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Merged
labkey-adam merged 10 commits into from
Mar 18, 2025
Merged

DisplayColumn refactor #858

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d0373d6
DisplayColumn refactor
labkey-adam Mar 12, 2025
cb2b80a
Remove unused methods from DisplayColumn, refactor
labkey-adam Mar 12, 2025
8676dd0
renderInputHtml(), renderDetailsCaptionCell(), and renderHiddenFormIn…
labkey-adam Mar 13, 2025
60e1f6b
Migrate renderGridCellContents() and renderDetailsCellContents()
labkey-adam Mar 13, 2025
08c6e00
Clean up
labkey-adam Mar 14, 2025
5acf567
CR CR
labkey-adam Mar 14, 2025
2717fb7
Better scripty stuff
labkey-adam Mar 14, 2025
bb7a995
Fix assay upload wizard
labkey-adam Mar 14, 2025
2ad8a49
Don't encode NBSP. Code cleanup. Delete unused class
labkey-jeckels Mar 17, 2025
160e9ca
Clean up a few unnecessary wrappings
labkey-adam Mar 17, 2025
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1 change: 0 additions & 1 deletion flow/src/org/labkey/flow/controllers/executescript/ChooseRunsRegion.java
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Expand Up @@ -33,7 +33,6 @@
import org.labkey.flow.data.FlowWell;

import java.io.File;
import java.io.IOException;
import java.util.List;

import static org.labkey.api.util.DOM.Attribute.colspan;
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23 changes: 12 additions & 11 deletions flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java
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Expand Up @@ -46,7 +46,7 @@
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.SimpleNamedObject;
import org.labkey.api.util.StringExpression;
import org.labkey.api.util.element.Input;
import org.labkey.api.util.element.Input.InputBuilder;
import org.labkey.api.view.GridView;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.flow.analysis.model.ISampleInfo;
Expand Down Expand Up @@ -335,7 +335,7 @@ protected void renderExtraRecordSelectorContent(RenderContext ctx, HtmlWriter ou
{
// Add a hidden input for spring form binding -- if this value is posted, the row was unchecked.
out.write(
new Input.InputBuilder()
new InputBuilder<>()
.type("hidden")
.name(SpringActionController.FIELD_MARKER + getRecordSelectorName(ctx))
.value(0)
Expand Down Expand Up @@ -369,23 +369,23 @@ public MatchedFlagDisplayColumn()
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
{
Boolean match = ctx.get(MATCHED_FLAG_FIELD_KEY, Boolean.class);
if (match != null)
{
out.write("<img src=\"");
out.write(AppProps.getInstance().getContextPath());
oldWriter.write("<img src=\"");
oldWriter.write(AppProps.getInstance().getContextPath());
if (match)
{
out.write("/_images/check.png\" />");
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(out);
PageFlowUtil.popupHelp(HtmlString.of("Matched the previously imported FCS file '" + fileName + "'"), "Matched").appendTo(oldWriter);
}
else
{
out.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(out);
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);
}
}
}
Expand Down Expand Up @@ -504,7 +504,7 @@ protected String getSelectInputDisplayValue(NamedObject entry)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
super.renderGridCellContents(ctx, out);

