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 45f5824358..e33c1fd314 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.FormHandlerAction; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.ReadOnlyApiAction; @@ -95,7 +96,7 @@ 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 dd37618a8f..c45dbaa1d3 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.*; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineService; @@ -53,7 +54,7 @@ */ 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 842917a1a2..e47da59dda 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.action.UrlProvider; import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.pipeline.PipeRoot; 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 new file mode 100644 index 0000000000..e69de29bb2 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 { - 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 d8e4405b86..c9a4d612d9 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; @@ -54,7 +55,7 @@ */ 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;