We don't need the Log4J 1.2 API in these locations - unfortunately it…

… still comes in via CMLXOM and JENA but better for now.
cdk · Dec 22, 2021 · a207f62 · a207f62
1 parent 68b78c6
commit a207f62
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Showing 34 changed files with 8 additions and 158 deletions.
diff --git a/descriptor/fingerprint/pom.xml b/descriptor/fingerprint/pom.xml
@@ -50,11 +50,6 @@
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/descriptor/ionpot/pom.xml b/descriptor/ionpot/pom.xml
@@ -29,11 +29,6 @@
             <artifactId>jama</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>

diff --git a/descriptor/qsar/pom.xml b/descriptor/qsar/pom.xml
@@ -36,11 +36,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/descriptor/qsaratomic/pom.xml b/descriptor/qsaratomic/pom.xml
@@ -48,11 +48,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/descriptor/qsarbond/pom.xml b/descriptor/qsarbond/pom.xml
@@ -48,11 +48,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/descriptor/qsarcml/pom.xml b/descriptor/qsarcml/pom.xml
@@ -29,10 +29,6 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/descriptor/qsarionpot/pom.xml b/descriptor/qsarionpot/pom.xml
@@ -29,11 +29,6 @@
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>gov.nist.math</groupId>
             <artifactId>jama</artifactId>

diff --git a/descriptor/qsarmolecular/pom.xml b/descriptor/qsarmolecular/pom.xml
@@ -48,11 +48,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/descriptor/qsarprotein/pom.xml b/descriptor/qsarprotein/pom.xml
@@ -36,11 +36,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/display/render/pom.xml b/display/render/pom.xml
@@ -28,11 +28,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/display/renderawt/pom.xml b/display/renderawt/pom.xml
@@ -32,11 +32,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/display/renderbasic/pom.xml b/display/renderbasic/pom.xml
@@ -37,11 +37,6 @@
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/display/renderextra/pom.xml b/display/renderextra/pom.xml
@@ -28,11 +28,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/misc/diff/pom.xml b/misc/diff/pom.xml
@@ -33,11 +33,6 @@
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/misc/test-extra/pom.xml b/misc/test-extra/pom.xml
@@ -47,11 +47,6 @@
             </exclusions>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -508,17 +508,17 @@
             </dependency>
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
-                <artifactId>log4j-1.2-api</artifactId>
+                <artifactId>log4j-api</artifactId>
                 <version>2.17.0</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
-                <artifactId>log4j-api</artifactId>
+                <artifactId>log4j-core</artifactId>
                 <version>2.17.0</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
-                <artifactId>log4j-core</artifactId>
+                <artifactId>log4j-1.2-api</artifactId>
                 <version>2.17.0</version>
             </dependency>
         </dependencies>

diff --git a/storage/inchi/pom.xml b/storage/inchi/pom.xml
@@ -23,10 +23,6 @@
             <artifactId>jna-inchi-core</artifactId>
             <version>1.0.1</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/storage/io/pom.xml b/storage/io/pom.xml
@@ -49,11 +49,6 @@
             </exclusions>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/storage/ioformats/pom.xml b/storage/ioformats/pom.xml
@@ -40,11 +40,6 @@
             </exclusions>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/storage/iordf/pom.xml b/storage/iordf/pom.xml
@@ -60,6 +60,11 @@
             <artifactId>log4j-1.2-api</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java b/storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java
@@ -22,9 +22,6 @@
  */
 package org.openscience.cdk.io.rdf;
 
-import org.apache.log4j.BasicConfigurator;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -50,8 +47,6 @@ public static void setup() {
 
     @Test
     public void testWriteMolecule() throws Exception {
-        BasicConfigurator.configure();
-        Logger.getRootLogger().setLevel(Level.ERROR);
         StringWriter output = new StringWriter();
         CDKOWLWriter writer = new CDKOWLWriter(output);
 

diff --git a/storage/libiocml/pom.xml b/storage/libiocml/pom.xml
@@ -33,10 +33,6 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/storage/libiomd/pom.xml b/storage/libiomd/pom.xml
@@ -25,10 +25,6 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/storage/pdb/pom.xml b/storage/pdb/pom.xml
@@ -32,11 +32,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/storage/pdbcml/pom.xml b/storage/pdbcml/pom.xml
@@ -29,10 +29,6 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/storage/smiles/pom.xml b/storage/smiles/pom.xml
@@ -62,11 +62,6 @@
             </exclusions>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

diff --git a/tool/builder3d/pom.xml b/tool/builder3d/pom.xml
@@ -44,11 +44,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-core</artifactId>

diff --git a/tool/charges/pom.xml b/tool/charges/pom.xml
@@ -36,11 +36,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>

diff --git a/tool/forcefield/pom.xml b/tool/forcefield/pom.xml
@@ -46,11 +46,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>

diff --git a/tool/formula/pom.xml b/tool/formula/pom.xml
@@ -33,11 +33,6 @@
             <artifactId>jama</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>xom</groupId>
             <artifactId>xom</artifactId>

diff --git a/tool/pcore/pom.xml b/tool/pcore/pom.xml
@@ -36,11 +36,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-data</artifactId>

diff --git a/tool/sdg/pom.xml b/tool/sdg/pom.xml
@@ -35,11 +35,6 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>