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Merged
labkey-adam merged 4 commits into from
Jun 10, 2025
Merged

Migrate renderDataRegion() and renderView() to HtmlWriter #892

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c6f3bdf
Migrate renderDataRegion() and renderView() to HtmlWriter
labkey-adam Jun 5, 2025
c1fddc8
Migrate WebPartView.renderView() to HtmlWriter
labkey-adam Jun 5, 2025
80ccf14
Migrate MS2 setup webparts
labkey-adam Jun 6, 2025
4d01cc0
Setting can render itself
labkey-adam Jun 7, 2025
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8 changes: 3 additions & 5 deletions luminex/src/org/labkey/luminex/query/ExclusionUIDisplayColumn.java
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Expand Up @@ -30,8 +30,6 @@
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;
import java.util.Set;

import static org.labkey.api.util.DOM.Attribute.alt;
Expand Down Expand Up @@ -103,7 +101,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
boolean canEdit = _container.hasPermission(_user, UpdatePermission.class);
Boolean excluded = (Boolean)ctx.get(getColumnInfo().getFieldKey());

HtmlString img = excluded.booleanValue() ?
DOM.Renderable img = excluded.booleanValue() ?
getImgTag("excluded.png", exclusionComment, id, canEdit) :
getImgTag("included.png", "Click to add a well or replicate group exclusion", id, canEdit);

Expand All @@ -120,7 +118,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
}
}

private HtmlString getImgTag(String png, String titleAlt, String id, boolean canEdit)
private DOM.Renderable getImgTag(String png, String titleAlt, String id, boolean canEdit)
{
DOM._Attributes att = at(src, AppProps.getInstance().getContextPath() + "/luminex/exclusion/" + png)
.at(height, 16)
Expand All @@ -130,6 +128,6 @@ private HtmlString getImgTag(String png, String titleAlt, String id, boolean can
if (canEdit)
att.at(title, titleAlt).at(alt, titleAlt);

return DOM.createHtmlFragment(IMG(att));
return IMG(att);
}
}
69 changes: 52 additions & 17 deletions ms2/src/org/labkey/ms2/pipeline/MS2PipelineProvider.java
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Expand Up @@ -15,21 +15,29 @@
*/
package org.labkey.ms2.pipeline;

import org.labkey.api.data.Container;
import org.labkey.api.module.Module;
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineDirectory;
import org.labkey.api.pipeline.PipelineProvider;
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.util.DOM;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.WebPartView;
import org.labkey.api.data.Container;
import org.labkey.api.module.Module;
import org.labkey.api.writer.HtmlWriter;

import java.io.PrintWriter;
import java.util.Arrays;

import static org.labkey.api.util.DOM.Attribute.style;
import static org.labkey.api.util.DOM.TABLE;
import static org.labkey.api.util.DOM.TD;
import static org.labkey.api.util.DOM.TR;
import static org.labkey.api.util.DOM.at;

/**
*/
public class MS2PipelineProvider extends PipelineProvider
{
static String name = "MS2";
Expand Down Expand Up @@ -66,20 +74,47 @@ public SetupWebPart()
}

@Override
protected void renderView(Object model, PrintWriter out)
protected void renderView(Object model, HtmlWriter out)
{
ViewContext context = getViewContext();
if (!context.getContainer().hasPermission(context.getUser(), InsertPermission.class))
return;
StringBuilder html = new StringBuilder();
html.append("<table><tr><td style=\"font-weight:bold;\">MS2 specific settings:</td></tr>");
ActionURL buttonURL = new ActionURL(PipelineController.SetupClusterSequenceDBAction.class, context.getContainer());
html.append("<tr><td>&nbsp;&nbsp;&nbsp;&nbsp;")
.append("<a href=\"").append(buttonURL.getLocalURIString()).append("\">Set FASTA root</a>")
.append(" - Specify the location on the web server where FASTA sequence files will be located.</td></tr>");
renderSettings(context, "MS2", out, new Setting(buttonURL, "Set FASTA root", "Specify the location on the web server where FASTA sequence files will be located."));
}
}

html.append("</table>");
out.write(html.toString());
public record Setting(ActionURL url, String text, String description)
{
// Standard "Set defaults" setting
public Setting(ActionURL url, String name)
{
this(url, "Set defaults", "Specify the default XML parameters file for " + name + ".");
}

