Merge branch 'develop' into TASK-4158

opencb · Feb 6, 2024 · 1f6d639 · 1f6d639
2 parents b428f41 + b03fded
commit 1f6d639
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Showing 11 changed files with 33 additions and 29 deletions.
diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -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/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java b/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.formats.variant.annotation.io;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Test;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;

diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -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-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java b/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.models.alignment;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import org.opencb.biodata.models.core.Region;
 
 import java.io.IOException;

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.models.clinical.pedigree;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.Phenotype;
 

diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -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/...ta-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java b/...ta-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceKmers.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceKmers.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceStats.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceStats.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/pom.xml b/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>org.opencb.biodata</groupId>
     <artifactId>biodata</artifactId>
-    <version>2.13.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>Biodata</name>
@@ -38,19 +38,20 @@
 
     <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>5.0.0-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>
+        <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 +230,11 @@
                 <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 +409,9 @@
                             <ignoredUnusedDeclaredDependencies>
                                 <ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
                             </ignoredUnusedDeclaredDependencies>
+                            <ignoredNonTestScopedDependencies>
+                                <ignoredNonTestScopedDependency>*</ignoredNonTestScopedDependency>
+                            </ignoredNonTestScopedDependencies>
                         </configuration>
                     </execution>
                 </executions>