From d1443702fbb50a0e3f7718156d4a14bc49eb862d Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 16 May 2023 12:10:43 +0200
Subject: [PATCH 01/10] pom: Clean dependencies #TASK-2095

---
 .github/workflows/test-analysis.yml |   3 +-
 cellbase-app/pom.xml                | 108 +++++++++++++-
 cellbase-client/pom.xml             |  58 ++++++--
 cellbase-core/pom.xml               |  60 +++++---
 cellbase-lib/pom.xml                | 137 +++++++++++++----
 cellbase-server/pom.xml             |  77 +++++++---
 pom.xml                             | 221 ++++++++++++++++++++++++----
 7 files changed, 548 insertions(+), 116 deletions(-)

diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
index 7795e5773..aec31781b 100644
--- a/.github/workflows/test-analysis.yml
+++ b/.github/workflows/test-analysis.yml
@@ -20,7 +20,8 @@ on:
         type: string
         required: true
 env:
-  xb_version: "1.6.1"
+  xb_version: "1.7.0"
+  
 jobs:
   test:
     name: Test and push Sonar analysis
diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index 5c19ea43d..0f23b50d2 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -28,25 +28,121 @@
             <artifactId>cellbase-server</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-formats</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-lib</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.cellbase</groupId>
+            <artifactId>cellbase-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-tools</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-models</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.cellbase</groupId>
+            <artifactId>cellbase-lib</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-api</artifactId>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-mongodb</artifactId>
             <scope>test</scope>
         </dependency>
+
+        <!-- General dependencies -->
         <dependency>
-            <groupId>org.junit.platform</groupId>
-            <artifactId>junit-platform-engine</artifactId>
-            <scope>test</scope>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.jsonwebtoken</groupId>
+            <artifactId>jjwt-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-lang</groupId>
+            <artifactId>commons-lang</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.jsonwebtoken</groupId>
+            <artifactId>jjwt-impl</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.rocksdb</groupId>
+            <artifactId>rocksdbjni</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>bson</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-util-ajax</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.github.samtools</groupId>
+            <artifactId>htsjdk</artifactId>
+        </dependency>
+
+        <!-- Test dependencies -->
         <dependency>
             <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-engine</artifactId>
+            <artifactId>junit-jupiter-api</artifactId>
             <scope>test</scope>
         </dependency>
+
     </dependencies>
 
     <build>
diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 4cb59a780..467907343 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -19,17 +19,22 @@
             <artifactId>cellbase-core</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.core</groupId>
-            <artifactId>jersey-client</artifactId>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-models</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.inject</groupId>
-            <artifactId>jersey-hk2</artifactId>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-core</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.containers</groupId>
-            <artifactId>jersey-container-servlet</artifactId>
-            <scope>test</scope>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-formats</artifactId>
+        </dependency>
+
+        <!-- General dependencies -->
+        <dependency>
+            <groupId>org.glassfish.jersey.core</groupId>
+            <artifactId>jersey-client</artifactId>
         </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
@@ -42,19 +47,44 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.junit.platform</groupId>
-            <artifactId>junit-platform-engine</artifactId>
-            <scope>test</scope>
+            <groupId>com.fasterxml.jackson.dataformat</groupId>
+            <artifactId>jackson-dataformat-yaml</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-engine</artifactId>
-            <scope>test</scope>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.avro</groupId>
+            <artifactId>avro</artifactId>
+        </dependency>
+
+        <!-- Test dependencies -->
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-all</artifactId>
+            <artifactId>hamcrest-core</artifactId>
             <scope>test</scope>
         </dependency>
     </dependencies>
 </project>
+
diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
index ec34893f7..474c72c88 100644
--- a/cellbase-core/pom.xml
+++ b/cellbase-core/pom.xml
@@ -18,7 +18,24 @@
             <groupId>org.opencb.biodata</groupId>
             <artifactId>biodata-tools</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-lib</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-models</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-formats</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-core</artifactId>
+        </dependency>
 
