Migrate to renderGridCellContents(RenderContext, HtmlWriter)

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

@@ -44,10 +44,10 @@
 import org.labkey.api.security.User;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.HtmlString;
+import org.labkey.api.util.InputBuilder;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.SimpleNamedObject;
 import org.labkey.api.util.StringExpression;
-import org.labkey.api.util.InputBuilder;
 import org.labkey.api.view.GridView;
 import org.labkey.api.writer.HtmlWriter;
 import org.labkey.flow.analysis.model.ISampleInfo;
@@ -58,8 +58,6 @@
 import org.labkey.flow.util.KeywordUtil;
 import org.springframework.validation.Errors;
 
-import java.io.IOException;
-import java.io.Writer;
 import java.sql.ResultSet;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -72,6 +70,10 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import static org.labkey.api.util.DOM.Attribute.src;
+import static org.labkey.api.util.DOM.IMG;
+import static org.labkey.api.util.DOM.at;
+
 public class SamplesConfirmGridView extends GridView
 {
     public static final Logger LOG = LogManager.getLogger(SamplesConfirmGridView.class);
@@ -368,23 +370,23 @@ public MatchedFlagDisplayColumn()
         }
 
         @Override
-        public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
+        public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
         {
             Boolean match = ctx.get(MATCHED_FLAG_FIELD_KEY, Boolean.class);
             if (match != null)
             {
-                oldWriter.write("<img src=\"");
-                oldWriter.write(AppProps.getInstance().getContextPath());
+                IMG(
+                    at(src, AppProps.getInstance().getContextPath() + (match ? "/_images/check.png" : "/_images/cancel.png"))
+                ).appendTo(out);
+
                 if (match)
                 {
-                    oldWriter.write("/_images/check.png\" />");
                     String fileName = ctx.get(SAMPLE_NAME_FIELD_KEY, String.class);
-                    PageFlowUtil.popupHelp(HtmlString.of("Matched the previously imported FCS file '" + fileName + "'"), "Matched").appendTo(oldWriter);
+                    out.write(PageFlowUtil.popupHelp(HtmlString.of("Matched the previously imported FCS file '" + fileName + "'"), "Matched"));
                 }
                 else
                 {
-                    oldWriter.write("/_images/cancel.png\" />");
-                    PageFlowUtil.popupHelp(HtmlString.of("Failed to match a previously imported FCS file. Please manually select a matching FCS file or skip importing this row."), "Not matched").appendTo(oldWriter);
+                    out.write(PageFlowUtil.popupHelp(HtmlString.of("Failed to match a previously imported FCS file. Please manually select a matching FCS file or skip importing this row."), "Not matched"));
                 }
             }
         }

flow/src/org/labkey/flow/query/FlowSchema.java

@@ -16,6 +16,7 @@
 
 package org.labkey.flow.query;
 
+import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -25,7 +26,28 @@
 import org.labkey.api.assay.AssayService;
 import org.labkey.api.cache.Cache;
 import org.labkey.api.cache.CacheManager;
-import org.labkey.api.data.*;
+import org.labkey.api.data.AbstractTableInfo;
+import org.labkey.api.data.BaseColumnInfo;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.DataColumn;
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DisplayColumn;
+import org.labkey.api.data.DisplayColumnFactory;
+import org.labkey.api.data.FilterInfo;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.MaterializedQueryHelper;
+import org.labkey.api.data.MutableColumnInfo;
+import org.labkey.api.data.NullColumnInfo;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.Table;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.WrappedColumnInfo;
 import org.labkey.api.exp.PropertyColumn;
 import org.labkey.api.exp.PropertyDescriptor;
 import org.labkey.api.exp.api.DataType;
@@ -70,6 +92,8 @@
 import org.labkey.api.study.assay.SpecimenForeignKey;
 import org.labkey.api.study.publish.StudyPublishService;
 import org.labkey.api.util.ContainerContext;
+import org.labkey.api.util.HtmlString;
+import org.labkey.api.util.LinkBuilder;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.StringExpressionFactory;
 import org.labkey.api.view.ActionURL;
@@ -100,10 +124,7 @@
 import org.labkey.flow.view.FlowQueryView;
 import org.springframework.validation.BindException;
 
-import jakarta.servlet.http.HttpServletRequest;
 import java.beans.PropertyChangeEvent;
-import java.io.IOException;
-import java.io.Writer;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -447,37 +468,26 @@ public TableInfo getLookupTableInfo()
         return ret;
     }
 
