pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<!--
  ~ Copyright 2015-2017 OpenCB
  ~
  ~ Licensed under the Apache License, Version 2.0 (the "License");
  ~ you may not use this file except in compliance with the License.
  ~ You may obtain a copy of the License at
  ~
  ~     http://www.apache.org/licenses/LICENSE-2.0
  ~
  ~ Unless required by applicable law or agreed to in writing, software
  ~ distributed under the License is distributed on an "AS IS" BASIS,
  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  ~ See the License for the specific language governing permissions and
  ~ limitations under the License.
  -->

<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xmlns="http://maven.apache.org/POM/4.0.0"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>org.opencb.opencga</groupId>
    <artifactId>opencga</artifactId>
    <version>3.0.2-SNAPSHOT</version>
    <packaging>pom</packaging>

    <name>OpenCGA</name>
    <description>OpenCGA projects implements a big data platform for genomic data analysis</description>
    <url>http://docs.opencb.org/display/opencga/</url>

    <modules>
        <module>opencga-core</module>
        <module>opencga-app</module>
        <module>opencga-catalog</module>
        <module>opencga-master</module>
        <module>opencga-analysis</module>
        <module>opencga-storage</module>
        <module>opencga-client</module>
        <module>opencga-server</module>
        <module>opencga-clinical</module>
        <module>opencga-test</module>
    </modules>

    <properties>
        <pyopencga.version>3.0.2</pyopencga.version>
        <opencgar.version>3.0.2</opencgar.version>
        <cellbase.version>6.0.0</cellbase.version>
        <biodata.version>3.0.0</biodata.version>
        <java-common-libs.version>5.0.0</java-common-libs.version>
        <iva.version>3.0.0</iva.version>
        <oskar.version>0.2.0</oskar.version>

        <jackson.version>2.14.3</jackson.version>
        <jersey.version>2.30.1</jersey.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>
        <slf4j.version>1.7.36</slf4j.version>
        <log4j2.version>2.17.2</log4j2.version>
        <solr.version>8.11.2</solr.version>
        <jjwt.version>0.11.2</jjwt.version>
<!--        <jetty.version>9.4.17.v20190418</jetty.version>-->
        <jetty.version>9.4.51.v20230217</jetty.version>
        <jetty-for-hadoop-test.version>${jetty.version}</jetty-for-hadoop-test.version>
        <guava.version>28.0-jre</guava.version>
        <htsjdk.version>2.23.0</htsjdk.version>
        <snpeff.version>4.3.1</snpeff.version>
        <mongodb-driver.version>4.8.2</mongodb-driver.version>
        <commons-io.version>2.8.0</commons-io.version>
        <commons-lang3.version>3.14.0</commons-lang3.version>
        <commons-codec.version>1.7</commons-codec.version>
        <reflections.version>0.9.10</reflections.version>
        <mockito.version>2.2.27</mockito.version>
        <findbugs-annotations.version>2.0.1</findbugs-annotations.version>
        <junit.version>4.13.2</junit.version>
        <jline.version>3.12.1</jline.version>
        <javax-mail.version>1.4.7</javax-mail.version>
        <hamcrest-core.version>1.3</hamcrest-core.version>
        <ga4gh.version>0.6.0a5</ga4gh.version>
        <jansi.version>2.4.0</jansi.version>
        <jakarta.ws.rs-api.version>2.1.6</jakarta.ws.rs-api.version>
        <jcommander.version>1.69</jcommander.version>
        <jackson-codehaus.version>1.9.13</jackson-codehaus.version>
        <adal4j.version>1.6.3</adal4j.version>
        <microsoft-graph.version>1.4.0</microsoft-graph.version>
        <json-smart.version>2.3</json-smart.version>
        <gson.version>2.8.0</gson.version>
        <nimbus-jose-jwt.version>9.31</nimbus-jose-jwt.version>
        <azure-client.version>1.5.4</azure-client.version>
        <azure-batch.version>4.0.1</azure-batch.version>
        <!-- Cannot upgrade the version until we upgrade GRPC version -->
        <azure.version>1.13.0</azure.version>
        <azure.optional>true</azure.optional>
        <azure-storage-blob.version>11.0.0</azure-storage-blob.version>
        <httpclient.version>4.5.6</httpclient.version>
        <oauth2-oidc-sdk.version>5.64.4</oauth2-oidc-sdk.version>
        <passay.version>1.6.1</passay.version>
        <kubernetes.version>4.3.0</kubernetes.version>
        <javax.servlet-api.version>3.1.0</javax.servlet-api.version>
        <ant.version>1.10.12</ant.version>
        <httpcore.version>4.4.13</httpcore.version>
        <log4j.version>1.2.17</log4j.version>
        <javax.ws.rs-api.version>2.0.1</javax.ws.rs-api.version>
        <jmeter.version>5.0</jmeter.version>
        <ApacheJMeter_components.version>5.0</ApacheJMeter_components.version>
        <grep4j.version>1.8.7</grep4j.version>
        <redisson.version>2.2.0</redisson.version>
        <jsr305.version>3.0.2</jsr305.version>
        <commons-compress.version>1.4.1</commons-compress.version>
        <rxjava.version>2.2.0</rxjava.version>
        <client-runtime.version>2.1.0</client-runtime.version>
        <reactive-streams.version>1.0.0</reactive-streams.version>
        <snappy-java.version>1.1.8.2</snappy-java.version>
        <parquet-avro.version>${parquet-common.version}</parquet-avro.version>
        <jorphan.version>5.0</jorphan.version>

        <opencga.war.name>opencga</opencga.war.name>
        <opencga.env.file>opencga-env.sh</opencga.env.file>

