Update log4j to 2 - v15

igvteam · Dec 11, 2021 · 40aa5e0 · 40aa5e0
1 parent 19e3edf
commit 40aa5e0
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diff --git a/build.gradle b/build.gradle
diff --git a/lib_build/proguard_full_client.cfg b/lib_build/proguard_full_client.cfg
@@ -59,7 +59,7 @@
 -dontnote org.broad.igv.util.RuntimeUtils
 
 # Keep Apache logging classes due to runtime issues.  This rule can likely be far more aggressive but hasn't been tuned.
--keep,includedescriptorclasses class org.apache.log4j.**,org.apache.logging.** {
+-keep,includedescriptorclasses class org.apache.logging.log4j.**,org.apache.logging.** {
      *;
 }
 

diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
@@ -17,7 +17,6 @@
     requires java.sql;
     requires java.xml;
     requires jdk.xml.dom;
-    requires log4j;
     requires org.apache.logging.log4j;
     requires org.apache.logging.log4j.core;
     requires swing.layout;

diff --git a/src/main/java/org/broad/igv/DirectoryManager.java b/src/main/java/org/broad/igv/DirectoryManager.java
@@ -26,8 +26,8 @@
 package org.broad.igv;
 
 import org.apache.commons.io.FileUtils;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.*;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.core.LoggerContext;
 import org.apache.logging.log4j.core.appender.RollingFileAppender;
@@ -58,7 +58,7 @@
  */
 public class DirectoryManager {
 
-    private static Logger log = Logger.getLogger(DirectoryManager.class);
+    private static Logger log = LogManager.getLogger(DirectoryManager.class);
 
     private static File USER_HOME;
     private static File USER_DIRECTORY;    // FileSystemView.getFileSystemView().getDefaultDirectory();

diff --git a/src/main/java/org/broad/igv/Globals.java b/src/main/java/org/broad/igv/Globals.java
@@ -25,7 +25,7 @@
 
 package org.broad.igv;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.renderer.SequenceRenderer;
 
 import java.io.IOException;
@@ -39,7 +39,7 @@
  * Date: Feb 3, 2010
  */
 public class Globals {
-    private static Logger log = Logger.getLogger(Globals.class);
+    private static Logger log = LogManager.getLogger(Globals.class);
 
     public static final int DESIGN_DPI = 96;
     public static final DecimalFormat DECIMAL_FORMAT = new DecimalFormat();

diff --git a/src/main/java/org/broad/igv/aws/S3LoadDialog.java b/src/main/java/org/broad/igv/aws/S3LoadDialog.java
@@ -25,7 +25,7 @@
 
 package org.broad.igv.aws;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.apache.commons.lang3.tuple.Triple;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.util.MessageUtils;
@@ -55,7 +55,7 @@
 
 public class S3LoadDialog extends JDialog {
 
-    private static Logger log = Logger.getLogger(S3LoadDialog.class);
+    private static Logger log = LogManager.getLogger(S3LoadDialog.class);
 
     private final DefaultTreeModel treeModel;
     String selectedId;

diff --git a/src/main/java/org/broad/igv/batch/BatchRunner.java b/src/main/java/org/broad/igv/batch/BatchRunner.java
@@ -25,7 +25,7 @@
 
 package org.broad.igv.batch;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.Globals;
 import org.broad.igv.exceptions.DataLoadException;
 import org.broad.igv.feature.genome.GenomeManager;
@@ -40,7 +40,7 @@
 
 public class BatchRunner implements NamedRunnable {
 
-    private static Logger log = Logger.getLogger(BatchRunner.class);
+    private static Logger log = LogManager.getLogger(BatchRunner.class);
 
     private String inputFile;
     private IGV igv;

diff --git a/src/main/java/org/broad/igv/batch/CommandExecutor.java b/src/main/java/org/broad/igv/batch/CommandExecutor.java
@@ -30,7 +30,7 @@
 
 package org.broad.igv.batch;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.Locus;
 import org.broad.igv.feature.Range;
@@ -66,7 +66,7 @@
 
 public class CommandExecutor {
 
-    private static Logger log = Logger.getLogger(CommandExecutor.class);
+    private static Logger log = LogManager.getLogger(CommandExecutor.class);
 
     private File snapshotDirectory;
     private IGV igv;

diff --git a/src/main/java/org/broad/igv/batch/CommandListener.java b/src/main/java/org/broad/igv/batch/CommandListener.java
@@ -26,7 +26,7 @@
 package org.broad.igv.batch;
 
 import biz.source_code.base64Coder.Base64Coder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.google.OAuthUtils;
@@ -53,7 +53,7 @@ public class CommandListener implements Runnable {
 
     public static int currentListenerPort = -1;
 
