From 33902d3b30bd2b3fe5acc90f657dd5ee49f327b7 Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Mon, 13 Jul 2020 07:17:41 -0700 Subject: [PATCH] Item 7490: upgrade log4j --- src/org/labkey/mq/MqDatahandler.java | 2 +- src/org/labkey/mq/MqExperimentImporter.java | 7 ++++--- src/org/labkey/mq/MqManager.java | 5 +++-- src/org/labkey/mq/model/ExperimentGroupManager.java | 5 +++-- 4 files changed, 11 insertions(+), 8 deletions(-) diff --git a/src/org/labkey/mq/MqDatahandler.java b/src/org/labkey/mq/MqDatahandler.java index c03a750..1a48c0b 100644 --- a/src/org/labkey/mq/MqDatahandler.java +++ b/src/org/labkey/mq/MqDatahandler.java @@ -1,6 +1,6 @@ package org.labkey.mq; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; diff --git a/src/org/labkey/mq/MqExperimentImporter.java b/src/org/labkey/mq/MqExperimentImporter.java index 5b6cd8e..bd1c036 100644 --- a/src/org/labkey/mq/MqExperimentImporter.java +++ b/src/org/labkey/mq/MqExperimentImporter.java @@ -3,7 +3,8 @@ 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.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.data.SqlExecutor; @@ -33,11 +34,11 @@ import org.labkey.mq.model.TMTChannel; import org.labkey.mq.model.TMTInfo; import org.labkey.mq.parser.EvidenceParser; -import org.labkey.mq.parser.SummaryTemplateParser; import org.labkey.mq.parser.ModifiedPeptidesParser; import org.labkey.mq.parser.MqParserException; import org.labkey.mq.parser.PeptidesParser; import org.labkey.mq.parser.ProteinGroupsParser; +import org.labkey.mq.parser.SummaryTemplateParser; import org.labkey.mq.query.ModifiedPeptideManager; import java.io.File; @@ -68,7 +69,7 @@ public class MqExperimentImporter private PipelineJob _contextJob; // Use system logger for bugs & system problems, and in cases where we don't have a pipeline logger - protected static Logger _systemLog = Logger.getLogger(MqExperimentImporter.class); + protected static Logger _systemLog = LogManager.getLogger(MqExperimentImporter.class); protected final XarContext _context; public static final int STATUS_RUNNING = 0; diff --git a/src/org/labkey/mq/MqManager.java b/src/org/labkey/mq/MqManager.java index 8723fae..5124282 100644 --- a/src/org/labkey/mq/MqManager.java +++ b/src/org/labkey/mq/MqManager.java @@ -16,7 +16,8 @@ package org.labkey.mq; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlException; import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; import org.jetbrains.annotations.NotNull; @@ -62,7 +63,7 @@ public class MqManager { - private static Logger _log = Logger.getLogger(MqManager.class); + private static Logger _log = LogManager.getLogger(MqManager.class); private MqManager() { diff --git a/src/org/labkey/mq/model/ExperimentGroupManager.java b/src/org/labkey/mq/model/ExperimentGroupManager.java index c1ba6d5..fffbd3a 100644 --- a/src/org/labkey/mq/model/ExperimentGroupManager.java +++ b/src/org/labkey/mq/model/ExperimentGroupManager.java @@ -1,12 +1,13 @@ package org.labkey.mq.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; /** * Created by vsharma on 2/3/2016. */ public class ExperimentGroupManager { - private static Logger _log = Logger.getLogger(ExperimentGroupManager.class); + private static Logger _log = LogManager.getLogger(ExperimentGroupManager.class); }