From 4662ff606964619e7a9c500e0375a3426ab74eaf Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Tue, 7 Jul 2020 13:36:49 -0700 Subject: [PATCH 1/3] Item 7490: Migration from log4j1 to log4j2 - update java methods and package names --- .../org/labkey/elisa/ElisaDataHandler.java | 3 +- .../elispot/AbstractElispotDataHandler.java | 3 +- .../labkey/elispot/ElispotDataHandler.java | 3 +- .../org/labkey/elispot/ElispotManager.java | 5 +- .../flow/analysis/model/ExternalAnalysis.java | 5 +- .../org/labkey/flow/analysis/model/FCS.java | 5 +- .../labkey/flow/analysis/model/FCSHeader.java | 5 +- .../flow/analysis/model/WorkspaceParser.java | 5 +- .../labkey/flow/analysis/web/FCSAnalyzer.java | 5 +- .../flow/persist/AnalysisSerializer.java | 3 +- .../org/labkey/flow/persist/AttributeSet.java | 5 +- .../flow/controllers/FlowController.java | 5 +- .../flow/controllers/ReportsController.java | 5 +- .../flow/controllers/WorkspaceData.java | 5 +- .../attribute/AttributeController.java | 5 +- .../editscript/EditScriptForm.java | 5 +- .../editscript/ScriptController.java | 5 +- .../editscript/UploadAnalysisForm.java | 5 +- .../AnalysisScriptController.java | 5 +- .../ChooseRunsToAnalyzeForm.java | 5 +- .../executescript/SamplesConfirmGridView.java | 5 +- .../flow/controllers/run/RunController.java | 5 +- .../flow/controllers/well/WellController.java | 5 +- .../labkey/flow/data/FieldSubstitution.java | 5 +- .../org/labkey/flow/data/FlowExperiment.java | 5 +- .../org/labkey/flow/data/FlowProtocol.java | 5 +- flow/src/org/labkey/flow/data/FlowRun.java | 5 +- flow/src/org/labkey/flow/data/FlowWell.java | 5 +- .../labkey/flow/persist/AttributeCache.java | 5 +- .../flow/persist/AttributeSetHelper.java | 5 +- .../flow/persist/FlowContainerListener.java | 5 +- .../labkey/flow/persist/FlowDataHandler.java | 3 +- .../org/labkey/flow/persist/FlowManager.java | 5 +- .../flow/query/AttributeForeignKey.java | 5 +- .../labkey/flow/query/FlowPropertySet.java | 5 +- .../org/labkey/flow/script/AnalyzeJob.java | 5 +- .../labkey/flow/script/FlowExperimentJob.java | 3 +- flow/src/org/labkey/flow/script/FlowJob.java | 3 +- .../org/labkey/flow/script/KeywordsJob.java | 5 +- .../labkey/flow/script/ScriptXarSource.java | 5 +- .../src/org/labkey/flow/view/GraphColumn.java | 5 +- .../org/labkey/flow/view/JobStatusView.java | 5 +- .../org/labkey/luminex/LuminexController.java | 5 +- .../labkey/luminex/LuminexDataHandler.java | 11 +- .../org/labkey/luminex/LuminexManager.java | 5 +- .../src/org/labkey/luminex/LuminexModule.java | 2 +- .../luminex/LuminexRunAsyncContext.java | 109 +++++++++--------- .../labkey/microarray/MicroarrayManager.java | 5 +- .../matrix/ExpressionMatrixDataHandler.java | 5 +- .../pipeline/GeneDataPipelineProvider.java | 5 +- .../org/labkey/api/ms2/MS2Service.java | 3 +- .../ms2/BibliospecSpectrumRenderer.java | 5 +- .../org/labkey/ms2/CompareServiceImpl.java | 5 +- ms2/src/org/labkey/ms2/CumulativeTimer.java | 3 +- ms2/src/org/labkey/ms2/DeltaScanColumn.java | 5 +- ms2/src/org/labkey/ms2/Hydrophobicity3.java | 5 +- ms2/src/org/labkey/ms2/MS2Controller.java | 5 +- ms2/src/org/labkey/ms2/MS2Fraction.java | 3 +- ms2/src/org/labkey/ms2/MS2Importer.java | 5 +- ms2/src/org/labkey/ms2/MS2Manager.java | 5 +- ms2/src/org/labkey/ms2/MS2Peptide.java | 5 +- ms2/src/org/labkey/ms2/MS2Run.java | 5 +- ms2/src/org/labkey/ms2/MS2ServiceImpl.java | 3 +- ms2/src/org/labkey/ms2/MascotDatImporter.java | 3 +- .../ms2/PepXmlExperimentDataHandler.java | 3 +- ms2/src/org/labkey/ms2/PepXmlImporter.java | 3 +- ms2/src/org/labkey/ms2/PeptideImporter.java | 3 +- ms2/src/org/labkey/ms2/Protein.java | 5 +- .../ProteinProphetExperimentDataHandler.java | 3 +- .../labkey/ms2/ProteinProphetImporter.java | 5 +- ms2/src/org/labkey/ms2/SpectrumImporter.java | 5 +- .../ProteinExpressionMatrixDataHandler.java | 5 +- .../ms2/peptideview/AbstractMS2RunView.java | 5 +- .../ms2/pipeline/MS2PipelineManager.java | 5 +- .../ms2/pipeline/SearchServiceImpl.java | 5 +- .../ms2/pipeline/mascot/MascotClientImpl.java | 5 +- .../rollup/FractionRollupPipelineJob.java | 3 +- .../pipeline/tandem/XTandemPipelineJob.java | 3 +- .../tandem/XTandemSearchProtocol.java | 5 +- .../org/labkey/ms2/protein/FastaDbLoader.java | 3 +- .../org/labkey/ms2/protein/ParserTree.java | 3 +- .../labkey/ms2/protein/ProteinManager.java | 5 +- .../labkey/ms2/protein/XMLProteinHandler.java | 3 +- .../protein/organism/GuessOrgByParsing.java | 5 +- .../labkey/ms2/protein/tools/GoLoader.java | 5 +- .../tools/ProteinDictionaryHelpers.java | 5 +- .../labkey/ms2/protein/uniprot/uniprot.java | 3 +- .../uniprot/uniprot_entry_organism_name.java | 3 +- .../PeptideAggregrationDisplayColumn.java | 5 +- ms2/src/org/labkey/ms2/reader/MS2Loader.java | 3 +- .../org/labkey/ms2/reader/MS2XmlLoader.java | 3 +- .../labkey/ms2/reader/MascotDatLoader.java | 3 +- .../org/labkey/ms2/reader/PepXmlLoader.java | 7 +- .../labkey/ms2/reader/Q3AnalysisSummary.java | 5 +- ms2/src/org/labkey/ms2/reader/Q3Handler.java | 5 +- .../ms2/reader/SequentialMzxmlIterator.java | 5 +- .../ms2/reader/SimpleXMLEventRewriter.java | 5 +- .../org/labkey/ms2/reader/TarIterator.java | 5 +- .../ms2/reader/XPressAnalysisSummary.java | 5 +- .../org/systemsbiology/jrap/MSXMLParser.java | 5 +- nab/src/org/labkey/nab/NabDataHandler.java | 5 +- nab/src/org/labkey/nab/NabManager.java | 5 +- .../labkey/nab/SinglePlateNabDataHandler.java | 3 +- .../HighThroughputNabDataHandler.java | 3 +- .../labkey/viability/GuavaDataHandler.java | 3 +- .../labkey/viability/ViabilityManager.java | 5 +- .../ViabilitySpecimenChangeListener.java | 3 +- .../viability/ViabilityTsvDataHandler.java | 3 +- 108 files changed, 347 insertions(+), 240 deletions(-) diff --git a/elisa/src/org/labkey/elisa/ElisaDataHandler.java b/elisa/src/org/labkey/elisa/ElisaDataHandler.java index 4dbc9513af..f95cea6d23 100644 --- a/elisa/src/org/labkey/elisa/ElisaDataHandler.java +++ b/elisa/src/org/labkey/elisa/ElisaDataHandler.java @@ -18,7 +18,8 @@ import org.apache.commons.lang3.math.NumberUtils; import org.apache.commons.math3.stat.regression.SimpleRegression; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.assay.AbstractAssayTsvDataHandler; import org.labkey.api.assay.AssayDataType; import org.labkey.api.assay.AssayProvider; diff --git a/elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java b/elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java index ece8e94e0a..e893be9ec5 100644 --- a/elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java +++ b/elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.elispot; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.ConvertHelper; import org.labkey.api.exp.ExperimentException; diff --git a/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java b/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java index f714c0d40b..9c059fb193 100644 --- a/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java +++ b/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.data.statistics.MathStat; diff --git a/elispotassay/src/org/labkey/elispot/ElispotManager.java b/elispotassay/src/org/labkey/elispot/ElispotManager.java index f56e0ba7e6..c25c0f30a9 100644 --- a/elispotassay/src/org/labkey/elispot/ElispotManager.java +++ b/elispotassay/src/org/labkey/elispot/ElispotManager.java @@ -15,7 +15,8 @@ */ package org.labkey.elispot; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.ConcurrentCaseInsensitiveSortedMap; @@ -48,7 +49,7 @@ */ public class ElispotManager { - private static final Logger _log = Logger.getLogger(ElispotManager.class); + private static final Logger _log = LogManager.getLogger(ElispotManager.class); private static final ElispotManager _instance = new ElispotManager(); public static final String ELISPOT_RUNDATA_TABLE_NAME = "rundata"; diff --git a/flow/enginesrc/org/labkey/flow/analysis/model/ExternalAnalysis.java b/flow/enginesrc/org/labkey/flow/analysis/model/ExternalAnalysis.java index e0b0de337b..5c146859eb 100644 --- a/flow/enginesrc/org/labkey/flow/analysis/model/ExternalAnalysis.java +++ b/flow/enginesrc/org/labkey/flow/analysis/model/ExternalAnalysis.java @@ -15,7 +15,8 @@ */ package org.labkey.flow.analysis.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.collections.CaseInsensitiveMapWrapper; import org.labkey.api.collections.CaseInsensitiveTreeSet; import org.labkey.api.writer.FileSystemFile; @@ -42,7 +43,7 @@ */ public class ExternalAnalysis extends BaseWorkspace implements Serializable { - public static final Logger LOG = Logger.getLogger(ExternalAnalysis.class); + public static final Logger LOG = LogManager.getLogger(ExternalAnalysis.class); protected Map _sampleInfos = new CaseInsensitiveMapWrapper<>(new LinkedHashMap<>()); protected Set _compensationMatrices = new LinkedHashSet<>(); diff --git a/flow/enginesrc/org/labkey/flow/analysis/model/FCS.java b/flow/enginesrc/org/labkey/flow/analysis/model/FCS.java index e8e5ab92cc..c901145587 100644 --- a/flow/enginesrc/org/labkey/flow/analysis/model/FCS.java +++ b/flow/enginesrc/org/labkey/flow/analysis/model/FCS.java @@ -17,7 +17,8 @@ import org.apache.commons.io.filefilter.IOFileFilter; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.util.StringUtilsLabKey; import java.io.*; @@ -32,7 +33,7 @@ */ public class FCS extends FCSHeader { - static private final Logger _log = Logger.getLogger(FCS.class); + static private final Logger _log = LogManager.getLogger(FCS.class); boolean bigEndian; DataFrame rawData; public static List supportedVersions = new ArrayList<>(Arrays.asList("FCS2.0","FCS3.0","FCS3.1")); diff --git a/flow/enginesrc/org/labkey/flow/analysis/model/FCSHeader.java b/flow/enginesrc/org/labkey/flow/analysis/model/FCSHeader.java index cabcf6ddf2..cd930a62d8 100644 --- a/flow/enginesrc/org/labkey/flow/analysis/model/FCSHeader.java +++ b/flow/enginesrc/org/labkey/flow/analysis/model/FCSHeader.java @@ -17,7 +17,8 @@ package org.labkey.flow.analysis.model; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.search.AbstractDocumentParser; @@ -43,7 +44,7 @@ public class FCSHeader { public static final String CONTENT_TYPE = "application/vnd.isac.fcs"; - private static final Logger LOG = Logger.getLogger(FCSHeader.class); + private static final Logger LOG = LogManager.getLogger(FCSHeader.class); private Map keywords = new CaseInsensitiveHashMap<>(); int dataLast; diff --git a/flow/enginesrc/org/labkey/flow/analysis/model/WorkspaceParser.java b/flow/enginesrc/org/labkey/flow/analysis/model/WorkspaceParser.java index 4e80d6fcf3..4a4a7bada2 100644 --- a/flow/enginesrc/org/labkey/flow/analysis/model/WorkspaceParser.java +++ b/flow/enginesrc/org/labkey/flow/analysis/model/WorkspaceParser.java @@ -15,7 +15,8 @@ */ package org.labkey.flow.analysis.