Log4j updates

harmjanwestra · Jan 18, 2023 · 5998632 · 5998632
1 parent 75b906a
commit 5998632
Show file tree

Hide file tree

Showing 103 changed files with 763 additions and 632 deletions.
diff --git a/...nalyzer/src/main/java/nl/umcg/bondermj/microbialmetanalysis/BinaryMicrobePcaAnalysis.java b/...nalyzer/src/main/java/nl/umcg/bondermj/microbialmetanalysis/BinaryMicrobePcaAnalysis.java
@@ -89,7 +89,7 @@ public BinaryMicrobePcaAnalysis(String settingsFile, String textToReplace, Strin
 		try {
 			run((maxResults + tmpbuffersize));
 		} catch (IOException ex) {
-			Logger.getLogger(BinaryMicrobePcaAnalysis.class.getName()).log(Level.SEVERE, null, ex);
+			throw new RuntimeException(ex);
 		}
 
 	}

diff --git a/...Analyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/BinaryMetaAnalysisSettings.java b/...Analyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/BinaryMetaAnalysisSettings.java
@@ -673,7 +673,7 @@ void save() {
         try {
             config.save(output + "metasettings.xml");
         } catch (ConfigurationException ex) {
-            Logger.getLogger(BinaryMetaAnalysisSettings.class.getName()).log(Level.SEVERE, null, ex);
+            throw new RuntimeException(ex);
         }
 
     }

diff --git a/...ryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysis.java b/...ryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysis.java
@@ -71,7 +71,7 @@ public InternalMetaAnalysis(String settingsFile, String textToReplace, String re
 		try {
 			run();
 		} catch (IOException ex) {
-			Logger.getLogger(InternalMetaAnalysis.class.getName()).log(Level.SEVERE, null, ex);
+			throw new RuntimeException(ex);
 		}
 		//ToDo, check for non overlapping sites.
 		//Check allele assesed?

diff --git a/...alyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysisSettings.java b/...alyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysisSettings.java
@@ -152,7 +152,7 @@ void save() {
         try {
             config.save(output + "metasettings.xml");
         } catch (ConfigurationException ex) {
-            Logger.getLogger(InternalMetaAnalysisSettings.class.getName()).log(Level.SEVERE, null, ex);
+            throw new RuntimeException(ex);
         }
 
     }

diff --git a/...rah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/CheckZScoreMeanAndVariance.java b/...rah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/CheckZScoreMeanAndVariance.java
@@ -43,7 +43,7 @@ public CheckZScoreMeanAndVariance(String settingsFile, String textToReplace, Str
 			runPerDataset();
 		} catch (IOException ex) {
 			ex.printStackTrace();
-			Logger.getLogger(BinaryMetaAnalysis.class.getName()).log(Level.SEVERE, null, ex);
+			throw new RuntimeException(ex);
 		}
 
 	}

diff --git a/...trah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/ld/SortedBinaryZScoreFile.java b/...trah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/ld/SortedBinaryZScoreFile.java
@@ -55,7 +55,7 @@ public SortedBinaryZScoreFile(File datasetloc, boolean r) throws IOException {
 	}
 
 	private void openrowdata() throws IOException {
-		String rowfile = loc.replaceAll("-data.dat", "-combos.txt.gz");
+		String rowfile = loc.getAbsolutePath().replaceAll("-data.dat", "-combos.txt.gz");
 		rowdata = new TextFile(rowfile, TextFile.R);
 
 		availableGenes = new LinkedHashMap<>();
@@ -157,7 +157,7 @@ public void skipTo(String gene) throws IllegalAccessException, IOException {
 			}
 
 			is.close();
-			FileChannel ch = FileChannel.open(Paths.get(loc), StandardOpenOption.READ);
+			FileChannel ch = FileChannel.open(Paths.get(loc.getAbsolutePath()), StandardOpenOption.READ);
 			is = new DataInputStream(Channels.newInputStream(ch.position(lookuppositioninbinaryfile)));
 
 
@@ -183,7 +183,7 @@ public void close() throws IOException {
 			rowdata.close();
 		} else {
 			super.close();
-			File f = new File(this.loc);
+			File f = this.loc;
 
 			long length = f.length();
 			System.out.println(length + " bytes (" + Gpio.humanizeFileSize(length) + ") written to " + f.getAbsolutePath());
@@ -195,7 +195,7 @@ public void close() throws IOException {
 	}
 
 	public String getName() {
-		File f = new File(this.loc);
+		File f = this.loc;
 		String name = f.getName().replaceAll("-data.dat", "");
 		return name;
 	}

diff --git a/Decon2/Decon-eQTL/src/main/java/main/java/decon_eQTL/DeconvolutionLogger.java b/Decon2/Decon-eQTL/src/main/java/main/java/decon_eQTL/DeconvolutionLogger.java
@@ -14,7 +14,7 @@
 
