Cross-folder instrument utilization report

resources/queries/targetedms/InstrumentUtilizationByDay.query.xml

@@ -0,0 +1,25 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="InstrumentUtilizationByDay" tableDbType="TABLE">
+                <tableTitle>Runs by Day</tableTitle>
+                <columns>
+                    <column columnName="AcquisitionDate">
+                        <columnTitle>Date</columnTitle>
+                        <formatString>Date</formatString>
+                    </column>
+                    <column columnName="RunCount">
+                        <columnTitle>Skyline Document Count</columnTitle>
+                    </column>
+                    <column columnName="ReplicateCount">
+                        <columnTitle>Replicate Count</columnTitle>
+                        <url>/targetedms-showInstrument.view?name=${InstrumentNickname}&amp;utilizationTab=samples&amp;SampleFile.AcquiredTime~dateeq=${AcquisitionDate:date('yyyy-MM-dd')}</url>
+                    </column>
+                    <column columnName="InstrumentNickname">
+                        <columnTitle>Instrument</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

resources/queries/targetedms/InstrumentUtilizationByDay.sql

@@ -0,0 +1,23 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+-- Number of sample files and runs acquired per day, by instrument, across all folders the user can read.
+-- Consumed by the instrument utilization calendar and the "Runs by Day" grid on the Show Instrument page.
+SELECT
+    CAST(AcquisitionDay AS TIMESTAMP) AS AcquisitionDate,
+    COUNT(*) AS ReplicateCount,
+    COUNT(DISTINCT RunId) AS RunCount,
+    InstrumentNickname
+FROM
+    (SELECT
+        CAST(YEAR(AcquiredTime) AS VARCHAR) || '-' ||
+            (CASE WHEN MONTH(AcquiredTime) < 10 THEN '0' ELSE '' END) || CAST(MONTH(AcquiredTime) AS VARCHAR) || '-' ||
+            (CASE WHEN DAYOFMONTH(AcquiredTime) < 10 THEN '0' ELSE '' END) || CAST(DAYOFMONTH(AcquiredTime) AS VARCHAR) AS AcquisitionDay,
+        ReplicateId.RunId AS RunId,
+        InstrumentNickname
+    FROM targetedms.SampleFile
+    WHERE AcquiredTime IS NOT NULL) X
+GROUP BY AcquisitionDay, InstrumentNickname

resources/queries/targetedms/InstrumentUtilizationByMonth.query.xml

@@ -0,0 +1,25 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="InstrumentUtilizationByMonth" tableDbType="TABLE">
+                <tableTitle>Runs by Month</tableTitle>
+                <columns>
+                    <column columnName="MonthStart">
+                        <columnTitle>Month</columnTitle>
+                        <formatString>yyyy-MM</formatString>
+                    </column>
+                    <column columnName="RunCount">
+                        <columnTitle>Skyline Document Count</columnTitle>
+                    </column>
+                    <column columnName="ReplicateCount">
+                        <columnTitle>Replicate Count</columnTitle>
+                        <url>/targetedms-showInstrument.view?name=${InstrumentNickname}&amp;utilizationTab=samples&amp;SampleFile.AcquiredTime~dategte=${MonthStart:date('yyyy-MM-dd')}&amp;SampleFile.AcquiredTime~datelt=${MonthEnd:date('yyyy-MM-dd')}</url>
+                    </column>
+                    <column columnName="InstrumentNickname">
+                        <columnTitle>Instrument</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

resources/queries/targetedms/InstrumentUtilizationByMonth.sql

@@ -0,0 +1,23 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+-- Number of sample files and runs acquired per month, by instrument, across all folders the user can read.
+-- Consumed by the "Runs by Month" grid on the Show Instrument page.
+SELECT
+    CAST(MonthStart || '-01' AS TIMESTAMP) AS MonthStart,
+    TIMESTAMPADD('SQL_TSI_MONTH', 1, CAST(MonthStart || '-01' AS TIMESTAMP)) AS MonthEnd,
+    COUNT(*) AS ReplicateCount,
+    COUNT(DISTINCT RunId) AS RunCount,
+    InstrumentNickname
+FROM
+    (SELECT
+        CAST(YEAR(AcquiredTime) AS VARCHAR) || '-' ||
+            (CASE WHEN MONTH(AcquiredTime) < 10 THEN '0' ELSE '' END) || CAST(MONTH(AcquiredTime) AS VARCHAR) AS MonthStart,
+        ReplicateId.RunId AS RunId,
+        InstrumentNickname
+    FROM targetedms.SampleFile
+    WHERE AcquiredTime IS NOT NULL) X
+GROUP BY MonthStart, InstrumentNickname

src/org/labkey/targetedms/TargetedMSController.java

@@ -4815,6 +4815,8 @@ public ShowInstrumentAction()
         }
 
         private static final String FOLDER_SUMMARY = "FolderSummary";
+        private static final String UTILIZATION_BY_DAY = "UtilizationByDay";
+        private static final String UTILIZATION_BY_MONTH = "UtilizationByMonth";
 
         private InstrumentForm _form;
 
