Migrated logging from JCL to SLF4J; updated dependencies.

biopax-validator-client/pom.xml

@@ -20,6 +20,12 @@
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>fluent-hc</artifactId>
 			<version>4.5.14</version>
+			<exclusions>
+				<exclusion>
+					<groupId>commons-logging</groupId>
+					<artifactId>commons-logging</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
@@ -29,14 +35,25 @@
 		<dependency>
 			<groupId>jakarta.xml.bind</groupId>
 			<artifactId>jakarta.xml.bind-api</artifactId>
-			<version>4.0.0</version>
 		</dependency>
 		<dependency>
 			<groupId>com.sun.xml.bind</groupId>
 			<artifactId>jaxb-impl</artifactId>
-			<version>4.0.3</version>
 			<scope>runtime</scope>
 		</dependency>
+		<dependency>
+			<!--  httpcomponents use JCL -->
+			<groupId>org.slf4j</groupId>
+			<artifactId>jcl-over-slf4j</artifactId>
+			<scope>runtime</scope>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>runtime</scope>
+			<optional>true</optional>
+		</dependency>
 	</dependencies>
 
 	<build>

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

biopax-validator-client/src/test/resources/logback.xml → biopax-validator-client/src/test/resources/logback-test.xml

@@ -9,7 +9,7 @@
             <outputPatternAsHeader>true</outputPatternAsHeader>
         </encoder>
     </appender>
-    <root level="info">
+    <root level="debug">
         <appender-ref ref="console"/>
     </root>
 </configuration>

biopax-validator-web/pom.xml

@@ -166,6 +166,7 @@
         </configuration>
       </plugin>
       <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-dependency-plugin</artifactId>
         <version>3.6.0</version>
         <executions>
@@ -323,19 +324,15 @@
       <artifactId>slf4j-api</artifactId>
     </dependency>
     <dependency>
+      <!-- due to org.obo in biopax-validator uses log4j impl -->
       <groupId>org.slf4j</groupId>
-      <artifactId>jcl-over-slf4j</artifactId>
-      <scope>runtime</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.slf4j</groupId>
-      <artifactId>jul-to-slf4j</artifactId>
+      <artifactId>log4j-over-slf4j</artifactId>
       <scope>runtime</scope>
     </dependency>
     <dependency>
-      <!-- due to org.obo in biopax-validator uses log4j impl -->
+      <!--  obo and httpcomponents use JCL -->
       <groupId>org.slf4j</groupId>
-      <artifactId>log4j-over-slf4j</artifactId>
+      <artifactId>jcl-over-slf4j</artifactId>
       <scope>runtime</scope>
     </dependency>
     <dependency>

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

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<Rule<?>> 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<Rule<?>> 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));
 				}
 			}
 		});

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

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;

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;

distr/pom.xml

@@ -78,6 +78,25 @@
 			<type>war</type>
 			<scope>runtime</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>log4j-over-slf4j</artifactId>
+			<scope>runtime</scope>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<!--  obo and httpcomponents use JCL -->
+			<groupId>org.slf4j</groupId>
+			<artifactId>jcl-over-slf4j</artifactId>
+			<scope>runtime</scope>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>runtime</scope>
+			<optional>true</optional>
+		</dependency>
 	</dependencies>
 
 </project>

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;

distr/src/main/resources/logback.xml

@@ -9,9 +9,6 @@
             <outputPatternAsHeader>true</outputPatternAsHeader>
         </encoder>
     </appender>
-<!--    <logger name="org.springframework" level="info"/>-->
-<!--    <logger name="AspectJ Weaver" level="info"/>-->
-<!--    <logger name="org.biopax.ols" level="error"/>-->
     <logger name="org.biopax.psidev" level="error"/>
     <root level="info">
         <appender-ref ref="console"/>

obo-fetcher/pom.xml

@@ -34,6 +34,14 @@
 					<artifactId>jms</artifactId>
 					<groupId>javax.jms</groupId>
 				</exclusion>
+				<exclusion>
+					<groupId>log4j</groupId>
+					<artifactId>log4j</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>commons-logging</groupId>
+					<artifactId>commons-logging</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>

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<String, Term> ontologyTerms = new HashMap<>(5000);
     protected String ONTOLOGY_DEFINITION;
     protected String FULL_NAME;

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;