LabKey · labkey-adam · Mar 3, 2025 · Mar 1, 2025 · Mar 3, 2025
diff --git a/flow/src/org/labkey/flow/script/WorkspaceJob.java b/flow/src/org/labkey/flow/script/WorkspaceJob.java
@@ -203,13 +203,13 @@ private List<String> filterSamples(Workspace workspace, List<String> sampleIDs)
         if (flowProtocol != null)
             analysisFilter = flowProtocol.getFCSAnalysisFilter();
 
-        if (analysisFilter != null && analysisFilter.getClauses().size() > 0)
+        if (analysisFilter != null && !analysisFilter.getClauses().isEmpty())
         {
             info("Using protocol FCS analysis filter: " + analysisFilter.getFilterText());
 
             User user = User.getSearchUser();
             Container c = flowProtocol.getContainer();
-            TableInfo fcsFilesTable = new FlowSchema(user, c).getTable(FlowTableType.FCSFiles, ContainerFilter.current(c));
+            TableInfo fcsFilesTable = new FlowSchema(user, c).getTable(FlowTableType.FCSFiles, ContainerFilter.current(this));
 
             List<String> filteredSampleIDs = new ArrayList<>(sampleIDs.size());
             for (String sampleID : sampleIDs)

diff --git a/luminex/src/org/labkey/luminex/LuminexController.java b/luminex/src/org/labkey/luminex/LuminexController.java
@@ -657,7 +657,7 @@ public Object execute(LuminexSaveExclusionsForm form, BindException errors) thro
             PipelineService.get().queueJob(job);
 
             response.put("success", true);
-            response.put(ActionURL.Param.returnUrl.name(), urlProvider(AssayUrls.class).getShowUploadJobsURL(getContainer(), form.getProtocol(getContainer()), ContainerFilter.current(getContainer())));
+            response.put(ActionURL.Param.returnUrl.name(), urlProvider(AssayUrls.class).getShowUploadJobsURL(getContainer(), form.getProtocol(getContainer()), ContainerFilter.current(this)));
             return response;
         }
     }

diff --git a/luminex/src/org/labkey/luminex/model/AnalyteSinglePointControl.java b/luminex/src/org/labkey/luminex/model/AnalyteSinglePointControl.java
@@ -21,9 +21,6 @@
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.query.FieldKey;
 import org.labkey.luminex.LuminexDataHandler;
-import org.labkey.luminex.model.AbstractLuminexControlAnalyte;
-import org.labkey.luminex.model.Analyte;
-import org.labkey.luminex.model.SinglePointControl;
 import org.labkey.luminex.query.AnalyteSinglePointControlTable;
 import org.labkey.luminex.query.LuminexProtocolSchema;
 
@@ -80,7 +77,7 @@ public void updateQCFlags(LuminexProtocolSchema schema)
         SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("Analyte"), analyte.getRowId());
         filter.addCondition(FieldKey.fromParts("SinglePointControl"), control.getRowId());
         AnalyteSinglePointControlTable analyteSinglePointControlTable = schema.createAnalyteSinglePointControlTable(null, true);
-        analyteSinglePointControlTable.setContainerFilter(ContainerFilter.EVERYTHING);
+        analyteSinglePointControlTable.setContainerFilter(ContainerFilter.EVERYTHING_UNSAFE);
         Double average = new TableSelector(analyteSinglePointControlTable, Collections.singleton("AverageFiBkgd"), filter, null).getObject(Double.class);
 
         LuminexDataHandler.insertOrUpdateAnalyteSinglePointControlQCFlags(schema.getUser(), run, schema.getProtocol(), this, analyte, control, runIsotypeConjugate.get("Isotype"), runIsotypeConjugate.get("Conjugate"), average);

diff --git a/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java b/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java
@@ -80,7 +80,7 @@ public AnalyteSinglePointControlTable(final LuminexProtocolSchema schema, Contai
         // Get the average of the non-excluded FI-Background values for this control
         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.EVERYTHING, false);
+        LuminexDataTable dataTable = schema.createDataTable(ContainerFilter.EVERYTHING_UNSAFE, false);
         List<ColumnInfo> dataColumns = Arrays.asList(dataTable.getColumn("FlaggedAsExcluded"), dataTable.getColumn("FIBackground"), dataTable.getColumn("Description"), dataTable.getColumn("Data"), dataTable.getColumn("Analyte"));
         avgFiSQL.append(QueryService.get().getSelectSQL(dataTable, dataColumns, null, null, Table.ALL_ROWS, 0, false));
         avgFiSQL.append(") dr, ");

diff --git a/luminex/src/org/labkey/luminex/query/GuideSetCurveFitTable.java b/luminex/src/org/labkey/luminex/query/GuideSetCurveFitTable.java
@@ -40,7 +40,7 @@ public GuideSetCurveFitTable(LuminexProtocolSchema schema, ContainerFilter cf, S
     {
         super(schema.getDbSchema(), LuminexProtocolSchema.GUIDE_SET_CURVE_FIT_TABLE_NAME, schema, cf);
         if (null== cf)
-            _containerFilter = ContainerFilter.current(schema.getContainer());
+            _containerFilter = ContainerFilter.current(schema);
         _curveType = curveType;
         setDescription("Contains one row per curve fit/guide set combination, and contains average and other statistics for all of the matching runs");
 