@@ -4846,11 +4848,31 @@ protected QueryView createQueryView(InstrumentForm form, BindException errors, b
                 TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
                 return schema.createView(getViewContext(), settings, errors);
             }
+            if (UTILIZATION_BY_DAY.equalsIgnoreCase(dataRegion))
+            {
+                QuerySettings settings = new QuerySettings(getViewContext(), UTILIZATION_BY_DAY, "InstrumentUtilizationByDay");
+                settings.setBaseSort(new Sort("-AcquisitionDate"));
+                settings.setBaseFilter(new SimpleFilter(FieldKey.fromParts("InstrumentNickname"), form.getName()));
+                settings.setContainerFilterName(ContainerFilter.Type.AllFolders.name());
+                settings.setFieldKeys(List.of(FieldKey.fromParts("AcquisitionDate"), FieldKey.fromParts("RunCount"), FieldKey.fromParts("ReplicateCount")));
+                TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+                return schema.createView(getViewContext(), settings, errors);
+            }
+            if (UTILIZATION_BY_MONTH.equalsIgnoreCase(dataRegion))
+            {
+                QuerySettings settings = new QuerySettings(getViewContext(), UTILIZATION_BY_MONTH, "InstrumentUtilizationByMonth");
+                settings.setBaseSort(new Sort("-MonthStart"));
+                settings.setBaseFilter(new SimpleFilter(FieldKey.fromParts("InstrumentNickname"), form.getName()));
+                settings.setContainerFilterName(ContainerFilter.Type.AllFolders.name());
+                settings.setFieldKeys(List.of(FieldKey.fromParts("MonthStart"), FieldKey.fromParts("RunCount"), FieldKey.fromParts("ReplicateCount")));
+                TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+                return schema.createView(getViewContext(), settings, errors);
+            }
             throw new NotFoundException("Unknown dataRegion: " + dataRegion);
         }
 
         @Override
-        public ModelAndView getView(InstrumentForm form, BindException errors)
+        public ModelAndView getView(InstrumentForm form, BindException errors) throws Exception
         {
             if (form.getName() == null)
             {
@@ -4868,29 +4890,94 @@ public ModelAndView getView(InstrumentForm form, BindException errors)
 
             VBox result = new VBox();
 
+            VBox instrumentInfoView = new VBox();
             for (InstrumentNickname name : names)
             {
                 var nameView = new JspView<>("/org/labkey/targetedms/view/nickname.jsp", name);
                 nameView.setTitle("Instrument Info");
                 nameView.setFrame(WebPartView.FrameType.PORTAL);
-                result.addView(nameView);
+                instrumentInfoView.addView(nameView);
             }
 
             QueryView folderSummaryView = createQueryView(form, errors, false, FOLDER_SUMMARY);
             folderSummaryView.setTitle("Summary by Folder");
             folderSummaryView.setFrame(WebPartView.FrameType.PORTAL);
 
-            QueryView sampleFileView = createQueryView(form, errors, false, TargetedMSSchema.TABLE_SAMPLE_FILE);
-            sampleFileView.setTitle("Samples from " + form.getName());
-            sampleFileView.setFrame(WebPartView.FrameType.PORTAL);
-
-            result.addView(folderSummaryView);
-            result.addView(sampleFileView);
+            // Instrument info is narrow; pair it with the folder summary grid in a two-column row so the
+            // otherwise-empty space to the right of the info panel is put to use.
+            var infoRowView = new JspView<>("/org/labkey/targetedms/view/instrumentInfoRow.jsp",
+                    new InstrumentInfoRowBean(instrumentInfoView, folderSummaryView));
+            infoRowView.setFrame(WebPartView.FrameType.NONE);
+            result.addView(infoRowView);
+
+            QueryView byDayView = createInitializedQueryView(form, errors, false, UTILIZATION_BY_DAY);
+            byDayView.setFrame(WebPartView.FrameType.NONE);
+            QueryView byMonthView = createInitializedQueryView(form, errors, false, UTILIZATION_BY_MONTH);
+            byMonthView.setFrame(WebPartView.FrameType.NONE);
+            QueryView sampleFileView = createInitializedQueryView(form, errors, false, TargetedMSSchema.TABLE_SAMPLE_FILE);
+            sampleFileView.setFrame(WebPartView.FrameType.NONE);
+
+            var utilizationView = new JspView<>("/org/labkey/targetedms/view/instrumentUtilization.jsp",
+                    new InstrumentUtilizationBean(byDayView, byMonthView, sampleFileView));
+            utilizationView.setTitle("Instrument Utilization Across Folders");
+            utilizationView.setFrame(WebPartView.FrameType.PORTAL);
+            result.addView(utilizationView);
 
