Updated logging dep. and cfg., Spring; removed println, etc.

BioPAX · Feb 4, 2024 · ec8a5d6 · ec8a5d6
1 parent 8b91a48
commit ec8a5d6
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Showing 13 changed files with 60 additions and 62 deletions.
diff --git a/biopax-validator-client/src/main/resources/logback.xml b/biopax-validator-client/src/main/resources/logback.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+  <contextListener class="ch.qos.logback.classic.jul.LevelChangePropagator">
+    <resetJUL>true</resetJUL>
+  </contextListener>
+  <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
+    <encoder>
+      <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>
+      <outputPatternAsHeader>true</outputPatternAsHeader>
+    </encoder>
+  </appender>
+  <root level="info">
+    <appender-ref ref="console"/>
+  </root>
+</configuration>
diff --git a/biopax-validator-client/src/test/java/BiopaxValidatorClientTest.java b/biopax-validator-client/src/test/java/BiopaxValidatorClientTest.java
@@ -39,7 +39,7 @@ public void testClientHtml() throws IOException {
 		);
 //		System.out.println(baos);
     }
-	
+
 	@Test
 	public void testClientXml() throws IOException, JAXBException {
 		BiopaxValidatorClient client = new BiopaxValidatorClient();
@@ -52,13 +52,13 @@ public void testClientXml() throws IOException, JAXBException {
 		ValidatorResponse resp = client.unmarshal(baos.toString());
 
 		Assertions.assertAll(
-			() -> Assertions.assertTrue(baos.size()>0),
-			() -> Assertions.assertNotNull(resp),
-			() -> Assertions.assertEquals(2, resp.getValidation().size())
+				() -> Assertions.assertTrue(baos.size()>0),
+				() -> Assertions.assertNotNull(resp),
+				() -> Assertions.assertEquals(2, resp.getValidation().size())
 		);
-		
-		System.out.println(resp.getValidation().get(0).getSummary()
-				+ "; cases: " + resp.getValidation().get(0).getTotalProblemsFound());
-    }
+
+//		System.out.println(resp.getValidation().get(0).getSummary()
+//				+ "; cases: " + resp.getValidation().get(0).getTotalProblemsFound());
+	}
 
 }
diff --git a/biopax-validator-web/src/main/resources/logback.xml b/biopax-validator-web/src/main/resources/logback.xml
@@ -3,6 +3,8 @@
   <contextListener class="ch.qos.logback.classic.jul.LevelChangePropagator">
     <resetJUL>true</resetJUL>
   </contextListener>
+  <!-- JMX and additional logback init info -->
+  <jmxConfigurator/>
   <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
     <encoder>
       <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>

diff --git a/biopax-validator/src/test/java/LoadTimeWeavingIT.java b/biopax-validator/src/test/java/LoadTimeWeavingIT.java
@@ -73,8 +73,8 @@ public void unknownProperty() { // important!
 		);
 		biopaxValidator.validate(validation);
 		assertEquals(5,validation.getError().size());
-		validation.getError().stream().forEach(e -> System.out.println(e + ": " + e.getErrorCase().size() + " case(s); "
-				+ e.getErrorCase().stream().map(ErrorCaseType::toString).collect(Collectors.joining())));
+//		validation.getError().stream().forEach(e -> System.out.println(e + ": " + e.getErrorCase().size() + " case(s); "
+//				+ e.getErrorCase().stream().map(ErrorCaseType::toString).collect(Collectors.joining())));
 	}
 
 	@Test

diff --git a/distr/pom.xml b/distr/pom.xml
@@ -78,22 +78,6 @@
 			<type>war</type>
 			<scope>runtime</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>jcl-over-slf4j</artifactId>
-			<scope>runtime</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>log4j-over-slf4j</artifactId>
-			<scope>runtime</scope>
-		</dependency>
-		<dependency>
-			<groupId>ch.qos.logback</groupId>
-			<artifactId>logback-classic</artifactId>
-			<version>1.4.12</version>
-			<scope>runtime</scope>
-		</dependency>
 	</dependencies>
 
 </project>
diff --git a/distr/src/main/etc/bin/validate.sh b/distr/src/main/etc/bin/validate.sh
@@ -8,7 +8,7 @@ echo Running BioPAX Validator...
 JDK_JAVA_OPTIONS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"
 VALIDATOR_OPTS="-javaagent:lib/spring-instrument-${spring-framework.version}.jar -Xmx2g -Dfile.encoding=UTF-8 -Djava.security.egd=file:/dev/./urandom"
 
-# run the validator with an alternative log4j.properties and obo.properties, e.g., from current directory -
+# run the validator with an alternative log4j.properties/logback.xml or obo.properties, e.g., from current directory -
 #$JAVA_HOME/bin/java -cp .:biopax-validator.jar $VALIDATOR_OPTS org.biopax.validator.Main "$1" "$2" "$3" "$4" "$5" "$6" "$7"
 
 # run with built-in logging and OBO properties (from the default classpath)

diff --git a/distr/src/main/etc/log4j.properties b/distr/src/main/etc/log4j.properties
diff --git a/distr/src/main/java/org/biopax/validator/Main.java b/distr/src/main/java/org/biopax/validator/Main.java
@@ -201,16 +201,12 @@ private static String outFileName(Validation result) {
 
 
   public static Collection<Resource> getResourcesToValidate(String input) throws IOException {
-    Set<Resource> setRes = new HashSet<Resource>();
+    Set<Resource> setRes = new HashSet<>();
 
