pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<!--
  ~ The Exomiser - A tool to annotate and prioritize genomic variants
  ~
  ~ Copyright (c) 2016-2022 Queen Mary University of London.
  ~ Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
  ~
  ~ This program is free software: you can redistribute it and/or modify
  ~ it under the terms of the GNU Affero General Public License as
  ~ published by the Free Software Foundation, either version 3 of the
  ~ License, or (at your option) any later version.
  ~
  ~ This program is distributed in the hope that it will be useful,
  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  ~ GNU Affero General Public License for more details.
  ~
  ~ You should have received a copy of the GNU Affero General Public License
  ~ along with this program.  If not, see <http://www.gnu.org/licenses/>.
  -->

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 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.monarchinitiative.exomiser</groupId>
    <artifactId>exomiser</artifactId>
    <version>14.0.0</version>
    <packaging>pom</packaging>

    <name>exomiser</name>
    <description>A toolkit for filtering variants and prioritising genes by phenotype from whole genome or whole exome VCF files.</description>
    <url>https://github.com/exomiser/Exomiser</url>
    <inceptionYear>2012</inceptionYear>

    <licenses>
        <license>
            <name>GNU AFFERO GENERAL PUBLIC LICENSE, Version 3 (AGPL-3.0)</name>
            <url>http://opensource.org/licenses/AGPL-3.0</url>
        </license>
    </licenses>

    <developers>
        <developer>
            <name>Jules Jacobsen</name>
            <email>j.jacobsen@qmul.ac.uk</email>
            <organization>Queen Mary University of London</organization>
            <organizationUrl>http://qmul.ac.uk</organizationUrl>
        </developer>
        <developer>
            <name>Damian Smedley</name>
            <email>d.smedley@qmul.ac.uk</email>
            <organization>Queen Mary University of London</organization>
            <organizationUrl>http://qmul.ac.uk</organizationUrl>
        </developer>
        <developer>
            <name>Peter Robinson</name>
            <email>peter.robinson@jax.org</email>
            <organization>The Jackson Laboratory for Genomic Medicine</organization>
            <organizationUrl>https://www.jax.org/</organizationUrl>
        </developer>
    </developers>

    <scm>
        <connection>scm:git:git://github.com/exomiser/Exomiser.git</connection>
        <developerConnection>scm:git:git@github.com:exomiser/Exomiser.git</developerConnection>
        <url>https://github.com/exomiser/Exomiser/tree/master</url>
    </scm>

    <ciManagement>
        <system>Circle CI</system>
        <url>https://circleci.com/gh/exomiser/Exomiser</url>
    </ciManagement>

    <modules>
        <module>phenix-repository</module>
        <module>exomiser-core</module>
        <module>exomiser-spring-boot-autoconfigure</module>
        <module>exomiser-spring-boot-starter</module>
        <module>exomiser-spring-boot-test</module>
        <module>exomiser-cli</module>
        <module>exomiser-data-genome</module>
        <module>exomiser-data-phenotype</module>
        <module>exomiser-rest-prioritiser</module>
        <module>exomiser-web</module>
    </modules>

    <properties>
        <java.version>17</java.version>
        <maven.build.timestamp.format>yyyy-MM-dd HH:mm</maven.build.timestamp.format>
        <build.timestamp>${maven.build.timestamp}</build.timestamp>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.organization>The Monarch Initiative</project.organization>
        <sonar.host.url>https://sonarcloud.io</sonar.host.url>
        <sonar.organization>exomiser</sonar.organization>
        <sonar.language>java</sonar.language>
        <jannovar.version>0.41</jannovar.version>
        <svart.version>2.0.0-RC6</svart.version>
        <htsjdk.version>3.0.5</htsjdk.version>
        <guava.version>31.1-jre</guava.version>
        <protobuf.version>3.21.12</protobuf.version>
        <spring-boot.version>3.2.3</spring-boot.version>
        <!-- H2 version 1.4.200 was used for 2309 and below, 2.1.214 is part of Spring boot 3.1.1 the file formats and
        API for the MVStore are different so consider very hard if this needs updating.-->
        <h2.version>2.2.224</h2.version>
        <!-- flway needs to be limited for it to support migrations on the H2 version used above -->
        <flyway.version>10.6.0</flyway.version>
        <docker.base.image>
            gcr.io/distroless/java17-debian11@sha256:d5a7bb2b1bcd09d9b7ba7f7b13df39cbb2ab2ff73a0ab834a5769e59229af2f8
        </docker.base.image>
        <docker.registry>docker.io</docker.registry>
        <docker.repository>exomiser</docker.repository>
        <!--    These properties are use for the README.md  -->
        <genome.data.version>2402</genome.data.version>
        <phenotype.data.version>2402</phenotype.data.version>
    </properties>

    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>org.springframework.boot</groupId>
                <artifactId>spring-boot-dependencies</artifactId>
                <version>${spring-boot.version}</version>
                <type>pom</type>
                <scope>import</scope>
            </dependency>
        </dependencies>
    </dependencyManagement>

