diff --git a/BinaryMetaAnalyzer/src/main/java/nl/umcg/bondermj/microbialmetanalysis/BinaryMicrobePcaAnalysis.java b/BinaryMetaAnalyzer/src/main/java/nl/umcg/bondermj/microbialmetanalysis/BinaryMicrobePcaAnalysis.java index 5e74b6950..5d22ec4eb 100644 --- a/BinaryMetaAnalyzer/src/main/java/nl/umcg/bondermj/microbialmetanalysis/BinaryMicrobePcaAnalysis.java +++ b/BinaryMetaAnalyzer/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/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/BinaryMetaAnalysisSettings.java b/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/BinaryMetaAnalysisSettings.java index 53425005f..b27e3e367 100644 --- a/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/BinaryMetaAnalysisSettings.java +++ b/BinaryMetaAnalyzer/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/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysis.java b/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysis.java index 6d6018fb1..ecd264190 100644 --- a/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysis.java +++ b/BinaryMetaAnalyzer/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/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysisSettings.java b/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysisSettings.java index 7f0ce6e08..f4d7869be 100644 --- a/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/InternalMetaAnalysisSettings.java +++ b/BinaryMetaAnalyzer/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/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/CheckZScoreMeanAndVariance.java b/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/CheckZScoreMeanAndVariance.java index 8c9cd34e8..009cca6c7 100644 --- a/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/CheckZScoreMeanAndVariance.java +++ b/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/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/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/ld/SortedBinaryZScoreFile.java b/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/ld/SortedBinaryZScoreFile.java index 0400a3d8d..18d84e683 100644 --- a/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/binarymetaanalyzer/westrah/binarymetaanalyzer/posthoc/ld/SortedBinaryZScoreFile.java +++ b/BinaryMetaAnalyzer/src/main/java/nl/umcg/westrah/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 index 0813c16b7..b9ad93709 100644 --- 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 index d97bbfe00..fe188d115 100644 --- a/Downstreamer/pom.xml +++ b/Downstreamer/pom.xml @@ -122,16 +122,6 @@ progressbar 0.7.2 - - org.apache.logging.log4j - log4j-core - 2.19.0 - - - org.apache.logging.log4j - log4j-api - 2.19.0 - org.apache.poi poi-ooxml @@ -146,14 +136,6 @@ com.facebook.presto.hive hive-apache - - log4j-core - log4j-core - - - log4j-api - log4j-api - diff --git a/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/Downstreamer.java b/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/Downstreamer.java index 523e1a5c6..d0f4cc57f 100644 --- a/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/Downstreamer.java +++ b/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/Downstreamer.java @@ -281,7 +281,7 @@ 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() @@ -289,7 +289,7 @@ public static void initializeLoggers(Level loggingLevel, File logFile) throws IO .build(); PatternLayout loggingLayoutReduced = PatternLayout.newBuilder() - .withPattern("[%level] %d{HH:mm:ss} - %msg%n") + .withPattern("%msg%n") .build(); // Stdout appender diff --git a/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/runners/DownstreamerEnrichment.java b/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/runners/DownstreamerEnrichment.java index 87fe773aa..9b4ff1a5a 100644 --- a/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/runners/DownstreamerEnrichment.java +++ b/Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/runners/DownstreamerEnrichment.java @@ -177,7 +177,7 @@ public static DownstreamerStep2Results enrichmentAnalysis(OptionsModeEnrichment //TODO papamters List pathwayRegeressionResults = DownstreamerRegressionEngine.performDownstreamerRegression(null, null, null, null, null, blockDiagonalIndices, true, true, true); - final DoubleMatrixDataset pathwayPvalues = new DoubleMatrixDataset<>(pathwayData.getColObjects(), ) + final DoubleMatrixDataset 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 index 196c20378..8ec9cf0e7 100644 --- 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 index a833f74b4..0d0894c85 100644 --- 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 index 91c2ea466..6c10b2e10 100644 --- 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 { diff --git a/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/InfoOnlyLogLayout.java b/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/InfoOnlyLogLayout.java index ce0f9181e..f5ca7087e 100644 --- a/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/InfoOnlyLogLayout.java +++ b/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/InfoOnlyLogLayout.java @@ -1,41 +1,41 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ -package nl.systemsgenetics.gadocommandline; - -import org.apache.log4j.Layout; -import org.apache.log4j.Level; -import org.apache.log4j.spi.LoggingEvent; - -/** - * - * @author patri - */ -public class InfoOnlyLogLayout extends Layout { - - StringBuffer sbuf = new StringBuffer(128); - - @Override - public String format(LoggingEvent event) { - if (event.getLevel() == Level.INFO) { - sbuf.setLength(0); - sbuf.append(event.getRenderedMessage()); - sbuf.append(LINE_SEP); - return sbuf.toString(); - } else { - return ""; - } - } - - @Override - public boolean ignoresThrowable() { - return false; - } - - @Override - public void activateOptions() { - } - -} +///* +// * To change this license header, choose License Headers in Project Properties. +// * To change this template file, choose Tools | Templates +// * and open the template in the editor. +// */ +//package nl.systemsgenetics.gadocommandline; +// +//import org.apache.log4j.Layout; +//import org.apache.log4j.Level; +//import org.apache.log4j.spi.LoggingEvent; +// +///** +// * +// * @author patri +// */ +//public class InfoOnlyLogLayout extends Layout { +// +// StringBuffer sbuf = new StringBuffer(128); +// +// @Override +// public String format(LoggingEvent event) { +// if (event.getLevel() == Level.INFO) { +// sbuf.setLength(0); +// sbuf.append(event.getRenderedMessage()); +// sbuf.append(LINE_SEP); +// return sbuf.toString(); +// } else { +// return ""; +// } +// } +// +// @Override +// public boolean ignoresThrowable() { +// return false; +// } +// +// @Override +// public void activateOptions() { +// } +// +//} diff --git a/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/ProcessCaseHpo.java b/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/ProcessCaseHpo.java index d0570ebd4..0290e0521 100644 --- a/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/ProcessCaseHpo.java +++ b/GadoCommandline/src/main/java/nl/systemsgenetics/gadocommandline/ProcessCaseHpo.java @@ -20,7 +20,8 @@ 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.Ontology; import org.biojava.nbio.ontology.Term; @@ -29,7 +30,7 @@ */ public class ProcessCaseHpo { - private static final Logger LOGGER = Logger.getLogger(ProcessCaseHpo.class); + private static final Logger LOGGER = LogManager.getLogger(ProcessCaseHpo.class); /** * @param options diff --git a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/benchmark/Benchmark.java b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/benchmark/Benchmark.java index c37cf8717..ba17a1f64 100644 --- a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/benchmark/Benchmark.java +++ b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/benchmark/Benchmark.java @@ -113,7 +113,7 @@ public static void main(String[] args) { } } catch (ParseException ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (IOException e) { e.printStackTrace(); } diff --git a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Configuration.java b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Configuration.java index fd405b1bd..32e855d06 100644 --- a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Configuration.java +++ b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Configuration.java @@ -7,7 +7,8 @@ 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; import org.molgenis.genotype.GenotypeDataException; import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats; @@ -29,7 +30,7 @@ public class Configuration { static { - LOGGER = Logger.getLogger(Configuration.class); + LOGGER = LogManager.getLogger(Configuration.class); OPTIONS = new Options(); diff --git a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Main.java b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Main.java index a4e8c7406..b3d2ee3b7 100644 --- a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Main.java +++ b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/geneticriskscorecalculator/Main.java @@ -12,8 +12,14 @@ import org.apache.commons.cli.ParseException; import org.apache.log4j.FileAppender; import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.log4j.SimpleLayout; +import org.apache.logging.log4j.core.Appender; +import org.apache.logging.log4j.core.LoggerContext; +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.RandomAccessGenotypeData; import org.molgenis.genotype.multipart.IncompatibleMultiPartGenotypeDataException; @@ -24,196 +30,224 @@ */ public class Main { - //private static final String VERSION = ResourceBundle.getBundle("verion").getString("application.version"); - private static final String VERSION = "0.0.1"; - - private static final String HEADER - = " /---------------------------------------\\\n" - + " | Genetic Risk Score Calculator |\n" - + " | |\n" - + " | Rudi Alberts |\n" - + " | |\n" - + " | Patrick Deelen |\n" - + " | |\n" - + " | |\n" - + " | Dasha Zhernakova, Marijke v/d Sijde, |\n" - + " | Marc Jan Bonder, Harm-Jan Westra, |\n" - + " | Lude Franke, Morris Swertz |\n" - + " | |\n" - + " | Genomics Coordination Center |\n" - + " | Department of Genetics |\n" - + " | University Medical Center Groningen |\n" - + " \\---------------------------------------/"; - private static final Logger LOGGER = Logger.getLogger(Main.class); - private static final DateFormat DATE_TIME_FORMAT = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); - private static final Date currentDataTime = new Date(); - private static final Pattern TAB_PATTERN = Pattern.compile("\\t"); - - public static void main(String[] args) { - - System.out.println(HEADER); - System.out.println(); - System.out.println(" --- Version: " + VERSION + " ---"); - System.out.println(); - System.out.println("More information: http://molgenis.org/systemsgenetics"); - System.out.println(); - - System.out.println("Current date and time: " + DATE_TIME_FORMAT.format(currentDataTime)); - System.out.println(); - - System.out.flush(); //flush to make sure header is before errors - try { - Thread.sleep(25); //Allows flush to complete - } catch (InterruptedException ex) { - } - - if (args.length == 0) { - Configuration.printHelp(); - System.exit(1); - } - - final Configuration configuration; - try { - configuration = new Configuration(args); - } catch (ParseException ex) { - System.err.println("Invalid command line arguments: "); - System.err.println(ex.getMessage()); - System.err.println(); - Configuration.printHelp(); - System.exit(1); - return; - } - - final File outputFile = configuration.getOutputFile(); - final File outputFolder = outputFile.getParentFile(); - if (outputFolder != null && !outputFolder.exists()) { - if (!outputFolder.mkdirs()) { - System.err.println("Failed to create ouput folder at: " + outputFolder.getAbsolutePath()); - System.exit(1); - } - } - - final File logFile = new File(outputFile.getAbsolutePath() + ".log"); - startLogging(logFile, true); - - final RandomAccessGenotypeData inputGenotypes; - try { - inputGenotypes = configuration.getInputDataType().createGenotypeData(configuration.getInputPaths(), 100); - System.out.println("Loading reference data complete"); - LOGGER.info("Loading reference data complete"); - } catch (IOException ex) { - System.err.println("Unable to load reference genotypes file."); - LOGGER.fatal("Unable to load reference genotypes file.", ex); - System.exit(1); - return; - } catch (IncompatibleMultiPartGenotypeDataException ex) { - System.err.println("Unable to load reference genotypes file."); - LOGGER.fatal("Unable to load reference genotypes file.", ex); - System.exit(1); - return; - } catch (GenotypeDataException ex) { - System.err.println("Unable to load reference genotypes file."); - LOGGER.fatal("Unable to load reference genotypes file.", ex); - System.exit(1); - return; - } - int debug = 0; - - int index = 0; - int index2 = 0; - for (String mySample : inputGenotypes.getSampleNames()) { - if (index < 5) { - System.out.println("Samplename: " + mySample); - } - index++; - } - - final String onlyCount = configuration.getOnlyCount(); - final String harmonizedData = configuration.getHarmonizedData(); - final double inclusionThreshold = configuration.getInclusionThreshold(); - - - - - - GwasCatalogLoader gwasCatalogLoader = new GwasCatalogLoader(); - List geneticRiskScoreCalculators = gwasCatalogLoader.getGeneticRiskScoreCalculators(configuration.getRisksnpsFile().toString()); - - List phenotypes = new ArrayList(); - for (GeneticRiskScoreCalculator calculator : geneticRiskScoreCalculators) { - phenotypes.add(calculator.getPhenotype()); - System.out.println("USING PHENOTYPE: **" + calculator.getPhenotype() + "**"); - } - - // List phenotypes = Arrays.asList("Height", "Migraine"); // fixed size list - - RiskScoreMatrix riskScoreMatrix = new RiskScoreMatrix(inputGenotypes.getSampleNames(), phenotypes); - - for (GeneticRiskScoreCalculator calculator : geneticRiskScoreCalculators) { - TObjectDoubleHashMap riskScores = calculator.calculateRiskScores(inputGenotypes, onlyCount, harmonizedData, inclusionThreshold); - index = 0; - for (String sample : inputGenotypes.getSampleNames()) { - riskScoreMatrix.setRiskScore(sample, calculator.getPhenotype(), riskScores.get(sample)); - if (index < 3) { - System.out.println("sample:" + sample); - System.out.println("phenotype:" + calculator.getPhenotype()); - System.out.println("score:" + riskScores.get(sample)); - } - index++; - //System.out.println("sample:" + calculator.getPhenotype()); - } - - } - - // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_1094", "Height")); - // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_0727", "Height")); - // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_1094", "Migraine")); - // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_0727", "Migraine")); - - System.out.println("GET A SCORE ROWS: " + riskScoreMatrix.rows()); - System.out.println("GET A SCORE COLS: " + riskScoreMatrix.cols()); - - try { - riskScoreMatrix.save(outputFile); - } catch (IOException ex) { - System.err.println("Could not save output file to: " + outputFile.getAbsolutePath()); - LOGGER.fatal("Could not save output file to: " + outputFile.getAbsolutePath(), ex); - System.exit(1); - return; - } - System.out.println("Risk score calculation complete"); - LOGGER.info("Risk score calculation complete"); - - } + //private static final String VERSION = ResourceBundle.getBundle("verion").getString("application.version"); + private static final String VERSION = "0.0.1"; + + private static final String HEADER + = " /---------------------------------------\\\n" + + " | Genetic Risk Score Calculator |\n" + + " | |\n" + + " | Rudi Alberts |\n" + + " | |\n" + + " | Patrick Deelen |\n" + + " | |\n" + + " | |\n" + + " | Dasha Zhernakova, Marijke v/d Sijde, |\n" + + " | Marc Jan Bonder, Harm-Jan Westra, |\n" + + " | Lude Franke, Morris Swertz |\n" + + " | |\n" + + " | Genomics Coordination Center |\n" + + " | Department of Genetics |\n" + + " | University Medical Center Groningen |\n" + + " \\---------------------------------------/"; + private static final Logger LOGGER = LogManager.getLogger(Main.class); + private static final DateFormat DATE_TIME_FORMAT = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); + private static final Date currentDataTime = new Date(); + private static final Pattern TAB_PATTERN = Pattern.compile("\\t"); + + public static void main(String[] args) { + + System.out.println(HEADER); + System.out.println(); + System.out.println(" --- Version: " + VERSION + " ---"); + System.out.println(); + System.out.println("More information: http://molgenis.org/systemsgenetics"); + System.out.println(); + + System.out.println("Current date and time: " + DATE_TIME_FORMAT.format(currentDataTime)); + System.out.println(); + + System.out.flush(); //flush to make sure header is before errors + try { + Thread.sleep(25); //Allows flush to complete + } catch (InterruptedException ex) { + } + + if (args.length == 0) { + Configuration.printHelp(); + System.exit(1); + } + + final Configuration configuration; + try { + configuration = new Configuration(args); + } catch (ParseException ex) { + System.err.println("Invalid command line arguments: "); + System.err.println(ex.getMessage()); + System.err.println(); + Configuration.printHelp(); + System.exit(1); + return; + } + + final File outputFile = configuration.getOutputFile(); + final File outputFolder = outputFile.getParentFile(); + if (outputFolder != null && !outputFolder.exists()) { + if (!outputFolder.mkdirs()) { + System.err.println("Failed to create ouput folder at: " + outputFolder.getAbsolutePath()); + System.exit(1); + } + } + + final File logFile = new File(outputFile.getAbsolutePath() + ".log"); + startLogging(logFile, true); + + final RandomAccessGenotypeData inputGenotypes; + try { + inputGenotypes = configuration.getInputDataType().createGenotypeData(configuration.getInputPaths(), 100); + System.out.println("Loading reference data complete"); + LOGGER.info("Loading reference data complete"); + } catch (IOException ex) { + System.err.println("Unable to load reference genotypes file."); + LOGGER.fatal("Unable to load reference genotypes file.", ex); + System.exit(1); + return; + } catch (IncompatibleMultiPartGenotypeDataException ex) { + System.err.println("Unable to load reference genotypes file."); + LOGGER.fatal("Unable to load reference genotypes file.", ex); + System.exit(1); + return; + } catch (GenotypeDataException ex) { + System.err.println("Unable to load reference genotypes file."); + LOGGER.fatal("Unable to load reference genotypes file.", ex); + System.exit(1); + return; + } + int debug = 0; + + int index = 0; + int index2 = 0; + for (String mySample : inputGenotypes.getSampleNames()) { + if (index < 5) { + System.out.println("Samplename: " + mySample); + } + index++; + } + + final String onlyCount = configuration.getOnlyCount(); + final String harmonizedData = configuration.getHarmonizedData(); + final double inclusionThreshold = configuration.getInclusionThreshold(); + + GwasCatalogLoader gwasCatalogLoader = new GwasCatalogLoader(); + List geneticRiskScoreCalculators = gwasCatalogLoader.getGeneticRiskScoreCalculators(configuration.getRisksnpsFile().toString()); + + List phenotypes = new ArrayList(); + for (GeneticRiskScoreCalculator calculator : geneticRiskScoreCalculators) { + phenotypes.add(calculator.getPhenotype()); + System.out.println("USING PHENOTYPE: **" + calculator.getPhenotype() + "**"); + } + + // List phenotypes = Arrays.asList("Height", "Migraine"); // fixed size list + RiskScoreMatrix riskScoreMatrix = new RiskScoreMatrix(inputGenotypes.getSampleNames(), phenotypes); + + for (GeneticRiskScoreCalculator calculator : geneticRiskScoreCalculators) { + TObjectDoubleHashMap riskScores = calculator.calculateRiskScores(inputGenotypes, onlyCount, harmonizedData, inclusionThreshold); + index = 0; + for (String sample : inputGenotypes.getSampleNames()) { + riskScoreMatrix.setRiskScore(sample, calculator.getPhenotype(), riskScores.get(sample)); + if (index < 3) { + System.out.println("sample:" + sample); + System.out.println("phenotype:" + calculator.getPhenotype()); + System.out.println("score:" + riskScores.get(sample)); + } + index++; + //System.out.println("sample:" + calculator.getPhenotype()); + } + + } + + // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_1094", "Height")); + // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_0727", "Height")); + // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_1094", "Migraine")); + // System.out.println("GET A SCORE: " + riskScoreMatrix.getRiskScore("LLDeep_0727", "Migraine")); + System.out.println("GET A SCORE ROWS: " + riskScoreMatrix.rows()); + System.out.println("GET A SCORE COLS: " + riskScoreMatrix.cols()); + + try { + riskScoreMatrix.save(outputFile); + } catch (IOException ex) { + System.err.println("Could not save output file to: " + outputFile.getAbsolutePath()); + LOGGER.fatal("Could not save output file to: " + outputFile.getAbsolutePath(), ex); + System.exit(1); + return; + } + System.out.println("Risk score calculation complete"); + LOGGER.info("Risk score calculation complete"); + + } // get sample dosages - // 0,1,2 .... 1.5 1.4 1.33434 - // imputation not sure .... in between aa ab bb - - private static void startLogging(File logFile, boolean debugMode) { - - try { - FileAppender logAppender = new FileAppender(new SimpleLayout(), logFile.getCanonicalPath(), false); - Logger.getRootLogger().removeAllAppenders(); - Logger.getRootLogger().addAppender(logAppender); - if (debugMode) { - LOGGER.setLevel(Level.DEBUG); - } else { - LOGGER.setLevel(Level.INFO); - } - } catch (IOException e) { - System.err.println("Failed to create logger: " + e.getMessage()); - System.exit(1); - } - - LOGGER.info( - "\n" + HEADER); - LOGGER.info("Version: " + VERSION); - LOGGER.info("Current date and time: " + DATE_TIME_FORMAT.format(currentDataTime)); - LOGGER.info("Log level: " + LOGGER.getLevel()); - - System.out.println("Started logging"); - System.out.println(); - } + // 0,1,2 .... 1.5 1.4 1.33434 + // imputation not sure .... in between aa ab bb + + private static void startLogging(File logFile, boolean debugMode) { + + try { + + if (debugMode) { + Configurator.setRootLevel(org.apache.logging.log4j.Level.DEBUG); + } else { + Configurator.setRootLevel(org.apache.logging.log4j.Level.INFO); + } + LoggerContext context = LoggerContext.getContext(false); + org.apache.logging.log4j.core.config.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(); + + // Log file appender + org.apache.logging.log4j.core.appender.FileAppender file = org.apache.logging.log4j.core.appender.FileAppender.newBuilder() + .setName("file") + .setLayout(loggingLayoutFull) + .withFileName(logFile.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(file, org.apache.logging.log4j.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); + } + + LOGGER.info( + "\n" + HEADER); + LOGGER.info( + "Version: " + VERSION); + LOGGER.info( + "Current date and time: " + DATE_TIME_FORMAT.format(currentDataTime)); + LOGGER.info( + "Log level: " + LOGGER.getLevel()); + + System.out.println( + "Started logging"); + System.out.println(); + } } - diff --git a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/CalculateSimpleGeneticRiskScore.java b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/CalculateSimpleGeneticRiskScore.java index e3169e59e..ce7ee1791 100644 --- a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/CalculateSimpleGeneticRiskScore.java +++ b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/CalculateSimpleGeneticRiskScore.java @@ -164,7 +164,7 @@ static DoubleMatrixDataset calculate(RandomAccessGenotypeData ge excludeList.add(riskE2.getRsName()); } } catch (LdCalculatorException ex) { - Logger.getLogger(CalculateSimpleGeneticRiskScore.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } @@ -178,7 +178,7 @@ static DoubleMatrixDataset calculate(RandomAccessGenotypeData ge out.close(); } } catch (IOException ex) { - Logger.getLogger(CalculateSimpleGeneticRiskScore.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } p.iterate(); @@ -266,7 +266,7 @@ static DoubleMatrixDataset calculateTwoStages(RandomAccessGenoty excludeList.add(riskE2.getRsName()); } } catch (LdCalculatorException ex) { - Logger.getLogger(CalculateSimpleGeneticRiskScore.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } } @@ -349,7 +349,7 @@ static DoubleMatrixDataset calculateTwoStages(RandomAccessGenoty excludeList.add(riskE2.getRsName()); } } catch (LdCalculatorException ex) { - Logger.getLogger(CalculateSimpleGeneticRiskScore.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } } @@ -362,7 +362,7 @@ static DoubleMatrixDataset calculateTwoStages(RandomAccessGenoty out.close(); } } catch (IOException ex) { - Logger.getLogger(CalculateSimpleGeneticRiskScore.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } p.iterate(); diff --git a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/Main.java b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/Main.java index 1f0083854..913c8bca6 100644 --- a/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/Main.java +++ b/GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/Main.java @@ -155,7 +155,7 @@ public static void main(String[] args) { sumRisks = cmd.hasOption('s'); } catch (ParseException ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { @@ -176,7 +176,7 @@ public static void main(String[] args) { } } catch (IOException ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } @@ -308,7 +308,7 @@ private static THashMapcommons-cli 1.2 - - org.apache.logging.log4j - log4j-core - 2.17.2 - net.sf.jsci jsci diff --git a/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/Aligner.java b/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/Aligner.java index 910e0d7e4..a95590116 100644 --- a/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/Aligner.java +++ b/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/Aligner.java @@ -18,7 +18,8 @@ import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.IntStream; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.RandomAccessGenotypeData; import org.molgenis.genotype.modifiable.ModifiableGeneticVariant; import org.molgenis.genotype.modifiable.ModifiableGenotypeData; @@ -33,7 +34,7 @@ */ public class Aligner { - private static Logger LOGGER = Logger.getLogger(GenotypeHarmonizer.class); + private static Logger LOGGER = LogManager.getLogger(GenotypeHarmonizer.class); /** * @param study data to align diff --git a/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizer.java b/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizer.java index 9ef5ae01b..6dd2f61e9 100644 --- a/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizer.java +++ b/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizer.java @@ -13,10 +13,17 @@ import java.util.regex.Pattern; import org.apache.commons.cli.ParseException; -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.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +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.*; import org.molgenis.genotype.modifiable.ModifiableGenotypeData; import org.molgenis.genotype.multipart.IncompatibleMultiPartGenotypeDataException; @@ -53,7 +60,7 @@ class GenotypeHarmonizer { + " | Genomics Coordination Center |\n" + " | University Medical Center Groningen |\n" + " \\---------------------------------------/"; - private static final Logger LOGGER = Logger.getLogger(GenotypeHarmonizer.class); + private static final Logger LOGGER = LogManager.getLogger(GenotypeHarmonizer.class); private static final DateFormat DATE_TIME_FORMAT = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); /** * The lowest allowed minimum for the number of SNPs needed to align on @@ -108,14 +115,46 @@ public static void main(String... args) throws InterruptedException { } try { - FileAppender logAppender = new FileAppender(new SimpleLayout(), parameters.getLogFile().getCanonicalPath(), false); - LOGGER.getRootLogger().removeAllAppenders(); - LOGGER.getRootLogger().addAppender(logAppender); + if (parameters.isDebugMode()) { - LOGGER.setLevel(Level.DEBUG); + Configurator.setRootLevel(Level.DEBUG); } else { - LOGGER.