-    private static Logger log = Logger.getLogger(CommandListener.class);
+    private static Logger log = LogManager.getLogger(CommandListener.class);
 
     private static CommandListener listener;
     private static final String CRLF = "\r\n";

diff --git a/src/main/java/org/broad/igv/bbfile/BBFileHeader.java b/src/main/java/org/broad/igv/bbfile/BBFileHeader.java
@@ -38,7 +38,7 @@
 
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.LittleEndianInputStream;
 
 import java.io.ByteArrayInputStream;
@@ -50,7 +50,7 @@
 **/
 public class BBFileHeader {
 
-    private static Logger log = Logger.getLogger(BBFileHeader.class);
+    private static Logger log = LogManager.getLogger(BBFileHeader.class);
 
     // defines bigBed/bigwig Header Format types
     static public final int BBFILE_HEADER_SIZE = 64;

diff --git a/src/main/java/org/broad/igv/bbfile/BBFileReader.java b/src/main/java/org/broad/igv/bbfile/BBFileReader.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.stream.IGVSeekableBufferedStream;
 import org.broad.igv.util.stream.IGVSeekableStreamFactory;
 
@@ -91,7 +91,7 @@ public class BBFileReader {
 
     public static final long BBFILE_HEADER_OFFSET = 0;
 
-    private static Logger log = Logger.getLogger(BBFileReader.class);
+    private static Logger log = LogManager.getLogger(BBFileReader.class);
 
     private SeekableStream fis;      // BBFile input stream handle
     private long fileOffset;           // file offset for next item to be read

diff --git a/src/main/java/org/broad/igv/bbfile/BBTotalSummaryBlock.java b/src/main/java/org/broad/igv/bbfile/BBTotalSummaryBlock.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.LittleEndianInputStream;
 
 import java.io.ByteArrayInputStream;
@@ -46,7 +46,7 @@
 * */
 public class BBTotalSummaryBlock {
 
-    private static Logger log = Logger.getLogger(BBTotalSummaryBlock.class);
+    private static Logger log = LogManager.getLogger(BBTotalSummaryBlock.class);
 
     public static final int TOTAL_SUMMARY_BLOCK_SIZE = 40;
 

diff --git a/src/main/java/org/broad/igv/bbfile/BBZoomLevelFormat.java b/src/main/java/org/broad/igv/bbfile/BBZoomLevelFormat.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.LittleEndianInputStream;
 
 import java.io.ByteArrayInputStream;
@@ -57,7 +57,7 @@
 * */
 public class BBZoomLevelFormat {
 
-    private static Logger log = Logger.getLogger(BBZoomLevelFormat.class);
+    private static Logger log = LogManager.getLogger(BBZoomLevelFormat.class);
 
     // size of zoom level format header is 4 byte; only accounts for zoomCount of Table O
     public static final int ZOOM_FORMAT_HEADER_SIZE = 4;

diff --git a/src/main/java/org/broad/igv/bbfile/BBZoomLevelHeader.java b/src/main/java/org/broad/igv/bbfile/BBZoomLevelHeader.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.LittleEndianInputStream;
 
 import java.io.ByteArrayInputStream;
@@ -49,7 +49,7 @@
 * */
 public class BBZoomLevelHeader {
 
-    private static Logger log = Logger.getLogger(BBZoomLevelHeader.class);
+    private static Logger log = LogManager.getLogger(BBZoomLevelHeader.class);
 
     static public final int ZOOM_LEVEL_HEADER_SIZE = 24;
 

diff --git a/src/main/java/org/broad/igv/bbfile/BBZoomLevels.java b/src/main/java/org/broad/igv/bbfile/BBZoomLevels.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.stream.IGVSeekableBufferedStream;
 
 import java.util.ArrayList;
@@ -54,7 +54,7 @@
 * */
 public class BBZoomLevels {
 
-    private static Logger log = Logger.getLogger(BBZoomLevels.class);
+    private static Logger log = LogManager.getLogger(BBZoomLevels.class);
 
     // defines the zoom headers access
     //private SeekableStream fis;       // BBFile handle

diff --git a/src/main/java/org/broad/igv/bbfile/BPTree.java b/src/main/java/org/broad/igv/bbfile/BPTree.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.LittleEndianInputStream;
 
 import java.io.ByteArrayInputStream;
@@ -69,7 +69,7 @@
 **/
 public class BPTree {
 
-    private static Logger log = Logger.getLogger(BPTree.class);
+    private static Logger log = LogManager.getLogger(BPTree.class);
 
     public static final int BPTREE_NODE_FORMAT_SIZE = 4;   // node format size
     public static final int BPTREE_NODE_ITEM_SIZE = 8;     // Plus keySize to be added

diff --git a/src/main/java/org/broad/igv/bbfile/BPTreeChildNode.java b/src/main/java/org/broad/igv/bbfile/BPTreeChildNode.java
@@ -25,7 +25,7 @@
 
 package org.broad.igv.bbfile;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 
 import java.util.ArrayList;
 
