pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>

	<parent>
		<groupId>org.springframework.boot</groupId>
		<artifactId>spring-boot-starter-parent</artifactId>
		<version>3.4.1</version>
	</parent>

	<groupId>org.cbioportal</groupId>
	<artifactId>cbioportal</artifactId>
	<version>6.0.24-SNAPSHOT</version>

	<description>cBioPortal for Cancer Genomics</description>

	<properties>
		<maven.compiler.release>21</maven.compiler.release>
		<sonar.java.source>21</sonar.java.source>
        <java.version>21</java.version>
        <maven.compiler.source>21</maven.compiler.source>
        <maven.compiler.target>21</maven.compiler.target>
		<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
		<timestamp>${maven.build.timestamp}</timestamp>
		<!--        TODO replace with version of cbioportal frontend with compatible
        login url-->
		<frontend.groupId>com.github.cbioportal</frontend.groupId>
		<frontend.version>v6.0.23</frontend.version>

        <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
		<db.version>2.13.1</db.version>

		<!-- Version properties for dependencies that should have same version. -->
		<!-- The rest can be set in the dependencyManagement section -->
		<spring.social.version>1.1.6.RELEASE</spring.social.version>

		<jackson.version>2.12.5</jackson.version>
		<mysql-connector.version>8.0.28</mysql-connector.version>
        <mysql.version>8.2.0</mysql.version>
		<springfox.version>3.0.0</springfox.version>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

		<!-- Sonar -->
		<sonar.projectKey>cBioPortal_cbioportal</sonar.projectKey>
		<sonar.moduleKey>${project.groupId}:${project.artifactId}</sonar.moduleKey>
		<sonar.organization>cbioportal</sonar.organization>
		<sonar.host.url>https://sonarcloud.io</sonar.host.url>
		<sonar.coverage.exclusions>**src/test/**/*.*</sonar.coverage.exclusions>

		<!-- JaCoCo Properties -->
		<jacoco.version>0.8.11</jacoco.version>
		<sonar.java.coveragePlugin>jacoco</sonar.java.coveragePlugin>
		<sonar.dynamicAnalysis>reuseReports</sonar.dynamicAnalysis>
		<sonar.language>java</sonar.language>
		<sonar.coverage.jacoco.xmlReportPaths>
			${project.basedir}/target/site/jacoco/jacoco.xml</sonar.coverage.jacoco.xmlReportPaths>


		<db.test.driver>com.mysql.jdbc.Driver</db.test.driver>
		<!-- For MySQL < 5.5 change 'default_storage_engine' to 'storage_engine' -->
		<db.test.url>
			jdbc:mysql://127.0.0.1:3306/cgds_test?sessionVariables=default_storage_engine=InnoDB&amp;allowLoadLocalInfile=true</db.test.url>
		<db.test.username>cbio_user</db.test.username>
		<db.test.password>somepassword</db.test.password>

		<!--For tomcat instances, the scope to tomcat catalina lib should be provided. this prop is used in portal module.-->
		<tomcat.catalina.scope>provided</tomcat.catalina.scope>
		<tomcat.session.timeout>720</tomcat.session.timeout>


		<!-- Unknown -->
		<io.swagger.version>1.6.3</io.swagger.version>
		<mybatis.starter.version>3.0.4</mybatis.starter.version>
		<testcontainers.version>1.19.4</testcontainers.version>
		<mockserver.version>5.15.0</mockserver.version>
		<opensaml.version>4.1.1</opensaml.version>


		<!-- Third Party -->
		<redisson.version>3.22.0</redisson.version>
		<commons-math3.version>3.6.1</commons-math3.version>
		<springdoc.version>2.8.3</springdoc.version>
		<apache-commons-collections.version>4.4</apache-commons-collections.version>
		<io-jsonwebtoken.version>0.11.2</io-jsonwebtoken.version>
		<mongodb_bson.version>4.11.0</mongodb_bson.version>
		<google_guava.version>32.1.3-jre</google_guava.version>
		<commons_codec.version>1.16.0</commons_codec.version>
		<commons_validator.version>1.7</commons_validator.version>
		<simple_java_bitly.version>1.1</simple_java_bitly.version>
		<ehcache.version>3.7.1</ehcache.version>
		<json_simple.version>1.1.1</json_simple.version>
		<mongo_java_driver.version>3.12.14</mongo_java_driver.version>
		<datumbox.version>0.8.2</datumbox.version>
		<dasniko-testcontainer-keycloak.version>3.2.0</dasniko-testcontainer-keycloak.version>
		<selenium_chrome_driver.version>3.14.0</selenium_chrome_driver.version>
        <selenium.version>4.17.0</selenium.version>
		<sentry.version>7.1.0</sentry.version>
        <clickhouse_testcontainer.version>1.19.7</clickhouse_testcontainer.version>
        <bouncy_castle.version>1.78</bouncy_castle.version>