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(); + + + // Log file appender + FileAppender file = FileAppender.newBuilder() + .setName("file") + .setLayout(loggingLayoutFull) + .withFileName(parameters.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(file, 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); diff --git a/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizerParamaters.java b/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizerParamaters.java index e96cf3a7a..68aed10ae 100644 --- a/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizerParamaters.java +++ b/Genotype-Harmonizer/src/main/java/nl/umcg/deelenp/genotypeharmonizer/GenotypeHarmonizerParamaters.java @@ -14,7 +14,8 @@ import org.apache.commons.cli.ParseException; import org.apache.commons.cli.PosixParser; import org.apache.commons.lang3.EnumUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.GenotypeDataException; import org.molgenis.genotype.GenotypedDataWriterFormats; import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats; @@ -86,7 +87,7 @@ public class GenotypeHarmonizerParamaters { static { - LOGGER = Logger.getLogger(GenotypeHarmonizerParamaters.class); + LOGGER = LogManager.getLogger(GenotypeHarmonizerParamaters.class); OPTIONS = new Options(); diff --git a/Genotype-IO/pom.xml b/Genotype-IO/pom.xml index cd3a6e739..dde6e3d0f 100644 --- a/Genotype-IO/pom.xml +++ b/Genotype-IO/pom.xml @@ -17,11 +17,16 @@ 11 - - org.apache.logging.log4j - log4j-core - 2.19.0 - + + org.apache.logging.log4j + log4j-core + 2.19.0 + + + org.apache.logging.log4j + log4j-api + 2.19.0 + org.molgenis vcf-io diff --git a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/ExtendSnpProbeCombinationsFile.java b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/ExtendSnpProbeCombinationsFile.java index e8846b0e1..d36ba5f8f 100644 --- a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/ExtendSnpProbeCombinationsFile.java +++ b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/ExtendSnpProbeCombinationsFile.java @@ -31,13 +31,13 @@ public static void main(String[] args) throws Exception { try { initialPairs = readInitialPairs(initialReplicationList); } catch (IOException ex) { - Logger.getLogger(ExtendSnpProbeCombinationsFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { metaphlanMatrix = DoubleMatrixDataset.loadDoubleData(fileNameMetaphlanTable); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } if(metaphlanMatrix!=null && initialPairs!=null){ ArrayList rows = metaphlanMatrix.getRowObjects(); @@ -45,7 +45,7 @@ public static void main(String[] args) throws Exception { try { writeFullReplicationList(rows, initialPairs, fullReplicationList); } catch (IOException ex) { - Logger.getLogger(ExtendSnpProbeCombinationsFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeAndFilter.java b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeAndFilter.java index eaa42e02d..3e8c7e544 100644 --- a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeAndFilter.java +++ b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeAndFilter.java @@ -35,7 +35,7 @@ public static void main(String[] args) throws Exception { try { metaphlanMatrix = DoubleMatrixDataset.loadDoubleData(fileNameMetaphlanTable); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } if(scaleToPercent){ @@ -56,7 +56,7 @@ public static void main(String[] args) throws Exception { try { metaphlanMatrix.save(fileNameMetaphlanTable+additionToFileName+".tsv"); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeToReadsPerMillion.java b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeToReadsPerMillion.java index 57e450d96..24748236e 100644 --- a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeToReadsPerMillion.java +++ b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/NormalizeToReadsPerMillion.java @@ -34,14 +34,14 @@ public static void main(String[] args) throws Exception { try { readStats = readReadStatsFile(fileNameReadStatistics); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } DoubleMatrixDataset metaphlanMatrix = null; try { metaphlanMatrix = DoubleMatrixDataset.loadDoubleData(fileNameMetaphlanTable); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } if(cladeNormalization){ @@ -49,7 +49,7 @@ public static void main(String[] args) throws Exception { try { cladeSizeInformation = readCladeSizeInfo(cladeInformationFile); } catch (IOException ex) { - Logger.getLogger(NormalizeToReadsPerMillion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } metaphlanMatrix = normalizeWithCladeSize(metaphlanMatrix, cladeSizeInformation); } @@ -63,7 +63,7 @@ public static void main(String[] args) throws Exception { try { metaphlanMatrix.save(fileNameMetaphlanTable+".cladeNorm.normalized.tsv"); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintDatasetPerEntry.java b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintDatasetPerEntry.java index 36abdb63b..533bc366e 100644 --- a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintDatasetPerEntry.java +++ b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintDatasetPerEntry.java @@ -45,7 +45,7 @@ public static void main(String[] args) throws Exception { try { bugMatrix = DoubleMatrixDataset.loadDoubleData(inputTable); } catch (IOException ex) { - Logger.getLogger(PrintDatasetPerEntry.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } //Write matrix with direct filtering on X number of bugs in the individual cohort. @@ -71,7 +71,7 @@ private static void writeTablesToFile(DoubleMatrixDataset bugMat try { relevantBugMatrix.save(outputFolder+"matrix_"+i+"_CuttOfNumber_"+cutOffNumber+"_incPercentage"+minPercentage+".tsv"); } catch (IOException ex) { - Logger.getLogger(PrintDatasetPerEntry.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } i++; diff --git a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintPerDatasetCuttOff.java b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintPerDatasetCuttOff.java index 1c526d486..a8211b7da 100644 --- a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintPerDatasetCuttOff.java +++ b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintPerDatasetCuttOff.java @@ -58,7 +58,7 @@ public static void main(String[] args) throws Exception { try { bugMatrix = DoubleMatrixDataset.loadDoubleData(inputTable); } catch (IOException ex) { - Logger.getLogger(PrintPerDatasetCuttOff.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } //Write matrix with direct filtering on X number of bugs in the individual cohort. @@ -78,7 +78,7 @@ private static HashMap> readGTMInformation(String gtmFol try { informationPerDataset.put(F.getName().split("_")[0], readFileSample(F)); } catch (IOException ex) { - Logger.getLogger(PrintPerDatasetCuttOff.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } @@ -113,7 +113,7 @@ private static void writeTablesToFile(HashMap> Informati try { relevantBugMatrix.save(outputFolder+"matrix_"+dataset.getKey()+"_CuttOfNumber_"+cutOffNumber+"_incPercentage"+minPercentage+".tsv"); } catch (IOException ex) { - Logger.getLogger(PrintPerDatasetCuttOff.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } } diff --git a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintTablePerLevel.java b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintTablePerLevel.java index 580912997..b68eefaae 100644 --- a/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintTablePerLevel.java +++ b/MetaGenomicDataProcessing/src/main/java/umcg/genetics/tableAdaption/PrintTablePerLevel.java @@ -30,20 +30,20 @@ public static void main(String[] args) throws Exception { try { metaphlanMatrix = DoubleMatrixDataset.loadDoubleData(fileNameMetaphlanTable); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } if (kraken) { try { writeMatrixPerLevelKraken(metaphlanMatrix, fileNameMetaphlanTable); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } else { try { writeMatrixPerLevelMetaphlan(metaphlanMatrix, fileNameMetaphlanTable); } catch (IOException ex) { - Logger.getLogger(PrintTablePerLevel.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/PatricksToolbox/pom.xml b/PatricksToolbox/pom.xml index 64c1b8936..d44ec00ac 100644 --- a/PatricksToolbox/pom.xml +++ b/PatricksToolbox/pom.xml @@ -118,11 +118,6 @@ progressbar 0.7.2 - - org.apache.logging.log4j - log4j-core - 2.17.1 - org.apache.poi poi-ooxml diff --git a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/InfoOnlyLogLayout.java b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/InfoOnlyLogLayout.java index 2930d4eb0..e6fa1dfd2 100644 --- a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/InfoOnlyLogLayout.java +++ b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/InfoOnlyLogLayout.java @@ -1,41 +1,41 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ -package nl.systemsgenetics.toolbox; - -import org.apache.log4j.Layout; -import org.apache.log4j.Level; -import org.apache.log4j.spi.LoggingEvent; - -/** - * - * @author patri - */ -public class InfoOnlyLogLayout extends Layout { - - StringBuffer sbuf = new StringBuffer(128); - - @Override - public String format(LoggingEvent event) { - if (event.getLevel() == Level.INFO) { - sbuf.setLength(0); - sbuf.append(event.getRenderedMessage()); - sbuf.append(LINE_SEP); - return sbuf.toString(); - } else { - return ""; - } - } - - @Override - public boolean ignoresThrowable() { - return false; - } - - @Override - public void activateOptions() { - } - -} +///* +// * To change this license header, choose License Headers in Project Properties. +// * To change this template file, choose Tools | Templates +// * and open the template in the editor. +// */ +//package nl.systemsgenetics.toolbox; +// +//import org.apache.log4j.Layout; +//import org.apache.log4j.Level; +//import org.apache.log4j.spi.LoggingEvent; +// +///** +// * +// * @author patri +// */ +//public class InfoOnlyLogLayout extends Layout { +// +// StringBuffer sbuf = new StringBuffer(128); +// +// @Override +// public String format(LoggingEvent event) { +// if (event.getLevel() == Level.INFO) { +// sbuf.setLength(0); +// sbuf.append(event.getRenderedMessage()); +// sbuf.append(LINE_SEP); +// return sbuf.toString(); +// } else { +// return ""; +// } +// } +// +// @Override +// public boolean ignoresThrowable() { +// return false; +// } +// +// @Override +// public void activateOptions() { +// } +// +//} diff --git a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Main.java b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Main.java index 658d3e3de..4b8f3963e 100644 --- a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Main.java +++ b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Main.java @@ -14,11 +14,17 @@ 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.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +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; @@ -33,7 +39,7 @@ public class Main { public static final DecimalFormat LARGE_INT_FORMAT = new DecimalFormat("###,###"); 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(Main.class); + private static final Logger LOGGER = LogManager.getLogger(Main.class); private static final String HEADER = " /---------------------------------------\\\n" + " | Patrick's Toolbox |\n" @@ -86,23 +92,54 @@ public static void main(String[] args) throws InterruptedException { return; } - 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("Downstreamer" + 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, options.isDebugMode() ? Level.DEBUG : Level.INFO, null); + rootLoggerConfig.addAppender(file, 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); diff --git a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Options.java b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Options.java index e60207bb1..efdda12cc 100644 --- a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Options.java +++ b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Options.java @@ -13,7 +13,8 @@ import org.apache.commons.cli.OptionBuilder; 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; import org.molgenis.genotype.GenotypeDataException; import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats; @@ -24,7 +25,7 @@ public class Options { private static final org.apache.commons.cli.Options OPTIONS; - private static final Logger LOGGER = Logger.getLogger(Options.class); + private static final Logger LOGGER = LogManager.getLogger(Options.class); private static final SimpleFeature HLA = new SimpleFeature("6", 20000000, 40000000); private final Mode mode; diff --git a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Utils.java b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Utils.java index 9698b3479..27968d1be 100644 --- a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Utils.java +++ b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/Utils.java @@ -16,7 +16,8 @@ import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.RandomAccessGenotypeData; import org.molgenis.genotype.sampleFilter.SampleFilter; import org.molgenis.genotype.sampleFilter.SampleIdIncludeFilter; @@ -32,7 +33,7 @@ */ public class Utils { - private static final Logger LOGGER = Logger.getLogger(Utils.class); + private static final Logger LOGGER = LogManager.getLogger(Utils.class); public static RandomAccessGenotypeData loadGenotypes(Options options, Collection variantsToInclude) throws IOException { final RandomAccessGenotypeData referenceGenotypeData; diff --git a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/picalo/OverlapPicEqtlWithGwas.java b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/picalo/OverlapPicEqtlWithGwas.java index 1afd6c80b..b8212e48f 100644 --- a/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/picalo/OverlapPicEqtlWithGwas.java +++ b/PatricksToolbox/src/main/java/nl/systemsgenetics/toolbox/picalo/OverlapPicEqtlWithGwas.java @@ -25,7 +25,8 @@ import java.util.zip.GZIPInputStream; import nl.systemsgenetics.toolbox.Options; import nl.systemsgenetics.toolbox.Utils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.RandomAccessGenotypeData; import org.molgenis.genotype.util.LdCalculator; import org.molgenis.genotype.variant.GeneticVariant; @@ -40,7 +41,7 @@ */ public class OverlapPicEqtlWithGwas { - private static final Logger LOGGER = Logger.getLogger(OverlapPicEqtlWithGwas.class); + private static final Logger LOGGER = LogManager.getLogger(OverlapPicEqtlWithGwas.class); public static void overlap(Options options) throws IOException, Exception { diff --git a/cellTypeSpecificAlleleSpecificExpression/src/main/java/nl/systemsgenetics/cellTypeSpecificAlleleSpecificExpression/MainEntryPoint.java b/cellTypeSpecificAlleleSpecificExpression/src/main/java/nl/systemsgenetics/cellTypeSpecificAlleleSpecificExpression/MainEntryPoint.java index 775e98b31..e5b33a8df 100644 --- a/cellTypeSpecificAlleleSpecificExpression/src/main/java/nl/systemsgenetics/cellTypeSpecificAlleleSpecificExpression/MainEntryPoint.java +++ b/cellTypeSpecificAlleleSpecificExpression/src/main/java/nl/systemsgenetics/cellTypeSpecificAlleleSpecificExpression/MainEntryPoint.java @@ -17,7 +17,8 @@ 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; import org.jdom.IllegalDataException; import org.molgenis.genotype.GenotypeInfo; @@ -41,7 +42,7 @@ public class MainEntryPoint { static { - LOGGER = Logger.getLogger(GenotypeInfo.class); + LOGGER = LogManager.getLogger(GenotypeInfo.class); OPTIONS = new Options(); diff --git a/eQTLInteractionAnalyser/src/main/java/nl/systemsgenetics/eqtlinteractionanalyser/eqtlinteractionanalyser/TestEQTLDatasetForInteractions.java b/eQTLInteractionAnalyser/src/main/java/nl/systemsgenetics/eqtlinteractionanalyser/eqtlinteractionanalyser/TestEQTLDatasetForInteractions.java index e81440581..b043df2ea 100644 --- a/eQTLInteractionAnalyser/src/main/java/nl/systemsgenetics/eqtlinteractionanalyser/eqtlinteractionanalyser/TestEQTLDatasetForInteractions.java +++ b/eQTLInteractionAnalyser/src/main/java/nl/systemsgenetics/eqtlinteractionanalyser/eqtlinteractionanalyser/TestEQTLDatasetForInteractions.java @@ -575,7 +575,7 @@ public final String performInteractionAnalysis(String[] covsToCorrect, String[] System.out.println(task + 1 + " tasks processed"); } } catch (ExecutionException ex) { - Logger.getLogger(PerformInteractionAnalysisPermutationTask.