 'INFO');
+        }
+    }
+
     if (!helper.isETL()) {
 
         if (row.QCStateLabel) {

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

@@ -43,6 +43,14 @@
                             <fkDisplayColumnName>title</fkDisplayColumnName>
                         </fk>
                     </column>
+                    <column columnName="conceptId">
+                        <columnTitle>Conception Id</columnTitle>
+                        <fk>
+                            <fkDbSchema>nbri_ehr</fkDbSchema>
+                            <fkTable>Conception</fkTable>
+                            <fkColumnName>ConceptId</fkColumnName>
+                        </fk>
+                    </column>
                     <column columnName="remark"/>
                     <column columnName="performedby"/>
                 </columns>

nbri_ehr/resources/queries/study/pregnancy.js

@@ -4,9 +4,28 @@
  * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
  */
 require("ehr/triggers").initScript(this);
+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);
 
+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) {
+            EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id does not match any conception record', 'WARN');
+        }
+
+        //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;
+        if (triggerHelper.totalRecords('study', 'pregnancy', 'conceptId', row.conceptId) > conceptIdThreshold) {
+            EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id is already used by another pregnancy outcome record', 'INFO');
+        }
+
+        if (triggerHelper.totalRecords('study', 'birth', 'conceptId', row.conceptId) > 0) {
+            EHR.Server.Utils.addError(scriptErrors, 'conceptId', 'This conception Id is already used by a birth record', 'INFO');
+        }
+    }
+});
+
 EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.ON_BECOME_PUBLIC, 'study', 'pregnancy', function(scriptErrors, helper, row, oldRow) {
     if (!helper.isETL()) {
 

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

@@ -21,6 +21,14 @@
                             <fkDisplayColumnName>title</fkDisplayColumnName>
                         </fk>
                     </column>
+                    <column columnName="conceptId">
+                        <columnTitle>Conception Id</columnTitle>
+                        <fk>
+                            <fkDbSchema>nbri_ehr</fkDbSchema>
+                            <fkTable>Conception</fkTable>
+                            <fkColumnName>ConceptId</fkColumnName>
+                        </fk>
+                    </column>
                 </columns>
             </table>
         </tables>

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

@@ -221,6 +221,9 @@
             <column columnName="birthProtocol">
                 <datatype>varchar</datatype>
             </column>
+            <column columnName="conceptId">
+                <datatype>varchar</datatype>
+            </column>
         </columns>
     </table>
     <table tableName="blood" tableDbType="TABLE">
@@ -1364,6 +1367,9 @@
                 <datatype>varchar</datatype>
                 <rangeURI>http://cpas.fhcrc.org/exp/xml#fileLink</rangeURI>
             </column>
+            <column columnName="conceptId">
+                <datatype>varchar</datatype>
+            </column>
         </columns>
     </table>
     <table tableName="notes" tableDbType="TABLE">

nbri_ehr/resources/reports/additionalReports.tsv

@@ -49,4 +49,5 @@ behaviorRemarks	Behavior	query	Behavior Remarks	true		study	BehaviorClinRemarks
 clinObsBehavior	Behavior	query	Observations	true		study	behaviorObservations			date	false	false		qcstate/publicdata	This report contains one record for each encounter with each animal, including surergies, exams, procedures, etc.
 clinremarks	Clinical	query	Clinical Remarks	true		study	ClinicalClinRemarks			date	false	false		qcstate/publicdata	This report contains the clinical remarks entered about each animal
 physicalExam	Clinical	query	Exam History	True		study	physicalExam			date	false	false		qcstate/publicdata	This report displays physical exam data for the selected animal
-historicalOther	General	query	Historical	True		study	historicalOther			date	false	false		qcstate/publicdata	This report displays historical events from legacy systems
+historicalOther	General	query	Historical	True		study	historicalOther			date	false	false		qcstate/publicdata	This report displays historical events from legacy systems
+conceptionsByDam	Reproductive Management	query	Conceptions by Dam	true		nbri_ehr	ConceptionsByDam			ConceptDate	false	false		qcstate/publicdata	This report displays conception records where the selected animal is the dam

nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-26.000-26.001.sql

@@ -0,0 +1,26 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+CREATE TABLE nbri_ehr.Conception
+(
+    RowId               SERIAL NOT NULL,
+    ConceptId           VARCHAR(100),
+    ConceptDate         TIMESTAMP,
+    ConceptTermDate     TIMESTAMP,
+    Remark              TEXT,
+    Dam                 VARCHAR(100),
+    Sire                VARCHAR(100),
+    TaskId              ENTITYID,
+    QCState             INTEGER,
+    Container           entityId NOT NULL,
+    Created             TIMESTAMP,
+    CreatedBy           USERID,
+    Modified            TIMESTAMP,
+    ModifiedBy          USERID,
+    CONSTRAINT PK_CONCEPTION PRIMARY KEY (RowId),
+    CONSTRAINT UQ_CONCEPTION_ConceptId UNIQUE (ConceptId),
+    CONSTRAINT FK_CONCEPTION_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId)
+);
+CREATE INDEX IX_Nbri_Ehr_Conception_Container ON nbri_ehr.Conception (Container);

nbri_ehr/resources/schemas/nbri_ehr.xml

@@ -569,4 +569,29 @@
         </columns>
     </table>
 
+    <table tableName="Conception" tableDbType="TABLE">
+        <tableTitle>Conception</tableTitle>
+        <auditLogging>DETAILED</auditLogging>
+        <columns>
+            <column columnName="RowId"/>
+            <column columnName="ConceptId"/>
+            <column columnName="ConceptDate">
+                <formatString>Date</formatString>
+            </column>
+            <column columnName="ConceptTermDate">
+                <formatString>Date</formatString>
+            </column>
+            <column columnName="Remark"/>
+            <column columnName="Dam"/>
+            <column columnName="Sire"/>
+            <column columnName="TaskId"/>
+            <column columnName="QCState"/>
+            <column columnName="Container"/>
+            <column columnName="Created"/>
+            <column columnName="CreatedBy"/>
+            <column columnName="Modified"/>
+            <column columnName="ModifiedBy"/>
+        </columns>
+    </table>
+
 </tables>

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

@@ -71,6 +71,11 @@ EHR.model.DataModelManager.registerMetadata('Birth', {
             },
             'Id/demographics/gender': {
                 allowBlank: false
+            },
+            conceptId: {
+                columnConfig: {
+                    width: 150
+                }
             }
         }
     }

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

@@ -0,0 +1,66 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+EHR.model.DataModelManager.registerMetadata('Conception', {
+    allQueries: {
+
+    },
+    byQuery: {
+        'nbri_ehr.Conception': {
+            RowId: {
+                allowBlank: true,
+                nullable: true,
+                hidden: true
+            },
+            ConceptId: {
+                allowBlank: false,
+                nullable: false,
+                columnConfig: {
+                    width: 200
+                },
+            },
+            ConceptDate: {
+                xtype: 'datefield',
+                extFormat: LABKEY.extDefaultDateFormat,
+                columnConfig: {
+                    width: 200
+                },
+            },
+            ConceptTermDate: {
+                xtype: 'datefield',
+                extFormat: LABKEY.extDefaultDateFormat,
+                columnConfig: {
+                    width: 200
+                },
+            },
+            Dam: {
+                xtype: 'ehr-animalfield',
+                lookups: false,
+                allowBlank: false,
+                nullable: false,
+                columnConfig: {
+                    width: 200
+                },
+            },
+            Sire: {
+                xtype: 'ehr-animalfield',
+                lookups: false,
+                columnConfig: {
+                    width: 200
+                },
+            },
+            Remark: {
+                height: 75,
+                editorConfig: {
+                    resizeDirections: 's'
+                },
+                columnConfig: {
+                    width: 300
+                },
+            }
+        },
+
+    }
+});

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

@@ -24,6 +24,11 @@ EHR.model.DataModelManager.registerMetadata('Pregnancy', {
             result: {
                 allowBlank: false,
                 nullable: false,
+            },
+            conceptId: {
+                columnConfig: {
+                    width: 150
+                }
             }
         },
 

nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRModule.java

@@ -80,7 +80,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 26.000;
+        return 26.001;
     }
 
     @Override
@@ -236,6 +236,7 @@ private void registerDataEntry()
         EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIChemistryImportFormType.class, this));
         EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRISerologyImportFormType.class, this));
         EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIRearrivalFormType.class, this));
+        EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIConceptionFormType.class, this));
     }
 
     @Override