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xerces.impl.Constants; import org.apache.xerces.parsers.DOMParser; import org.apache.xerces.util.SymbolTable; @@ -520,7 +521,7 @@ public void parse(InputSource inputSource) throws SAXException, IOException } catch (RuntimeException x) { - Logger.getLogger(FlowJoWorkspace.class).error("Unexpected error", x); + LogManager.getLogger(FlowJoWorkspace.class).error("Unexpected error", x); throw x; } } diff --git a/flow/enginesrc/org/labkey/flow/analysis/web/FCSAnalyzer.java b/flow/enginesrc/org/labkey/flow/analysis/web/FCSAnalyzer.java index 96e368f38e..2086d20755 100644 --- a/flow/enginesrc/org/labkey/flow/analysis/web/FCSAnalyzer.java +++ b/flow/enginesrc/org/labkey/flow/analysis/web/FCSAnalyzer.java @@ -16,7 +16,8 @@ package org.labkey.flow.analysis.web; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.jfree.chart.ChartRenderingInfo; import org.jfree.chart.JFreeChart; @@ -51,7 +52,7 @@ public class FCSAnalyzer { public static final SubsetSpec compSubset = new SubsetSpec(null, PopulationName.fromString("comp")); - private static final Logger _log = Logger.getLogger(FCSAnalyzer.class); + private static final Logger _log = LogManager.getLogger(FCSAnalyzer.class); private static final FCSAnalyzer _instance = new FCSAnalyzer(); private static final int GRAPH_HEIGHT = 300; private static final int GRAPH_WIDTH = 300; diff --git a/flow/enginesrc/org/labkey/flow/persist/AnalysisSerializer.java b/flow/enginesrc/org/labkey/flow/persist/AnalysisSerializer.java index a6c1b249a3..5b2dd9b1c6 100644 --- a/flow/enginesrc/org/labkey/flow/persist/AnalysisSerializer.java +++ b/flow/enginesrc/org/labkey/flow/persist/AnalysisSerializer.java @@ -17,7 +17,8 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.junit.Assert; import org.junit.Test; diff --git a/flow/enginesrc/org/labkey/flow/persist/AttributeSet.java b/flow/enginesrc/org/labkey/flow/persist/AttributeSet.java index 7c282a04cc..3e8ec1c4b8 100644 --- a/flow/enginesrc/org/labkey/flow/persist/AttributeSet.java +++ b/flow/enginesrc/org/labkey/flow/persist/AttributeSet.java @@ -17,7 +17,8 @@ package org.labkey.flow.persist; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.fhcrc.cpas.exp.xml.DataBaseType; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -51,7 +52,7 @@ public class AttributeSet implements Serializable { - private static final Logger LOG = Logger.getLogger(AttributeSet.class); + private static final Logger LOG = LogManager.getLogger(AttributeSet.class); ObjectType _type; URI _uri; diff --git a/flow/src/org/labkey/flow/controllers/FlowController.java b/flow/src/org/labkey/flow/controllers/FlowController.java index a60cd39791..4e88f1a2c0 100644 --- a/flow/src/org/labkey/flow/controllers/FlowController.java +++ b/flow/src/org/labkey/flow/controllers/FlowController.java @@ -16,7 +16,8 @@ package org.labkey.flow.controllers; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.SimpleViewAction; import org.labkey.api.admin.AdminUrls; @@ -79,7 +80,7 @@ public class FlowController extends BaseFlowController { - private static final Logger _log = Logger.getLogger(FlowController.class); + private static final Logger _log = LogManager.getLogger(FlowController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(FlowController.class); diff --git a/flow/src/org/labkey/flow/controllers/ReportsController.java b/flow/src/org/labkey/flow/controllers/ReportsController.java index 1b85c22868..e826e6bcc3 100644 --- a/flow/src/org/labkey/flow/controllers/ReportsController.java +++ b/flow/src/org/labkey/flow/controllers/ReportsController.java @@ -15,7 +15,8 @@ */ package org.labkey.flow.controllers; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.ConfirmAction; @@ -69,7 +70,7 @@ */ public class ReportsController extends BaseFlowController { - private static final Logger _log = Logger.getLogger(ReportsController.class); + private static final Logger _log = LogManager.getLogger(ReportsController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(ReportsController.class); public ReportsController() diff --git a/flow/src/org/labkey/flow/controllers/WorkspaceData.java b/flow/src/org/labkey/flow/controllers/WorkspaceData.java index bd2f825cc3..9fb5f81cfa 100644 --- a/flow/src/org/labkey/flow/controllers/WorkspaceData.java +++ b/flow/src/org/labkey/flow/controllers/WorkspaceData.java @@ -16,7 +16,8 @@ package org.labkey.flow.controllers; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineService; @@ -59,7 +60,7 @@ public class WorkspaceData implements Serializable { - static final private Logger _log = Logger.getLogger(WorkspaceData.class); + static final private Logger _log = LogManager.getLogger(WorkspaceData.class); String path; String name; diff --git a/flow/src/org/labkey/flow/controllers/attribute/AttributeController.java b/flow/src/org/labkey/flow/controllers/attribute/AttributeController.java index 2452e82d9a..40b660c57d 100644 --- a/flow/src/org/labkey/flow/controllers/attribute/AttributeController.java +++ b/flow/src/org/labkey/flow/controllers/attribute/AttributeController.java @@ -16,7 +16,8 @@ package org.labkey.flow.controllers.attribute; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.ConfirmAction; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.ReturnUrlForm; @@ -52,7 +53,7 @@ */ public class AttributeController extends BaseFlowController { - private static final Logger _log = Logger.getLogger(AttributeController.class); + private static final Logger _log = LogManager.getLogger(AttributeController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(AttributeController.class); diff --git a/flow/src/org/labkey/flow/controllers/editscript/EditScriptForm.java b/flow/src/org/labkey/flow/controllers/editscript/EditScriptForm.java index 43c005f5ac..d0110f8a36 100644 --- a/flow/src/org/labkey/flow/controllers/editscript/EditScriptForm.java +++ b/flow/src/org/labkey/flow/controllers/editscript/EditScriptForm.java @@ -16,7 +16,8 @@ package org.labkey.flow.controllers.editscript; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.fhcrc.cpas.flow.script.xml.ScriptDocument; import org.jetbrains.annotations.NotNull; import org.labkey.api.security.permissions.UpdatePermission; @@ -52,7 +53,7 @@ public class EditScriptForm extends FlowObjectForm { - static private Logger _log = Logger.getLogger(EditScriptForm.class); + static private Logger _log = LogManager.getLogger(EditScriptForm.class); private static int MAX_WELLS_TO_POLL = 15; public ScriptDocument analysisDocument; diff --git a/flow/src/org/labkey/flow/controllers/editscript/ScriptController.java b/flow/src/org/labkey/flow/controllers/editscript/ScriptController.java index 5d470d37eb..c796f90fd8 100644 --- a/flow/src/org/labkey/flow/controllers/editscript/ScriptController.java +++ b/flow/src/org/labkey/flow/controllers/editscript/ScriptController.java @@ -17,7 +17,8 @@ package org.labkey.flow.controllers.editscript; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlCursor; import org.apache.xmlbeans.XmlObject; import org.fhcrc.cpas.flow.script.xml.AnalysisDef; @@ -96,7 +97,7 @@ */ public class ScriptController extends BaseFlowController { - private static Logger _log = Logger.getLogger(ScriptController.class); + private static Logger _log = LogManager.getLogger(ScriptController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(ScriptController.class); diff --git a/flow/src/org/labkey/flow/controllers/editscript/UploadAnalysisForm.java b/flow/src/org/labkey/flow/controllers/editscript/UploadAnalysisForm.java index aaf2b643dd..65639e90fe 100644 --- a/flow/src/org/labkey/flow/controllers/editscript/UploadAnalysisForm.java +++ b/flow/src/org/labkey/flow/controllers/editscript/UploadAnalysisForm.java @@ -17,7 +17,8 @@ package org.labkey.flow.controllers.editscript; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.util.SessionHelper; import org.labkey.flow.analysis.model.Analysis; import org.labkey.flow.analysis.model.StatisticSet; @@ -29,7 +30,7 @@ public class UploadAnalysisForm extends EditScriptForm { - private static final Logger _log = Logger.getLogger(UploadAnalysisForm.class); + private static final Logger _log = LogManager.getLogger(UploadAnalysisForm.class); private String token; private int existingStatCount = 0; diff --git a/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java b/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java index 9df06acaa7..6e71bdf2ce 100644 --- a/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java +++ b/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java @@ -18,7 +18,8 @@ import org.apache.commons.io.filefilter.DirectoryFileFilter; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.SimpleRedirectAction; import org.labkey.api.action.SimpleViewAction; @@ -96,7 +97,7 @@ public class AnalysisScriptController extends BaseFlowController { - private static final Logger _log = Logger.getLogger(AnalysisScriptController.class); + private static final Logger _log = LogManager.getLogger(AnalysisScriptController.class); public enum Action { diff --git a/flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java b/flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java index 42f1de8f57..b2fcbf36f4 100644 --- a/flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java +++ b/flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java @@ -17,7 +17,8 @@ package org.labkey.flow.controllers.executescript; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.DataRegionSelection; import org.labkey.api.data.Filter; import org.labkey.api.data.SimpleFilter; @@ -35,7 +36,7 @@ public class ChooseRunsToAnalyzeForm extends FlowQueryForm implements DataRegionSelection.DataSelectionKeyForm { - static private final Logger _log = Logger.getLogger(ChooseRunsToAnalyzeForm.class); + static private final Logger _log = LogManager.getLogger(ChooseRunsToAnalyzeForm.class); static private final String COMPOPTION_EXPERIMENTLSID = "experimentlsid:"; static private final String COMPOPTION_COMPID = "compid:"; diff --git a/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java b/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java index 855ca6e626..d646ad46b6 100644 --- a/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java +++ b/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java @@ -15,7 +15,8 @@ */ package org.labkey.flow.controllers.executescript; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.SpringActionController; import org.labkey.api.collections.NamedObject; import org.labkey.api.collections.NamedObjectList; @@ -71,7 +72,7 @@ */ public class SamplesConfirmGridView extends GridView { - public static final Logger LOG = Logger.getLogger(SamplesConfirmGridView.class); + public static final Logger LOG = LogManager.getLogger(SamplesConfirmGridView.class); /*package*/ public static String DATAREGION_NAME = "SamplesConfirm"; diff --git a/flow/src/org/labkey/flow/controllers/run/RunController.java b/flow/src/org/labkey/flow/controllers/run/RunController.java index 58c7782632..25a4a985ba 100644 --- a/flow/src/org/labkey/flow/controllers/run/RunController.java +++ b/flow/src/org/labkey/flow/controllers/run/RunController.java @@ -20,7 +20,8 @@ import com.fasterxml.jackson.annotation.JsonProperty; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.FormViewAction; @@ -117,7 +118,7 @@ public class RunController extends BaseFlowController { - private static final Logger _log = Logger.getLogger(RunController.class); + private static final Logger _log = LogManager.getLogger(RunController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(RunController.class); diff --git a/flow/src/org/labkey/flow/controllers/well/WellController.java b/flow/src/org/labkey/flow/controllers/well/WellController.java index 6f098e4496..6ade4ac74c 100644 --- a/flow/src/org/labkey/flow/controllers/well/WellController.java +++ b/flow/src/org/labkey/flow/controllers/well/WellController.java @@ -18,7 +18,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.DateUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.MutatingApiAction; @@ -98,7 +99,7 @@ public class WellController extends BaseFlowController { - private static final Logger _log = Logger.getLogger(WellController.class); + private static final Logger _log = LogManager.getLogger(WellController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(WellController.class); diff --git a/flow/src/org/labkey/flow/data/FieldSubstitution.java b/flow/src/org/labkey/flow/data/FieldSubstitution.java index ce6ef878d5..4bc26ec46c 100644 --- a/flow/src/org/labkey/flow/data/FieldSubstitution.java +++ b/flow/src/org/labkey/flow/data/FieldSubstitution.java @@ -17,7 +17,8 @@ package org.labkey.flow.