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } /*} //If gene annotation not provided, use all gene pairs @@ -602,7 +602,7 @@ public final String performInteractionAnalysis(String[] covsToCorrect, String[] System.out.println(task + 1 + " tasks processed"); } } catch (ExecutionException ex) { - Logger.getLogger(PerformInteractionAnalysisPermutationTask.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(PerformInteractionAnalysisPermutationTask.class.getName()).log(Level.SEVERE, null, ex); } } }*/ diff --git a/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeMultipleTfbsOverlap.java b/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeMultipleTfbsOverlap.java index d7c0f3769..04b4929d6 100644 --- a/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeMultipleTfbsOverlap.java +++ b/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeMultipleTfbsOverlap.java @@ -76,7 +76,7 @@ public static void main(String[] args) { peakData = readMultipleTfbsInformation(inputFolderTfbsData); } catch (IOException ex) { - Logger.getLogger(EncodeMultipleTfbsOverlap.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { @@ -96,7 +96,7 @@ public static void main(String[] args) { } outWriter.close(); } catch (IOException ex) { - Logger.getLogger(EncodeMultipleTfbsOverlap.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeTfbsOverlap.java b/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeTfbsOverlap.java index 33bfa1b78..ef836b1e1 100644 --- a/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeTfbsOverlap.java +++ b/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/EncodeTfbsOverlap.java @@ -44,7 +44,7 @@ public static void main(String[] args) { peakData = readTfbsInformation(inputFolderTfbsData); } catch (IOException ex) { - Logger.getLogger(EncodeTfbsOverlap.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { @@ -58,7 +58,7 @@ public static void main(String[] args) { } outWriter.close(); } catch (IOException ex) { - Logger.getLogger(EncodeTfbsOverlap.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/RoadMapCHmm.java b/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/RoadMapCHmm.java index d9459e04d..5edf2e0be 100644 --- a/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/RoadMapCHmm.java +++ b/eqtl-functional-enrichment/src/main/java/nl/systemsgenetics/eqtlannotation/RoadMapCHmm.java @@ -39,7 +39,7 @@ public static void main(String[] args) { peakData = readCHmmInformation(inputFolderTfbsData); } catch (IOException ex) { - Logger.getLogger(EncodeTfbsOverlap.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } // writeContacts(qtlSnps, peakData, outputFile); @@ -157,7 +157,7 @@ private static void writeContacts(ArrayList qtlSnps, HashMap qtlSnps, HashMap qtlSnps, HashMapgenetica-libraries 1.0.10-SNAPSHOT - - org.apache.logging.log4j - log4j-core - 2.17.2 - nl.systemsgenetics Genotype-IO diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/Ase.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/Ase.java index 88d6231bc..fba00b36c 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/Ase.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/Ase.java @@ -27,12 +27,17 @@ import java.util.Map; import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; +import java.util.logging.LogManager; import java.util.regex.Pattern; import org.apache.commons.cli.ParseException; -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.Level; +import org.apache.logging.log4j.Logger; +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.layout.PatternLayout; import org.molgenis.genotype.GenotypeDataException; import org.molgenis.genotype.RandomAccessGenotypeData; import org.molgenis.genotype.multipart.IncompatibleMultiPartGenotypeDataException; @@ -49,8 +54,8 @@ public class Ase { private static final String VERSION = Main.VERSION; - private static final String HEADER = - " /---------------------------------------\\\n" + private static final String HEADER + = " /---------------------------------------\\\n" + " | Allele Specific Expression Mapper |\n" + " | |\n" + " | Patrick Deelen |\n" @@ -64,7 +69,7 @@ public class Ase { + " | Department of Genetics |\n" + " | University Medical Center Groningen |\n" + " \\---------------------------------------/"; - private static final Logger LOGGER = Logger.getLogger(Ase.class); + private static final Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(Ase.class); private static final DateFormat DATE_TIME_FORMAT = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); private static final Date currentDataTime = new Date(); private static final Pattern TAB_PATTERN = Pattern.compile("\\t"); @@ -194,7 +199,6 @@ public static void main(String[] args) { //We have reference genotypes. This means a lot of random access to this single genotype data which slowed down the analyis a lot. //Chucking the analysis will be used so that we can efficiently cache the reference genotypes. - final int chunkSize = configuration.getChunkSize(); for (String chr : referenceGenotypes.getSeqNames()) { @@ -225,7 +229,6 @@ public static void main(String[] args) { } - } final boolean encounteredBaseQuality = aseResults.isEncounteredBaseQuality(); @@ -236,7 +239,7 @@ public static void main(String[] args) { if (configuration.isMappabilityTrackSet()) { System.out.println("Start loading mappability track"); - + int removeNoMappabilityInfo = 0; int removeLowMappability = 0; @@ -263,7 +266,6 @@ public static void main(String[] args) { return; } - for (Iterator aseIterator = aseResults.iterator(); aseIterator.hasNext();) { AseVariantAppendable ase = aseIterator.next(); List aseMappabilities = mappabilities.searchPosition(ase.getChr(), ase.getPos()); @@ -293,7 +295,6 @@ public static void main(String[] args) { } - AseVariantAppendable[] aseVariants = new AseVariantAppendable[aseResults.getCount()]; { int i = 0; @@ -302,17 +303,15 @@ public static void main(String[] args) { ++i; } } - + AseCalculator.startAseCalculators(aseVariants, configuration.getThreads()); System.out.println("Completed ASE calculations"); - + //int numberOfTests = aseVariants.length; //double bonferroniCutoff = 0.05 / numberOfTests; //System.out.println("Performed " + DEFAULT_NUMBER_FORMATTER.format(numberOfTests) + " tests. Bonferroni FWER 0.05 cut-off: " + bonferroniCutoff); //LOGGER.info("Performed " + DEFAULT_NUMBER_FORMATTER.format(numberOfTests) + " tests. Bonferroni FWER 0.05 cut-off: " + bonferroniCutoff); - - Arrays.sort(aseVariants); final PerChrIntervalTree gtfAnnotations; @@ -337,7 +336,6 @@ public static void main(String[] args) { gtfAnnotations = null; } - for (MultipleTestingCorrectionMethod correctionMethod : EnumSet.of(MultipleTestingCorrectionMethod.NONE, MultipleTestingCorrectionMethod.BONFERRONI, MultipleTestingCorrectionMethod.HOLM, MultipleTestingCorrectionMethod.BH)) { File outputFileBonferroni = new File(configuration.getOutputFolder(), correctionMethod == MultipleTestingCorrectionMethod.NONE ? "ase.txt" : "ase_" + correctionMethod.toString().toLowerCase() + ".txt"); @@ -353,7 +351,6 @@ public static void main(String[] args) { LOGGER.info("Completed writing " + DEFAULT_NUMBER_FORMATTER.format(writtenResults) + " " + correctionMethod.toString().toLowerCase() + " significant ASE variants"); } - } catch (UnsupportedEncodingException ex) { throw new RuntimeException(ex); } catch (FileNotFoundException ex) { @@ -386,20 +383,26 @@ public static void main(String[] args) { private static void startLogging(File logFile, boolean debugMode) { - try { - FileAppender logAppender = new FileAppender(new SimpleLayout(), logFile.getCanonicalPath(), false); - Logger.getRootLogger().removeAllAppenders(); - Logger.getRootLogger().addAppender(logAppender); - if (debugMode) { - LOGGER.setLevel(Level.DEBUG); - } else { - LOGGER.setLevel(Level.INFO); - } - } catch (IOException e) { - System.err.println("Failed to create logger: " + e.getMessage()); - System.exit(1); + if (debugMode) { + Configurator.setRootLevel(Level.DEBUG); + } else { + Configurator.setRootLevel(Level.INFO); } + LoggerContext context = LoggerContext.getContext(false); + Configuration config = context.getConfiguration(); + + PatternLayout loggingLayoutReduced = PatternLayout.newBuilder() + .withPattern("[%level] %d{HH:mm:ss} - %msg%n") + .build(); + + // Stdout appender + ConsoleAppender stdOut = ConsoleAppender.newBuilder() + .setName("stdout") + .setLayout(loggingLayoutReduced) + .build(); + stdOut.start(); + LOGGER.info( "\n" + HEADER); LOGGER.info("Version: " + VERSION); @@ -494,7 +497,6 @@ private static int printAseResults(final File outputFile, final AseVariantAppend ++counter; - outputWriter.append(String.valueOf(aseVariant.getMle().getRatioP())); outputWriter.append('\t'); outputWriter.append(String.valueOf(aseVariant.getMle().getRatioD())); @@ -529,7 +531,6 @@ private static int printAseResults(final File outputFile, final AseVariantAppend List elements = gtfAnnotations.searchPosition(aseVariant.getChr(), aseVariant.getPos()); - boolean first = true; for (GffElement element : elements) { @@ -613,14 +614,10 @@ private static int printAseResults(final File outputFile, final AseVariantAppend // outputWriter.append(altMeanBaseQualities); // // } - - - outputWriter.append('\n'); } - outputWriter.close(); return counter; @@ -657,15 +654,14 @@ protected static class ThreadErrorHandler implements UncaughtExceptionHandler { @Override public void uncaughtException(Thread t, Throwable e) { - if(e instanceof OutOfMemoryError){ + if (e instanceof OutOfMemoryError) { System.err.println("Error: out of memory, use -Xmx##g -Xms##g to reserve more memory, see manual for more information."); LOGGER.fatal("Out of memory, use -Xmx##g -Xms##g to reserve more memory, see manual for more information.", e); } else { System.err.println("Fatal error: " + e.getMessage()); LOGGER.fatal("Fatal error: ", e); } - - + System.exit(1); } } @@ -707,7 +703,7 @@ private static void loadAseData(List inputFiles, AseResults aseResults, Se } if (showFileProgress) { - + int currentCount = fileCounter.get(); if (currentCount > nextReport) { @@ -720,7 +716,5 @@ private static void loadAseData(List inputFiles, AseResults aseResults, Se } while (running); } - - - -} \ No newline at end of file + +} diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseConfiguration.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseConfiguration.java index 026e21b82..79295c189 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseConfiguration.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseConfiguration.java @@ -20,7 +20,8 @@ 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.LogManager; +import org.apache.logging.log4j.Logger; import org.molgenis.genotype.GenotypeDataException; import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats; @@ -55,7 +56,7 @@ public class AseConfiguration { static { - LOGGER = Logger.getLogger(AseConfiguration.class); + LOGGER = LogManager.getLogger(AseConfiguration.class); OPTIONS = new Options(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMle.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMle.java index e690a640f..a439866ed 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMle.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMle.java @@ -5,7 +5,8 @@ import java.math.BigDecimal; import java.math.MathContext; import java.math.RoundingMode; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; /** * @@ -25,7 +26,7 @@ public class AseMle { private static final double[] a = new double[171]; private static final int NTOP = 2000; private static final double[] aa = new double[NTOP]; - private static final Logger LOGGER = Logger.getLogger(AseMle.class); + private static final Logger LOGGER = LogManager.getLogger(AseMle.class); private static final BigDecimal probabilityStep = new BigDecimal(0.001); private static final MathContext mathContextProbability = new MathContext(3, RoundingMode.HALF_UP);//Must fit step percision protected static final double[] probabilities; diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleBeta.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleBeta.java index a6f2d2fa3..1eb5b2389 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleBeta.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleBeta.java @@ -5,7 +5,8 @@ import java.math.BigDecimal; import java.math.MathContext; import java.math.RoundingMode; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; /** * @@ -26,7 +27,7 @@ public class AseMleBeta { private static final double[] a = new double[171]; private static final int NTOP = 2000; private static final double[] aa = new double[NTOP]; - private static final Logger LOGGER = Logger.getLogger(AseMleBeta.class); + private static final Logger LOGGER = LogManager.getLogger(AseMleBeta.class); private static final BigDecimal probabilityStep = new BigDecimal(0.001); private static final MathContext mathContextProbability = new MathContext(3, RoundingMode.HALF_UP);//Must fit step percision protected static final double[] probabilities; diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleNegative.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleNegative.java index da3251901..0879f86ac 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleNegative.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/AseMleNegative.java @@ -5,7 +5,8 @@ import java.math.BigDecimal; import java.math.MathContext; import java.math.RoundingMode; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; /** * @@ -25,7 +26,7 @@ public class AseMleNegative { private static final double[] a = new double[171]; private static final int NTOP = 2000; private static final double[] aa = new double[NTOP]; - private static final Logger LOGGER = Logger.getLogger(AseMleNegative.class); + private static final Logger LOGGER = LogManager.getLogger(AseMleNegative.class); private static final BigDecimal probabilityStep = new BigDecimal(0.001); private static final MathContext mathContextProbability = new MathContext(3, RoundingMode.HALF_UP);//Must fit step percision protected static final double[] probabilities; diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/ReadCountsLoader.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/ReadCountsLoader.java index 834e6a0e5..2fd93d927 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/ReadCountsLoader.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/ase/ReadCountsLoader.java @@ -11,7 +11,8 @@ import java.util.Map; import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.Allele; import org.molgenis.genotype.Alleles; import org.molgenis.genotype.GenotypeDataException; @@ -41,7 +42,7 @@ public class ReadCountsLoader implements Runnable { private final String chr; private final int start; private final int stop; - private static final Logger LOGGER = Logger.getLogger(ReadCountsLoader.class); + private static final Logger LOGGER = LogManager.getLogger(ReadCountsLoader.class); public ReadCountsLoader(Iterator inputFileIterator, AseResults aseResults, Set detectedSampleSet, AtomicInteger fileCounter, AseConfiguration configuration) { this(inputFileIterator, aseResults, detectedSampleSet, fileCounter, configuration, null); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisCalculationThread.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisCalculationThread.java index 154e7f17d..2d51713f1 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisCalculationThread.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisCalculationThread.java @@ -20,6 +20,7 @@ import java.util.logging.Logger; import java.util.zip.DataFormatException; import java.util.zip.Inflater; +import org.apache.logging.log4j.LogManager; /** * @author harmjan @@ -197,7 +198,7 @@ protected void analyze(MetaAnalysisWorkPackage pack) { zscores = inflate(data, ds[d].getNumProbes()); // pack.setData(d, null); } catch (DataFormatException ex) { - Logger.getLogger(MetaAnalysisCalculationThread.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisPlotThread.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisPlotThread.java index dc61d0d38..823dcae79 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisPlotThread.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaAnalysisPlotThread.java @@ -11,6 +11,7 @@ import java.util.logging.Level; import java.util.logging.Logger; import java.util.zip.DataFormatException; +import org.apache.logging.log4j.LogManager; import umcg.genetica.io.trityper.bin.BinaryResultSNP; import umcg.genetica.math.stats.Descriptives; @@ -119,7 +120,7 @@ protected void analyze(MetaAnalysisWorkPackage pack) { zscores = inflate(data, ds[d].getNumProbes()); // pack.setData(d, null); } catch (DataFormatException ex) { - Logger.getLogger(MetaAnalysisCalculationThread.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } if (zscores != null) { diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaSettings.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaSettings.java index 1e553f7aa..f9fbbd2dd 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaSettings.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/MetaSettings.java @@ -10,6 +10,7 @@ import java.util.ArrayList; import java.util.logging.Level; import java.util.logging.Logger; +import org.apache.logging.log4j.LogManager; /** * @author harm-jan @@ -502,7 +503,7 @@ void save() { try { config.save(output + "metasettings.xml"); } catch (ConfigurationException ex) { - Logger.getLogger(MetaSettings.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CalcThread.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CalcThread.java index a7336d198..f8ac39bdc 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CalcThread.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CalcThread.java @@ -4,10 +4,10 @@ */ package eqtlmappingpipeline.binarymeta.meta.cis; +import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread; import java.util.HashMap; import java.util.concurrent.ArrayBlockingQueue; -import java.util.logging.Level; -import java.util.logging.Logger; +import org.apache.logging.log4j.LogManager; import umcg.genetica.containers.Pair; /** @@ -38,9 +38,9 @@ public void run() { output.offer(result); } } catch (InterruptedException ex) { - Logger.getLogger(CalcThread.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } catch (Exception ex) { - Logger.getLogger(CalcThread.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisAnalysis.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisAnalysis.java index 988d5216b..51a49e765 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisAnalysis.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisAnalysis.java @@ -5,6 +5,7 @@ package eqtlmappingpipeline.binarymeta.meta.cis; import com.itextpdf.text.DocumentException; +import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread; import eqtlmappingpipeline.metaqtl3.FDR; import eqtlmappingpipeline.metaqtl3.graphics.EQTLDotPlot; import eqtlmappingpipeline.binarymeta.meta.MetaAnalyze; @@ -16,6 +17,7 @@ import java.util.*; import java.util.logging.Level; import java.util.logging.Logger; +import org.apache.logging.log4j.LogManager; import umcg.genetica.console.ProgressBar; import umcg.genetica.containers.Pair; import umcg.genetica.io.Gpio; @@ -58,7 +60,7 @@ public static void main(String[] args) { CisAnalysis c = new CisAnalysis(config); c.run(); } catch (IOException ex) { - Logger.getLogger(CisAnalysis.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } } } @@ -147,7 +149,7 @@ public void run() throws IOException { try { edp.draw(m_settings.getOutput() + "/eQTLsFDR" + m_settings.getFdrthreshold() + ".txt", m_settings.getOutput() + "/DotPlot-FDR" + m_settings.getFdrthreshold() + ".pdf", EQTLDotPlot.Output.PDF); // "/eQTLsFDR" + fdrCutOff + ".txt", outputReportsDir + "/eQTLsFDR" + fdrCutOff + "DotPlot.png" } catch (DocumentException ex) { - Logger.getLogger(CisAnalysis.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } edp = null; } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisBinaryConverter.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisBinaryConverter.java index 41876be25..5346b6001 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisBinaryConverter.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/CisBinaryConverter.java @@ -4,6 +4,7 @@ */ package eqtlmappingpipeline.binarymeta.meta.cis; +import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread; import eqtlmappingpipeline.binarymeta.meta.MetaSettings; import java.io.IOException; import java.nio.ByteBuffer; @@ -12,6 +13,7 @@ import java.util.logging.Logger; import java.util.zip.DataFormatException; import java.util.zip.Inflater; +import org.apache.logging.log4j.LogManager; import umcg.genetica.console.ProgressBar; import umcg.genetica.io.Gpio; import umcg.genetica.io.bin.BinaryFile; @@ -39,7 +41,7 @@ public static void main(String[] args) { try { c.run(); } catch (IOException ex) { - Logger.getLogger(CisBinaryConverter.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } } private final MetaSettings m_settings; @@ -160,7 +162,7 @@ public void run() throws IOException { // pb.iterate(); // snp++; } catch (DataFormatException ex) { - Logger.getLogger(CisBinaryConverter.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } pb.iterate(); } @@ -172,7 +174,7 @@ public void run() throws IOException { // System.out.println("Waiting for result thread..."); // completor.join(); // } catch (InterruptedException ex) { -// Logger.getLogger(CisBinaryConverter.class.getName()).log(Level.SEVERE, null, ex); +// LogManager.getLogger(CisBinaryConverter.class.getName()).log(Level.SEVERE, null, ex); // } dataset.close(); dataset = null; diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/UnzipTask.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/UnzipTask.java index d13bf301f..e2acf4def 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/UnzipTask.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/UnzipTask.java @@ -4,6 +4,7 @@ */ package eqtlmappingpipeline.binarymeta.meta.cis; +import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread; import java.nio.ByteBuffer; import java.util.ArrayList; import java.util.HashMap; @@ -12,6 +13,7 @@ import java.util.logging.Logger; import java.util.zip.DataFormatException; import java.util.zip.Inflater; +import org.apache.logging.log4j.LogManager; import umcg.genetica.containers.Pair; import umcg.genetica.io.trityper.bin.BinaryResultDataset; import umcg.genetica.io.trityper.bin.BinaryResultSNP; @@ -67,7 +69,7 @@ public Pair> call() throws Exception { byte[] data = ds.getMatrix().readDeflated(pointer, nextpointer, ds.getNumProbes()); zscores = inflate(data, ds.getNumProbes()); } catch (DataFormatException ex) { - Logger.getLogger(CisAnalysis.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } for (int probe = 0; probe < probes.size(); probe++) { diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/ZScoreLoaderTask.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/ZScoreLoaderTask.java index 0e00cf7a5..0384431f3 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/ZScoreLoaderTask.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/meta/cis/ZScoreLoaderTask.java @@ -4,6 +4,7 @@ */ package eqtlmappingpipeline.binarymeta.meta.cis; +import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread; import java.nio.ByteBuffer; import java.util.ArrayList; import java.util.HashMap; @@ -12,6 +13,7 @@ import java.util.logging.Logger; import java.util.zip.DataFormatException; import java.util.zip.Inflater; +import org.apache.logging.log4j.LogManager; import umcg.genetica.containers.Pair; import umcg.genetica.io.trityper.bin.BinaryResultDataset; import umcg.genetica.io.trityper.bin.BinaryResultSNP; @@ -67,7 +69,7 @@ public Pair call() throws Exception { byte[] data = ds[d].getMatrix().readDeflated(pointer, nextpointer, ds[d].getNumProbes()); zscores = inflate(data, ds[d].getNumProbes()); } catch (DataFormatException ex) { - Logger.getLogger(CisAnalysis.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/util/Filter.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/util/Filter.java index 628fa188f..62c0d2107 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/util/Filter.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/binarymeta/util/Filter.java @@ -5,6 +5,7 @@ package eqtlmappingpipeline.binarymeta.util; import com.itextpdf.text.DocumentException; +import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread; import eqtlmappingpipeline.metaqtl3.FDR; import eqtlmappingpipeline.metaqtl3.FDR.FDRMethod; import eqtlmappingpipeline.metaqtl3.graphics.EQTLDotPlot; @@ -13,6 +14,7 @@ import java.util.HashSet; import java.util.logging.Level; import java.util.logging.Logger; +import org.apache.logging.log4j.LogManager; import umcg.genetica.io.Gpio; import umcg.genetica.io.text.TextFile; @@ -84,7 +86,7 @@ public void run(String indir, String probetranslationfile, String requestedAnnot try { edp.draw(outdir + "/eQTLsFDR" + 0.05 + ".txt", outdir + "/DotPlot-FDR" + 0.05 + ".png", EQTLDotPlot.Output.PDF); // "/eQTLsFDR" + fdrCutOff + ".txt", outputReportsDir + "/eQTLsFDR" + fdrCutOff + "DotPlot.png" } catch (DocumentException ex) { - Logger.getLogger(Filter.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(MetaAnalysisCalculationThread.class.getName()).log(org.apache.logging.log4j.Level.FATAL, ex); } edp = null; diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/interactionanalysis/InteractionAnalysisDetermineDirection.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/interactionanalysis/InteractionAnalysisDetermineDirection.java index dee78d1dc..9ab4b0385 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/interactionanalysis/InteractionAnalysisDetermineDirection.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/interactionanalysis/InteractionAnalysisDetermineDirection.java @@ -30,7 +30,8 @@ import org.apache.commons.math3.stat.ranking.NaNStrategy; import org.apache.commons.math3.stat.ranking.NaturalRanking; import org.apache.commons.math3.stat.ranking.RankingAlgorithm; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.Allele; import org.molgenis.genotype.Alleles; import org.molgenis.genotype.GenotypeDataException; @@ -60,7 +61,7 @@ public class InteractionAnalysisDetermineDirection { static { - LOGGER = Logger.getLogger(GenotypeInfo.class); + LOGGER = LogManager.getLogger(GenotypeInfo.class); OPTIONS = new Options(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl3/MetaQTL3.