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Merged
labkey-adam merged 1 commit into from
Apr 14, 2025
Merged

Simplify and expand use of LinkBuilder factory methods #875

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6 changes: 3 additions & 3 deletions flow/src/org/labkey/flow/controllers/attribute/summary.jsp
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Expand Up @@ -63,7 +63,7 @@
<% } %>
</td>
<td>
<%=link("edit").href(editURL.clone().addParameter(AttributeController.Param.rowId, primary._rowId))%>
<%=link("edit", editURL.clone().addParameter(AttributeController.Param.rowId, primary._rowId))%>
<%--<% if (totalCount == 0) { %>--%>
<%--<labkey:link href='<%=deleteURL.clone().addParameter(AttributeController.Param.rowId, primary._rowId)%>' text="delete"/>--%>
<%--<% } %>--%>
Expand All @@ -86,7 +86,7 @@
<% } %>
</td>
<td>
<%=link("edit").href(editURL.clone().addParameter(AttributeController.Param.rowId, alias._rowId))%>
<%=link("edit", editURL.clone().addParameter(AttributeController.Param.rowId, alias._rowId))%>
<%--<labkey:link href='<%=deleteURL.clone().addParameter(AttributeController.Param.rowId, alias._rowId)%>' text="delete"/>--%>
<%--<labkey:link href='<%=makePrimaryURL.clone().addParameter(AttributeController.Param.rowId, alias._rowId)%>' text="make primary"/>--%>
</td>
Expand All @@ -98,7 +98,7 @@
<td style="padding-left: 1.5em;">
</td>
<td>
<%=link("create alias").href(aliasURL.clone().addParameter(AttributeController.Param.rowId, primary._rowId))%>
<%=link("create alias", aliasURL.clone().addParameter(AttributeController.Param.rowId, primary._rowId))%>
</td>
<td>&nbsp;</td>
</tr>
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/compensation/showCompensation.jsp
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Expand Up @@ -191,7 +191,7 @@
<%}%>
</table>
<% } %>
<%=link("Download").href(flowComp.urlDownload()).nofollow()%><br>
<%=link("Download", flowComp.urlDownload()).nofollow()%><br>
<%
DiscussionService service = DiscussionService.get();
if (service != null)
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8 changes: 4 additions & 4 deletions flow/src/org/labkey/flow/controllers/editscript/showCompensationCalculation.jsp
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Expand Up @@ -58,9 +58,9 @@
<br/>
<p>
This compensation calculation may be edited in a number of ways:<br>
<%=link("Upload a FlowJo workspace").href(form.urlFor(ScriptController.UploadCompensationCalculationAction.class))%><br>
<%=link("Switch keywords or gates").href(form.urlFor(ScriptController.ChooseCompensationRunAction.class))%><br>
<%=link("Rename gates").href(form.getFlowScript().urlFor(ScriptController.EditGateTreeAction.class, FlowProtocolStep.calculateCompensation))%><br>
<%=link("Script main page").href(form.urlFor(AnalysisScriptController.BeginAction.class))%>
<%=link("Upload a FlowJo workspace", form.urlFor(ScriptController.UploadCompensationCalculationAction.class))%><br>
<%=link("Switch keywords or gates", form.urlFor(ScriptController.ChooseCompensationRunAction.class))%><br>
<%=link("Rename gates", form.getFlowScript().urlFor(ScriptController.EditGateTreeAction.class, FlowProtocolStep.calculateCompensation))%><br>
<%=link("Script main page", form.urlFor(AnalysisScriptController.BeginAction.class))%>
</p>
<% } %>
4 changes: 2 additions & 2 deletions flow/src/org/labkey/flow/controllers/executescript/showScript.jsp
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Expand Up @@ -69,7 +69,7 @@ The analysis section describes which gates in the analysis, as well as the stati
<% if (script.getRunCount() > 0) {
boolean showRuns = FlowPreference.showRuns.getBooleanValue(request);
if (showRuns) {
%><%=link("Hide Runs").href(url.clone().replaceParameter("showRuns", "0"))%><br/><%
%><%=link("Hide Runs", url.clone().replaceParameter("showRuns", "0"))%><br/><%

