From 45a5b74088cacd27ae44f382c07f656788d601c7 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Sun, 20 Jul 2025 13:55:14 -0700
Subject: [PATCH 1/2] Link crawler fixes

---
 snprc_ehr/resources/views/ehrAdmin.html       |  4 +-
 .../labkey/snprc_ehr/views/AnimalGroups.jsp   | 28 ++++-----
 .../snprc_ehr/views/AnimalsHierarchy.jsp      | 58 +++++++++----------
 .../snprc_ehr/views/EditLookupTables.jsp      |  4 +-
 .../test/tests/snprc_ehr/SNPRC_EHRTest.java   |  8 +++
 5 files changed, 55 insertions(+), 47 deletions(-)

diff --git a/snprc_ehr/resources/views/ehrAdmin.html b/snprc_ehr/resources/views/ehrAdmin.html
index b98c12c28..719944e0b 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'},
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 4d5d332a4..f056db9ae 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');
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 f2628467a..af5b6af47 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 {
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 d921018ce..fdea7db79 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'},
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 a3f2031ac..98a957415 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 90c45da12963fa259703f6260ff1c1907c017d14 Mon Sep 17 00:00:00 2001
From: Marty Pradere <martyp@labkey.com>
Date: Wed, 30 Jul 2025 09:30:48 -0700
Subject: [PATCH 2/2] comment

---
 .../test/src/org/labkey/test/tests/snprc_ehr/SNPRC_EHRTest.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 98a957415..30664db52 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
@@ -271,7 +271,7 @@ protected void importStudy()
     protected List<String> skipLinksForValidation()
     {
         List<String> links = new ArrayList<>(super.skipLinksForValidation());
-        links.add("snprc_ehr-BirthReport.view");
+        links.add("snprc_ehr-BirthReport.view"); // Not currently rendering in test project
         return links;
     }