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QC plots ignore date range when showing guide set with many replicates #1224

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QC plots ignore date range when showing guide set with many replicates #1224

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45625ca
QC plots ignore date range when showing guide set with many replicates
ankurjuneja Jun 4, 2026
f30e841
fix truncation of out-of-range points
ankurjuneja Jun 4, 2026
546f146
Merge branch 'release26.3-SNAPSHOT' into 26.3_fb_1206
ankurjuneja Jun 7, 2026
69ba601
code review findings
ankurjuneja Jun 8, 2026
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80 changes: 65 additions & 15 deletions webapp/TargetedMS/js/QCPlotHelperBase.js
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Original file line number Diff line number Diff line change
Expand Up @@ -330,17 +330,23 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
}


// ReferenceRangeSeries is used to separate series. Default to "InRange" and only
// promote to "GuideSet" on a match, so that a later non-matching guide set in the
// map cannot clobber the label back to "InRange" when multiple guide sets exist.
plotData['ReferenceRangeSeries'] = "InRange";
Ext4.Object.each(this.guideSetDataMap, function(guideSetId, guideSetData) {
// guideSetDataMap is keyed by guide set ID, so the iteration key guideSetId is a
// String (JS object keys are always strings), whereas plotData.guideSetId is a Number
// (set from the numeric server value in QCPlotHelperWrapper.processPlotDataRow).
// Parse the String key to an int so this is a type-safe === comparison and we don't
// rely on == coercion (mirrors the parseInt pattern in QCTrendPlotPanel.js).
const guideSetIdInt = parseInt(guideSetId, 10);
// for truncating out of range guideset data find first index of plotDate ending at guideset.trainingEnd
if (plotData.guideSetId === guideSetId && plotData.inGuideSetTrainingRange && guideSetData.TrainingEnd <= this.startDate) {
if (plotData.guideSetId === guideSetIdInt && plotData.inGuideSetTrainingRange && guideSetData.TrainingEnd <= this.startDate) {
this.filterPoints[frag][plotData.MetricId]['filterPointsFirstIndex'] = j + 1;
// ReferenceRangeSeries is used to separate series
plotData['ReferenceRangeSeries'] = "GuideSet";
return false; // stop once the matching guide set is found
}
else {
plotData['ReferenceRangeSeries'] = "InRange";
}

}, this);

// for truncating out of range guideset data find last index of plotData starting from this.startDate
Expand All @@ -365,20 +371,25 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
if (this.showExpRunRange && this.filterPoints) {

for (let i = 0; i < plotDataRows.length; i++) {
Ext4.Object.each(this.filterPoints[plotDataRows[i].SeriesLabel], function (metricId, filterPointsData) {
const seriesPoints = this.filterPoints && this.filterPoints[plotDataRows[i].SeriesLabel];
if (!seriesPoints) {
continue;
}
Ext4.Object.each(seriesPoints, function (metricId, filterPointsData) {
// no need to filter if less than 6 data points are present between reference end of guideset and startdate
if (filterPointsData['filterPointsFirstIndex'] && filterPointsData['filterPointsLastIndex']) {
if (filterPointsData['filterPointsLastIndex'] - filterPointsData['filterPointsFirstIndex'] < 6) {
this.filterQCPoints = false;
// set the startDate field = acquired time of the 1st point of 5 points before the experiment run range

this.getStartDateField().setValue(this.formatDate(plotDataRows[i].data[filterPointsData['filterPointsFirstIndex']].AcquiredTime));
// Fewer than 6 out-of-range points for this series/metric, so there is nothing to truncate
// for it. Flag only this entry rather than clearing the global this.filterQCPoints, so that
// other series still truncate and the separator / guide-set line break still render.
filterPointsData['skipTruncation'] = true;
// set the startDate field = acquired time of the point right before the experiment run range
this.setStartDateFromFilterIndex(plotDataRows[i], filterPointsData['filterPointsFirstIndex']);
}
else { // skip 5 points
filterPointsData['filterPointsLastIndex'] = filterPointsData['filterPointsLastIndex'] - 6;
// set the startDate field = acquired time of the 1st point of 5 points before the experiment run range
// adding 1 as the point is right after filter last index
this.getStartDateField().setValue(this.formatDate(plotDataRows[i].data[filterPointsData['filterPointsLastIndex'] + 1].AcquiredTime));
// set the startDate field = acquired time of the point right after the new filter last index
this.setStartDateFromFilterIndex(plotDataRows[i], filterPointsData['filterPointsLastIndex'] + 1);
}
}
}, this);
Expand All @@ -389,6 +400,42 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
this.renderPlots();
},

