diff --git a/.gitattributes b/.gitattributes index af623e919..983dc0af1 100644 --- a/.gitattributes +++ b/.gitattributes @@ -528,37 +528,6 @@ microarray/src/org/labkey/microarray/view/FeatureAnnotationSetQueryView.java -te microarray/src/org/labkey/microarray/view/uploadFeatureAnnotation.jsp -text ms2/api-src/org/labkey/api/util/massSpecDataFileType.java -text ms2/build.gradle -text -ms2/gwtsrc/org/labkey/ms2/pipeline/Search.gwt.xml -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/CutSite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/Enzyme.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/EnzymeComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/EnzymeParseException.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/GWTSearchServiceResult.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/GeneralInputXmlComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/InputXmlComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/MzXmlComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/OtherParametersComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/ParamParser.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/ParameterNames.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/PipelineConfigCallback.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/ProtocolComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/ResidueModComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/Search.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/SearchFormComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/SearchFormCompositeFactory.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/SearchFormException.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/SearchService.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/SearchServiceAsync.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/SequenceDbComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/TPPComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/mascot/MascotEnzymeComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/mascot/MascotResidueModComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/mascot/MascotSequenceDbComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/sequest/SequestResidueModComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/sequest/SimpleSequenceDbComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/tandem/XtandemInputXmlComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/tandem/XtandemResidueModComposite.java -text -ms2/gwtsrc/org/labkey/ms2/pipeline/client/tandem/XtandemSequenceDbComposite.java -text ms2/module.properties -text ms2/resources/credits/scripts.txt -text ms2/resources/queries/ms2/CometPeptides/ProteinProphet.qview.xml -text @@ -697,8 +666,6 @@ ms2/src/org/labkey/ms2/pipeline/PipelineController.java -text ms2/src/org/labkey/ms2/pipeline/ProteinProphetPipelineJob.java -text ms2/src/org/labkey/ms2/pipeline/ProteinProphetPipelineProvider.java -text ms2/src/org/labkey/ms2/pipeline/QuantitationAlgorithm.java -text -ms2/src/org/labkey/ms2/pipeline/SearchFormUtil.java -text -ms2/src/org/labkey/ms2/pipeline/SearchServiceImpl.java -text ms2/src/org/labkey/ms2/pipeline/Sqt2PinTask.java -text ms2/src/org/labkey/ms2/pipeline/TPPTask.java -text ms2/src/org/labkey/ms2/pipeline/UnknownMS2Run.java -text @@ -789,7 +756,6 @@ ms2/src/org/labkey/ms2/proteinCoverageMapHeader.jsp -text ms2/src/org/labkey/ms2/proteinDisambiguation.jsp -text ms2/src/org/labkey/ms2/proteinSequence.jsp -text ms2/src/org/labkey/ms2/query/AbstractQueryCrosstabView.java -text -ms2/src/org/labkey/ms2/query/AbstractRunCompareView.java -text ms2/src/org/labkey/ms2/query/ComparePeptideTableInfo.java -text ms2/src/org/labkey/ms2/query/CompareProteinProphetTableInfo.java -text ms2/src/org/labkey/ms2/query/FastaRunMappingTable.java -text @@ -931,7 +897,6 @@ nab/src/org/labkey/nab/query/NabWellDataTable.java -text nab/src/org/labkey/nab/view/nabQC.jsp -text viability/module.properties -text viability/resources/schemas/dbscripts/postgresql/viability-0.00-16.10.sql -text -viability/resources/schemas/dbscripts/sqlserver/viability-0.00-14.20.sql -text viability/resources/schemas/viability.xml -text viability/src/org/labkey/viability/GuavaDataHandler.java -text viability/src/org/labkey/viability/ViabilityAssayDataHandler.java -text diff --git a/luminex/src/org/labkey/luminex/model/AnalyteSinglePointControl.java b/luminex/src/org/labkey/luminex/model/AnalyteSinglePointControl.java