+        <!-- General dependencies -->
         <dependency>
             <groupId>com.fasterxml.jackson.dataformat</groupId>
             <artifactId>jackson-dataformat-yaml</artifactId>
@@ -30,40 +47,49 @@
         <dependency>
             <groupId>io.jsonwebtoken</groupId>
             <artifactId>jjwt-api</artifactId>
-            <version>${jwt.version}</version>
         </dependency>
         <dependency>
             <groupId>io.jsonwebtoken</groupId>
             <artifactId>jjwt-impl</artifactId>
-            <version>${jwt.version}</version>
         </dependency>
         <dependency>
-            <groupId>io.jsonwebtoken</groupId>
-            <artifactId>jjwt-jackson</artifactId>
-            <version>${jwt.version}</version>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-slf4j-impl</artifactId>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-api</artifactId>
-            <scope>test</scope>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.junit.platform</groupId>
-            <artifactId>junit-platform-engine</artifactId>
-            <scope>test</scope>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-engine</artifactId>
-            <scope>test</scope>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-lang</groupId>
+            <artifactId>commons-lang</artifactId>
         </dependency>
+
+        <!-- Test dependencies -->
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-all</artifactId>
+            <artifactId>hamcrest-core</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
             <scope>test</scope>
         </dependency>
     </dependencies>
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index cc86b3d6d..7928d4e3c 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -18,63 +18,140 @@
             <groupId>org.opencb.cellbase</groupId>
             <artifactId>cellbase-core</artifactId>
         </dependency>
-<!--        <dependency>-->
-<!--            <groupId>org.opencb.commons</groupId>-->
-<!--            <artifactId>commons-lib</artifactId>-->
-<!--            <version>${java-common-libs.version}</version>-->
-<!--        </dependency>-->
         <dependency>
             <groupId>org.opencb.commons</groupId>
             <artifactId>commons-datastore-mongodb</artifactId>
-            <version>${java-common-libs.version}</version>
-            <exclusions>
-                <exclusion>
-                    <artifactId>slf4j-simple</artifactId>
-                    <groupId>org.slf4j</groupId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <!--<dependency>-->
-        <!--<groupId>org.opencb.bionetdb</groupId>-->
-        <!--<artifactId>bionetdb-core</artifactId>-->
-        <!--<version>${bionetdb.version}</version>-->
-        <!--</dependency>-->
+         </dependency>
         <dependency>
-            <groupId>org.eclipse.jetty</groupId>
-            <artifactId>jetty-util-ajax</artifactId>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-formats</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-lib</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-tools</artifactId>
         </dependency>
-
         <dependency>
-            <groupId>org.glassfish.jersey.core</groupId>
-            <artifactId>jersey-client</artifactId>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-models</artifactId>
         </dependency>
+
+
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>4.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-api</artifactId>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-lang</groupId>
+            <artifactId>commons-lang</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>mongodb-driver-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>mongodb-driver-sync</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.rocksdb</groupId>
+            <artifactId>rocksdbjni</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+        </dependency>
+       <dependency>
+            <groupId>commons-codec</groupId>
+            <artifactId>commons-codec</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>bson</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.xml.bind</groupId>
+            <artifactId>jakarta.xml.bind-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.poi</groupId>
+            <artifactId>poi</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.github.samtools</groupId>
+            <artifactId>htsjdk</artifactId>
+        </dependency>
+
+
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-util-ajax</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.junit.platform</groupId>
-            <artifactId>junit-platform-engine</artifactId>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-engine</artifactId>
+            <artifactId>junit-jupiter-api</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-all</artifactId>
+            <artifactId>hamcrest-core</artifactId>
             <scope>test</scope>
         </dependency>
     </dependencies>
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
index 10f0323b0..fc5910ae9 100644
--- a/cellbase-server/pom.xml
+++ b/cellbase-server/pom.xml
@@ -19,50 +19,89 @@
             <artifactId>cellbase-lib</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
-
-        <dependency>
-            <groupId>com.fasterxml.jackson.module</groupId>
-            <artifactId>jackson-module-jsonSchema</artifactId>
-        </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.containers</groupId>
-            <artifactId>jersey-container-servlet</artifactId>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-formats</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.inject</groupId>
-            <artifactId>jersey-hk2</artifactId>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-core</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.containers</groupId>
-            <artifactId>jersey-container-servlet-core</artifactId>
+            <groupId>org.opencb.cellbase</groupId>
+            <artifactId>cellbase-core</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.media</groupId>
-            <artifactId>jersey-media-multipart</artifactId>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-lib</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.glassfish.jersey.media</groupId>
-            <artifactId>jersey-media-json-jackson</artifactId>
+            <groupId>org.opencb.biodata</groupId>
+            <artifactId>biodata-models</artifactId>
         </dependency>
+
+        <!-- General dependencies -->
         <dependency>
-            <groupId>io.swagger</groupId>
-            <artifactId>swagger-jersey2-jaxrs</artifactId>
-            <version>1.6.5</version>
+            <groupId>com.fasterxml.jackson.module</groupId>
+            <artifactId>jackson-module-jsonSchema</artifactId>
         </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
             <artifactId>javax.servlet-api</artifactId>
-            <version>3.1.0</version>
             <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-server</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-util-ajax</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-webapp</artifactId>
         </dependency>
+        <dependency>
+            <groupId>io.swagger</groupId>
+            <artifactId>swagger-annotations</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>bson</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-lang</groupId>
+            <artifactId>commons-lang</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
     </dependencies>
 