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.query.FieldKey; import org.labkey.api.data.ColumnInfo; @@ -29,7 +30,7 @@ public class FieldSubstitution { - static final private Logger _log = Logger.getLogger(FieldSubstitution.class); + static final private Logger _log = LogManager.getLogger(FieldSubstitution.class); Object[] _parts; static public FieldSubstitution fromString(String s) { diff --git a/flow/src/org/labkey/flow/data/FlowExperiment.java b/flow/src/org/labkey/flow/data/FlowExperiment.java index 24253a567f..fd5fabf848 100644 --- a/flow/src/org/labkey/flow/data/FlowExperiment.java +++ b/flow/src/org/labkey/flow/data/FlowExperiment.java @@ -16,7 +16,8 @@ package org.labkey.flow.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpExperiment; @@ -46,7 +47,7 @@ */ public class FlowExperiment extends FlowObject { - static private final Logger _log = Logger.getLogger(FlowExperiment.class); + static private final Logger _log = LogManager.getLogger(FlowExperiment.class); static public String FlowExperimentRunExperimentName = "Flow Experiment Runs"; static public String FlowWorkspaceExperimentName = "Flow Workspace"; static public String DEFAULT_ANALYSIS_NAME = "Analysis"; diff --git a/flow/src/org/labkey/flow/data/FlowProtocol.java b/flow/src/org/labkey/flow/data/FlowProtocol.java index 3d61d925ab..df0b86f1f0 100644 --- a/flow/src/org/labkey/flow/data/FlowProtocol.java +++ b/flow/src/org/labkey/flow/data/FlowProtocol.java @@ -17,7 +17,8 @@ package org.labkey.flow.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.junit.Before; import org.junit.Test; @@ -96,7 +97,7 @@ public class FlowProtocol extends FlowObject { - static private final Logger _log = Logger.getLogger(FlowProtocol.class); + static private final Logger _log = LogManager.getLogger(FlowProtocol.class); static protected final String DEFAULT_PROTOCOL_NAME = "Flow"; static private final String SAMPLETYPE_NAME = "Samples"; diff --git a/flow/src/org/labkey/flow/data/FlowRun.java b/flow/src/org/labkey/flow/data/FlowRun.java index ce40a1ac71..927ad981b3 100644 --- a/flow/src/org/labkey/flow/data/FlowRun.java +++ b/flow/src/org/labkey/flow/data/FlowRun.java @@ -16,7 +16,8 @@ package org.labkey.flow.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.attachments.Attachment; import org.labkey.api.attachments.AttachmentService; @@ -58,7 +59,7 @@ public class FlowRun extends FlowObject { - private static final Logger _log = Logger.getLogger(FlowRun.class); + private static final Logger _log = LogManager.getLogger(FlowRun.class); public static final Comparator NAME_COMPARATOR = Comparator.comparing(FlowObject::getName); diff --git a/flow/src/org/labkey/flow/data/FlowWell.java b/flow/src/org/labkey/flow/data/FlowWell.java index 74ae6ddf7b..cf9b29d3e0 100644 --- a/flow/src/org/labkey/flow/data/FlowWell.java +++ b/flow/src/org/labkey/flow/data/FlowWell.java @@ -16,7 +16,8 @@ package org.labkey.flow.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.exp.api.DataType; import org.labkey.api.exp.api.ExpData; @@ -51,7 +52,7 @@ public class FlowWell extends FlowDataObject { - static private final Logger _log = Logger.getLogger(FlowWell.class); + static private final Logger _log = LogManager.getLogger(FlowWell.class); // For serialization protected FlowWell() {} diff --git a/flow/src/org/labkey/flow/persist/AttributeCache.java b/flow/src/org/labkey/flow/persist/AttributeCache.java index c32d7b2eda..1a40367af9 100644 --- a/flow/src/org/labkey/flow/persist/AttributeCache.java +++ b/flow/src/org/labkey/flow/persist/AttributeCache.java @@ -18,7 +18,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.BlockingCache; @@ -48,7 +49,7 @@ */ abstract public class AttributeCache, E extends AttributeCache.Entry> { - private static final Logger LOG = Logger.getLogger(AttributeCache.class); + private static final Logger LOG = LogManager.getLogger(AttributeCache.class); // container id -> list of names (sorted) private CacheLoader> BY_CONTAINER_LOADER = new CacheLoader>() diff --git a/flow/src/org/labkey/flow/persist/AttributeSetHelper.java b/flow/src/org/labkey/flow/persist/AttributeSetHelper.java index 66788e7f23..bf0d80dfc0 100644 --- a/flow/src/org/labkey/flow/persist/AttributeSetHelper.java +++ b/flow/src/org/labkey/flow/persist/AttributeSetHelper.java @@ -16,7 +16,8 @@ package org.labkey.flow.persist; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.data.SqlSelector; @@ -45,7 +46,7 @@ */ public class AttributeSetHelper { - private static final Logger LOG = Logger.getLogger(AttributeSetHelper.class); + private static final Logger LOG = LogManager.getLogger(AttributeSetHelper.class); public static AttributeSet fromData(ExpData data) diff --git a/flow/src/org/labkey/flow/persist/FlowContainerListener.java b/flow/src/org/labkey/flow/persist/FlowContainerListener.java index f93932dc35..f1e45ebc79 100644 --- a/flow/src/org/labkey/flow/persist/FlowContainerListener.java +++ b/flow/src/org/labkey/flow/persist/FlowContainerListener.java @@ -16,14 +16,15 @@ package org.labkey.flow.persist; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.security.User; public class FlowContainerListener extends ContainerManager.AbstractContainerListener { - static final private Logger _log = Logger.getLogger(FlowContainerListener.class); + static final private Logger _log = LogManager.getLogger(FlowContainerListener.class); /** * Delete all Flow data from the container. diff --git a/flow/src/org/labkey/flow/persist/FlowDataHandler.java b/flow/src/org/labkey/flow/persist/FlowDataHandler.java index 2e786fc5ac..791b3c8554 100644 --- a/flow/src/org/labkey/flow/persist/FlowDataHandler.java +++ b/flow/src/org/labkey/flow/persist/FlowDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.flow.persist; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; diff --git a/flow/src/org/labkey/flow/persist/FlowManager.java b/flow/src/org/labkey/flow/persist/FlowManager.java index 0b4a265250..5062bb9744 100644 --- a/flow/src/org/labkey/flow/persist/FlowManager.java +++ b/flow/src/org/labkey/flow/persist/FlowManager.java @@ -18,7 +18,8 @@ import org.apache.commons.collections4.iterators.ArrayIterator; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.audit.AuditLogService; @@ -83,7 +84,7 @@ public class FlowManager { private static final FlowManager instance = new FlowManager(); - private static final Logger _log = Logger.getLogger(FlowManager.class); + private static final Logger _log = LogManager.getLogger(FlowManager.class); private static final String SCHEMA_NAME = "flow"; static public FlowManager get() diff --git a/flow/src/org/labkey/flow/query/AttributeForeignKey.java b/flow/src/org/labkey/flow/query/AttributeForeignKey.java index 97a04bb8bf..45f97e808f 100644 --- a/flow/src/org/labkey/flow/query/AttributeForeignKey.java +++ b/flow/src/org/labkey/flow/query/AttributeForeignKey.java @@ -17,7 +17,8 @@ package org.labkey.flow.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.*; import org.labkey.api.query.AliasManager; import org.labkey.api.query.UserSchema; @@ -32,7 +33,7 @@ abstract public class AttributeForeignKey> extends AbstractForeignKey { - protected static final Logger LOG = Logger.getLogger(AttributeForeignKey.class); + protected static final Logger LOG = LogManager.getLogger(AttributeForeignKey.class); @Override public StringExpression getURL(ColumnInfo parent) diff --git a/flow/src/org/labkey/flow/query/FlowPropertySet.java b/flow/src/org/labkey/flow/query/FlowPropertySet.java index b9192ab534..3286dbf294 100644 --- a/flow/src/org/labkey/flow/query/FlowPropertySet.java +++ b/flow/src/org/labkey/flow/query/FlowPropertySet.java @@ -17,7 +17,8 @@ package org.labkey.flow.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.exp.query.ExpDataTable; import org.labkey.flow.analysis.model.PopulationName; @@ -38,7 +39,7 @@ public class FlowPropertySet { - static private final Logger _log = Logger.getLogger(FlowPropertySet.class); + static private final Logger _log = LogManager.getLogger(FlowPropertySet.class); private Container _container; private Collection _keywords; diff --git a/flow/src/org/labkey/flow/script/AnalyzeJob.java b/flow/src/org/labkey/flow/script/AnalyzeJob.java index 7ae0d5b222..307aca43e0 100644 --- a/flow/src/org/labkey/flow/script/AnalyzeJob.java +++ b/flow/src/org/labkey/flow/script/AnalyzeJob.java @@ -18,7 +18,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.flow.data.FlowProtocol; @@ -32,7 +33,7 @@ public class AnalyzeJob extends ScriptJob { - private static Logger _log = Logger.getLogger(AnalyzeJob.class); + private static Logger _log = LogManager.getLogger(AnalyzeJob.class); int[] _runIds; diff --git a/flow/src/org/labkey/flow/script/FlowExperimentJob.java b/flow/src/org/labkey/flow/script/FlowExperimentJob.java index 43e7086d8a..07a9c4f818 100644 --- a/flow/src/org/labkey/flow/script/FlowExperimentJob.java +++ b/flow/src/org/labkey/flow/script/FlowExperimentJob.java @@ -15,7 +15,8 @@ */ package org.labkey.flow.script; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.fhcrc.cpas.exp.xml.ExperimentRunType; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; diff --git a/flow/src/org/labkey/flow/script/FlowJob.java b/flow/src/org/labkey/flow/script/FlowJob.java index caefabd994..d318f7c89e 100644 --- a/flow/src/org/labkey/flow/script/FlowJob.java +++ b/flow/src/org/labkey/flow/script/FlowJob.java @@ -16,7 +16,8 @@ package org.labkey.flow.script; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineJob; diff --git a/flow/src/org/labkey/flow/script/KeywordsJob.java b/flow/src/org/labkey/flow/script/KeywordsJob.java index 928f87de8d..a20fb2cd03 100644 --- a/flow/src/org/labkey/flow/script/KeywordsJob.java +++ b/flow/src/org/labkey/flow/script/KeywordsJob.java @@ -18,7 +18,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.view.ViewBackgroundInfo; @@ -39,7 +40,7 @@ */ public class KeywordsJob extends ScriptJob { - private static final Logger _log = Logger.getLogger(KeywordsJob.class); + private static final Logger _log = LogManager.getLogger(KeywordsJob.class); private final List _paths; private final Container _targetStudy; diff --git a/flow/src/org/labkey/flow/script/ScriptXarSource.java b/flow/src/org/labkey/flow/script/ScriptXarSource.java index 121bdc76f4..74944805f0 100644 --- a/flow/src/org/labkey/flow/script/ScriptXarSource.java +++ b/flow/src/org/labkey/flow/script/ScriptXarSource.java @@ -16,7 +16,8 @@ package org.labkey.flow.script; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; import org.labkey.api.data.Container; @@ -33,7 +34,7 @@ public class ScriptXarSource extends XarSource { - private static final Logger _log = Logger.getLogger(ScriptXarSource.class); + private static final Logger _log = LogManager.getLogger(ScriptXarSource.class); File _root; File _workingDirectory; File _logFile; diff --git a/flow/src/org/labkey/flow/view/GraphColumn.java b/flow/src/org/labkey/flow/view/GraphColumn.java index 42a8419828..8e1a98206c 100644 --- a/flow/src/org/labkey/flow/view/GraphColumn.java +++ b/flow/src/org/labkey/flow/view/GraphColumn.java @@ -16,7 +16,8 @@ package org.labkey.flow.view; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; @@ -41,7 +42,7 @@ public class GraphColumn extends DataColumn public static final String SEP = "~~~"; private static final String INCLUDE_UTIL_SCRIPT = "~~~Flow/util.js~~~"; - private Logger _log = Logger.getLogger(GraphColumn.class); + private Logger _log = LogManager.getLogger(GraphColumn.class); private FlowQuerySettings.ShowGraphs _showGraphs; public GraphColumn(ColumnInfo colinfo) diff --git a/flow/src/org/labkey/flow/view/JobStatusView.java b/flow/src/org/labkey/flow/view/JobStatusView.java index 4fe1568739..353e67b1bc 100644 --- a/flow/src/org/labkey/flow/view/JobStatusView.java +++ b/flow/src/org/labkey/flow/view/JobStatusView.java @@ -16,13 +16,14 @@ package org.labkey.flow.view; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.view.JspView; import org.labkey.flow.data.FlowStatus; public class JobStatusView extends JspView { - private static Logger _log = Logger.getLogger(JobStatusView.class); + private static Logger _log = LogManager.getLogger(JobStatusView.class); public JobStatusView(FlowStatus model) { diff --git a/luminex/src/org/labkey/luminex/LuminexController.java b/luminex/src/org/labkey/luminex/LuminexController.java index 60603b391f..af76b243c1 100644 --- a/luminex/src/org/labkey/luminex/LuminexController.java +++ b/luminex/src/org/labkey/luminex/LuminexController.java @@ -17,7 +17,8 @@ package org.labkey.luminex; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.ExportAction; @@ -108,7 +109,7 @@ */ public class LuminexController extends SpringActionController { - private static final Logger _log = Logger.getLogger(LuminexController.class); + private static final Logger _log = LogManager.getLogger(LuminexController.class); private static final DefaultActionResolver _resolver = new DefaultActionResolver(LuminexController.class, LuminexUploadWizardAction.class); diff --git a/luminex/src/org/labkey/luminex/LuminexDataHandler.java b/luminex/src/org/labkey/luminex/LuminexDataHandler.java index 1d255c2fc8..6d62e4ee00 100644 --- a/luminex/src/org/labkey/luminex/LuminexDataHandler.java +++ b/luminex/src/org/labkey/luminex/LuminexDataHandler.java @@ -21,7 +21,8 @@ import org.apache.commons.collections4.ListUtils; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -140,7 +141,7 @@ public class LuminexDataHandler extends AbstractExperimentDataHandler implements public static final String NEGATIVE_BEAD_DISPLAY_NAME = "Subtract Negative Bead"; public static final Double MAX_CURVE_PARAM_VALUE = 10e37; // Issue 15200 - private static final Logger LOGGER = Logger.getLogger(LuminexDataHandler.class); + private static final Logger LOGGER = LogManager.getLogger(LuminexDataHandler.class); public static final int MINIMUM_TITRATION_SUMMARY_COUNT = 5; public static final int MINIMUM_TITRATION_RAW_COUNT = 10; @@ -557,8 +558,8 @@ private void saveDataRows(ExpRun expRun, User user, ExpProtocol protocol, Map getUnitTests() AssayQCFlagColumn.TestCase.class, LuminexDataHandler.TestCase.class, LuminexExcelParser.TestCase.class, - LuminexRunAsyncContext.TestCase.class, +// LuminexRunAsyncContext.TestCase.class, LuminexSaveExclusionsForm.TestCase.class ); } diff --git a/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java b/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java index 8dee6861c0..43ddf7e720 100644 --- a/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java +++ b/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java @@ -21,7 +21,8 @@ import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.assay.pipeline.AssayRunAsyncContext; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.luminex.model.SinglePointControl; import org.labkey.luminex.model.Titration; import org.labkey.luminex.query.LuminexProtocolSchema; @@ -263,57 +264,57 @@ public List getSinglePointControls() } - public static class TestCase extends Assert - { - - LuminexUnitTestContext testContext = new LuminexUnitTestContext(); - LuminexRunAsyncContext asyncContext; - - private static class StringLogger extends Logger - { - StringBuilder sb = new StringBuilder(); - private StringLogger() - { - super(""); - } - - @Override - public void info(Object append) - { - sb.append(append); - sb.append("\n"); - } - - public String toString() - { - return sb.toString(); - } - } - - @Test - public void checkLogging() throws Exception - { - asyncContext = new LuminexRunAsyncContext(testContext); - StringLogger sl = new StringLogger(); - asyncContext.logProperties(sl); - String output = sl.toString(); - - assert(output.contains("Analyte 1")); - assert(output.contains("Analyte 2")); - assert(output.contains("Batch Name: Name of the Batch")); - assert(output.contains("* New")); - assert(output.contains("Assay ID: Log Test")); - assert(output.contains("Run Comments: Test Comments")); - assert(output.contains("Run Name: Name of the Run")); - assert(output.contains("Name: Name of the Project")); - assert(output.contains("*PositivityThreshold: 50.0")); - assert(output.contains("*NegativeBead: Blank (3)")); - assert(output.contains("Standard: true")); - assert(output.contains("QC Control: false")); - assert(output.contains("Other Control: true")); - assert(output.contains("Unknown: false")); - assert(output.contains("Single Point Control: true")); - } - - } +// public static class TestCase extends Assert +// { +// +// LuminexUnitTestContext testContext = new LuminexUnitTestContext(); +// LuminexRunAsyncContext asyncContext; +// +// private static class StringLogger extends Logger +// { +// StringBuilder sb = new StringBuilder(); +// private StringLogger() +// { +// super(""); +// } +// +// @Override +// public void info(Object append) +// { +// sb.append(append); +// sb.append("\n"); +// } +// +// public String toString() +// { +// return sb.toString(); +// } +// } +// +// @Test +// public void checkLogging() throws Exception +// { +// asyncContext = new LuminexRunAsyncContext(testContext); +// StringLogger sl = new StringLogger(); +// asyncContext.logProperties(sl); +// String output = sl.toString(); +// +// assert(output.contains("Analyte 1")); +// assert(output.contains("Analyte 2")); +// assert(output.contains("Batch Name: Name of the Batch")); +// assert(output.contains("* New")); +// assert(output.contains("Assay ID: Log Test")); +// assert(output.contains("Run Comments: Test Comments")); +// assert(output.contains("Run Name: Name of the Run")); +// assert(output.contains("Name: Name of the Project")); +// assert(output.contains("*PositivityThreshold: 50.0")); +// assert(output.contains("*NegativeBead: Blank (3)")); +// assert(output.contains("Standard: true")); +// assert(output.contains("QC Control: false")); +// assert(output.contains("Other Control: true")); +// assert(output.contains("Unknown: false")); +// assert(output.contains("Single Point Control: true")); +// } +// +// } } diff --git a/microarray/src/org/labkey/microarray/MicroarrayManager.java b/microarray/src/org/labkey/microarray/MicroarrayManager.java index 313eca9ff4..3fb08209c8 100644 --- a/microarray/src/org/labkey/microarray/MicroarrayManager.java +++ b/microarray/src/org/labkey/microarray/MicroarrayManager.java @@ -16,7 +16,8 @@ package org.labkey.microarray; import org.apache.commons.lang3.ArrayUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -66,7 +67,7 @@ public class MicroarrayManager { private static final MicroarrayManager _instance = new MicroarrayManager(); - private static final Logger LOG = Logger.getLogger(MicroarrayManager.class); + private static final Logger LOG = LogManager.getLogger(MicroarrayManager.class); private MicroarrayManager() { diff --git a/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixDataHandler.java b/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixDataHandler.java index 5956949513..7633a86d3e 100644 --- a/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixDataHandler.java +++ b/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.microarray.matrix; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.Container; import org.labkey.api.data.DbSchema; @@ -55,7 +56,7 @@ public class ExpressionMatrixDataHandler extends AbstractMatrixDataHandler public static final String FEATURE_ID_COLUMN_NAME = "ID_REF"; public static final String FEATURE_ID_COLUMN_IMPORT_ALIAS = "feature_id"; - private static final Logger LOG = Logger.getLogger(ExpressionMatrixDataHandler.class); + private static final Logger LOG = LogManager.getLogger(ExpressionMatrixDataHandler.class); // CONSIDER: move this flag to the assay design // private static boolean autoCreateSamples = true; diff --git a/microarray/src/org/labkey/microarray/pipeline/GeneDataPipelineProvider.java b/microarray/src/org/labkey/microarray/pipeline/GeneDataPipelineProvider.java index e3f66df205..a5e955bbb8 100644 --- a/microarray/src/org/labkey/microarray/pipeline/GeneDataPipelineProvider.java +++ b/microarray/src/org/labkey/microarray/pipeline/GeneDataPipelineProvider.java @@ -16,7 +16,8 @@ package org.labkey.microarray.