From 3564cbb9084e4164b2e4916b8660bc5ca0d5dcf1 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 10 Feb 2024 20:01:38 -0500 Subject: [PATCH] Migrated logging from JCL to SLF4J; updated dependencies. --- biopax-validator-client/pom.xml | 21 +++++++- .../validator/BiopaxValidatorClient.java | 6 +-- .../{logback.xml => logback-test.xml} | 2 +- biopax-validator-web/pom.xml | 13 ++--- .../web/controller/ValidatorController.java | 6 +-- .../org/biopax/validator/BiopaxValidator.java | 48 +++++++++---------- .../biopax/validator/ExceptionsAspect.java | 6 +-- .../org/biopax/validator/utils/CoreUtils.java | 6 +-- .../biopax/validator/utils/OntologyUtils.java | 6 +-- distr/pom.xml | 19 ++++++++ .../main/java/org/biopax/validator/Main.java | 6 +-- distr/src/main/resources/logback.xml | 3 -- obo-fetcher/pom.xml | 8 ++++ .../ols/impl/BaseOBO2AbstractLoader.java | 6 +-- .../org/biopax/ols/impl/OBO2FormatParser.java | 6 +-- .../ontology_manager/impl/OboLoader.java | 8 ++-- .../impl/OntologyAccessImpl.java | 6 +-- .../impl/OntologyManagerImpl.java | 6 +-- .../src/test/resources/logback-test.xml | 2 +- pom.xml | 27 ++++++----- .../biopax/validator/api/AbstractAspect.java | 6 +-- .../org/biopax/validator/api/BaseRule.java | 8 ++-- .../validator/api/beans/Validation.java | 6 +-- 23 files changed, 134 insertions(+), 97 deletions(-) rename biopax-validator-client/src/test/resources/{logback.xml => logback-test.xml} (95%) diff --git a/biopax-validator-client/pom.xml b/biopax-validator-client/pom.xml index 143e1c96..bbaa01e4 100644 --- a/biopax-validator-client/pom.xml +++ b/biopax-validator-client/pom.xml @@ -20,6 +20,12 @@ org.apache.httpcomponents fluent-hc 4.5.14 + + + commons-logging + commons-logging + + org.apache.httpcomponents @@ -29,14 +35,25 @@ jakarta.xml.bind jakarta.xml.bind-api - 4.0.0 com.sun.xml.bind jaxb-impl - 4.0.3 runtime + + + org.slf4j + jcl-over-slf4j + runtime + true + + + ch.qos.logback + logback-classic + runtime + true + diff --git a/biopax-validator-client/src/main/java/org/biopax/validator/BiopaxValidatorClient.java b/biopax-validator-client/src/main/java/org/biopax/validator/BiopaxValidatorClient.java index 88ec0d8e..7be67ae0 100644 --- a/biopax-validator-client/src/main/java/org/biopax/validator/BiopaxValidatorClient.java +++ b/biopax-validator-client/src/main/java/org/biopax/validator/BiopaxValidatorClient.java @@ -8,8 +8,6 @@ import javax.xml.transform.Source; import javax.xml.transform.stream.StreamSource; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.http.Header; import org.apache.http.HttpEntity; import org.apache.http.client.fluent.Executor; @@ -18,6 +16,8 @@ import org.apache.http.entity.mime.MultipartEntityBuilder; import org.biopax.validator.jaxb.Behavior; import org.biopax.validator.jaxb.ValidatorResponse; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; /** * Simple (example) BioPAX Validator client @@ -27,7 +27,7 @@ * */ public class BiopaxValidatorClient { - private static final Log log = LogFactory.getLog(BiopaxValidatorClient.class); + private static final Logger log = LoggerFactory.getLogger(BiopaxValidatorClient.class); /** * Default BioPAX Validator's URL diff --git a/biopax-validator-client/src/test/resources/logback.xml b/biopax-validator-client/src/test/resources/logback-test.xml similarity index 95% rename from biopax-validator-client/src/test/resources/logback.xml rename to biopax-validator-client/src/test/resources/logback-test.xml index 6888824b..81c34ca6 100644 --- a/biopax-validator-client/src/test/resources/logback.xml +++ b/biopax-validator-client/src/test/resources/logback-test.xml @@ -9,7 +9,7 @@ true - + diff --git a/biopax-validator-web/pom.xml b/biopax-validator-web/pom.xml index 0d46d8a3..e9b22224 100644 --- a/biopax-validator-web/pom.xml +++ b/biopax-validator-web/pom.xml @@ -166,6 +166,7 @@ + org.apache.maven.plugins maven-dependency-plugin 3.6.0 @@ -323,19 +324,15 @@ slf4j-api + org.slf4j - jcl-over-slf4j - runtime - - - org.slf4j - jul-to-slf4j + log4j-over-slf4j runtime - + org.slf4j - log4j-over-slf4j + jcl-over-slf4j runtime diff --git a/biopax-validator-web/src/main/java/org/biopax/validator/web/controller/ValidatorController.java