     <build>
diff --git a/pom.xml b/pom.xml
index eb2297360..3742741e3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -29,13 +29,31 @@
         <jackson.version>2.11.4</jackson.version>
         <jersey.version>2.30.1</jersey.version>
         <slf4j.version>1.7.32</slf4j.version>
-        <log4j2.version>2.17.2</log4j2.version>
+        <log4j.version>2.17.2</log4j.version>
         <junit.platform.version>1.5.2</junit.platform.version>
         <junit.jupiter.version>5.5.2</junit.jupiter.version>
         <jacoco.version>0.8.8</jacoco.version>
         <jetty.version>9.4.17.v20190418</jetty.version>
         <jwt.version>0.11.5</jwt.version>
-
+        <swagger-annotations.version>1.6.5</swagger-annotations.version>
+        <javax.servlet-api.version>3.1.0</javax.servlet-api.version>
+        <poi.version>4.1.2</poi.version>
+        <mongodb.version>4.8.2</mongodb.version>
+        <junit.version>4.12</junit.version>
+        <commons-codec.version>1.13</commons-codec.version>
+        <jakarta.xml.bind-api.version>2.3.3</jakarta.xml.bind-api.version>
+        <guava.version>22.0</guava.version>
+        <avro.version>1.9.1</avro.version>
+        <hamcrest.version>1.3</hamcrest.version>
+        <htsjdk.version>2.23.0</htsjdk.version>
+        <grpc.version>1.48.0</grpc.version>
+        <commons-lang.version>2.4</commons-lang.version>
+        <commons-io.version>2.4</commons-io.version>
+        <jjwt.version>0.11.5</jjwt.version>
+        <commons-lang3.version>3.12.0</commons-lang3.version>
+        <jakarta.ws.rs-api.version>2.1.6</jakarta.ws.rs-api.version>
+        <commons-collections4.version>4.4</commons-collections4.version>
+        <jcommander.version>1.69</jcommander.version>
 
         <CELLBASE.WAR.NAME>cellbase</CELLBASE.WAR.NAME>
         <checkstyle.config.location>checkstyle.xml</checkstyle.config.location>
@@ -127,31 +145,33 @@
                 <groupId>org.opencb.biodata</groupId>
                 <artifactId>biodata-tools</artifactId>
                 <version>${biodata.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <artifactId>slf4j-simple</artifactId>
-                        <groupId>org.slf4j</groupId>
-                    </exclusion>
-                    <exclusion>
-                        <groupId>org.mortbay.jetty</groupId>
-                        <artifactId>servlet-api</artifactId>
-                    </exclusion>
-                    <exclusion>
-                        <artifactId>log4j</artifactId>
-                        <groupId>log4j</groupId>
-                    </exclusion>
-                    <exclusion>
-                        <groupId>org.apache.avro</groupId>
-                        <artifactId>avro-ipc</artifactId>
-                    </exclusion>
-                </exclusions>
+            </dependency>
+            <dependency>
+                <groupId>org.opencb.commons</groupId>
+                <artifactId>commons-datastore-core</artifactId>
+                <version>${java-common-libs.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.opencb.commons</groupId>
+                <artifactId>commons-lib</artifactId>
+                <version>${java-common-libs.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.opencb.biodata</groupId>
+                <artifactId>biodata-formats</artifactId>
+                <version>${biodata.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.opencb.biodata</groupId>
+                <artifactId>biodata-models</artifactId>
+                <version>${biodata.version}</version>
             </dependency>
 
