pom.xml

<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/maven-v4_0_0.xsd">

  <modelVersion>4.0.0</modelVersion>
  <groupId>org.cbioportal.annotation.pipeline</groupId>
  <artifactId>master</artifactId>
  <version>1.0.0</version>
  <name>Genome Nexus Variant Annotation Tools</name>
  <description>tools for annotating variants via genome nexus</description>
  <packaging>pom</packaging>
  <url>https://github.com/cbioportal/genome-nexus-annotation-pipeline/</url>

  <modules>
    <module>annotationPipeline</module>
    <module>annotator</module>
    <module>databaseAnnotator</module>
  </modules>

  <!-- inherit defaults from spring boot -->
  <parent>
    <groupId>org.springframework.boot</groupId>
    <artifactId>spring-boot-starter-parent</artifactId>
    <version>2.7.0</version>
  </parent>

  <properties>
    <java.version>17</java.version>
    <slf4j.version>1.7.30</slf4j.version>
    <spring.version>5.3.0</spring.version>
    <jackson.version>2.11.2</jackson.version>
  </properties>

  <dependencies>
    <dependency>
      <groupId>org.springframework.boot</groupId>
      <artifactId>spring-boot-starter-batch</artifactId>
        <exclusions>
          <exclusion>
            <groupId>org.slf4j</groupId>
            <artifactId>log4j-over-slf4j</artifactId>
          </exclusion>
          <exclusion>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
          </exclusion>
        </exclusions>
    </dependency>
    <dependency>
      <groupId>org.springframework.boot</groupId>
      <artifactId>spring-boot-starter-test</artifactId>
    </dependency>
    <!-- slf4j -->
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-log4j12</artifactId>
      <version>${slf4j.version}</version>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-api</artifactId>
      <version>${slf4j.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.batch</groupId>
      <artifactId>spring-batch-test</artifactId>
    </dependency>

    <!-- cbioportal -->
    <dependency>
      <groupId>com.github.averyniceday.cbioportal</groupId>
      <artifactId>core</artifactId>
      <version>7db494c4a3</version>
      <exclusions>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-core</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <!-- spring embedded datasource for testing -->
    <dependency>
      <groupId>com.h2database</groupId>
      <artifactId>h2</artifactId>
      <version>1.3.156</version>
    </dependency>
      <!-- https://mvnrepository.com/artifact/org.xerial/sqlite-jdbc -->
    <dependency>
      <groupId>org.xerial</groupId>
      <artifactId>sqlite-jdbc</artifactId>
      <version>3.34.0</version>
    </dependency>
    <!-- allows junit3 or juni4 tests to run in the juni5 environment -->
    <dependency>
      <groupId>org.junit.vintage</groupId>
      <artifactId>junit-vintage-engine</artifactId>
      <version>5.8.2</version>
      <scope>test</scope>
    </dependency>
    <!-- api client -->
    <dependency>
      <groupId>com.github.genome-nexus.genome-nexus-java-api-client</groupId>
      <artifactId>genomeNexusPublicApiClient</artifactId>
      <version>600501017ef64be14cfb36679babec30da9200ca</version>
    </dependency>
    <dependency>
      <groupId>com.github.genome-nexus.genome-nexus-java-api-client</groupId>
      <artifactId>genomeNexusInternalApiClient</artifactId>
      <version>600501017ef64be14cfb36679babec30da9200ca</version>
    </dependency>
  </dependencies>

  <repositories>
    <repository>
      <id>jitpack.io</id>
      <url>https://jitpack.io</url>
    </repository>
  </repositories>

  <build>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <configuration>
          <useSystemClassLoader>false</useSystemClassLoader>
          <properties>
            <includeTags>junit5</includeTags>
          </properties>
        </configuration>
      </plugin>
    </plugins>
  </build>

</project>