// Render this Setting as a Renderable
private DOM.Renderable renderable()
{
return TR(TD(
HtmlString.NBSP,
HtmlString.NBSP,
HtmlString.NBSP,
HtmlString.NBSP,
LinkBuilder.simpleLink(text(), url()), " - " + description()
));
}
}

public static void renderSettings(ViewContext context, String name, HtmlWriter out, Setting... settings)
{
if (!context.getContainer().hasPermission(context.getUser(), InsertPermission.class))
return;

TABLE(
TR(TD(
at(style, "font-weight:bold;"),
name + "-specific settings:"
)),
Arrays.stream(settings)
.map(Setting::renderable)
).appendTo(out);
}
}
21 changes: 5 additions & 16 deletions ms2/src/org/labkey/ms2/pipeline/comet/CometPipelineProvider.java
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Expand Up @@ -22,24 +22,21 @@
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineActionConfig;
import org.labkey.api.pipeline.PipelineDirectory;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.WebPartView;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.ms2.pipeline.AbstractMS2SearchPipelineProvider;
import org.labkey.ms2.pipeline.AbstractMS2SearchProtocolFactory;
import org.labkey.ms2.pipeline.MS2PipelineManager;
import org.labkey.ms2.pipeline.MS2PipelineProvider;
import org.labkey.ms2.pipeline.MS2PipelineProvider.Setting;
import org.labkey.ms2.pipeline.PipelineController;

import java.io.PrintWriter;
import java.util.Collections;
import java.util.List;

/**
* User: jeckels
* Date: September 17, 2013
*/
public class CometPipelineProvider extends AbstractMS2SearchPipelineProvider<CometSearchTask.Factory>
{
private static final String ACTION_LABEL = "Comet Peptide Search";
Expand Down Expand Up @@ -98,18 +95,11 @@ public SetupWebPart()
}

@Override
protected void renderView(Object model, PrintWriter out)
protected void renderView(Object model, HtmlWriter out)
{
ViewContext context = getViewContext();
if (!context.getContainer().hasPermission(context.getUser(), InsertPermission.class))
return;
StringBuilder html = new StringBuilder();
html.append("<table><tr><td style=\"font-weight:bold;\">Comet specific settings:</td></tr>");
ActionURL setDefaultsURL = new ActionURL(PipelineController.SetCometDefaultsAction.class, context.getContainer());
html.append("<tr><td>&nbsp;&nbsp;&nbsp;&nbsp;")
.append("<a href=\"").append(setDefaultsURL.getLocalURIString()).append("\">Set defaults</a>")
.append(" - Specify the default XML parameters file for Comet.</td></tr></table>");
out.write(html.toString());
MS2PipelineProvider.renderSettings(context, "Comet", out, new Setting(setDefaultsURL, "Comet"));
}
}

Expand All @@ -118,5 +108,4 @@ public AbstractMS2SearchProtocolFactory getProtocolFactory()
{
return CometSearchProtocolFactory.get();
}

}
31 changes: 8 additions & 23 deletions ms2/src/org/labkey/ms2/pipeline/mascot/MascotCPipelineProvider.java
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Expand Up @@ -21,29 +21,23 @@
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineActionConfig;
import org.labkey.api.pipeline.PipelineDirectory;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.WebPartView;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.ms2.MS2Controller;
import org.labkey.ms2.pipeline.AbstractMS2SearchPipelineProvider;
import org.labkey.ms2.pipeline.AbstractMS2SearchProtocolFactory;
import org.labkey.ms2.pipeline.MS2PipelineManager;
import org.labkey.ms2.pipeline.MS2PipelineProvider;
import org.labkey.ms2.pipeline.MS2PipelineProvider.Setting;
import org.labkey.ms2.pipeline.PipelineController;

import java.io.IOException;
import java.io.PrintWriter;
import java.util.Collections;
import java.util.List;