BindException errors = new NullSafeBindException(new Object(), "fake");
FlowSchema schema = new FlowSchema(context);
Expand All @@ -88,7 +88,7 @@ The analysis section describes which gates in the analysis, as well as the stati
view.getSettings().getBaseFilter().addCondition(FieldKey.fromParts("AnalysisScript", "RowId"), script.getScriptId(), CompareType.EQUAL);
include(view, out);
} else {
%><%=link("Show Runs").href(url.clone().replaceParameter("showRuns", "1"))%><%
%><%=link("Show Runs", url.clone().replaceParameter("showRuns", "1"))%><%
}
} %>
</div>
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30 changes: 15 additions & 15 deletions flow/src/org/labkey/flow/controllers/protocol/showProtocol.jsp
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Expand Up @@ -36,36 +36,36 @@
Upload sample information and match samples with FCSFiles.<br>
<% if (sampleType == null) { %>
No samples have been uploaded in this folder.<br>
<%=link("Create new sample type").href(protocol.urlCreateSampleType())%><br>
<%=link("Create new sample type", protocol.urlCreateSampleType())%><br>
<% } else { %>
<%=link("Show sample type").href(protocol.getSampleTypeDetailsURL(sampleType, getContainer()))%><br>
<%=link("Show samples joined to FCS Files").href(protocol.urlShowSamples())%><br>
<%=link("Upload more samples from a spreadsheet").href(protocol.urlUploadSamples())%><br>
<% if (protocol.getSampleTypeJoinFields().size() != 0) { %>
<%=link("Modify sample join fields").href(protocol.urlFor(JoinSampleTypeAction.class))%><br>
<%=link("Show sample type", protocol.getSampleTypeDetailsURL(sampleType, getContainer()))%><br>
<%=link("Show samples joined to FCS Files", protocol.urlShowSamples())%><br>
<%=link("Upload more samples from a spreadsheet", protocol.urlUploadSamples())%><br>
<% if (!protocol.getSampleTypeJoinFields().isEmpty()) { %>
<%=link("Modify sample join fields", protocol.urlFor(JoinSampleTypeAction.class))%><br>
<% } else { %>
<%=link("Join samples to FCS File Data").href(protocol.urlFor(JoinSampleTypeAction.class))%><br>
<%=link("Join samples to FCS File Data", protocol.urlFor(JoinSampleTypeAction.class))%><br>
<% } %>
<% } %>
</p>
<p><b>FCS Analysis Display Names</b><br>
When you analyze an FCS file, the FCS analysis can be given a name composed from keyword values from the FCS file.<br>
<%=link("Change FCS Analyses Names").href(protocol.urlFor(ProtocolController.EditFCSAnalysisNameAction.class))%>
<%=link("Change FCS Analyses Names", protocol.urlFor(ProtocolController.EditFCSAnalysisNameAction.class))%>
</p>
<p><b>FCS Analysis Filter</b><br>
You can choose to only analyze FCS files where the keywords match certain criteria.<br>
<%=link("Edit FCS Analysis Filter").href(protocol.urlFor(ProtocolController.EditFCSAnalysisFilterAction.class))%>
<%=link("Edit FCS Analysis Filter", protocol.urlFor(ProtocolController.EditFCSAnalysisFilterAction.class))%>
</p>
<p><b>Metadata</b><br>
Identify participant visit/date columns and
columns used to subtract background from stimulated wells.<br>
<%=link("Edit Metadata").href(protocol.urlFor(ProtocolController.EditICSMetadataAction.class))%>
<%=link("Edit Metadata", protocol.urlFor(ProtocolController.EditICSMetadataAction.class))%>
</p>
<p><b>Manage Names and Aliases</b><br>
Create and remove names and aliases for Keywords, Statistics, and Graphs.<br>
<%=link("Case sensitivity").href(protocol.urlFor(AttributeController.CaseSensitivityAction.class).addReturnUrl(getActionURL()))%><br/>
<%=link("Delete Unused").href(protocol.urlFor(AttributeController.DeleteUnusedAction.class).addReturnUrl(getActionURL()))%><br/>
<%=link("Manage Keywords").href(protocol.urlFor(AttributeController.SummaryAction.class).addParameter(AttributeController.Param.type, AttributeType.keyword.name()))%><br/>
<%=link("Manage Statistics").href(protocol.urlFor(AttributeController.SummaryAction.class).addParameter(AttributeController.Param.type, AttributeType.statistic.name()))%><br/>
<%=link("Manage Graphs").href(protocol.urlFor(AttributeController.SummaryAction.class).addParameter(AttributeController.Param.type, AttributeType.graph.name()))%><br/>
<%=link("Case sensitivity", protocol.urlFor(AttributeController.CaseSensitivityAction.class).addReturnUrl(getActionURL()))%><br/>
<%=link("Delete Unused", protocol.urlFor(AttributeController.DeleteUnusedAction.class).addReturnUrl(getActionURL()))%><br/>
<%=link("Manage Keywords", protocol.urlFor(AttributeController.SummaryAction.class).addParameter(AttributeController.Param.type, AttributeType.keyword.name()))%><br/>
<%=link("Manage Statistics", protocol.urlFor(AttributeController.SummaryAction.class).addParameter(AttributeController.Param.type, AttributeType.statistic.name()))%><br/>
<%=link("Manage Graphs", protocol.urlFor(AttributeController.SummaryAction.class).addParameter(AttributeController.Param.type, AttributeType.graph.name()))%><br/>
</p>
6 changes: 3 additions & 3 deletions flow/src/org/labkey/flow/controllers/protocol/showSamples2.jsp
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Expand Up @@ -75,14 +75,14 @@

