Easy metrics based on replicate and precursor annotation values

api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java

@@ -33,6 +33,7 @@ public class QCMetricConfiguration implements Comparable<QCMetricConfiguration>
     private String _yAxisLabel;
     private Double _upperBound;
     private Double _lowerBound;
+    private String _annotationName;
 
     public int getId()
     {
@@ -164,6 +165,16 @@ public void setLowerBound(Double lowerBound)
         _lowerBound = lowerBound;
     }
 
+    public String getAnnotationName()
+    {
+        return _annotationName;
+    }
+
+    public void setAnnotationName(String annotationName)
+    {
+        _annotationName = annotationName;
+    }
+
     public JSONObject toJSON(){
         JSONObject jsonObject = new JSONObject();
         jsonObject.put("id", _id);
@@ -195,6 +206,9 @@ public JSONObject toJSON(){
         if (_upperBound != null) {
             jsonObject.put("upperBound", _upperBound);
         }
+        if (_annotationName != null) {
+            jsonObject.put("annotationName", _annotationName);
+        }
 
         return jsonObject;
     }

resources/queries/targetedms/qcMetricsConfig.sql

@@ -30,7 +30,8 @@ SELECT
        qmc.MaxTimeValue,
        qmc.TimeValueOption,
        qmc.TraceName,
-       qmc.YAxisLabel
+       qmc.YAxisLabel,
+       qmc.AnnotationName
 FROM
       qcmetricconfiguration qmc
 FULL JOIN   qcenabledmetrics qem

resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql

@@ -0,0 +1 @@
+ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN AnnotationName VARCHAR(200);

resources/schemas/targetedms.xml

@@ -1358,6 +1358,7 @@
             <column columnName="TimeValueOption"/>
             <column columnName="TraceName"/>
             <column columnName="YAxisLabel"/>
+            <column columnName="AnnotationName"/>
         </columns>
     </table>
     <table tableName="QCMetricExclusion" tableDbType="TABLE">

resources/views/configureQCMetric.html

@@ -59,11 +59,14 @@
             });
 
             qcMetricsTable += '</table><br>' +
-                    '<button type="button" class="labkey-button primary" id="saveButton" style="margin-right: 20px;">Save</button>' +
-                    '<button type="button" class="labkey-button" id="cancelButton" style="margin-right: 20px;">Cancel</button>' +
-                    '<button type="button" class="labkey-button" id="createNewCustomMetricButton" style="margin-right: 20px;">Add New Custom Metric</button>' +
-                    '<button type="button" class="labkey-button" id="createNewTraceMetricButton" style="margin-right: 20px;">Add New Trace Metric</button>' +
+                    '<div style="display:flex;flex-wrap:wrap;gap:8px;">' +
+                    '<button type="button" class="labkey-button primary" id="saveButton">Save</button>' +
+                    '<button type="button" class="labkey-button" id="cancelButton">Cancel</button>' +
+                    '<button type="button" class="labkey-button" id="createNewCustomMetricButton">Add New Custom Metric</button>' +
+                    '<button type="button" class="labkey-button" id="createNewTraceMetricButton">Add New Trace Metric</button>' +
+                    '<button type="button" class="labkey-button" id="createNewAnnotationMetricButton">Add Annotation-Backed Metric</button>' +
                     '<button type="button" class="labkey-button" id="clearCacheButton">Clear Cached Metric Values</button>' +
+                    '</div>' +
                     '</form><br>Edits to queries backing existing custom metrics require a manual cache clearing to display the updated results.</p>';
 
             jQuery('#qcMetricsTable').html(qcMetricsTable);
@@ -80,7 +83,10 @@
                 LABKEY.internal.ConfigureQCMetrics.addNewMetric('custom');
             });
             jQuery('#createNewTraceMetricButton').click(function() {
-                LABKEY.internal.ConfigureQCMetrics.addNewMetric('trace')
+                LABKEY.internal.ConfigureQCMetrics.addNewMetric('trace');
+            });
+            jQuery('#createNewAnnotationMetricButton').click(function() {
+                LABKEY.internal.ConfigureQCMetrics.addNewMetric('annotation');
             });
             jQuery('#clearCacheButton').click(function() {
                 jQuery('#qcMetricsError').text('Clearing cached metrics...');
@@ -169,7 +175,10 @@
 
