flat protein/molecule list for a Skyline document

resources/queries/protein/Sequences.query.xml

@@ -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>

resources/queries/targetedms/Protein/.qview.xml

@@ -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>

resources/schemas/dbscripts/postgresql/targetedms-26.006-26.007.sql

@@ -0,0 +1,34 @@
+ALTER TABLE targetedms.Runs ADD COLUMN ProteinCount INT;
+
+UPDATE targetedms.Runs r
+SET ProteinCount = (
+    SELECT COUNT(*)
+    FROM targetedms.Protein p
+    JOIN targetedms.PeptideGroup pg ON p.PeptideGroupId = pg.Id
+    WHERE pg.RunId = r.Id
+);
+
+-- Redefine PeptideGroupCount: groups containing at least one peptide
+UPDATE targetedms.Runs r
+SET PeptideGroupCount = (
+    SELECT COUNT(DISTINCT pg.Id)
+    FROM targetedms.PeptideGroup pg
+    JOIN targetedms.GeneralMolecule gm ON gm.PeptideGroupId = pg.Id
+    JOIN targetedms.Peptide p ON p.Id = gm.Id
+    WHERE pg.RunId = r.Id
+);
+
+ALTER TABLE targetedms.Runs ADD COLUMN MoleculeGroupCount INT;
+
+UPDATE targetedms.Runs r
+SET MoleculeGroupCount = (
+    SELECT COUNT(DISTINCT pg.Id)
+    FROM targetedms.PeptideGroup pg
+    JOIN targetedms.GeneralMolecule gm ON gm.PeptideGroupId = pg.Id
+    JOIN targetedms.Molecule m ON m.Id = gm.Id
+    WHERE pg.RunId = r.Id
+);
+
+ALTER TABLE targetedms.Runs ALTER COLUMN MoleculeGroupCount SET NOT NULL;
+ALTER TABLE targetedms.Runs ALTER COLUMN PeptideGroupCount SET NOT NULL;
+ALTER TABLE targetedms.Runs ALTER COLUMN ProteinCount SET NOT NULL;

resources/schemas/targetedms.xml

@@ -179,15 +179,23 @@
             <column columnName="DocumentGUID"/>
             <column columnName="PeptideGroupCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showPeptideGroupList.view?id=${Id}</url>
+            </column>
+            <column columnName="MoleculeGroupCount">
+                <formatString>#,###</formatString>
+                <url>/targetedms-showMoleculeGroupList.view?id=${Id}</url>
+            </column>
+            <column columnName="ProteinCount">
+                <formatString>#,###</formatString>
+                <url>/targetedms-showProteinList.view?id=${Id}</url>
             </column>
             <column columnName="PeptideCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showPeptideList.view?id=${Id}</url>
             </column>
             <column columnName="SmallMoleculeCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showMoleculeList.view?id=${Id}</url>
             </column>
             <column columnName="PrecursorCount">
                 <formatString>#,###</formatString>

src/org/labkey/targetedms/SkylineDocImporter.java

@@ -144,6 +144,9 @@ public class SkylineDocImporter
     protected static final Logger _systemLog = LogHelper.getLogger(SkylineDocImporter.class, "Imports Skyline documents");
     protected final XarContext _context;
     private int blankLabelIndex;
+    private int _importedPeptideGroupCount = 0;
+    private int _importedMoleculeGroupCount = 0;
+    private int _importedProteinCount = 0;
 
     private final LocalDirectory _localDirectory;
     private final PipeRoot _pipeRoot;
@@ -450,7 +453,9 @@ private void importSkylineDoc(TargetedMSRun run, File f) throws XMLStreamExcepti
             int auditLogEntriesCount = importer.importAuditLogFile(_user, _auditLogFile, parser.getDocumentGUID(), run);
 
             run.setAuditLogEntriesCount(auditLogEntriesCount);
-            run.setPeptideGroupCount(parser.getPeptideGroupCount());
+            run.setPeptideGroupCount(_importedPeptideGroupCount);
+            run.setMoleculeGroupCount(_importedMoleculeGroupCount);
+            run.setProteinCount(_importedProteinCount);
             run.setPeptideCount(parser.getPeptideCount());
             run.setSmallMoleculeCount(parser.getSmallMoleculeCount());
             run.setPrecursorCount(parser.getPrecursorCount());
@@ -1357,10 +1362,12 @@ else if(!pepGroup.isDecoy())
         if(peptideCount > 0)
         {
             _log.debug(String.format("Total peptides inserted: %d", peptideCount));
+            _importedPeptideGroupCount++;
         }
         if(moleculeCount > 0)
         {
             _log.debug(String.format("Total molecules inserted: %d", moleculeCount));
+            _importedMoleculeGroupCount++;
         }
     }
 
