Tag script blocks with nonce

OConnor/resources/views/inventory_specimen_available.html

@@ -1,5 +1,5 @@
 <div id="a"></div>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=scriptNonce%>">
 
     // called once Ext is ready
     var initSpecimenAvailable = function() {

OConnorExperiments/src/org/labkey/oconnorexperiments/view/workbookSearch.jsp

@@ -46,7 +46,7 @@
     <%=button("Search").submit(true)%>
 </form>
 </td></tr></table>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=getScriptNonce()%>">
     Ext.onReady(function(){
         new Ext.form.TextField({
             applyTo: 'wbsearch-id',

OConnorExperiments/test/src/org/labkey/test/tests/OConnorListTest.java

@@ -39,13 +39,13 @@
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class OConnorListTest extends BaseWebDriverTest implements PostgresOnlyTest
 {
-    private static String PROJECT_NAME = "OConnorTestProject";
-    private static String FOLDER_ZIP_FILE = "OConnor_Test.folder.zip";
-    private static String[] MODULES = {"OConnor", "OConnorExperiments"};
-    private static String[] SPECIMEN_TYPES = {"type1", "type2", "type3", "type4"};
-    private static String[] EXPERIMENT_TYPES = {"name1", "name2", "name3", "name4"};
-    private static String[] DISABLED_SPECIMEN_TYPES = {"disabledtype1", "disabledtype2"};
-    private static String[] DISABLED_EXPERIMENT_TYPES = {"disabledname1", "disabledname2"};
+    private static final String PROJECT_NAME = "OConnorTestProject";
+    private static final String FOLDER_ZIP_FILE = "OConnor_Test.folder.zip";
+    private static final String[] MODULES = {"OConnor", "OConnorExperiments"};
+    private static final String[] SPECIMEN_TYPES = {"type1", "type2", "type3", "type4"};
+    private static final String[] EXPERIMENT_TYPES = {"name1", "name2", "name3", "name4"};
+    private static final String[] DISABLED_SPECIMEN_TYPES = {"disabledtype1", "disabledtype2"};
+    private static final String[] DISABLED_EXPERIMENT_TYPES = {"disabledname1", "disabledname2"};
 
     @Nullable
     @Override
@@ -176,7 +176,7 @@ public void testAvailableDDValues()
             assertTextNotPresent(d_option);
         }
         //check available specimen types
-        beginAt("/oconnor/OConnorTestProject/inventory_specimen_available.view?");
+        beginAt("/OConnorTestProject/oconnor-inventory_specimen_available.view");
         waitForText("Inventory Specimen Available");
         shortWait().until(ExpectedConditions.elementToBeClickable(Locator.linkWithSpan("Add new specimens")));
         click(Locator.linkWithSpan("Add new specimens"));

genotyping/resources/views/illuminaSampleSheetExport.html

@@ -1,8 +1,8 @@
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=scriptNonce%>">
     LABKEY.requiresExt4ClientAPI();
     LABKEY.requiresScript('/genotyping/IlluminaExportPanel.js');
 </script>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=scriptNonce%>">
 
 Ext4.onReady(function(){
     var webpart = <%=webpartContext%>;

genotyping/src/org/labkey/genotyping/GenotypingController.java

@@ -2247,7 +2247,7 @@ private String stripSubType(String name, STRDiscrepancies form)
                 return name;
             }
             // Strip off subtype suffix, if any
-            while (name.length() > 0 && !Character.isDigit(name.charAt(name.length() - 1)))
+            while (!name.isEmpty() && !Character.isDigit(name.charAt(name.length() - 1)))
             {
                 name = name.substring(0, name.length() - 1);
             }
@@ -2266,19 +2266,19 @@ public void addNavTrail(NavTree root)
     public static class STRDiscrepancies extends ProtocolIdForm
     {
         private boolean ignoreSubtype;
-        private Map<String, Set<String>> discrepancies;
+        private final Map<String, Set<String>> discrepancies;
 
         public STRDiscrepancies()
         {
             this.discrepancies = new TreeMap<>();
         }
 