                 const op = 'update';
                 if (clickedQcMetricConfig.TraceName) {
-                    LABKEY.internal.ConfigureQCMetrics.showTraceMetricWindow(op, clickedQcMetricConfig)
+                    LABKEY.internal.ConfigureQCMetrics.showTraceMetricWindow(op, clickedQcMetricConfig);
+                }
+                else if (clickedQcMetricConfig.AnnotationName) {
+                    LABKEY.internal.ConfigureQCMetrics.showAnnotationMetricWindow(op, clickedQcMetricConfig);
                 }
                 else {
                     LABKEY.internal.ConfigureQCMetrics.showCustomMetricWindow(op, clickedQcMetricConfig);
@@ -242,13 +251,27 @@
                 });
             },
 
+            showAnnotationMetricWindow: function (op, clickedMetric) {
+                const windowConfig = {
+                    parent: this,
+                    operation: op
+                };
+                if (clickedMetric) {
+                    windowConfig.metric = clickedMetric;
+                }
+                Panorama.Window.AddAnnotationMetricWindow.show(windowConfig);
+            },
+
             addNewMetric: function (metricType) {
                 const op = 'insert';
                 if (metricType === 'custom') {
                     this.showCustomMetricWindow(op);
                 }
                 else if (metricType === 'trace') {
-                    this.showTraceMetricWindow(op)
+                    this.showTraceMetricWindow(op);
+                }
+                else if (metricType === 'annotation') {
+                    this.showAnnotationMetricWindow(op);
                 }
             },
 

resources/views/configureQCMetric.view.xml

@@ -7,6 +7,7 @@
         <dependency path="Ext4"/>
         <dependency path="PanoramaPremium/window/AddNewMetricWindow.js"/>
         <dependency path="PanoramaPremium/window/AddNewTraceMetricWindow.js"/>
+        <dependency path="PanoramaPremium/window/AddNewAnnotationMetricWindow.js"/>
         <dependency path="TargetedMS/js/misc.js"/>
     </dependencies>
 </view>

