Merge remote-tracking branch 'remotes/origin/release24.11-SNAPSHOT' into 24.11_fb_optimizeChromImport

Author: nickshulman

src/org/labkey/targetedms/parser/SkylineBinaryParser.java

@@ -25,7 +25,6 @@
 import org.labkey.targetedms.parser.skyd.CacheHeaderStruct;
 import org.labkey.targetedms.parser.skyd.CachedFileHeaderStruct;
 import org.labkey.targetedms.parser.skyd.ChromGroupHeaderInfo;
-import org.labkey.targetedms.parser.skyd.ChromPeak;
 import org.labkey.targetedms.parser.skyd.ChromTransition;
 import org.labkey.targetedms.parser.skyd.StructSerializer;
 
@@ -37,7 +36,6 @@
 import java.nio.ByteBuffer;
 import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
-import java.nio.channels.SeekableByteChannel;
 import java.util.EnumSet;
 import java.util.List;
 import java.util.Objects;
@@ -62,7 +60,6 @@ public class SkylineBinaryParser
     private CacheHeaderStruct _cacheHeaderStruct;
 
     private ChromGroupHeaderInfo[] _chromatograms;
-    private float[] _allPeaksRt;
     private byte[] _seqBytes;
     private List<ChromatogramGroupId> _chromatogramGroupIds;
 
@@ -120,7 +117,6 @@ public void parse() throws IOException
 
         parseChromatogramGroupIds();
         parseFiles();
-        parsePeaks();
         _log.debug("Starting to load chromatogram headers");
         parseChromatograms();
         _log.debug("Done loading chromatogram headers");
@@ -200,19 +196,6 @@ private String readStringOfByteLength(InputStream inputStream, int length) throw
         return new String(buffer, _cacheFormat.getCharset());
     }
 
-    private void parsePeaks() throws IOException
-    {
-        _channel.position(_cacheHeaderStruct.getLocationPeaks());
-        ChromPeak[] chromPeaks = _cacheFormat.chromPeakSerializer()
-                .readArray(Channels.newInputStream(_channel), _cacheHeaderStruct.getNumPeaks());
-        _allPeaksRt = new float[chromPeaks.length];
-
-        for (int i = 0; i < chromPeaks.length; i++)
-        {
-            _allPeaksRt[i] = chromPeaks[i].getRetentionTime();
-        }
-    }
-
     private void parseChromatogramGroupIds() throws IOException
     {
         if (_cacheFormat.getFormatVersion().compareTo(CacheFormatVersion.Eighteen) < 0)
@@ -251,11 +234,6 @@ private void parseChromatograms() throws IOException
                 Channels.newInputStream(_channel), _cacheHeaderStruct.getNumChromatograms());
     }
 
-    public SeekableByteChannel getChannel()
-    {
-        return _channel;
-    }
-
     final int getCacheFileSize()
     {
         return _cacheFiles != null ? _cacheFiles.length : 0;

webapp/TargetedMS/js/QCSummaryPanel.js

@@ -299,7 +299,17 @@ Ext4.define('LABKEY.targetedms.QCSummary', {
     renderContainerSampleFileStats: function (params) {
         let container = params.container;
         let sampleFiles = params.sampleFiles;
-        let metrics = sampleFiles[0].Metrics;
+        let metrics = [];
+        let seenMetrics = {};
+        Ext4.iterate(sampleFiles, function (sampleFile) {
+            Ext4.iterate(sampleFile.Metrics, function (metric) {
+                if (!seenMetrics[metric.MetricId]) {
+                    metrics.push(metric);
+                    seenMetrics[metric.MetricId] = true;
+                }
+            });
+        });
+
         let showMetrics = LABKEY.ActionURL.getAction().toLowerCase() === 'qcSummaryHistory'.toLowerCase();
         let tableWidth = container.width - 100;
         let html = '';
@@ -340,8 +350,17 @@ Ext4.define('LABKEY.targetedms.QCSummary', {
 
 
             if (showMetrics) {
-                Ext4.each(sampleFile.Metrics, function (metric) {
-                    html += '<td><div class="sample-file-item" style="text-align: right">' + Ext4.util.Format.htmlEncode(metric.Value) + '</div></td>';
+                Ext4.each(metrics, function (metric) {
+                    let isMetricPresent = false;
+                    Ext4.each(sampleFile.Metrics, function (item) {
+                        if (metric.MetricId === item.MetricId) {
+                            isMetricPresent = true;
+                            html += '<td><div class="sample-file-item" style="text-align: right">' + Ext4.util.Format.htmlEncode(item.Value) + '</div></td>';
+                        }
+                    });
+                    if (!isMetricPresent) {
+                        html += '<td><div class="sample-file-item" style="text-align: right">N/A</div></td>';
+                    }
                 });
             }
             if (sampleFile.IgnoreForAllMetric) {