    <dependencies>
        <dependency>
            <groupId>org.monarchinitiative.svart</groupId>
            <artifactId>svart</artifactId>
            <version>${svart.version}</version>
        </dependency>
        <!--DI framework -->
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-core</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context-support</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-jdbc</artifactId>
            <type>jar</type>
        </dependency>
        <!--H2 is a very versatile and highly compatible pure java DB-->
        <dependency>
            <groupId>com.h2database</groupId>
            <artifactId>h2</artifactId>
            <version>${h2.version}</version>
        </dependency>
        <!--https://github.com/brettwooldridge/HikariCP/wiki/FAQ#q-how-to-i-properly-enable-preparedstatement-caching-for-postgresql-->
        <!--        <dependency>-->
        <!--            <groupId>com.impossibl.pgjdbc-ng</groupId>-->
        <!--            <artifactId>pgjdbc-ng</artifactId>-->
        <!--            <version>0.4</version>-->
        <!--        </dependency>-->
        <!--HikariCP is a "zero-overhead" production ready JDBC connection pool.
        https://github.com/brettwooldridge/HikariCP -->
        <dependency>
            <groupId>com.zaxxer</groupId>
            <artifactId>HikariCP</artifactId>
        </dependency>

        <!-- Need to override guava to version 21.0 which  contains the Java 8 Collectors support on immutable Collections
        used by exomiser-core-->
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
            <version>${guava.version}</version>
        </dependency>
        <!-- https://mvnrepository.com/artifact/com.google.protobuf/protobuf-java -->
        <dependency>
            <groupId>com.google.protobuf</groupId>
            <artifactId>protobuf-java</artifactId>
            <version>${protobuf.version}</version>
        </dependency>
        <dependency>
            <groupId>com.google.protobuf</groupId>
            <artifactId>protobuf-java-util</artifactId>
            <version>${protobuf.version}</version>
        </dependency>
        <!--JSON + YAML deps-->
        <dependency>
            <groupId>com.fasterxml.jackson.dataformat</groupId>
            <artifactId>jackson-dataformat-yaml</artifactId>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.dataformat</groupId>
            <artifactId>jackson-dataformat-protobuf</artifactId>
        </dependency>

        <!--Test dependencies-->
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-test</artifactId>
            <scope>test</scope>
            <exclusions>
                <exclusion>
                    <groupId>org.junit.vintage</groupId>
                    <artifactId>junit-vintage-engine</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <!-- Required to run Mockito with JUnit Jupiter-->
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-junit-jupiter</artifactId>
            <scope>test</scope>
        </dependency>
        <!-- ByteBuddy 1.9.0+ required for compiling on Java 11 -->
        <dependency>
            <groupId>net.bytebuddy</groupId>
            <artifactId>byte-buddy</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>
    
    <build>
        <pluginManagement>
            <plugins>
                <plugin>
                    <groupId>com.google.cloud.tools</groupId>
                    <artifactId>jib-maven-plugin</artifactId>
                    <version>3.3.0</version>
                </plugin>
            </plugins>
        </pluginManagement>
        <plugins>
            <plugin>
                <!-- n.b. the wrapper plugin is completely broken and will only work on Maven 3.7.0+ -->
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-wrapper-plugin</artifactId>
                <version>3.0.1</version>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.11.0</version>
                <configuration>
                    <source>${java.version}</source>
                    <target>${java.version}</target>
                    <parameters>true</parameters>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>3.0.0</version>
                <!-- Don't enable parallel tests as these will fail in the autoconfigure module due to MVStore
                only being able to be opened once by any given JVM -->
                <!--                <configuration>-->
                <!--                    <forkCount>0</forkCount>-->
                <!--                </configuration>-->
            </plugin>
            <plugin>
                <groupId>org.sonarsource.scanner.maven</groupId>
                <artifactId>sonar-maven-plugin</artifactId>
                <version>3.7.0.1746</version>
            </plugin>
            <plugin>
                <groupId>org.jacoco</groupId>
                <artifactId>jacoco-maven-plugin</artifactId>
                <version>0.8.10</version>
                <executions>
                    <execution>
                        <id>prepare-agent</id>
                        <goals>
                            <goal>prepare-agent</goal>
                        </goals>
                    </execution>
                    <execution>
                        <id>report</id>
                        <phase>test</phase>
                        <goals>
                            <goal>report</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
    <profiles>
        <profile>
            <id>coverage</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.jacoco</groupId>
                        <artifactId>jacoco-maven-plugin</artifactId>
                        <version>0.8.10</version>
                        <executions>
                            <execution>
                                <id>prepare-agent</id>
                                <goals>
                                    <goal>prepare-agent</goal>
                                </goals>
                            </execution>
                            <execution>
                                <id>report</id>
                                <goals>
                                    <goal>report</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>
</project>