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flat protein/molecule list for a Skyline document #1208

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288e462
flat protein/molecule list for a Skyline document
ankurjuneja May 11, 2026
4c015f9
match columns with Skyline file
ankurjuneja May 12, 2026
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13 changes: 13 additions & 0 deletions resources/queries/protein/Sequences.query.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="Sequences" tableDbType="TABLE">
<columns>
<column columnName="ProtSequence">
<displayWidth>200</displayWidth>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
16 changes: 16 additions & 0 deletions resources/queries/targetedms/Protein/.qview.xml
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@@ -0,0 +1,16 @@
<customView xmlns="http://labkey.org/data/xml/queryCustomView" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
label="Proteins" canOverride="true">
<columns>
<column name="Label" />
<column name="Description" />
<column name="Accession" />
<column name="PreferredName" />
<column name="Gene" />
<column name="Species" />

<column name="SequenceId/ProtSequence" />
<column name="Note" />

</columns>

</customView>
2 changes: 1 addition & 1 deletion resources/schemas/targetedms.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -179,7 +179,7 @@
<column columnName="DocumentGUID"/>
<column columnName="PeptideGroupCount">
<formatString>#,###</formatString>
<url>/targetedms-showPrecursorList.view?id=${Id}</url>
<url>/targetedms-showProteinList.view?id=${Id}</url>
</column>
<column columnName="PeptideCount">
<formatString>#,###</formatString>
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47 changes: 47 additions & 0 deletions src/org/labkey/targetedms/TargetedMSController.java
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Expand Up @@ -4534,6 +4534,53 @@ public String getDataRegionNameSmallMolecule()
}
}

@RequiresPermission(ReadPermission.class)
public class ShowProteinListAction extends SimpleViewAction<RunDetailsForm>
{
private static final String DATA_REGION_NAME = "ProteinList";

@Override
public ModelAndView getView(RunDetailsForm form, BindException errors)
{
if (!form.hasRunId())
throw new RedirectException(new ActionURL(ShowListAction.class, getContainer()));

TargetedMSRun run = validateRun(form.getId());

TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
QuerySettings settings;
String title;

if (run.getPeptideCount() > 0)
{
settings = new QuerySettings(getViewContext(), DATA_REGION_NAME, TargetedMSSchema.TABLE_PROTEIN);
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@labkey-jeckels labkey-jeckels May 13, 2026

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A file can have both proteins and small molecules. If so, we need to show both, like we do in other actions. I suggest making this action a subclass of ShowRunSplitDetailsAction and following the pattern from other subclasses.

settings.setBaseFilter(new SimpleFilter(FieldKey.fromParts("PeptideGroupId", "RunId"), form.getId()));
title = "Proteins";
}
else
{
settings = new QuerySettings(getViewContext(), DATA_REGION_NAME, TargetedMSSchema.TABLE_PEPTIDE_GROUP);
settings.setBaseFilter(new SimpleFilter(FieldKey.fromParts("RunId"), form.getId()));
title = "Molecule Lists";
}

settings.setContainerFilterName(null);
QueryView view = schema.createView(getViewContext(), settings, errors);
view.setAllowableContainerFilterTypes();
view.setShowDetailsColumn(false);
view.setShowFilterDescription(false);
view.setFrame(WebPartView.FrameType.PORTAL);
view.setTitle(title);
return view;
}

@Override
public void addNavTrail(NavTree root)
{
root.addChild("Targeted MS Runs", getShowListURL(getContainer()));
}
}

@RequiresPermission(ReadPermission.class)
public class ShowGroupComparisonAction extends ShowRunSplitDetailsAction<GroupComparisonView>
{
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5 changes: 4 additions & 1 deletion src/org/labkey/targetedms/view/runSummaryView.jsp
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Expand Up @@ -52,6 +52,9 @@
ActionURL precursorListAction = new ActionURL(TargetedMSController.ShowPrecursorListAction.class, getContainer());
precursorListAction.addParameter("id", run.getId());

ActionURL proteinListAction = new ActionURL(TargetedMSController.ShowProteinListAction.class, getContainer());
proteinListAction.addParameter("id", run.getId());

ActionURL ptmReportAction = new ActionURL(TargetedMSController.ShowPTMReportAction.class, getContainer());
ptmReportAction.addParameter("id", run.getId());

Expand Down Expand Up @@ -94,7 +97,7 @@
</div>
&nbsp;
<div>
<a href="<%= h(precursorListAction) %>"><%= h(StringUtilsLabKey.pluralize(run.getPeptideGroupCount(), peptideGroupLabel))%></a>,
<a href="<%= h(proteinListAction) %>"><%= h(StringUtilsLabKey.pluralize(run.getPeptideGroupCount(), peptideGroupLabel))%></a>,
<% if (run.getPeptideCount() > 0) { %><a href="<%= h(precursorListAction) %>"><%= h(StringUtilsLabKey.pluralize(run.getPeptideCount(), "peptide"))%></a>,<% } %>
<% if (run.getSmallMoleculeCount() > 0) { %><a href="<%= h(precursorListAction + "#Small Molecule Precursor List") %>"><%= h(StringUtilsLabKey.pluralize(run.getSmallMoleculeCount(), "small molecule"))%></a>,<% } %>
<a href="<%= h(precursorListAction) %>"><%= h(StringUtilsLabKey.pluralize(run.getPrecursorCount(), "precursor"))%></a>,
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