Epic 5658: HTML filtering improvements

flow/src/org/labkey/flow/controllers/compensation/showCompensation.jsp

@@ -18,16 +18,17 @@
 <%@ page import="org.labkey.api.announcements.DiscussionService" %>
 <%@ page import="org.labkey.api.jsp.JspLoader" %>
 <%@ page import="org.labkey.api.security.permissions.UpdatePermission" %>
+<%@ page import="org.labkey.api.util.HtmlString" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.api.view.JspView" %>
 <%@ page import="org.labkey.flow.FlowPreference" %>
 <%@ page import="org.labkey.flow.analysis.model.CompensationMatrix" %>
 <%@ page import="org.labkey.flow.analysis.web.GraphSpec" %>
 <%@ page import="org.labkey.flow.controllers.FlowParam" %>
-<%@ page import="org.labkey.flow.controllers.well.WellController" %>
+<%@ page import="org.labkey.flow.controllers.well.WellController"%>
 <%@ page import="org.labkey.flow.data.FlowCompensationMatrix"%>
 <%@ page import="org.labkey.flow.data.FlowDataType"%>
-<%@ page import="org.labkey.flow.data.FlowRun"%>
+<%@ page import="org.labkey.flow.data.FlowRun" %>
 <%@ page import="org.labkey.flow.data.FlowWell" %>
 <%@ page import="org.labkey.flow.view.GraphDataRegion" %>
 <%@ page import="org.labkey.flow.view.SetCommentView" %>
@@ -99,7 +100,7 @@
     </tr>
     <% for (int iChannel = 0; iChannel < channelCount; iChannel++)
     {
-        _HtmlString className = getShadeRowClass(iChannel);
+        HtmlString className = getShadeRowClass(iChannel);
     %>
     <tr class="labkey-row">
         <td class="labkey-column-header <%=className%>" style="text-align:right;"><%=h(channelNames[iChannel])%></td>
@@ -111,19 +112,22 @@
     <%}%>
 </table>
 
+<%
+    final FlowRun run = flowComp.getRun();
 
-
-    <% final FlowRun run = flowComp.getRun();
     if (run == null)
     {
         return;
     }
+
     final List<FlowWell> appWells = (List<FlowWell>) run.getDatas(FlowDataType.CompensationControl);
-    final Map<String, FlowWell> wellMap = new HashMap();
+    final Map<String, FlowWell> wellMap = new HashMap<>();
+
     for (FlowWell well : appWells)
     {
         wellMap.put(well.getName(), well);
     }
+
     abstract class Callback
     {
         String title;
@@ -138,22 +142,24 @@
 
     final String graphSize = FlowPreference.graphSize.getValue(request);
     Callback[] callbacks = new Callback[]
+    {
+        new Callback("Uncompensated Graphs")
+        {
+            @Override
+            String render(int iChannel, int iChannelValue)
             {
-                    new Callback("Uncompensated Graphs")
-                    {
-                        String render(int iChannel, int iChannelValue)
-                        {
-                            return compImg(wellMap.get(channelNames[iChannel] + "+"), channelNames[iChannelValue], graphSize);
-                        }
-                    },
-                    new Callback("Compensated Graphs")
-                    {
-                        String render(int iChannel, int iChannelValue)
-                        {
-                            return compImg(wellMap.get(channelNames[iChannel] + "+"), "<" + channelNames[iChannelValue] + ">", graphSize);
-                        }
-                    }
-            };
+                return compImg(wellMap.get(channelNames[iChannel] + "+"), channelNames[iChannelValue], graphSize);
+            }
+        },
+        new Callback("Compensated Graphs")
+        {
+            @Override
+            String render(int iChannel, int iChannelValue)
+            {
+                return compImg(wellMap.get(channelNames[iChannel] + "+"), "<" + channelNames[iChannelValue] + ">", graphSize);
+            }
+        }
+    };
 %>
 <br/>
 <% include(new JspView(JspLoader.createPage(GraphDataRegion.class, "setGraphSize.jsp")), out);%>

flow/src/org/labkey/flow/controllers/executescript/ChooseRunsView.java

@@ -40,11 +40,13 @@ public ChooseRunsView(ChooseRunsToAnalyzeForm form)
         _form = form;
     }
 