        <opencga.hadoop.thirdparty.version>1.0.0-SNAPSHOT</opencga.hadoop.thirdparty.version>

        <opencga-hadoop-shaded.id.default>hdp3.1</opencga-hadoop-shaded.id.default>
        <opencga-hadoop-shaded.id>${opencga-hadoop-shaded.id.default}</opencga-hadoop-shaded.id>
        <opencga-hadoop-lib.artifactId>opencga-storage-hadoop-lib-${opencga-hadoop-shaded.id}</opencga-hadoop-lib.artifactId>
        <opencga-hadoop-shaded.artifactId>opencga-hadoop-shaded-${opencga-hadoop-shaded.id}</opencga-hadoop-shaded.artifactId>

        <opencga-storage-hadoop-compat.id-default>hbase2.0</opencga-storage-hadoop-compat.id-default>
        <opencga-storage-hadoop-compat.id>${opencga-storage-hadoop-compat.id-default}</opencga-storage-hadoop-compat.id>

        <sonar.organization>opencb</sonar.organization>
        <sonar.host.url>https://sonarcloud.io</sonar.host.url>

        <!-- This prevents findbugs plugin to check all the dependency locations -->
        <dependency.locations.enabled>false</dependency.locations.enabled>
        <maven.compiler.source>1.8</maven.compiler.source>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <surefire.skipDefaultTestExecution>false</surefire.skipDefaultTestExecution>
        <surefire.testFailureIgnore>false</surefire.testFailureIgnore>
        <maven-surefire-plugin.version>3.1.0</maven-surefire-plugin.version>
        <parquet-hadoop.version>${parquet-common.version}</parquet-hadoop.version>
        <parquet-common.version>1.7.0</parquet-common.version>
        <commons-logging.version>1.1.3</commons-logging.version>
        <jcl-over-slf4j.version>1.7.24</jcl-over-slf4j.version>
        <servlet-api.version>2.5-20081211</servlet-api.version>


        <!--TO REMOVE:
            The version of Java (11.0.21) used to run this analysis is deprecated, and SonarCloud no longer supports it. Please upgrade to Java 17 or later.
            As a temporary measure, you can set the property 'sonar.scanner.force-deprecated-java-version' to 'true' to continue using Java 11.0.21
            This workaround will only be effective until January 28, 2024. After this date, all scans using the deprecated Java 11 will fail.
         -->
        <sonar.scanner.force-deprecated-java-version>true</sonar.scanner.force-deprecated-java-version>
        <kryo.version>2.23.0</kryo.version>

        <lombok.version>1.18.30</lombok.version>
        <maven-war-plugin.version>3.4.0</maven-war-plugin.version>
    </properties>

    <scm>
        <url>https://github.com/opencb/opencga</url>
        <connection>scm:git:git://github.com/opencb/opencga.git</connection>
        <developerConnection>scm:git:git@github.com:opencb/opencga.git</developerConnection>
    </scm>

    <licenses>
        <license>
            <name>Apache License, Version 2</name>
            <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
        </license>
    </licenses>

    <developers>
        <developer>
            <id>imedina</id>
            <name>Nacho</name>
            <email>igmecas@gmail.com</email>
        </developer>
        <developer>
            <id>j-coll</id>
            <name>Jacobo</name>
            <email>jacobo167@gmail.com</email>
        </developer>
        <developer>
            <id>pfurio</id>
            <name>Pedro</name>
            <email>pedrofurio@gmail.com</email>
        </developer>
        <developer>
            <id>jtarraga</id>
            <name>Joaquin</name>
            <email>joaquintarraga@gmail.com</email>
        </developer>
        <developer>
            <id>juanfeSanahuja</id>
            <name>Juanfe</name>
            <email>juanfesanahuja@gmail.com</email>
        </developer>
    </developers>

    <mailingLists>
        <mailingList>
            <name>OpenCB Mailing List</name>
            <archive>https://groups.google.com/forum/#!forum/opencb</archive>
            <post>opencb@googlegroups.com</post>
        </mailingList>
    </mailingLists>

    <repositories>
        <repository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
            <snapshots>
                <enabled>true</enabled>
                <updatePolicy>daily</updatePolicy>
            </snapshots>
        </repository>
        <repository>
            <id>github</id>
            <url>https://maven.pkg.github.com/opencb</url>
            <snapshots>
                <enabled>true</enabled>
            </snapshots>
        </repository>
    </repositories>

    <dependencyManagement>
        <dependencies>
            <!-- Intra-module dependencies -->
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-core</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-catalog</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-analysis</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-master</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-client</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-storage-app</artifactId>
                <version>${project.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.opencb.opencga</groupId>
                        <artifactId>opencga-storage-hadoop-${opencga-hadoop-shaded.id.default}</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-test</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-storage-core</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-storage-hadoop-core</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-storage-hadoop-core</artifactId>
                <version>${project.version}</version>
                <type>test-jar</type>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-storage-core</artifactId>
                <version>${project.version}</version>
                <type>test-jar</type>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-catalog</artifactId>
                <version>${project.version}</version>
                <type>test-jar</type>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-analysis</artifactId>
                <version>${project.version}</version>
                <type>test-jar</type>
            </dependency>
            <dependency>
                <groupId>org.opencb.opencga</groupId>
                <artifactId>opencga-server</artifactId>
                <version>${project.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.opencb.opencga</groupId>
                        <artifactId>opencga-storage-hadoop-${opencga-hadoop-shaded.id.default}</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>