             <!-- General dependencies -->
             <dependency>
                 <groupId>io.grpc</groupId>
                 <artifactId>grpc-all</artifactId>
-                <version>1.48.0</version>
+                <version>${grpc.version}</version>
             </dependency>
             <dependency>
                 <groupId>com.fasterxml.jackson.module</groupId>
@@ -231,42 +251,163 @@
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
                 <artifactId>log4j-slf4j-impl</artifactId>
-                <version>${log4j2.version}</version>
+                <version>${log4j.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
                 <artifactId>log4j-core</artifactId>
-                <version>${log4j2.version}</version>
+                <version>${log4j.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-api</artifactId>
+                <version>${log4j.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.junit.jupiter</groupId>
                 <artifactId>junit-jupiter-api</artifactId>
                 <version>${junit.jupiter.version}</version>
-                <scope>test</scope>
             </dependency>
             <dependency>
                 <groupId>org.junit.platform</groupId>
                 <artifactId>junit-platform-engine</artifactId>
                 <version>${junit.platform.version}</version>
-                <scope>test</scope>
             </dependency>
             <dependency>
                 <groupId>org.junit.jupiter</groupId>
                 <artifactId>junit-jupiter-engine</artifactId>
                 <version>${junit.jupiter.version}</version>
-                <scope>test</scope>
             </dependency>
             <dependency>
                 <groupId>org.junit.jupiter</groupId>
                 <artifactId>junit-jupiter-params</artifactId>
                 <version>${junit.jupiter.version}</version>
-                <scope>test</scope>
+            </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-annotations</artifactId>
+                <version>${jackson.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>io.jsonwebtoken</groupId>
+                <artifactId>jjwt-api</artifactId>
+                <version>${jjwt.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>io.jsonwebtoken</groupId>
+                <artifactId>jjwt-impl</artifactId>
+                <version>${jjwt.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-lang3</artifactId>
+                <version>${commons-lang3.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-collections4</artifactId>
+                <version>${commons-collections4.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>jakarta.ws.rs</groupId>
+                <artifactId>jakarta.ws.rs-api</artifactId>
+                <version>${jakarta.ws.rs-api.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-io</groupId>
+                <artifactId>commons-io</artifactId>
+                <version>${commons-io.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-lang</groupId>
+                <artifactId>commons-lang</artifactId>
+                <version>${commons-lang.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.rocksdb</groupId>
+                <artifactId>rocksdbjni</artifactId>
+                <version>4.5.1</version>
+            </dependency>
+            <dependency>
+                <groupId>com.beust</groupId>
+                <artifactId>jcommander</artifactId>
+                <version>${jcommander.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>com.github.samtools</groupId>
+                <artifactId>htsjdk</artifactId>
+                <version>${htsjdk.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.hamcrest</groupId>
+                <artifactId>hamcrest-core</artifactId>
+                <version>${hamcrest.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.hamcrest</groupId>
                 <artifactId>hamcrest-all</artifactId>
-                <version>1.3</version>
-                <scope>test</scope>
+                <version>${hamcrest.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.avro</groupId>
+                <artifactId>avro</artifactId>
+                <version>${avro.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>com.google.guava</groupId>
+                <artifactId>guava</artifactId>
+                <version>${guava.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>jakarta.xml.bind</groupId>
+                <artifactId>jakarta.xml.bind-api</artifactId>
+                <version>${jakarta.xml.bind-api.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-codec</groupId>
+                <artifactId>commons-codec</artifactId>
+                <version>${commons-codec.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>junit</groupId>
+                <artifactId>junit</artifactId>
+                <version>${junit.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.mongodb</groupId>
+                <artifactId>mongodb-driver-sync</artifactId>
+                <version>${mongodb.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.mongodb</groupId>
+                <artifactId>mongodb-driver-core</artifactId>
+                <version>${mongodb.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.mongodb</groupId>
+                <artifactId>bson</artifactId>
+                <version>${mongodb.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi-ooxml</artifactId>
+                <version>${poi.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi</artifactId>
+                <version>${poi.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>javax.servlet</groupId>
+                <artifactId>javax.servlet-api</artifactId>
+                <version>${javax.servlet-api.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>io.swagger</groupId>
+                <artifactId>swagger-annotations</artifactId>
+                <version>${swagger-annotations.version}</version>
             </dependency>
         </dependencies>
     </dependencyManagement>
@@ -276,6 +417,28 @@
         <testSourceDirectory>src/test/java</testSourceDirectory>
 
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <version>3.5.0</version>
+                <executions>
+                    <execution>
+                        <id>analyze</id>
+                        <goals>
+                            <goal>analyze-only</goal>
+                        </goals>
+                        <configuration>
+                            <failOnWarning>true</failOnWarning>
+                            <ignoredUnusedDeclaredDependencies>
+                                <ignoredUnusedDeclaredDependency>org.eclipse.jetty:jetty-util-ajax</ignoredUnusedDeclaredDependency>
+                            </ignoredUnusedDeclaredDependencies>
+                            <ignoredNonTestScopedDependencies>
+                                <ignoredNonTestScopedDependency>org.apache.avro:avro</ignoredNonTestScopedDependency>
+                            </ignoredNonTestScopedDependencies>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>

From 06194e281f1aee800fb14da57bb80e776269ff4a Mon Sep 17 00:00:00 2001
From: imedina <igmecas@gmail.com>
Date: Tue, 16 May 2023 23:56:14 +0100
Subject: [PATCH 02/10] pom: minor improvement

---
 cellbase-lib/pom.xml | 1 -
 pom.xml              | 8 +++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index 7928d4e3c..0fc0516d0 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -43,7 +43,6 @@
             <artifactId>biodata-models</artifactId>
         </dependency>
 
