Speed up single point control Average Fi Bkgd calculation

luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java

@@ -28,7 +28,6 @@
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableSelector;
-import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.query.ExprColumn;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.InvalidKeyException;
@@ -81,18 +80,13 @@ public AnalyteSinglePointControlTable(final LuminexProtocolSchema schema, Contai
         SQLFragment avgFiSQL = new SQLFragment("(SELECT AVG(dr.FIBackground) FROM (");
         // TODO ContainerFilter -- Do we really want a non-permission checking container filter here?
         LuminexDataTable dataTable = schema.createDataTable(ContainerFilter.getUnsafeEverythingFilter(), false);
-        List<ColumnInfo> dataColumns = Arrays.asList(dataTable.getColumn("FlaggedAsExcluded"), dataTable.getColumn("FIBackground"), dataTable.getColumn("Description"), dataTable.getColumn("Data"), dataTable.getColumn("Analyte"));
+        List<ColumnInfo> dataColumns = Arrays.asList(dataTable.getColumn("FlaggedAsExcluded"), dataTable.getColumn("FIBackground"), dataTable.getColumn("SinglePointControl"), dataTable.getColumn("Analyte"));
         avgFiSQL.append(QueryService.get().getSelectBuilder(dataTable).columns(dataColumns).buildSqlFragment());
-        avgFiSQL.append(") dr, ");
-        avgFiSQL.append(ExperimentService.get().getTinfoData(), "d");
-        avgFiSQL.append(", ");
-        avgFiSQL.append(LuminexProtocolSchema.getTableInfoSinglePointControl(), "spc");
-        avgFiSQL.append(" WHERE dr.Description = spc.Name AND dr.Data = d.RowId AND d.RunId = spc.RunId ");
-        avgFiSQL.append(" AND dr.Analyte = ");
+        avgFiSQL.append(") dr WHERE dr.SinglePointControl = ");
         avgFiSQL.append(ExprColumn.STR_TABLE_ALIAS);
-        avgFiSQL.append(".AnalyteId AND spc.RowId = ");
+        avgFiSQL.append(".SinglePointControlId AND dr.Analyte = ");
         avgFiSQL.append(ExprColumn.STR_TABLE_ALIAS);
-        avgFiSQL.append(".SinglePointControlId AND dr.FlaggedAsExcluded = ?)");
+        avgFiSQL.append(".AnalyteId AND dr.FlaggedAsExcluded = ?)");
         avgFiSQL.add(false);
 
         ExprColumn avgFiColumn = new ExprColumn(this, "AverageFiBkgd", avgFiSQL, JdbcType.DOUBLE);

luminex/test/src/org/labkey/test/tests/luminex/LuminexSinglePointTest.java

@@ -18,11 +18,17 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.query.QueryKey;
+import org.labkey.remoteapi.CommandResponse;
 import org.labkey.remoteapi.Connection;
 import org.labkey.remoteapi.assay.GetProtocolCommand;
 import org.labkey.remoteapi.assay.Protocol;
 import org.labkey.remoteapi.assay.ProtocolResponse;
 import org.labkey.remoteapi.assay.SaveProtocolCommand;
+import org.labkey.remoteapi.query.Filter;
+import org.labkey.remoteapi.query.Row;
+import org.labkey.remoteapi.query.SelectRowsCommand;
+import org.labkey.remoteapi.query.SelectRowsResponse;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.SortDirection;
@@ -32,11 +38,14 @@
 import org.labkey.test.components.html.BootstrapMenu;
 import org.labkey.test.pages.ReactAssayDesignerPage;
 import org.labkey.test.pages.luminex.LeveyJenningsPlotWindow;
+import org.labkey.test.util.APIAssayHelper;
 import org.labkey.test.util.DataRegionTable;
 import org.labkey.test.util.luminex.LuminexGuideSetHelper;
+import org.labkey.test.util.luminex.LuminexSaveExclusionCommand;
 
 import java.util.Arrays;
 import java.util.Calendar;
+import java.util.List;
 import java.util.Map;
 import java.util.TreeMap;
 