            <!-- OpenCB dependencies -->
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-lib</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-datastore-core</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-datastore-mongodb</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-datastore-solr</artifactId>
                <version>${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>
                <exclusions>
                    <exclusion>
                        <groupId>com.google.protobuf</groupId>
                        <artifactId>protobuf-lite</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.mortbay.jetty</groupId>
                        <artifactId>servlet-api</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.mortbay.jetty</groupId>
                <artifactId>servlet-api</artifactId>
                <version>${servlet-api.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.biodata</groupId>
                <artifactId>biodata-tools</artifactId>
                <version>${biodata.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.apache.avro</groupId>
                        <artifactId>avro-ipc</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.opencb.cellbase</groupId>
                <artifactId>cellbase-core</artifactId>
                <version>${cellbase.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.cellbase</groupId>
                <artifactId>cellbase-client</artifactId>
                <version>${cellbase.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-log4j12</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.opencb.oskar</groupId>
                <artifactId>oskar-analysis</artifactId>
                <version>${oskar.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-log4j12</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>

            <!-- General dependencies -->
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-collections4</artifactId>
                <version>${collections.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-lang3</artifactId>
                <version>${commons-lang3.version}</version>
            </dependency>
            <dependency>
                <groupId>commons-io</groupId>
                <artifactId>commons-io</artifactId>
                <version>${commons-io.version}</version>
            </dependency>
            <dependency>
                <groupId>commons-codec</groupId>
                <artifactId>commons-codec</artifactId>
                <version>${commons-codec.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-api</artifactId>
                <version>${slf4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.logging.log4j</groupId>
                <artifactId>log4j-core</artifactId>
                <version>${log4j2.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.logging.log4j</groupId>
                <artifactId>log4j-api</artifactId>
                <version>${log4j2.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.logging.log4j</groupId>
                <artifactId>log4j-slf4j-impl</artifactId>
                <version>${log4j2.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-core</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-databind</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-annotations</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.datatype</groupId>
                <artifactId>jackson-datatype-joda</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.dataformat</groupId>
                <artifactId>jackson-dataformat-yaml</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.dataformat</groupId>
                <artifactId>jackson-dataformat-xml</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.dataformat</groupId>
                <artifactId>jackson-dataformat-cbor</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.jmeter</groupId>
                <artifactId>ApacheJMeter_components</artifactId>
                <version>${ApacheJMeter_components.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.solr</groupId>
                <artifactId>solr-solrj</artifactId>
                <version>${solr.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.solr</groupId>
                <artifactId>solr-core</artifactId>
                <version>${solr.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.solr</groupId>
                <artifactId>solr-test-framework</artifactId>
                <version>${solr.version}</version>
                <scope>test</scope>
                <exclusions>
                    <exclusion>
                        <groupId>com.google.protobuf</groupId>
                        <artifactId>protobuf-java</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-slf4j-impl</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-1.2-api</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-api</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-web</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.apache.jmeter</groupId>
                <artifactId>ApacheJMeter_core</artifactId>
                <version>${jmeter.version}</version>
                <exclusions>
                    <exclusion>
                        <artifactId>mongo-java-driver</artifactId>
                        <groupId>org.mongodb</groupId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-slf4j-impl</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-1.2-api</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-api</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-core</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>com.beust</groupId>
                        <artifactId>jcommander</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.apache.jmeter</groupId>
                <artifactId>ApacheJMeter_http</artifactId>
                <version>${jmeter.version}</version>
                <exclusions>
                    <exclusion>
                        <artifactId>mongo-java-driver</artifactId>
                        <groupId>org.mongodb</groupId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-slf4j-impl</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-1.2-api</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.apache.jmeter</groupId>
                <artifactId>ApacheJMeter_java</artifactId>
                <version>${jmeter.version}</version>
                <exclusions>
                    <exclusion>
                        <artifactId>mongo-java-driver</artifactId>
                        <groupId>org.mongodb</groupId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-slf4j-impl</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.logging.log4j</groupId>
                        <artifactId>log4j-1.2-api</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.apache.jmeter</groupId>
                <artifactId>jorphan</artifactId>
                <version>${jorphan.version}</version>
            </dependency>
            <dependency>
                <groupId>javax.ws.rs</groupId>
                <artifactId>javax.ws.rs-api</artifactId>
                <version>${javax.ws.rs-api.version}</version>
            </dependency>
            <dependency>
                <groupId>org.jline</groupId>
                <artifactId>jline-reader</artifactId>
                <version>${jline.version}</version>
            </dependency>
            <dependency>
                <groupId>org.jline</groupId>
                <artifactId>jline-terminal</artifactId>