-
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
diff --git a/pom.xml b/pom.xml
index 3742741e3..2630e2455 100644
--- a/pom.xml
+++ b/pom.xml
@@ -42,7 +42,7 @@
         <junit.version>4.12</junit.version>
         <commons-codec.version>1.13</commons-codec.version>
         <jakarta.xml.bind-api.version>2.3.3</jakarta.xml.bind-api.version>
-        <guava.version>22.0</guava.version>
+        <guava.version>19.0</guava.version>
         <avro.version>1.9.1</avro.version>
         <hamcrest.version>1.3</hamcrest.version>
         <htsjdk.version>2.23.0</htsjdk.version>
@@ -145,6 +145,12 @@
                 <groupId>org.opencb.biodata</groupId>
                 <artifactId>biodata-tools</artifactId>
                 <version>${biodata.version}</version>
+                <exclusions>
+                    <exclusion>
+                        <groupId>org.opencb.ga4gh</groupId>
+                        <artifactId>ga4gh</artifactId>
+                    </exclusion>
+                </exclusions>
             </dependency>
             <dependency>
                 <groupId>org.opencb.commons</groupId>

From 9c405dc6ffa2641e80bfd318c51e0d90fce51840 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 11 Oct 2023 16:16:13 +0200
Subject: [PATCH 03/10] Update version pom

---
 cellbase-app/pom.xml    | 2 +-
 cellbase-client/pom.xml | 2 +-
 cellbase-core/pom.xml   | 2 +-
 cellbase-lib/pom.xml    | 2 +-
 cellbase-server/pom.xml | 2 +-
 pom.xml                 | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index 0f23b50d2..5a0f3a0bf 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.4.1-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 467907343..15ab96376 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.4.1-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
index 474c72c88..dfe95b02c 100644
--- a/cellbase-core/pom.xml
+++ b/cellbase-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.4.1-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index 0fc0516d0..c2d97de7b 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.4.1-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
index fc5910ae9..f50bf0bf0 100644
--- a/cellbase-server/pom.xml
+++ b/cellbase-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.4.1-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/pom.xml b/pom.xml
index 2630e2455..b3c472f52 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>5.4.1-SNAPSHOT</version>
+    <version>5.8.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>

From 276c9d648e08ffb28c3f8754f6d222f9c5fb97f8 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 11 Oct 2023 16:21:26 +0200
Subject: [PATCH 04/10] Clean Poms TASK-2095

---
 cellbase-lib/pom.xml    | 2 --
 cellbase-server/pom.xml | 1 -
 pom.xml                 | 4 ----
 3 files changed, 7 deletions(-)

diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index c2d97de7b..a95967e58 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -131,8 +131,6 @@
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
         </dependency>
-
-
         <dependency>
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-util-ajax</artifactId>
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
index f50bf0bf0..1f5fb9515 100644
--- a/cellbase-server/pom.xml
+++ b/cellbase-server/pom.xml
@@ -39,7 +39,6 @@
             <groupId>org.opencb.biodata</groupId>
             <artifactId>biodata-models</artifactId>
         </dependency>
-
         <!-- General dependencies -->
         <dependency>
             <groupId>com.fasterxml.jackson.module</groupId>
diff --git a/pom.xml b/pom.xml
index 8caff8536..a3b15950c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -57,10 +57,8 @@
 
         <CELLBASE.WAR.NAME>cellbase</CELLBASE.WAR.NAME>
         <checkstyle.config.location>checkstyle.xml</checkstyle.config.location>
-
         <sonar.organization>opencb</sonar.organization>
         <sonar.host.url>https://sonarcloud.io</sonar.host.url>
-
         <maven.compiler.source>1.8</maven.compiler.source>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     </properties>
@@ -172,7 +170,6 @@
                 <artifactId>biodata-models</artifactId>
                 <version>${biodata.version}</version>
             </dependency>
-
             <!-- General dependencies -->
             <dependency>
                 <groupId>io.grpc</groupId>
@@ -304,7 +301,6 @@
                 <artifactId>jjwt-impl</artifactId>
                 <version>${jjwt.version}</version>
             </dependency>
-
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-lang3</artifactId>

From b5fe4da48195100cee415ef4dce3105b471d904d Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Fri, 13 Oct 2023 13:18:30 +0200
Subject: [PATCH 05/10] poms: update dependencies #TASK-2095

---
 cellbase-app/pom.xml    | 4 ----
 cellbase-client/pom.xml | 4 ++++
 cellbase-lib/pom.xml    | 4 ++++
 pom.xml                 | 6 ++++++
 4 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index 5a0f3a0bf..a65df02b2 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -83,10 +83,6 @@
             <groupId>commons-lang</groupId>
             <artifactId>commons-lang</artifactId>
         </dependency>
-        <dependency>
-            <groupId>io.jsonwebtoken</groupId>
-            <artifactId>jjwt-impl</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 15ab96376..02a4607eb 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -32,6 +32,10 @@
         </dependency>
 