/**
* MascotCPipelineProvider class
* <p/>
* Created: Nov 1, 2005
*
* @author bmaclean
*/
public class MascotCPipelineProvider extends AbstractMS2SearchPipelineProvider<MascotSearchTask.Factory>
{
public static String name = "Mascot";
Expand Down Expand Up @@ -107,23 +101,15 @@ public SetupWebPart()
}

@Override
protected void renderView(Object model, PrintWriter out)
protected void renderView(Object model, HtmlWriter out)
{
ViewContext context = getViewContext();
if (!context.getContainer().hasPermission(context.getUser(), InsertPermission.class))
return;
StringBuilder html = new StringBuilder();
html.append("<table><tr><td style=\"font-weight:bold;\">Mascot specific settings:</td></tr>");
ActionURL setDefaultsURL = new ActionURL(PipelineController.SetMascotDefaultsAction.class, context.getContainer());
html.append("<tr><td>&nbsp;&nbsp;&nbsp;&nbsp;")
.append("<a href=\"").append(setDefaultsURL.getLocalURIString()).append("\">Set defaults</a>")
.append(" - Specify the default XML parameters file for Mascot.</td></tr>");
ActionURL configMascotURL = new ActionURL(MS2Controller.MascotConfigAction.class, context.getContainer());
html.append("<tr><td>&nbsp;&nbsp;&nbsp;&nbsp;")
.append("<a href=\"").append(configMascotURL.getLocalURIString()).append("\">Configure Mascot Server</a>")
.append(" - Specify connection information for the Mascot Server.</td></tr>");
html.append("</table>");
out.write(html.toString());
MS2PipelineProvider.renderSettings(context, "Mascot", out,
new Setting(setDefaultsURL, "Mascot"),
new Setting(configMascotURL, "Configure Mascot Server", "Specify connection information for the Mascot Server.")
);
}
}

Expand All @@ -141,5 +127,4 @@ private MascotConfig ensureMascotConfig(Container container) throws IOException
throw new IOException("Mascot Server has not been configured.");
return config;
}

}
11 changes: 7 additions & 4 deletions ms2/src/org/labkey/ms2/pipeline/mascot/MascotRun.java
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Expand Up @@ -35,9 +35,10 @@
import org.labkey.ms2.peptideview.QueryPeptideMS2RunView;
import org.springframework.web.servlet.ModelAndView;

import java.io.PrintWriter;
import java.util.Map;

import static org.labkey.api.util.DOM.DIV;

public class MascotRun extends MS2Run
{
private String mascotFile;
Expand Down Expand Up @@ -147,11 +148,13 @@ protected ModelAndView getAdditionalPeptideSummaryView(ViewContext viewContext,
}
else
{
return new WebPartView(title) {
return new WebPartView<>(title) {
@Override
protected void renderView(Object model, PrintWriter out)
protected void renderView(Object model, HtmlWriter out)
{
out.write("<div>Use the 'Standard' grouping to view this information.</div>");
DIV(
"Use the 'Standard' grouping to view this information."
).appendTo(out);
}
};
}
Expand Down
21 changes: 4 additions & 17 deletions ms2/src/org/labkey/ms2/pipeline/sequest/SequestPipelineProvider.java
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Expand Up @@ -22,25 +22,20 @@
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineActionConfig;
import org.labkey.api.pipeline.PipelineDirectory;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.WebPartView;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.ms2.pipeline.AbstractMS2SearchPipelineProvider;
import org.labkey.ms2.pipeline.AbstractMS2SearchProtocolFactory;
import org.labkey.ms2.pipeline.MS2PipelineManager;
import org.labkey.ms2.pipeline.MS2PipelineProvider;
import org.labkey.ms2.pipeline.PipelineController;

import java.io.PrintWriter;
import java.util.Collections;
import java.util.List;