Expand All @@ -515,7 +515,8 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
String sampleId = ctx.get(SAMPLE_ID_FIELD_KEY, String.class);
for (FlowFCSFile candidate : candidates)
{
out.write("<input type='hidden' name='selectedSamples.rows[" + sampleId + "].candidateFile' value='" + candidate.getRowId() + "'>\n");
out.write(new InputBuilder<>().type("hidden").name("selectedSamples.rows[" + sampleId + "].candidateFile").value(candidate.getRowId()));
out.write("\n");
}
}
}
Expand Down
17 changes: 9 additions & 8 deletions flow/src/org/labkey/flow/query/FlowSchema.java
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Expand Up @@ -74,6 +74,7 @@
import org.labkey.api.util.StringExpressionFactory;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ViewContext;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.flow.analysis.web.FCSAnalyzer;
import org.labkey.flow.analysis.web.StatisticSpec;
import org.labkey.flow.controllers.FlowController;
Expand Down Expand Up @@ -454,7 +455,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
return new DataColumn(colInfo)
{
@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
{
String targetStudyId = (String)getBoundColumn().getValue(ctx);
if (targetStudyId != null && targetStudyId.length() > 0)
Expand All @@ -467,11 +468,11 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
var urlProvider = PageFlowUtil.urlProvider(ProjectUrls.class);
if (study != null && urlProvider != null)
{
out.write("<a href=\"");
out.write(PageFlowUtil.filter(urlProvider.getBeginURL(c)));
out.write("\">");
out.write(study.getLabel().replaceAll(" ", "&nbsp;"));
out.write("</a>");
oldWriter.write("<a href=\"");
oldWriter.write(PageFlowUtil.filter(urlProvider.getBeginURL(c)));
oldWriter.write("\">");
oldWriter.write(study.getLabel().replaceAll(" ", "&nbsp;"));
oldWriter.write("</a>");
}
}
}
Expand Down Expand Up @@ -881,12 +882,12 @@ public String renderURL(RenderContext ctx)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
{
String url = renderURL(ctx);
if (url != null)
{
out.write(PageFlowUtil.iconLink("fa fa-download", null).href(url).toString());
oldWriter.write(PageFlowUtil.iconLink("fa fa-download", null).href(url).toString());
}
}
};
Expand Down
6 changes: 2 additions & 4 deletions flow/src/org/labkey/flow/view/GraphColumn.java
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Expand Up @@ -39,8 +39,6 @@
import org.labkey.flow.controllers.well.WellController;
import org.labkey.flow.query.FlowQuerySettings;

import java.io.Writer;

import static org.labkey.api.util.DOM.Attribute.alt;
import static org.labkey.api.util.DOM.Attribute.height;
import static org.labkey.api.util.DOM.Attribute.src;
Expand Down Expand Up @@ -125,9 +123,9 @@ protected FlowQuerySettings.ShowGraphs showGraphs(RenderContext ctx)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out)
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
renderGraph(ctx, HtmlWriter.of(out));
renderGraph(ctx, out);
}

public void renderGraph(RenderContext ctx, HtmlWriter out)
Expand Down
11 changes: 6 additions & 5 deletions flow/src/org/labkey/flow/webparts/AnalysisScriptsWebPart.java
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Expand Up @@ -35,6 +35,7 @@
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;
Expand Down Expand Up @@ -151,7 +152,7 @@ public FlowScript getScript(RenderContext ctx)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
{
FlowScript script = getScript(ctx);
if (script != null)
Expand All @@ -161,21 +162,21 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
if (script.hasStep(FlowProtocolStep.calculateCompensation))
{
ActionURL url = script.urlFor(AnalysisScriptController.ChooseRunsToAnalyzeAction.class, FlowProtocolStep.calculateCompensation);
out.write("<a href='" + PageFlowUtil.filter(url) + "'>Compensation</a>");
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);
out.write(and);
out.write("<a href='" + PageFlowUtil.filter(url) + "'>Statistics and Graphs</a>");
oldWriter.write(and);
oldWriter.write("<a href='" + PageFlowUtil.filter(url) + "'>Statistics and Graphs</a>");
}

}
else
{
out.write("&nbsp;");
oldWriter.write("&nbsp;");
}
}
}
Expand Down
47 changes: 34 additions & 13 deletions luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java
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Expand Up @@ -18,6 +18,7 @@

import jakarta.servlet.ServletException;
import org.apache.commons.collections4.keyvalue.MultiKey;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.action.LabKeyError;
import org.labkey.api.action.SpringActionController;
Expand Down Expand Up @@ -53,11 +54,13 @@
import org.labkey.api.study.assay.ParticipantVisitResolverType;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.element.Input;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.InsertView;
import org.labkey.api.view.JspView;
import org.labkey.api.view.VBox;
import org.labkey.api.view.ViewServlet;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.luminex.model.Analyte;
import org.labkey.luminex.model.SinglePointControl;
import org.labkey.luminex.model.Titration;
Expand Down Expand Up @@ -85,6 +88,10 @@
import java.util.Set;
import java.util.TreeSet;

