Cache precursor-scoped metrics for better reporting performance

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

@@ -24,7 +24,6 @@ public class QCMetricConfiguration implements Comparable<QCMetricConfiguration>
     private String _name;
     private String _queryName;
     private boolean _precursorScoped;
-    private String _enabledQueryName;
     private QCMetricStatus _status;
     private String _traceName;
     private Double _minTimeValue;
@@ -75,16 +74,6 @@ public void setPrecursorScoped(boolean precursorScoped)
         _precursorScoped = precursorScoped;
     }
 
-    public String getEnabledQueryName()
-    {
-        return _enabledQueryName;
-    }
-
-    public void setEnabledQueryName(String enabledQueryName)
-    {
-        _enabledQueryName = enabledQueryName;
-    }
-
     public QCMetricStatus getStatus()
     {
         return _status;
@@ -182,9 +171,6 @@ public JSONObject toJSON(){
         jsonObject.put("queryName", _queryName);
         jsonObject.put("precursorScoped",  _precursorScoped);
         jsonObject.put("metricStatus", getStatus() == null ? QCMetricStatus.DEFAULT.toString() : getStatus().toString());
-        if (_enabledQueryName != null) {
-            jsonObject.put("enabledQueryName", _enabledQueryName);
-        }
         if (_traceName != null) {
             jsonObject.put("traceName", _traceName);
         }

resources/queries/targetedms/QCMetric_massErrorTransition.sql

@@ -18,11 +18,12 @@ SELECT * FROM (
                       pci.Id AS PrecursorChromInfoId,
                       SampleFileId AS SampleFileId,
                       -- Use the error from the most intense transition associated with the precursor
-                      (SELECT COALESCE(MassErrorPPM, -1000) AS MetricValue
+                      (SELECT COALESCE(MassErrorPPM, -100000) AS MetricValue
                        FROM TransitionChromInfo tci
                        WHERE TransitionId.Charge IS NOT NULL
                          AND tci.PrecursorChromInfoId = pci.Id
                          AND Area IS NOT NULL
                        ORDER BY Area DESC, Id LIMIT 1) AS MetricValue FROM PrecursorChromInfo pci
  ) X
 WHERE MetricValue IS NOT NULL
+AND MetricValue != -100000

resources/queries/targetedms/QCMetric_peakArea.sql

@@ -17,4 +17,9 @@ SELECT
   Id AS PrecursorChromInfoId,
   SampleFileId AS SampleFileId,
   TotalArea AS MetricValue
-FROM PrecursorChromInfo
+FROM PrecursorChromInfo
+WHERE
+    -- Ensure we have precursor areas for peptides or small molecules
+    EXISTS (SELECT * FROM QCMetricEnabled_precursorArea)
+    -- Ensure we have transition areas for peptides or small molecules
+    AND EXISTS (SELECT * FROM QCMetricEnabled_transitionArea)

resources/queries/targetedms/QCMetric_precursorArea.sql

@@ -14,7 +14,9 @@
  * limitations under the License.
  */
 SELECT
-  Id AS PrecursorChromInfoId,
-  SampleFileId AS SampleFileId,
-  TotalPrecursorArea AS MetricValue
-FROM PrecursorChromInfo
+    Id AS PrecursorChromInfoId,
+    SampleFileId AS SampleFileId,
+    TotalPrecursorArea AS MetricValue
+FROM PrecursorChromInfo
+WHERE
+    EXISTS (SELECT * FROM QCMetricEnabled_precursorArea)

resources/queries/targetedms/QCMetric_transitionArea.sql

@@ -17,4 +17,6 @@ SELECT
   Id AS PrecursorChromInfoId,
   SampleFileId AS SampleFileId,
   TotalNonPrecursorArea AS MetricValue
-FROM PrecursorChromInfo
+FROM PrecursorChromInfo
+WHERE
+  EXISTS (SELECT * FROM QCMetricEnabled_transitionArea)

resources/queries/targetedms/qcMetricsConfig.sql

@@ -20,7 +20,6 @@ SELECT
        qmc.QueryName,
        qmc.PrecursorScoped,
        qmc.Container, -- including to lock out editing pre-configured qc metrics,
-       qmc.EnabledQueryName,
        qem.Status,
        CASE WHEN qem.metric IS NULL THEN FALSE
             ELSE TRUE END AS Inserted,

resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql

@@ -0,0 +1,21 @@
+CREATE TABLE targetedms.QCMetricCache
+(
+    Container       entityid NOT NULL,
+    MetricId        INT NOT NULL,
+    PrecursorChromInfoId BIGINT,
+    SampleFileId    BIGINT NOT NULL,
+    MetricValue     REAL,
+    SeriesLabel     VARCHAR(200),
+
+    CONSTRAINT PK_QCMetricCache PRIMARY KEY (Container, MetricId, PrecursorChromInfoId),
+    CONSTRAINT FK_QCMetricCache_PrecursorChromInfoId FOREIGN KEY (PrecursorChromInfoId) REFERENCES targetedms.PrecursorChromInfo(Id),
+    CONSTRAINT FK_QCMetricCache_SampleFileId FOREIGN KEY (SampleFileId) REFERENCES targetedms.SampleFile(Id),
+    CONSTRAINT FK_QCMetricCache_MetricIdId FOREIGN KEY (MetricId) REFERENCES targetedms.QCMetricConfiguration(Id),
+    CONSTRAINT FK_QCMetricCache_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId)
+);
+
+CREATE INDEX IDX_QCMetricCache_PrecursorChromInfoId ON targetedms.QCMetricCache(PrecursorChromInfoId);
+CREATE INDEX IDX_QCMetricCache_SampleFileId ON targetedms.QCMetricCache(SampleFileId);
+CREATE INDEX IDX_QCMetricCache_MetricId ON targetedms.QCMetricCache(MetricId);
+
+ALTER TABLE targetedms.QCMetricConfiguration DROP COLUMN EnabledQueryName;

resources/schemas/targetedms.xml

@@ -1349,7 +1349,6 @@
             <column columnName="Name"/>
             <column columnName="QueryName"/>
             <column columnName="PrecursorScoped"/>
-            <column columnName="EnabledQueryName"/>
             <column columnName="TraceValue"/>
             <column columnName="MinTimeValue"/>
             <column columnName="MaxTimeValue"/>
@@ -1940,4 +1939,14 @@
             <column columnName="Nickname"/>
         </columns>
     </table>
+    <table tableName="QCMetricCache" tableDbType="TABLE">
+        <columns>
+            <column columnName="Container"/>
+            <column columnName="MetricId"/>
+            <column columnName="PrecursorChromInfoId"/>
+            <column columnName="SampleFileId"/>
+            <column columnName="MetricValue"/>
+            <column columnName="SeriesLabel"/>
+        </columns>
+    </table>
 </tables>

resources/views/configureQCMetric.html

@@ -4,7 +4,8 @@
 </p>
 
 <div id="qcMetricsTable">Loading...</div>
-<div id="qcMetricsError"></div>
+<div id="qcMetricsError" class="labkey-error"></div>
+<div id="linkToRawTable"></div>
 <script type="text/javascript" nonce="<%=scriptNonce%>">
 
     if (!LABKEY.internal)
@@ -28,9 +29,9 @@
                                 '</tr>';
 
             jQuery.each(qcMetrics, function (index, row) {
-                var rowClass = index % 2 === 1 ? "labkey-row" : "labkey-alternate-row";
+                const rowClass = index % 2 === 1 ? "labkey-row" : "labkey-alternate-row";
                 configRows.push({metric: row.id, name: row.name, Status: row.Status, Inserted: row.Inserted});
-                var editLock = row.Container === LABKEY.container.id;
+                const editLock = row.Container === LABKEY.container.id;
 
                 qcMetricsTable += '<tr class="' + rowClass + '">';
 
@@ -57,12 +58,13 @@
                 qcMetricsTable += '</tr>';
             });
 
-            qcMetricsTable += '</table>' + '<br>' +
+            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">Add New Trace Metric</button>' +
-                    '</form>';
+                    '<button type="button" class="labkey-button" id="createNewTraceMetricButton" style="margin-right: 20px;">Add New Trace Metric</button>' +
+                    '<button type="button" class="labkey-button" id="clearCacheButton">Clear Cached Metric Values</button>' +
+                    '</form><br>Edits to queries backing existing custom metrics require a manual cache clearing to display the updated results.</p>';
 
             jQuery('#qcMetricsTable').html(qcMetricsTable);
 
