[bot] Fast-forward for 26.3.10

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/protein/Sequences.query.xml

@@ -0,0 +1,13 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="Sequences" tableDbType="TABLE">
+                <columns>
+                    <column columnName="ProtSequence">
+                        <displayWidth>200</displayWidth>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

resources/queries/targetedms/Protein/.qview.xml

@@ -0,0 +1,16 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+            label="Proteins" canOverride="true">
+    <columns>
+        <column name="Label" />
+        <column name="Description" />
+        <column name="Accession" />
+        <column name="PreferredName" />
+        <column name="Gene" />
+        <column name="Species" />
+
+        <column name="SequenceId/ProtSequence" />
+        <column name="Note" />
+
+    </columns>
+
+</customView>

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-26.006-26.007.sql

@@ -0,0 +1,34 @@
+ALTER TABLE targetedms.Runs ADD COLUMN ProteinCount INT;
+
+UPDATE targetedms.Runs r
+SET ProteinCount = (
+    SELECT COUNT(*)
+    FROM targetedms.Protein p
+    JOIN targetedms.PeptideGroup pg ON p.PeptideGroupId = pg.Id
+    WHERE pg.RunId = r.Id
+);
+
+-- Redefine PeptideGroupCount: groups containing at least one peptide
+UPDATE targetedms.Runs r
+SET PeptideGroupCount = (
+    SELECT COUNT(DISTINCT pg.Id)
+    FROM targetedms.PeptideGroup pg
+    JOIN targetedms.GeneralMolecule gm ON gm.PeptideGroupId = pg.Id
+    JOIN targetedms.Peptide p ON p.Id = gm.Id
+    WHERE pg.RunId = r.Id
+);
+
+ALTER TABLE targetedms.Runs ADD COLUMN MoleculeGroupCount INT;
+
+UPDATE targetedms.Runs r
+SET MoleculeGroupCount = (
+    SELECT COUNT(DISTINCT pg.Id)
+    FROM targetedms.PeptideGroup pg
+    JOIN targetedms.GeneralMolecule gm ON gm.PeptideGroupId = pg.Id
+    JOIN targetedms.Molecule m ON m.Id = gm.Id
+    WHERE pg.RunId = r.Id
+);
+
+ALTER TABLE targetedms.Runs ALTER COLUMN MoleculeGroupCount SET NOT NULL;
+ALTER TABLE targetedms.Runs ALTER COLUMN PeptideGroupCount SET NOT NULL;
+ALTER TABLE targetedms.Runs ALTER COLUMN ProteinCount SET NOT NULL;

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

@@ -0,0 +1 @@
+ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN AnnotationName VARCHAR(255);

resources/schemas/targetedms.xml

@@ -179,15 +179,23 @@
             <column columnName="DocumentGUID"/>
             <column columnName="PeptideGroupCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showPeptideGroupList.view?id=${Id}</url>
+            </column>
+            <column columnName="MoleculeGroupCount">
+                <formatString>#,###</formatString>
+                <url>/targetedms-showMoleculeGroupList.view?id=${Id}</url>
+            </column>
+            <column columnName="ProteinCount">
+                <formatString>#,###</formatString>
+                <url>/targetedms-showProteinList.view?id=${Id}</url>
             </column>
             <column columnName="PeptideCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showPeptideList.view?id=${Id}</url>
             </column>
             <column columnName="SmallMoleculeCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showMoleculeList.view?id=${Id}</url>
             </column>
             <column columnName="PrecursorCount">
                 <formatString>#,###</formatString>
@@ -1358,6 +1366,7 @@
             <column columnName="TimeValueOption"/>
             <column columnName="TraceName"/>
             <column columnName="YAxisLabel"/>
+            <column columnName="AnnotationName"/>
         </columns>
     </table>
     <table tableName="QCMetricExclusion" tableDbType="TABLE">

resources/views/configureQCMetric.html

@@ -12,6 +12,10 @@
         LABKEY.internal = {};
 
     LABKEY.internal.ConfigureQCMetrics = new function () {
+        const METRIC_TYPE_CUSTOM = 'custom';
+        const METRIC_TYPE_TRACE = 'trace';
+        const METRIC_TYPE_ANNOTATION = 'annotation';
+
         let qcMetrics;
         let qcMetricsTable ='';
         let configRows = [];
@@ -36,7 +40,7 @@
                 qcMetricsTable += '<tr class="' + rowClass + '">';
 
                 qcMetricsTable += '<td>' + (editLock ? '<a id="editLink' + row.id + '" href="#">' : '' ) + LABKEY.Utils.encodeHtml(row.name) + '</td>' + (editLock ? '</a>' : '' );
-                qcMetricsTable += '<td>' + (row.PrecursorScoped ? 'Precursor' : 'Run') + '</td>';
+                qcMetricsTable += '<td>' + (row.PrecursorScoped ? 'Precursor' : 'Replicate') + '</td>';
 
                 if (row.EffectiveStatus === 'NoData') {
                     qcMetricsTable += '<td id=\"' + LABKEY.Utils.encodeHtml(row.name) + '\">No data in this folder</td>';
@@ -59,11 +63,14 @@
             });
 
             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);
@@ -77,10 +84,13 @@
                 LABKEY.internal.ConfigureQCMetrics.resetQCMetrics();
             });
             jQuery('#createNewCustomMetricButton').click(function() {
-                LABKEY.internal.ConfigureQCMetrics.addNewMetric('custom');
+                LABKEY.internal.ConfigureQCMetrics.addNewMetric(METRIC_TYPE_CUSTOM);
             });
             jQuery('#createNewTraceMetricButton').click(function() {
-                LABKEY.internal.ConfigureQCMetrics.addNewMetric('trace')
+                LABKEY.internal.ConfigureQCMetrics.addNewMetric(METRIC_TYPE_TRACE);
+            });
+            jQuery('#createNewAnnotationMetricButton').click(function() {
+                LABKEY.internal.ConfigureQCMetrics.addNewMetric(METRIC_TYPE_ANNOTATION);
             });
             jQuery('#clearCacheButton').click(function() {
                 jQuery('#qcMetricsError').text('Clearing cached metrics...');
@@ -169,7 +179,10 @@
 
                 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);
@@ -181,22 +194,11 @@
             },
 
             showCustomMetricWindow: function (op, clickedMetric) {
-                LABKEY.Query.getSchemas({
-                    scope: this,
-                    containerPath: LABKEY.container.id,
-                    success:  function(schemasInfo) {
-                        const windowConfig = {
-                            parent: this,
-                            schemas: schemasInfo.schemas,
-                            operation: op
-                        };
-
-                        if (clickedMetric) {
-                            windowConfig.metric = clickedMetric;
-                        }
-                        Ext4.create('Panorama.Window.AddCustomMetricWindow', windowConfig).show();
-                    }
-                });
+                const windowConfig = { operation: op };
+                if (clickedMetric) {
+                    windowConfig.metric = clickedMetric;
+                }
+                Panorama.Window.AddCustomMetricWindow.show(windowConfig);
             },
 
             showTraceMetricWindow: function (op, clickedMetric) {
@@ -242,13 +244,27 @@
                 });
             },
 
+            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') {
+                if (metricType === METRIC_TYPE_CUSTOM) {
                     this.showCustomMetricWindow(op);
                 }
-                else if (metricType === 'trace') {
-                    this.showTraceMetricWindow(op)
+                else if (metricType === METRIC_TYPE_TRACE) {
+                    this.showTraceMetricWindow(op);
+                }
+                else if (metricType === METRIC_TYPE_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>