cbioportal
Used in:
components
- OverviewOverview
- VersionsVersions
- DependentsDependents
- DependenciesDependencies
<dependency> <groupId>io.github.cbioportal</groupId> <artifactId>cbioportal</artifactId> <version>ef4570dde5acc2a92c8f91df4bb5da7e4ea6ff1c</version> </dependency>
<?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>io.github.cbioportal</groupId> <artifactId>cbioportal</artifactId> <version>ef4570dde5acc2a92c8f91df4bb5da7e4ea6ff1c</version> <packaging>jar</packaging> <description>cBioPortal for Cancer Genomics</description> <properties> <m2e.apt.activation>jdt_apt</m2e.apt.activation> <!-- <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>${maven.build.timestamp}</timestamp> <!-- TODO replace with version of cbioportal frontend with compatible login url--> <frontend.groupId>io.github.cbioportal</frontend.groupId> <frontend.artifactId>frontend-cbioportal</frontend.artifactId> <frontend.version>b15f3ae780bc208731124b3d001995172f5d9693</frontend.version> <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL --> <db.version>2.13.1</db.version> <!-- Version properties for dependencies that should have same version. --> <!-- The rest can be set in the dependencyManagement section --> <spring.social.version>1.1.6.RELEASE</spring.social.version> <jackson.version>2.12.5</jackson.version> <mysql-connector.version>8.0.28</mysql-connector.version> <mysql.version>8.2.0</mysql.version> <springfox.version>3.0.0</springfox.version> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding> <!-- Sonar --> <sonar.projectKey>cBioPortal_cbioportal</sonar.projectKey> <sonar.moduleKey>${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&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> <mapstruct.version>1.6.3</mapstruct.version> <!-- No sure what these are for --> <bundle.symbolicName.prefix>org.mskcc</bundle.symbolicName.prefix> <bundle.namespace>org.mskcc.mondrian</bundle.namespace> <!-- Maven Central --> <mavenCentralDeploymentName>Deployment</mavenCentralDeploymentName> </properties> <!-- Maven Central Requirements --> <name>${project.groupId}:${project.artifactId}</name> <url>https://www.cbioportal.org</url> <licenses> <license> <name>GNU AFFERO GENERAL PUBLIC LICENSE v3.0</name> <url>https://www.gnu.org/licenses/agpl-3.0.html</url> </license> </licenses> <developers> <developer> <name>Zain Nasir</name> <email>nasirz1@mskcc.org</email> <organization>Memorial Sloan Kettering Cancer Center</organization> <organizationUrl>https://www.mskcc.org/</organizationUrl> </developer> </developers> <scm> <connection>scm:git:git://github.com/cBioPortal/cbioportal.git</connection> <developerConnection>scm:git:ssh://github.com:cBioPortal/cbioportal.git</developerConnection> <url>https://github.com/cBioPortal/cbioportal/tree/master</url> </scm> <dependencies> <dependency> <groupId>org.springframework.boot</groupId> <artifactId>spring-boot-starter</artifactId> </dependency> <dependency> <groupId>org.springframework.boot</groupId> <artifactId>spring-boot-starter-test</artifactId> <scope>test</scope> </dependency> <dependency> <groupId>org.junit.vintage</groupId> <artifactId>junit-vintage-engine</artifactId> <scope>test</scope> </dependency> <dependency> <groupId>org.slf4j</groupId> <artifactId>slf4j-api</artifactId> </dependency> <dependency> <groupId>ch.qos.logback</groupId> <artifactId>logback-core</artifactId> </dependency> <dependency> <groupId>ch.qos.logback</groupId> <artifactId>logback-classic</artifactId> </dependency> <dependency> <groupId>pl.pragmatists</groupId> <artifactId>JUnitParams</artifactId> <version>1.1.0</version> <scope>test</scope> </dependency> <dependency> <groupId>org.springframework.boot</groupId> <artifactId>spring-boot-starter-web</artifactId> </dependency> <dependency> <groupId>org.springframework.boot</groupId> <artifactId>spring-boot-starter-validation</artifactId> </dependency> <dependency> <groupId>org.mybatis.spring.boot</groupId> <artifactId>mybatis-spring-boot-starter</artifactId> <version>${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>${mockserver.version}</version> <scope>test</scope> <exclusions> <exclusion> <groupId>javax.servlet</groupId> <artifactId>javax.servlet-api</artifactId> </exclusion> </exclusions> </dependency> <dependency> <groupId>com.github.dasniko</groupId> <artifactId>testcontainers-keycloak</artifactId> <version>${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> <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> <dependency> <groupId>org.mapstruct</groupId> <artifactId>mapstruct</artifactId> <version>${mapstruct.version}</version> </dependency> <!