[bot] Fast-forward for 25.7.16

GeneticsCore/resources/etls/MHC_Typing.xml

@@ -22,6 +22,21 @@
                 </alternateKeys>
             </destination>
         </transform>
+
+        <transform id="rc" type="TaskrefTransformStep">
+            <taskref ref="org.labkey.primeseq.etl.VerifyRowCount">
+                <settings>
+                    <setting name="sourceRemoteSource" value="PRIMESEQ_MHC"/>
+                    <setting name="sourceSchema" value="geneticscore"/>
+                    <setting name="sourceQuery" value="mhc_data"/>
+                    <setting name="sourceColumn" value="objectId"/>
+
+                    <setting name="destSchema" value="geneticscore"/>
+                    <setting name="destQuery" value="mhc_data"/>
+                    <setting name="destColumn" value="objectId"/>
+                </settings>
+            </taskref>
+        </transform>
     </transforms>
 
     <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified">

onprc_ehr/resources/etls/CageAuditLog.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+Created by: Kollil, 10/16/2025
+Created a new ETL process for the cage audit log data.
+This query runs daily at 8:30Pm to capture the snapshot of the cage inventory
+-->
+
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>CageAuditLog</name>
+    <description>Executes onprc_ehr.p_CageAuditHistoryProcess daily (no load)</description>
+    <transforms>
+        <!-- Calls a DB stored procedure that simply executes the query -->
+        <transform id="RunCageAuditLog" type="StoredProcedure">
+            <description>Run stored proc p_CageAuditHistoryProcess</description>
+            <procedure schemaName="onprc_ehr" procedureName="p_CageAuditHistoryProcess" useTransaction="false"/>
+        </transform>
+    </transforms>
+
+    <schedule>
+        <!--Runs daily 8:30pm-->
+        <cron expression="0 30 20 * * ?"/>
+    </schedule>
+
+</etl>

onprc_ehr/resources/queries/study/parentageSummary.sql

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2013-2017 LabKey Corporation
+ * Copyright (c) 2013-2016 LabKey Corporation
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -21,9 +21,9 @@ SELECT
   p.method
 
 FROM study.parentage p
-WHERE p.qcstate.publicdata = true and p.enddateCoalesced <= now()
+WHERE p.qcstate.publicdata = true and p.enddate is null
 
-UNION ALL
+UNION
 
 SELECT
   b.Id,
@@ -34,15 +34,16 @@ SELECT
 
 FROM study.birth b
 WHERE b.dam is not null and b.qcstate.publicdata = true
-
-UNION ALL
+And 'dam' not in (select k.relationship from study.parentage k where k.Id = b.Id and k.enddate is null)
+UNION
 
 SELECT
-    b.Id,
-    b.date,
-    b.sire,
+    a.Id,
+    a.date,
+    a.sire,
     'Sire' as relationship,
     'Observed' as method
 
-FROM study.birth b
-WHERE b.sire is not null and b.qcstate.publicdata = true
+FROM study.birth a
+WHERE a.sire is not null and a.qcstate.publicdata = true
+ And 'sire' not in (select k.relationship from study.parentage k where k.Id = a.Id and k.enddate is null)

onprc_ehr/resources/scripts/onprc_ehr/onprc_triggers.js

@@ -568,59 +568,6 @@ exports.init = function(EHR){
         }
     });
 