                <version>${jline.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-server</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-webapp</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-servlet</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-http</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-io</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-util</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-util-ajax</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-xml</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-rewrite</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-security</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-client</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-project</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-alpn-client</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.eclipse.jetty</groupId>
                <artifactId>jetty-alpn-java-client</artifactId>
                <version>${jetty.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.core</groupId>
                <artifactId>jersey-client</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.core</groupId>
                <artifactId>jersey-common</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.core</groupId>
                <artifactId>jersey-server</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.containers</groupId>
                <artifactId>jersey-container-servlet-core</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.containers</groupId>
                <artifactId>jersey-container-servlet</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.inject</groupId>
                <artifactId>jersey-hk2</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.media</groupId>
                <artifactId>jersey-media-json-jackson</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.media</groupId>
                <artifactId>jersey-media-multipart</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.media</groupId>
                <artifactId>jersey-media-jaxb</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>io.jsonwebtoken</groupId>
                <artifactId>jjwt-api</artifactId>
                <version>${jjwt.version}</version>
            </dependency>
            <dependency>
                <groupId>io.jsonwebtoken</groupId>
                <artifactId>jjwt-impl</artifactId>
                <version>${jjwt.version}</version>
            </dependency>
            <dependency>
                <groupId>io.jsonwebtoken</groupId>
                <artifactId>jjwt-jackson</artifactId>
                <version>${jjwt.version}</version>
            </dependency>
            <dependency>
                <groupId>com.google.protobuf</groupId>
                <artifactId>protobuf-java</artifactId>
                <version>${protobuf.version}</version>
            </dependency>
            <dependency>
                <groupId>com.google.protobuf</groupId>
                <artifactId>protobuf-java-util</artifactId>
                <version>${protobuf.version}</version>
            </dependency>
            <dependency>
                <groupId>com.google.code.findbugs</groupId>
                <artifactId>annotations</artifactId>
                <version>${findbugs-annotations.version}</version>
            </dependency>
            <dependency>
                <groupId>io.grpc</groupId>
                <artifactId>grpc-all</artifactId>
                <version>${grpc.version}</version>
            </dependency>
            <dependency>
                <groupId>io.grpc</groupId>
                <artifactId>grpc-api</artifactId>
                <version>${grpc.version}</version>
            </dependency>
            <dependency>
                <groupId>io.grpc</groupId>
                <artifactId>grpc-protobuf</artifactId>
                <version>${grpc.version}</version>
            </dependency>
            <dependency>
                <groupId>io.grpc</groupId>
                <artifactId>grpc-stub</artifactId>
                <version>${grpc.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.avro</groupId>
                <artifactId>avro</artifactId>
                <version>${avro.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-api</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.apache.avro</groupId>
                <artifactId>avro-ipc</artifactId>
                <version>${avro.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.avro</groupId>
                <artifactId>avro-mapred</artifactId>
                <version>${avro.version}</version>
                <classifier>hadoop2</classifier>
            </dependency>
            <dependency>
                <groupId>org.mongodb</groupId>
                <artifactId>mongodb-driver-core</artifactId>
                <version>${mongodb-driver.version}</version>
            </dependency>
            <dependency>
                <groupId>org.mongodb</groupId>
                <artifactId>mongodb-driver-sync</artifactId>
                <version>${mongodb-driver.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.parquet</groupId>
                <artifactId>parquet-common</artifactId>
                <version>${parquet-common.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>jcl-over-slf4j</artifactId>
                <version>${jcl-over-slf4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.mongodb</groupId>
                <artifactId>bson</artifactId>
                <version>${mongodb-driver.version}</version>
            </dependency>
            <dependency>
                <groupId>commons-logging</groupId>
                <artifactId>commons-logging</artifactId>
                <version>${commons-logging.version}</version>
            </dependency>
            <dependency>
                <groupId>javax.mail</groupId>
                <artifactId>mail</artifactId>
                <version>${javax-mail.version}</version>
            </dependency>
            <dependency>
                <groupId>org.reflections</groupId>
                <artifactId>reflections</artifactId>
                <version>${reflections.version}</version>
            </dependency>
            <dependency>
                <groupId>com.github.samtools</groupId>
                <artifactId>htsjdk</artifactId>
                <version>${htsjdk.version}</version>
            </dependency>
            <dependency>
                <groupId>com.databricks</groupId>
                <artifactId>SnpEff</artifactId>
                <version>${snpeff.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.parquet</groupId>
                <artifactId>parquet-avro</artifactId>
                <version>${parquet-avro.version}</version>
            </dependency>
            <dependency>
                <groupId>com.google.guava</groupId>
                <artifactId>guava</artifactId>
                <version>${guava.version}</version>
            </dependency>
            <dependency>
                <groupId>org.hamcrest</groupId>
                <artifactId>hamcrest-core</artifactId>
                <version>${hamcrest-core.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.ga4gh</groupId>
                <artifactId>ga4gh</artifactId>
                <version>${ga4gh.version}</version>
            </dependency>
            <dependency>
                <groupId>org.fusesource.jansi</groupId>
                <artifactId>jansi</artifactId>
                <version>${jansi.version}</version>
            </dependency>
            <dependency>
                <groupId>jakarta.ws.rs</groupId>
                <artifactId>jakarta.ws.rs-api</artifactId>
                <version>${jakarta.ws.rs-api.version}</version>
            </dependency>
            <dependency>
                <groupId>com.beust</groupId>
                <artifactId>jcommander</artifactId>
                <version>${jcommander.version}</version>