         <!-- General dependencies -->
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-lib</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index a95967e58..aa3e2387e 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -131,6 +131,10 @@
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.codehaus.jackson</groupId>
+            <artifactId>jackson-mapper-asl</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-util-ajax</artifactId>
diff --git a/pom.xml b/pom.xml
index a3b15950c..6a7fc1200 100644
--- a/pom.xml
+++ b/pom.xml
@@ -27,6 +27,7 @@
         <biodata.version>2.12.0-SNAPSHOT</biodata.version>
         <bionetdb.version>0.1.0</bionetdb.version>
         <jackson.version>2.11.4</jackson.version>
+        <jackson-asl.version>1.9.13</jackson-asl.version>
         <jersey.version>2.30.1</jersey.version>
         <slf4j.version>1.7.32</slf4j.version>
         <log4j.version>2.17.2</log4j.version>
@@ -411,6 +412,11 @@
                 <artifactId>swagger-annotations</artifactId>
                 <version>${swagger-annotations.version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.codehaus.jackson</groupId>
+                <artifactId>jackson-mapper-asl</artifactId>
+                <version>${jackson-asl.version}</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 

From 647bfe1960853ad1d8ad296b7699cb02b164e023 Mon Sep 17 00:00:00 2001
From: imedina <igmecas@gmail.com>
Date: Fri, 13 Oct 2023 16:33:44 +0100
Subject: [PATCH 06/10] pom: upgrade dependency plugin version

---
 cellbase-lib/pom.xml |  4 +++
 pom.xml              | 64 ++++++++++++++++----------------------------
 2 files changed, 27 insertions(+), 41 deletions(-)

diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index aa3e2387e..0bc93eeff 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -135,6 +135,10 @@
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
         </dependency>
+        <dependency>
+            <groupId>io.jsonwebtoken</groupId>
+            <artifactId>jjwt-api</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-util-ajax</artifactId>
diff --git a/pom.xml b/pom.xml
index 6a7fc1200..737612635 100644
--- a/pom.xml
+++ b/pom.xml
@@ -425,28 +425,6 @@
         <testSourceDirectory>src/test/java</testSourceDirectory>
 
         <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-dependency-plugin</artifactId>
-                <version>3.5.0</version>
-                <executions>
-                    <execution>
-                        <id>analyze</id>
-                        <goals>
-                            <goal>analyze-only</goal>
-                        </goals>
-                        <configuration>
-                            <failOnWarning>true</failOnWarning>
-                            <ignoredUnusedDeclaredDependencies>
-                                <ignoredUnusedDeclaredDependency>org.eclipse.jetty:jetty-util-ajax</ignoredUnusedDeclaredDependency>
-                            </ignoredUnusedDeclaredDependencies>
-                            <ignoredNonTestScopedDependencies>
-                                <ignoredNonTestScopedDependency>org.apache.avro:avro</ignoredNonTestScopedDependency>
-                            </ignoredNonTestScopedDependencies>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
@@ -524,25 +502,6 @@
                     </execution>
                 </executions>
             </plugin>
-<!--            <plugin>-->
-<!--                <groupId>org.jacoco</groupId>-->
-<!--                <artifactId>jacoco-maven-plugin</artifactId>-->
-<!--                <version>${jacoco.version}</version>-->
-<!--                <executions>-->
-<!--                    <execution>-->
-<!--                        <goals>-->
-<!--                            <goal>prepare-agent</goal>-->
-<!--                        </goals>-->
-<!--                    </execution>-->
-<!--                    <execution>-->
-<!--                        <id>report</id>-->
-<!--                        <phase>test</phase>-->
-<!--                        <goals>-->
-<!--                            <goal>report</goal>-->
-<!--                        </goals>-->
-<!--                    </execution>-->
-<!--                </executions>-->
-<!--            </plugin>-->
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
@@ -582,6 +541,29 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <version>3.6.0</version>
+                <executions>
+                    <execution>
+                        <id>analyze</id>
+                        <goals>
+                            <goal>analyze-only</goal>
+                        </goals>
+                        <configuration>
+                            <failOnWarning>true</failOnWarning>
+                            <ignoredUnusedDeclaredDependencies>
+                                <ignoredUnusedDeclaredDependency>org.eclipse.jetty:jetty-util-ajax</ignoredUnusedDeclaredDependency>
+                            </ignoredUnusedDeclaredDependencies>
+                            <ignoredNonTestScopedDependencies>
+                                <ignoredNonTestScopedDependency>org.apache.avro:avro</ignoredNonTestScopedDependency>
+                                <ignoredNonTestScopedDependency>io.jsonwebtoken:jjwt-api</ignoredNonTestScopedDependency>
+                            </ignoredNonTestScopedDependencies>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 