/**
* User: billnelson@uky.edu
* Date: Aug 24, 2006
* Time: 12:45:45 PM
*/
public class SequestPipelineProvider extends AbstractMS2SearchPipelineProvider<SequestSearchTask.Factory>
{
private static final String ACTION_LABEL = "Sequest Peptide Search";
Expand Down Expand Up @@ -110,18 +105,11 @@ public SetupWebPart()
}

@Override
protected void renderView(Object model, PrintWriter out)
protected void renderView(Object model, HtmlWriter out)
{
ViewContext context = getViewContext();
if (!context.getContainer().hasPermission(context.getUser(), InsertPermission.class))
return;
StringBuilder html = new StringBuilder();
html.append("<table><tr><td style=\"font-weight:bold;\">Sequest specific settings:</td></tr>");
ActionURL setDefaultsURL = new ActionURL(PipelineController.SetSequestDefaultsAction.class, context.getContainer());
html.append("<tr><td>&nbsp;&nbsp;&nbsp;&nbsp;")
.append("<a href=\"").append(setDefaultsURL.getLocalURIString()).append("\">Set defaults</a>")
.append(" - Specify the default XML parameters file for Sequest.</td></tr></table>");
out.write(html.toString());
MS2PipelineProvider.renderSettings(context, "Sequest", out, new MS2PipelineProvider.Setting(setDefaultsURL, "Sequest"));
}
}

Expand All @@ -130,5 +118,4 @@ public AbstractMS2SearchProtocolFactory getProtocolFactory()
{
return SequestSearchProtocolFactory.get();
}

}
22 changes: 5 additions & 17 deletions ms2/src/org/labkey/ms2/pipeline/tandem/XTandemPipelineProvider.java
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Expand Up @@ -21,25 +21,21 @@
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineActionConfig;
import org.labkey.api.pipeline.PipelineDirectory;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.WebPartView;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.ms2.pipeline.AbstractMS2SearchPipelineProvider;
import org.labkey.ms2.pipeline.AbstractMS2SearchProtocolFactory;
import org.labkey.ms2.pipeline.MS2PipelineManager;
import org.labkey.ms2.pipeline.MS2PipelineProvider;
import org.labkey.ms2.pipeline.MS2PipelineProvider.Setting;
import org.labkey.ms2.pipeline.PipelineController;

import java.io.PrintWriter;
import java.util.Collections;
import java.util.List;

/**
* Created: Nov 1, 2005
*
* @author bmaclean
*/
public class XTandemPipelineProvider extends AbstractMS2SearchPipelineProvider<XTandemSearchTask.Factory>
{
public static String name = "X! Tandem";
Expand Down Expand Up @@ -98,18 +94,11 @@ public SetupWebPart()
}

@Override
protected void renderView(Object model, PrintWriter out)
protected void renderView(Object model, HtmlWriter out)
{
ViewContext context = getViewContext();
if (!context.getContainer().hasPermission(context.getUser(), InsertPermission.class))
return;
StringBuilder html = new StringBuilder();
html.append("<table><tr><td style=\"font-weight:bold;\">X! Tandem specific settings:</td></tr>");
ActionURL setDefaultsURL = new ActionURL(PipelineController.SetTandemDefaultsAction.class, context.getContainer());
html.append("<tr><td>&nbsp;&nbsp;&nbsp;&nbsp;")
.append("<a href=\"").append(setDefaultsURL.getLocalURIString()).append("\">Set defaults</a>")
.append(" - Specify the default XML parameters file for X! Tandem.</td></tr></table>");
out.write(html.toString());
MS2PipelineProvider.renderSettings(context, "X! Tandem", out, new Setting(setDefaultsURL, "X! Tandem"));
}
}

Expand All @@ -118,5 +107,4 @@ public AbstractMS2SearchProtocolFactory getProtocolFactory()
{
return XTandemSearchProtocolFactory.get();
}

}