[bot] Merge 26.6 to develop

src/org/labkey/targetedms/TargetedMSController.java

@@ -3185,8 +3185,31 @@ public void addNavTrail(NavTree root)
         }
     }
 
+    /**
+     * Reading library spectra from a large library file can take many seconds over network storage, especially for large
+     * EncyclopeDIA libraries. To protect public folders from aggressive bots, do not show library spectra to guests when
+     * the library is large. Show the login prompt instead.
+     * Returns true (and adds the login view) when the library spectrum should be withheld.
+     */
+    private boolean addGuestSpectrumGate(TargetedMSRun run, VBox vbox)
+    {
+        if (!LibrarySpectrumMatchGetter.blockSpectraForGuest(getUser(), run.getId()))
+        {
+            return false;
+        }
+        HtmlView loginView = getLoginView(getViewContext(), getContainer());
+        loginView.setTitle("Library Spectrum");
+        loginView.setFrame(WebPartView.FrameType.PORTAL);
+        vbox.addView(loginView);
+        return true;
+    }
+
     private void addSpectrumViews(TargetedMSRun run, VBox vbox, Precursor precursor, BindException errors)
     {
+        if (addGuestSpectrumGate(run, vbox))
+        {
+            return;
+        }
         PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
         if (null != root)
         {
@@ -3205,6 +3228,10 @@ private void addSpectrumViews(TargetedMSRun run, VBox vbox, Precursor precursor,
 
     private void addSpectrumViews(TargetedMSRun run, VBox vbox, Peptide peptide, BindException errors)
     {
+        if (addGuestSpectrumGate(run, vbox))
+        {
+            return;
+        }
         PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
         if (null != root)
         {
@@ -3289,6 +3316,13 @@ public Object execute(SpectrumDataForm form, BindException errors)
             }
             TargetedMSRun run = TargetedMSManager.getRunForGeneralMolecule(peptide.getId());
 
+            // Apply the same guest gate as the spectrum views (see LibrarySpectrumMatchGetter.blockSpectraForGuest).
+            if (LibrarySpectrumMatchGetter.blockSpectraForGuest(getUser(), run.getId()))
+            {
+                response.put("error", "Login to view this data");
+                return response;
+            }
+
             List<PeptideSettings.SpectrumLibrary> libraries = LibraryManager.getLibraries(run.getId());
             PeptideSettings.SpectrumLibrary library = null;
             for (PeptideSettings.SpectrumLibrary lib : libraries)

src/org/labkey/targetedms/chart/ChromatogramDataset.java

@@ -900,6 +900,13 @@ public void build()
 
         protected List<LibrarySpectrumMatchGetter.PeptideIdRtInfo> getPeptideIdRetentionTimes()
         {
+            // Skip peptide-ID retention-time markers for guests when the library is large. Reading large libraries can be slow over network storage.
+            // See LibrarySpectrumMatchGetter.blockSpectraForGuest.
+            if (LibrarySpectrumMatchGetter.blockSpectraForGuest(_user, _run.getId()))
+            {
+                return Collections.emptyList();
+            }
+
             SampleFile sampleFile = ReplicateManager.getSampleFile(_pChromInfo.getSampleFileId());
 
             // TODO: May want to move LocalDirectory up to controller, where others are created. Sharing probably desired.

src/org/labkey/targetedms/view/precursorConflictResolutionView.jsp

@@ -119,12 +119,12 @@ $(document).ready(function () {
         {
             row.child.hide();
             tr.removeClass('shown');
-            $("." + cls).children('img').attr('src', "<%=getWebappURL("_images/plus.gif")%>");
+            $("." + cls).children('img').attr('src', "<%=getWebappURL("_images/plus.gif")%>").attr('alt', 'Expand row details');
         }
         else {
             row.child.show();
             tr.addClass('shown');
-            $("." + cls).children('img').attr('src', "<%=getWebappURL("_images/minus.gif")%>");
+            $("." + cls).children('img').attr('src', "<%=getWebappURL("_images/minus.gif")%>").attr('alt', 'Collapse row details');
         }
 
         if(!srcTd.hasClass('content_loaded'))
@@ -271,7 +271,7 @@ function toggleCheckboxSelection(element)
              <!--<td class="representative newPrecursor <%=precursor.getNewPrecursorId()%>"><%=precursor.getNewPrecursorId()%></td>-->
              <td class="representative details-control newPrecursor <%=precursor.getNewPrecursorId()%>">
                 <span class="<%=precursor.getNewPrecursorId()%>_<%=precursor.getOldPrecursorId()%>">
-                     <img src="<%=getWebappURL("_images/plus.gif")%>"/>
+                     <img src="<%=getWebappURL("_images/plus.gif")%>" alt="Expand row details"/>
                  </span>
              </td>
              <td class="representative newPrecursor <%=precursor.getNewPrecursorId()%>">
@@ -291,7 +291,7 @@ function toggleCheckboxSelection(element)
              <!--<td class="oldPrecursor <%=precursor.getNewPrecursorId()%>"><%=precursor.getOldPrecursorId()%></td>-->
              <td class="details-control oldPrecursor <%=precursor.getNewPrecursorId()%>">
                 <span class="<%=precursor.getNewPrecursorId()%>_<%=precursor.getOldPrecursorId()%>">
-                     <img src="<%=getWebappURL("_images/plus.gif")%>"/>
+                     <img src="<%=getWebappURL("_images/plus.gif")%>" alt="Expand row details"/>
                  </span>
              </td>
              <td class="oldPrecursor <%=precursor.getNewPrecursorId()%>">

