removed log4j dependencies and added slf4j bridges

sirius-ms · Dec 16, 2021 · a3ad947 · a3ad947
1 parent 7f30f13
commit a3ad947
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Showing 4 changed files with 16 additions and 11 deletions.
diff --git a/build.gradle b/build.gradle
@@ -132,9 +132,12 @@ allprojects {
 
         annotationProcessor "de.unijena.bioinf.ms:processor:$siriusVersion"
         compile 'net.sf.trove4j:core:3.1.0'
-        //switched from 'net.sf.trove4j:trove4j:3.0.3' which seems to be buggy and no longer supported
+
         compile "org.jetbrains:annotations:$jetbrains_version"
-        compile group: 'org.slf4j', name: 'slf4j-api', version: "$slf4j_version"
+
+        compile "org.slf4j:log4j-over-slf4j:$slf4j_version"
+        compile "org.slf4j:jcl-over-slf4j:$slf4j_version"
+        compile "org.slf4j:slf4j-api:$slf4j_version"
 
         testCompile group: 'junit', name: 'junit', version: '4.12'
 
@@ -143,6 +146,15 @@ allprojects {
 //        compile "cplex:cplex:12.7.1"
     }
 
+    configurations {
+        //replaced by log4j-over-slf4j
+        runtime.exclude group: "log4j", module: "log4j"
+        compile.exclude group: "log4j", module: "log4j"
+        //replaced by jcl-over-slf4j
+        runtime.exclude group: "commons-logging", module: "commons-logging"
+        compile.exclude group: "commons-logging", module: "commons-logging"
+    }
+
     //there are some outdated incompatible trove dependencies in some libs.
     // this is to exclude them and enforce the one we need.
     configurations {

diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/core/ApplicationCore.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/core/ApplicationCore.java
@@ -29,7 +29,6 @@
 import de.unijena.bioinf.webapi.WebAPI;
 import org.apache.commons.configuration2.PropertiesConfiguration;
 import org.apache.commons.configuration2.ex.ConfigurationException;
-import org.apache.log4j.Level;
 import org.jbibtex.BibTeXDatabase;
 import org.jbibtex.BibTeXParser;
 import org.jetbrains.annotations.NotNull;
@@ -81,13 +80,6 @@ public static void measureTime(String message) {
             t1 = System.currentTimeMillis();
         measureTime("Start AppCore");
         try {
-//            System.setProperty("de.unijena.bioinf.jjobs.DEBUG", "true");
-
-//            System.out.println("LD ==> " + System.getProperty("java.library.path"));
-            System.setProperty("org.apache.commons.logging.Log", "org.apache.commons.logging.impl.NoOpLog");
-            org.apache.log4j.Logger.getLogger("net.sf.jnati").setLevel(Level.WARN);
-
-
             System.setProperty("de.unijena.bioinf.ms.propertyLocations", "sirius_frontend.build.properties");
 
             final String version = PropertyManager.getProperty("de.unijena.bioinf.siriusFrontend.version");

diff --git a/sirius_cli/src/main/resources/logging.properties b/sirius_cli/src/main/resources/logging.properties
@@ -30,6 +30,7 @@ java.awt.level=WARNING
 sun.awt.level=WARNING
 javax.swing.level=WARNING
 org.reflections8.level=SEVERE
+net.sf.jnati.level=WARNING
 # Handlers
 # -----------------------------------------
 # --- ConsoleHandler ---

diff --git a/sirius_cli/src/main/resources/sirius_frontend.build.properties b/sirius_cli/src/main/resources/sirius_frontend.build.properties
@@ -1,5 +1,5 @@
 #here you can provide properties that may be needed during build- AND during runtime and should not be editable by the user at runtime
-de.unijena.bioinf.siriusFrontend.version=4.9.11-SNAPSHOT
+de.unijena.bioinf.siriusFrontend.version=4.9.12-SNAPSHOT
 
 de.unijena.bioinf.sirius.version=4.6.1
 de.unijena.bioinf.fingerid.version=1.6.0