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl3/MetaQTL3.java index 7ced0c0e2..bcd2c09fe 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl3/MetaQTL3.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl3/MetaQTL3.java @@ -1236,7 +1236,7 @@ public void mapEQTLs() throws IOException { edp.draw(m_settings.outputReportsDir + "/eQTLsFDR" + m_settings.fdrCutOff + ".txt.gz", m_settings.outputReportsDir + "/DotPlot-FDR" + m_settings.fdrCutOff + ".pdf", EQTLDotPlot.Output.PDF); // "/eQTLsFDR" + fdrCutOff + ".txt", outputReportsDir + "/eQTLsFDR" + fdrCutOff + "DotPlot.png" } } catch (DocumentException ex) { - Logger.getLogger(MetaQTL3.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } edp = null; } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4.java index 476ffb3b9..6590ece8f 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4.java @@ -16,7 +16,8 @@ import java.util.concurrent.ExecutorCompletionService; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.RandomAccessGenotypeData; import org.molgenis.genotype.variant.GeneticVariant; import umcg.genetica.console.ProgressBar; @@ -44,7 +45,7 @@ public class MetaQTL4 { private ArrayList availableTraits; private TObjectIntHashMap availableTraitsHash; //int as value private GeneticVariant[][] geneticVariantIndex; - private static final Logger LOG = Logger.getLogger(MetaQTL4.class); + private static final Logger LOG = LogManager.getLogger(MetaQTL4.class); public MetaQTL4(MetaQTL4Settings settings) throws IOException, Exception { LOG.info("WARNING: MetaQTL4 is experimental code!"); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4ConsoleUI.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4ConsoleUI.java index 6215c33e5..46367f726 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4ConsoleUI.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4ConsoleUI.java @@ -1,6 +1,7 @@ package eqtlmappingpipeline.metaqtl4; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; /** * An awesome MetaQTL4 @@ -8,7 +9,7 @@ */ public class MetaQTL4ConsoleUI { - private static final Logger logger = Logger.getLogger(MetaQTL4ConsoleUI.class); + private static final Logger logger = LogManager.getLogger(MetaQTL4ConsoleUI.class); public MetaQTL4ConsoleUI(String[] args) { if (args.length < 1) { diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4Dataset.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4Dataset.java index 906563fdc..e380af384 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4Dataset.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/MetaQTL4Dataset.java @@ -12,7 +12,8 @@ import java.util.List; import java.util.Map; import java.util.Set; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.GenotypeData; import org.molgenis.genotype.RandomAccessGenotypeData; import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats; @@ -38,7 +39,7 @@ public class MetaQTL4Dataset { private final HashMap genotypeToTraitCoupling; private int[] intGenotypeToTraitCoupling; private final String genotypeDataLocation; - private static final Logger LOG = Logger.getLogger(MetaQTL4Dataset.class); + private static final Logger LOG = LogManager.getLogger(MetaQTL4Dataset.class); public MetaQTL4Dataset(MetaQTL4DatasetSettings settings) throws IOException { this(settings.getTraitDataLocation(), null, settings.getGenotypeLocation(), settings.getGenotypeFormat(), null, settings.getGenotypeToTraitCoupling()); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/SingleDatasetAnalysis.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/SingleDatasetAnalysis.java index 0e245f5c4..c2f94fae6 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/SingleDatasetAnalysis.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/metaqtl4/SingleDatasetAnalysis.java @@ -16,7 +16,8 @@ import java.util.concurrent.ExecutorCompletionService; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.molgenis.genotype.variant.GeneticVariant; import umcg.genetica.console.ProgressBar; import umcg.genetica.containers.Pair; @@ -40,7 +41,7 @@ public class SingleDatasetAnalysis { private MetaQTL4Dataset dataset; private ArrayList availableTraits; private TObjectIntHashMap availableTraitsHash; //int as value - private static final Logger LOG = Logger.getLogger(SingleDatasetAnalysis.class); + private static final Logger LOG = LogManager.getLogger(SingleDatasetAnalysis.class); private Integer[] traitIndex; public SingleDatasetAnalysis(MetaQTL4Settings settings) throws IOException, Exception { diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/textmeta/FixedEffectMetaAnalysis.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/textmeta/FixedEffectMetaAnalysis.java index 677fa7825..c965497e6 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/textmeta/FixedEffectMetaAnalysis.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/textmeta/FixedEffectMetaAnalysis.java @@ -192,7 +192,7 @@ public void run(String filesDir, String output, Integer minimalNrDatasets, Integ } catch (InterruptedException e) { e.printStackTrace(); } catch (ExecutionException ex) { - Logger.getLogger(FixedEffectMetaAnalysis.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/GetStatistics.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/GetStatistics.java index 2621f778f..395dee8ff 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/GetStatistics.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/GetStatistics.java @@ -32,14 +32,14 @@ public static void main(String[] args){ try { informationPerEntry = readAndProcessPermutation(inputFilePermutation); } catch (IOException ex) { - Logger.getLogger(GetStatistics.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { // processRealData(inputFileReal, informationPerEntry, outputFile); processRealData2(readAndProcessPermutation(inputFileReal), informationPerEntry, outputFile); } catch (IOException ex) { - Logger.getLogger(GetStatistics.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorBlockbased.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorBlockbased.java index 93066d5f5..4e3c856b8 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorBlockbased.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorBlockbased.java @@ -350,7 +350,7 @@ private static HashMap> readInQtlTransformB try { qtls = readInQtlInformation(in, inProxies, probeMap, snpMap, permutationFile, renameSnpProxie); } catch (IOException ex) { - Logger.getLogger(HiCQTLAnnotatorBlockbased.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } HashMap> desiredContacts; HashSet keysAdded = new HashSet<>(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorSnpBased.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorSnpBased.java index e3ca5fbe0..077baea1a 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorSnpBased.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLAnnotatorSnpBased.java @@ -365,7 +365,7 @@ private static HashMap> readInQtlInformatio try { qtls = readInQtlInformation(in, inProxies, probeMap, snpMap, permutationFile, renameSnpProxie); } catch (IOException ex) { - Logger.getLogger(HiCQTLAnnotatorSnpBased.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } HashMap> desiredContacts = new HashMap>(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLProbeAnnotatorSnpBased.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLProbeAnnotatorSnpBased.java index 561f30664..98b6afcb8 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLProbeAnnotatorSnpBased.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/HiC/HiCQTLProbeAnnotatorSnpBased.java @@ -175,7 +175,7 @@ private static HashMap> readInQtlProbeInfor try { qtls = HiCQTLAnnotatorSnpBased.readInQtlInformation(in, null, probeMap, snpMap, permutationFile, renameSnpProxie); } catch (IOException ex) { - Logger.getLogger(HiCQTLProbeAnnotatorSnpBased.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } HashMap> desiredContacts = new HashMap<>(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtWestraReplication.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtWestraReplication.java index be9635eea..6fd471603 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtWestraReplication.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtWestraReplication.java @@ -24,7 +24,8 @@ import org.apache.commons.cli.ParseException; import org.apache.commons.cli.PosixParser; 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.molgenis.genotype.Allele; import org.molgenis.genotype.Alleles; import org.molgenis.genotype.GenotypeDataException; @@ -75,7 +76,7 @@ public class ModuleEqtWestraReplication { } EXTRA_COL_FROM_REPLICATION[12] = 0; - LOGGER = Logger.getLogger(GenotypeInfo.class); + LOGGER = LogManager.getLogger(GenotypeInfo.class); OPTIONS = new Options(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlGeuvadisReplication.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlGeuvadisReplication.java index 66bd0cb06..e57c605e1 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlGeuvadisReplication.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlGeuvadisReplication.java @@ -24,7 +24,8 @@ import org.apache.commons.cli.ParseException; import org.apache.commons.cli.PosixParser; 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.molgenis.genotype.GenotypeDataException; import org.molgenis.genotype.GenotypeInfo; import org.molgenis.genotype.RandomAccessGenotypeData; @@ -60,7 +61,7 @@ public class ModuleEqtlGeuvadisReplication { static { - LOGGER = Logger.getLogger(GenotypeInfo.class); + LOGGER = LogManager.getLogger(GenotypeInfo.class); OPTIONS = new Options(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlNeutrophilReplication.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlNeutrophilReplication.java index c233c68fb..89033eeb0 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlNeutrophilReplication.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/ModuleEqtlNeutrophilReplication.java @@ -24,7 +24,8 @@ import org.apache.commons.cli.ParseException; import org.apache.commons.cli.PosixParser; 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.molgenis.genotype.GenotypeDataException; import org.molgenis.genotype.GenotypeInfo; import org.molgenis.genotype.RandomAccessGenotypeData; @@ -63,7 +64,7 @@ public class ModuleEqtlNeutrophilReplication { static { - LOGGER = Logger.getLogger(GenotypeInfo.class); + LOGGER = LogManager.getLogger(GenotypeInfo.class); OPTIONS = new Options(); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/NoLdSnpProbeListCreator.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/NoLdSnpProbeListCreator.java index eb21fa49b..e284ff444 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/NoLdSnpProbeListCreator.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/NoLdSnpProbeListCreator.java @@ -168,7 +168,7 @@ public static void main(String[] args) throws UnsupportedEncodingException, File logOutput += "Chr filter:\t" + chrF + "\n"; } } catch (ParseException ex) { - Logger.getLogger(NoLdSnpProbeListCreator.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } System.out.println(logOutput); diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLDotPlotter.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLDotPlotter.java index f7865fb65..7289cc117 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLDotPlotter.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLDotPlotter.java @@ -23,9 +23,9 @@ public void plot(String file) { EQTLDotPlot edp = new EQTLDotPlot(); edp.draw(file, file + "EQTLDotPlot.pdf", EQTLDotPlot.Output.PDF); } catch (IOException ex) { - Logger.getLogger(QTLDotPlotter.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (DocumentException ex) { - Logger.getLogger(QTLDotPlotter.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLFileCompare.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLFileCompare.java index f62fc0bf9..14b5fe1ed 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLFileCompare.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/QTLFileCompare.java @@ -105,9 +105,9 @@ public QTLFileCompare(String[] args) { compareOverlapAndZScoreDirectionTwoEQTLFilesMj(file1, file2, out, pCut, pCut2, matchOnGeneName, matchSnpOnPos, splitGeneNames); } } catch (IOException ex) { - Logger.getLogger(QTLFileCompare.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (Exception ex) { - Logger.getLogger(QTLFileCompare.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } else { diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/RegressCisEffectsFromGeneExpressionData.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/RegressCisEffectsFromGeneExpressionData.java index 95f04a539..e3bd47b5b 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/RegressCisEffectsFromGeneExpressionData.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/RegressCisEffectsFromGeneExpressionData.java @@ -166,9 +166,9 @@ public RegressCisEffectsFromGeneExpressionData(String settingsFile, String eQTLF try { m_settings.load(settingsFile); } catch (IOException ex) { - Logger.getLogger(RegressCisEffectsFromGeneExpressionData.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (ConfigurationException ex) { - Logger.getLogger(RegressCisEffectsFromGeneExpressionData.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } int numDatasets = m_settings.datasetSettings.size(); @@ -183,9 +183,9 @@ public RegressCisEffectsFromGeneExpressionData(String settingsFile, String eQTLF try { m_gg[i] = new TriTyperGeneticalGenomicsDataset(m_settings.datasetSettings.get(i), null); } catch (IOException ex) { - Logger.getLogger(RegressCisEffectsFromGeneExpressionData.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (Exception ex) { - Logger.getLogger(RegressCisEffectsFromGeneExpressionData.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } if (m_gg[i].isExpressionDataLoadedCorrectly()) { @@ -209,9 +209,9 @@ public RegressCisEffectsFromGeneExpressionData(String settingsFile, String eQTLF try { eqr.regressOutEQTLEffects(eQTLFile, true, m_gg); } catch (IOException ex) { - Logger.getLogger(RegressCisEffectsFromGeneExpressionData.