<% if (st == null) { %>
No samples have been imported in this folder.<br>
<%=link("Create sample type").href(protocol.urlCreateSampleType())%><br>
<%=link("Create sample type", protocol.urlCreateSampleType())%><br>
<% } else { %>
<p>
There are <a id="all-samples" href="<%=h(protocol.getSampleTypeDetailsURL(st, getContainer()))%>"><%=sampleCount%> sample descriptions</a> in this folder.<br>

<% if (sampleTypeJoinFields.size() == 0) { %>
<% if (sampleTypeJoinFields.isEmpty()) { %>
<p>
<%=link("Join samples to FCS File Data").href(protocol.urlFor(JoinSampleTypeAction.class))%><br>
<%=link("Join samples to FCS File Data", protocol.urlFor(JoinSampleTypeAction.class))%><br>
No sample join fields have been defined yet. The samples are linked to the FCS files using keywords. When new samples are added or FCS files are loaded, new links will be created.
<% } else { %>
Samples are joined to FCSFiles by the following properties (<a href="<%=h(protocol.urlFor(JoinSampleTypeAction.class))%>">edit</a>):
Expand Down
2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/controllers/run/download.jsp
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Expand Up @@ -48,7 +48,7 @@
%>
</ul>
<br>
<%=link("Download FCS Files anyway?").href(model.run.urlFor(RunController.DownloadAction.class).addParameter("skipMissing", true))%>
<%=link("Download FCS Files anyway?", model.run.urlFor(RunController.DownloadAction.class).addParameter("skipMissing", true))%>
</p>