-    EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'assignment', function(helper, scriptErrors, row, oldRow){
-        // note: if this is automatically generated from death/departure, allow an incomplete record
-        // alerts will flag these
-        if (row.enddate && !row.releaseCondition && !helper.isGeneratedByServer()){
-            EHR.Server.Utils.addError(scriptErrors, 'releaseCondition', 'Must provide the release condition when the release date is set', 'WARN');
-        }
-
-        if (row.enddate && !row.releaseType && !helper.isGeneratedByServer()){
-            EHR.Server.Utils.addError(scriptErrors, 'releaseType', 'Must provide the release type when the release date is set', 'WARN');
-        }
-
-        //update condition on release
-        //Modified: 5-13-2019  R.Blasa
-        if (!helper.isETL() && helper.getEvent() == 'update' && oldRow){
-            if (EHR.Server.Security.getQCStateByLabel(row.QCStateLabel).PublicData && EHR.Server.Security.getQCStateByLabel(oldRow.QCStateLabel).PublicData){
-                if (row.releaseCondition && row.enddate && row.releaseCondition != 206){
-                    var msg = triggerHelper.checkForConditionDowngrade(row.Id, row.enddate, row.releaseCondition);
-                    if (msg){
-                        EHR.Server.Utils.addError(scriptErrors, 'releaseCondition', msg, 'INFO');
-                    }
-                    else {
-                        triggerHelper.updateAnimalCondition(row.Id, row.enddate, row.releaseCondition);
-                    }
-                }
-            }
-        }
-
-        // we want to record the date a record was marked endded, in addition to the actual end itself
-        // NOTE: we only do this when both enddate and releaseType are entered
-        if (!row.enddatefinalized && row.enddate && row.releaseCondition && EHR.Server.Security.getQCStateByLabel(row.QCStateLabel).PublicData){
-            //note: if ended in the future, defer to that date
-            row.enddatefinalized = new Date();
-            if (row.enddate.getTime() > row.enddatefinalized.getTime()){
-                row.enddatefinalized = row.enddate;
-            }
-        }
-
-        //check for condition downgrade for assign condition
-        if (!helper.isETL() && row.Id && row.assignCondition){
-            var msg = triggerHelper.checkForConditionDowngrade(row.Id, row.date, row.assignCondition);
-            if (msg){
-                EHR.Server.Utils.addError(scriptErrors, 'assignCondition', msg, 'INFO');
-            }
-        }
-
-        //check for condition downgrade for assign condition
-        if (!helper.isETL() && row.Id && row.date && row.assignCondition){
-            var msg = triggerHelper.checkForConditionDowngrade(row.Id, row.date, row.assignCondition);
-            if (msg){
-                EHR.Server.Utils.addError(scriptErrors, 'assignCondition', msg, 'INFO');
-            }
-        }
-    });
 
     EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.ON_BECOME_PUBLIC, 'study', 'assignment', function(scriptErrors, helper, row, oldRow){
         //Modified: 5-9-2019  R.Blasa  Prevent flag enttrie for terminal monkey ids
@@ -1307,6 +1254,86 @@ exports.init = function(EHR){
                 }
             }
         });
+        //     Added 10-17-2025  R. Blasa
+        EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'assignment', EHR.Server.TriggerManager.Events.BEFORE_UPSERT);
+        EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'assignment', function(helper, scriptErrors, row, oldRow){
+            if (!helper.isETL()){
+                //note: the the date field is handled above by removeTimeFromDate
+                EHR.Server.Utils.removeTimeFromDate(row, scriptErrors, 'enddate');
+                EHR.Server.Utils.removeTimeFromDate(row, scriptErrors, 'projectedRelease');
+            }
+
+
+            //check number of allowed animals at assign/approve time
+            if (!helper.isETL() && !helper.isQuickValidation() && helper.doStandardProtocolCountValidation() &&
+                    //this is designed to always perform the check on imports, but also updates where the Id was changed
+                    !(oldRow && oldRow.Id && oldRow.Id==row.Id) &&
+                    row.Id && row.project && row.date
+            ){
+                var assignmentsInTransaction = helper.getProperty('assignmentsInTransaction');
+                assignmentsInTransaction = assignmentsInTransaction || [];
+
+                var msgs = helper.getJavaHelper().verifyProtocolCounts(row.Id, row.project, assignmentsInTransaction);
+                if (msgs){
+                    msgs = msgs.split("<>");
+                    for (var i=0;i<msgs.length;i++){
+                        EHR.Server.Utils.addError(scriptErrors, 'project', msgs[i], 'WARN');
+                    }
+                }
+            }
+
+                // note: if this is automatically generated from death/departure, allow an incomplete record
+                // alerts will flag these
+                if (row.enddate && !row.releaseCondition && !helper.isGeneratedByServer()){
+                    EHR.Server.Utils.addError(scriptErrors, 'releaseCondition', 'Must provide the release condition when the release date is set', 'WARN');
+                }
+
+                if (row.enddate && !row.releaseType && !helper.isGeneratedByServer()){
+                    EHR.Server.Utils.addError(scriptErrors, 'releaseType', 'Must provide the release type when the release date is set', 'WARN');
+                }
+
+                //update condition on release
+                //Modified: 5-13-2019  R.Blasa
+                if (!helper.isETL() && helper.getEvent() == 'update' && oldRow){
+                    if (EHR.Server.Security.getQCStateByLabel(row.QCStateLabel).PublicData && EHR.Server.Security.getQCStateByLabel(oldRow.QCStateLabel).PublicData){
+                        if (row.releaseCondition && row.enddate && row.releaseCondition != 206){
+                            var msg = triggerHelper.checkForConditionDowngrade(row.Id, row.enddate, row.releaseCondition);
+                            if (msg){
+                                EHR.Server.Utils.addError(scriptErrors, 'releaseCondition', msg, 'INFO');
+                            }
+                            else {
+                                triggerHelper.updateAnimalCondition(row.Id, row.enddate, row.releaseCondition);
+                            }
+                        }
+                    }
+                }
+
+                // we want to record the date a record was marked endded, in addition to the actual end itself
+                // NOTE: we only do this when both enddate and releaseType are entered
+                if (!row.enddatefinalized && row.enddate && row.releaseCondition && EHR.Server.Security.getQCStateByLabel(row.QCStateLabel).PublicData){
+                    //note: if ended in the future, defer to that date
+                    row.enddatefinalized = new Date();
+                    if (row.enddate.getTime() > row.enddatefinalized.getTime()){
+                        row.enddatefinalized = row.enddate;
+                    }
+                }
+
+                //check for condition downgrade for assign condition
+                if (!helper.isETL() && row.Id && row.assignCondition){
+                    var msg = triggerHelper.checkForConditionDowngrade(row.Id, row.date, row.assignCondition);
+                    if (msg){
+                        EHR.Server.Utils.addError(scriptErrors, 'assignCondition', msg, 'INFO');
+                    }
+                }
+
+                //check for condition downgrade for assign condition
+                if (!helper.isETL() && row.Id && row.date && row.assignCondition){
+                    var msg = triggerHelper.checkForConditionDowngrade(row.Id, row.date, row.assignCondition);
+                    if (msg){
+                        EHR.Server.Utils.addError(scriptErrors, 'assignCondition', msg, 'INFO');
+                    }
+                }
+        });
 