@@ -47,7 +47,7 @@
 * */
 public class BPTreeChildNode implements BPTreeNode{
 
-    private static Logger log = Logger.getLogger(BPTreeChildNode.class);
+    private static Logger log = LogManager.getLogger(BPTreeChildNode.class);
     private final boolean isLeafNode = false;
 
     private long nodeIndex;    // index for node in B+ tree organization

diff --git a/src/main/java/org/broad/igv/bbfile/BPTreeChildNodeItem.java b/src/main/java/org/broad/igv/bbfile/BPTreeChildNodeItem.java
@@ -25,7 +25,7 @@
 
 package org.broad.igv.bbfile;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 
 /**
  * Created by IntelliJ IDEA.
@@ -39,7 +39,7 @@
  */
 public class BPTreeChildNodeItem implements BPTreeNodeItem {
 
-    private static Logger log = Logger.getLogger(BPTreeChildNodeItem.class);
+    private static Logger log = LogManager.getLogger(BPTreeChildNodeItem.class);
     private final boolean isLeafItem = false;
     private long itemIndex;     // item index in child node list
 

diff --git a/src/main/java/org/broad/igv/bbfile/BPTreeHeader.java b/src/main/java/org/broad/igv/bbfile/BPTreeHeader.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.LittleEndianInputStream;
 
 import java.io.ByteArrayInputStream;
@@ -48,7 +48,7 @@
  * */
 public class  BPTreeHeader {
 
-    private static Logger log = Logger.getLogger(BPTreeHeader.class);
+    private static Logger log = LogManager.getLogger(BPTreeHeader.class);
 
     static public final int BPTREE_HEADER_SIZE = 32;
 

diff --git a/src/main/java/org/broad/igv/bbfile/BPTreeLeafNode.java b/src/main/java/org/broad/igv/bbfile/BPTreeLeafNode.java
@@ -25,7 +25,7 @@
 
 package org.broad.igv.bbfile;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 
 import java.util.ArrayList;
 
@@ -45,7 +45,7 @@
 * */
 public class BPTreeLeafNode implements BPTreeNode{
 
-    private static Logger log = Logger.getLogger(BPTreeLeafNode.class);
+    private static Logger log = LogManager.getLogger(BPTreeLeafNode.class);
     private final boolean isLeafNode = true;
 
     private long nodeIndex;    // index for node in B+ tree organization

diff --git a/src/main/java/org/broad/igv/bbfile/BPTreeLeafNodeItem.java b/src/main/java/org/broad/igv/bbfile/BPTreeLeafNodeItem.java
@@ -32,14 +32,14 @@
  */
 package org.broad.igv.bbfile;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 
 /*
  *   Container class for B+ tree leaf node.
 * */
 public class BPTreeLeafNodeItem implements BPTreeNodeItem {
 
-    private static Logger log = Logger.getLogger(BPTreeLeafNodeItem.class);
+    private static Logger log = LogManager.getLogger(BPTreeLeafNodeItem.class);
     private final boolean isLeafItem = true;
     private long leafIndex;    // leaf index in B+ tree item list
 

diff --git a/src/main/java/org/broad/igv/bbfile/BedFeature.java b/src/main/java/org/broad/igv/bbfile/BedFeature.java
@@ -25,7 +25,7 @@
 
 package org.broad.igv.bbfile;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 
 /**
  * Created by IntelliJ IDEA.
@@ -71,7 +71,7 @@
 * */
 public class BedFeature {
 
-    private static Logger log = Logger.getLogger(BedFeature.class);
+    private static Logger log = LogManager.getLogger(BedFeature.class);
 
     private int itemIndex;     // data record index
 

diff --git a/src/main/java/org/broad/igv/bbfile/BigBedDataBlock.java b/src/main/java/org/broad/igv/bbfile/BigBedDataBlock.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 import org.broad.igv.util.CompressionUtils;
 import org.broad.igv.util.LittleEndianInputStream;
 
@@ -51,7 +51,7 @@
 * */
 public class BigBedDataBlock {
 
-    private static Logger log = Logger.getLogger(BigBedDataBlock.class);
+    private static Logger log = LogManager.getLogger(BigBedDataBlock.class);
 
     // Bed data block access variables   - for reading in bed records from a file
     private long fileOffset;       // Bed data block file offset

diff --git a/src/main/java/org/broad/igv/bbfile/BigBedIterator.java b/src/main/java/org/broad/igv/bbfile/BigBedIterator.java
@@ -26,7 +26,7 @@
 package org.broad.igv.bbfile;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.*;
 
 import java.util.*;
 
@@ -39,7 +39,7 @@
  */
 public class BigBedIterator implements Iterator<BedFeature> {
 
-    private static Logger log = Logger.getLogger(BigBedIterator.class);
+    private static Logger log = LogManager.getLogger(BigBedIterator.class);
 
     //specification of chromosome selection region
     private RPChromosomeRegion selectionRegion;  // selection region for iterator