From d3da01dbe1a24a018f1bd05a45c35fee2866cf38 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Wed, 16 Jul 2025 06:27:06 -0700
Subject: [PATCH 1/5] test exception

---
 .../org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java    | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java b/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java
index a3f2031a..98a95741 100644
--- a/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java
+++ b/snprc_ehr/test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java
@@ -267,6 +267,14 @@ protected void importStudy()
         importFolderFromPath(++_pipelineJobCount);
     }
 
+    @Override
+    protected List<String> skipLinksForValidation()
+    {
+        List<String> links = new ArrayList<>(super.skipLinksForValidation());
+        links.add("snprc_ehr-BirthReport.view");
+        return links;
+    }
+
     protected void initSND()
     {
         goToProjectHome();

From 8f83b717050c2c1d08e3ad3755b950cb30748597 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Wed, 16 Jul 2025 06:27:28 -0700
Subject: [PATCH 2/5] Remove unused lookups

---
 snprc_ehr/src/org/labkey/snprc_ehr/views/EditLookupTables.jsp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/views/EditLookupTables.jsp b/snprc_ehr/src/org/labkey/snprc_ehr/views/EditLookupTables.jsp
index d921018c..fdea7db7 100644
--- a/snprc_ehr/src/org/labkey/snprc_ehr/views/EditLookupTables.jsp
+++ b/snprc_ehr/src/org/labkey/snprc_ehr/views/EditLookupTables.jsp
@@ -93,8 +93,8 @@
                     {queryName: 'drug_categories', schemaName: 'ehr_lookups', title: 'Drug Categories'},
                     {queryName: 'conc_units', schemaName: 'ehr_lookups', title: 'Drug Concentration Units'},
                     {queryName: 'dosage_units', schemaName: 'ehr_lookups', title: 'Drug Dosage Units'},
-                    {queryName: 'ValidDSGroup', schemaName: 'ehr_lookups', title: 'Diagnosis Groups'},
-                    {queryName: 'ValidDXList', schemaName: 'ehr_lookups', title: 'Diagnosis Lists'},
+                    // {queryName: 'ValidDSGroup', schemaName: 'ehr_lookups', title: 'Diagnosis Groups'},
+                    // {queryName: 'ValidDXList', schemaName: 'ehr_lookups', title: 'Diagnosis Lists'},
                     {queryName: 'volume_units', schemaName: 'ehr_lookups', title: 'Drug Volume Units'},
                     //{queryName: 'drug_defaults', schemaName: 'ehr_lookups', title: 'Drug Default Values'},
                     {queryName: 'routes', schemaName: 'ehr_lookups', title: 'Drug Routes'},

From bc73e046321acf5d7a7cfb73c6fd4183eb840617 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Wed, 16 Jul 2025 06:27:50 -0700
Subject: [PATCH 3/5] Fix a couple broken links

---
 snprc_ehr/resources/views/ehrAdmin.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/snprc_ehr/resources/views/ehrAdmin.html b/snprc_ehr/resources/views/ehrAdmin.html
index b98c12c2..719944e0 100644
--- a/snprc_ehr/resources/views/ehrAdmin.html
+++ b/snprc_ehr/resources/views/ehrAdmin.html
@@ -20,8 +20,8 @@
                 {name: 'Set EHR Module Properties', url: '<%=contextPath%><%=containerPath%>/core-modulePropertyAdmin.view?moduleName=EHR'},
                 {name: 'Configure SSRS Properties', url: '<%=contextPath%><%=containerPath%>/snprc_ehr-ssrsConfig.view'},
                 {name: 'Update Study QCStates', url: '<%=contextPath%><%=containerPath%>/ehr-ensureQCStates.view'},
-                {name: 'Verify Dataset Resources', url: '<%=contextPath%><%=containerPath%>/ehr-verifyDatasetResources.view}'},
-                {name: 'Verify Dataset Columns', url: '<%=contextPath%><%=containerPath%>/snprc_ehr-validateDataSetCols.view'},
+                {name: 'Verify Dataset Resources', url: '<%=contextPath%><%=containerPath%>/ehr-verifyDatasetResources.view'},
+                {name: 'Verify Dataset Columns', url: '<%=contextPath%><%=containerPath%>/ehr-validateDataSetCols.view'},
                 {name: 'Verify EHR Schema Indexes Are Compressed', url: '<%=contextPath%><%=containerPath%>/ehr-ensureEHRSchemaIndexes.view'},
                 {name: 'Cache Demographics On All Living Animals', url: '<%=contextPath%><%=containerPath%>/ehr-cacheLivingAnimals.view'},
                 {name: 'Cache Demographics On All Animals', url: '<%=contextPath%><%=containerPath%>/ehr-cacheLivingAnimals.view?includeAll=true'},

From 6520cd912338d9dcde4f34ae87b9345e55d561ec Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Wed, 16 Jul 2025 06:28:07 -0700
Subject: [PATCH 4/5] CSP updates

---
 .../snprc_ehr/views/AnimalsHierarchy.jsp      | 58 +++++++++----------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalsHierarchy.jsp b/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalsHierarchy.jsp
index f2628467..af5b6af4 100644
--- a/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalsHierarchy.jsp
+++ b/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalsHierarchy.jsp
@@ -44,36 +44,36 @@
 