             return result;
         }
     }
 
+    public static class InstrumentUtilizationBean
+    {
+        private final QueryView _byDayView;
+        private final QueryView _byMonthView;
+        private final QueryView _sampleFileView;
+
+        public InstrumentUtilizationBean(QueryView byDayView, QueryView byMonthView, QueryView sampleFileView)
+        {
+            _byDayView = byDayView;
+            _byMonthView = byMonthView;
+            _sampleFileView = sampleFileView;
+        }
+
+        public QueryView getByDayView()
+        {
+            return _byDayView;
+        }
+
+        public QueryView getByMonthView()
+        {
+            return _byMonthView;
+        }
+
+        public QueryView getSampleFileView()
+        {
+            return _sampleFileView;
+        }
+    }
+
+    public static class InstrumentInfoRowBean
+    {
+        private final HttpView _infoView;
+        private final HttpView _summaryView;
+
+        public InstrumentInfoRowBean(HttpView infoView, HttpView summaryView)
+        {
+            _infoView = infoView;
+            _summaryView = summaryView;
+        }
+
+        public HttpView getInfoView()
+        {
+            return _infoView;
+        }
+
+        public HttpView getSummaryView()
+        {
+            return _summaryView;
+        }
+    }
+
     @RequiresPermission(ReadPermission.class)
     public class ShowReplicatesAction extends ShowRunSingleDetailsAction<RunDetailsForm>
     {

src/org/labkey/targetedms/query/SampleFileTable.java

@@ -184,7 +184,10 @@ public SampleFileTable(TargetedMSSchema schema, ContainerFilter cf, @Nullable Ta
             // Do a query to look across the entire server for samples where the name matches with names from the
             // targetedms.SampleFiles table, as currently filtered by the SampleFileTable (container and/or run)
             SQLFragment sql = new SQLFragment("SELECT DISTINCT m.Container, m.CpasType FROM (\n");
-            sql.append("SELECT COALESCE(ra.value, sf.SampleId, sf.SampleName) AS SampleIdentifier FROM \n");
+            // DISTINCT collapses the many sample files that share an identifier down to the distinct set, so the
+            // planner builds the hash on this small side and scans exp.material once as the probe (instead of
+            // hashing and spilling the entire, server-wide material table).
+            sql.append("SELECT DISTINCT COALESCE(ra.value, sf.SampleId, sf.SampleName) AS SampleIdentifier FROM \n");
             sql.append(TargetedMSManager.getTableInfoSampleFile(), "sf");
             sql.append(" INNER JOIN \n");
             sql.append(TargetedMSManager.getTableInfoReplicate(), "rep");

src/org/labkey/targetedms/view/instrumentInfoRow.jsp

@@ -0,0 +1,74 @@
+<%
+    /*
+     * Copyright (c) 2026 LabKey Corporation
+     *
+     * Licensed under the Apache License, Version 2.0 (the "License");
+     * you may not use this file except in compliance with the License.
+     * You may obtain a copy of the License at
+     *
+     *     http://www.apache.org/licenses/LICENSE-2.0
+     *
+     * Unless required by applicable law or agreed to in writing, software
+     * distributed under the License is distributed on an "AS IS" BASIS,
+     * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+     * See the License for the specific language governing permissions and
+     * limitations under the License.
+     */
+%>
+<%@ page import="org.labkey.api.view.HttpView" %>
+<%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.labkey.targetedms.TargetedMSController.InstrumentInfoRowBean" %>
+<%@ page extends="org.labkey.api.jsp.JspBase" %>
+<%
+    JspView<InstrumentInfoRowBean> me = HttpView.currentView();
+    InstrumentInfoRowBean bean = me.getModelBean();
+%>
+<div class="row" id="lk-instrument-info-row">
+    <div class="col-md-5">
+        <% me.include(bean.getInfoView(), out); %>
+    </div>
+    <div class="col-md-7" style="max-width: 100%; overflow-x: auto;">
+        <% me.include(bean.getSummaryView(), out); %>
+    </div>
+</div>
+
+<script type="text/javascript" nonce="<%=getScriptNonce()%>">
+(function() {
+    // Match the height of the two side-by-side web part panels
+    function equalizeHeights() {
+        var cols = document.querySelectorAll('#lk-instrument-info-row > [class*="col-"]');
+        var panels = [];
+        for (var i = 0; i < cols.length; i++) {
+            var panel = cols[i].querySelector('.panel');
+            if (panel) {
+                panels.push(panel);
+            }
+        }
+        if (panels.length < 2) {
+            return;
+        }
+
+        // Reset before measuring so re-runs (e.g. on resize) don't accumulate.
+        panels.forEach(function(p) { p.style.minHeight = ''; });
+
+        // If the columns have wrapped onto separate rows, leave their natural heights alone.
+        var firstTop = panels[0].getBoundingClientRect().top;
+        var sameRow = panels.every(function(p) { return Math.abs(p.getBoundingClientRect().top - firstTop) < 1; });
+        if (!sameRow) {
+            return;
+        }
+
+        var tallest = 0;
+        panels.forEach(function(p) { tallest = Math.max(tallest, p.offsetHeight); });
+        panels.forEach(function(p) { p.style.minHeight = tallest + 'px'; });
+    }
+
+    if (document.readyState !== 'loading') {
+        equalizeHeights();
+    }
+    else {
+        document.addEventListener('DOMContentLoaded', equalizeHeights);
+    }
+    window.addEventListener('resize', equalizeHeights);
+})();
+</script>