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 http://maven.apache.org/xsd/maven-4.0.0.xsd">
  <!-- meta data -->
  <modelVersion>4.0.0</modelVersion>
  <groupId>org.mskcc.cbio</groupId>
  <artifactId>master</artifactId>
  <packaging>pom</packaging>
  <name>Portal Master</name>
  <!-- project version is generated through git or can be passed as
	   PROJECT_VERSION env variable (see version.sh) -->
  <version>0-unknown-version-SNAPSHOT</version>
  <description>master maven module</description>

  <scm>
    <developerConnection>scm:git:https://github.com/cBioPortal/cbioportal.git</developerConnection>
  </scm>

  <repositories>
    <repository>
      <id>spring-milestones</id>
      <name>Spring Milestones</name>
      <url>http://repo.spring.io/milestone</url>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
    </repository>
  </repositories>
  <pluginRepositories>
    <pluginRepository>
      <id>jitpack.io</id>
      <url>https://jitpack.io</url>
    </pluginRepository>
  </pluginRepositories>

  <profiles>
    <profile>
      <id>public</id>
      <activation>
        <activeByDefault>true</activeByDefault>
      </activation>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
      </properties>
    <build>
    <plugins>
          <plugin>
            <groupId>com.github.cbioportal.maven-external-version</groupId>
            <artifactId>maven-external-version-plugin</artifactId>
            <version>f09c2b9608744881111f24e55d55a91e54e6cb5f</version>
            <extensions>true</extensions>
            <configuration>
              <strategy hint="script">
                <script>./version.sh</script>
              </strategy>
            </configuration>
          </plugin>
          <plugin>
            <groupId>org.jacoco</groupId>
            <artifactId>jacoco-maven-plugin</artifactId>
             <version>${jacoco-maven-plugin.version}</version>
             <executions>
                <!--
                    Prepares the property pointing to the JaCoCo runtime agent which
                    is passed as VM argument when Maven the Surefire plugin is executed.
                -->
                <execution>
                    <id>pre-unit-test</id>
                    <phase>process-test-classes</phase>
                    <goals>
                        <goal>prepare-agent</goal>
                    </goals>
                    <configuration>
                        <!-- Sets the path to the file which contains the execution data. -->
                        <destFile>${project.build.directory}/coverage-reports/jacoco-ut.exec</destFile>
                        <!--
                            Sets the name of the property containing the settings
                            for JaCoCo runtime agent.
                        -->
                        <propertyName>argLine</propertyName>
                    </configuration>
                </execution>
                <!--
                    Ensures that the code coverage report for unit tests is created after
                    unit tests have been run.
                -->
                <execution>
                    <id>post-unit-test</id>
                    <phase>test</phase>
                    <goals>
                        <goal>report</goal>
                    </goals>
                    <configuration>
                        <!-- Sets the path to the file which contains the execution data. -->
                        <dataFile>${project.build.directory}/coverage-reports/jacoco-ut.exec</dataFile>
                        <!-- Sets the output directory for the code coverage report. -->
                        <outputDirectory>${project.build.directory}/coverage-reports/jacoco-ut</outputDirectory>
                    </configuration>
                </execution>
             </executions>
          </plugin>
          <!-- copy portal.properties.EXAMPLE and log4j.properties.EXAMPLE if they don't exist -->
          <plugin>
            <artifactId>maven-antrun-plugin</artifactId>
            <version>1.8</version>
            <!-- only needs to be executed for parent pom -->
            <inherited>false</inherited>
            <executions>
              <execution>
                <phase>validate</phase>
                <goals>
                  <goal>run</goal>
                </goals>
                <configuration>
                  <target>
                    <taskdef resource="net/sf/antcontrib/antlib.xml" classpathref="maven.dependency.classpath" />
                    <if>
                      <not>
                        <available file="${basedir}/src/main/resources/portal.properties" />
                      </not>
                      <then>
                        <copy file="${basedir}/src/main/resources/portal.properties.EXAMPLE" tofile="${basedir}/src/main/resources/portal.properties" />
                      </then>
                    </if>
                    <if>
                      <not>
                        <available file="${basedir}/src/main/resources/log4j.properties" />
                      </not>
                      <then>
                        <copy file="${basedir}/src/main/resources/log4j.properties.EXAMPLE" tofile="${basedir}/src/main/resources/log4j.properties" />
                      </then>
                    </if>
                  </target>
                </configuration>
              </execution>
            </executions>
            <dependencies>
              <dependency>
                <groupId>ant-contrib</groupId>
                <artifactId>ant-contrib</artifactId>
                <version>1.0b3</version>
                <exclusions>
                    <exclusion>
                        <groupId>ant</groupId>
                        <artifactId>ant</artifactId>
                    </exclusion>
                </exclusions>
              </dependency>
              <dependency>
                <groupId>org.apache.ant</groupId>
                <artifactId>ant-nodeps</artifactId>
                <version>1.8.1</version>
              </dependency>
            </dependencies>
          </plugin>
          <!-- Generate test DB schema without key `UQ_MUTATION_EVENT_DETAILS` to accommodate H2 MySQL driver not supporting partial indexes -->
          <plugin>
            <artifactId>exec-maven-plugin</artifactId>
            <groupId>org.codehaus.mojo</groupId>
            <version>1.6.0</version>
            <inherited>false</inherited>
            <executions>
              <execution>
                <id>Generate Test DB schema</id>
                <phase>integration-test</phase>
                <goals>
                  <goal>exec</goal>
                </goals>
                <configuration>
                  <executable>${basedir}/db-scripts/src/main/resources/gen-cgds-test-schema.sh</executable>
                </configuration>
              </execution>
            </executions>
        </plugin>
          <plugin>
            <groupId>pl.project13.maven</groupId>
            <artifactId>git-commit-id-plugin</artifactId>
            <version>2.2.4</version>
                <executions>
                    <execution>
                        <id>get-the-git-infos</id>
                        <goals>
                            <goal>revision</goal>
                        </goals>
                        <!-- *NOTE*: The default phase of revision is initialize, but in case you want to change it, you can do so by adding the phase here -->
                        <phase>initialize</phase>
                    </execution>
                    <execution>
                        <id>validate-the-git-infos</id>
                        <goals>
                            <goal>validateRevision</goal>
                        </goals>
                        <!-- *NOTE*: The default phase of validateRevision is verify, but in case you want to change it, you can do so by adding the phase here -->
                        <phase>package</phase>
                    </execution>
                </executions>
            <configuration>
                <generateGitPropertiesFile>true</generateGitPropertiesFile>
                <gitDescribe>
                    <tags>true</tags>
                </gitDescribe>
            </configuration>
          </plugin>
    </plugins>
    </build>
    </profile>
    <profile>
      <id>external</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.PortalImporterTool</importer-main-class>
        <final-war-name>cbioportal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>heroku</id>

