Updated dependencies

opencb · Jan 3, 2024 · df4bcba · df4bcba
1 parent 6fca9b1
commit df4bcba
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Showing 4 changed files with 21 additions and 15 deletions.
diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
@@ -88,11 +88,11 @@
             <groupId>org.apache.avro</groupId>
             <artifactId>avro</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
             <scope>test</scope>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
@@ -74,10 +74,10 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -90,10 +90,10 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -38,19 +38,19 @@
 
     <properties>
         <!-- All dependency versions must be defined here -->
-        <java-common-libs.version>4.13.0-SNAPSHOT</java-common-libs.version>
-        <jackson.version>2.11.4</jackson.version>
+        <java-common-libs.version>4.12.0-SNAPSHOT</java-common-libs.version>
+        <jackson.version>2.14.3</jackson.version>
         <collections.version>4.4</collections.version>
         <avro.version>1.7.7</avro.version>
         <protobuf.version>3.11.4</protobuf.version>
         <grpc.version>1.28.1</grpc.version>
-        <htsjdk.version>2.23.0</htsjdk.version>
-        <slf4j.version>1.7.32</slf4j.version>
+        <htsjdk.version>3.0.5</htsjdk.version>
+        <slf4j.version>1.7.36</slf4j.version>
         <jsr.version>3.0.2</jsr.version>
-        <commons-lang.version>3.12.0</commons-lang.version>
-        <jackson-mapper.version>1.9.13</jackson-mapper.version>
+        <commons-lang.version>3.14.0</commons-lang.version>
+       <!-- <jackson-mapper.version>2.9.9</jackson-mapper.version>-->
         <guava.version>19.0</guava.version>
-        <commons-io.version>2.4</commons-io.version>
+        <commons-io.version>2.12.0</commons-io.version>
         <biojava-core.version>5.0.0</biojava-core.version>
         <ga4gh.version>0.6.0a5</ga4gh.version>
         <SnpEff.version>4.3.1</SnpEff.version>
@@ -229,11 +229,11 @@
                 <artifactId>commons-lang3</artifactId>
                 <version>${commons-lang.version}</version>
             </dependency>
-            <dependency>
+           <!-- <dependency>
                 <groupId>org.codehaus.jackson</groupId>
                 <artifactId>jackson-mapper-asl</artifactId>
                 <version>${jackson-mapper.version}</version>
-            </dependency>
+            </dependency>-->
             <dependency>
                 <groupId>org.apache.avro</groupId>
                 <artifactId>avro</artifactId>
@@ -408,6 +408,12 @@
                             <ignoredUnusedDeclaredDependencies>
                                 <ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
                             </ignoredUnusedDeclaredDependencies>
+                            <ignoredNonTestScopedDependencies>
+                                <ignoredNonTestScopedDependency>*</ignoredNonTestScopedDependency>
+                            </ignoredNonTestScopedDependencies>
+                            <ignoredUsedUndeclaredDependencies>
+                                <usedUndeclaredDependency>org.codehaus.jackson:jackson-mapper-asl*</usedUndeclaredDependency>
+                            </ignoredUsedUndeclaredDependencies>
                         </configuration>
                     </execution>
                 </executions>