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipeRoot; @@ -43,7 +44,7 @@ public class GeneDataPipelineProvider extends PipelineProvider private static final String GENE_DATA_BASE_URL_PARAMETER_NAME = "org.labkey.microarray.geneDataBaseURL"; private static final String GENE_DATA_FILE_ROOT_PARAMETER_NAME = "org.labkey.microarray.geneDataFileRoot"; - private static final Logger LOG = Logger.getLogger(GeneDataPipelineProvider.class); + private static final Logger LOG = LogManager.getLogger(GeneDataPipelineProvider.class); public GeneDataPipelineProvider(MicroarrayModule module) { diff --git a/ms2/api-src/org/labkey/api/ms2/MS2Service.java b/ms2/api-src/org/labkey/api/ms2/MS2Service.java index aa378a5a2c..2771d91591 100644 --- a/ms2/api-src/org/labkey/api/ms2/MS2Service.java +++ b/ms2/api-src/org/labkey/api/ms2/MS2Service.java @@ -16,7 +16,8 @@ package org.labkey.api.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.SimpleFilter; diff --git a/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java b/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java index 6ff5ee3534..110f1cd478 100644 --- a/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java +++ b/ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.junit.Assert; import org.junit.Test; import org.labkey.api.data.RuntimeSQLException; @@ -54,7 +55,7 @@ */ public class BibliospecSpectrumRenderer implements SpectrumRenderer { - private static final Logger LOG = Logger.getLogger(BibliospecSpectrumRenderer.class); + private static final Logger LOG = LogManager.getLogger(BibliospecSpectrumRenderer.class); private final ViewContext _context; diff --git a/ms2/src/org/labkey/ms2/CompareServiceImpl.java b/ms2/src/org/labkey/ms2/CompareServiceImpl.java index 95a8e9f4ed..cbf98ef1a3 100644 --- a/ms2/src/org/labkey/ms2/CompareServiceImpl.java +++ b/ms2/src/org/labkey/ms2/CompareServiceImpl.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.gwt.client.model.GWTComparisonResult; import org.labkey.api.gwt.server.BaseRemoteService; import org.labkey.api.query.ComparisonCrosstabView; @@ -40,7 +41,7 @@ */ public class CompareServiceImpl extends BaseRemoteService implements CompareService { - private static Logger _log = Logger.getLogger(CompareServiceImpl.class); + private static Logger _log = LogManager.getLogger(CompareServiceImpl.class); public CompareServiceImpl(ViewContext context) { diff --git a/ms2/src/org/labkey/ms2/CumulativeTimer.java b/ms2/src/org/labkey/ms2/CumulativeTimer.java index 442ae98429..05022dd4e5 100644 --- a/ms2/src/org/labkey/ms2/CumulativeTimer.java +++ b/ms2/src/org/labkey/ms2/CumulativeTimer.java @@ -18,7 +18,8 @@ import org.apache.commons.collections4.OrderedMap; import org.apache.commons.collections4.map.ListOrderedMap; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.util.Formats; /** diff --git a/ms2/src/org/labkey/ms2/DeltaScanColumn.java b/ms2/src/org/labkey/ms2/DeltaScanColumn.java index 4b02077de8..3b9fc11a0b 100644 --- a/ms2/src/org/labkey/ms2/DeltaScanColumn.java +++ b/ms2/src/org/labkey/ms2/DeltaScanColumn.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.arrays.DoubleArray; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.RenderContext; @@ -38,7 +39,7 @@ */ public class DeltaScanColumn extends AbstractPeptideDisplayColumn { - private static final Logger _log = Logger.getLogger(DeltaScanColumn.class); + private static final Logger _log = LogManager.getLogger(DeltaScanColumn.class); private ColumnInfo _fractionColInfo; private ColumnInfo _scanColInfo; diff --git a/ms2/src/org/labkey/ms2/Hydrophobicity3.java b/ms2/src/org/labkey/ms2/Hydrophobicity3.java index e6b6c49dce..153d9d3bf5 100644 --- a/ms2/src/org/labkey/ms2/Hydrophobicity3.java +++ b/ms2/src/org/labkey/ms2/Hydrophobicity3.java @@ -1,6 +1,7 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.reader.Readers; import java.io.BufferedReader; @@ -46,7 +47,7 @@ public class Hydrophobicity3 { /* translation of the ReadParmFile perl routine. This does not read a parameter */ /* file; it makes static initializers for the parameter data. */ - static Logger _log = Logger.getLogger(Hydrophobicity3.class); + static Logger _log = LogManager.getLogger(Hydrophobicity3.class); public static String VERSION = "Krokhin,3.0"; private static class AAParams { diff --git a/ms2/src/org/labkey/ms2/MS2Controller.java b/ms2/src/org/labkey/ms2/MS2Controller.java index b86bf6f8f6..86c7840315 100644 --- a/ms2/src/org/labkey/ms2/MS2Controller.java +++ b/ms2/src/org/labkey/ms2/MS2Controller.java @@ -17,7 +17,8 @@ import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.jfree.chart.imagemap.ImageMapUtilities; @@ -205,7 +206,7 @@ public class MS2Controller extends SpringActionController { private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(MS2Controller.class); - private static final Logger _log = Logger.getLogger(MS2Controller.class); + private static final Logger _log = LogManager.getLogger(MS2Controller.class); /** Bogus view name to use as a marker for showing the standard peptide view instead of a custom view or the .lastFilter view */ private static final String STANDARD_VIEW_NAME = "~~~~~~StandardView~~~~~~~"; private static final String MS2_VIEWS_CATEGORY = "MS2Views"; diff --git a/ms2/src/org/labkey/ms2/MS2Fraction.java b/ms2/src/org/labkey/ms2/MS2Fraction.java index 95d686b7f5..ae4e455604 100644 --- a/ms2/src/org/labkey/ms2/MS2Fraction.java +++ b/ms2/src/org/labkey/ms2/MS2Fraction.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import java.io.Serializable; diff --git a/ms2/src/org/labkey/ms2/MS2Importer.java b/ms2/src/org/labkey/ms2/MS2Importer.java index b32d7d7284..26172e4eef 100644 --- a/ms2/src/org/labkey/ms2/MS2Importer.java +++ b/ms2/src/org/labkey/ms2/MS2Importer.java @@ -18,7 +18,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.data.SQLFragment; @@ -82,7 +83,7 @@ public abstract class MS2Importer protected Logger _log = null; // Use system logger for bugs & system problems, and in cases where we don't have a pipeline logger - protected static Logger _systemLog = Logger.getLogger(MS2Importer.class); + protected static Logger _systemLog = LogManager.getLogger(MS2Importer.class); protected final XarContext _context; public MS2Importer(XarContext context, User user, Container c, String description, String fullFileName, Logger log) diff --git a/ms2/src/org/labkey/ms2/MS2Manager.java b/ms2/src/org/labkey/ms2/MS2Manager.java index 995b4640be..eb76508272 100644 --- a/ms2/src/org/labkey/ms2/MS2Manager.java +++ b/ms2/src/org/labkey/ms2/MS2Manager.java @@ -17,7 +17,8 @@ package org.labkey.ms2; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; import org.jetbrains.annotations.NotNull; import org.labkey.api.cache.Cache; @@ -110,7 +111,7 @@ */ public class MS2Manager { - private static Logger _log = Logger.getLogger(MS2Manager.class); + private static Logger _log = LogManager.getLogger(MS2Manager.class); private static PeptideIndexCache _peptideIndexCache = new PeptideIndexCache(); diff --git a/ms2/src/org/labkey/ms2/MS2Peptide.java b/ms2/src/org/labkey/ms2/MS2Peptide.java index 5660ee5f51..4dd01b6406 100644 --- a/ms2/src/org/labkey/ms2/MS2Peptide.java +++ b/ms2/src/org/labkey/ms2/MS2Peptide.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.util.Pair; import org.labkey.ms2.protein.fasta.Peptide; import org.labkey.ms2.reader.LibraQuantResult; @@ -28,7 +29,7 @@ public class MS2Peptide { - private static Logger _log = Logger.getLogger(MS2Peptide.class); + private static Logger _log = LogManager.getLogger(MS2Peptide.class); public static final double pMass = 1.007276; // Mass of a proton, according to X! Tandem diff --git a/ms2/src/org/labkey/ms2/MS2Run.java b/ms2/src/org/labkey/ms2/MS2Run.java index 57b0b3a873..872ac0fe5e 100644 --- a/ms2/src/org/labkey/ms2/MS2Run.java +++ b/ms2/src/org/labkey/ms2/MS2Run.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.SqlSelector; @@ -34,7 +35,7 @@ public abstract class MS2Run implements Serializable { - private static Logger _log = Logger.getLogger(MS2Run.class); + private static Logger _log = LogManager.getLogger(MS2Run.class); protected final static String[] EMPTY_STRING_ARRAY = new String[0]; diff --git a/ms2/src/org/labkey/ms2/MS2ServiceImpl.java b/ms2/src/org/labkey/ms2/MS2ServiceImpl.java index 7eca2583a1..18d797b9eb 100644 --- a/ms2/src/org/labkey/ms2/MS2ServiceImpl.java +++ b/ms2/src/org/labkey/ms2/MS2ServiceImpl.java @@ -27,7 +27,8 @@ import org.labkey.ms2.pipeline.mascot.MascotClientImpl; import org.labkey.ms2.query.PeptidesTableInfo; import org.labkey.ms2.query.MS2Schema; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; /** * User: jeckels diff --git a/ms2/src/org/labkey/ms2/MascotDatImporter.java b/ms2/src/org/labkey/ms2/MascotDatImporter.java index a696cdc01a..7fe821b672 100644 --- a/ms2/src/org/labkey/ms2/MascotDatImporter.java +++ b/ms2/src/org/labkey/ms2/MascotDatImporter.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.RuntimeSQLException; import org.labkey.api.exp.XarContext; diff --git a/ms2/src/org/labkey/ms2/PepXmlExperimentDataHandler.java b/ms2/src/org/labkey/ms2/PepXmlExperimentDataHandler.java index e4fb277e77..56b391af25 100644 --- a/ms2/src/org/labkey/ms2/PepXmlExperimentDataHandler.java +++ b/ms2/src/org/labkey/ms2/PepXmlExperimentDataHandler.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; diff --git a/ms2/src/org/labkey/ms2/PepXmlImporter.java b/ms2/src/org/labkey/ms2/PepXmlImporter.java index 0cc8441c8b..b4ecbf7dc7 100644 --- a/ms2/src/org/labkey/ms2/PepXmlImporter.java +++ b/ms2/src/org/labkey/ms2/PepXmlImporter.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.RuntimeSQLException; import org.labkey.api.exp.XarContext; diff --git a/ms2/src/org/labkey/ms2/PeptideImporter.java b/ms2/src/org/labkey/ms2/PeptideImporter.java index 814e52d3d6..93c777badb 100644 --- a/ms2/src/org/labkey/ms2/PeptideImporter.java +++ b/ms2/src/org/labkey/ms2/PeptideImporter.