Item 7490: upgrade log4j (#46)

Author: labkey-ankurj

OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java

@@ -20,7 +20,8 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.directory.api.ldap.model.exception.LdapException;
 import org.apache.directory.api.ldap.model.exception.LdapOperationException;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.action.ApiResponse;
@@ -48,7 +49,7 @@ public class OpenLdapSyncController extends SpringActionController
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(OpenLdapSyncController.class);
     public static final String NAME = "openldapsync";
 
-    private static Logger _log = Logger.getLogger(OpenLdapSyncController.class);
+    private static Logger _log = LogManager.getLogger(OpenLdapSyncController.class);
 
     public OpenLdapSyncController()
     {

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapConnectionWrapper.java

@@ -14,7 +14,8 @@
 import org.apache.directory.ldap.client.api.DefaultPoolableLdapConnectionFactory;
 import org.apache.directory.ldap.client.api.LdapConnection;
 import org.apache.directory.ldap.client.api.LdapConnectionConfig;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -34,7 +35,7 @@ public class LdapConnectionWrapper
     private LdapConnectionConfig _cfg = null;
     private LdapConnection _connection = null;
     private LdapSettings _settings;
-    private static final Logger _log = Logger.getLogger(LdapConnectionWrapper.class);
+    private static final Logger _log = LogManager.getLogger(LdapConnectionWrapper.class);
     private boolean doLog = false;
 
     public LdapConnectionWrapper() throws LdapException

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapEntry.java

@@ -4,7 +4,8 @@
 import org.apache.directory.api.ldap.model.entry.Entry;
 import org.apache.directory.api.ldap.model.exception.LdapInvalidAttributeValueException;
 import org.apache.directory.api.ldap.model.name.Dn;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.security.ValidEmail;
 
 /**
@@ -15,7 +16,7 @@
  */
 public class LdapEntry
 {
-    private static final Logger _log = Logger.getLogger(LdapEntry.class);
+    private static final Logger _log = LogManager.getLogger(LdapEntry.class);
 
     private Entry _entry;
     protected LdapSettings _settings;

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapScheduler.java

@@ -1,7 +1,8 @@
 package org.labkey.openldapsync.ldap;
 
 import org.apache.directory.api.ldap.model.exception.LdapException;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.quartz.DailyTimeIntervalScheduleBuilder;
 import org.quartz.JobBuilder;
 import org.quartz.JobDetail;
@@ -18,7 +19,7 @@
 public class LdapScheduler
 {
     private static final LdapScheduler _instance = new LdapScheduler();
-    private static final Logger _log = Logger.getLogger(LdapScheduler.class);
+    private static final Logger _log = LogManager.getLogger(LdapScheduler.class);
     private static JobDetail _job = null;
     private Integer _frequency = null;
 

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java

@@ -4,7 +4,8 @@
 import org.apache.directory.api.ldap.model.exception.LdapException;
 import org.apache.directory.api.ldap.model.exception.LdapInvalidDnException;
 import org.apache.directory.api.ldap.model.name.Dn;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.junit.After;
 import org.junit.Assert;
 import org.junit.Before;
@@ -68,7 +69,7 @@
  */
 public class LdapSyncRunner implements Job
 {
-    private static final Logger _log = Logger.getLogger(LdapSyncRunner.class);
+    private static final Logger _log = LogManager.getLogger(LdapSyncRunner.class);
     private LdapSettings _settings;
     private LdapConnectionWrapper _wrapper;
     private Map<String, LdapSyncModel> _syncedRecordMap = new HashMap<>();

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/GenomeTrigger.java

@@ -15,7 +15,8 @@
  */
 package org.labkey.api.sequenceanalysis;
 
-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.security.User;
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java

@@ -17,7 +17,8 @@
 
 import htsjdk.samtools.util.StringUtil;
 import org.apache.commons.io.IOUtils;
-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.data.ContainerManager;
@@ -54,7 +55,7 @@
  */
 public class RefNtSequenceModel implements Serializable
 {
-    private static final Logger _log = Logger.getLogger(RefNtSequenceModel.class);
+    private static final Logger _log = LogManager.getLogger(RefNtSequenceModel.class);
 
     private int _rowid;
     private String _name;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -16,7 +16,8 @@
 package org.labkey.api.sequenceanalysis;
 
 
-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.laboratory.NavItem;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java

@@ -1,7 +1,8 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.apache.commons.io.FileUtils;
-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.ConvertHelper;
 import org.labkey.api.pipeline.PipelineJobException;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineContext.java

@@ -15,7 +15,8 @@
  */
 package org.labkey.api.sequenceanalysis.pipeline;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.WorkDirectory;