b/biopax-validator-web/src/main/java/org/biopax/validator/web/controller/ValidatorController.java index ce1a82ed..e798c05c 100644 --- a/biopax-validator-web/src/main/java/org/biopax/validator/web/controller/ValidatorController.java +++ b/biopax-validator-web/src/main/java/org/biopax/validator/web/controller/ValidatorController.java @@ -8,8 +8,8 @@ import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.paxtools.normalizer.Normalizer; import org.biopax.validator.api.beans.Behavior; import org.biopax.validator.api.beans.Validation; @@ -34,7 +34,7 @@ public class ValidatorController { private ValidatorAdapter service; - private final static Log log = LogFactory.getLog(ValidatorController.class); + private final static Logger log = LoggerFactory.getLogger(ValidatorController.class); private final static String NEWLINE = System.getProperty ( "line.separator" ); @Autowired diff --git a/biopax-validator/src/main/java/org/biopax/validator/BiopaxValidator.java b/biopax-validator/src/main/java/org/biopax/validator/BiopaxValidator.java index 37e452d1..cb70f7e0 100644 --- a/biopax-validator/src/main/java/org/biopax/validator/BiopaxValidator.java +++ b/biopax-validator/src/main/java/org/biopax/validator/BiopaxValidator.java @@ -7,8 +7,8 @@ import java.util.concurrent.Executors; import java.util.concurrent.TimeUnit; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.paxtools.controller.ModelUtils; import org.biopax.paxtools.converter.LevelUpgrader; import org.biopax.paxtools.io.SimpleIOHandler; @@ -40,7 +40,7 @@ * @author rodche */ public class BiopaxValidator implements Validator { - private static final Log log = LogFactory.getLog(BiopaxValidator.class); + private static final Logger log = LoggerFactory.getLogger(BiopaxValidator.class); @Autowired private Set> rules; @@ -191,7 +191,7 @@ public void run() { } catch (Throwable t) { //if we're here, there is probably a bug in the rule or validator! String id = validation.identify(obj); - log.fatal(rule + ".check(" + id + log.error(rule + ".check(" + id + ") threw the exception: " + t.toString(), t); // anyway, report it almost normally (for a user to see this in the results too) validation.addError(utils.createError(id, "exception", @@ -204,27 +204,25 @@ public void run() { private void execute(ExecutorService exec, final Set> rules, final Validation validation, final Object obj) { - exec.execute(new Runnable() { - @SuppressWarnings("unchecked") //obj can be either Model or a BPE - public void run() { - for(Rule rule : rules) { - Behavior behavior = utils.getRuleBehavior(rule.getClass().getName(), - validation.getProfile()); - if (behavior == Behavior.IGNORE) - continue; // skip disabled rule - - try { - if (rule.canCheck(obj)) - rule.check(validation, obj); - } catch (Throwable t) { - //if we're here, there is probably a bug in the rule or validator! - String id = validation.identify(obj); - log.fatal(rule + ".check(" + id - + ") threw the exception: " + t.toString(), t); - // anyway, report it almost normally (for a user to see this in the results too) - validation.addError(utils.createError(id, "exception", - rule.getClass().getName(), null, false, t)); - } + //obj can be either Model or a BPE + exec.execute(() -> { + for(Rule rule : rules) { + Behavior behavior = utils.getRuleBehavior(rule.getClass().getName(), +validation.getProfile()); + if (behavior == Behavior.IGNORE) + continue; // skip disabled rule + + try { + if (rule.canCheck(obj)) + rule.check(validation, obj); + } catch (Throwable t) { + //if we're here, there is probably a bug in the rule or validator! + String id = validation.identify(obj); + log.error(rule + ".check(" + id + + ") threw the exception: " + t.toString(), t); + // anyway, report it almost normally (for a user to see this in the results too) + validation.addError(utils.createError(id, "exception", + rule.getClass().getName(), null, false, t)); } } }); diff --git a/biopax-validator/src/main/java/org/biopax/validator/ExceptionsAspect.java b/biopax-validator/src/main/java/org/biopax/validator/ExceptionsAspect.java index cc859b6e..6525519c 100644 --- a/biopax-validator/src/main/java/org/biopax/validator/ExceptionsAspect.java +++ b/biopax-validator/src/main/java/org/biopax/validator/ExceptionsAspect.java @@ -3,8 +3,8 @@ import java.lang.reflect.Method; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.aspectj.lang.JoinPoint; import org.aspectj.lang.ProceedingJoinPoint; import org.aspectj.lang.annotation.