Fb assay qc 5364

luminex/src/org/labkey/luminex/LuminexDataHandler.java

@@ -684,6 +684,7 @@ private void insertCVQCFlags(User user, ExpRun expRun, List<LuminexDataRow> data
     {
         LuminexWellGroup wellGroup = analyte.buildWellGroup(dataRows);
         List<LuminexWell> allReplicates = wellGroup.getWellData(true); // combine replicates and get mean MFI and %CV
+        AssayProvider provider = AssayService.get().getProvider(expRun);
 
         Set<CVQCFlag> newCVQCFlags = new HashSet<>();
         for (LuminexWell replicate : allReplicates)
@@ -701,7 +702,7 @@ private void insertCVQCFlags(User user, ExpRun expRun, List<LuminexDataRow> data
                 if (!newCVQCFlags.contains(newQcFlag))
                 {
                     newCVQCFlags.add(newQcFlag);
-                    Table.insert(user, ExperimentService.get().getTinfoAssayQCFlag(), newQcFlag);
+                    AssayService.get().saveFlag(expRun.getContainer(), user, provider, newQcFlag);
                 }
             }
         }
@@ -851,7 +852,7 @@ public static void insertOrUpdateAnalyteSinglePointControlQCFlags(User user, Exp
         {
             if (!existingQCFlags.contains(newQCFlag))
             {
-                Table.insert(user, ExperimentService.get().getTinfoAssayQCFlag(), newQCFlag);
+                AssayService.get().saveFlag(expRun.getContainer(), user, provider, newQCFlag);
             }
         }
 
@@ -860,7 +861,7 @@ public static void insertOrUpdateAnalyteSinglePointControlQCFlags(User user, Exp
         {
             if (!newQCFlags.contains(existingAnalyteTitrationQCFlag))
             {
-                Table.delete(ExperimentService.get().getTinfoAssayQCFlag(), existingAnalyteTitrationQCFlag.getRowId());
+                AssayService.get().deleteFlag(expRun.getContainer(), user, provider, existingAnalyteTitrationQCFlag);
             }
         }
     }
@@ -1520,7 +1521,7 @@ else if (guideSetRow.isAucEnabled() && curveFit.getCurveType().equals("Trapezoid
         {
             if (!existingAnalyteTitrationQCFlags.contains(newAnalyteTitrationQCFlag))
             {
-                Table.insert(user, ExperimentService.get().getTinfoAssayQCFlag(), newAnalyteTitrationQCFlag);
+                AssayService.get().saveFlag(expRun.getContainer(), user, provider, newAnalyteTitrationQCFlag);
             }
         }
 
@@ -1529,7 +1530,7 @@ else if (guideSetRow.isAucEnabled() && curveFit.getCurveType().equals("Trapezoid
         {
             if (!newAnalyteTitrationQCFlags.contains(existingAnalyteTitrationQCFlag))
             {
-                Table.delete(ExperimentService.get().getTinfoAssayQCFlag(), existingAnalyteTitrationQCFlag.getRowId());
+                AssayService.get().deleteFlag(expRun.getContainer(), user, provider, existingAnalyteTitrationQCFlag);
             }
         }
     }

luminex/src/org/labkey/luminex/LuminexModule.java

@@ -17,12 +17,14 @@
 package org.labkey.luminex;
 
 import org.jetbrains.annotations.NotNull;
+import org.labkey.api.assay.AssayDefaultFlagHandler;
+import org.labkey.api.assay.AssayFlagHandler;
+import org.labkey.api.assay.AssayQCFlagColumn;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.property.PropertyService;
 import org.labkey.api.module.DefaultModule;
 import org.labkey.api.module.ModuleContext;
-import org.labkey.api.study.assay.AssayQCFlagColumn;
 import org.labkey.api.study.assay.AssayService;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.WebPartFactory;
@@ -72,6 +74,8 @@ public void doStartup(ModuleContext moduleContext)
         AssayService.get().registerAssayProvider(new LuminexAssayProvider());
         PropertyService.get().registerDomainKind(new LuminexAnalyteDomainKind());
         PropertyService.get().registerDomainKind(new LuminexDataDomainKind());
+
+        AssayFlagHandler.registerHandler(AssayService.get().getProvider(LuminexAssayProvider.NAME), new AssayDefaultFlagHandler());
     }
 
     @Override

nab/src/org/labkey/nab/NabAssayController.java

@@ -1055,7 +1055,7 @@ public ApiResponse execute(QCControlInfo form, BindException errors) throws Exce
                             DilutionManager.clearWellExclusions(scope.getSqlDialect(), form.getRunId());
 