+    @Override
     protected boolean canDelete()
     {
         return false;
     }
 
+    @Override
     protected DataRegion createDataRegion()
     {
         DataRegion rgn = new ChooseRunsRegion(_form);
@@ -53,6 +55,7 @@ protected DataRegion createDataRegion()
     }
 
 
+    @Override
     public DataView createDataView()
     {
         DataView ret = super.createDataView();
@@ -68,19 +71,22 @@ public DataView createDataView()
     }
 
 
+    @Override
     protected void populateButtonBar(DataView view, ButtonBar bb)
     {
         view.getDataRegion().setShowRecordSelectors(true);
         bb.add(new ActionButton(AnalysisScriptController.AnalyzeSelectedRunsAction.class, "Analyze selected runs"));
     }
 
 
+    @Override
     protected boolean verboseErrors()
     {
         return false;
     }
 
 
+    @Override
     protected ActionURL urlFor(QueryAction action)
     {
         switch (action)

flow/src/org/labkey/flow/view/FlowQueryView.java

@@ -121,11 +121,13 @@ protected void configureDataRegion(DataRegion rgn)
         rgn.setShowPaginationCount(false);
     }
 
+    @Override
     public User getUser()
     {
         return getViewContext().getUser();
     }
 
+    @Override
     protected void renderView(Object model, HttpServletRequest request, HttpServletResponse response) throws Exception
     {
         if (!isPrintView())
@@ -164,6 +166,7 @@ protected void renderView(Object model, HttpServletRequest request, HttpServletR
         super.renderView(model, request, response);
     }
 
+    @Override
     public FlowQuerySettings getSettings()
     {
         return (FlowQuerySettings) super.getSettings();
@@ -202,18 +205,21 @@ protected boolean subtractBackground()
         return getSettings().getSubtractBackground();
     }
 
+    @Override
     protected URLHelper urlChangeView()
     {
         URLHelper ret = super.urlChangeView();
         ret.deleteParameter(FlowParam.experimentId.toString());
         return ret;
     }
 
+    @Override
     public FlowSchema getSchema()
     {
         return (FlowSchema) super.getSchema();
     }
 
+    @Override
     protected void populateButtonBar(DataView view, ButtonBar bar)
     {
         if (showAnalysisFolderButton() && getSchema().getRun() == null /*&& getSchema().getScript() == null*/)
@@ -329,6 +335,7 @@ else if (queryName.equals(FlowTableType.FCSFiles.toString()) || queryName.equals
         return panelButton;
     }
 
+    @Override
     public List<DisplayColumn> getDisplayColumns()
     {
         if (_displayColumns != null)
@@ -358,6 +365,7 @@ protected boolean hasGraphs()
         return __hasGraphs;
     }
 
+    @Override
     public NavTrailConfig getNavTrailConfig()
     {
         NavTrailConfig ntc = super.getNavTrailConfig();
@@ -391,6 +399,7 @@ else if (schema.getExperiment() != null)
         return ntc;
     }
 
+    @Override
     protected ColumnHeaderType getColumnHeaderType()
     {
         return ColumnHeaderType.FieldKey;

flow/src/org/labkey/flow/webparts/AnalysesWebPart.java

@@ -52,6 +52,7 @@ public AnalysesWebPart(ViewContext context, Portal.WebPart wp)
         setButtonBarPosition(DataRegion.ButtonBarPosition.TOP);
     }
 
+    @Override
     protected void populateButtonBar(DataView view, ButtonBar bar)
     {
         super.populateButtonBar(view, bar);

flow/src/org/labkey/flow/webparts/AnalysisScriptsWebPart.java

@@ -75,6 +75,7 @@ public AnalysisScriptsWebPart(ViewContext portalCtx, Portal.WebPart wp)
         setButtonBarPosition(DataRegion.ButtonBarPosition.TOP);
     }
 
+    @Override
     public List<DisplayColumn> getDisplayColumns()
     {
         List<DisplayColumn> ret = new ArrayList<>();
@@ -93,6 +94,7 @@ public List<DisplayColumn> getDisplayColumns()
         return ret;
     }
 