*; @@ -31,7 +31,7 @@ @Aspect public class ExceptionsAspect extends AbstractAspect { - private static final Log log = LogFactory.getLog(ExceptionsAspect.class); + private static final Logger log = LoggerFactory.getLogger(ExceptionsAspect.class); @Autowired @Override diff --git a/biopax-validator/src/main/java/org/biopax/validator/utils/CoreUtils.java b/biopax-validator/src/main/java/org/biopax/validator/utils/CoreUtils.java index c38060d7..8f146bb6 100644 --- a/biopax-validator/src/main/java/org/biopax/validator/utils/CoreUtils.java +++ b/biopax-validator/src/main/java/org/biopax/validator/utils/CoreUtils.java @@ -3,8 +3,8 @@ import org.apache.commons.text.StringEscapeUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.validator.api.ValidatorUtils; import org.biopax.validator.api.beans.*; import org.springframework.beans.factory.annotation.Configurable; @@ -24,7 +24,7 @@ */ @Configurable public class CoreUtils implements ValidatorUtils { - private static final Log logger = LogFactory.getLog(CoreUtils.class); + private static final Logger logger = LoggerFactory.getLogger(CoreUtils.class); public static final int DEFAULT_MAX_ERRORS = 10000; private Locale locale; diff --git a/biopax-validator/src/main/java/org/biopax/validator/utils/OntologyUtils.java b/biopax-validator/src/main/java/org/biopax/validator/utils/OntologyUtils.java index aa777c44..6ab05262 100644 --- a/biopax-validator/src/main/java/org/biopax/validator/utils/OntologyUtils.java +++ b/biopax-validator/src/main/java/org/biopax/validator/utils/OntologyUtils.java @@ -5,8 +5,8 @@ import org.apache.commons.collections15.collection.CompositeCollection; import org.apache.commons.lang3.StringUtils; import org.apache.commons.text.StringEscapeUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.paxtools.model.BioPAXFactory; import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.level3.ControlledVocabulary; @@ -36,7 +36,7 @@ */ public class OntologyUtils implements CvUtils, CvFactory, XrefUtils { - private final static Log log = LogFactory.getLog(OntologyUtils.class); + private final static Logger log = LoggerFactory.getLogger(OntologyUtils.class); //see the post-construct init() method, where the following fields get initialized private OntologyManager ontologyManager; diff --git a/distr/pom.xml b/distr/pom.xml index 4875a727..dbeca6ce 100644 --- a/distr/pom.xml +++ b/distr/pom.xml @@ -78,6 +78,25 @@ war runtime + + org.slf4j + log4j-over-slf4j + runtime + true + + + + org.slf4j + jcl-over-slf4j + runtime + true + + + ch.qos.logback + logback-classic + runtime + true + diff --git a/distr/src/main/java/org/biopax/validator/Main.java b/distr/src/main/java/org/biopax/validator/Main.java index 14bd0e38..565bd76b 100644 --- a/distr/src/main/java/org/biopax/validator/Main.java +++ b/distr/src/main/java/org/biopax/validator/Main.java @@ -1,8 +1,8 @@ package org.biopax.validator; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.paxtools.io.SimpleIOHandler; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.normalizer.Normalizer; @@ -31,7 +31,7 @@ * @author rodche */ public class Main { - static final Log log = LogFactory.getLog(Main.class); + static final Logger log = LoggerFactory.getLogger(Main.class); static ApplicationContext ctx; static boolean autofix = false; static int maxErrors = 0; diff --git a/distr/src/main/resources/logback.xml b/distr/src/main/resources/logback.xml index 5dfe1e0c..5e9450ed 100644 --- a/distr/src/main/resources/logback.xml +++ b/distr/src/main/resources/logback.xml @@ -9,9 +9,6 @@ true - - - diff --git a/obo-fetcher/pom.xml b/obo-fetcher/pom.xml index 6e123b44..4c6faaf6 100644 --- a/obo-fetcher/pom.xml +++ b/obo-fetcher/pom.xml @@ -34,6 +34,14 @@ jms javax.jms + + log4j + log4j + + + commons-logging + commons-logging + diff --git a/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java b/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java index