<p>
Expand Down
3 changes: 2 additions & 1 deletion flow/src/org/labkey/flow/reports/PositivityFlowReport.java
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Expand Up @@ -26,6 +26,7 @@
import org.labkey.api.query.AliasManager;
import org.labkey.api.query.FieldKey;
import org.labkey.api.reports.report.ReportDescriptor;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Tuple3;
import org.labkey.api.view.ActionURL;
Expand Down Expand Up @@ -178,7 +179,7 @@ public HttpView renderReport(ViewContext context) throws Exception

return HtmlView.unsafe(
"<p class='labkey-error'>Positivity report requires configuring flow experiment metadata for study and background information before running.</p>" +
PageFlowUtil.link("Edit Metadata").href(editICSMetadataURL));
LinkBuilder.labkeyLink("Edit Metadata", editICSMetadataURL));
}
else
{
Expand Down
2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/reports/editPositivityReport.jsp
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Expand Up @@ -70,7 +70,7 @@
The positivity report requires metadata describing the sample and background information
of the flow experiment before it can be run.
<br>
<%=link("Edit Metadata").href(editICSMetadataURL)%>
<%=link("Edit Metadata", editICSMetadataURL)%>
</p>
<% } %>

Expand Down
2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/query/ExclusionUIDisplayColumn.java
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Expand Up @@ -112,7 +112,7 @@ 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) + ");";
new LinkBuilder(img).href("#").onClick(onClick).clearClasses().appendTo(oldWriter);
LinkBuilder.simpleLink(img).href("#").onClick(onClick).appendTo(oldWriter);
}
else
{
Expand Down
3 changes: 1 addition & 2 deletions luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java
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Expand Up @@ -662,9 +662,8 @@ else if (pdfs.size() > 1)
}

HtmlString image = HtmlString.unsafe("<img src=\"" + AppProps.getInstance().getContextPath() + "/_images/sigmoidal_curve.png\" />");
new LinkBuilder(image)
LinkBuilder.simpleLink(image)
.onMouseOver("return showHelpDiv(this, 'Titration Curves', " + PageFlowUtil.jsString(PageFlowUtil.filter(sb.toString())) + ");")
.clearClasses()
.appendTo(oldWriter);
}
}
Expand Down
3 changes: 1 addition & 2 deletions luminex/src/org/labkey/luminex/view/guideSetConfirmDelete.jsp
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Expand Up @@ -61,8 +61,7 @@
<% for (GuideSet gs : guideSets) { %>
<li>
<%
new LinkBuilder("Guide Set " + gs.getGuideSetId() + ": " + gs.getComment())
.href("#")
LinkBuilder.labkeyLink("Guide Set " + gs.getGuideSetId() + ": " + gs.getComment(), "#")
.attributes(Map.of(tabindex.name(), "-1"))
.onClick("createGuideSetWindow(" + bean.getProtocol().getRowId() + ", " + gs.getGuideSetId() + ", false)")
.appendTo(out);
Expand Down
6 changes: 3 additions & 3 deletions ms2/src/org/labkey/ms2/MS2Controller.java
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Expand Up @@ -658,7 +658,7 @@ private LinkBuilder modificationHref(MS2Run run)

onClick.append(", 100); return false;");

return PageFlowUtil.link("Show Modifications").onClick(onClick.toString()).id("modificationsLink");
return LinkBuilder.labkeyLink("Show Modifications").onClick(onClick.toString()).id("modificationsLink");
}

private DOM.Renderable appendMods(Map<String, String> mods, String heading)
Expand Down Expand Up @@ -826,10 +826,10 @@ public ModelAndView getView(DetailsForm form, BindException errors) throws Excep