 public class DeconvolutionLogger {
 	static private FileHandler outfilePath;
-	protected final static Logger log = Logger.getLogger(Logger.GLOBAL_LOGGER_NAME);
+	protected final static Logger log = LogManager.getLogger(Logger.GLOBAL_LOGGER_NAME);
 	static public void setup(String outputDir, Boolean noConsole) throws IOException {
 		// get the global logger to configure it
 		LogManager.getLogManager().reset();

diff --git a/Downstreamer/pom.xml b/Downstreamer/pom.xml
@@ -122,16 +122,6 @@
 			<artifactId>progressbar</artifactId>
 			<version>0.7.2</version>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-core</artifactId>
-			<version>2.19.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-api</artifactId>
-			<version>2.19.0</version>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi-ooxml</artifactId>
@@ -146,14 +136,6 @@
 					<groupId>com.facebook.presto.hive</groupId>
 					<artifactId>hive-apache</artifactId>
 				</exclusion>
-				<exclusion>
-					<groupId>log4j-core</groupId>
-					<artifactId>log4j-core</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>log4j-api</groupId>
-					<artifactId>log4j-api</artifactId>
-				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>

diff --git a/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/Downstreamer.java b/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/Downstreamer.java
@@ -281,15 +281,15 @@ public static void main(String[] args) throws InterruptedException {
 
     public static void initializeLoggers(Level loggingLevel, File logFile) throws IOException {
         Configurator.setRootLevel(loggingLevel);
-        LoggerContext context  = LoggerContext.getContext(false);
+        LoggerContext context = LoggerContext.getContext(false);
         Configuration config = context.getConfiguration();
 
         PatternLayout loggingLayoutFull = PatternLayout.newBuilder()
                 .withPattern("[%level] %d{ABSOLUTE} - %c{1} - %msg%n")
                 .build();
 
         PatternLayout loggingLayoutReduced = PatternLayout.newBuilder()
-                .withPattern("[%level] %d{HH:mm:ss} - %msg%n")
+                .withPattern("%msg%n")
                 .build();
 
         // Stdout appender

diff --git a/...treamer/src/main/java/nl/systemsgenetics/downstreamer/runners/DownstreamerEnrichment.java b/...treamer/src/main/java/nl/systemsgenetics/downstreamer/runners/DownstreamerEnrichment.java
@@ -177,7 +177,7 @@ public static DownstreamerStep2Results enrichmentAnalysis(OptionsModeEnrichment
 			//TODO papamters
 			List<LinearRegressionResult> pathwayRegeressionResults = DownstreamerRegressionEngine.performDownstreamerRegression(null, null, null, null, null, blockDiagonalIndices, true, true, true);
 
-			final DoubleMatrixDataset<String, String> pathwayPvalues = new DoubleMatrixDataset<>(pathwayData.getColObjects(), )
+			final DoubleMatrixDataset<String, String> pathwayPvalues = new DoubleMatrixDataset<>(pathwayData.getColObjects(), gwasGenePvalues.getColObjects());
 
 
 		}

diff --git a/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/GadoCommandline.java b/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/GadoCommandline.java
@@ -5,21 +5,25 @@
  */
 package nl.systemsgenetics.gadocommandline;
 
-import java.io.File;
 import java.io.IOException;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.ResourceBundle;
 import org.apache.commons.cli.ParseException;
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.FileAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.core.Appender;
+import org.apache.logging.log4j.core.LoggerContext;
+import org.apache.logging.log4j.core.appender.ConsoleAppender;
+import org.apache.logging.log4j.core.appender.FileAppender;
+import org.apache.logging.log4j.core.config.Configuration;
+import org.apache.logging.log4j.core.config.Configurator;
+import org.apache.logging.log4j.core.config.LoggerConfig;
+import org.apache.logging.log4j.core.layout.PatternLayout;
 import org.molgenis.genotype.GenotypeDataException;
 import org.molgenis.genotype.multipart.IncompatibleMultiPartGenotypeDataException;
-import org.molgenis.genotype.tabix.TabixFileNotFoundException;
 
 /**
  *
@@ -29,7 +33,7 @@ public class GadoCommandline {
 
 	public static final String VERSION = ResourceBundle.getBundle("verion").getString("application.version");
 	private static final DateFormat DATE_TIME_FORMAT = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
-	private static final Logger LOGGER = Logger.getLogger(GadoCommandline.class);
+	private static final Logger LOGGER = LogManager.getLogger(GadoCommandline.class);
 	private static final String HEADER
 			= "  /---------------------------------------\\\n"
 			+ "  |                 GADO                  |\n"
@@ -41,7 +45,7 @@ public class GadoCommandline {
 	 * @param args the command line arguments
 	 */
 	public static void main(String[] args) {
-		
+
 		System.out.println(HEADER);
 		System.out.println();
 		System.out.println("          --- Version: " + VERSION + " ---");
@@ -57,7 +61,8 @@ public static void main(String[] args) {
 		System.out.flush(); //flush to make sure header is before errors
 		try {
 			Thread.sleep(25); //Allows flush to complete
-		} catch (InterruptedException ex) {}
+		} catch (InterruptedException ex) {
+		}
 