                             // clear out prior qc flags
-                            Table.delete(ExperimentService.get().getTinfoAssayQCFlag(), new SimpleFilter(FieldKey.fromParts("runId"), form.getRunId()));
+                            AssayService.get().deleteFlagsForRun(getContainer(), getUser(), provider, form.getRunId());
                             Set<String> excludedWells = new HashSet<>();
                             Collection<Integer> wellRowIds = new HashSet<>();
 
@@ -1065,7 +1065,7 @@ public ApiResponse execute(QCControlInfo form, BindException errors) throws Exce
 
                                 // add the assay qc flag for the exclusions
                                 NabWellQCFlag flag = new NabWellQCFlag(form.getRunId(), well);
-                                Table.insert(getUser(), ExperimentService.get().getTinfoAssayQCFlag(), flag);
+                                AssayService.get().saveFlag(getContainer(), getUser(), provider, flag);
                             }
 
                             // get the rowid's for the wells to exclude
@@ -1257,9 +1257,10 @@ public ApiResponse execute(RenderAssayBean form, BindException errors)
             {
                 List<WellExclusion> exclusions = new ArrayList<>();
                 Map<String, NabWellQCFlag> qcFlagMap = new HashMap<>();
+                AssayProvider provider = AssayService.get().getProvider(run);
 
                 // get the saved assay QC flags to pull comment information from
-                for (NabWellQCFlag flag : new TableSelector(ExperimentService.get().getTinfoAssayQCFlag(), new SimpleFilter(FieldKey.fromParts("runId"), form.getRowId()), null).getArrayList(NabWellQCFlag.class))
+                for (NabWellQCFlag flag : AssayService.get().getFlags(provider, form.getRowId(), NabWellQCFlag.class))
                 {
                     qcFlagMap.put(flag.getKey1(), flag);
                 }

nab/src/org/labkey/nab/NabModule.java

@@ -16,7 +16,9 @@
 package org.labkey.nab;
 
 import org.jetbrains.annotations.NotNull;
+import org.labkey.api.assay.AssayDefaultFlagHandler;
 import org.labkey.api.data.ContainerManager;
+import org.labkey.api.assay.AssayFlagHandler;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.property.PropertyService;
 import org.labkey.api.module.DefaultModule;
@@ -99,6 +101,13 @@ public void doStartup(ModuleContext moduleContext)
         ExperimentService.get().registerExperimentDataHandler(new SinglePlateDilutionNabDataHandler());
         ContainerManager.addContainerListener(new NabContainerListener());
 
+        // register QC flag handlers for supported assays
+        AssayFlagHandler handler = new AssayDefaultFlagHandler();
+
+        AssayFlagHandler.registerHandler(AssayService.get().getProvider(NabAssayProvider.NAME), handler);
+        AssayFlagHandler.registerHandler(new CrossPlateDilutionNabAssayProvider(), handler);
+        AssayFlagHandler.registerHandler(new SinglePlateDilutionNabAssayProvider(), handler);
+
         PropertyService.get().registerDomainKind(new NabVirusDomainKind());
     }
 

nab/src/org/labkey/nab/query/NabProtocolSchema.java

@@ -31,18 +31,15 @@
 import org.labkey.api.data.DatabaseCache;
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.DisplayColumnFactory;
-import org.labkey.api.data.JdbcType;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.exp.query.ExpRunTable;
-import org.labkey.api.query.ExprColumn;
 import org.labkey.api.query.QuerySettings;
 import org.labkey.api.security.User;
 import org.labkey.api.study.assay.AssayDataLinkDisplayColumn;
 import org.labkey.api.study.assay.AssayProtocolSchema;
 import org.labkey.api.study.assay.AssayProvider;
-import org.labkey.api.study.assay.AssayQCFlagColumn;
 import org.labkey.api.study.assay.RunListDetailsQueryView;
 import org.labkey.api.study.query.ResultsQueryView;
 import org.labkey.api.study.query.RunListQueryView;
@@ -101,15 +98,6 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
         return runTable;
     }
 
-    @Override
-    protected void addQCFlagColumn(ExpRunTable runTable)
-    {
-        runTable.addColumn(new AssayQCFlagColumn(runTable, getSchemaName(), false));
-        var qcEnabled = runTable.addColumn(new ExprColumn(runTable, "QCFlagsEnabled", AssayQCFlagColumn.createSQLFragment(runTable.getSqlDialect(), "Enabled"), JdbcType.VARCHAR));
-        qcEnabled.setLabel("QC Flags Enabled State");
-        qcEnabled.setHidden(true);
-    }
-
     @Nullable
     @Override
     protected ResultsQueryView createDataQueryView(ViewContext context, QuerySettings settings, BindException errors)