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/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<groupId>cloudgene</groupId>
	<artifactId>cloudgene</artifactId>
	<version>2.8.5</version>

	<name>Cloudgene</name>
	<url>http://www.cloudgene.io</url>
	<organization>
		<name>Lukas Forer and Sebastian Schoenherr</name>
	</organization>

	<developers>
		<developer>
			<id>lukfor</id>
			<name>Lukas Forer</name>
			<email>lukas.forer@i-med.ac.at</email>
			<url>http://www.forer.it</url>
			<organization>Medical University of Innsbruck</organization>
		</developer>
		<developer>
			<id>seb</id>
			<name>Sebastian Schoenherr</name>
			<email>sebastian.schoenherr@i-med.ac.at</email>
			<url>https://seppinho.github.io</url>
			<organization>Medical University of Innsbruck</organization>
		</developer>
	</developers>

	<properties>
		<java.version>1.8</java.version>
		<restlet.version>2.3.12</restlet.version>
		<hadoop.version>2.6.0-cdh5.16.1</hadoop.version>
		<node.version>v18.17.1</node.version>
		<npm.version>9.6.7</npm.version>
		<webapp>${basedir}/src/main/html/webapp</webapp>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
	</properties>

	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>com.amazonaws</groupId>
				<artifactId>aws-java-sdk-bom</artifactId>
				<version>1.12.153</version>
				<type>pom</type>
				<scope>import</scope>
			</dependency>
		</dependencies>
	</dependencyManagement>

	<repositories>
		<repository>
			<id>maven-restlet</id>
			<name>Restlet Framework repository</name>
			<url>https://maven.restlet.talend.com</url>
		</repository>

		<repository>
			<id>genepi-maven</id>
			<name>genepi-maven</name>
			<url>https://genepi.i-med.ac.at/maven</url>
		</repository>

		<repository>
			<id>cloudera</id>
			<name>Cloudera repository</name>
			<url>https://repository.cloudera.com/artifactory/cloudera-repos/</url>
		</repository>

	</repositories>

	<!-- **** Dependencies **** -->

	<dependencies>

		<dependency>
			<groupId>cloudgene</groupId>
			<artifactId>cloudgene-java-sdk</artifactId>
			<version>1.0.2</version>
		</dependency>

		<dependency>
			<groupId>genepi</groupId>
			<artifactId>genepi-io</artifactId>
			<version>1.2.0</version>
			<exclusions>
				<exclusion>
					<groupId>log4j</groupId>
					<artifactId>log4j</artifactId>
				</exclusion>
			</exclusions>
		</dependency>
		<dependency>
				<groupId>commons-dbutils</groupId>
				<artifactId>commons-dbutils</artifactId>
				<version>1.7</version>
			</dependency>
	
			<dependency>
				<groupId>commons-dbcp</groupId>
				<artifactId>commons-dbcp</artifactId>
				<version>1.4</version>
			</dependency>
		<dependency>
			<groupId>genepi</groupId>
			<artifactId>genepi-hadoop</artifactId>
			<version>mr1-1.4.1</version>
			<exclusions>
				<exclusion>
					<groupId>org.apache.hadoop</groupId>
					<artifactId>hadoop-client</artifactId>
				</exclusion>
				<exclusion>
					<groupId>org.apache.httpcomponents</groupId>
					<artifactId>httpcore</artifactId>
				</exclusion>
				<exclusion>
					<groupId>org.apache.httpcomponents</groupId>
					<artifactId>httpclient</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>mysql</groupId>
			<artifactId>mysql-connector-java</artifactId>
			<version>8.0.32</version>
		</dependency>

		<dependency>
			<groupId>com.h2database</groupId>
			<artifactId>h2</artifactId>
			<version>2.2.220</version>
		</dependency>

		<dependency>
			<groupId>org.restlet.jse</groupId>
			<artifactId>org.restlet</artifactId>
			<version>${restlet.version}</version>
		</dependency>

		<dependency>
			<groupId>org.restlet.jse</groupId>
			<artifactId>org.restlet.ext.jetty</artifactId>
			<version>${restlet.version}</version>
		</dependency>

		<dependency>
			<groupId>org.restlet.jse</groupId>
			<artifactId>org.restlet.ext.json</artifactId>
			<version>${restlet.version}</version>
		</dependency>

		<dependency>
			<groupId>org.restlet.jee</groupId>
			<artifactId>org.restlet.ext.html</artifactId>
			<version>${restlet.version}</version>
		</dependency>

		<dependency>
			<groupId>org.restlet.jee</groupId>
			<artifactId>org.restlet.ext.fileupload</artifactId>
			<version>${restlet.version}</version>
		</dependency>

