Easy metrics based on replicate and precursor annotation values #1210
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN AnnotationName VARCHAR(200); | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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'; | ||
|
labkey-jeckels marked this conversation as resolved.
|
||
| } | ||
|
|
||
| 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, | ||
|
ankurjuneja marked this conversation as resolved.
Outdated
|
||
| 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, | ||
|
ankurjuneja marked this conversation as resolved.
Outdated
|
||
| 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;">' | ||
|
labkey-jeckels marked this conversation as resolved.
|
||
| + '<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); | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -231,7 +231,7 @@ public String getName() | |
| @Override | ||
| public Double getSchemaVersion() | ||
| { | ||
| return 26.008; | ||
| } | ||
|
|
||
| @Override | ||
|
|
||
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.