		<!-- No sure what these are for -->
		<bundle.symbolicName.prefix>org.mskcc</bundle.symbolicName.prefix>
		<bundle.namespace>org.mskcc.mondrian</bundle.namespace>
	</properties>

	<dependencies>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-test</artifactId>
			<scope>test</scope>
		</dependency>
        <dependency>
            <groupId>org.junit.vintage</groupId>
            <artifactId>junit-vintage-engine</artifactId>
            <scope>test</scope>
        </dependency>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
		</dependency>
		<dependency>
			<groupId>ch.qos.logback</groupId>
			<artifactId>logback-core</artifactId>
		</dependency>
		<dependency>
			<groupId>ch.qos.logback</groupId>
			<artifactId>logback-classic</artifactId>
		</dependency>
		<dependency>
			<groupId>pl.pragmatists</groupId>
			<artifactId>JUnitParams</artifactId>
			<version>1.1.0</version>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-web</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-validation</artifactId>
		</dependency>
		<dependency>
			<groupId>org.mybatis.spring.boot</groupId>
			<artifactId>mybatis-spring-boot-starter</artifactId>
			<version>${mybatis.starter.version}</version>
		</dependency>
		<dependency>
			<groupId>org.redisson</groupId>
			<artifactId>redisson</artifactId>
			<version>${redisson.version}</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math3</artifactId>
			<version>${commons-math3.version}</version>
		</dependency>
		<dependency>
			<groupId>org.springdoc</groupId>
			<artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
			<version>${springdoc.version}</version>
		</dependency>
		<dependency>
			<groupId>org.springframework.security</groupId>
			<artifactId>spring-security-core</artifactId>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-collections4</artifactId>
			<version>${apache-commons-collections.version}</version>
		</dependency>
		<dependency>
			<groupId>io.jsonwebtoken</groupId>
			<artifactId>jjwt-api</artifactId>
			<version>${io-jsonwebtoken.version}</version>
		</dependency>
		<dependency>
			<groupId>io.jsonwebtoken</groupId>
			<artifactId>jjwt-impl</artifactId>
			<version>${io-jsonwebtoken.version}</version>
		</dependency>
		<dependency>
			<groupId>io.jsonwebtoken</groupId>
			<artifactId>jjwt-jackson</artifactId>
			<version>${io-jsonwebtoken.version}</version>
		</dependency>
		<dependency>
			<groupId>com.google.guava</groupId>
			<artifactId>guava</artifactId>
			<version>${google_guava.version}</version>
		</dependency>
		<dependency>
			<groupId>commons-codec</groupId>
			<artifactId>commons-codec</artifactId>
			<version>${commons_codec.version}</version>
		</dependency>
		<dependency>
			<groupId>commons-validator</groupId>
			<artifactId>commons-validator</artifactId>
			<version>${commons_validator.version}</version>
		</dependency>
		<dependency>
			<groupId>com.github.romain-warnan</groupId>
			<artifactId>simple-java-bitly</artifactId>
			<version>${simple_java_bitly.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>org.apache.httpcomponents</groupId>
                    <artifactId>httpclient</artifactId>
                </exclusion>
            </exclusions>
		</dependency>
		<dependency>
			<groupId>org.ehcache</groupId>
			<artifactId>ehcache</artifactId>
			<version>${ehcache.version}</version>
		</dependency>
		<dependency>
			<groupId>com.googlecode.json-simple</groupId>
			<artifactId>json-simple</artifactId>
			<version>${json_simple.version}</version>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-cache</artifactId>
		</dependency>
		<dependency>
			<groupId>com.datumbox</groupId>
			<artifactId>datumbox-framework-lib</artifactId>
			<version>${datumbox.version}</version>
		</dependency>
		<dependency>
			<groupId>org.springframework.security</groupId>
			<artifactId>spring-security-config</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.security</groupId>
			<artifactId>spring-security-web</artifactId>
		</dependency>
        <dependency>
            <groupId>org.springframework.security</groupId>
            <artifactId>spring-security-jwt</artifactId>
            <version>1.1.1.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>com.auth0</groupId>
            <artifactId>jwks-rsa</artifactId>
            <version>0.22.1</version>
        </dependency>
        <dependency>
            <groupId>com.mysql</groupId>
            <artifactId>mysql-connector-j</artifactId>
            <version>${mysql.version}</version>
        </dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-thymeleaf</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.security</groupId>
			<artifactId>spring-security-test</artifactId>
			<scope>test</scope>
		</dependency>
        <dependency>
            <groupId>org.seleniumhq.selenium</groupId>
            <artifactId>selenium-java</artifactId>
            <version>${selenium.version}</version>
            <scope>test</scope>
        </dependency>
		<dependency>
			<groupId>org.testcontainers</groupId>
			<artifactId>testcontainers</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.testcontainers</groupId>
			<artifactId>mysql</artifactId>
			<scope>test</scope>
		</dependency>
        <dependency>
            <groupId>org.testcontainers</groupId>
            <artifactId>mockserver</artifactId>
            <scope>test</scope> 
        </dependency>
        <dependency>
            <groupId>org.mock-server</groupId>
            <artifactId>mockserver-client-java</artifactId>
            <version>${mockserver.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>com.github.dasniko</groupId>
            <artifactId>testcontainers-keycloak</artifactId>
            <version>${dasniko-testcontainer-keycloak.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
			<groupId>org.testcontainers</groupId>
			<artifactId>selenium</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>com.h2database</groupId>
			<artifactId>h2</artifactId>
			<scope>test</scope>
		</dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-data-mongodb</artifactId>
        </dependency>
		<!-- JitPack Publishing -->
		<dependency>
			<groupId>com.github.jitpack</groupId>
			<artifactId>maven-simple</artifactId>
			<version>0.1</version>
		</dependency>