            </dependency>
            <dependency>
                <groupId>com.microsoft.azure</groupId>
                <artifactId>adal4j</artifactId>
                <version>${adal4j.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-simple</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>com.microsoft.graph</groupId>
                <artifactId>microsoft-graph</artifactId>
                <version>${microsoft-graph.version}</version>
            </dependency>
            <dependency>
                <groupId>net.minidev</groupId>
                <artifactId>json-smart</artifactId>
                <version>${json-smart.version}</version>
            </dependency>
            <dependency>
                <groupId>com.google.code.gson</groupId>
                <artifactId>gson</artifactId>
                <version>${gson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.nimbusds</groupId>
                <artifactId>nimbus-jose-jwt</artifactId>
                <version>${nimbus-jose-jwt.version}</version>
            </dependency>
            <dependency>
                <groupId>com.microsoft.azure</groupId>
                <artifactId>azure-client-runtime</artifactId>
                <version>${azure-client.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-simple</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>com.microsoft.azure</groupId>
                <artifactId>azure-client-authentication</artifactId>
                <version>${azure-client.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-simple</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.apache.httpcomponents</groupId>
                <artifactId>httpclient</artifactId>
                <version>${httpclient.version}</version>
            </dependency>
            <dependency>
                <groupId>com.nimbusds</groupId>
                <artifactId>oauth2-oidc-sdk</artifactId>
                <version>${oauth2-oidc-sdk.version}</version>
            </dependency>
            <dependency>
                <groupId>org.passay</groupId>
                <artifactId>passay</artifactId>
                <version>${passay.version}</version>
            </dependency>
            <dependency>
                <groupId>com.microsoft.azure</groupId>
                <artifactId>azure-batch</artifactId>
                <version>${azure-batch.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-simple</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>io.fabric8</groupId>
                <artifactId>kubernetes-client</artifactId>
                <version>${kubernetes.version}</version>
            </dependency>
            <dependency>
                <groupId>io.fabric8</groupId>
                <artifactId>kubernetes-model</artifactId>
                <version>${kubernetes.version}</version>
            </dependency>
            <dependency>
                <groupId>javax.servlet</groupId>
                <artifactId>javax.servlet-api</artifactId>
                <version>${javax.servlet-api.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.ant</groupId>
                <artifactId>ant</artifactId>
                <version>${ant.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.httpcomponents</groupId>
                <artifactId>httpcore</artifactId>
                <version>${httpcore.version}</version>
            </dependency>
            <dependency>
                <groupId>log4j</groupId>
                <artifactId>log4j</artifactId>
                <version>${log4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.codehaus.jackson</groupId>
                <artifactId>jackson-core-asl</artifactId>
                <version>${jackson-codehaus.version}</version>
            </dependency>
            <dependency>
                <groupId>org.mockito</groupId>
                <artifactId>mockito-core</artifactId>
                <version>${mockito.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>${junit.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-report-plugin</artifactId>
                <version>${maven-surefire-plugin.version}</version>
                <type>maven-plugin</type>
            </dependency>
            <dependency>
                <groupId>com.googlecode.grep4j</groupId>
                <artifactId>grep4j</artifactId>
                <version>${grep4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.projectlombok</groupId>
                <artifactId>lombok</artifactId>
                <version>${lombok.version}</version>
                <scope>provided</scope>
            </dependency>
            <dependency>
                <groupId>org.redisson</groupId>
                <artifactId>redisson</artifactId>
                <version>${redisson.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>io.netty</groupId>
                        <artifactId>netty-codec</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>io.netty</groupId>
                        <artifactId>netty-common</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>io.netty</groupId>
                        <artifactId>netty-handler</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>io.netty</groupId>
                        <artifactId>netty-buffer</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>io.netty</groupId>
                        <artifactId>netty-transport</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.reactivestreams</groupId>
                <artifactId>reactive-streams</artifactId>
                <version>${reactive-streams.version}</version>
            </dependency>
            <dependency>
                <groupId>com.microsoft.rest.v2</groupId>
                <artifactId>client-runtime</artifactId>
                <version>${client-runtime.version}</version>
            </dependency>
            <dependency>
                <groupId>com.microsoft.azure</groupId>
                <artifactId>azure-storage-blob</artifactId>
                <version>${azure-storage-blob.version}</version>
                <optional>${azure.optional}</optional>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-simple</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>com.google.code.findbugs</groupId>
                <artifactId>jsr305</artifactId>
                <version>${jsr305.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-compress</artifactId>
                <version>${commons-compress.version}</version>
            </dependency>
            <dependency>
                <groupId>io.reactivex.rxjava2</groupId>
                <artifactId>rxjava</artifactId>
                <version>${rxjava.version}</version>
            </dependency>
            <dependency>
                <groupId>org.xerial.snappy</groupId>
                <artifactId>snappy-java</artifactId>
                <version>${snappy-java.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.parquet</groupId>
                <artifactId>parquet-hadoop</artifactId>
                <version>${parquet-hadoop.version}</version>
            </dependency>
            <dependency>
                <groupId>org.jline</groupId>
                <artifactId>jline-terminal-jna</artifactId>
                <version>${jline.version}</version>
            </dependency>
            <dependency>
                <groupId>com.microsoft.azure</groupId>
                <artifactId>azure</artifactId>
                <version>${azure.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-simple</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>com.esotericsoftware.kryo</groupId>
                <artifactId>kryo</artifactId>
                <version>${kryo.version}</version>
            </dependency>