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.SqlExecutor; diff --git a/ms2/src/org/labkey/ms2/Protein.java b/ms2/src/org/labkey/ms2/Protein.java index 8dc5446e00..26dabd0427 100644 --- a/ms2/src/org/labkey/ms2/Protein.java +++ b/ms2/src/org/labkey/ms2/Protein.java @@ -17,7 +17,8 @@ package org.labkey.ms2; import org.junit.Assert; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.junit.Test; import org.labkey.api.util.HtmlString; @@ -28,7 +29,7 @@ public class Protein { - private static Logger _log = Logger.getLogger(Protein.class); + private static Logger _log = LogManager.getLogger(Protein.class); private double _mass; private String _sequence; diff --git a/ms2/src/org/labkey/ms2/ProteinProphetExperimentDataHandler.java b/ms2/src/org/labkey/ms2/ProteinProphetExperimentDataHandler.java index 92f60db42a..fa61ae6804 100644 --- a/ms2/src/org/labkey/ms2/ProteinProphetExperimentDataHandler.java +++ b/ms2/src/org/labkey/ms2/ProteinProphetExperimentDataHandler.java @@ -27,7 +27,8 @@ import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.api.security.User; import org.labkey.ms2.pipeline.TPPTask; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import javax.xml.stream.XMLStreamException; import java.io.File; diff --git a/ms2/src/org/labkey/ms2/ProteinProphetImporter.java b/ms2/src/org/labkey/ms2/ProteinProphetImporter.java index fccb49d652..f768b0eeba 100644 --- a/ms2/src/org/labkey/ms2/ProteinProphetImporter.java +++ b/ms2/src/org/labkey/ms2/ProteinProphetImporter.java @@ -17,7 +17,8 @@ package org.labkey.ms2; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.data.SQLFragment; @@ -62,7 +63,7 @@ */ public class ProteinProphetImporter { - private static final Logger _log = Logger.getLogger(ProteinProphetImporter.class); + private static final Logger _log = LogManager.getLogger(ProteinProphetImporter.class); private final File _file; private final String _experimentRunLSID; diff --git a/ms2/src/org/labkey/ms2/SpectrumImporter.java b/ms2/src/org/labkey/ms2/SpectrumImporter.java index 73263ef63f..fe3a454950 100644 --- a/ms2/src/org/labkey/ms2/SpectrumImporter.java +++ b/ms2/src/org/labkey/ms2/SpectrumImporter.java @@ -16,7 +16,8 @@ package org.labkey.ms2; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.DbSchema; import org.labkey.api.util.NetworkDrive; import org.labkey.api.util.Pair; @@ -39,7 +40,7 @@ */ public class SpectrumImporter { - private static Logger _systemLog = Logger.getLogger(SpectrumImporter.class); + private static Logger _systemLog = LogManager.getLogger(SpectrumImporter.class); private static final int SQL_BATCH_SIZE = 100; private Logger _log = null; diff --git a/ms2/src/org/labkey/ms2/matrix/ProteinExpressionMatrixDataHandler.java b/ms2/src/org/labkey/ms2/matrix/ProteinExpressionMatrixDataHandler.java index 749d10f8ba..17890c81b5 100644 --- a/ms2/src/org/labkey/ms2/matrix/ProteinExpressionMatrixDataHandler.java +++ b/ms2/src/org/labkey/ms2/matrix/ProteinExpressionMatrixDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.ms2.matrix; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbSchema; import org.labkey.api.data.RuntimeSQLException; @@ -53,7 +54,7 @@ public class ProteinExpressionMatrixDataHandler extends AbstractMatrixDataHandler { public static final String PROTEIN_SEQ_ID_COLUMN_NAME = "Molecule Identifier"; - private static final Logger LOG = Logger.getLogger(ProteinExpressionMatrixDataHandler.class); + private static final Logger LOG = LogManager.getLogger(ProteinExpressionMatrixDataHandler.class); public ProteinExpressionMatrixDataHandler() { diff --git a/ms2/src/org/labkey/ms2/peptideview/AbstractMS2RunView.java b/ms2/src/org/labkey/ms2/peptideview/AbstractMS2RunView.java index 45eaaec58d..98119f4c3a 100644 --- a/ms2/src/org/labkey/ms2/peptideview/AbstractMS2RunView.java +++ b/ms2/src/org/labkey/ms2/peptideview/AbstractMS2RunView.java @@ -16,7 +16,8 @@ package org.labkey.ms2.peptideview; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ButtonBar; import org.labkey.api.data.ColumnHeaderType; @@ -81,7 +82,7 @@ */ public abstract class AbstractMS2RunView { - private static Logger _log = Logger.getLogger(AbstractMS2RunView.class); + private static Logger _log = LogManager.getLogger(AbstractMS2RunView.class); private final Container _container; private final User _user; diff --git a/ms2/src/org/labkey/ms2/pipeline/MS2PipelineManager.java b/ms2/src/org/labkey/ms2/pipeline/MS2PipelineManager.java index 6f174576c9..6f98454405 100644 --- a/ms2/src/org/labkey/ms2/pipeline/MS2PipelineManager.java +++ b/ms2/src/org/labkey/ms2/pipeline/MS2PipelineManager.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.pipeline.*; import org.labkey.api.pipeline.cmd.ConvertTaskId; @@ -43,7 +44,7 @@ */ public class MS2PipelineManager { - private static Logger _log = Logger.getLogger(MS2PipelineProvider.class); + private static Logger _log = LogManager.getLogger(MS2PipelineProvider.class); private static final String DEFAULT_FASTA_DIR = "databases"; public static final String SEQUENCE_DB_ROOT_TYPE = "SEQUENCE_DATABASE"; diff --git a/ms2/src/org/labkey/ms2/pipeline/SearchServiceImpl.java b/ms2/src/org/labkey/ms2/pipeline/SearchServiceImpl.java index e398dd9a78..b873befaba 100644 --- a/ms2/src/org/labkey/ms2/pipeline/SearchServiceImpl.java +++ b/ms2/src/org/labkey/ms2/pipeline/SearchServiceImpl.java @@ -17,7 +17,8 @@ package org.labkey.ms2.pipeline; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.gwt.server.BaseRemoteService; import org.labkey.api.pipeline.PipeRoot; @@ -48,7 +49,7 @@ public class SearchServiceImpl extends BaseRemoteService implements SearchService { - private static Logger _log = Logger.getLogger(SearchServiceImpl.class); + private static Logger _log = LogManager.getLogger(SearchServiceImpl.class); private GWTSearchServiceResult results= new GWTSearchServiceResult(); private AbstractMS2SearchPipelineProvider provider; private AbstractMS2SearchProtocol protocol; diff --git a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java index 71cea2e36c..7bb29ae641 100644 --- a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java +++ b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java @@ -25,7 +25,8 @@ import org.apache.http.entity.mime.content.FileBody; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.junit.Assert; import org.junit.Assume; import org.junit.Test; @@ -79,7 +80,7 @@ public class MascotClientImpl implements SearchClient { - private static final Logger _log = Logger.getLogger(MascotClientImpl.class); + private static final Logger _log = LogManager.getLogger(MascotClientImpl.class); private final Logger _instanceLogger; diff --git a/ms2/src/org/labkey/ms2/pipeline/rollup/FractionRollupPipelineJob.java b/ms2/src/org/labkey/ms2/pipeline/rollup/FractionRollupPipelineJob.java index c9e30db670..0a25ca8f43 100644 --- a/ms2/src/org/labkey/ms2/pipeline/rollup/FractionRollupPipelineJob.java +++ b/ms2/src/org/labkey/ms2/pipeline/rollup/FractionRollupPipelineJob.java @@ -17,7 +17,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.TaskId; import org.labkey.api.pipeline.file.AbstractFileAnalysisJob; diff --git a/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemPipelineJob.java b/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemPipelineJob.java index 7900c2a590..854037ab6a 100644 --- a/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemPipelineJob.java +++ b/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemPipelineJob.java @@ -17,7 +17,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.pipeline.*; import org.labkey.api.pipeline.file.AbstractFileAnalysisJob; import org.labkey.api.view.ViewBackgroundInfo; diff --git a/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java b/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java index 7c09bdb89a..ae6e1ee53e 100644 --- a/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java +++ b/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2.pipeline.tandem; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory; @@ -36,7 +37,7 @@ */ public class XTandemSearchProtocol extends AbstractMS2SearchProtocol { - private static Logger _log = Logger.getLogger(XTandemSearchProtocol.class); + private static Logger _log = LogManager.getLogger(XTandemSearchProtocol.class); public XTandemSearchProtocol(String name, String description, String xml) { diff --git a/ms2/src/org/labkey/ms2/protein/FastaDbLoader.java b/ms2/src/org/labkey/ms2/protein/FastaDbLoader.java index d985eb0670..43a134c5c6 100644 --- a/ms2/src/org/labkey/ms2/protein/FastaDbLoader.java +++ b/ms2/src/org/labkey/ms2/protein/FastaDbLoader.java @@ -17,7 +17,8 @@ package org.labkey.ms2.protein; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.junit.Assert; import org.junit.Test; import org.labkey.api.data.SqlExecutor; diff --git a/ms2/src/org/labkey/ms2/protein/ParserTree.java b/ms2/src/org/labkey/ms2/protein/ParserTree.java index f4beff3f27..998846ddfe 100644 --- a/ms2/src/org/labkey/ms2/protein/ParserTree.java +++ b/ms2/src/org/labkey/ms2/protein/ParserTree.java @@ -18,7 +18,8 @@ import org.labkey.ms2.protein.uniprot.uniprot; import org.labkey.ms2.protein.uniprot.*; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import java.util.Map; import java.util.HashMap; diff --git a/ms2/src/org/labkey/ms2/protein/ProteinManager.java b/ms2/src/org/labkey/ms2/protein/ProteinManager.java index 182171efe8..cede25b40e 100644 --- a/ms2/src/org/labkey/ms2/protein/ProteinManager.java +++ b/ms2/src/org/labkey/ms2/protein/ProteinManager.java @@ -21,7 +21,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.SpringActionController; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -84,7 +85,7 @@ */ public class ProteinManager { - private static final Logger LOG = Logger.getLogger(ProteinManager.class); + private static final Logger LOG = LogManager.getLogger(ProteinManager.class); private static final String SCHEMA_NAME = "prot"; public static final int RUN_FILTER = 1; diff --git a/ms2/src/org/labkey/ms2/protein/XMLProteinHandler.java b/ms2/src/org/labkey/ms2/protein/XMLProteinHandler.java index 1cd946c74b..ced7b26a0e 100644 --- a/ms2/src/org/labkey/ms2/protein/XMLProteinHandler.java +++ b/ms2/src/org/labkey/ms2/protein/XMLProteinHandler.java @@ -22,7 +22,8 @@ import org.xml.sax.Attributes; import org.xml.sax.XMLReader; import org.labkey.ms2.protein.tools.REProperties; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import java.io.File; import java.util.HashSet; diff --git a/ms2/src/org/labkey/ms2/protein/organism/GuessOrgByParsing.java b/ms2/src/org/labkey/ms2/protein/organism/GuessOrgByParsing.java index cc6861e0d6..d1f80a9880 100644 --- a/ms2/src/org/labkey/ms2/protein/organism/GuessOrgByParsing.java +++ b/ms2/src/org/labkey/ms2/protein/organism/GuessOrgByParsing.java @@ -16,7 +16,8 @@ package org.labkey.ms2.protein.organism; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.DbSchema; import org.labkey.api.data.SqlSelector; import org.labkey.ms2.protein.ProteinManager; @@ -36,7 +37,7 @@ public class GuessOrgByParsing extends Timer implements OrganismGuessStrategy private Map _cache = new HashMap<>(); private static final DbSchema _schema = ProteinManager.getSchema(); private static final String CACHED_MISS_VALUE = "GuessOrgByParsing.CACHED_MISS_VALUE"; - private static Logger _log = Logger.getLogger(GuessOrgByParsing.class); + private static Logger _log = LogManager.getLogger(GuessOrgByParsing.class); private static final String _organismFromTaxIdSql = "SELECT " + _schema.getSqlDialect().concatenate("genus", "' '", "species") + " FROM " + diff --git a/ms2/src/org/labkey/ms2/protein/tools/GoLoader.java b/ms2/src/org/labkey/ms2/protein/tools/GoLoader.java index 27d2606b01..e207ade8da 100644 --- a/ms2/src/org/labkey/ms2/protein/tools/GoLoader.java +++ b/ms2/src/org/labkey/ms2/protein/tools/GoLoader.java @@ -18,7 +18,8 @@ import org.apache.commons.compress.archivers.tar.TarArchiveEntry; import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbScope; @@ -58,7 +59,7 @@ */ public abstract class GoLoader { - private static final Logger _log = Logger.getLogger(GoLoader.class); + private static final Logger _log = LogManager.getLogger(GoLoader.class); private static final String GOTERM_FILE = "term.txt"; private static final String GOTERM2TERM_FILE = "term2term.txt"; diff --git a/ms2/src/org/labkey/ms2/protein/tools/ProteinDictionaryHelpers.java b/ms2/src/org/labkey/ms2/protein/tools/ProteinDictionaryHelpers.java index 55556ca811..52d15b9696 100644 --- a/ms2/src/org/labkey/ms2/protein/tools/ProteinDictionaryHelpers.java +++ b/ms2/src/org/labkey/ms2/protein/tools/ProteinDictionaryHelpers.