From f8dc56473fbff0ca6190d77d4e32be2c8f394eb7 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 19 Oct 2023 12:58:22 +0200
Subject: [PATCH 07/10] pom: Added ignoredUnusedDeclaredDependency for all
 dependencies #TASK-2095

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 6a7fc1200..714943789 100644
--- a/pom.xml
+++ b/pom.xml
@@ -438,7 +438,7 @@
                         <configuration>
                             <failOnWarning>true</failOnWarning>
                             <ignoredUnusedDeclaredDependencies>
-                                <ignoredUnusedDeclaredDependency>org.eclipse.jetty:jetty-util-ajax</ignoredUnusedDeclaredDependency>
+                                <ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
                             </ignoredUnusedDeclaredDependencies>
                             <ignoredNonTestScopedDependencies>
                                 <ignoredNonTestScopedDependency>org.apache.avro:avro</ignoredNonTestScopedDependency>

From ff974bf9e6aa6c254ff59d0bd363dd0a1ee677ee Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 19 Oct 2023 13:30:44 +0200
Subject: [PATCH 08/10] pom: Added develop dependencies to review #TASK-2095

---
 cellbase-app/pom.xml    | 13 +++++++++++++
 cellbase-client/pom.xml | 27 +++++++++++++++++++++++++++
 cellbase-core/pom.xml   | 25 +++++++++++++++++++++++++
 cellbase-lib/pom.xml    | 27 +++++++++++++++++++++++++++
 cellbase-server/pom.xml | 27 +++++++++++++++++++++++++++
 pom.xml                 | 14 ++++++++++++--
 6 files changed, 131 insertions(+), 2 deletions(-)

diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index a65df02b2..e22c63e91 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -139,6 +139,19 @@
             <scope>test</scope>
         </dependency>
 
+        <!--TODO Review -->
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.platform</groupId>
+            <artifactId>junit-platform-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+
     </dependencies>
 
     <build>
diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 02a4607eb..63106b459 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -89,6 +89,33 @@
             <artifactId>hamcrest-core</artifactId>
             <scope>test</scope>
         </dependency>
+
+        <!--TODO Review -->
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest-all</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.inject</groupId>
+            <artifactId>jersey-hk2</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.containers</groupId>
+            <artifactId>jersey-container-servlet</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.platform</groupId>
+            <artifactId>junit-platform-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+
     </dependencies>
 </project>
 
diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
index dfe95b02c..62d86797c 100644
--- a/cellbase-core/pom.xml
+++ b/cellbase-core/pom.xml
@@ -92,6 +92,31 @@
             <artifactId>junit-jupiter-api</artifactId>
             <scope>test</scope>
         </dependency>
+
+        <!--TODO Review -->
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest-all</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-slf4j-impl</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.platform</groupId>
+            <artifactId>junit-platform-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>io.jsonwebtoken</groupId>
+            <artifactId>jjwt-jackson</artifactId>
+        </dependency>
     </dependencies>
 
     <build>
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index 0bc93eeff..72525f8fd 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -159,5 +159,32 @@
             <artifactId>hamcrest-core</artifactId>
             <scope>test</scope>
         </dependency>
+
+        <!--TODO Review -->
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-util-ajax</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.core</groupId>
+            <artifactId>jersey-client</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest-all</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.platform</groupId>
+            <artifactId>junit-platform-engine</artifactId>
+            <scope>test</scope>
+        </dependency>
+
     </dependencies>
 </project>
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
index 1f5fb9515..5571e2282 100644
--- a/cellbase-server/pom.xml
+++ b/cellbase-server/pom.xml
@@ -101,6 +101,33 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
+
+        <!--TODO Review -->
+        <dependency>
+            <groupId>io.swagger</groupId>
+            <artifactId>swagger-jersey2-jaxrs</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.inject</groupId>
+            <artifactId>jersey-hk2</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.media</groupId>
+            <artifactId>jersey-media-json-jackson</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.containers</groupId>
+            <artifactId>jersey-container-servlet</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.containers</groupId>
+            <artifactId>jersey-container-servlet-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.media</groupId>
+            <artifactId>jersey-media-multipart</artifactId>
+        </dependency>
+
     </dependencies>
 