@@ -102,11 +102,11 @@ public SQLFragment getFromSQL()
         result.append("at.GuideSetId,\n");
         result.append("cf.CurveType FROM \n");
 
-        AnalyteTitrationTable analyteTitrationTable = (AnalyteTitrationTable)_userSchema.getTable(LuminexProtocolSchema.ANALYTE_TITRATION_TABLE_NAME, ContainerFilter.EVERYTHING);
+        AnalyteTitrationTable analyteTitrationTable = (AnalyteTitrationTable)_userSchema.getTable(LuminexProtocolSchema.ANALYTE_TITRATION_TABLE_NAME, ContainerFilter.EVERYTHING_UNSAFE);
         result.append(analyteTitrationTable, "at");
         result.append(", ");
 
-        CurveFitTable curveFitTable = (CurveFitTable)_userSchema.getTable(LuminexProtocolSchema.CURVE_FIT_TABLE_NAME, ContainerFilter.EVERYTHING);
+        CurveFitTable curveFitTable = (CurveFitTable)_userSchema.getTable(LuminexProtocolSchema.CURVE_FIT_TABLE_NAME, ContainerFilter.EVERYTHING_UNSAFE);
         result.append(curveFitTable, "cf");
 
         result.append(" WHERE at.AnalyteId = cf.AnalyteId AND at.TitrationId = cf.TitrationId AND at.GuideSetId IS NOT NULL AND at.IncludeInGuideSetCalculation = ?\n");

diff --git a/luminex/src/org/labkey/luminex/query/GuideSetTable.java b/luminex/src/org/labkey/luminex/query/GuideSetTable.java
@@ -167,7 +167,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
 
         addFIColumns(LuminexProtocolSchema.getTableInfoAnalyteTitration(), "MaxFI", "TitrationMax", "Titration Max", "GuideSetId");
         AnalyteSinglePointControlTable analyteSinglePointControlTable = schema.createAnalyteSinglePointControlTable(cf, false);
-        analyteSinglePointControlTable.setContainerFilter(ContainerFilter.EVERYTHING);
+        analyteSinglePointControlTable.setContainerFilter(ContainerFilter.EVERYTHING_UNSAFE);
         addFIColumns(analyteSinglePointControlTable, "AverageFiBkgd", "SinglePointControl", "Single Point Control", "GuideSet");
 
         SQLFragment controlTypeSql = new SQLFragment("(SELECT CASE WHEN IsTitration=" + this.getSqlDialect().getBooleanTRUE() +" THEN 'Titration' ELSE 'SinglePoint' END)");

diff --git a/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java b/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java
@@ -154,7 +154,7 @@ public synchronized List<String> getCurveTypes()
         {
             QueryDefinition queryDef = QueryService.get().createQueryDef(getUser(), _container, this, "query");
             queryDef.setSql("SELECT DISTINCT CurveType FROM \"" + CURVE_FIT_TABLE_NAME+ "\"");
-            queryDef.setContainerFilter(ContainerFilter.EVERYTHING);
+            queryDef.setContainerFilter(ContainerFilter.EVERYTHING_UNSAFE);
 
             ArrayList<QueryException> errors = new ArrayList<>();
             TableInfo table = queryDef.getTable(this, errors, false);

diff --git a/ms2/src/org/labkey/ms2/peptideview/QueryPeptideMS2RunView.java b/ms2/src/org/labkey/ms2/peptideview/QueryPeptideMS2RunView.java
@@ -231,7 +231,7 @@ private PeptidesTableInfo createPeptideTable(MS2Schema schema)
                 runTypes.add(run.getRunType());
             }
             boolean highestScoreFlag = _url.getParameter("highestScore") != null;
-            _peptidesTable =  new PeptidesTableInfo(schema, _url.clone(), ContainerFilter.current(schema.getContainer()), runTypes.toArray(new MS2RunType[0]), highestScoreFlag);
+            _peptidesTable =  new PeptidesTableInfo(schema, _url.clone(), ContainerFilter.current(schema), runTypes.toArray(new MS2RunType[0]), highestScoreFlag);
             // Manually apply the metadata
             _peptidesTable.overlayMetadata(_peptidesTable.getPublicName(), schema, new ArrayList<>());
         }