-        public void insertDiscrepancy(String name, String disrepancy)
+        public void insertDiscrepancy(String name, String discrepancy)
         {
             if (!discrepancies.containsKey(name))
                 discrepancies.put(name, new TreeSet<>());
             //NOTE: this might be better as a set...
-            discrepancies.get(name).add(disrepancy);
+            discrepancies.get(name).add(discrepancy);
         }
 
         public boolean isEmpty()
@@ -2303,7 +2303,7 @@ public void setIgnoreSubtype(boolean ignoreSubtype)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class AggregatedResultsReportAction extends BaseAssayAction<ProtocolIdForm>
+    public static class AggregatedResultsReportAction extends BaseAssayAction<ProtocolIdForm>
     {
         private ExpProtocol _protocol;
 
@@ -2338,8 +2338,6 @@ public ModelAndView getView(AssignmentForm form, BindException errors)
             if (form.getRowId() == -1)
                 errors.reject(ERROR_MSG, "Error: Please provide an rowId for the AnimalAnalysis table.");
 
-
-
             return new JspView<>("/org/labkey/genotyping/view/editHaplotypeAssignment.jsp", form, errors);
         }
 

genotyping/src/org/labkey/genotyping/view/analyze.jsp

@@ -42,7 +42,7 @@
 <labkey:errors/>
 <div id="form"></div>
 
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=getScriptNonce()%>">
     var samples = [
 <%
     String sep = "";

genotyping/src/org/labkey/genotyping/view/configure.jsp

@@ -45,7 +45,7 @@
     ActionURL haplotypeEditDomainURL = PropertyService.get().getDomainKind(schema.getDomainURI(GenotypingQuerySchema.TableType.Haplotype.name())).urlCreateDefinition(GenotypingQuerySchema.NAME, GenotypingQuerySchema.TableType.Haplotype.name(), getContainer(), getUser());
     haplotypeEditDomainURL.addReturnURL(getActionURL());
 %>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=getScriptNonce()%>">
     var queries = {};
 
     function update(query, hiddenId, divId)

genotyping/src/org/labkey/genotyping/view/editHaplotypeAssignment.jsp

@@ -48,7 +48,7 @@
 <%
     }
 %>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=getScriptNonce()%>">
 
     Ext4.onReady(function(){
         LABKEY.Query.selectRows({

genotyping/src/org/labkey/genotyping/view/haplotypeAssignmentReport.jsp

@@ -44,7 +44,7 @@
 <br/>
 <div id='<%=h(queryWebPartDivId)%>'></div>
 
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=getScriptNonce()%>">
 
     Ext4.onReady(function(){
         // lookup the Animal IDs if there were any selected from the results grid

genotyping/src/org/labkey/genotyping/view/importHaplotypeAssignments.jsp

@@ -39,7 +39,7 @@
 %>
 <div id="<%=h(copyPasteDivId)%>"></div>
 
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=getScriptNonce()%>">
     var expectedHeaders = [];
     <%
     for (Map.Entry<String, HaplotypeColumnMappingProperty> property : HaplotypeAssayProvider.getColumnMappingProperties(bean.getProtocol()).entrySet())

genotyping/src/org/labkey/genotyping/view/strDiscrepancies.jsp

@@ -35,10 +35,10 @@
 <p>
     <form method="GET" action="<%= h(reportURL)%>">
         <input type="hidden" name="rowId" value="<%= model.getRowId() %>" />
-        <input type="checkbox" name="ignoreSubtype" <%= text(model.isIgnoreSubtype() ? "checked" : "") %> onclick="this.form.submit();" /> Ignore haplotype subtype distinctions ('a', 'b', 'c', etc suffixes on the haplotype names)
+        <input type="checkbox" name="ignoreSubtype" id="ignoreSubtype"<%=checked(model.isIgnoreSubtype())%>/> Ignore haplotype subtype distinctions ('a', 'b', 'c', etc suffixes on the haplotype names)
     </form>
 </p>
-
+<%addHandler("ignoreSubtype", "click", "this.form.submit();");%>
 <table class="labkey-data-region labkey-show-borders">
     <tr>
         <td class="labkey-column-header">Animal Id</td>