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>
  <version>1.2.4</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>

  <profiles>
    <profile>
      <id>mskcc</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>mskcc</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>genie</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>genie</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>private</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>private</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>triage</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>triage</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>gdac</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>gdac-portal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>su2c</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>su2c-portal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>public</id>
      <activation>
        <activeByDefault>true</activeByDefault>
      </activation>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>cbioportal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>prostate</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>prostate-portal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>kras</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>kras</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>target</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>target-portal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>glioma</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>glioma-portal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>acc</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>acc-portal</final-war-name>
      </properties>
    </profile>
    <profile>
      <id>ctd2-dashboard</id>
      <properties>
        <importer-main-class>org.mskcc.cbio.importer.Admin</importer-main-class>
        <final-war-name>ctd2-dashboard-portal</final-war-name>
      </properties>
    </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>
          <!-- copy portal.properties.EXAMPLE and log4j.properties.EXAMPLE -->
          <plugin>
            <artifactId>maven-antrun-plugin</artifactId>
            <!-- only needs to be executed for parent pom -->
            <inherited>false</inherited>
            <executions>
              <execution>
                <phase>validate</phase>
                <goals>
                  <goal>run</goal>
                </goals>
                <configuration>
                  <tasks>
                    <copy
                    file="${basedir}/src/main/resources/portal.properties.EXAMPLE"
                    tofile="${basedir}/src/main/resources/portal.properties" />
                    <copy
                    file="${basedir}/src/main/resources/log4j.properties.EXAMPLE"
                    tofile="${basedir}/src/main/resources/log4j.properties" />
                  </tasks>
                </configuration>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>

  <properties>
    <slf4j.version>1.6.6</slf4j.version>
    <spring.version>4.0.4.RELEASE</spring.version>
    <spring.context.support.version>4.1.2.RELEASE</spring.context.support.version>
    <spring.integration.version>4.1.0.RELEASE</spring.integration.version>
    <spring.security.version>3.2.5.RELEASE</spring.security.version>
    <spring.security.saml.version>1.0.0.RELEASE</spring.security.saml.version>
    <mybatis.spring.version>1.2.2</mybatis.spring.version>
    <spring.social.version>1.1.0.RELEASE</spring.social.version>
    <org.springframework.social.google-version>1.0.0.RELEASE</org.springframework.social.google-version>
    <mybatis.version>3.2.7</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>

    <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
    <db.version>1.2.1</db.version>

  </properties>

  <modules>
    <module>portal</module>
    <module>core</module>
    <module>business</module>
    <module>web</module>
  </modules>

  <dependencies>
    <!-- apache commons logging -->
    <dependency>
      <groupId>log4j</groupId>
      <artifactId>apache-log4j-extras</artifactId>
      <version>1.1</version>
    </dependency>
    <dependency>
      <groupId>commons-dbcp</groupId>
      <artifactId>commons-dbcp</artifactId>
      <version>1.4</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>4.3.4</version>
    </dependency>
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpcore</artifactId>
      <version>4.3.2</version>
    </dependency>
    <!-- junit -->
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.8.2</version>
    </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>${spring.version}</version>
    </dependency>
    <!-- spring security -->
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-acl</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-config</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-core</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-ldap</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-openid</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security.extensions</groupId>
      <artifactId>spring-security-saml2-core</artifactId>
      <version>${spring.security.saml.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-taglibs</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.security</groupId>
      <artifactId>spring-security-web</artifactId>
      <version>${spring.security.version}</version>
    </dependency>
    <dependency>
      <groupId>org.mybatis</groupId>
      <artifactId>mybatis-spring</artifactId>
      <version>${mybatis.spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.mybatis</groupId>
      <artifactId>mybatis</artifactId>
      <version>${mybatis.version}</version>
    </dependency>
    <!-- Spring Social -->
    <dependency>
      <groupId>org.springframework.social</groupId>
      <artifactId>spring-social-config</artifactId>
      <version>${spring.social.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.social</groupId>
      <artifactId>spring-social-core</artifactId>
      <version>${spring.social.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.social</groupId>
      <artifactId>spring-social-security</artifactId>
      <version>${spring.social.version}</version>
    </dependency>
    <dependency>
      <groupId>org.springframework.social</groupId>
      <artifactId>spring-social-web</artifactId>
      <version>${spring.social.version}</version>
    </dependency>
    <!-- Spring Social Google-->
    <dependency>
      <groupId>org.springframework.social</groupId>
      <artifactId>spring-social-google</artifactId>
      <version>${org.springframework.social.google-version}</version>
    </dependency>
    <!-- guava -->
    <dependency>
      <groupId>com.google.guava</groupId>
      <artifactId>guava</artifactId>
      <version>19.0</version>
    </dependency>
  </dependencies>

  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>true</filtering>
        <includes>
          <include>**/portal.properties</include>
        </includes>
      </resource>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>false</filtering>
        <excludes>
          <exclude>**/portal.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>
  </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>