 		GadoOptions options;
 
@@ -80,24 +85,55 @@ public static void main(String[] args) {
 				System.exit(1);
 			}
 		}
-
-		try {
-			FileAppender logFileAppender = new FileAppender(new SimpleLayout(), options.getLogFile().getCanonicalPath(), false);
-			ConsoleAppender logConsoleInfoAppender = new ConsoleAppender(new InfoOnlyLogLayout());
-			Logger.getRootLogger().removeAllAppenders();
-			Logger.getRootLogger().addAppender(logFileAppender);
 
-			LOGGER.info("DEPICT" + VERSION);
-			LOGGER.info("Current date and time: " + startDateTime);
-
-			Logger.getRootLogger().addAppender(logConsoleInfoAppender);
+		try {
 
 			if (options.isDebugMode()) {
-				Logger.getRootLogger().setLevel(Level.DEBUG);
+				Configurator.setRootLevel(Level.DEBUG);
 			} else {
-				Logger.getRootLogger().setLevel(Level.INFO);
+				Configurator.setRootLevel(Level.INFO);
 			}
+			LoggerContext context = LoggerContext.getContext(false);
+			Configuration config = context.getConfiguration();
+
+			PatternLayout loggingLayoutFull = PatternLayout.newBuilder()
+					.withPattern("[%level] %d{ABSOLUTE} - %c{1} - %msg%n")
+					.build();
+
+			PatternLayout loggingLayoutReduced = PatternLayout.newBuilder()
+					.withPattern("%msg%n")
+					.build();
+
+			// Stdout appender
+			ConsoleAppender stdOut = ConsoleAppender.newBuilder()
+					.setName("stdout")
+					.setLayout(loggingLayoutReduced)
+					.build();
+			stdOut.start();
+
+			// Log file appender
+			FileAppender file = FileAppender.newBuilder()
+					.setName("file")
+					.setLayout(loggingLayoutFull)
+					.withFileName(options.getLogFile().getCanonicalPath())
+					.build();
+			file.start();
+
+			// Make sure any existing loggers are removed
+			for (Appender appender : context.getRootLogger().getAppenders().values()) {
+				context.getRootLogger().removeAppender(appender);
+			}
+
+			// Add the appenders to the root logger
+			Logger rootLogger = context.getRootLogger();
+			LoggerConfig rootLoggerConfig = config.getRootLogger();
+
+			rootLoggerConfig.addAppender(stdOut, Level.INFO, null);
+			rootLoggerConfig.addAppender(file, options.isDebugMode() ? Level.DEBUG : Level.INFO, null);
+			config.addLogger(rootLogger.getName(), rootLoggerConfig);
 
+			context.updateLoggers(config);
+
 		} catch (IOException e) {
 			System.err.println("Failed to create logger: " + e.getMessage());
 			System.exit(1);
@@ -145,9 +181,9 @@ public static void main(String[] args) {
 			}
 			System.exit(1);
 		}
-		
+
 		LOGGER.info("Analysis completed");
-		
+
 	}
 
 }
diff --git a/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/GadoOptions.java b/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/GadoOptions.java
@@ -13,7 +13,8 @@
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 
 /**
  *
@@ -22,7 +23,7 @@
 public class GadoOptions {
 
 	private static final Options OPTIONS;
-	private static final Logger LOGGER = Logger.getLogger(GadoOptions.class);
+	private static final Logger LOGGER = LogManager.getLogger(GadoOptions.class);
 
 	private final GadoMode mode;
 

diff --git a/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/HpoGenePrioritisation.java b/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/HpoGenePrioritisation.java
@@ -25,7 +25,8 @@
 import java.util.Map;
 import java.util.zip.GZIPInputStream;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.biojava.nbio.ontology.Term;
 import umcg.genetica.math.matrix2.DoubleMatrixDataset;
 
@@ -35,7 +36,7 @@
 public class HpoGenePrioritisation {
 
 	private static final NumberFormat Z_FORMAT = new DecimalFormat("#0.0##");
-	private static final Logger LOGGER = Logger.getLogger(HpoGenePrioritisation.class);
+	private static final Logger LOGGER = LogManager.getLogger(HpoGenePrioritisation.class);
 
 	public static void prioritize(GadoOptions options) throws IOException, ParseException, Exception {