String nextPrevStr = "";
if (null != previousURL) {
nextPrevStr += PageFlowUtil.link("Previous").href(previousURL);
nextPrevStr += LinkBuilder.labkeyLink("Previous", previousURL);
}
if (null != nextURL) {
nextPrevStr += PageFlowUtil.link("Next").href(nextURL);
nextPrevStr += LinkBuilder.labkeyLink("Next", nextURL);
}
if (!nextPrevStr.isEmpty()) {
result.addView(HtmlView.unsafe(nextPrevStr));
Expand Down
6 changes: 3 additions & 3 deletions ms2/src/org/labkey/ms2/runSummary.jsp
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Expand Up @@ -76,17 +76,17 @@ if (null != bean.quantAlgorithm)

if (null != run.getParamsFileName() && null != run.getPath())
{ %>
<%=link("Show " + run.getParamsFileName()).href(urlFor(MS2Controller.ShowParamsFileAction.class).addParameter("run", run.getRun())).id("paramFileLink").target("paramFile")%><%
<%=link("Show " + run.getParamsFileName(), urlFor(MS2Controller.ShowParamsFileAction.class).addParameter("run", run.getRun())).id("paramFileLink").target("paramFile")%><%
}

if (run.getHasPeptideProphet())
{ %>
<%=link("Show Peptide Prophet Details").href(urlFor(MS2Controller.ShowPeptideProphetDetailsAction.class).addParameter("run", run.getRun())).id("peptideProphetDetailsLink").target("peptideProphetSummary")%><%
<%=link("Show Peptide Prophet Details", urlFor(MS2Controller.ShowPeptideProphetDetailsAction.class).addParameter("run", run.getRun())).id("peptideProphetDetailsLink").target("peptideProphetSummary")%><%
}

if (run.hasProteinProphet())
{ %>
<%=link("Show Protein Prophet Details").href(urlFor(MS2Controller.ShowProteinProphetDetailsAction.class).addParameter("run", run.getRun())).id("proteinProphetDetailsLink").target("proteinProphetSummary")%><%
<%=link("Show Protein Prophet Details", urlFor(MS2Controller.ShowProteinProphetDetailsAction.class).addParameter("run", run.getRun())).id("proteinProphetDetailsLink").target("proteinProphetSummary")%><%
} %>
</div>
</td></tr>
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2 changes: 1 addition & 1 deletion protein/api-src/org/labkey/api/protein/ProteinManager.java
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Expand Up @@ -298,7 +298,7 @@ public static HtmlString makeFullAnchorLink(String url, String target, String tx
if (null == url)
return HtmlString.of(txt);

return new LinkBuilder(txt).href(url).target(target).clearClasses().getHtmlString();
return LinkBuilder.simpleLink(txt, url).target(target).getHtmlString();
}

public static List<HtmlString> makeFullAnchorLinks(Collection<String> idents, String target, String identType)
Expand Down
5 changes: 3 additions & 2 deletions protein/src/org/labkey/protein/ProteinController.java
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Expand Up @@ -104,6 +104,7 @@
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.HtmlStringBuilder;
import org.labkey.api.util.JobRunner;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.TestContext;
import org.labkey.api.util.URLHelper;
Expand Down Expand Up @@ -394,13 +395,13 @@ public MenuButton createQueryPickerButton(String label)
{
url = new ActionURL(ShowAnnotationSetAction.class, getContainer());
url.addParameter("CustomAnnotation.queryName", settings.getQueryName());
header.append("This view shows your protein list with all the proteins that match. If more than one sequence matches you will get multiple rows. ").append(PageFlowUtil.link("show without proteins").href(url));
header.append("This view shows your protein list with all the proteins that match. If more than one sequence matches you will get multiple rows. ").append(LinkBuilder.labkeyLink("show without proteins", url));
}
else
{
url = new ActionURL(ShowAnnotationSetWithSequencesAction.class, getContainer());
url.addParameter("CustomAnnotation.queryName", settings.getQueryName());
header.append("This view shows just the data uploaded as part of the list. ").append(PageFlowUtil.link("show with matching proteins loaded into this server").href(url));
header.append("This view shows just the data uploaded as part of the list. ").append(LinkBuilder.labkeyLink("show with matching proteins loaded into this server", url));
}

HtmlView linkView = new HtmlView(header);
Expand Down