c129920f..e0c560a8 100644 --- a/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java +++ b/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java @@ -1,7 +1,7 @@ package org.biopax.ols.impl; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.ols.Annotation; import org.biopax.ols.Constants; import org.biopax.ols.DbXref; @@ -27,7 +27,7 @@ * @author Richard Cote */ public abstract class BaseOBO2AbstractLoader implements Loader { - protected static Log logger = LogFactory.getLog(BaseOBO2AbstractLoader.class); + protected static Logger logger = LoggerFactory.getLogger(BaseOBO2AbstractLoader.class); protected HashMap ontologyTerms = new HashMap<>(5000); protected String ONTOLOGY_DEFINITION; protected String FULL_NAME; diff --git a/obo-fetcher/src/main/java/org/biopax/ols/impl/OBO2FormatParser.java b/obo-fetcher/src/main/java/org/biopax/ols/impl/OBO2FormatParser.java index dbca172e..70fa785f 100644 --- a/obo-fetcher/src/main/java/org/biopax/ols/impl/OBO2FormatParser.java +++ b/obo-fetcher/src/main/java/org/biopax/ols/impl/OBO2FormatParser.java @@ -1,7 +1,7 @@ package org.biopax.ols.impl; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.ols.Parser; import org.obo.dataadapter.OBOAdapter; import org.obo.dataadapter.OBOFileAdapter; @@ -20,7 +20,7 @@ * @version $Id: AbstractParser.java,v 1.9 2008/04/16 13:49:44 rglcote Exp $ */ public class OBO2FormatParser implements Parser { - private static Log logger = LogFactory.getLog(OBO2FormatParser.class); + private static Logger logger = LoggerFactory.getLogger(OBO2FormatParser.class); private OBOSession session; diff --git a/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OboLoader.java b/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OboLoader.java index e7d19df6..581eb989 100644 --- a/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OboLoader.java +++ b/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OboLoader.java @@ -1,7 +1,7 @@ package org.biopax.psidev.ontology_manager.impl; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.ols.TermRelationship; import org.biopax.ols.TermSynonym; import org.biopax.ols.impl.BaseOBO2AbstractLoader; @@ -25,7 +25,7 @@ * @since 
30-Sep-2005
*/ public class OboLoader extends BaseOBO2AbstractLoader { - public static final Log log = LogFactory.getLog( OboLoader.class ); + public static final Logger log = LoggerFactory.getLogger( OboLoader.class ); public OboLoader( ) { } @@ -50,7 +50,7 @@ public OntologyAccess parseOboFile( File file, String ontologyID) { setParser(new OBO2FormatParser(file.getAbsolutePath())); process(); } catch ( Exception e ) { - log.fatal("Parse failed", e); + log.error("Parse failed", e); } return buildOntology(ontologyID); } diff --git a/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyAccessImpl.java b/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyAccessImpl.java index 318d719c..944a4b6d 100644 --- a/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyAccessImpl.java +++ b/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyAccessImpl.java @@ -1,7 +1,7 @@ package org.biopax.psidev.ontology_manager.impl; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.psidev.ontology_manager.OntologyAccess; import org.biopax.psidev.ontology_manager.OntologyTermI; @@ -20,7 +20,7 @@ public class OntologyAccessImpl implements OntologyAccess, Serializable { private static final long serialVersionUID = 1L; - public static final Log log = LogFactory.getLog( OntologyAccessImpl.class ); + public static final Logger log = LoggerFactory.getLogger( OntologyAccessImpl.class ); private String name; diff --git a/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyManagerImpl.java b/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyManagerImpl.java index b72c1b55..acf937ff 100644 --- a/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyManagerImpl.java +++ b/obo-fetcher/src/main/java/org/biopax/psidev/ontology_manager/impl/OntologyManagerImpl.java @@ -1,7 +1,7 @@ package org.biopax.psidev.ontology_manager.impl; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.psidev.ontology_manager.OntologyAccess; import org.biopax.psidev.ontology_manager.OntologyManager; import