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (Exception e) { - Logger.getLogger(RegressCisEffectsFromGeneExpressionData.class.getName()).log(Level.SEVERE, null, e); + throw new RuntimeException(e); } } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/SummarizeQtlSummaries.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/SummarizeQtlSummaries.java index 51172c6e6..73cc50432 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/SummarizeQtlSummaries.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/SummarizeQtlSummaries.java @@ -27,7 +27,7 @@ public static void main(String[] args) { try { processData(fileList, filenameContains); } catch (IOException ex) { - Logger.getLogger(SummarizeQtlSummaries.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/UtilConsoleGUI.java b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/UtilConsoleGUI.java index a1c86919d..ecf467182 100644 --- a/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/UtilConsoleGUI.java +++ b/eqtl-mapping-pipeline/src/main/java/eqtlmappingpipeline/util/UtilConsoleGUI.java @@ -526,13 +526,13 @@ public UtilConsoleGUI(String[] args) { try { NoLdSnpProbeListCreator.main(Arrays.copyOfRange(args, 2, args.length)); } catch (UnsupportedEncodingException ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (FileNotFoundException ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (IOException ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (Exception ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } break; @@ -555,9 +555,9 @@ public UtilConsoleGUI(String[] args) { p.alternativeInitialize(settingsfile, in, inexp, null, annot, gte, out, true, true, perm, snpfile, threads, sortsnps); p.performeQTLMappingOverEigenvectorMatrixAndReNormalize(out, stepSize, max, nreqtls); } catch (IOException ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } catch (Exception ex) { - Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/genetica-libraries/pom.xml b/genetica-libraries/pom.xml index 77586d110..511888cd1 100644 --- a/genetica-libraries/pom.xml +++ b/genetica-libraries/pom.xml @@ -79,11 +79,6 @@ commons-io 2.11.0 - - commons-logging - commons-logging - 1.1.1 - org.apache.commons commons-math3 diff --git a/genetica-libraries/src/main/java/umcg/genetica/graphics/ForestPlot.java b/genetica-libraries/src/main/java/umcg/genetica/graphics/ForestPlot.java index e5e0784b0..6f6f637cf 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/graphics/ForestPlot.java +++ b/genetica-libraries/src/main/java/umcg/genetica/graphics/ForestPlot.java @@ -20,7 +20,6 @@ import java.text.DecimalFormat; import java.util.Arrays; import java.util.Locale; -import java.util.logging.Logger; import javax.imageio.ImageIO; import umcg.genetica.io.trityper.util.ChrAnnotation; @@ -59,7 +58,7 @@ public enum Output { private static final Color red2Color = new Color(242, 101, 94, 25); private static final Color gray1Color = new Color(237, 237, 237); private static final Color gray2Color = new Color(247, 247, 247); - private static final Logger LOGGER = Logger.getLogger(Heatmap.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(ForestPlot.class); private static final Stroke dashed = new BasicStroke(1, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 0, new float[]{4}, 0); private static final Stroke line2pt = new BasicStroke(2, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND); private static final Stroke line = new BasicStroke(1, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND); diff --git a/genetica-libraries/src/main/java/umcg/genetica/graphics/Heatmap.java b/genetica-libraries/src/main/java/umcg/genetica/graphics/Heatmap.java index 9549ebdb7..035fd89bd 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/graphics/Heatmap.java +++ b/genetica-libraries/src/main/java/umcg/genetica/graphics/Heatmap.java @@ -32,7 +32,7 @@ public class Heatmap { private static final int LEGEND_Y = 10; private static final int LEGEND_WIDTH = 200; private static final int LEGEND_HEIGHT = 100; - private static final Logger LOGGER = Logger.getLogger(Heatmap.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(ForestPlot.class); public enum Output { diff --git a/genetica-libraries/src/main/java/umcg/genetica/gwas/Independifier.java b/genetica-libraries/src/main/java/umcg/genetica/gwas/Independifier.java index 47a5e05d2..da727cf18 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/gwas/Independifier.java +++ b/genetica-libraries/src/main/java/umcg/genetica/gwas/Independifier.java @@ -4,7 +4,6 @@ */ package umcg.genetica.gwas; -import gnu.trove.map.hash.THashMap; import gnu.trove.map.hash.TObjectIntHashMap; import java.io.IOException; import java.util.ArrayList; @@ -12,8 +11,8 @@ import java.util.List; import java.util.Map; import java.util.Vector; -import java.util.logging.Level; -import java.util.logging.Logger; +import org.apache.logging.log4j.Level; +import umcg.genetica.graphics.ForestPlot; import umcg.genetica.io.text.TextFile; import umcg.genetica.io.trityper.SNP; import umcg.genetica.io.trityper.SNPLoader; @@ -29,7 +28,7 @@ */ public class Independifier { - private static final Logger LOGGER = Logger.getLogger(Independifier.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(ForestPlot.class); TriTyperGenotypeData genotypeData; final SNPLoader snpLoader; Map> permDatasets; diff --git a/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortInterChrContacts.java b/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortInterChrContacts.java index 960415c40..951c9d52d 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortInterChrContacts.java +++ b/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortInterChrContacts.java @@ -11,9 +11,9 @@ import java.io.InputStreamReader; import java.util.ArrayList; import java.util.Collections; -import java.util.logging.Level; -import java.util.logging.Logger; import org.apache.commons.lang3.StringUtils; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; import umcg.genetica.io.text.TextFile; /** @@ -27,14 +27,14 @@ public static void readNonSortedWriteSorted(String fileToReads, String fileToWri try { contacts = readRawInterContactInformation(fileToReads); } catch (IOException ex) { - Logger.getLogger(SortInterChrContacts.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(SortInterChrContacts.class).log(Level.FATAL, ex); } Collections.sort(contacts); try { writeRawInterContactInformation(contacts, fileToWrite); } catch (IOException ex) { - Logger.getLogger(SortInterChrContacts.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(SortInterChrContacts.class).log(Level.FATAL, ex); } } diff --git a/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortIntraChrContacts.java b/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortIntraChrContacts.java index 72d2ef75e..498cdcabd 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortIntraChrContacts.java +++ b/genetica-libraries/src/main/java/umcg/genetica/io/chrContacts/SortIntraChrContacts.java @@ -11,9 +11,8 @@ import java.io.InputStreamReader; import java.util.ArrayList; import java.util.Collections; -import java.util.logging.Level; -import java.util.logging.Logger; import org.apache.commons.lang3.StringUtils; +import org.apache.logging.log4j.LogManager; import umcg.genetica.io.text.TextFile; /** @@ -27,14 +26,14 @@ public static void readNonSortedWriteSorted(String fileToReads, String fileToWri try { contacts = readRawIntraContactInformation(fileToReads); } catch (IOException ex) { - Logger.getLogger(SortIntraChrContacts.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(SortInterChrContacts.class).log(org.apache.logging.log4j.Level.FATAL, ex); } Collections.sort(contacts); try { writeRawIntraContactInformation(contacts, fileToWrite); } catch (IOException ex) { - Logger.getLogger(SortIntraChrContacts.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(SortInterChrContacts.class).log(org.apache.logging.log4j.Level.FATAL, ex); } contacts = null; } diff --git a/genetica-libraries/src/main/java/umcg/genetica/io/geofiles/ParseTextTable.java b/genetica-libraries/src/main/java/umcg/genetica/io/geofiles/ParseTextTable.java index 62efe3f87..2bc6139a4 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/io/geofiles/ParseTextTable.java +++ b/genetica-libraries/src/main/java/umcg/genetica/io/geofiles/ParseTextTable.java @@ -8,13 +8,11 @@ import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D; import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D; import java.io.IOException; -import java.util.HashSet; import java.util.LinkedHashMap; import java.util.LinkedHashSet; -import java.util.logging.Level; -import java.util.logging.Logger; import java.util.regex.Pattern; import org.apache.commons.lang.math.NumberUtils; +import org.apache.logging.log4j.Level; import umcg.genetica.io.text.TextFile; import umcg.genetica.math.matrix2.DoubleMatrixDataset; @@ -26,7 +24,7 @@ public class ParseTextTable { private static Pattern SPLIT_ON_TAB = Pattern.compile("\\t"); protected static final String ENCODING = "ISO-8859-1"; - static final Logger LOGGER = Logger.getLogger(DoubleMatrixDataset.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(ParseTextTable.class); /** * Geo text tables for HT12 v3 / v4 data @@ -79,7 +77,7 @@ public static DoubleMatrixDataset parseGeoTables(String fileInpu } } } else if(colMap.containsKey(colName)) { - LOGGER.warning("Duplicated column name:" + colName + "! In file: " + fileInput); + LOGGER.warn("Duplicated column name:" + colName + "! In file: " + fileInput); throw new IOException("Problem with parsing file"); } else if (debug) { @@ -144,14 +142,14 @@ else if (debug) { } row++; } else { - LOGGER.warning("Duplicated row name: "+data[columnOffset - 1]); + LOGGER.warn("Duplicated row name: "+data[columnOffset - 1]); System.out.println(str); throw new IOException("Problem in reading file."); } } } if (!correctData) { - LOGGER.warning("Your data contains NaN/unparseable values!"); + LOGGER.warn("Your data contains NaN/unparseable values!"); } in.close(); diff --git a/genetica-libraries/src/main/java/umcg/genetica/io/probemapping/reading.java b/genetica-libraries/src/main/java/umcg/genetica/io/probemapping/reading.java index 8be83b722..dd2aa1892 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/io/probemapping/reading.java +++ b/genetica-libraries/src/main/java/umcg/genetica/io/probemapping/reading.java @@ -5,7 +5,6 @@ package umcg.genetica.io.probemapping; import gnu.trove.map.hash.THashMap; -import java.awt.TextField; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; @@ -18,11 +17,12 @@ import java.util.LinkedHashMap; import java.util.Set; import java.util.TreeMap; -import java.util.logging.Level; -import java.util.logging.Logger; import java.util.regex.Pattern; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; import umcg.genetica.containers.Pair; import umcg.genetica.containers.Triple; +import umcg.genetica.io.chrContacts.SortInterChrContacts; import umcg.genetica.io.text.TextFile; import umcg.genetica.math.matrix.DoubleMatrixDataset; @@ -1030,7 +1030,7 @@ public static DoubleMatrixDataset readDoubleMatrixFile(String ei tmp = new DoubleMatrixDataset(eigenVectorFile, null, rowsToInclude); } } catch (IOException ex) { - Logger.getLogger(reading.class.getName()).log(Level.SEVERE, null, ex); + LogManager.getLogger(SortInterChrContacts.class).log(Level.FATAL, ex); } return (tmp); diff --git a/genetica-libraries/src/main/java/umcg/genetica/io/text/converters/NetworkConverter.java b/genetica-libraries/src/main/java/umcg/genetica/io/text/converters/NetworkConverter.java index 9739b38f5..799906c5c 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/io/text/converters/NetworkConverter.java +++ b/genetica-libraries/src/main/java/umcg/genetica/io/text/converters/NetworkConverter.java @@ -12,8 +12,7 @@ import java.util.List; import java.util.Map; import java.util.Set; -import java.util.logging.Level; -import java.util.logging.Logger; +import org.apache.logging.log4j.Level; import umcg.genetica.io.text.TextFile; /** @@ -22,7 +21,7 @@ */ public class NetworkConverter { - private static final Logger LOGGER = Logger.getLogger(NetworkConverter.