resources/web/PanoramaPremium/window/AddNewAnnotationMetricWindow.js

@@ -0,0 +1,226 @@
+/*
+ * Copyright (c) 2025 LabKey Corporation. All rights reserved. No portion of this work may be reproduced in
+ * any form or by any electronic or mechanical means without written permission from LabKey Corporation.
+ */
+
+(function($) {
+    window.Panorama = window.Panorama || {};
+    window.Panorama.Window = window.Panorama.Window || {};
+
+    const DIALOG_ID = 'lk-annotation-metric-dialog';
+    let _config = null;
+    let _allAnnotations = [];
+
+    function closeDialog() {
+        $('#' + DIALOG_ID).remove();
+    }
+
+    function showError(msg) {
+        $('#lk-annotation-metric-error').text(msg).show();
+    }
+
+    function clearErrors() {
+        $('#lk-annotation-metric-error').hide().text('');
+        $('#lk-annotation-metric-name, #lk-annotation-metric-ylabel, #lk-annotation-name-select')
+            .css('border-color', '');
+    }
+
+    function markInvalid($field) {
+        $field.css('border-color', 'red');
+    }
+
+    function validate() {
+        clearErrors();
+        let isValid = true;
+
+        if (!$('#lk-annotation-metric-name').val().trim()) {
+            markInvalid($('#lk-annotation-metric-name'));
+            isValid = false;
+        }
+        if (!$('#lk-annotation-metric-ylabel').val().trim()) {
+            markInvalid($('#lk-annotation-metric-ylabel'));
+            isValid = false;
+        }
+        if (!$('#lk-annotation-name-select').val()) {
+            markInvalid($('#lk-annotation-name-select'));
+            isValid = false;
+        }
+
+        if (!isValid) {
+            showError('Please fill in all required fields.');
+        }
+        return isValid;
+    }
+
+    function getAnnotationTarget() {
+        return $('input[name="annotationType"]:checked').val() === 'precursor'
+            ? 'precursor_result'
+            : 'replicate';
+    }
+
+    function getFilteredAnnotations() {
+        const target = getAnnotationTarget();
+        const seen = {};
+        const result = [];
+        _allAnnotations.forEach(function(row) {
+            const targets = (row['Targets'] || '').split(',').map(function(s) { return s.trim(); });
+            if (targets.indexOf(target) >= 0 && !seen[row['Name']]) {
+                seen[row['Name']] = true;
+                result.push(row['Name']);
+            }
+        });
+        result.sort();
+        return result;
+    }
+
+    function refreshAnnotationsSelect() {
+        const $select = $('#lk-annotation-name-select');
+        const currentVal = $select.val();
+        $select.empty().append($('<option>').val('').text('-- Select annotation --'));
+        getFilteredAnnotations().forEach(function(name) {
+            $select.append($('<option>').val(name).text(name));
+        });
+
+        const metric = _config && _config.metric;
+        if (_config.operation === 'update' && metric && metric.AnnotationName) {
+            $select.val(metric.AnnotationName);
+        } else if (currentVal) {
+            $select.val(currentVal);
+        }
+    }
+
+    function checkMetricNameExists(metricName, callback) {
+        const filterArray = [LABKEY.Filter.create('Name', metricName, LABKEY.Filter.Types.EQUAL)];
+        if (_config.operation === 'update' && _config.metric) {
+            filterArray.push(LABKEY.Filter.create('id', _config.metric.id, LABKEY.Filter.Types.NOT_EQUAL));
+        }
+        LABKEY.Query.selectRows({
+            containerPath: LABKEY.container.id,
+            schemaName: 'targetedms',
+            queryName: 'qcmetricconfiguration',
+            filterArray: filterArray,
+            success: function(data) { callback(data.rows.length > 0); },
+            failure: function() { callback(false); }
+        });
+    }
+
+    function save() {
+        if (!validate()) return;
+
+        const metricName = $('#lk-annotation-metric-name').val().trim();
+        checkMetricNameExists(metricName, function(exists) {
+            if (exists) {
+                showError('A metric with the name "' + LABKEY.Utils.encodeHtml(metricName) + '" already exists. Please choose a different name.');
+                markInvalid($('#lk-annotation-metric-name'));
+                return;
+            }
+
+            const newMetric = {
+                Name: metricName,
+                QueryName: 'QCAnnotationMetric',
+                YAxisLabel: $('#lk-annotation-metric-ylabel').val().trim(),
+                PrecursorScoped: $('input[name="annotationType"]:checked').val() === 'precursor',
+                AnnotationName: $('#lk-annotation-name-select').val()
+            };
+            if (_config.operation === 'update') {
+                newMetric.id = _config.metric.id;
+            }
+
+            LABKEY.Query.saveRows({
+                containerPath: LABKEY.container.id,
+                commands: [{ schemaName: 'targetedms', queryName: 'qcmetricconfiguration', command: _config.operation, rows: [newMetric] }],
+                method: 'POST',
+                success: function() { window.location.reload(); },
+                failure: function(response) {
+                    showError((response && (response.exception || response.message)) || 'Error saving metric');
+                }
+            });
+        });
+    }
+
+    function deleteMetric() {
+        if (!confirm('This will delete the "' + _config.metric.name + '" metric. Are you sure?')) return;
