Skip to content

Eliminate class-loading deadlock warning in ContainerFilter #867

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
labkey-adam merged 1 commit into from
Apr 1, 2025
Merged

Eliminate class-loading deadlock warning in ContainerFilter #867

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 0 additions & 35 deletions .gitattributes
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/model/AnalyteSinglePointControl.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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<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, ");
Expand Down
4 changes: 2 additions & 2 deletions luminex/src/org/labkey/luminex/query/GuideSetCurveFitTable.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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");
Expand Down
2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/query/GuideSetTable.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)");
Expand Down
2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ 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_UNSAFE);
queryDef.setContainerFilter(ContainerFilter.getUnsafeEverythingFilter());

ArrayList<QueryException> errors = new ArrayList<>();
TableInfo table = queryDef.getTable(this, errors, false);
Expand Down
6 changes: 3 additions & 3 deletions ms2/src/org/labkey/ms2/query/MS2Schema.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"))));
}

Expand Down Expand Up @@ -701,7 +701,7 @@ public TableInfo getLookupTableInfo()
@Override
public TableInfo getLookupTableInfo()
{
return createPeptidesTable(ContainerFilter.EVERYTHING_UNSAFE, MS2RunType.values());
return createPeptidesTable(ContainerFilter.getUnsafeEverythingFilter(), MS2RunType.values());
}
});

Expand Down Expand Up @@ -906,7 +906,7 @@ public List<MS2Run> getRuns()

protected SQLFragment getPeptideSelectSQL(SimpleFilter filter, Collection<FieldKey> 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);
}

Expand Down
2 changes: 1 addition & 1 deletion ms2/src/org/labkey/ms2/query/SpectraCountTableInfo.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
}
});
Expand Down
2 changes: 1 addition & 1 deletion viability/src/org/labkey/viability/ViabilityManager.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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<FieldKey> fields = new ArrayList<>();
FieldKey resultId = FieldKey.fromParts("ResultID");
Expand Down