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(NetworkConverter.class); // prevent instantiation, only static factory methods private NetworkConverter() { @@ -34,7 +33,7 @@ public static void convertPlainTextDoubleMatrixToPlainTextEdgeList(String matrix String line = in.readLine(); String[] split = line.split(infileDelimiter); String[] nodes = Arrays.copyOfRange(split, 1, split.length); - LOGGER.log(Level.FINE, "{0} nodes in {1}", new Object[]{nodes.length, matrixfile}); + LOGGER.log(Level.DEBUG, "{0} nodes in {1}", new Object[]{nodes.length, matrixfile}); TextFile out = new TextFile(outfile, TextFile.W); int lineNr = 1; @@ -63,7 +62,7 @@ public static void convertPlainTextDoubleMatrixToPlainTextEdgeList(String matrix } in.close(); out.close(); - LOGGER.log(Level.FINE, "{0} edges from {1} written to ''{2}''", new Object[]{nrEdges, matrixfile, outfile}); + LOGGER.log(Level.DEBUG, "{0} edges from {1} written to ''{2}''", new Object[]{nrEdges, matrixfile, outfile}); } public static void writeGMTFileBasedOnGeneSetFileAndMappingFileRemovingDuplicateGeneSets(String genesetfile, String mappingfile, String mappingdelimiter, String gmtfile) throws IOException { @@ -91,7 +90,7 @@ public static void writeGMTFileBasedOnGeneSetFileAndMappingFileRemovingDuplicate String code = split[0].trim(); String name = code2name.get(code); if (name == null) { - LOGGER.log(Level.WARNING, "No annotation for gene set ''{0}''", code); + LOGGER.log(Level.WARN, "No annotation for gene set ''{0}''", code); } else { String genes = Arrays.asList(Arrays.copyOfRange(split, 1, split.length)).toString(); System.out.println(genes); diff --git a/genetica-libraries/src/main/java/umcg/genetica/io/trityper/ConvertDoubleMatrixDataToTriTyper.java b/genetica-libraries/src/main/java/umcg/genetica/io/trityper/ConvertDoubleMatrixDataToTriTyper.java index b89b700b5..70c9fda72 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/io/trityper/ConvertDoubleMatrixDataToTriTyper.java +++ b/genetica-libraries/src/main/java/umcg/genetica/io/trityper/ConvertDoubleMatrixDataToTriTyper.java @@ -20,8 +20,6 @@ import java.io.FileWriter; import java.io.IOException; import java.util.HashSet; -import java.util.logging.Level; -import java.util.logging.Logger; import java.util.regex.Pattern; /** @@ -79,7 +77,7 @@ public static void main(String[] args) throws IOException, Exception { removeNanRow = cmd.hasOption("R"); } catch (org.apache.commons.cli.ParseException ex) { - Logger.getLogger(ConvertDoubleMatrixDataToTriTyper.class.getName()).log(Level.SEVERE, null, ex); + org.apache.logging.log4j.LogManager.getLogger(ConvertDoubleMatrixDataToTriTyper.class).log(org.apache.logging.log4j.Level.FATAL, ex); } diff --git a/genetica-libraries/src/main/java/umcg/genetica/io/trityper/converters/FinalReportToTriTyper.java b/genetica-libraries/src/main/java/umcg/genetica/io/trityper/converters/FinalReportToTriTyper.java index 2311417cc..c73b254d7 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/io/trityper/converters/FinalReportToTriTyper.java +++ b/genetica-libraries/src/main/java/umcg/genetica/io/trityper/converters/FinalReportToTriTyper.java @@ -935,7 +935,7 @@ public static void main(String[] args) { try { new FinalReportToTriTyper(inputFile, outputDir, isIlluminaFinalReportFile, delimiter, decimalSeparator); } catch (IOException ex) { - Logger.getLogger(FinalReportToTriTyper.class.getName()).log(Level.SEVERE, null, ex); + org.apache.logging.log4j.LogManager.getLogger(FinalReportToTriTyper.class).log(org.apache.logging.log4j.Level.FATAL, ex); } } } diff --git a/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDataset.java b/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDataset.java index 2ffaf2b4b..f504ad0da 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDataset.java +++ b/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDataset.java @@ -22,11 +22,11 @@ import java.util.concurrent.ExecutorCompletionService; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; -import java.util.logging.Level; -import java.util.logging.Logger; import java.util.regex.Pattern; +import org.apache.logging.log4j.Level; import umcg.genetica.console.ProgressBar; import umcg.genetica.containers.Triple; +import umcg.genetica.graphics.ForestPlot; import umcg.genetica.io.concurrent.DoubleParseTask; import umcg.genetica.io.text.TextFile; import umcg.genetica.math.matrix.DoubleMatrixDatasetAC.LoadLabels; @@ -43,7 +43,7 @@ public class DoubleMatrixDataset extends DoubleMatrixDatasetAC { // LOAD_BOTH, LOAD_ROWS, LOAD_COLUMNS, DONT_LOAD // }; - private static final Logger LOGGER = Logger.getLogger(DoubleMatrixDataset.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(ForestPlot.class); public double[][] rawData = null; //public int nrRows = 0; //public int nrCols = 0; @@ -347,7 +347,7 @@ private void loadExpressionData(String fileName, String delimiter) throws IOExce } pb.close(); if (!correctData) { - LOGGER.warning("Your data contains NaN/unparseable values!"); + LOGGER.warn("Your data contains NaN/unparseable values!"); } in.close(); recalculateHashMaps(); @@ -597,7 +597,7 @@ private void loadRowObjects(String fileName) throws FileNotFoundException, IOExc rowObjects.add((T) ois.readObject()); } } catch (ClassNotFoundException ex) { - Logger.getLogger(DoubleMatrixDataset.class.getName()).log(Level.SEVERE, "Error with row objects", ex); + System.err.println("Error with row objects"); ex.printStackTrace(); } bis.close(); @@ -660,7 +660,7 @@ private void loadColumnObjects(String fileName) throws FileNotFoundException, IO colObjects.add((U) ois.readObject()); } } catch (ClassNotFoundException ex) { - Logger.getLogger(DoubleMatrixDataset.class.getName()).log(Level.SEVERE, "Error with column objects", ex); + System.err.println("Error with column objects"); ex.printStackTrace(); } bis.close(); diff --git a/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDatasetRA.java b/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDatasetRA.java index 041313e0c..11ea05f71 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDatasetRA.java +++ b/genetica-libraries/src/main/java/umcg/genetica/math/matrix/DoubleMatrixDatasetRA.java @@ -6,9 +6,8 @@ import java.io.*; import java.util.*; -import java.util.logging.Level; -import java.util.logging.Logger; - +import org.apache.logging.log4j.Level; +import umcg.genetica.graphics.ForestPlot; /** * * @author lude, juha @@ -16,7 +15,7 @@ @Deprecated public class DoubleMatrixDatasetRA extends DoubleMatrixDatasetAC { - private static final Logger LOGGER = Logger.getLogger(DoubleMatrixDatasetRA.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(ForestPlot.class); public int nrColsTotal = 0; public Set rowsToInclude = null; public Set colsToInclude = null; diff --git a/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/DoubleMatrixDataset.java b/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/DoubleMatrixDataset.java index e6a5e5363..2d2fa2597 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/DoubleMatrixDataset.java +++ b/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/DoubleMatrixDataset.java @@ -46,7 +46,7 @@ */ public class DoubleMatrixDataset { - static final Logger LOGGER = Logger.getLogger(DoubleMatrixDataset.class.getName()); + private static final org.apache.logging.log4j.Logger LOGGER = org.apache.logging.log4j.LogManager.getLogger(DoubleMatrixDataset.class); protected DoubleMatrix2D matrix; protected LinkedHashMap hashRows; @@ -663,7 +663,7 @@ public static DoubleMatrixDataset loadSubsetOfTextDoubleData(Str desiredColIds.add(new Pair<>(s, storedCols)); storedCols++; } else if (colMap.containsKey(colName)) { - LOGGER.warning("Duplicated column name!"); + LOGGER.warn("Duplicated column name!"); throw new Exception("Duplicated column are not allowed. Tried to add: " + colName); } } @@ -701,13 +701,12 @@ public static DoubleMatrixDataset loadSubsetOfTextDoubleData(Str storingRow++; } else if (rowMap.containsKey(data[0])) { - LOGGER.warning("Duplicated row name!"); throw new Exception("Duplicated row are not allowed. Tried to add: " + data[0]); } } } if (!correctData.get()) { - LOGGER.warning("Your data contains NaN/unparseable values!"); + LOGGER.warn("Your data contains NaN/unparseable values!"); } in.close(); diff --git a/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/MergeDoubleMatrices.java b/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/MergeDoubleMatrices.java index c143bb742..2a838cf2b 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/MergeDoubleMatrices.java +++ b/genetica-libraries/src/main/java/umcg/genetica/math/matrix2/MergeDoubleMatrices.java @@ -10,8 +10,6 @@ import java.util.ArrayList; import java.util.HashSet; import java.util.LinkedHashMap; -import java.util.logging.Level; -import java.util.logging.Logger; import umcg.genetica.console.ProgressBar; /** @@ -208,7 +206,7 @@ public static DoubleMatrixDataset combineBasedOnRows(ArrayList combineBasedOnCols(ArrayList readDoubleMatrixFile(String e tmp = new DoubleMatrixDataset(eigenVectorFile, null, rowsToInclude);//, "\t"); } } catch (IOException ex) { - Logger.getLogger(AssociatingPcasWithAnnotation.class.getName()).log(Level.SEVERE, null, ex); + org.apache.logging.log4j.LogManager.getLogger(AssociatingPcasWithAnnotation.class).log(org.apache.logging.log4j.Level.FATAL, ex); } return (tmp); diff --git a/genetica-libraries/src/main/java/umcg/genetica/methylation/MethylationAssociatoingAnnotationWithValues.java b/genetica-libraries/src/main/java/umcg/genetica/methylation/MethylationAssociatoingAnnotationWithValues.java index c62cf017c..9adace817 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/methylation/MethylationAssociatoingAnnotationWithValues.java +++ b/genetica-libraries/src/main/java/umcg/genetica/methylation/MethylationAssociatoingAnnotationWithValues.java @@ -191,7 +191,7 @@ private static DoubleMatrixDataset readDoubleMatrixFile(String e try { tmp = new DoubleMatrixDataset(eigenVectorFile, "\t"); } catch (IOException ex) { - Logger.getLogger(MethylationAssociatoingAnnotationWithValues.class.getName()).log(Level.SEVERE, null, ex); + org.apache.logging.log4j.LogManager.getLogger(MethylationAssociatoingAnnotationWithValues.class).log(org.apache.logging.log4j.Level.FATAL, ex); } return (tmp); @@ -606,7 +606,7 @@ private static void associateAnovaScoreAndItemOfInterest(DoubleMatrixDataset parseTCGAData_lvl1(String file try { dataset3.save(fileOutputFolder + "/TCGADataBeta.txt"); } catch (IOException ex) { - Logger.getLogger(ParseTcgaMethylationFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } ArrayList> tmp = new ArrayList>(3); @@ -280,7 +280,7 @@ public static DoubleMatrixDataset parseTCGAData450As27K_lvl1(Str try { dataset3.save(fileOutputFolder + "TCGA_450K-27K_DataBeta.txt"); } catch (IOException ex) { - Logger.getLogger(ParseTcgaMethylationFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } ArrayList> tmp = new ArrayList>(3); @@ -416,17 +416,17 @@ public static ArrayList> parseTCGAData_lvl1_ try { dataset1.save(fileOutputFolder + "/TCGADataM.txt"); } catch (IOException ex) { - Logger.getLogger(ParseTcgaMethylationFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { dataset2.save(fileOutputFolder + "/TCGADataU.txt"); } catch (IOException ex) { - Logger.getLogger(ParseTcgaMethylationFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { dataset3.save(fileOutputFolder + "/TCGADataBeta.txt"); } catch (IOException ex) { - Logger.getLogger(ParseTcgaMethylationFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } ArrayList> tmp = new ArrayList>(3); @@ -532,7 +532,7 @@ public static DoubleMatrixDataset parseTCGAData_lvl3(String file try { dataset1.save(fileOut); } catch (IOException ex) { - Logger.getLogger(ParseTcgaMethylationFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } System.out.println(dataset1.colObjects.toString()); diff --git a/genetica-libraries/src/main/java/umcg/genetica/util/ConverteMappingAndSnpFile.java b/genetica-libraries/src/main/java/umcg/genetica/util/ConverteMappingAndSnpFile.java index 8687b580a..b0368d1c3 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/util/ConverteMappingAndSnpFile.java +++ b/genetica-libraries/src/main/java/umcg/genetica/util/ConverteMappingAndSnpFile.java @@ -161,7 +161,7 @@ private static void remapPositionsAndSnps(LinkedHashSet OrderingEst, Has out.close(); out2.close(); } catch (IOException ex) { - Logger.getLogger(ConverteMappingAndSnpFile.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } diff --git a/genetica-libraries/src/main/java/umcg/genetica/util/WriteExtendedFastaOfInterestRegion.java b/genetica-libraries/src/main/java/umcg/genetica/util/WriteExtendedFastaOfInterestRegion.java index 05d0b00db..01634db2b 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/util/WriteExtendedFastaOfInterestRegion.java +++ b/genetica-libraries/src/main/java/umcg/genetica/util/WriteExtendedFastaOfInterestRegion.java @@ -51,21 +51,21 @@ public static void main(String[] args) { interestStrings = readFileWithPositionsBed(fileWithPositions); } } catch (Exception ex) { - Logger.getLogger(WriteExtendedFastaOfInterestRegion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } System.out.println(" done"); try { System.out.print("Reading reference FASTA ......"); refGen = new ReferenceGenomeFasta(new File(referenceFasta), ReferenceGenomeFasta.HUMAN_NORMAL_CHR); } catch (Exception ex) { - Logger.getLogger(WriteExtendedFastaOfInterestRegion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } System.out.println(" done"); if (refGen != null && interestStrings != null) { try { writeFastaIncDirectionGuessing(refGen, interestStrings, outputFile, maxScore, minDiff); } catch (IOException ex) { - Logger.getLogger(WriteExtendedFastaOfInterestRegion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } @@ -180,7 +180,7 @@ private static void writeFastaIncDirectionGuessing(ReferenceGenomeFasta refGen, } } catch (Exception ex) { - Logger.getLogger(WriteExtendedFastaOfInterestRegion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } } diff --git a/genetica-libraries/src/main/java/umcg/genetica/util/WriteFastaOfInterestRegion.java b/genetica-libraries/src/main/java/umcg/genetica/util/WriteFastaOfInterestRegion.java index 2a20b511c..cd11e8591 100644 --- a/genetica-libraries/src/main/java/umcg/genetica/util/WriteFastaOfInterestRegion.java +++ b/genetica-libraries/src/main/java/umcg/genetica/util/WriteFastaOfInterestRegion.java @@ -47,21 +47,21 @@ public static void main(String[] args) { interestStrings = readBedFileWithPositions(fileWithPositions); } } catch (Exception ex) { - Logger.getLogger(WriteFastaOfInterestRegion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } try { System.out.println("Reading reference FASTA."); refGen = new ReferenceGenomeFasta(new File(referenceFasta), ReferenceGenomeFasta.HUMAN_NORMAL_CHR); } catch (Exception ex) { - Logger.getLogger(WriteFastaOfInterestRegion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } if (refGen != null && interestStrings != null) { try { writeFasta(refGen, interestStrings, outputFile); } catch (IOException ex) { - Logger.getLogger(WriteFastaOfInterestRegion.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } } @@ -149,7 +149,7 @@ private static void writeFasta(ReferenceGenomeFasta refGen, HashMap dataset, try { evd.factor(new DenseMatrix(CorMatrix.toArray())); } catch (NotConvergedException ex) { - Logger.getLogger(DoPcoa.class.getName()).log(Level.SEVERE, null, ex); + throw new RuntimeException(ex); } //System.out.println(dataset.columns()); diff --git a/javaPoCA/src/main/java/nl/umcg/bondermj/pcoa/PcoaParamaters.java b/javaPoCA/src/main/java/nl/umcg/bondermj/pcoa/PcoaParamaters.java index 7ee03d29c..40ca96ec3 100644 --- a/javaPoCA/src/main/java/nl/umcg/bondermj/pcoa/PcoaParamaters.java +++ b/javaPoCA/src/main/java/nl/umcg/bondermj/pcoa/PcoaParamaters.java @@ -12,7 +12,8 @@ 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; /** * @@ -49,7 +50,7 @@ public enum PackageToUse { static { - LOGGER = Logger.getLogger(PcoaParamaters.class); + LOGGER = LogManager.getLogger(PcoaParamaters.class); OPTIONS = new Options();