diff --git a/ms2/src/org/labkey/ms2/query/MS2Schema.java b/ms2/src/org/labkey/ms2/query/MS2Schema.java
@@ -651,7 +651,7 @@ public void getProteinGroupSelectSQL(MS2Controller.PeptideFilteringComparisonFor
             filter.addUrlFilters(url, "InternalName");
         }
         ProteinGroupTableInfo tableInfo = new ProteinGroupTableInfo(this, null, false);
-        tableInfo.setContainerFilter(ContainerFilter.EVERYTHING);
+        tableInfo.setContainerFilter(ContainerFilter.EVERYTHING_UNSAFE);
         sql.append(getSelectSQL(tableInfo, filter, Collections.singleton(FieldKey.fromParts("RowId"))));
     }
 
@@ -701,7 +701,7 @@ public TableInfo getLookupTableInfo()
             @Override
             public TableInfo getLookupTableInfo()
             {
-                return createPeptidesTable(ContainerFilter.EVERYTHING, MS2RunType.values());
+                return createPeptidesTable(ContainerFilter.EVERYTHING_UNSAFE, MS2RunType.values());
             }
         });
 
@@ -906,7 +906,7 @@ public List<MS2Run> getRuns()
 
     protected SQLFragment getPeptideSelectSQL(SimpleFilter filter, Collection<FieldKey> fieldKeys)
     {
-        TableInfo tiFiltered = getTable(HiddenTableType.PeptidesFilter.name(), ContainerFilter.EVERYTHING, true, false);
+        TableInfo tiFiltered = getTable(HiddenTableType.PeptidesFilter.name(), ContainerFilter.EVERYTHING_UNSAFE, true, false);
         return getSelectSQL(tiFiltered, filter, fieldKeys);
     }
 
@@ -1555,7 +1555,7 @@ public TableInfo getLookupTableInfo()
 
     public TableInfo createPeptidesTableInfo()
     {
-        return createPeptidesTableInfo(true, ContainerFilter.current(getContainer()), null, null);
+        return createPeptidesTableInfo(true, ContainerFilter.current(this), null, null);
     }
 
     public TableInfo createPeptidesTableInfo(boolean includeFeatureFk, ContainerFilter containerFilter, SimpleFilter filter, Iterable<FieldKey> defaultColumns)

diff --git a/ms2/src/org/labkey/ms2/query/PeptidesTableInfo.java b/ms2/src/org/labkey/ms2/query/PeptidesTableInfo.java
@@ -67,7 +67,7 @@ public class PeptidesTableInfo extends FilteredTable<MS2Schema>
 
     public PeptidesTableInfo(MS2Schema schema)
     {
-        this(schema, new ActionURL(MS2Controller.BeginAction.class, schema.getContainer()), ContainerFilter.current(schema.getContainer()), MS2RunType.values(), false);
+        this(schema, new ActionURL(MS2Controller.BeginAction.class, schema.getContainer()), ContainerFilter.current(schema), MS2RunType.values(), false);
     }
 
     public PeptidesTableInfo(MS2Schema schema, ContainerFilter containerFilter, MS2RunType[] runTypes)

diff --git a/ms2/src/org/labkey/ms2/query/SpectraCountTableInfo.java b/ms2/src/org/labkey/ms2/query/SpectraCountTableInfo.java
@@ -142,7 +142,7 @@ public SpectraCountTableInfo(MS2Schema ms2Schema, SpectraCountConfiguration conf
             public TableInfo getLookupTableInfo()
             {
                 ExpRunTable result = (ExpRunTable)MS2Schema.TableType.MS2SearchRuns.createTable(_userSchema, getContainerFilter());
-                result.setContainerFilter(ContainerFilter.EVERYTHING);
+                result.setContainerFilter(ContainerFilter.EVERYTHING_UNSAFE);
                 return result;
             }
         });

diff --git a/viability/src/org/labkey/viability/ViabilityManager.java b/viability/src/org/labkey/viability/ViabilityManager.java
@@ -372,7 +372,7 @@ public static void updateSpecimenAggregates(User user, Container c, @NotNull Ass
     @Nullable
     private static SQLFragment specimenAggregates(ViabilityAssaySchema schema, ExpRun run)
     {
-        ViabilityAssaySchema.ResultSpecimensTable rs = schema.createResultSpecimensTable(ContainerFilter.EVERYTHING);
+        ViabilityAssaySchema.ResultSpecimensTable rs = schema.createResultSpecimensTable(ContainerFilter.EVERYTHING_UNSAFE);
 
         List<FieldKey> fields = new ArrayList<>();
         FieldKey resultId = FieldKey.fromParts("ResultID");