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Issue 50945: Show counts per metric for outliers in QC Summary view of all replicates #953

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merged 4 commits into from
Aug 28, 2024
Merged

Issue 50945: Show counts per metric for outliers in QC Summary view of all replicates #953

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59a1c04
Issue 50945: Show counts per metric for outliers in QC Summary view o…
ankurjuneja Aug 23, 2024
e2eee07
Merge branch 'develop' into fb_Issue50945
ankurjuneja Aug 27, 2024
80eb0da
fix when to show full table vs summary
ankurjuneja Aug 27, 2024
4fe4588
code review suggestion - html encode
ankurjuneja Aug 27, 2024
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18 changes: 11 additions & 7 deletions resources/views/peptideSummary.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,10 @@
margin-top: 1em;
}

.outlier-count {
text-align: right
}

</style>

<label for="date-range">Date Range:</label>
Expand Down Expand Up @@ -161,7 +165,7 @@
function generateTable(data) {
$('#fom-loading').hide();
const tableContainer = document.getElementById('table-container');
let tableHTML = '<table id="heatmap-table" class="heatmap-table">';
let tableHTML = '<table id="heatmap-table" class="table-condensed labkey-data-region-legacy labkey-show-borders">';
tableHTML += '<thead><tr><th></th>';

for (let i = 0; i < data.metrics.length; i++) {
Expand Down Expand Up @@ -191,7 +195,7 @@
for (let j = 0; j < data.metrics.length; j++) {
let metric = data.metrics[j];
if (data.peptideOutliers[i].outlierCountsPerMetric[metric]) {
tableHTML += '<td>' + data.peptideOutliers[i].outlierCountsPerMetric[metric] + '</td>';
tableHTML += '<td class="outlier-count">' + data.peptideOutliers[i].outlierCountsPerMetric[metric] + '</td>';
if (!totalOutliersByMetric[metric]) {
totalOutliersByMetric[metric] = 0;
}
Expand All @@ -200,11 +204,11 @@

}
else {
tableHTML += '<td>0</td>';
tableHTML += '<td class="outlier-count">0</td>';
}

if (j === data.metrics.length - 1) {
tableHTML += '<td><b>' + LABKEY.Utils.encodeHtml(data.peptideOutliers[i].totalOutliers) + '</b></td>';
tableHTML += '<td class="outlier-count"><b>' + LABKEY.Utils.encodeHtml(data.peptideOutliers[i].totalOutliers) + '</b></td>';
}
}
tableHTML += '</tr>';
Expand All @@ -215,13 +219,13 @@
for (let i = 0; i < data.metrics.length; i++) {
if (totalOutliersByMetric[data.metrics[i]]) {
sumOfOutliers += totalOutliersByMetric[data.metrics[i]];
tableHTML += '<td><b>' + LABKEY.Utils.encodeHtml(totalOutliersByMetric[data.metrics[i]]) + '</b></td>';
tableHTML += '<td class="outlier-count"><b>' + LABKEY.Utils.encodeHtml(totalOutliersByMetric[data.metrics[i]]) + '</b></td>';
}
else {
tableHTML += '<td><b>0</b></td>';
tableHTML += '<td class="outlier-count"><b>0</b></td>';
}
}
tableHTML += '<td><b>' + sumOfOutliers + '</b></td>';
tableHTML += '<td class="outlier-count"><b>' + sumOfOutliers + '</b></td>';
tableHTML += '</tbody></table>';
tableContainer.innerHTML = tableHTML;

Expand Down
105 changes: 66 additions & 39 deletions webapp/TargetedMS/js/QCSummaryPanel.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,7 @@ Ext4.define('LABKEY.targetedms.QCSummary', {
getContainerSummaryView: function (container, hasChildren, width) {
container.viewCmpId = Ext4.id();
container.autoQcCalloutId = Ext4.id();
container.width = width;

var config = {
id: container.viewCmpId,
Expand Down Expand Up @@ -296,49 +297,75 @@ Ext4.define('LABKEY.targetedms.QCSummary', {
},

renderContainerSampleFileStats: function (params) {
var container = params.container;
var html = '<table class="table-condensed labkey-data-region-legacy labkey-show-borders">';
html += '<thead><tr><td></td></td><td class="labkey-column-header">Replicate Name</td><td class="labkey-column-header">Acquired</td><td class="labkey-column-header">Outliers</td></tr></thead>';
var sampleFiles = params.sampleFiles;
Ext4.iterate(sampleFiles, function (sampleFile) {
// create a new div id for each sampleFile to use for the hover details callout
sampleFile.calloutId = Ext4.id();

var totalOutliers = sampleFile.Value;

var iconCls;
if (sampleFile.IgnoreForAllMetric)
iconCls = 'fa-ban qc-none';
else if (totalOutliers > 0)
iconCls = 'fa-times-rectangle qc-error';
else
iconCls = 'fa-check qc-correct';
html += '<tr id="' + sampleFile.calloutId + '"><td>'
+ '<span class="fa ' + iconCls + '" style="width: 1em; text-align: center"></span></td><td><div class="sample-file-item">' + Ext4.util.Format.htmlEncode(sampleFile.ReplicateName) + '</div></td><td><div class="sample-file-item-acquired">' + Ext4.util.Format.date(sampleFile.AcquiredTime ? new Date(sampleFile.AcquiredTime) : null, LABKEY.extDefaultDateTimeFormat || 'Y-m-d H:i:s') + '</div></td>';