     File fileOrDir = new File(input);
     if (fileOrDir.isDirectory()) {
       // validate all the OWL files in the folder
-      FilenameFilter filter = new FilenameFilter() {
-        public boolean accept(File dir, String name) {
-          return (name.endsWith(".owl"));
-        }
-      };
+      FilenameFilter filter = (dir, name) -> (name.endsWith(".owl"));
       for (String s : fileOrDir.list(filter)) {
         String uri = "file:" + fileOrDir.getCanonicalPath() + File.separator + s;
         setRes.add(ctx.getResource(uri));

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
@@ -705,7 +705,7 @@ private DbXref createDbXref(Dbxref xref, int xrefType) {
             retval.setAccession(safeTrim(xref.getDatabaseID()));
 //            if (retval.getAccession() != null && retval.getAccession().length() > 512) {
             if (retval.getAccession() != null && retval.getAccession().length() > 256) {
-                System.out.println("retval.getAccession().length() = " + retval.getAccession().length());
+//                System.out.println("retval.getAccession().length() = " + retval.getAccession().length());
                 logger.warn("dbxref accession longer than allowed database column length: " + retval.getAccession());
                 retval.setAccession(retval.getAccession().substring(0, 256));
 //                retval.setAccession(retval.getAccession().substring(0, 512));

diff --git a/obo-fetcher/src/test/java/LocalOntologyTest.java b/obo-fetcher/src/test/java/LocalOntologyTest.java
@@ -225,12 +225,6 @@ public void getAllParents_unknown_accession() {
 		Assertions.assertEquals(0, parents.size());
 	}
 
-	private void printTerms(Collection<OntologyTermI> terms) {
-		for (OntologyTermI term : terms) {
-			System.out.println(term);
-		}
-	}
-
 	@Test
 	public final void testSearchTermByName() {
 		Set<OntologyTermI> term = manager.searchTermByName("O-phospho-L-serine");

diff --git a/obo-fetcher/src/test/resources/log4j.properties b/obo-fetcher/src/test/resources/log4j.properties
diff --git a/obo-fetcher/src/test/resources/logback.xml → ...tcher/src/test/resources/logback-test.xml b/obo-fetcher/src/test/resources/logback.xml → ...tcher/src/test/resources/logback-test.xml
@@ -3,13 +3,15 @@
     <contextListener class="ch.qos.logback.classic.jul.LevelChangePropagator">
         <resetJUL>true</resetJUL>
     </contextListener>
+    <!-- To enable JMX Management (also prints additional logback initializing info)-->
+    <jmxConfigurator/>
     <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
         <encoder>
             <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>
             <outputPatternAsHeader>true</outputPatternAsHeader>
         </encoder>
     </appender>
-    <root level="info">
+    <root level="debug">
         <appender-ref ref="console"/>
     </root>
 </configuration>
diff --git a/pom.xml b/pom.xml
@@ -175,7 +175,8 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
     <github.global.server>github</github.global.server>
-    <spring-framework.version>5.3.29</spring-framework.version>
+    <spring-framework.version>5.3.31</spring-framework.version>
+    <slf4j.version>2.0.11</slf4j.version>
     <agent>${settings.localRepository}/org/springframework/spring-instrument/${spring-framework.version}/spring-instrument-${spring-framework.version}.jar</agent>
     <paxtools.version>6.0.0-SNAPSHOT</paxtools.version>
     <license.licenseName>MIT</license.licenseName>
@@ -382,17 +383,22 @@
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>slf4j-api</artifactId>
-        <version>2.0.7</version>
+        <version>${slf4j.version}</version>
       </dependency>
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>log4j-over-slf4j</artifactId>
-        <version>2.0.7</version>
+        <version>${slf4j.version}</version>
       </dependency>
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>jcl-over-slf4j</artifactId>
-        <version>2.0.7</version>
+        <version>${slf4j.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>org.slf4j</groupId>
+        <artifactId>jul-to-slf4j</artifactId>
+        <version>${slf4j.version}</version>
       </dependency>
       <dependency>
         <groupId>ch.qos.logback</groupId>
@@ -561,12 +567,26 @@
       <!-- one of obo-fetcher's deps uses log4j directly-->
       <groupId>org.slf4j</groupId>
       <artifactId>log4j-over-slf4j</artifactId>
-      <scope>test</scope>
+      <scope>runtime</scope>
+      <optional>true</optional>
+    </dependency>
+    <dependency>
+      <groupId>org.slf4j</groupId>
+      <artifactId>jcl-over-slf4j</artifactId>
+      <scope>runtime</scope>
+      <optional>true</optional>
+    </dependency>
+    <dependency>
+      <groupId>org.slf4j</groupId>
+      <artifactId>jul-to-slf4j</artifactId>
+      <scope>runtime</scope>
+      <optional>true</optional>
     </dependency>
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
-      <scope>test</scope>
+      <scope>runtime</scope>
+      <optional>true</optional>
     </dependency>
   </dependencies>