 </script>
 
-<script src="<%= contextPath %>/LDK/Utils.js"></script>
-<script src="<%= contextPath %>/LDK/Assert.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/AnimalsByNodeTreeStore.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/panels/AnimalsByNodeTreePanel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/panels/AnimalsByNodeReportsContainer.js"></script>
-<script src="<%= contextPath %>/LDK/panel/ContentResizingPanel.js"></script>
-<script src="<%= contextPath %>/LDK/ConvertUtils.js"></script>
-<script src="<%= contextPath %>/LDK/QueryHelper.js"></script>
-<script src="<%= contextPath %>/LDK/SelectRowsRow.js"></script>
-<script src="<%= contextPath %>/LDK/panel/QueryPanel.js"></script>
-<script src="<%= contextPath %>/LDK/field/NumberField.js"></script>
-<script src="<%= contextPath %>/LDK/panel/WebpartPanel.js"></script>
-<script src="<%= contextPath %>/LDK/panel/GraphPanel.js"></script>
-<script src="<%= contextPath %>/ehr/data/ClinicalHistoryStore.js"></script>
-<script src="<%= contextPath %>/ehr/panel/ClinicalHistoryPanel.js"></script>
-<script src="<%= contextPath %>/ehr/panel/SnapshotPanel.js"></script>
-<script src="<%= contextPath %>/ehr/panel/SmallFormSnapshotPanel.js"></script>
+<script src="<%= contextPath %>/LDK/Utils.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/Assert.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/AnimalsByNodeTreeStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/panels/AnimalsByNodeTreePanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/panels/AnimalsByNodeReportsContainer.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/panel/ContentResizingPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/ConvertUtils.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/QueryHelper.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/SelectRowsRow.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/panel/QueryPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/field/NumberField.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/panel/WebpartPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/panel/GraphPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/data/ClinicalHistoryStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/panel/ClinicalHistoryPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/panel/SnapshotPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/panel/SmallFormSnapshotPanel.js" nonce="<%=getScriptNonce()%>"></script>
 
-<script src="<%= contextPath %>/ehr/panel/WeightSummaryPanel.js"></script>
-<script src="<%= contextPath %>/ehr/panel/WeightGraphPanel.js"></script>
-<script src="<%= contextPath %>/ehr/utils.js"></script>
-<script src="<%= contextPath %>/ehr/DemographicsCache.js"></script>
-<script src="<%= contextPath %>/ehr/panel/KinShipPanel.js"></script>
-<script src="<%= contextPath %>/LDK/panel/DetailsPanel.js"></script>
-<script src="<%= contextPath %>/LDK/panel/MultiRecordDetailsPanel.js"></script>
-<script src="<%= contextPath %>/ehr/panel/BloodSummaryPanel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/Panel/BloodSummaryPanel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/Panel/ClinicalHistoryPanel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/DemographicsRecord.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/snprcOverrides.js"></script>
+<script src="<%= contextPath %>/ehr/panel/WeightSummaryPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/panel/WeightGraphPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/utils.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/DemographicsCache.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/panel/KinShipPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/panel/DetailsPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/LDK/panel/MultiRecordDetailsPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/ehr/panel/BloodSummaryPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/Panel/BloodSummaryPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/Panel/ClinicalHistoryPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/DemographicsRecord.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/snprcOverrides.js" nonce="<%=getScriptNonce()%>"></script>
 
 <style>
     .x4-grid-tree-node-expanded .location .x4-tree-icon-parent, .location .x4-tree-icon-parent {

From 99e6d27ab18e3a0add91f4fef8dd17404b2081d1 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Thu, 17 Jul 2025 15:13:21 -0700
Subject: [PATCH 5/5] Another csp violation

---
 .../labkey/snprc_ehr/views/AnimalGroups.jsp   | 28 +++++++++----------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalGroups.jsp b/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalGroups.jsp
index 4d5d332a..f056db9a 100644
--- a/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalGroups.jsp
+++ b/snprc_ehr/src/org/labkey/snprc_ehr/views/AnimalGroups.jsp
@@ -30,23 +30,23 @@
 <%
     HtmlString contextPath = getContextPath();
 %>
-<script src="<%= contextPath %>/snprc_ehr/lib/models/GroupCategoryModel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/models/GroupMemberModel.js"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/models/GroupCategoryModel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/models/GroupMemberModel.js" nonce="<%=getScriptNonce()%>"></script>
 
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/GroupCategoriesStore.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/SpeciesStore.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/AnimalGroupsStore.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/AnimalsComboStore.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/YesNoStore.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/GenderStore.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/stores/GroupMembersStore.js"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/GroupCategoriesStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/SpeciesStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/AnimalGroupsStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/AnimalsComboStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/YesNoStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/GenderStore.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/stores/GroupMembersStore.js" nonce="<%=getScriptNonce()%>"></script>
 
-<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupCategoriesGridPanel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupCategoryFormPanel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupMembersGridPanel.js"></script>
-<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupsGridPanel.js"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupCategoriesGridPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupCategoryFormPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupMembersGridPanel.js" nonce="<%=getScriptNonce()%>"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/panels/GroupsGridPanel.js" nonce="<%=getScriptNonce()%>"></script>
 
-<script src="<%= contextPath %>/snprc_ehr/lib/windows/AssignAnimalsToGroupWindow.js"></script>
+<script src="<%= contextPath %>/snprc_ehr/lib/windows/AssignAnimalsToGroupWindow.js" nonce="<%=getScriptNonce()%>"></script>
 <style>
     .trash-btn {
         background-image: url('<%=contextPath%>/snprc_ehr/lib/images/trash-bin.png');