if (sampleFile.IgnoreForAllMetric) {
html += '<td><div class="sample-file-item-total-outliers" style="text-align: center">excluded</div></td>';
}
else {
html += '<td style="text-align: right"><div class="sample-file-item-total-outliers">' + totalOutliers + "</div></td>"
}
html += '</tr>';
let container = params.container;
let sampleFiles = params.sampleFiles;
let metrics = sampleFiles[0].Metrics;
let showMetrics = container.fileCount <= sampleFiles.length && metrics && metrics.length > 0;
let tableWidth = container.width - 100;
let html = '';
let thead = '';
if (showMetrics) {
html = '<table class="table-condensed labkey-data-region-legacy labkey-show-borders" style="width: ' + tableWidth + 'px">';
thead = '<thead><tr><td></td></td><td class="labkey-column-header">Replicate Name</td><td class="labkey-column-header">Acquired</td>';
Ext4.each(metrics, function (item) {
thead += '<td class="labkey-column-header">' + Ext4.util.Format.htmlEncode(item.MetricLabel) + '</td>';
});
html += '</table>';
if (container.fileCount > sampleFiles.length) {
html += '<div class="qc-summary-text"><a href="' + LABKEY.ActionURL.buildURL('targetedms', 'qcSummaryHistory.view', container.path) + '">View all ' + container.fileCount + ' replicates and utilization calendar <span class="fa fa-calendar"></span></a></div>';
thead += '<td class="labkey-column-header"><b>Total</b></td>';
}
else {
html = '<table class="table-condensed labkey-data-region-legacy labkey-show-borders">';
thead = '<thead><tr><td></td></td><td class="labkey-column-header">Replicate Name</td><td class="labkey-column-header">Acquired</td><td class="labkey-column-header">Outliers</td>';
}

thead += '</tr></thead>';
html += thead;

Ext4.iterate(sampleFiles, function (sampleFile) {
// create a new div id for each sampleFile to use for the hover details callout
sampleFile.calloutId = Ext4.id();

var totalOutliers = sampleFile.Value;

var iconCls;
if (sampleFile.IgnoreForAllMetric)
iconCls = 'fa-ban qc-none';
else if (totalOutliers > 0)
iconCls = 'fa-times-rectangle qc-error';
else
iconCls = 'fa-check qc-correct';
html += '<tr id="' + sampleFile.calloutId + '"><td>'
+ '<span class="fa ' + iconCls + '" style="width: 1em; text-align: center"></span></td><td><div class="sample-file-item">' + Ext4.util.Format.htmlEncode(sampleFile.ReplicateName) + '</div></td><td><div class="sample-file-item-acquired" style="text-wrap: nowrap">' + Ext4.util.Format.date(sampleFile.AcquiredTime ? new Date(sampleFile.AcquiredTime) : null, LABKEY.extDefaultDateTimeFormat || 'Y-m-d H:i:s') + '</div></td>';
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We should HTML encode the formatted time just to be safe.




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>';
});
}
var sampleFilesDiv = Ext4.get('qc-summary-samplefiles-' + container.id);
sampleFilesDiv.update(html);
sampleFilesDiv.removeCls('sample-file-details-loading');
if (sampleFile.IgnoreForAllMetric) {
html += '<td><div class="sample-file-item-total-outliers" style="text-align: center"><b>excluded</b></div></td>';
}
else {
html += '<td><div class="sample-file-item-total-outliers" style="text-align: right"><b>' + totalOutliers + "</b></div></td>"
}
html += '</tr>';
});
html += '</table>';
if (container.fileCount > sampleFiles.length) {
html += '<div class="qc-summary-text"><a href="' + LABKEY.ActionURL.buildURL('targetedms', 'qcSummaryHistory.view', container.path) + '">View all ' + container.fileCount + ' replicates and utilization calendar <span class="fa fa-calendar"></span></a></div>';
}
var sampleFilesDiv = Ext4.get('qc-summary-samplefiles-' + container.id);
sampleFilesDiv.update(html);
sampleFilesDiv.removeCls('sample-file-details-loading');

// since the height of the panel will change from adding up to three lines of text, need to reset the size of the view
this.doLayout();
// since the height of the panel will change from adding up to three lines of text, need to reset the size of the view
this.doLayout();

// add a hover listener for each of the sample file divs
Ext4.iterate(sampleFiles, function (sampleFile) {
this.showSampleFileStatsDetails(sampleFile.calloutId, sampleFile);
}, this);
// add a hover listener for each of the sample file divs
Ext4.iterate(sampleFiles, function (sampleFile) {
this.showSampleFileStatsDetails(sampleFile.calloutId, sampleFile);
}, this);
},

showSampleFileStatsDetails : function(divId, sampleFile) {
Expand Down