@@ -1381,6 +1388,7 @@ private void insertProtein(Protein protein)
             proteinService.ensureIdentifiers(seqId, identifierMap);
         }
         Table.insert(null, TargetedMSManager.getTableInfoProtein(), protein);
+        _importedProteinCount++;
     }
 
     private static final String SKYLINE_IDENT_TYPE = "Skyline";

src/org/labkey/targetedms/TargetedMSController.java

@@ -258,9 +258,11 @@
 import org.labkey.targetedms.view.CalibrationCurvesView;
 import org.labkey.targetedms.view.ChromatogramGridView;
 import org.labkey.targetedms.view.ChromatogramsDataRegion;
+import org.labkey.targetedms.view.DocumentGeneralMoleculesView;
+import org.labkey.targetedms.view.DocumentPeptideGroupView;
+import org.labkey.targetedms.view.DocumentProteinView;
 import org.labkey.targetedms.view.DocumentPrecursorsView;
 import org.labkey.targetedms.view.DocumentTransitionsView;
-import org.labkey.targetedms.view.DocumentView;
 import org.labkey.targetedms.view.FiguresOfMeritView;
 import org.labkey.targetedms.view.GroupComparisonView;
 import org.labkey.targetedms.view.InstrumentSummaryWebPart;
@@ -4377,7 +4379,7 @@ public void addNavTrail(NavTree root, TargetedMSRun run)
     // Action to display a document's transition or precursor list, with both proteomics and small molecule views
     // ------------------------------------------------------------------------
     @RequiresPermission(ReadPermission.class)
-    public abstract class ShowRunSplitDetailsAction<VIEWTYPE extends DocumentView> extends AbstractShowRunDetailsAction<RunDetailsForm, VIEWTYPE>
+    public abstract class ShowRunSplitDetailsAction<VIEWTYPE extends QueryView> extends AbstractShowRunDetailsAction<RunDetailsForm, VIEWTYPE>
     {
         public ShowRunSplitDetailsAction()
         {
@@ -4496,16 +4498,16 @@ public ShowPrecursorListAction(ViewContext ctx)
         @Override
         protected DocumentPrecursorsView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
         {
-            DocumentPrecursorsView view;
-            if(PeptidePrecursorsView.DATAREGION_NAME.equals(dataRegion))
+            DocumentPrecursorsView view = null;
+            if (PeptidePrecursorsView.DATAREGION_NAME.equals(dataRegion))
             {
                 view = new PeptidePrecursorsView(getViewContext(),
                         new TargetedMSSchema(getUser(), getContainer()),
                         TargetedMSSchema.TABLE_EXPERIMENT_PRECURSOR,
                         form.getId(),
                         forExport);
             }
-            else
+            else if (SmallMoleculePrecursorsView.DATAREGION_NAME.equals(dataRegion))
             {
                 view = new SmallMoleculePrecursorsView(getViewContext(),
                         new TargetedMSSchema(getUser(), getContainer()),
@@ -4514,9 +4516,12 @@ protected DocumentPrecursorsView createQueryView(RunDetailsForm form, BindExcept
                         forExport);
             }
 
-            view.setShowExportButtons(true);
-            view.setShowDetailsColumn(false);
-            view.setButtonBarPosition(DataRegion.ButtonBarPosition.BOTH);
+            if (view != null)
+            {
+                view.setShowExportButtons(true);
+                view.setShowDetailsColumn(false);
+                view.setButtonBarPosition(DataRegion.ButtonBarPosition.BOTH);
+            }
 
             return view;
         }
@@ -4534,6 +4539,102 @@ public String getDataRegionNameSmallMolecule()
         }
     }
 