src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java

@@ -16,6 +16,7 @@
 package org.labkey.targetedms.view.spectrum;
 
 import org.apache.commons.io.FilenameUtils;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.cache.BlockingCache;
@@ -24,6 +25,7 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.security.User;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSRun;
 import org.labkey.targetedms.TargetedMSSchema;
@@ -42,6 +44,8 @@
 import org.labkey.targetedms.query.PeptideManager;
 import org.labkey.targetedms.query.PrecursorManager;
 
+import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -58,8 +62,64 @@
  */
 public class LibrarySpectrumMatchGetter
 {
+    private static final Logger LOG = LogHelper.getLogger(LibrarySpectrumMatchGetter.class, "Matches library spectra and retention times for the library spectrum viewer");
+
     private static final int CACHE_SIZE = 10;
 
+    // Reading library spectra and retention times from large spectrum libraries can be slow over network storage.
+    // For EncyclopeDIA .elib we read one row per source file for the peptide. This can be hundreds of rows and the needed
+    // columns are not in the index, so each table row lookup is a separate network round-trip on GPFS.
+    // For BiblioSpec .blib we scan the unindexed RetentionTimes table for the RT of the peptide in all the scans and source
+    // files.
+    // PanoramaWeb has large files of both types, so the size gate covers both library types. To protect public folders from
+    // aggressive bots, library spectra are not shown to guests when the library file is at or above this size. Guests are
+    // asked to log in instead.
+    private static final long GUEST_SPECTRUM_LIBRARY_SIZE_LIMIT = 500L * 1024 * 1024; // 500 MB
+
+    /**
+     * Returns true if library spectra should NOT be shown to the given user for the given run,
+     * i.e. the user is a guest and the run references a supported spectrum library file that is at
+     * or above {@link #GUEST_SPECTRUM_LIBRARY_SIZE_LIMIT}. Logged-in users are never blocked, and
+     * small libraries are read in place as before.
+     */
+    public static boolean blockSpectraForGuest(User user, long runId)
+    {
+        if (!user.isGuest())
+        {
+            return false;
+        }
+        for (Path libPath : LibraryManager.getLibraryFilePaths(runId).values())
+        {
+            if (isLargeSpectrumLibrary(libPath))
+            {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    private static boolean isLargeSpectrumLibrary(Path libPath)
+    {
+        // Only .elib/.blib libraries are read for spectra; ignore anything we cannot read.
+        if (libPath == null || getReaderForLibrary(FileUtil.getFileName(libPath)) == null)
+        {
+            return false;
+        }
+        try
+        {
+            // Files.size throws NoSuchFileException if the file is missing, so a separate Files.exists
+            // check is unnecessary and would add a second filesystem round-trip on network storage.
+            return Files.size(libPath) >= GUEST_SPECTRUM_LIBRARY_SIZE_LIMIT;
+        }
+        catch (IOException e)
+        {
+            // If we cannot stat the file it is missing or unreadable, in which case the
+            // downstream library read will fail too.
+            LOG.warn("Could not determine size of spectrum library file " + libPath, e);
+            return false;
+        }
+    }
+
     private static final BlockingCache<PrecursorKey, List<PeptideIdRtInfo>> _peptideIdRtsCache =
             CacheManager.getBlockingCache(CACHE_SIZE, CacheManager.DAY, "TargetedMS peptide ID retention times",
                     (precursor, argument) -> {

test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java

@@ -901,6 +901,36 @@ public String toString()
         }
     }
 
+    public void performYAxisZoom(QCPlot qcPlot)
+    {
+        WebElement plotEl = qcPlot.getPlot();
+        WebElement overlay = elementCache().yZoomOverlay.findElement(plotEl);
+        getWrapper().scrollIntoView(overlay);
+
+        int clickOffset = 40;
+        new Actions(getWrapper().getDriver())
+                .moveToElement(overlay, 0, -clickOffset)
+                .click()
+                .moveToElement(overlay, 0, clickOffset)
+                .click()
+                .perform();
+
+        WebDriverWrapper.waitFor(() -> !elementCache().yZoomConfirmBtn.findElements(plotEl).isEmpty(),
+                "Zoom buttons did not appear after y-axis clicks", WAIT_FOR_JAVASCRIPT);
+
+        elementCache().yZoomConfirmBtn.findElement(plotEl).click();
+    }
+
+    public boolean isZoomActive(QCPlot qcPlot)
+    {
+        return !elementCache().yZoomBorder.findElements(qcPlot.getPlot()).isEmpty();
+    }
+
+    public void clickResetZoom(QCPlot qcPlot)
+    {
+        elementCache().yZoomOverlay.findElement(qcPlot.getPlot()).click();
+    }
+
     public class Elements extends BodyWebPart<?>.ElementCache
     {
         WebElement startDate = Locator.css("#start-date-field input").findWhenNeeded(this);
@@ -936,6 +966,9 @@ public class Elements extends BodyWebPart<?>.ElementCache
         WebElement plotPanel = Locator.css("div.tiledPlotPanel").findWhenNeeded(this);
         WebElement paginationPanel = Locator.css("div.plotPaginationHeaderPanel").findWhenNeeded(this);
         Locator extFormDisplay = Locator.css("div.x4-form-display-field");
+        Locator.CssLocator yZoomOverlay = Locator.css("svg rect.y-zoom-overlay");
+        Locator.CssLocator yZoomConfirmBtn = Locator.css("svg g.y-zoom-btn-zoom rect");
+        Locator.CssLocator yZoomBorder = Locator.css("svg rect.y-zoom-border");
         Locator.CssLocator guideSetTrainingRect = Locator.css("svg rect.training");
         Locator.CssLocator experimentRangeRect = Locator.css("svg rect.expRange");
         Locator.CssLocator guideSetSvgButton = Locator.css("svg g.guideset-svg-button text");