-- Add OSGi dependency needed because compile time of org.ehcache --> <!-- ehcache should be removed --> <dependency> <groupId>org.osgi</groupId> <artifactId>org.osgi.service.component.annotations</artifactId> <version>1.5.1</version> <scope>provided</scope> </dependency> </dependencies> <dependencyManagement> <dependencies> <dependency> <groupId>org.testcontainers</groupId> <artifactId>testcontainers-bom</artifactId> <version>${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.apache.maven.plugins</groupId> <artifactId>maven-compiler-plugin</artifactId> <version>3.13.0</version> <configuration> <release>21</release> <annotationProcessorPaths> <path> <groupId>org.mapstruct</groupId> <artifactId>mapstruct-processor</artifactId> <version>${mapstruct.version}</version> </path> </annotationProcessorPaths> </configuration> </plugin> <plugin> <groupId>org.springframework.boot</groupId> <artifactId>spring-boot-maven-plugin</artifactId> <executions> <execution> <id>repackage</id> <configuration> <classifier>exec</classifier> </configuration> </execution> </executions> </plugin> <!-- write git version properties file (git.properties) --> <plugin> <groupId>io.github.git-commit-id</groupId> <artifactId>git-commit-id-maven-plugin</artifactId> <version>5.0.0</version> <executions> <execution> <id>get-the-git-infos</id> <phase>initialize</phase> <goals> <goal>revision</goal> </goals> </execution> <execution> <id>validate-the-git-infos</id> <phase>package</phase> <goals> <goal>validateRevision</goal> </goals> </execution> </executions> <configuration> <dotGitDirectory>${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>${frontend.artifactId}</artifactId> <version>${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> <!-- Maven Central Plugins --> <plugin> <groupId>org.sonatype.central</groupId> <artifactId>central-publishing-maven-plugin</artifactId> <version>0.7.0</version> <extensions>true</extensions> <configuration> <publishingServerId>central</publishingServerId> <autoPublish>true</autoPublish> <waitUntil>published</waitUntil> <deploymentName>${mavenCentralDeploymentName}</deploymentName> </configuration> </plugin> <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-source-plugin</artifactId> <version>3.3.0</version> <executions> <execution> <id>attach-sources</id> <phase>verify</phase> <goals> <goal>jar-no-fork</goal> </goals> </execution> </executions> </plugin> <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-gpg-plugin</artifactId> <version>3.1.0</version> <executions> <execution> <id>sign-artifacts</id> <phase>verify</phase> <goals> <goal>sign</goal> </goals> </execution> </executions> <configuration> <gpgArguments> <arg>--pinentry-mode</arg> <arg>loopback</arg> </gpgArguments> </configuration> </plugin> <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-source-plugin</artifactId> <version>3.3.0</version> <executions> <execution> <id>attach-sources</id> <phase>verify</phase> <goals> <goal>jar-no-fork</goal> </goals> </execution> </executions> </plugin> <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-javadoc-plugin</artifactId> <version>3.6.3</version> <executions> <execution> <id>attach-javadoc</id> <goals> <goal>jar</goal> </goals> </execution> </executions> <configuration> <stylesheet>java</stylesheet> <doclint>none</doclint> </configuration> </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> <!-- 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>