		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-oauth2-client</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-oauth2-resource-server</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.security</groupId>
			<artifactId>spring-security-saml2-service-provider</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.session</groupId>
			<artifactId>spring-session-data-redis</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-data-redis</artifactId>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-devtools</artifactId>
			<scope>runtime</scope>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>io.sentry</groupId>
			<artifactId>sentry-spring-boot-starter-jakarta</artifactId>
			<version>${sentry.version}</version>
		</dependency>
        <dependency>
            <groupId>org.apache.httpcomponents.client5</groupId>
            <artifactId>httpclient5</artifactId>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>com.clickhouse</groupId>
            <artifactId>clickhouse-jdbc</artifactId>
            <version>0.6.2</version>
            <!-- use uber jar with all dependencies included, change classifier
            to http for smaller jar -->
            <classifier>all</classifier>
        </dependency>
        <dependency>
            <groupId>org.testcontainers</groupId>
            <artifactId>clickhouse</artifactId>
            <version>${clickhouse_testcontainer.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.mybatis.spring.boot</groupId>
            <artifactId>mybatis-spring-boot-test-autoconfigure</artifactId>
            <version>3.0.3</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-testcontainers</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>org.testcontainers</groupId>
                <artifactId>testcontainers-bom</artifactId>
                <version>${testcontainers.version}</version>
                <type>pom</type>
                <scope>import</scope>
            </dependency>
        </dependencies>
    </dependencyManagement>
    
	<build>
		<finalName>cbioportal</finalName>
		<pluginManagement>
			<plugins>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-wrapper-plugin</artifactId>
					<version>3.2.0</version>
				</plugin>
			</plugins>
		</pluginManagement>

		<filters>
			<filter>src/main/resources/application.properties</filter>
			<filter>src/main/resources/maven.properties</filter>
		</filters>

		<resources>
			<!-- copy over resources directory into classpath of product -->
			<resource>
				<directory>src/main/resources</directory>
				<filtering>true</filtering>
				<excludes>
					<exclude>artwork/**</exclude>
					<exclude>content/**</exclude>
					<exclude>tutorials/**</exclude>
					<exclude>webapp/**</exclude>
					<exclude>templates/**</exclude>
					<exclude>*.pdf</exclude>
					<exclude>db-scripts/**</exclude>

				</excludes>
			</resource>
			<resource>
				<directory>src/main/resources</directory>
				<filtering>false</filtering>
				<includes>
					<include>webapp/**</include>
					<include>templates/**</include>
				</includes>
			</resource>
			<!-- copy over database schema and migration logic into classpath of
			product -->
			<resource>
				<directory>src/main/resources/db-scripts</directory>
				<targetPath>db-scripts</targetPath>
				<filtering>false</filtering>
				<includes>
					<include>cgds.sql</include>
					<include>migration.sql</include>
                    <include>clickhouse/clickhouse.sql</include>
                    <include>clickhouse/materialized_views.sql</include>
				</includes>
			</resource>
		</resources>
        <testResources>
            <testResource>
                <directory>src/main/resources/db-scripts</directory>
                <filtering>false</filtering>
                <includes>
                    <include>clickhouse/clickhouse.sql</include>
                    <include>clickhouse/materialized_views.sql</include>
                </includes> 
            </testResource>
            <testResource>
                <directory>src/test/resources</directory>
                <filtering>false</filtering>
            </testResource>
        </testResources>

		<plugins>
			<plugin>
				<groupId>org.springframework.boot</groupId>
				<artifactId>spring-boot-maven-plugin</artifactId>
				<executions>
					<execution>
						<id>repackage</id>
						<configuration>
							<classifier>exec</classifier>
						</configuration>
					</execution>
				</executions>
			</plugin>