test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java

@@ -1147,6 +1147,56 @@ private void verifyRow(DataRegionTable drt, int row, String sampleName, String s
         assertEquals(skylineDocName, drt.getDataAsText(row, "File"));
     }
 
+    @Test
+    public void testQCPlotYAxisZoom()
+    {
+        PanoramaDashboard qcDashboard = new PanoramaDashboard(this);
+        QCPlotsWebPart qcPlotsWebPart = qcDashboard.getQcPlotsWebPart();
+        qcPlotsWebPart.filterQCPlotsToInitialData(PRECURSORS.length, true);
+
+        List<QCPlot> plots = qcPlotsWebPart.getPlots();
+        assertTrue("Expected at least 2 plots for y-axis zoom test", plots.size() >= 2);
+
+        // 1. Verify zooming is possible: drag on y-axis, confirm zoom, border appears
+        log("Verifying y-axis zoom can be applied");
+        qcPlotsWebPart.performYAxisZoom(plots.get(0));
+        waitForElement(Locator.css("svg rect.y-zoom-border"), WAIT_FOR_JAVASCRIPT);
+
+        plots = qcPlotsWebPart.getPlots();
+        QCPlot firstPlot = plots.get(0);
+        QCPlot secondPlot = plots.get(1);
+
+        assertTrue("Zoom border should appear on first plot after zoom", qcPlotsWebPart.isZoomActive(firstPlot));
+
+        // 2. Verify zoom is per-plot: second plot is unaffected
+        log("Verifying zoom is independent per plot");
+        assertFalse("Second plot should not be zoomed", qcPlotsWebPart.isZoomActive(secondPlot));
+
+        // 3. Verify reset works: clicking the zoomed y-axis (zoom-out cursor) resets zoom
+        log("Verifying clicking the y-axis resets zoom on the target plot");
+        qcPlotsWebPart.clickResetZoom(firstPlot);
+        waitForElementToDisappear(Locator.css("svg rect.y-zoom-border"), WAIT_FOR_JAVASCRIPT);
+
+        plots = qcPlotsWebPart.getPlots();
+        firstPlot = plots.get(0);
+
+        assertFalse("Zoom border should be gone after reset", qcPlotsWebPart.isZoomActive(firstPlot));
+
+        // 4. Verify zoom is not persisted after page reload
+        log("Verifying zoom state is cleared on page reload");
+        qcPlotsWebPart.performYAxisZoom(firstPlot);
+        waitForElement(Locator.css("svg rect.y-zoom-border"), WAIT_FOR_JAVASCRIPT);
+
+        refresh();
+        qcDashboard = new PanoramaDashboard(this);
+        qcPlotsWebPart = qcDashboard.getQcPlotsWebPart();
+
+        plots = qcPlotsWebPart.getPlots();
+        firstPlot = plots.get(0);
+
+        assertFalse("Zoom should not persist after page reload", qcPlotsWebPart.isZoomActive(firstPlot));
+    }
+
     private void createAndInsertAnnotations()
     {
         clickTab("Annotations");

webapp/TargetedMS/css/qcTrendPlotReport.css

@@ -70,6 +70,7 @@
     font-size: 18px;
     padding: 0 8px;
     border: solid #c0c0c0 1px;
+    background: none;
 }
 .qc-paging-prev {
     border-right-width: 0;
@@ -115,4 +116,24 @@
 
 .qc-combined-tree-legend .qc-tree-precursor:hover {
     background-color: #f0f0f0;
-}
+}
+
+.y-zoom-overlay {
+    cursor: zoom-in;
+}
+
+.y-zoom-pending-line {
+    stroke: rgba(20, 204, 201, 1);
+    stroke-width: 2px;
+    stroke-dasharray: 6, 3;
+}
+
+.y-zoom-selection {
+    fill: rgba(20, 204, 201, 0.3);
+    stroke: rgba(20, 204, 201, 1);
+    stroke-width: 1px;
+}
+
+.y-zoom-buttons g {
+    cursor: pointer;
+}