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2.protein.tools; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.DbScope; import org.labkey.api.data.SqlExecutor; @@ -47,7 +48,7 @@ */ public class ProteinDictionaryHelpers { - private static final Logger _log = Logger.getLogger(ProteinDictionaryHelpers.class); + private static final Logger _log = LogManager.getLogger(ProteinDictionaryHelpers.class); private static final String FILE = "/MS2/externalData/ProtSprotOrgMap.txt"; private static final int SPOM_BATCH_SIZE = 1000; diff --git a/ms2/src/org/labkey/ms2/protein/uniprot/uniprot.java b/ms2/src/org/labkey/ms2/protein/uniprot/uniprot.java index f4d0c83847..46b51708c7 100644 --- a/ms2/src/org/labkey/ms2/protein/uniprot/uniprot.java +++ b/ms2/src/org/labkey/ms2/protein/uniprot/uniprot.java @@ -16,7 +16,8 @@ package org.labkey.ms2.protein.uniprot; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.CoreSchema; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.dialect.SqlDialect; diff --git a/ms2/src/org/labkey/ms2/protein/uniprot/uniprot_entry_organism_name.java b/ms2/src/org/labkey/ms2/protein/uniprot/uniprot_entry_organism_name.java index ca9fd0ada7..128cda0e42 100644 --- a/ms2/src/org/labkey/ms2/protein/uniprot/uniprot_entry_organism_name.java +++ b/ms2/src/org/labkey/ms2/protein/uniprot/uniprot_entry_organism_name.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2.protein.uniprot; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.xml.sax.*; import org.labkey.ms2.protein.*; diff --git a/ms2/src/org/labkey/ms2/query/PeptideAggregrationDisplayColumn.java b/ms2/src/org/labkey/ms2/query/PeptideAggregrationDisplayColumn.java index 835b1f971f..0243298c46 100644 --- a/ms2/src/org/labkey/ms2/query/PeptideAggregrationDisplayColumn.java +++ b/ms2/src/org/labkey/ms2/query/PeptideAggregrationDisplayColumn.java @@ -16,7 +16,8 @@ package org.labkey.ms2.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.*; import org.labkey.api.util.ResultSetUtil; @@ -36,7 +37,7 @@ public abstract class PeptideAggregrationDisplayColumn extends SimpleDisplayColu private ColumnInfo _groupingColumn; private ColumnInfo _peptideColumn; - private static final Logger LOG = Logger.getLogger(PeptideAggregrationDisplayColumn.class); + private static final Logger LOG = LogManager.getLogger(PeptideAggregrationDisplayColumn.class); private boolean _loggedError = false; public PeptideAggregrationDisplayColumn(ColumnInfo groupingColumn, ColumnInfo peptideColumn, String caption) diff --git a/ms2/src/org/labkey/ms2/reader/MS2Loader.java b/ms2/src/org/labkey/ms2/reader/MS2Loader.java index ee82e8923f..2deb03b70e 100644 --- a/ms2/src/org/labkey/ms2/reader/MS2Loader.java +++ b/ms2/src/org/labkey/ms2/reader/MS2Loader.java @@ -16,7 +16,8 @@ package org.labkey.ms2.reader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.ms2.MS2Modification; diff --git a/ms2/src/org/labkey/ms2/reader/MS2XmlLoader.java b/ms2/src/org/labkey/ms2/reader/MS2XmlLoader.java index 7684aefddb..be9986c5b2 100644 --- a/ms2/src/org/labkey/ms2/reader/MS2XmlLoader.java +++ b/ms2/src/org/labkey/ms2/reader/MS2XmlLoader.java @@ -16,7 +16,8 @@ package org.labkey.ms2.reader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.reader.SimpleXMLStreamReader; import org.labkey.api.util.PossiblyGZIPpedFileInputStreamFactory; diff --git a/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java b/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java index 418d4e55f6..949797885b 100644 --- a/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java +++ b/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java @@ -16,7 +16,8 @@ package org.labkey.ms2.reader; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; diff --git a/ms2/src/org/labkey/ms2/reader/PepXmlLoader.java b/ms2/src/org/labkey/ms2/reader/PepXmlLoader.java index d6ed974cea..56111f9b10 100644 --- a/ms2/src/org/labkey/ms2/reader/PepXmlLoader.java +++ b/ms2/src/org/labkey/ms2/reader/PepXmlLoader.java @@ -17,7 +17,8 @@ package org.labkey.ms2.reader; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.reader.SimpleXMLStreamReader; import org.labkey.ms2.MS2Modification; import org.labkey.ms2.protein.fasta.Protein; @@ -310,7 +311,7 @@ public PeptideIterator getPeptideIterator() public static class PeptideIterator implements Iterator { - private static Logger _log = Logger.getLogger(PepXmlLoader.class); + private static Logger _log = LogManager.getLogger(PepXmlLoader.class); private SimpleXMLStreamReader _parser; private PepXmlPeptide _peptide = null; @@ -425,7 +426,7 @@ public static class PepXmlPeptide extends MS2Loader.Peptide //then all elements are null except the actual modifications. Index+1 = position of mod private ModifiedAminoAcid[] _modifiedAminoAcids = null; // TODO Delete this? This doesn't seem to be used ??? - private static Logger _log = Logger.getLogger(PepXmlPeptide.class); + private static Logger _log = LogManager.getLogger(PepXmlPeptide.class); protected static PepXmlPeptide getNextPeptide(SimpleXMLStreamReader parser, MS2ModificationList modifications, PepXmlFraction fraction) throws XMLStreamException diff --git a/ms2/src/org/labkey/ms2/reader/Q3AnalysisSummary.java b/ms2/src/org/labkey/ms2/reader/Q3AnalysisSummary.java index dab6dac4c7..b379b76074 100644 --- a/ms2/src/org/labkey/ms2/reader/Q3AnalysisSummary.java +++ b/ms2/src/org/labkey/ms2/reader/Q3AnalysisSummary.java @@ -18,7 +18,8 @@ import org.labkey.ms2.reader.SimpleXMLEventRewriter; import org.labkey.api.reader.SimpleXMLStreamReader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import javax.xml.stream.XMLStreamException; @@ -27,7 +28,7 @@ */ public class Q3AnalysisSummary extends RelativeQuantAnalysisSummary { - private static Logger _log = Logger.getLogger(Q3AnalysisSummary.class); + private static Logger _log = LogManager.getLogger(Q3AnalysisSummary.class); private static final float DEFAULT_MASSTOL = .1f; diff --git a/ms2/src/org/labkey/ms2/reader/Q3Handler.java b/ms2/src/org/labkey/ms2/reader/Q3Handler.java index 954e2ccc94..85ffecd3a8 100644 --- a/ms2/src/org/labkey/ms2/reader/Q3Handler.java +++ b/ms2/src/org/labkey/ms2/reader/Q3Handler.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2.reader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.reader.SimpleXMLStreamReader; import javax.xml.stream.XMLStreamException; @@ -31,7 +32,7 @@ public class Q3Handler extends PepXmlAnalysisResultHandler { public static final String ANALYSIS_TYPE = "q3"; - static Logger _log = Logger.getLogger(PepXmlAnalysisResult.class); + static Logger _log = LogManager.getLogger(PepXmlAnalysisResult.class); @Override protected Q3Result getResult(SimpleXMLStreamReader parser) throws XMLStreamException diff --git a/ms2/src/org/labkey/ms2/reader/SequentialMzxmlIterator.java b/ms2/src/org/labkey/ms2/reader/SequentialMzxmlIterator.java index 04d6551f65..bb04077ae9 100644 --- a/ms2/src/org/labkey/ms2/reader/SequentialMzxmlIterator.java +++ b/ms2/src/org/labkey/ms2/reader/SequentialMzxmlIterator.java @@ -19,7 +19,8 @@ import org.labkey.api.util.NetworkDrive; import org.labkey.api.util.PossiblyGZIPpedFileInputStreamFactory; import org.labkey.api.reader.SimpleXMLStreamReader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.GDuration; import org.systemsbiology.jrap.Scan; @@ -34,7 +35,7 @@ */ public class SequentialMzxmlIterator extends AbstractMzxmlIterator { - private static Logger _log = Logger.getLogger(SequentialMzxmlIterator.class); + private static Logger _log = LogManager.getLogger(SequentialMzxmlIterator.class); private File _file; private InputStream _in; diff --git a/ms2/src/org/labkey/ms2/reader/SimpleXMLEventRewriter.java b/ms2/src/org/labkey/ms2/reader/SimpleXMLEventRewriter.java index bf6682a76f..65daaa822a 100644 --- a/ms2/src/org/labkey/ms2/reader/SimpleXMLEventRewriter.java +++ b/ms2/src/org/labkey/ms2/reader/SimpleXMLEventRewriter.java @@ -15,7 +15,8 @@ */ package org.labkey.ms2.reader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import java.io.FileInputStream; import java.io.IOException; @@ -49,7 +50,7 @@ */ public class SimpleXMLEventRewriter { - private static Logger _log = Logger.getLogger(SimpleXMLEventRewriter.class); + private static Logger _log = LogManager.getLogger(SimpleXMLEventRewriter.class); private static XMLEventFactory eventFactory = XMLEventFactory.newInstance(); private static DatatypeFactory typeFactory = null; diff --git a/ms2/src/org/labkey/ms2/reader/TarIterator.java b/ms2/src/org/labkey/ms2/reader/TarIterator.java index b64240475a..b66a79c55b 100644 --- a/ms2/src/org/labkey/ms2/reader/TarIterator.java +++ b/ms2/src/org/labkey/ms2/reader/TarIterator.java @@ -17,7 +17,8 @@ import org.apache.commons.compress.archivers.tar.TarArchiveEntry; import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.arrays.FloatArray; import org.labkey.ms2.FloatParser; import org.labkey.ms2.MS2Importer; @@ -39,7 +40,7 @@ */ public class TarIterator implements SimpleScanIterator { - private static final Logger _log = Logger.getLogger(TarIterator.class); + private static final Logger _log = LogManager.getLogger(TarIterator.class); private static final int STREAM_BUFFER_SIZE = 128 * 1024; private String _dtaFileNamePrefix = null; diff --git a/ms2/src/org/labkey/ms2/reader/XPressAnalysisSummary.java b/ms2/src/org/labkey/ms2/reader/XPressAnalysisSummary.java index 2c7007f8dd..d8ca241c4d 100644 --- a/ms2/src/org/labkey/ms2/reader/XPressAnalysisSummary.java +++ b/ms2/src/org/labkey/ms2/reader/XPressAnalysisSummary.java @@ -16,7 +16,8 @@ package org.labkey.ms2.reader; import net.systemsbiology.regisWeb.pepXML.XpressratioSummaryDocument; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.labkey.ms2.reader.RelativeQuantAnalysisSummary; import org.labkey.api.reader.SimpleXMLStreamReader; @@ -29,7 +30,7 @@ */ public class XPressAnalysisSummary extends RelativeQuantAnalysisSummary { - private static Logger _log = Logger.getLogger(XPressAnalysisSummary.class); + private static Logger _log = LogManager.getLogger(XPressAnalysisSummary.class); public static final String analysisType = "xpress"; diff --git a/ms2/src/org/systemsbiology/jrap/MSXMLParser.java b/ms2/src/org/systemsbiology/jrap/MSXMLParser.java index 10a1d862b9..4640cee5df 100644 --- a/ms2/src/org/systemsbiology/jrap/MSXMLParser.java +++ b/ms2/src/org/systemsbiology/jrap/MSXMLParser.java @@ -38,7 +38,8 @@ ******************************************************************************/ package org.systemsbiology.jrap; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.xml.sax.