			<!-- write git version properties file (git.properties) -->
			<plugin>
				<groupId>io.github.git-commit-id</groupId>
				<artifactId>git-commit-id-maven-plugin</artifactId>
				<version>5.0.0</version>
				<executions>
					<execution>
						<id>get-the-git-infos</id>
						<phase>initialize</phase>
						<goals>
							<goal>revision</goal>
						</goals>
					</execution>
					<execution>
						<id>validate-the-git-infos</id>
						<phase>package</phase>
						<goals>
							<goal>validateRevision</goal>
						</goals>
					</execution>
				</executions>
				<configuration>
					<dotGitDirectory>${project.basedir}/.git</dotGitDirectory>
					<generateGitPropertiesFile>true</generateGitPropertiesFile>
					<generateGitPropertiesFilename>
						${project.build.outputDirectory}/git.properties</generateGitPropertiesFilename>
					<commitIdGenerationMode>full</commitIdGenerationMode>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-dependency-plugin</artifactId>
				<executions>
					<execution>
						<id>unpack</id>
						<phase>prepare-package</phase>
						<goals>
							<goal>unpack</goal>
						</goals>
						<configuration>
							<artifactItems>
								<artifactItem>
									<groupId>${frontend.groupId}</groupId>
									<artifactId>cbioportal-frontend</artifactId>
									<version>${frontend.version}</version>
									<type>jar</type>
									<outputDirectory>
										${project.build.directory}/classes</outputDirectory>
									<excludes>*index*</excludes>
									<overWrite>true</overWrite>
								</artifactItem>
							</artifactItems>
						</configuration>
					</execution>
				</executions>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-wrapper-plugin</artifactId>
			</plugin>
			<plugin>
				<groupId>org.jacoco</groupId>
				<artifactId>jacoco-maven-plugin</artifactId>
				<version>${jacoco.version}</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>
						<configuration>
							<formats>
								<format>XML</format>
							</formats>
						</configuration>
					</execution>
				</executions>
			</plugin>

            <!-- config for unit and integration tests -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <configuration>
                    <skipTests>${skipTests}</skipTests>
                    <excludes>
                        <exclude>**/*IntegrationTest.java</exclude>
                    </excludes>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-failsafe-plugin</artifactId>
                <configuration>
                    <skipTests>${skipITs}</skipTests>
                    <includes>
                        <include>**/*IntegrationTest.java</include>
                    </includes>
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>integration-test</goal>
                            <goal>verify</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
	</build>

	<reporting>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-javadoc-plugin</artifactId>
				<configuration>
					<doclet>org.umlgraph.doclet.UmlGraphDoc</doclet>
					<docletArtifact>
						<groupId>org.umlgraph</groupId>
						<artifactId>umlgraph</artifactId>
						<version>5.6</version>
					</docletArtifact>
					<additionalparam>-views -all</additionalparam>
					<useStandardDocletOptions>true</useStandardDocletOptions>
				</configuration>
			</plugin>
		</plugins>
	</reporting>

	<pluginRepositories>
		<!-- needed for the maven-external-version-plugin -->
		<pluginRepository>
			<id>jboss-third-party</id>
			<url>
				https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
		</pluginRepository>
		<pluginRepository>
			<id>maven-snapshots</id>
			<url>https://repository.apache.org/content/repositories/snapshots/</url>
		</pluginRepository>
		<pluginRepository>
			<id>maven-shade-plugin</id>
			<url>
				https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-shade-plugin</url>
		</pluginRepository>
	</pluginRepositories>


	<repositories>
		<repository>
			<id>jitpack.io</id>
			<url>https://jitpack.io</url>
		</repository>
		<!-- needed for the maven-external-version-plugin -->
		<repository>
			<id>jboss-third-party</id>
			<url>
				https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
		</repository>
		<!-- needed for the opensaml dependency -->
		<repository>
			<id>shiboleth</id>
			<url>
				https://build.shibboleth.net/nexus/content/repositories/releases/</url>
		</repository>
		<!-- needed for keycloak test containers -->
		<repository>
			<id>maven-central</id>
			<url>https://repo1.maven.org/maven2/</url>
		</repository>
	</repositories>

	<profiles>
		<profile>
			<id>default</id>
			<activation>
				<activeByDefault>true</activeByDefault>
			</activation>
			<properties>
				<skipTests>false</skipTests>
				<!-- skipITs is an official Maven param; do not rename-->
				<skipITs>true</skipITs>
			</properties>
		</profile>
		<profile>
			<id>integration-test</id>
			<properties>
				<skipTests>true</skipTests>
				<!-- skipITs is an official Maven param; do not rename-->
				<skipITs>false</skipITs>
			</properties>
		</profile>
	</profiles>

</project>