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

/**
* Adds Analyte Properties as third wizard step, handles analyte and titration definition input view UI and post, saves
* last entered default values for analyte domain and standard properties
Expand Down Expand Up @@ -421,21 +428,26 @@ else if (titrationEntry.getValue().isStandard())
view.getDataRegion().addGroup(new DisplayColumnGroup(cols, titrationEntry.getKey(), true)
{
@Override
public void writeSameCheckboxCell(RenderContext ctx, Writer out) throws IOException
public void writeSameCheckboxCell(RenderContext ctx, HtmlWriter out)
{
String titrationCellName = PageFlowUtil.filter(getTitrationColumnCellName(titrationEntry.getValue().getName()));
String groupName = ColumnInfo.propNameFromName(getColumns().get(0).getFormFieldName(ctx));
String id = groupName + "CheckBox";
out.write("<td name='" + titrationCellName + "' style='display:" + (hideCell ? "none" : "table-cell") + "' >");
out.write("<input type=checkbox name='" + id + "' id='" + id + "'>");

TD(
at(style, "display:" + (hideCell ? "none" : "table-cell")).
name(titrationCellName),
new Input.InputBuilder<>().type("checkbox").name(id).id(id)

).appendTo(out);

StringBuilder onchange = new StringBuilder("b = this.checked;");
for (DisplayColumn col : getColumns())
{
onchange.append("document.getElementsByName('").append(col.getFormFieldName(ctx)).append("')[0].style.display = b ? 'none' : 'block';\n");
}
onchange.append("if (b) { ").append(groupName).append("Updated(); }");
HttpView.currentPageConfig().addHandler(id, "change", onchange.toString());
out.write("</td>");
}

@Override
Expand Down Expand Up @@ -548,7 +560,7 @@ private boolean toShowStandardCheckboxColumn(boolean errorReshow, Set<Titration>
return (errorReshow && requestParamValue.equals("true")) || (!errorReshow && standardTitrations.contains(standard));
}

private DisplayColumnFactory createAnalytePropertyDisplayColumnFactory(final String inputName, final String displayName)
private DisplayColumnFactory createAnalytePropertyDisplayColumnFactory(final String inputName, final @NotNull String displayName)
{
return colInfo -> new DataColumn(colInfo)
{
Expand All @@ -559,21 +571,30 @@ public String getFormFieldName(RenderContext ctx)
}

@Override
public void renderTitle(RenderContext ctx, Writer out) throws IOException
public HtmlString getTitle(RenderContext ctx)
{
out.write(displayName);
return HtmlString.of(displayName);
}

@Override
public void renderDetailsCaptionCell(RenderContext ctx, Writer out, @Nullable String cls) throws IOException
public void renderDetailsCaptionCell(RenderContext ctx, HtmlWriter out, @Nullable String cls)
{
out.write("<td class=\"control-header-label\">");
Writer oldWriter = out.unwrap();

renderTitle(ctx, out);
String sb = "Type: " + getBoundColumn().getFriendlyTypeName() + "\n";
PageFlowUtil.popupHelp(HtmlString.of(sb), displayName).appendTo(out);
try
{
oldWriter.write("<td class=\"control-header-label\">");

out.write("</td>");
oldWriter.write(getTitle(ctx).toString());
String sb = "Type: " + getBoundColumn().getFriendlyTypeName() + "\n";
PageFlowUtil.popupHelp(HtmlString.of(sb), displayName).appendTo(oldWriter);

oldWriter.write("</td>");
}
catch (IOException e)
{
throw new RuntimeException(e);
}
}
};
}
Expand Down
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