		<dependency>
			<groupId>org.restlet.jee</groupId>
			<artifactId>org.restlet.ext.slf4j</artifactId>
			<version>${restlet.version}</version>
			<exclusions>
				<exclusion>
					<groupId>org.slf4j</groupId>
					<artifactId>slf4j-api</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.restlet.jee</groupId>
			<artifactId>org.restlet.ext.freemarker</artifactId>
			<version>${restlet.version}</version>
		</dependency>

		<dependency>
			<groupId>org.codehaus.groovy</groupId>
			<artifactId>groovy-all</artifactId>
			<version>3.0.17</version>
			<type>pom</type>
		</dependency>

		<dependency>
			<groupId>org.apache.ivy</groupId>
			<artifactId>ivy</artifactId>
			<version>2.5.2</version>
		</dependency>

		<!-- Logging -->

		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-api</artifactId>
			<version>2.19.0</version>
		</dependency>

		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-core</artifactId>
			<version>2.19.0</version>
		</dependency>

		<!-- use slf4j with log4j2 -->
		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-slf4j-impl</artifactId>
			<version>2.19.0</version>
		</dependency>

		<!-- use apache commons with log4j2 -->
		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-jcl</artifactId>
			<version>2.19.0</version>
		</dependency>

		<!-- End Logging -->

		<dependency>
			<groupId>commons-io</groupId>
			<artifactId>commons-io</artifactId>
			<version>2.11.0</version>
		</dependency>

		<dependency>
		    <groupId>com.contrastsecurity</groupId>
		    <artifactId>yamlbeans</artifactId>
		    <version>1.17</version>
		</dependency>

		<dependency>
		    <groupId>org.apache.velocity</groupId>
		    <artifactId>velocity-engine-core</artifactId>
		    <version>2.3</version>
		</dependency>


		<dependency>
			<groupId>com.nimbusds</groupId>
			<artifactId>nimbus-jose-jwt</artifactId>
			<version>9.19</version>
		</dependency>

		<dependency>
			<groupId>net.sf.json-lib</groupId>
			<artifactId>json-lib</artifactId>
			<version>2.4</version>
			<classifier>jdk15</classifier>
		</dependency>

		<dependency>
			<groupId>com.sun.mail</groupId>
			<artifactId>javax.mail</artifactId>
			<version>1.6.2</version>
		</dependency>

		<dependency>
			<groupId>org.quartz-scheduler</groupId>
			<artifactId>quartz</artifactId>
			<version>2.3.2</version>
			<exclusions>
				<exclusion>
					<groupId>org.slf4j</groupId>
					<artifactId>slf4j-api</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.quartz-scheduler</groupId>
			<artifactId>quartz-jobs</artifactId>
			<version>2.3.2</version>
		</dependency>

		<dependency>
			<groupId>net.lingala.zip4j</groupId>
			<artifactId>zip4j</artifactId>
			<version>2.11.3</version>
		</dependency>

		<dependency>
			<groupId>net.gpedro.integrations.slack</groupId>
			<artifactId>slack-webhook</artifactId>
			<version>1.4.0</version>
		</dependency>

		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<version>32.0.0-jre</version>
		</dependency>

		<dependency>
			<groupId>com.amazonaws</groupId>
			<artifactId>aws-java-sdk-s3</artifactId>
		</dependency>

		<dependency>
			<groupId>com.amazonaws</groupId>
			<artifactId>aws-java-sdk-sts</artifactId>
		</dependency>

		<dependency>
			<groupId>org.springframework.security</groupId>
			<artifactId>spring-security-crypto</artifactId>
			<version>5.8.1</version>
		</dependency>

		<!-- Test Dependencies -->

		<dependency>
			<groupId>org.bouncycastle</groupId>
			<artifactId>bcprov-jdk15on</artifactId>
			<version>1.70</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>org.apache.hadoop</groupId>
			<artifactId>hadoop-hdfs</artifactId>
			<version>${hadoop.version}</version>
			<scope>test</scope>
			<type>test-jar</type>
		</dependency>

		<dependency>
			<groupId>org.apache.hadoop</groupId>
			<artifactId>hadoop-hdfs</artifactId>
			<version>${hadoop.version}</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>org.apache.hadoop</groupId>
			<artifactId>hadoop-common</artifactId>
			<version>${hadoop.version}</version>
			<scope>test</scope>
			<exclusions>
				<exclusion>
					<groupId>org.apache.httpcomponents</groupId>
					<artifactId>httpcore</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<dependency>
			<groupId>org.apache.hadoop</groupId>
			<artifactId>hadoop-common</artifactId>
			<version>${hadoop.version}</version>
			<scope>test</scope>
			<type>test-jar</type>
		</dependency>