        </dependencies>
    </dependencyManagement>

    <build>
        <sourceDirectory>src/main/java</sourceDirectory>
        <testSourceDirectory>src/test/java</testSourceDirectory>

        <pluginManagement>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-jar-plugin</artifactId>
                    <version>3.2.0</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-shade-plugin</artifactId>
                    <version>3.5.1</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-surefire-report-plugin</artifactId>
                    <version>${maven-surefire-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-war-plugin</artifactId>
                    <version>${maven-war-plugin.version}</version>
                </plugin>
            </plugins>
        </pluginManagement>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.10.1</version>
                <configuration>
                    <source>${maven.compiler.source}</source>
                    <target>${maven.compiler.source}</target>
                    <showDeprecation>true</showDeprecation>
                    <showWarnings>true</showWarnings>
                    <meminitial>128m</meminitial>
                    <maxmem>512m</maxmem>
                    <encoding>${project.build.sourceEncoding}</encoding>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-resources-plugin</artifactId>
                <version>3.2.0</version>
                <configuration>
                    <encoding>${project.build.sourceEncoding}</encoding>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-checkstyle-plugin</artifactId>
                <version>2.17</version>
                <dependencies>
                    <dependency>
                        <groupId>com.puppycrawl.tools</groupId>
                        <artifactId>checkstyle</artifactId>
                        <version>8.1</version>
                    </dependency>
                </dependencies>
                <configuration>
                    <configLocation>checkstyle.xml</configLocation>
                    <excludes>
                        org/opencb/opencga/core/**,
                        org/opencb/opencga/app/**,
                        org/opencb/opencga/analysis/**,
                        org/opencb/opencga/server/**,
                        org/opencb/opencga/test/**,
                        org/opencb/opencga/storage/app/**,
                        org/opencb/opencga/client/rest/clients/**,
                        org/opencb/opencga/storage/alignment/**,
                        org/opencb/opencga/storage/variant/**,
                        org/opencb/opencga/storage/datamanagers/**,
                        org/opencb/opencga/storage/hadoop/variant/models/protobuf/**,
                        org/opencb/opencga/storage/server/grpc/**,
                    </excludes>
                    <resourceExcludes>
                        benchmark/jmeter/**
                    </resourceExcludes>
                </configuration>
                <executions>
                    <execution>
                        <id>validate</id>
                        <phase>validate</phase>
                        <configuration>
                            <configLocation>checkstyle.xml</configLocation>
                        </configuration>
                        <goals>
                            <goal>check</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-site-plugin</artifactId>
                <version>3.9.1</version>
            </plugin>
            <plugin>
                <groupId>org.jacoco</groupId>
                <artifactId>jacoco-maven-plugin</artifactId>
                <version>0.8.8</version>
                <executions>
                    <execution>
                        <id>default-prepare-agent</id>
                        <goals>
                            <goal>prepare-agent</goal>
                        </goals>
                    </execution>
                    <execution>
                        <id>default-report</id>
                        <goals>
                            <goal>report</goal>
                        </goals>
                    </execution>
                    <execution>
                        <id>default-check</id>
                        <goals>
                            <goal>check</goal>
                        </goals>
                        <configuration>
                            <rules>
                                <!--                                <rule>-->
                                <!--                                    <element>BUNDLE</element>-->
                                <!--                                    <limits>-->
                                <!--                                        <limit>-->
                                <!--                                            <counter>COMPLEXITY</counter>-->
                                <!--                                            <value>COVEREDRATIO</value>-->
                                <!--                                            <minimum>0.60</minimum>-->
                                <!--                                        </limit>-->
                                <!--                                    </limits>-->
                                <!--                                </rule>-->
                            </rules>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>${maven-surefire-plugin.version}</version>
                <executions>
                    <execution>
                        <id>default-test</id>
                        <configuration>
                            <skip>${surefire.skipDefaultTestExecution}</skip>
                            <forkCount>1</forkCount>
                            <reuseForks>false</reuseForks>
                            <!--<argLine>-Xmx1024m -XX:MaxPermSize=256m</argLine>-->
                        </configuration>
                    </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>*</ignoredUnusedDeclaredDependency>
                            </ignoredUnusedDeclaredDependencies>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
    <reporting>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-project-info-reports-plugin</artifactId>
                <version>2.9</version>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-report-plugin</artifactId>
                <version>${maven-surefire-plugin.version}</version>
            </plugin>
            <plugin>
                <groupId>com.github.spotbugs</groupId>
                <artifactId>spotbugs-maven-plugin</artifactId>
                <version>3.1.12.2</version>
            </plugin>
        </plugins>
    </reporting>

    <profiles>
        <profile>
            <id>prod-war</id>
            <activation>
                <activeByDefault>false</activeByDefault>
            </activation>
            <properties>
                <opencga.war.name>opencga</opencga.war.name>
            </properties>
        </profile>
        <profile>
            <id>default-config</id>
            <activation>
                <!-- Do not use "activeByDefault" as it might get deactivated when using any hadoop profile -->
                <property>
                    <name>!skipDefaultConfig</name>
                </property>
            </activation>
            <properties>
                <opencga.war.name>opencga-${project.parent.version}</opencga.war.name>

                <!-- General -->
                <OPENCGA.INSTALLATION.DIR>/opt/opencga</OPENCGA.INSTALLATION.DIR>
                <OPENCGA.USER.WORKSPACE>/opt/opencga/sessions</OPENCGA.USER.WORKSPACE>
                <OPENCGA.ANALYSIS.SCRATCH.DIR></OPENCGA.ANALYSIS.SCRATCH.DIR>
                <OPENCGA.DB.PREFIX>opencga</OPENCGA.DB.PREFIX>
                <OPENCGA.EXECUTION.MODE>LOCAL</OPENCGA.EXECUTION.MODE>

                <!-- Client -->
                <OPENCGA.CLIENT.REST.HOST>https://ws.opencb.org/opencga-prod</OPENCGA.CLIENT.REST.HOST>
                <OPENCGA.CLIENT.GRPC.HOST>localhost:9091</OPENCGA.CLIENT.GRPC.HOST>

                <OPENCGA.SERVER.REST.PORT>9090</OPENCGA.SERVER.REST.PORT>
                <OPENCGA.SERVER.GRPC.PORT>9091</OPENCGA.SERVER.GRPC.PORT>
                <OPENCGA.MONITOR.PORT>9092</OPENCGA.MONITOR.PORT>

                <!-- Catalog -->
                <OPENCGA.CATALOG.DB.HOSTS>localhost:27017</OPENCGA.CATALOG.DB.HOSTS>
                <OPENCGA.CATALOG.DB.USER></OPENCGA.CATALOG.DB.USER>
                <OPENCGA.CATALOG.DB.PASSWORD></OPENCGA.CATALOG.DB.PASSWORD>
                <OPENCGA.CATALOG.DB.AUTHENTICATION_DATABASE></OPENCGA.CATALOG.DB.AUTHENTICATION_DATABASE>
                <OPENCGA.CATALOG.DB.CONNECTIONS_PER_HOST>20</OPENCGA.CATALOG.DB.CONNECTIONS_PER_HOST>
                <OPENCGA.CATALOG.SEARCH.HOST>http://localhost:8983/solr/</OPENCGA.CATALOG.SEARCH.HOST>
                <OPENCGA.CATALOG.SEARCH.TIMEOUT>30000</OPENCGA.CATALOG.SEARCH.TIMEOUT>
                <OPENCGA.CATALOG.SEARCH.BATCH>2000</OPENCGA.CATALOG.SEARCH.BATCH>