-    private static final DisplayColumnFactory _targetStudyDisplayColumnFactory = new DisplayColumnFactory()
+    private static final DisplayColumnFactory _targetStudyDisplayColumnFactory = colInfo -> new DataColumn(colInfo)
     {
         @Override
-        public DisplayColumn createRenderer(ColumnInfo colInfo)
+        public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
         {
-            return new DataColumn(colInfo)
+            String targetStudyId = (String)getBoundColumn().getValue(ctx);
+            if (targetStudyId != null && !targetStudyId.isEmpty())
             {
-                @Override
-                public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
+                Container c = ContainerManager.getForId(targetStudyId);
+                if (c != null)
                 {
-                    String targetStudyId = (String)getBoundColumn().getValue(ctx);
-                    if (targetStudyId != null && targetStudyId.length() > 0)
+                    var ss = StudyService.get();
+                    Study study = null == ss ? null : ss.getStudy(c);
+                    var urlProvider = PageFlowUtil.urlProvider(ProjectUrls.class);
+                    if (study != null && urlProvider != null)
                     {
-                        Container c = ContainerManager.getForId(targetStudyId);
-                        if (c != null)
-                        {
-                            var ss = StudyService.get();
-                            Study study = null == ss ? null : ss.getStudy(c);
-                            var urlProvider = PageFlowUtil.urlProvider(ProjectUrls.class);
-                            if (study != null && urlProvider != null)
-                            {
-                                oldWriter.write("<a href=\"");
-                                oldWriter.write(PageFlowUtil.filter(urlProvider.getBeginURL(c)));
-                                oldWriter.write("\">");
-                                oldWriter.write(study.getLabel().replaceAll(" ", "&nbsp;"));
-                                oldWriter.write("</a>");
-                            }
-                        }
+                        LinkBuilder.simpleLink(HtmlString.unsafe(PageFlowUtil.filter(study.getLabel()).replaceAll(" ", "&nbsp;")), urlProvider.getBeginURL(c)).appendTo(out);
                     }
                 }
-            };
+            }
         }
     };
 
@@ -487,6 +497,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
      *
      *  basically rejoins what is effectively a vertically partitioned table (ACKK)
      */
+    // TODO: Delete this? Unused!
     class JoinFlowDataTable extends AbstractTableInfo implements ExpDataTable
     {
         final ExpDataTable _expData;
@@ -882,12 +893,12 @@ public String renderURL(RenderContext ctx)
                         }
 
                         @Override
-                        public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
+                        public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
                         {
                             String url = renderURL(ctx);
                             if (url != null)
                             {
-                                oldWriter.write(PageFlowUtil.iconLink("fa fa-download", null).href(url).toString());
+                                out.write(PageFlowUtil.iconLink("fa fa-download", null).href(url));
                             }
                         }
                     };

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

@@ -17,7 +17,6 @@
 package org.labkey.flow.webparts;
 
 import org.jetbrains.annotations.NotNull;
-import org.labkey.api.stats.ColumnAnalyticsProvider;
 import org.labkey.api.data.ActionButton;
 import org.labkey.api.data.ButtonBar;
 import org.labkey.api.data.ColumnInfo;
@@ -28,26 +27,20 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.query.AliasedColumn;
 import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.stats.ColumnAnalyticsProvider;
 import org.labkey.api.util.HtmlString;
-import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.DataView;
 import org.labkey.api.view.Portal;
 import org.labkey.api.view.SimpleWebPartFactory;
 import org.labkey.api.view.ViewContext;
-import org.labkey.api.writer.HtmlWriter;
 import org.labkey.flow.controllers.editscript.ScriptController;
-import org.labkey.flow.controllers.executescript.AnalysisScriptController;
-import org.labkey.flow.data.FlowProtocolStep;
-import org.labkey.flow.data.FlowScript;
 import org.labkey.flow.query.FlowQuerySettings;
 import org.labkey.flow.query.FlowSchema;
 import org.labkey.flow.query.FlowTableType;
 import org.labkey.flow.view.FlowQueryView;
 import org.springframework.web.servlet.mvc.Controller;
 