*; import org.xml.sax.helpers.XMLReaderFactory; @@ -53,7 +54,7 @@ */ public final class MSXMLParser { - static Logger _log = Logger.getLogger(MSXMLParser.class); + static Logger _log = LogManager.getLogger(MSXMLParser.class); // // Protected class members diff --git a/nab/src/org/labkey/nab/NabDataHandler.java b/nab/src/org/labkey/nab/NabDataHandler.java index 9c908aa71f..fb382d87a9 100644 --- a/nab/src/org/labkey/nab/NabDataHandler.java +++ b/nab/src/org/labkey/nab/NabDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.nab; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.plate.AbstractPlateBasedAssayProvider; import org.labkey.api.assay.dilution.DilutionAssayRun; @@ -53,7 +54,7 @@ */ public abstract class NabDataHandler extends DilutionDataHandler { - public static final Logger LOG = Logger.getLogger(NabDataHandler.class); + public static final Logger LOG = LogManager.getLogger(NabDataHandler.class); public static final DataType NAB_TRANSFORMED_DATA_TYPE = new DataType("AssayRunNabTransformedData"); // a marker data type public static final String NAB_DATA_ROW_LSID_PREFIX = "AssayRunNabDataRow"; diff --git a/nab/src/org/labkey/nab/NabManager.java b/nab/src/org/labkey/nab/NabManager.java index c6d4b36c4d..0a3cce02e4 100644 --- a/nab/src/org/labkey/nab/NabManager.java +++ b/nab/src/org/labkey/nab/NabManager.java @@ -16,7 +16,8 @@ package org.labkey.nab; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.DbSchema; @@ -60,7 +61,7 @@ */ public class NabManager extends AbstractNabManager { - private static final Logger _log = Logger.getLogger(NabManager.class); + private static final Logger _log = LogManager.getLogger(NabManager.class); private static final NabManager _instance = new NabManager(); private NabManager() diff --git a/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java b/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java index 6a0ff66a56..8284470084 100644 --- a/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java +++ b/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.nab; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.poi.openxml4j.exceptions.InvalidFormatException; import org.apache.poi.ss.usermodel.Workbook; import org.jetbrains.annotations.NotNull; diff --git a/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java b/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java index 31f898b3e6..ca4e31ab52 100644 --- a/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java +++ b/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.nab.multiplate; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.assay.dilution.DilutionManager; import org.labkey.api.assay.dilution.SampleProperty; import org.labkey.api.assay.dilution.WellDataRow; diff --git a/viability/src/org/labkey/viability/GuavaDataHandler.java b/viability/src/org/labkey/viability/GuavaDataHandler.java index 5f37ad1c94..a920948fc2 100644 --- a/viability/src/org/labkey/viability/GuavaDataHandler.java +++ b/viability/src/org/labkey/viability/GuavaDataHandler.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.beanutils.Converter; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.Lsid; diff --git a/viability/src/org/labkey/viability/ViabilityManager.java b/viability/src/org/labkey/viability/ViabilityManager.java index 71d8ee0f89..bafaa7c552 100644 --- a/viability/src/org/labkey/viability/ViabilityManager.java +++ b/viability/src/org/labkey/viability/ViabilityManager.java @@ -16,7 +16,8 @@ package org.labkey.viability; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -76,7 +77,7 @@ public class ViabilityManager { - private static final Logger LOG = org.apache.log4j.Logger.getLogger(ViabilityManager.class); + private static final Logger LOG = LogManager.getLogger(ViabilityManager.class); private static final ViabilityManager _instance = new ViabilityManager(); private ViabilityManager() diff --git a/viability/src/org/labkey/viability/ViabilitySpecimenChangeListener.java b/viability/src/org/labkey/viability/ViabilitySpecimenChangeListener.java index 888dea5d8c..7da474bebe 100644 --- a/viability/src/org/labkey/viability/ViabilitySpecimenChangeListener.java +++ b/viability/src/org/labkey/viability/ViabilitySpecimenChangeListener.java @@ -15,7 +15,8 @@ */ package org.labkey.viability; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.BaseSelector; import org.labkey.api.data.Container; import org.labkey.api.data.SQLFragment; diff --git a/viability/src/org/labkey/viability/ViabilityTsvDataHandler.java b/viability/src/org/labkey/viability/ViabilityTsvDataHandler.java index 9b08a274bf..7400b5069d 100644 --- a/viability/src/org/labkey/viability/ViabilityTsvDataHandler.java +++ b/viability/src/org/labkey/viability/ViabilityTsvDataHandler.java @@ -33,7 +33,8 @@ import org.labkey.api.assay.AssayService; import org.apache.commons.beanutils.converters.StringArrayConverter; import org.apache.commons.beanutils.Converter; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import java.io.File; import java.io.IOException; From f5a017c141c21811a87d5108aad0dd65f6c9ffe6 Mon Sep 17 00:00:00 2001 From: Ankur Juneja Date: Mon, 27 Jul 2020 11:48:18 -0700 Subject: [PATCH 2/3] Item 7554: LuminexRunAsyncContext test in commonAssays (#217) --- .../src/org/labkey/luminex/LuminexModule.java | 2 +- .../luminex/LuminexRunAsyncContext.java | 114 +++++++++--------- 2 files changed, 59 insertions(+), 57 deletions(-) diff --git a/luminex/src/org/labkey/luminex/LuminexModule.java b/luminex/src/org/labkey/luminex/LuminexModule.java index b13ab23c41..8321914473 100644 --- a/luminex/src/org/labkey/luminex/LuminexModule.java +++ b/luminex/src/org/labkey/luminex/LuminexModule.java @@ -101,7 +101,7 @@ public Set getUnitTests() AssayQCFlagColumn.TestCase.class, LuminexDataHandler.TestCase.class, LuminexExcelParser.TestCase.class, -// LuminexRunAsyncContext.TestCase.class, + LuminexRunAsyncContext.TestCase.class, LuminexSaveExclusionsForm.TestCase.class ); } diff --git a/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java b/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java index 43ddf7e720..f6a6bd7aa8 100644 --- a/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java +++ b/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java @@ -15,14 +15,16 @@ */ package org.labkey.luminex; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.simple.SimpleLogger; +import org.apache.logging.log4j.util.PropertiesUtil; import org.junit.Assert; import org.junit.Test; +import org.labkey.api.assay.pipeline.AssayRunAsyncContext; import org.labkey.api.data.ColumnInfo; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.property.DomainProperty; -import org.labkey.api.assay.pipeline.AssayRunAsyncContext; -import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.labkey.luminex.model.SinglePointControl; import org.labkey.luminex.model.Titration; import org.labkey.luminex.query.LuminexProtocolSchema; @@ -264,57 +266,57 @@ public List getSinglePointControls() } -// public static class TestCase extends Assert -// { -// -// LuminexUnitTestContext testContext = new LuminexUnitTestContext(); -// LuminexRunAsyncContext asyncContext; -// -// private static class StringLogger extends Logger -// { -// StringBuilder sb = new StringBuilder(); -// private StringLogger() -// { -// super(""); -// } -// -// @Override -// public void info(Object append) -// { -// sb.append(append); -// sb.append("\n"); -// } -// -// public String toString() -// { -// return sb.toString(); -// } -// } -// -// @Test -// public void checkLogging() throws Exception -// { -// asyncContext = new LuminexRunAsyncContext(testContext); -// StringLogger sl = new StringLogger(); -// asyncContext.logProperties(sl); -// String output = sl.toString(); -// -// assert(output.contains("Analyte 1")); -// assert(output.contains("Analyte 2")); -// assert(output.contains("Batch Name: Name of the Batch")); -// assert(output.contains("* New")); -// assert(output.contains("Assay ID: Log Test")); -// assert(output.contains("Run Comments: Test Comments")); -// assert(output.contains("Run Name: Name of the Run")); -// assert(output.contains("Name: Name of the Project")); -// assert(output.contains("*PositivityThreshold: 50.0")); -// assert(output.contains("*NegativeBead: Blank (3)")); -// assert(output.contains("Standard: true")); -// assert(output.contains("QC Control: false")); -// assert(output.contains("Other Control: true")); -// assert(output.contains("Unknown: false")); -// assert(output.contains("Single Point Control: true")); -// } -// -// } + public static class TestCase extends Assert + { + + LuminexUnitTestContext testContext = new LuminexUnitTestContext(); + LuminexRunAsyncContext asyncContext; + + private static class StringLogger extends SimpleLogger + { + StringBuilder sb = new StringBuilder(); + private StringLogger() + { + super("", Level.INFO, false, false, false, false, "", null, new PropertiesUtil(PropertiesUtil.getSystemProperties()), null); + } + + @Override + public void info(Object append) + { + sb.append(append); + sb.append("\n"); + } + + public String toString() + { + return sb.toString(); + } + } + + @Test + public void checkLogging() throws Exception + { + asyncContext = new LuminexRunAsyncContext(testContext); + StringLogger sl = new StringLogger(); + asyncContext.logProperties(sl); + String output = sl.toString(); + + assert(output.contains("Analyte 1")); + assert(output.contains("Analyte 2")); + assert(output.contains("Batch Name: Name of the Batch")); + assert(output.contains("* New")); + assert(output.contains("Assay ID: Log Test")); + assert(output.contains("Run Comments: Test Comments")); + assert(output.contains("Run Name: Name of the Run")); + assert(output.contains("Name: Name of the Project")); + assert(output.contains("*PositivityThreshold: 50.0")); + assert(output.contains("*NegativeBead: Blank (3)")); + assert(output.contains("Standard: true")); + assert(output.contains("QC Control: false")); + assert(output.contains("Other Control: true")); + assert(output.contains("Unknown: false")); + assert(output.contains("Single Point Control: true")); + } + + } } From 9e093e8f0df29bca4fc2eb6a2f519d80fb1ed561 Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Wed, 29 Jul 2020 17:49:32 -0700 Subject: [PATCH 3/3] override more specific method --- luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java b/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java index f6a6bd7aa8..1c9bd80477 100644 --- a/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java +++ b/luminex/src/org/labkey/luminex/LuminexRunAsyncContext.java @@ -281,9 +281,9 @@ private StringLogger() } @Override - public void info(Object append) + public void info(String message) { - sb.append(append); + sb.append(message); sb.append("\n"); }