     <build>
diff --git a/pom.xml b/pom.xml
index a6c41adac..ae1807958 100644
--- a/pom.xml
+++ b/pom.xml
@@ -35,7 +35,7 @@
         <junit.jupiter.version>5.5.2</junit.jupiter.version>
         <jacoco.version>0.8.8</jacoco.version>
         <jetty.version>9.4.17.v20190418</jetty.version>
-        <jwt.version>0.11.5</jwt.version>
+        <jjwt.version>0.11.5</jjwt.version>
         <swagger-annotations.version>1.6.5</swagger-annotations.version>
         <javax.servlet-api.version>3.1.0</javax.servlet-api.version>
         <poi.version>4.1.2</poi.version>
@@ -50,7 +50,6 @@
         <grpc.version>1.48.0</grpc.version>
         <commons-lang.version>2.4</commons-lang.version>
         <commons-io.version>2.4</commons-io.version>
-        <jjwt.version>0.11.5</jjwt.version>
         <commons-lang3.version>3.12.0</commons-lang3.version>
         <jakarta.ws.rs-api.version>2.1.6</jakarta.ws.rs-api.version>
         <commons-collections4.version>4.4</commons-collections4.version>
@@ -62,6 +61,7 @@
         <sonar.host.url>https://sonarcloud.io</sonar.host.url>
         <maven.compiler.source>1.8</maven.compiler.source>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <swagger-jersey2-jaxrs.version>1.6.5</swagger-jersey2-jaxrs.version>
     </properties>
     <scm>
         <url>https://github.com/opencb/cellbase</url>
@@ -417,6 +417,16 @@
                 <artifactId>jackson-mapper-asl</artifactId>
                 <version>${jackson-asl.version}</version>
             </dependency>
+            <dependency>
+                <groupId>io.jsonwebtoken</groupId>
+                <artifactId>jjwt-jackson</artifactId>
+                <version>${jjwt.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>io.swagger</groupId>
+                <artifactId>swagger-jersey2-jaxrs</artifactId>
+                <version>${swagger-jersey2-jaxrs.version}</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 

From 768606f2ec74f6e8d28de092f1310ee83ad2fc72 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 15 Nov 2023 13:00:04 +0100
Subject: [PATCH 09/10] pom: commons-datastore-mongodb not scoped test #2095

---
 cellbase-app/pom.xml |  7 ++++++-
 cellbase-lib/pom.xml | 14 +++++++-------
 pom.xml              |  3 +--
 3 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index e22c63e91..9933ed4aa 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -63,7 +63,12 @@
         <dependency>
             <groupId>org.opencb.commons</groupId>
             <artifactId>commons-datastore-mongodb</artifactId>
-            <scope>test</scope>
+            <exclusions>
+                <exclusion>
+                    <artifactId>slf4j-simple</artifactId>
+                    <groupId>org.slf4j</groupId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
         <!-- General dependencies -->
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index 72525f8fd..d497d9325 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -21,6 +21,12 @@
         <dependency>
             <groupId>org.opencb.commons</groupId>
             <artifactId>commons-datastore-mongodb</artifactId>
+            <exclusions>
+                <exclusion>
+                    <artifactId>slf4j-simple</artifactId>
+                    <groupId>org.slf4j</groupId>
+                </exclusion>
+            </exclusions>
          </dependency>
         <dependency>
             <groupId>org.opencb.biodata</groupId>
@@ -142,7 +148,6 @@
         <dependency>
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-util-ajax</artifactId>
-            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>junit</groupId>
@@ -161,12 +166,7 @@
         </dependency>
 
         <!--TODO Review -->
-        <dependency>
-            <groupId>org.eclipse.jetty</groupId>
-            <artifactId>jetty-util-ajax</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
+         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>
         </dependency>
diff --git a/pom.xml b/pom.xml
index ae1807958..febb92564 100644
--- a/pom.xml
+++ b/pom.xml
@@ -567,8 +567,7 @@
                                 <ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
                             </ignoredUnusedDeclaredDependencies>
                             <ignoredNonTestScopedDependencies>
-                                <ignoredNonTestScopedDependency>org.apache.avro:avro</ignoredNonTestScopedDependency>
-                                <ignoredNonTestScopedDependency>io.jsonwebtoken:jjwt-api</ignoredNonTestScopedDependency>
+                                <ignoredNonTestScopedDependency>*</ignoredNonTestScopedDependency>
                             </ignoredNonTestScopedDependencies>
                         </configuration>
                     </execution>

From 35e2c3e7faf1e02208c7f9cf08146edc7e91dc45 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 15 Nov 2023 16:07:47 +0100
Subject: [PATCH 10/10] pom: commons-collections4 added to client #2095

---
 cellbase-client/pom.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 63106b459..65aec2c9b 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -115,7 +115,10 @@
             <artifactId>junit-platform-engine</artifactId>
             <scope>test</scope>
         </dependency>
-
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+        </dependency>
     </dependencies>
 </project>