+
+        LABKEY.Query.saveRows({
+            containerPath: LABKEY.container.id,
+            commands: [
+                { schemaName: 'targetedms', queryName: 'qcenabledmetrics', command: 'delete', rows: [{ metric: _config.metric.id }] },
+                { schemaName: 'targetedms', queryName: 'qcmetricconfiguration', command: 'delete', rows: [{ id: _config.metric.id }] }
+            ],
+            method: 'POST',
+            success: function() { window.location.reload(); },
+            failure: function(response) {
+                showError((response && (response.exception || response.message)) || 'Error deleting metric');
+            }
+        });
+    }
+
+    function buildDialogHtml() {
+        const op = _config.operation;
+        const metric = _config.metric || {};
+        const isPrecursor = op === 'update' && metric.PrecursorScoped;
+        const title = op === 'insert' ? 'Add Annotation-Backed Metric' : 'Edit Annotation-Backed Metric';
+
+        return '<div id="' + DIALOG_ID + '" style="position:fixed;top:0;left:0;width:100%;height:100%;background:rgba(0,0,0,0.5);z-index:9999;display:flex;align-items:center;justify-content:center;">'
+            + '<div class="x4-window x4-window-default" style="min-width:480px;max-width:580px;">'
+            +   '<div class="x4-window-header x4-window-header-default x4-window-header-default-top" style="padding:4px 8px;border:none;">'
+            +     '<p class="x4-window-header-text-container-default" style="font-size:14px;margin:0;">' + LABKEY.Utils.encodeHtml(title) + '</p>'
+            +   '</div>'
+            +   '<div class="x4-window-body" style="background:white;padding:10px 12px;">'
+            +     '<table style="border-collapse:collapse;width:100%;">'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;"><label for="lk-annotation-metric-name">Metric Name *</label></td>'
+            +           '<td style="padding:5px 0;"><input type="text" id="lk-annotation-metric-name" style="width:100%;box-sizing:border-box;" value="' + LABKEY.Utils.encodeHtml(metric.name || '') + '"/></td></tr>'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;"><label for="lk-annotation-metric-ylabel">Y-Axis Label *</label></td>'
+            +           '<td style="padding:5px 0;"><input type="text" id="lk-annotation-metric-ylabel" style="width:100%;box-sizing:border-box;" value="' + LABKEY.Utils.encodeHtml(metric.YAxisLabel || '') + '"/></td></tr>'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;">Annotation Type</td>'
+            +           '<td style="padding:5px 0;">'
+            +             '<label style="margin-right:16px;"><input type="radio" name="annotationType" value="replicate"' + (!isPrecursor ? ' checked' : '') + '> Replicate</label>'
+            +             '<label><input type="radio" name="annotationType" value="precursor"' + (isPrecursor ? ' checked' : '') + '> Precursor</label>'
+            +           '</td></tr>'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;"><label for="lk-annotation-name-select">Annotation *</label></td>'
+            +           '<td style="padding:5px 0;"><select id="lk-annotation-name-select" style="width:100%;box-sizing:border-box;"><option value="">Loading...</option></select></td></tr>'
+            +     '</table>'
+            +     '<div id="lk-annotation-metric-error" class="labkey-error" style="display:none;margin-top:8px;"></div>'
+            +     '<div style="margin-top:12px;text-align:right;">'
+            +       '<button type="button" class="labkey-button" id="lk-annotation-metric-cancel">Cancel</button>'
+            +       (op === 'update' ? ' <button type="button" class="labkey-button" id="lk-annotation-metric-delete">Delete</button>' : '')
+            +       ' <button type="button" class="labkey-button primary" id="lk-annotation-metric-save">Save</button>'
+            +     '</div>'
+            +   '</div>'
+            + '</div>'
+            + '</div>';
+    }
+
+    window.Panorama.Window.AddAnnotationMetricWindow = {
+        show: function(config) {
+            _config = config;
+            _allAnnotations = [];
+
+            $('#' + DIALOG_ID).remove();
+            $('body').append(buildDialogHtml());
+
+            $('#lk-annotation-metric-cancel').on('click', closeDialog);
+            $('#lk-annotation-metric-save').on('click', save);
+            if (config.operation === 'update') {
+                $('#lk-annotation-metric-delete').on('click', deleteMetric);
+            }
+            $('input[name="annotationType"]').on('change', refreshAnnotationsSelect);
+
+            // close on overlay click
+            $('#' + DIALOG_ID).on('click', function(e) {
+                if (e.target === this) closeDialog();
+            });
+
+            LABKEY.Query.selectRows({
+                schemaName: 'targetedms',
+                queryName: 'AnnotationSettings',
+                columns: ['Name', 'Targets', 'Type'],
+                filterArray: [LABKEY.Filter.create('Type', 'number', LABKEY.Filter.Types.EQUAL)],
+                success: function(data) {
+                    _allAnnotations = data.rows || [];
+                    refreshAnnotationsSelect();
+                }
+            });
+        }
+    };
+})(jQuery);

src/org/labkey/targetedms/TargetedMSModule.java

@@ -231,7 +231,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.006;
+        return 26.008;
     }
 
     @Override