      <build>
        <plugins>
          <!-- copy files in heroku/ to root-->
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-resources-plugin</artifactId>
            <!-- only needs to be executed for parent pom -->
            <inherited>false</inherited>
            <version>2.7</version>
            <dependencies>
              <dependency>
                <groupId>org.apache.maven.shared</groupId>
                <artifactId>maven-filtering</artifactId>
                <version>1.3</version>
              </dependency>
            </dependencies>
            <executions>
              <execution>
                <id>copy-resources</id>
                <phase>validate</phase>
                <goals>
                  <goal>copy-resources</goal>
                </goals>
                <configuration>
                  <outputDirectory>.</outputDirectory>
                  <resources>
                    <resource>
                      <directory>heroku/</directory>
                      <filtering>true</filtering>
                    </resource>
                  </resources>
                </configuration>
              </execution>
            </executions>
          </plugin>
		  <!-- don't generate git.properties on heroku (unf doesn't work, since
			   .git directory is not accessible during build) -->
          <plugin>
            <groupId>pl.project13.maven</groupId>
            <artifactId>git-commit-id-plugin</artifactId>
                <executions>
                    <execution>
                        <id>get-the-git-infos</id>
						<phase>none</phase>
                    </execution>
                    <execution>
                        <id>validate-the-git-infos</id>
						<phase>none</phase>
                    </execution>
                </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>

  <properties>
    <frontend.version>v3.0.1</frontend.version>
    <frontend.groupId>com.github.cbioportal</frontend.groupId>
    <slf4j.version>1.6.6</slf4j.version>
    <spring.version>4.3.14.RELEASE</spring.version>
    <spring.context.support.version>4.3.14.RELEASE</spring.context.support.version>
    <spring.integration.version>4.3.14.RELEASE</spring.integration.version>
    <spring.security.version>5.0.7.RELEASE</spring.security.version>
    <spring.security.saml.version>1.0.3.RELEASE</spring.security.saml.version>
    <mybatis.spring.version>1.3.0</mybatis.spring.version>
    <mybatis.version>3.4.1</mybatis.version>
    <hibernate.version>3.6.9.Final</hibernate.version>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
    <bundle.symbolicName.prefix>org.mskcc</bundle.symbolicName.prefix>
    <bundle.namespace>org.mskcc.mondrian</bundle.namespace>
    <timestamp>${maven.build.timestamp}</timestamp>
    <maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
    <jacoco-maven-plugin.version>0.7.6.201602180812</jacoco-maven-plugin.version>
    <mockito.version>1.10.19</mockito.version>

    <final.war.name>cbioportal</final.war.name>

    <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</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>

    <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
    <db.version>2.9.0</db.version>
  </properties>

  <modules>
    <module>portal</module>
    <module>core</module>
    <module>business</module>
    <module>web</module>
    <module>model</module>
    <module>persistence</module>
    <module>service</module>
    <module>scripts</module>
    <module>db-scripts</module>
    <module>security</module>
  </modules>