		<dependency>
			<groupId>org.apache.hadoop</groupId>
			<artifactId>hadoop-test</artifactId>
			<version>2.6.0-mr1-cdh5.16.1</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.13.1</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>dumbster</groupId>
			<artifactId>dumbster</artifactId>
			<version>1.6</version>
			<scope>test</scope>
			<exclusions>
				<exclusion>
					<groupId>javax.activation</groupId>
					<artifactId>activation</artifactId>
				</exclusion>
				<exclusion>
					<groupId>javax.mail</groupId>
					<artifactId>mail</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

	</dependencies>

	<!-- **** Build **** -->

	<build>
		<resources>
			<resource>
				<directory>resources</directory>
				<excludes>
					<exclude>**/*.java</exclude>
				</excludes>
			</resource>

			<resource>
				<directory>src/main/sql</directory>
			</resource>
		</resources>

		<plugins>
			<plugin>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.1</version>
				<configuration>
					<source>${java.version}</source>
					<target>${java.version}</target>
				</configuration>
			</plugin>

			<!-- Create webapp for production -->

			<plugin>
				<groupId>com.github.eirslett</groupId>
				<artifactId>frontend-maven-plugin</artifactId>
				<version>1.11.0</version>
				<executions>
					<execution>
						<id>install node and npm</id>
						<goals>
							<goal>install-node-and-npm</goal>
						</goals>
						<configuration>
							<nodeVersion>${node.version}</nodeVersion>
							<npmVersion>${npm.version}</npmVersion>
							<workingDirectory>${webapp}</workingDirectory>
						</configuration>
					</execution>
					<execution>
						<id>npm install</id>
						<goals>
							<goal>npm</goal>
						</goals>
						<configuration>
							<arguments>install</arguments>
							<workingDirectory>${webapp}</workingDirectory>

						</configuration>
					</execution>
					<execution>
						<id>npm build prod</id>
						<goals>
							<goal>npm</goal>
						</goals>
						<phase>generate-resources</phase>
						<configuration>
							<arguments>run build</arguments>
							<npmInheritsProxyConfigFromMaven>false</npmInheritsProxyConfigFromMaven>
							<workingDirectory>${webapp}</workingDirectory>

						</configuration>
					</execution>
				</executions>
			</plugin>

			<!-- Build jar -->

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jar-plugin</artifactId>
				<version>3.1.0</version>
				<configuration>
					<archive>
						<manifest>
							<addClasspath>true</addClasspath>
							<classpathPrefix>lib/</classpathPrefix>
							<mainClass>cloudgene.mapred.Main</mainClass>
						</manifest>
						<manifestEntries>
							<Version>${project.version}</Version>
							<Build-Time>${maven.build.timestamp}</Build-Time>
						</manifestEntries>
					</archive>
				</configuration>

			</plugin>

			<!-- Build final directory structure and zip files -->

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-assembly-plugin</artifactId>
				<version>2.4</version>
				<executions>
					<execution>
						<id>create-assembly</id>
						<phase>package</phase>
						<goals>
							<goal>single</goal>
						</goals>
						<configuration>
							<descriptors>
								<descriptor>src/main/assembly/assembly.xml</descriptor>
							</descriptors>
						</configuration>
					</execution>
				</executions>
			</plugin>

			<!-- Build cloudgene installer -->

			<plugin>
				<groupId>com.github.hazendaz.maven</groupId>
				<artifactId>makeself-maven-plugin</artifactId>
				<version>1.0.0.beta3</version>
				<configuration>
					<archiveDir>cloudgene-${project.version}-assembly</archiveDir>
					<fileName>cloudgene-installer.sh</fileName>
					<label>Install Cloudgene ${project.version}</label>
					<notemp>true</notemp>
					<current>true</current>
					<nox11>true</nox11>
					<nowait>true</nowait>
				</configuration>
				<executions>
					<execution>
						<id>makeself</id>
						<goals>
							<goal>makeself</goal>
						</goals>
					</execution>
				</executions>
			</plugin>

			<!-- Code Coverage -->

			<plugin>
				<groupId>org.jacoco</groupId>
				<artifactId>jacoco-maven-plugin</artifactId>
				<version>0.8.5</version>
				<executions>
					<execution>
						<goals>
							<goal>prepare-agent</goal>
						</goals>
					</execution>
					<execution>
						<id>report</id>
						<phase>test</phase>
						<goals>
							<goal>report</goal>
						</goals>
					</execution>
				</executions>
			</plugin>

		</plugins>
	</build>

</project>