         //Added 10-5-2022  R.Blasa
         EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'matings', function (helper, scriptErrors, row, oldRow) {

onprc_ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java

@@ -394,6 +394,7 @@ protected String ensureFlagExists(final String category, final String name, fina
         SelectRowsCommand select1 = new SelectRowsCommand("ehr_lookups", "flag_values");
         select1.addFilter(new Filter("category", category, Filter.Operator.EQUAL));
         select1.addFilter(new Filter("value", name, Filter.Operator.EQUAL));
+        select1.addFilter(new Filter("datedisabled", null, Filter.Operator.ISBLANK));
         SelectRowsResponse resp = select1.execute(getApiHelper().getConnection(), getContainerPath());
 
         String objectid = resp.getRowCount().intValue() == 0 ? null : (String)resp.getRows().get(0).get("objectid");

onprc_ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest.java

@@ -43,6 +43,7 @@
 import org.labkey.test.components.BodyWebPart;
 import org.labkey.test.pages.ehr.AnimalHistoryPage;
 import org.labkey.test.pages.ehr.EnterDataPage;
+import org.labkey.test.pages.ehr.NotificationAdminPage;
 import org.labkey.test.util.DataRegionTable;
 import org.labkey.test.util.Ext4Helper;
 import org.labkey.test.util.LogMethod;
@@ -71,6 +72,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.function.Function;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
@@ -1975,5 +1977,104 @@ protected String getAnimalHistoryPath()
     {
         return ANIMAL_HISTORY_URL;
     }
-}
 
