diff --git a/flow/src/org/labkey/flow/script/WorkspaceJob.java b/flow/src/org/labkey/flow/script/WorkspaceJob.java index 59c45cf45b..f8395493ed 100644 --- a/flow/src/org/labkey/flow/script/WorkspaceJob.java +++ b/flow/src/org/labkey/flow/script/WorkspaceJob.java @@ -203,13 +203,13 @@ private List filterSamples(Workspace workspace, List 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 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 index df9bb76ce2..d2ddf29427 100644 --- 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 index 630edefd87..2dee9a1668 100644 --- 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 index 19553badab..d74536fee3 100644 --- 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 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 index 852a6fbfca..1cfe968d38 100644 --- 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 index cd830c6062..4992046ea4 100644 --- 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 index bfea017483..3ac19c4dc6 100644 --- 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 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 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 index adf8a55f2e..5fd7c32119 100644 --- 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 index 84e860c72a..ff936d95e9 100644 --- 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 getRuns() protected SQLFragment getPeptideSelectSQL(SimpleFilter filter, Collection 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 defaultColumns) diff --git a/ms2/src/org/labkey/ms2/query/PeptidesTableInfo.java b/ms2/src/org/labkey/ms2/query/PeptidesTableInfo.java index 639b64ae5b..13032abda3 100644 --- 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 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 index f5d4bde80c..d6af7af89d 100644 --- 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 index 364f0946a2..b5d9fa0506 100644 --- 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 fields = new ArrayList<>(); FieldKey resultId = FieldKey.fromParts("ResultID");