index 2dee9a166..5e26f2462 100644 --- a/luminex/src/org/labkey/luminex/model/AnalyteSinglePointControl.java +++ b/luminex/src/org/labkey/luminex/model/AnalyteSinglePointControl.java @@ -77,7 +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_UNSAFE); + analyteSinglePointControlTable.setContainerFilter(ContainerFilter.getUnsafeEverythingFilter()); 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 9414bdd31..8aa1f9bbb 100644 --- a/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java +++ b/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java @@ -81,7 +81,7 @@ 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_UNSAFE, false); + LuminexDataTable dataTable = schema.createDataTable(ContainerFilter.getUnsafeEverythingFilter(), 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 1cfe968d3..a707481ea 100644 --- a/luminex/src/org/labkey/luminex/query/GuideSetCurveFitTable.java +++ b/luminex/src/org/labkey/luminex/query/GuideSetCurveFitTable.java @@ -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_UNSAFE); + AnalyteTitrationTable analyteTitrationTable = (AnalyteTitrationTable)_userSchema.getTable(LuminexProtocolSchema.ANALYTE_TITRATION_TABLE_NAME, ContainerFilter.getUnsafeEverythingFilter()); result.append(analyteTitrationTable, "at"); result.append(", "); - CurveFitTable curveFitTable = (CurveFitTable)_userSchema.getTable(LuminexProtocolSchema.CURVE_FIT_TABLE_NAME, ContainerFilter.EVERYTHING_UNSAFE); + CurveFitTable curveFitTable = (CurveFitTable)_userSchema.getTable(LuminexProtocolSchema.CURVE_FIT_TABLE_NAME, ContainerFilter.getUnsafeEverythingFilter()); 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 6ef069f5e..4aa757fca 100644 --- a/luminex/src/org/labkey/luminex/query/GuideSetTable.java +++ b/luminex/src/org/labkey/luminex/query/GuideSetTable.java @@ -164,7 +164,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit addFIColumns(LuminexProtocolSchema.getTableInfoAnalyteTitration(), "MaxFI", "TitrationMax", "Titration Max", "GuideSetId"); AnalyteSinglePointControlTable analyteSinglePointControlTable = schema.createAnalyteSinglePointControlTable(cf, false); - analyteSinglePointControlTable.setContainerFilter(ContainerFilter.EVERYTHING_UNSAFE); + analyteSinglePointControlTable.setContainerFilter(ContainerFilter.getUnsafeEverythingFilter()); 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 a5a08e557..2a9891c74 100644 --- a/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java +++ b/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java @@ -155,7 +155,7 @@ 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_UNSAFE); + queryDef.setContainerFilter(ContainerFilter.getUnsafeEverythingFilter()); ArrayList errors = new ArrayList<>(); TableInfo table = queryDef.getTable(this, errors, false); diff --git a/ms2/src/org/labkey/ms2/query/MS2Schema.java b/ms2/src/org/labkey/ms2/query/MS2Schema.java index ff936d95e..ecd847b3e 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_UNSAFE); + tableInfo.setContainerFilter(ContainerFilter.getUnsafeEverythingFilter()); 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_UNSAFE, MS2RunType.values()); + return createPeptidesTable(ContainerFilter.getUnsafeEverythingFilter(), MS2RunType.values()); } }); @@ -906,7 +906,7 @@ public List getRuns() protected SQLFragment getPeptideSelectSQL(SimpleFilter filter, Collection fieldKeys) { - TableInfo tiFiltered = getTable(HiddenTableType.PeptidesFilter.name(), ContainerFilter.EVERYTHING_UNSAFE, true, false); + TableInfo tiFiltered = getTable(HiddenTableType.PeptidesFilter.name(), ContainerFilter.getUnsafeEverythingFilter(), true, false); return getSelectSQL(tiFiltered, filter, fieldKeys); } diff --git a/ms2/src/org/labkey/ms2/query/SpectraCountTableInfo.java b/ms2/src/org/labkey/ms2/query/SpectraCountTableInfo.java index d6af7af89..0e7bfdee0 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_UNSAFE); + result.setContainerFilter(ContainerFilter.getUnsafeEverythingFilter()); return result; } }); diff --git a/viability/src/org/labkey/viability/ViabilityManager.java b/viability/src/org/labkey/viability/ViabilityManager.java index b5d9fa050..2bec06129 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_UNSAFE); + ViabilityAssaySchema.ResultSpecimensTable rs = schema.createResultSpecimensTable(ContainerFilter.getUnsafeEverythingFilter()); List fields = new ArrayList<>(); FieldKey resultId = FieldKey.fromParts("ResultID");