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Merged
labkey-ankurj merged 7 commits into from
Aug 5, 2020
Merged

Item 7490: Migration from log4j1 to log4j2 #205

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4662ff6
Item 7490: Migration from log4j1 to log4j2 - update java methods and …
labkey-ankurj Jul 7, 2020
4074c3e
Merge branch 'develop' into fb_log4J_upgrade
labkey-ankurj Jul 15, 2020
db2ec38
Merge branch 'develop' into fb_log4J_upgrade
labkey-ankurj Jul 20, 2020
f5a017c
Item 7554: LuminexRunAsyncContext test in commonAssays (#217)
labkey-ankurj Jul 27, 2020
c02b0c3
Merge branch 'develop' into fb_log4j_upgrade
labkey-ankurj Jul 28, 2020
9e093e8
override more specific method
labkey-ankurj Jul 30, 2020
f433c07
Merge branch 'develop' into fb_log4J_upgrade
labkey-ankurj Aug 4, 2020
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3 changes: 2 additions & 1 deletion elisa/src/org/labkey/elisa/ElisaDataHandler.java
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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;
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3 changes: 2 additions & 1 deletion elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java
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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;
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3 changes: 2 additions & 1 deletion elispotassay/src/org/labkey/elispot/ElispotDataHandler.java
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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;
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5 changes: 3 additions & 2 deletions elispotassay/src/org/labkey/elispot/ElispotManager.java
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*/
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;
Expand Down Expand Up @@ -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";
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5 changes: 3 additions & 2 deletions flow/enginesrc/org/labkey/flow/analysis/model/ExternalAnalysis.java
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*/
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;
Expand All @@ -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<String, SampleInfo> _sampleInfos = new CaseInsensitiveMapWrapper<>(new LinkedHashMap<>());
protected Set<CompensationMatrix> _compensationMatrices = new LinkedHashSet<>();
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5 changes: 3 additions & 2 deletions flow/enginesrc/org/labkey/flow/analysis/model/FCS.java
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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.*;
Expand All @@ -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<String> supportedVersions = new ArrayList<>(Arrays.asList("FCS2.0","FCS3.0","FCS3.1"));
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5 changes: 3 additions & 2 deletions flow/enginesrc/org/labkey/flow/analysis/model/FCSHeader.java
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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;
Expand All @@ -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<String, String> keywords = new CaseInsensitiveHashMap<>();
int dataLast;
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5 changes: 3 additions & 2 deletions flow/enginesrc/org/labkey/flow/analysis/model/WorkspaceParser.java
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*/
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;
Expand Down Expand Up @@ -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;
}
}
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5 changes: 3 additions & 2 deletions flow/enginesrc/org/labkey/flow/analysis/web/FCSAnalyzer.java
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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;
Expand Down Expand Up @@ -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;
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3 changes: 2 additions & 1 deletion flow/enginesrc/org/labkey/flow/persist/AnalysisSerializer.java
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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;
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5 changes: 3 additions & 2 deletions flow/enginesrc/org/labkey/flow/persist/AttributeSet.java
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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;
Expand Down Expand Up @@ -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;
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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/FlowController.java
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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;
Expand Down Expand Up @@ -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);

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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/ReportsController.java
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*/
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;
Expand Down Expand Up @@ -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()
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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/WorkspaceData.java
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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;
Expand Down Expand Up @@ -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;
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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/attribute/AttributeController.java
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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;
Expand Down Expand Up @@ -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);

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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/editscript/EditScriptForm.java
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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;
Expand Down Expand Up @@ -52,7 +53,7 @@

public class EditScriptForm extends FlowObjectForm<FlowScript>
{
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;
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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/editscript/ScriptController.java
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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;
Expand Down Expand Up @@ -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);

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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/editscript/UploadAnalysisForm.java
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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;
Expand All @@ -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;
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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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
{
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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java
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Expand Up @@ -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;
Expand All @@ -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:";
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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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";

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5 changes: 3 additions & 2 deletions flow/src/org/labkey/flow/controllers/run/RunController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);

Expand Down
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