@@ -92,7 +101,7 @@ public void testAssayOverAPI() throws Exception
     }
 
     @Test
-    public void testSinglePoint()
+    public void testSinglePoint() throws Exception
     {
         importRun(file1, 1);
         importRun(file2, 2);
@@ -146,6 +155,43 @@ public void testSinglePoint()
         assertTextNotPresent(file4);
 
         verifyValueBasedGuideSet();
+
+        verifyWellExclusionRemovedFromAverage();
+    }
+
+    private void verifyWellExclusionRemovedFromAverage() throws Exception
+    {
+        String controlName = "IH5672";
+        String analyteName = "ENV1";
+        String excludedWell = "H11";
+
+        log("Exclude well " + excludedWell + " of single point control " + controlName + " for " + analyteName + " in " + file1);
+        Connection connection = createDefaultConnection();
+        SelectRowsCommand select = new SelectRowsCommand("assay.Luminex." + QueryKey.encodePart(TEST_ASSAY_LUM), "Data");
+        select.setColumns(List.of("Data", "Analyte", "Type", "SinglePointControl/Run/RowId"));
+        select.addFilter(new Filter("Data/Name", file1, Filter.Operator.EQUAL));
+        select.addFilter(new Filter("Description", controlName, Filter.Operator.EQUAL));
+        select.addFilter(new Filter("Analyte/Name", analyteName, Filter.Operator.EQUAL));
+        select.addFilter(new Filter("Well", excludedWell, Filter.Operator.EQUAL));
+        SelectRowsResponse selectResponse = select.execute(connection, getProjectName());
+        assertEquals("Expected one data row for the well to exclude", 1, selectResponse.getRowCount().intValue());
+        Row well = selectResponse.getRowset().iterator().next();
+
+        int assayId = new APIAssayHelper(this).getIdFromAssayName(TEST_ASSAY_LUM, getProjectName());
+        CommandResponse exclusionResponse = new LuminexSaveExclusionCommand(assayId, ((Number) well.getValue("SinglePointControl/Run/RowId")).longValue())
+                .addWellExclusion(((Number) well.getValue("Data")).longValue(), controlName, (String) well.getValue("Type"),
+                        excludedWell, ((Number) well.getValue("Analyte")).longValue(), "Exclude one single point control well")
+                .execute(connection, getProjectName());
+        beginAt((String) exclusionResponse.getParsedData().get("returnUrl"));
+        waitForPipelineJobsToComplete(6, false);
+
+        goToTestAssayHome();
+        BootstrapMenu.find(getDriver(), "view qc report").clickSubMenu(true, "view single point control qc report");
+        DataRegionTable tbl = new DataRegionTable("AnalyteSinglePointControl", getDriver());
+        tbl.setFilter("Analyte", "Equals", analyteName);
+        tbl.setSort("SinglePointControl/Run/Name", SortDirection.ASC);
+        assertEquals("Excluded well should be dropped from the average", "25.0", tbl.getDataAsText(0, "Average Fi Bkgd"));
+        assertEquals("Run without exclusions should be unchanged", "30.0", tbl.getDataAsText(1, "Average Fi Bkgd"));
     }
 
     private void verifyValueBasedGuideSet()

luminex/test/src/org/labkey/test/util/luminex/LuminexSaveExclusionCommand.java

@@ -0,0 +1,63 @@
+/*
+ * 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.
+ */
+package org.labkey.test.util.luminex;
+
+import org.json.JSONArray;
+import org.json.JSONObject;
+import org.labkey.remoteapi.CommandResponse;
+import org.labkey.remoteapi.PostCommand;
+
+/**
+ * Wrapper for luminex-saveExclusion.api, which queues a pipeline job to apply the exclusion commands.
+ */
+public class LuminexSaveExclusionCommand extends PostCommand<CommandResponse>
+{
+    private final int _assayId;
+    private final long _runId;
+    private final JSONArray _commands = new JSONArray();
+
+    public LuminexSaveExclusionCommand(int assayId, long runId)
+    {
+        super("luminex", "saveExclusion");
+        _assayId = assayId;
+        _runId = runId;
+    }
+
+    public LuminexSaveExclusionCommand addWellExclusion(long dataId, String description, String type, String well, long analyteRowId, String comment)
+    {
+        JSONObject command = new JSONObject();
+        command.put("command", "insert");
+        command.put("dataId", dataId);
+        command.put("description", description);
+        command.put("type", type);
+        command.put("well", well);
+        command.put("analyteRowIds", String.valueOf(analyteRowId));
+        command.put("comment", comment);
+        _commands.put(command);
+        return this;
+    }
+
+    @Override
+    public JSONObject getJsonObject()
+    {
+        JSONObject json = new JSONObject();
+        json.put("assayId", _assayId);
+        json.put("tableName", "WellExclusion");
+        json.put("runId", _runId);
+        json.put("commands", _commands);
+        return json;
+    }
+}