                <!-- Optimizations -->
                <OPENCGA_OPTIMIZATIONS_SIMPLIFY_PERMISSIONS>false</OPENCGA_OPTIMIZATIONS_SIMPLIFY_PERMISSIONS>

                <!-- Storage -->
                <OPENCGA.STORAGE.DEFAULT_ENGINE>hadoop</OPENCGA.STORAGE.DEFAULT_ENGINE>
                <OPENCGA.STORAGE.CACHE.HOST>localhost:6379</OPENCGA.STORAGE.CACHE.HOST>

                <!-- Storage Variants general -->
                <OPENCGA.STORAGE.VARIANT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.VARIANT.DB.HOSTS>
                <OPENCGA.STORAGE.VARIANT.DB.USER></OPENCGA.STORAGE.VARIANT.DB.USER>
                <OPENCGA.STORAGE.VARIANT.DB.PASSWORD></OPENCGA.STORAGE.VARIANT.DB.PASSWORD>
                <OPENCGA.STORAGE.SEARCH.HOST>http://localhost:8983/solr/</OPENCGA.STORAGE.SEARCH.HOST>
                <OPENCGA.STORAGE.SEARCH.CONFIG_SET>opencga-variant-configset-${project.parent.version}
                </OPENCGA.STORAGE.SEARCH.CONFIG_SET>
                <OPENCGA.STORAGE.SEARCH.TIMEOUT>30000</OPENCGA.STORAGE.SEARCH.TIMEOUT>
                <OPENCGA.STORAGE.CLINICAL.HOST>http://localhost:8983/solr/</OPENCGA.STORAGE.CLINICAL.HOST>
                <OPENCGA.STORAGE.CLINICAL.MANAGER>""</OPENCGA.STORAGE.CLINICAL.MANAGER>
                <OPENCGA.STORAGE.CLINICAL.TIMEOUT>30000</OPENCGA.STORAGE.CLINICAL.TIMEOUT>
                <OPENCGA.STORAGE.RGA.HOST>http://localhost:8983/solr/</OPENCGA.STORAGE.RGA.HOST>
                <OPENCGA.STORAGE.RGA.CONFIG_SET>opencga-rga-configset-${project.parent.version}
                </OPENCGA.STORAGE.RGA.CONFIG_SET>
                <OPENCGA.STORAGE.RGA.TIMEOUT>30000</OPENCGA.STORAGE.RGA.TIMEOUT>

                <!-- Storage Alignments general -->
                <OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>
                <OPENCGA.STORAGE.ALIGNMENT.DB.USER></OPENCGA.STORAGE.ALIGNMENT.DB.USER>
                <OPENCGA.STORAGE.ALIGNMENT.DB.PASSWORD></OPENCGA.STORAGE.ALIGNMENT.DB.PASSWORD>

                <!-- Storage-mongodb -->
                <OPENCGA.STORAGE.MONGODB.VARIANT.DB.AUTHENTICATION_DATABASE></OPENCGA.STORAGE.MONGODB.VARIANT.DB.AUTHENTICATION_DATABASE>
                <OPENCGA.STORAGE.MONGODB.VARIANT.DB.CONNECTIONS_PER_HOST>20
                </OPENCGA.STORAGE.MONGODB.VARIANT.DB.CONNECTIONS_PER_HOST>

                <!-- Storage-hadoop -->
                <OPENCGA.STORAGE.HADOOP.VARIANT.DB.USER></OPENCGA.STORAGE.HADOOP.VARIANT.DB.USER>
                <OPENCGA.STORAGE.HADOOP.VARIANT.DB.PASSWORD></OPENCGA.STORAGE.HADOOP.VARIANT.DB.PASSWORD>
                <OPENCGA.STORAGE.HADOOP.VARIANT.HBASE.NAMESPACE></OPENCGA.STORAGE.HADOOP.VARIANT.HBASE.NAMESPACE>

                <!-- Email server -->
                <OPENCGA.MAIL.HOST></OPENCGA.MAIL.HOST>
                <OPENCGA.MAIL.PORT></OPENCGA.MAIL.PORT>
                <OPENCGA.MAIL.USER></OPENCGA.MAIL.USER>
                <OPENCGA.MAIL.PASSWORD></OPENCGA.MAIL.PASSWORD>

                <!-- cellbase -->
                <OPENCGA.CELLBASE.REST.HOST>https://uk.ws.zettagenomics.com/cellbase/</OPENCGA.CELLBASE.REST.HOST>
                <OPENCGA.CELLBASE.VERSION>v5.2</OPENCGA.CELLBASE.VERSION>
            </properties>
        </profile>