+    @Override
     protected void populateButtonBar(DataView view, ButtonBar bar)
     {
         ActionButton btnNewScript = new ActionButton("Create Analysis Script", new ActionURL(ScriptController.NewProtocolAction.class, getContainer()));

ms1/src/org/labkey/ms1/view/FeatureDetailView.jsp

@@ -193,14 +193,14 @@
                 String nextFeatureCaption = "Next Feature >>";
 
                 if (model.getPrevFeatureId() < 0)
-                    out.write(PageFlowUtil.generateDisabledButton(prevFeatureCaption));
+                    out.print(PageFlowUtil.generateDisabledButton(prevFeatureCaption));
                 else
                     out.print(button(prevFeatureCaption).href(model.getPrevFeatureUrl()));
 
-                out.write("&nbsp;");
+                out.print("&nbsp;");
 
                 if (model.getNextFeatureId() < 0)
-                    out.write(PageFlowUtil.generateDisabledButton(nextFeatureCaption));
+                    out.print(PageFlowUtil.generateDisabledButton(nextFeatureCaption));
                 else
                     out.print(button(nextFeatureCaption).href(model.getNextFeatureUrl()));
             %>

ms2/src/org/labkey/ms2/compare/SpectraCountRReport.java

@@ -47,11 +47,13 @@ public enum Prop implements ReportDescriptor.ReportProperty
     }
 
 
+    @Override
     public Results generateResults(ViewContext context, boolean allowAsyncQuery) throws Exception
     {
         return getQueryView(context).getResults();
     }
 
+    @Override
     public HttpView renderDataView(ViewContext context) throws Exception
     {
         SpectraCountQueryView view = getQueryView(context);
@@ -101,11 +103,13 @@ private static String getRunList(ViewContext context)
         return context.getActionURL().getParameter(MS2Controller.PeptideFilteringFormElements.runList);
     }
 
+    @Override
     public String getType()
     {
         return TYPE;
     }
 
+    @Override
     public ActionURL getRunReportURL(ViewContext context)
     {
         if (hasValidParameters(context))
@@ -125,6 +129,7 @@ private boolean hasValidParameters(ViewContext context)
         return false;
     }
 
+    @Override
     public ActionURL getEditReportURL(ViewContext context)
     {
         // no editing from the manage page

ms2/src/org/labkey/ms2/mascotConfig.jsp

@@ -1,19 +1,19 @@
 <%
-    /*
-     * Copyright (c) 2015-2017 LabKey Corporation
-     *
-     * Licensed under the Apache License, Version 2.0 (the "License");
-     * you may not use this file except in compliance with the License.
-     * You may obtain a copy of the License at
-     *
-     *     http://www.apache.org/licenses/LICENSE-2.0
-     *
-     * Unless required by applicable law or agreed to in writing, software
-     * distributed under the License is distributed on an "AS IS" BASIS,
-     * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-     * See the License for the specific language governing permissions and
-     * limitations under the License.
-     */
+/*
+ * Copyright (c) 2015-2017 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page import="org.labkey.api.admin.AdminUrls"%>
@@ -22,14 +22,12 @@
 <%@ page import="org.labkey.api.util.PageFlowUtil" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
-<%@ page import="org.labkey.api.view.JspView" %>
 <%@ page import="org.labkey.ms2.MS2Controller" %>
 <%@ page import="org.labkey.ms2.pipeline.mascot.MascotConfig" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 
 <%=formatMissedErrors("form")%>
 <%
-    MS2Controller.MascotSettingsForm bean = ((JspView<MS2Controller.MascotSettingsForm>)HttpView.currentView()).getModelBean();
     Container container = HttpView.currentView().getViewContext().getContainer();
     MascotConfig mascotConfig = MascotConfig.findMascotConfig(container);
     boolean inherited = !mascotConfig.getContainer().equals(container);
@@ -65,7 +63,7 @@
     <input type="hidden" name="reset" value="false" id="resetInput" />
     <table class="lk-fields-table">
         <tr>
-            <td colspan=2>Configure Mascot settings (<%=text(new HelpTopic("configMascot").getSimpleLinkHtml("more info..."))%>)</td>
+            <td colspan=2>Configure Mascot settings (<%=new HelpTopic("configMascot").getSimpleLinkHtml("more info...")%>)</td>
         </tr> <%
             if (inherited) { %>
             <tr>