+    @RequiresPermission(ReadPermission.class)
+    public class ShowPeptideGroupListAction extends ShowRunSingleDetailsAction<RunDetailsForm>
+    {
+        public ShowPeptideGroupListAction()
+        {
+            super(RunDetailsForm.class, "Peptide Groups", TargetedMSSchema.TABLE_PEPTIDE_GROUP);
+        }
+
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            DocumentPeptideGroupView view = new DocumentPeptideGroupView(getViewContext(), schema, form.getId(),
+                    TargetedMSSchema.TABLE_PEPTIDE_GROUP, "Protein Groups");
+            view.setShowDetailsColumn(false);
+            view.setShowFilterDescription(false);
+            return view;
+        }
+    }
+
+    @RequiresPermission(ReadPermission.class)
+    public class ShowMoleculeGroupListAction extends ShowRunSingleDetailsAction<RunDetailsForm>
+    {
+        public ShowMoleculeGroupListAction()
+        {
+            super(RunDetailsForm.class, "Molecule Lists", TargetedMSSchema.TABLE_MOLECULE_GROUP);
+        }
+
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            DocumentPeptideGroupView view = new DocumentPeptideGroupView(getViewContext(), schema, form.getId(),
+                    TargetedMSSchema.TABLE_MOLECULE_GROUP, "Molecule Lists");
+            view.setShowDetailsColumn(false);
+            view.setShowFilterDescription(false);
+            return view;
+        }
+    }
+
+    @RequiresPermission(ReadPermission.class)
+    public class ShowProteinListAction extends ShowRunSingleDetailsAction<RunDetailsForm>
+    {
+        public ShowProteinListAction()
+        {
+            super(RunDetailsForm.class, "Proteins", TargetedMSSchema.TABLE_PROTEIN);
+        }
+
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            DocumentProteinView view = new DocumentProteinView(getViewContext(), schema, form.getId());
+            view.setShowDetailsColumn(false);
+            return view;
+        }
+    }
+
+    @RequiresPermission(ReadPermission.class)
+    public class ShowPeptideListAction extends ShowRunSingleDetailsAction<RunDetailsForm>
+    {
+        public ShowPeptideListAction()
+        {
+            super(RunDetailsForm.class, "Peptides", TargetedMSSchema.TABLE_PEPTIDE);
+        }
+
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            DocumentGeneralMoleculesView view = new DocumentGeneralMoleculesView(getViewContext(), schema, form.getId(),
+                    TargetedMSSchema.TABLE_PEPTIDE, "Peptides");
+            view.setShowDetailsColumn(false);
+            return view;
+        }
+    }
+
+    @RequiresPermission(ReadPermission.class)
+    public class ShowMoleculeListAction extends ShowRunSingleDetailsAction<RunDetailsForm>
+    {
+        public ShowMoleculeListAction()
+        {
+            super(RunDetailsForm.class, "Small Molecules", TargetedMSSchema.TABLE_MOLECULE);
+        }
+
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            DocumentGeneralMoleculesView view = new DocumentGeneralMoleculesView(getViewContext(), schema, form.getId(),
+                    TargetedMSSchema.TABLE_MOLECULE, "Small Molecules");
+            view.setShowDetailsColumn(false);
+            return view;
+        }
+    }
+
     @RequiresPermission(ReadPermission.class)
     public class ShowGroupComparisonAction extends ShowRunSplitDetailsAction<GroupComparisonView>
     {

src/org/labkey/targetedms/TargetedMSManager.java

@@ -2660,6 +2660,16 @@ public static boolean containerHasPeptides(Container container)
         return new SqlSelector(TargetedMSManager.getSchema(), new SQLFragment("SELECT Id FROM ", container, false).append(TargetedMSManager.getTableInfoRuns(), "r").append(" WHERE PeptideCount > 0 AND Container = ? AND Deleted = ?")).exists();
     }
 
+    public static boolean containerHasMoleculeGroups(Container container)
+    {
+        return new SqlSelector(TargetedMSManager.getSchema(), new SQLFragment("SELECT Id FROM ", container, false).append(TargetedMSManager.getTableInfoRuns(), "r").append(" WHERE MoleculeGroupCount > 0 AND Container = ? AND Deleted = ?")).exists();
+    }
+
+    public static boolean containerHasProteins(Container container)
+    {
+        return new SqlSelector(TargetedMSManager.getSchema(), new SQLFragment("SELECT Id FROM ", container, false).append(TargetedMSManager.getTableInfoRuns(), "r").append(" WHERE ProteinCount > 0 AND Container = ? AND Deleted = ?")).exists();
+    }
+
     public static boolean containerHasCalibrationCurves(Container container)
     {
         return new SqlSelector(TargetedMSManager.getSchema(), new SQLFragment("SELECT Id FROM ", container, false).append(TargetedMSManager.getTableInfoRuns(), "r").append(" WHERE CalibrationCurveCount > 0 AND Container = ? AND Deleted = ?")).exists();

src/org/labkey/targetedms/TargetedMSModule.java

@@ -231,7 +231,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.006;
+        return 26.007;
     }
 
     @Override

src/org/labkey/targetedms/TargetedMSRun.java

@@ -51,6 +51,8 @@ public class TargetedMSRun implements Serializable, ITargetedMSRun
     protected RunRepresentativeDataState _representativeDataState = NotRepresentative;
 
     protected int _peptideGroupCount;
+    protected int _moleculeGroupCount;
+    protected int _proteinCount;
     protected int _peptideCount;
     protected int _smallMoleculeCount;
     protected int _precursorCount;
@@ -249,6 +251,26 @@ public void setPeptideGroupCount(int peptideGroupCount)
         _peptideGroupCount = peptideGroupCount;
     }
 
+    public int getMoleculeGroupCount()
+    {
+        return _moleculeGroupCount;
+    }
+
+    public void setMoleculeGroupCount(int moleculeGroupCount)
+    {
+        _moleculeGroupCount = moleculeGroupCount;
+    }
+
+    public int getProteinCount()
+    {
+        return _proteinCount;
+    }
+
+    public void setProteinCount(int proteinCount)
+    {
+        _proteinCount = proteinCount;
+    }
+
     public int getPeptideCount()
     {
         return _peptideCount;