        <profile>
            <id>deploy-maven</id>
            <distributionManagement>
                <repository>
                    <id>ossrh</id>
                    <url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
                </repository>
                <snapshotRepository>
                    <id>ossrh</id>
                    <url>https://oss.sonatype.org/content/repositories/snapshots</url>
                </snapshotRepository>
            </distributionManagement>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-source-plugin</artifactId>
                        <version>3.2.0</version>
                        <executions>
                            <execution>
                                <id>attach-sources</id>
                                <goals>
                                    <goal>jar-no-fork</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-javadoc-plugin</artifactId>
                        <version>3.3.2</version>
                        <executions>
                            <execution>
                                <id>attach-javadocs</id>
                                <goals>
                                    <goal>jar</goal>
                                </goals>
                            </execution>
                        </executions>
                        <configuration>
                            <doclint>none</doclint>
                        </configuration>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-gpg-plugin</artifactId>
                        <version>1.6</version>
                        <executions>
                            <execution>
                                <id>sign-artifacts</id>
                                <phase>deploy</phase>
                                <goals>
                                    <goal>sign</goal>
                                </goals>
                                <configuration>
                                    <!-- Prevent `gpg` from using pinentry programs -->
                                    <gpgArguments>
                                        <arg>--pinentry-mode</arg>
                                        <arg>loopback</arg>
                                    </gpgArguments>
                                </configuration>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.sonatype.plugins</groupId>
                        <artifactId>nexus-staging-maven-plugin</artifactId>
                        <version>1.6.8</version>
                        <extensions>true</extensions>
                        <configuration>
                            <serverId>ossrh</serverId>
                            <nexusUrl>https://oss.sonatype.org/</nexusUrl>
                            <autoReleaseAfterClose>true</autoReleaseAfterClose>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>
        <profile>
            <id>deploy-github</id>
            <distributionManagement>
                <repository>
                    <id>github</id>
                    <name>GitHub OpenCB Apache Maven Packages</name>
                    <url>https://maven.pkg.github.com/opencb/opencga</url>
                </repository>
            </distributionManagement>
            <build>
            </build>
        </profile>

        <profile>
            <id>hdp3.1</id>
            <activation>
                <property>
                    <name>hadoop</name>
                    <value>hdp3.1</value>
                </property>
            </activation>
            <properties>
                <opencga-hadoop-shaded.id>hdp3.1</opencga-hadoop-shaded.id>
                <opencga-storage-hadoop-compat.id>hbase2.0</opencga-storage-hadoop-compat.id>
                <jetty-for-hadoop-test.version>9.3.25.v20180904</jetty-for-hadoop-test.version>
            </properties>
        </profile>
        <profile>
            <id>hdi5.1</id>
            <activation>
                <property>
                    <name>hadoop</name>
                    <value>hdi5.1</value>
                </property>
            </activation>
            <properties>
                <opencga-hadoop-shaded.id>hdi5.1</opencga-hadoop-shaded.id>
                <opencga-storage-hadoop-compat.id>hbase2.4</opencga-storage-hadoop-compat.id>
            </properties>
        </profile>
        <profile>
            <id>emr6.1</id>
            <activation>
                <property>
                    <name>hadoop</name>
                    <value>emr6.1</value>
                </property>
            </activation>
            <properties>
                <opencga-hadoop-shaded.id>emr6.1</opencga-hadoop-shaded.id>
                <opencga-storage-hadoop-compat.id>hbase2.2</opencga-storage-hadoop-compat.id>
                <!--  AWS changes the version of Jetty in their custom jar -->
                <jetty-for-hadoop-test.version>9.4.20.v20190813</jetty-for-hadoop-test.version>
            </properties>
        </profile>
        <profile>
            <id>emr6.13</id>
            <activation>
                <property>
                    <name>hadoop</name>
                    <value>emr6.13</value>
                </property>
            </activation>
            <properties>
                <opencga-hadoop-shaded.id>emr6.13</opencga-hadoop-shaded.id>
                <opencga-storage-hadoop-compat.id>hbase2.4</opencga-storage-hadoop-compat.id>
            </properties>
        </profile>
        <profile>
            <id>runShortTests</id>
            <properties>
                <surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
            </properties>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>${maven-surefire-plugin.version}</version>
                        <executions>
                            <execution>
                                <id>shortTestsExecution</id>
                                <phase>test</phase>
                                <goals>
                                    <goal>test</goal>
                                </goals>
                                <configuration>
                                    <testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
                                    <reuseForks>true</reuseForks>
                                    <forkCount>5</forkCount>
                                    <groups>org.opencb.opencga.core.testclassification.duration.ShortTests</groups>
                                </configuration>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
        <profile>
            <id>runMediumTests</id>
            <properties>
                <surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
            </properties>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>${maven-surefire-plugin.version}</version>
                        <executions>
                            <execution>
                                <id>mediumTestsExecution</id>
                                <phase>test</phase>
                                <goals>
                                    <goal>test</goal>
                                </goals>
                                <configuration>
                                    <testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
                                    <!--                            <reuseForks>true</reuseForks>-->
                                    <reuseForks>false</reuseForks>
                                    <forkCount>1</forkCount>
                                    <groups>org.opencb.opencga.core.testclassification.duration.MediumTests</groups>
                                </configuration>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
        <profile>
            <id>runLongTests</id>
            <properties>
                <surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
            </properties>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>${maven-surefire-plugin.version}</version>
                        <executions>
                            <execution>
                                <id>longTestsExecution</id>
                                <phase>test</phase>
                                <goals>
                                    <goal>test</goal>
                                </goals>
                                <configuration>
                                    <testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
                                    <reuseForks>false</reuseForks>
                                    <forkCount>1</forkCount>
                                    <groups>org.opencb.opencga.core.testclassification.duration.LongTests</groups>
                                </configuration>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
        <profile>
            <id>runUncategorizedTests</id>
            <properties>
                <surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
            </properties>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>${maven-surefire-plugin.version}</version>
                        <executions>
                            <execution>
                                <id>uncategorizedTestsExecution</id>
                                <phase>test</phase>
                                <goals>
                                    <goal>test</goal>
                                </goals>
                                <configuration>
                                    <testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
                                    <reuseForks>false</reuseForks>
                                    <forkCount>1</forkCount>
                                    <excludedGroups>
                                        org.opencb.opencga.core.testclassification.duration.ShortTests,org.opencb.opencga.core.testclassification.duration.MediumTests,org.opencb.opencga.core.testclassification.duration.LongTests
                                    </excludedGroups>
                                </configuration>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>

    </profiles>

</project>