-import java.io.IOException;
-import java.io.Writer;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -87,8 +80,6 @@ public List<DisplayColumn> getDisplayColumns()
         ColumnInfo colRowId = new AliasedColumn("RowId", table.getColumn("RowId"));
         if (getContainer().hasPermission(getUser(), UpdatePermission.class))
         {
-            // PerformAnalsysisColumn is too expensive
-            //ret.add(new PerformAnalysisColumn(colRowId));
             ret.add(new ScriptActionColumn("Copy", ScriptController.CopyAction.class, colRowId));
             ret.add(new ScriptActionColumn("Delete", ScriptController.DeleteAction.class, colRowId));
         }
@@ -131,54 +122,4 @@ public List<ColumnAnalyticsProvider> getAnalyticsProviders()
             return Collections.emptyList();
         }
     }
-
-    public class PerformAnalysisColumn extends DataColumn
-    {
-        public PerformAnalysisColumn(ColumnInfo col)
-        {
-            super(col);
-            setCaption("Execute Script");
-            setNoWrap(true);
-            setWidth("auto");
-        }
-
-        public FlowScript getScript(RenderContext ctx)
-        {
-            Object value = getBoundColumn().getValue(ctx);
-            if (!(value instanceof Number))
-                return null;
-            int id = ((Number) value).intValue();
-            return FlowScript.fromScriptId(id);
-        }
-
-        @Override
-        public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
-        {
-            FlowScript script = getScript(ctx);
-            if (script != null)
-            {
-                String and = "";
-
-                if (script.hasStep(FlowProtocolStep.calculateCompensation))
-                {
-                    ActionURL url = script.urlFor(AnalysisScriptController.ChooseRunsToAnalyzeAction.class, FlowProtocolStep.calculateCompensation);
-                    oldWriter.write("<a href='" + PageFlowUtil.filter(url) + "'>Compensation</a>");
-                    and = "<br>";
-                }
-
-                if (script.hasStep(FlowProtocolStep.analysis))
-                {
-                    ActionURL url = script.urlFor(AnalysisScriptController.ChooseRunsToAnalyzeAction.class, FlowProtocolStep.analysis);
-                    oldWriter.write(and);
-                    oldWriter.write("<a href='" + PageFlowUtil.filter(url) + "'>Statistics and Graphs</a>");
-                }
-
-            }
-            else
-            {
-                oldWriter.write("&nbsp;");
-            }
-        }
-    }
-
 }

luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java

@@ -121,7 +121,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
             return new JavaScriptDisplayColumn(colInfo, List.of("clientapi/ext3", "vis/vis", "luminex/LeveyJenningsPlotHelpers.js", "luminex/LeveyJenningsReport.css"))
             {
                 @Override
-                public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out)
+                public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
                 {
                     int protocolId = schema.getProtocol().getRowId();
                     int analyte = (int)ctx.get("analyte");
@@ -131,7 +131,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
 
                     HtmlString html = HtmlString.unsafe(String.format("<img src='%s' width='27' height='20'>", AppProps.getInstance().getContextPath() + "/luminex/ljPlotIcon.png"));
 
-                    renderLink(oldWriter, html, onClick, null);
+                    renderLink(out, html, onClick, null);
                 }
 
                 @Override

luminex/src/org/labkey/luminex/query/AnalyteTitrationTable.java

@@ -54,17 +54,11 @@
 import org.labkey.luminex.model.GuideSet;
 import org.labkey.luminex.model.Titration;
 
-import java.io.IOException;
-import java.io.Writer;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 
-/**
- * User: jeckels
- * Date: 7/8/11
- */
 public class AnalyteTitrationTable extends AbstractCurveFitPivotTable
 {
     public AnalyteTitrationTable(final LuminexProtocolSchema schema, ContainerFilter cf, boolean filter)
@@ -126,7 +120,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
             return new JavaScriptDisplayColumn(colInfo, List.of("clientapi/ext3", "vis/vis", "luminex/LeveyJenningsPlotHelpers.js", "luminex/LeveyJenningsReport.css"))
             {
                 @Override
-                public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
+                public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
                 {
                     int protocolId = schema.getProtocol().getRowId();
                     int analyte = (int)ctx.get("analyte");

luminex/src/org/labkey/luminex/query/ExclusionUIDisplayColumn.java

@@ -89,7 +89,7 @@ public HtmlString getTitle(RenderContext ctx)
     }
 
     @Override
-    public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
+    public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
     {
         String type = (String)ctx.get(_typeFieldKey);
         String description = (String)ctx.get(_descriptionFieldKey);
@@ -112,11 +112,11 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
             // add onclick handler to call the well exclusion window creation function
             String onClick = "openExclusionsWellWindow(" + _protocolId + ", " + runId + ", " + dataId + ", " +
                 jsString(wellID) + ", " + (description == null ? null : jsString(description)) + ", " + jsString(type) + ");";
-            LinkBuilder.simpleLink(img).href("#").onClick(onClick).appendTo(oldWriter);
+            LinkBuilder.simpleLink(img).href("#").onClick(onClick).appendTo(out);
         }
         else
         {
-            oldWriter.write(img.toString());
+            out.write(img);
         }
     }