@@ -80,14 +82,25 @@
             jQuery('#createNewTraceMetricButton').click(function() {
                 LABKEY.internal.ConfigureQCMetrics.addNewMetric('trace')
             });
+            jQuery('#clearCacheButton').click(function() {
+                jQuery('#qcMetricsError').text('Clearing cached metrics...');
+                LABKEY.Ajax.request({
+                    url: LABKEY.ActionURL.buildURL('targetedms', 'clearQCMetricsCache.api'),
+                    method: 'POST',
+                    success: function() {
+                        jQuery('#qcMetricsError').text('Cleared cached metrics.');
+                    },
+                    failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onError, this, true)
+                });
+            });
 
             jQuery.each(qcMetrics, function (index, row) {
                 jQuery('#editLink' + row.id).click(function (e) {
                     e.preventDefault();
                     LABKEY.internal.ConfigureQCMetrics.editMetric(jQuery('#editLink' + row.id).text());
                     return false;
                 });
-                jQuery('#select-' + row.id).change(function (e) {
+                jQuery('#select-' + row.id).change(function () {
                     refreshBoundsInputs(qcMetrics);
                 });
             });
@@ -103,7 +116,7 @@
         }
 
         function getReturnUrl() {
-            var returnUrl = LABKEY.ActionURL.getParameter('returnUrl');
+            const returnUrl = LABKEY.ActionURL.getParameter('returnUrl');
 
             if(returnUrl) {
                 return returnUrl;
@@ -125,30 +138,36 @@
                         qcMetrics = result.rows;
                         showQCMetrics();
                     },
-                    failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onError, this, true)
+                    failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onErrorClearLoading, this, true)
                 });
             },
 
+            onErrorClearLoading: function(exception, responseObj, response2){
+                this.onError(exception, responseObj, response2);
+                jQuery('#qcMetricsTable').text('');
+            },
+
             onError: function(exception, responseObj, response2){
                 console.error(arguments);
 
-                var msg = LABKEY.Utils.getMsgFromError(response2, exception, {
+                const msg = LABKEY.Utils.getMsgFromError(response2, exception, {
                     showExceptionClass: false,
                     msgPrefix: 'Error: '
                 });
 
                 jQuery('#qcMetricsError').text(msg);
+                jQuery('#linkToRawTable').html(LABKEY.Utils.textLink({href: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'targetedms', queryName: 'QCMetricConfiguration'}), text: 'View QC metrics table'}));
             },
 
             editMetric: function (metricName) {
-                var clickedQcMetricConfig = {};
+                let clickedQcMetricConfig = {};
                 jQuery.each(qcMetrics, function (index, row) {
                     if (row.name === metricName) {
                         clickedQcMetricConfig = row;
                     }
                 });
 
-                var op = 'update';
+                const op = 'update';
                 if (clickedQcMetricConfig.TraceName) {
                     LABKEY.internal.ConfigureQCMetrics.showTraceMetricWindow(op, clickedQcMetricConfig)
                 }
@@ -166,7 +185,7 @@
                     scope: this,
                     containerPath: LABKEY.container.id,
                     success:  function(schemasInfo) {
-                        var windowConfig = {
+                        const windowConfig = {
                             parent: this,
                             schemas: schemasInfo.schemas,
                             operation: op
@@ -188,25 +207,26 @@
                     filterArray: [LABKEY.Filter.create('TextId', null, LABKEY.Filter.Types.NOT_MISSING)],
                     success: function (sampleFileChromInfos) {
 
-                        var tracesPresent = false;
+                        let tracesPresent = false;
+                        let traces;
                         if (sampleFileChromInfos.rows && sampleFileChromInfos.rows.length > 0) {
-                            var rows = sampleFileChromInfos.rows;
-                            var uniqueTraces = [];
-                            var trace  = {};
+                            const rows = sampleFileChromInfos.rows;
+                            const uniqueTraces = [];
+                            const trace  = {};
 
-                            for (var i in rows) {
+                            for (let i in rows) {
                                 trace[rows[i]['TextId']] = rows[i];
                             }
 
-                            for (i in trace) {
+                            for (let i in trace) {
                                 uniqueTraces.push(trace[i]);
                             }
 
                             traces = uniqueTraces;
                             tracesPresent = true;
                         }
 
-                        var windowConfig = {
+                        const windowConfig = {
                             parent: this,
                             traces: tracesPresent ? traces : {} ,
                             tracesPresent: tracesPresent,
@@ -223,7 +243,7 @@
             },
 
             addNewMetric: function (metricType) {
-                var op = 'insert';
+                const op = 'insert';
                 if (metricType === 'custom') {
                     this.showCustomMetricWindow(op);
                 }
@@ -294,7 +314,7 @@
                     LABKEY.Query.saveRows({
                         commands: commands,
                         method: 'POST',
-                        success: function (data) {
+                        success: function () {
                             window.location = getReturnUrl();
                         },
                         failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onError, this, true)