org.biopax.psidev.ontology_manager.OntologyTermI; @@ -28,7 +28,7 @@ */ public class OntologyManagerImpl implements OntologyManager { - private static final Log log = LogFactory.getLog(OntologyManagerImpl.class); + private static final Logger log = LoggerFactory.getLogger(OntologyManagerImpl.class); private static final String TMPDIR = System.getProperty("java.io.tmpdir"); /** diff --git a/obo-fetcher/src/test/resources/logback-test.xml b/obo-fetcher/src/test/resources/logback-test.xml index 52c4d804..a2f51959 100644 --- a/obo-fetcher/src/test/resources/logback-test.xml +++ b/obo-fetcher/src/test/resources/logback-test.xml @@ -4,7 +4,7 @@ true - + %d %-5level [%thread] %logger{25} - %msg%n diff --git a/pom.xml b/pom.xml index 497029ba..4e089df9 100644 --- a/pom.xml +++ b/pom.xml @@ -67,6 +67,7 @@ org.sonatype.plugins nexus-staging-maven-plugin + 1.6.13 true ossrh @@ -100,6 +101,7 @@ maven-gpg-plugin org.apache.maven.plugins + 3.1.0 sign-artifacts @@ -118,7 +120,7 @@ scm:git:git://github.com/BioPAX/validator.git scm:git:git@github.com:BioPAX/validator.git - https://github.com/BioPAX/validator + https://github.com/BioPAX/validator/tree/master HEAD @@ -403,7 +405,7 @@ ch.qos.logback logback-classic - 1.4.12 + 1.4.14 org.springframework @@ -534,13 +536,13 @@ org.junit.jupiter junit-jupiter-api - 5.9.3 + 5.10.2 test org.junit.jupiter junit-jupiter-params - 5.9.3 + 5.10.2 test @@ -564,28 +566,27 @@ junit-jupiter-params - org.slf4j - log4j-over-slf4j - runtime - true + slf4j-api + org.slf4j - jcl-over-slf4j - runtime + log4j-over-slf4j + test true + org.slf4j - jul-to-slf4j - runtime + jcl-over-slf4j + test true ch.qos.logback logback-classic - runtime + test true diff --git a/validator-core/src/main/java/org/biopax/validator/api/AbstractAspect.java b/validator-core/src/main/java/org/biopax/validator/api/AbstractAspect.java index d0041373..ca37327a 100644 --- a/validator-core/src/main/java/org/biopax/validator/api/AbstractAspect.java +++ b/validator-core/src/main/java/org/biopax/validator/api/AbstractAspect.java @@ -6,8 +6,8 @@ import javax.xml.stream.XMLStreamException; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; /** * Basic class for the framework classes @@ -17,7 +17,7 @@ * @author rodche */ public abstract class AbstractAspect { - private static final Log log = LogFactory.getLog(AbstractAspect.class); + private static final Logger log = LoggerFactory.getLogger(AbstractAspect.class); /** * BioPAX Validator instance diff --git a/validator-core/src/main/java/org/biopax/validator/api/BaseRule.java b/validator-core/src/main/java/org/biopax/validator/api/BaseRule.java index 6c697b63..6772e1bc 100644 --- a/validator-core/src/main/java/org/biopax/validator/api/BaseRule.java +++ b/validator-core/src/main/java/org/biopax/validator/api/BaseRule.java @@ -5,8 +5,8 @@ import org.biopax.validator.api.beans.ErrorType; import org.biopax.validator.api.beans.Validation; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; /** * A validation rule. @@ -18,12 +18,12 @@ */ public abstract class BaseRule implements Rule { - protected Log logger; + protected Logger logger; protected ValidatorUtils utils; public BaseRule() { - logger = LogFactory.getLog(this.getClass()); + logger = LoggerFactory.getLogger(this.getClass()); } /** diff --git a/validator-core/src/main/java/org/biopax/validator/api/beans/Validation.java b/validator-core/src/main/java/org/biopax/validator/api/beans/Validation.java index 8dbdc505..99bb41f0 100644 --- a/validator-core/src/main/java/org/biopax/validator/api/beans/Validation.java +++ b/validator-core/src/main/java/org/biopax/validator/api/beans/Validation.java @@ -8,8 +8,8 @@ import jakarta.xml.bind.annotation.*; import org.apache.commons.text.StringEscapeUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.biopax.validator.api.Identifier; import org.biopax.validator.api.Rule; @@ -18,7 +18,7 @@ @XmlAccessorType(XmlAccessType.FIELD) public class Validation implements Serializable { private static final long serialVersionUID = 1L; - private static final Log log = LogFactory.getLog(Validation.class); + private static final Logger log = LoggerFactory.getLogger(Validation.class); @XmlTransient private Object model;