// Sets the start-date form field from the AcquiredTime of a point identified by a filterPoints index.
// The filterPoints indices (filterPointsFirstIndex / filterPointsLastIndex) are computed against
// this.fragmentPlotData[label].data, which has injected type:'missing' placeholder entries spliced in
// (see the "add any missing dates" block in processPlotData). plotDataRow.data is the raw server array:
// it has no missing entries and is the only place AcquiredTime is available, so a fragmentPlotData-space
// index cannot be used against it directly. Translate the index to raw-space by counting the non-missing
// entries before it, and guard the lookup so a stale/out-of-range index can never throw.
setStartDateFromFilterIndex: function(plotDataRow, fragIndex) {
if (!plotDataRow || fragIndex == null) {
return;
}
const fragData = this.fragmentPlotData[plotDataRow.SeriesLabel] && this.fragmentPlotData[plotDataRow.SeriesLabel].data;
if (!fragData || fragData.length === 0) {
return;
}
// Walk back to the nearest real (non-missing) entry at or before the requested index
let idx = Math.min(fragIndex, fragData.length - 1);
while (idx >= 0 && fragData[idx] && fragData[idx].type === 'missing') {
idx--;
}
if (idx < 0) {
return;
}
// raw index = number of non-missing entries strictly before idx (missing entries exist only in fragData)
let rawIndex = 0;
for (let k = 0; k < idx; k++) {
if (!fragData[k] || fragData[k].type !== 'missing') {
rawIndex++;
}
}
const rawPoint = plotDataRow.data[rawIndex];
if (rawPoint && rawPoint.AcquiredTime) {
this.getStartDateField().setValue(this.formatDate(rawPoint.AcquiredTime));
}
},

renderPlots: function() {
if (this.filterQCPoints) {
this.truncateOutOfRangeQCPoints();
Expand Down Expand Up @@ -434,7 +481,7 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
Ext4.Object.each(this.fragmentPlotData, function(label, fragmentData) {
// traverse plotData backwards from firstIndex to lastIndex and
// remove them from the array
if (this.filterQCPoints && this.filterPoints) {
if (this.filterQCPoints && this.filterPoints && this.filterPoints[label]) {

// when we're plotting two different metrics at the same time, then we
// have repeated dates (from oldest to newest for metric 1, and then oldest to newest for metric 2, all in the same array).
Expand All @@ -443,6 +490,9 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
const lab = label;

filterPointsReversed.forEach(metricId => {
if (this.filterPoints[lab][metricId]['skipTruncation']) {
return; // too few out-of-range points for this series/metric to truncate
}
let firstIndex = this.filterPoints[lab][metricId]['filterPointsFirstIndex'];
let lastIndex = this.filterPoints[lab][metricId]['filterPointsLastIndex'];

Expand Down
20 changes: 16 additions & 4 deletions webapp/TargetedMS/js/QCTrendPlotPanel.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2325,8 +2325,10 @@ Ext4.define('LABKEY.targetedms.QCTrendPlotPanel', {
.attr('stroke', color).attr('stroke-opacity', 0.1)
.attr('fill', color).attr('fill-opacity', 0.1)
.append("title")
.text(function (d) {
return "Selected replicate: " + Ext4.String.htmlEncode(plot.data[d.EndIndex].ReplicateName);
.text(function () {
// 'data' is the already-matched point for this replicate, don't index plot.data by
// seqValue (EndIndex), which breaks once out-of-range points have been truncated.
return "Selected replicate: " + Ext4.String.htmlEncode(data.ReplicateName);
});

this.sendSvgElementToBack(plot, outlierRect);
Expand Down Expand Up @@ -2399,8 +2401,18 @@ Ext4.define('LABKEY.targetedms.QCTrendPlotPanel', {
var pointsData = precursorInfo.data;
var expDataArr = [];

for (var i = startIndex; i <= endIndex; i++) {
expDataArr.push(pointsData[i].value);
// startIndex/endIndex are seqValues (x-axis positions), not array indices. Once out-of-range
// points are truncated, the array positions no longer line up with seqValue, so collect the
// experiment-range values by matching seqValue rather than indexing pointsData directly.
// In multi-series mode pointsData holds both metrics' points (the same seqValues repeated), so
// restrict to the primary metric - otherwise the experiment-range mean/std-dev/%CV would blend
// values from two different metrics into a single, meaningless statistic.
for (var i = 0; i < pointsData.length; i++) {
if (pointsData[i].seqValue >= startIndex && pointsData[i].seqValue <= endIndex
&& pointsData[i].MetricId === this.metric
&& pointsData[i].value !== undefined && pointsData[i].value !== null) {
expDataArr.push(pointsData[i].value);
}
}

var expMean = LABKEY.targetedms.PlotSettingsUtil.formatNumeric(LABKEY.vis.Stat.getMean(expDataArr));
Expand Down
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