  <dependencies>
    <!-- Spring Security for core and service -->
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-config</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-web</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-test</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <!-- apache commons logging -->
    <dependency>
      <groupId>log4j</groupId>
      <artifactId>apache-log4j-extras</artifactId>
      <version>1.1</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-dbcp2</artifactId>
      <version>2.1.1</version>
    </dependency>
    <dependency>
      <groupId>commons-beanutils</groupId>
      <artifactId>commons-beanutils</artifactId>
      <version>1.9.1</version>
    </dependency>
    <!-- Apache http components -->
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpclient</artifactId>
      <version>4.3.6</version>
    </dependency>
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpcore</artifactId>
      <version>4.3.2</version>
    </dependency>
    <!-- Apache commons lang -->
    <dependency>
      <groupId>commons-lang</groupId>
      <artifactId>commons-lang</artifactId>
      <version>2.4</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-lang3</artifactId>
      <version>3.5</version>
    </dependency>
    <!-- junit -->
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.12</version>
        <scope>test</scope>
    </dependency>
    <!-- log4j -->
    <dependency>
      <groupId>log4j</groupId>
      <artifactId>log4j</artifactId>
      <version>1.2.16</version>
    </dependency>
    <!-- mysql -->
    <dependency>
      <groupId>mysql</groupId>
      <artifactId>mysql-connector-java</artifactId>
      <version>5.1.16</version>
    </dependency>
    <!-- slf4j -->
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-log4j12</artifactId>
      <version>${slf4j.version}</version>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-api</artifactId>
      <version>${slf4j.version}</version>
    </dependency>
    <!-- spring -->
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-core</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-expression</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-beans</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-aop</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-context</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-context-support</artifactId>
      <version>${spring.context.support.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.integration</groupId>
      <artifactId>spring-integration-core</artifactId>
      <version>${spring.integration.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.integration</groupId>
      <artifactId>spring-integration-sftp</artifactId>
      <version>${spring.integration.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-tx</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-orm</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-jdbc</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-webmvc</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-web</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <!-- needed for @PreAuthorize and @PostFilter in core and service -->
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-core</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.mybatis</groupId>
      <artifactId>mybatis-spring</artifactId>
      <version>${mybatis.spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.mybatis</groupId>
      <artifactId>mybatis</artifactId>
      <version>${mybatis.version}</version>
    </dependency>
    <!-- guava -->
    <dependency>
      <groupId>com.google.guava</groupId>
      <artifactId>guava</artifactId>
      <version>19.0</version>
    </dependency>
    <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-math3</artifactId>
        <version>3.2</version>
    </dependency>
    <dependency>
      <groupId>org.mockito</groupId>
      <artifactId>mockito-core</artifactId>
      <version>${mockito.version}</version>
      <scope>test</scope>
        <exclusions>
            <exclusion>
                <artifactId>hamcrest-core</artifactId>
                <groupId>org.hamcrest</groupId>
            </exclusion>
        </exclusions>
    </dependency>
    <dependency>
        <groupId>org.hibernate</groupId>
        <artifactId>hibernate-validator</artifactId>
        <version>5.3.4.Final</version>
    </dependency>
    <dependency>
        <groupId>javax.el</groupId>
        <artifactId>javax.el-api</artifactId>
        <version>2.2.4</version>
    </dependency>
    <dependency>
        <groupId>org.glassfish.web</groupId>
        <artifactId>javax.el</artifactId>
        <version>2.2.4</version>
    </dependency>
  </dependencies>

  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>true</filtering>
        <includes>
          <include>**/portal.properties</include>
          <include>**/maven.properties</include>
          <include>**/git.properties</include>
        </includes>
      </resource>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>false</filtering>
        <excludes>
          <exclude>**/portal.properties</exclude>
          <exclude>**/maven.properties</exclude>
          <exclude>**/git.properties</exclude>
        </excludes>
      </resource>
    </resources>
    <!-- this plugin will allow us to share resources with children -->
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-resources-plugin</artifactId>
        <version>2.6</version>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-site-plugin</artifactId>
        <version>3.4</version>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-release-plugin</artifactId>
        <version>2.5.3</version>
      </plugin>
    </plugins>

    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.5.1</version>
          <configuration>
            <source>1.8</source>
            <target>1.8</target>
            <compilerArgs>
              <arg>-parameters</arg>
            </compilerArgs>
          </configuration>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>

  <reporting>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-javadoc-plugin</artifactId>
        <version>2.9</version>
        <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>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-jxr-plugin</artifactId>
        <version>2.5</version>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-project-info-reports-plugin</artifactId>
        <version>2.7</version>
      </plugin>
    </plugins>
  </reporting>

  <distributionManagement>
    <snapshotRepository>
      <id>portal.snapshots</id>
      <name>cBio Portal Snapshots Repository</name>
      <url>${portal.snapshot.url}</url>
    </snapshotRepository>
    <repository>
      <id>portal.releases</id>
      <name>cBio Portal Releases Repository</name>
      <url>${portal.release.url}</url>
    </repository>
  </distributionManagement>
</project>