+    @Test
+    public void testNotificationAdminAudits() throws Exception
+    {
+        // Ensure notification service is configured
+        setupNotificationService();
+
+        // Navigate to Notification Admin page
+        goToEHRFolder();
+        waitAndClickAndWait(Locators.bodyPanel().append(Locator.tagContainingText("a", "EHR Admin Page")));
+        waitAndClickAndWait(Locator.tagContainingText("a", "Notification Admin"));
+
+        // Record start time for audit filtering
+        LocalDateTime start = LocalDateTime.now().minusMinutes(5);
+
+        // Change Notification User and Reply Email, then save
+        NotificationAdminPage.beginAt(this);
+        String replyEmail = "ehr-notify@labkey.test";
+        Ext4FieldRef.getForLabel(this, "Notification User").setValue(PasswordUtil.getUsername());
+        Ext4FieldRef.getForLabel(this, "Reply Email").setValue(replyEmail);
+        click(Ext4Helper.Locators.ext4Button("Save"));
+        waitForElement(Ext4Helper.Locators.window("Success"));
+        waitAndClickAndWait(Ext4Helper.Locators.ext4Button("OK"));
+
+        // Identify two notifications by extracting their keys from the Run Report links
+        beginAt(WebTestHelper.getBaseURL() + "/ldk/" + getContainerPath() + "/notificationAdmin.view");
+        Locator links = Locator.tagContainingText("a", "Run Report In Browser");
+        waitFor(() -> links.findElements(getDriver()).size() >= 2, "Expected at least two notifications to be available", WAIT_FOR_PAGE);
+        List<WebElement> runLinks = links.findElements(getDriver());
+
+        List<String> notifKeys = new ArrayList<>();
+        for (int i = 0; i < Math.min(2, runLinks.size()); i++)
+        {
+            String href = runLinks.get(i).getAttribute("href");
+            int idx = href.indexOf("key=");
+            Assert.assertTrue("Could not locate notification key in href: " + href, idx > -1);
+            String key = href.substring(idx + 4);
+            notifKeys.add(key);
+        }
+
+        // Disable the two notifications and save
+        for (String key : notifKeys)
+        {
+            _ext4Helper.selectComboBoxItem(Ext4Helper.Locators.formItemWithInputNamed("status_" + key), Ext4Helper.TextMatchTechnique.EXACT, "Disabled");
+        }
+        click(Ext4Helper.Locators.ext4Button("Save"));
+        waitForElement(Ext4Helper.Locators.window("Success"));
+        waitAndClickAndWait(Ext4Helper.Locators.ext4Button("OK"));
+
+        // Re-enable the two notifications and save
+        for (String key : notifKeys)
+        {
+            _ext4Helper.selectComboBoxItem(Ext4Helper.Locators.formItemWithInputNamed("status_" + key), Ext4Helper.TextMatchTechnique.EXACT, "Enabled");
+        }
+        click(Ext4Helper.Locators.ext4Button("Save"));
+        waitForElement(Ext4Helper.Locators.window("Success"));
+        waitAndClickAndWait(Ext4Helper.Locators.ext4Button("OK"));
+
+        // Manage subscribed users on the first notification: add two users then remove one
+        Locator manageLink = Locator.tagContainingText("a", "Manage Subscribed Users/Groups").index(0);
+        waitAndClick(manageLink);
+        waitForElement(Ext4Helper.Locators.window("Manage Subscribed Users"));
+        Ext4ComboRef combo = Ext4ComboRef.getForLabel(this, "Add User Or Group");
+        combo.waitForStoreLoad();
+        _ext4Helper.selectComboBoxItem(Locator.id(combo.getId()), Ext4Helper.TextMatchTechnique.CONTAINS, DATA_ADMIN.getEmail());
+        Ext4FieldRef.waitForComponent(this, "field[fieldLabel^='Add User Or Group']");
+        combo = Ext4ComboRef.getForLabel(this, "Add User Or Group");
+        _ext4Helper.selectComboBoxItem(Locator.id(combo.getId()), Ext4Helper.TextMatchTechnique.CONTAINS, BASIC_SUBMITTER.getEmail());
+        waitAndClick(Ext4Helper.Locators.ext4Button("Close"));
+
+        // Re-open and remove one user
+        waitAndClick(manageLink);
+        waitForElement(Ext4Helper.Locators.window("Manage Subscribed Users"));
+        assertElementPresent(Ext4Helper.Locators.ext4Button("Remove"));
+        waitAndClick(Ext4Helper.Locators.ext4Button("Remove").index(0));
+        waitAndClick(Ext4Helper.Locators.ext4Button("Close"));
+
+        // Verify audit log entries in audit.SiteSettings for this container
+        sleep(1000);
+
+        Function<String, Integer> countAudit = (commentSubstring) -> {
+            try
+            {
+                SelectRowsCommand cmd = new SelectRowsCommand("auditLog", "AppPropsEvent");
+                cmd.addFilter(new Filter("Created", Date.from(start.atZone(ZoneId.systemDefault()).toInstant()), Filter.Operator.DATE_GTE));
+                cmd.addFilter(new Filter("Comment", commentSubstring, Filter.Operator.CONTAINS));
+                SelectRowsResponse resp = cmd.execute(getApiHelper().getConnection(), getContainerPath());
+                return resp.getRowCount().intValue();
+            }
+            catch (Exception e)
+            {
+                throw new RuntimeException(e);
+            }
+        };
+
+        Assert.assertTrue("Expected audit entry for reply-to email update", countAudit.apply("Notification reply-to email updated.") > 0);
+        Assert.assertTrue("Expected audit entry for service user update", countAudit.apply("Notification service user updated.") > 0);
+        Assert.assertTrue("Expected audit entry for notification enabled", countAudit.apply("has been enabled.") > 0);
+        Assert.assertTrue("Expected audit entry for subscription updates", countAudit.apply("Updated notification subscriptions for") > 0);
+    }
+}