pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<!--

    See the NOTICE file distributed with this work for additional
    information regarding copyright ownership.

    This is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as
    published by the Free Software Foundation; either version 2.1 of
    the License, or (at your option) any later version.

    This software is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
    Lesser General Public License for more details.

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    License along with this software; if not, write to the Free
    Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
    02110-1301 USA, or see the FSF site: http://www.fsf.org.

--><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/maven-v4_0_0.xsd">
  <modelVersion>4.0.0</modelVersion>

  <groupId>edu.toronto.cs.medsavant</groupId>
  <artifactId>medsavant-parent</artifactId>
  <version>1.3-SNAPSHOT</version>
  <packaging>pom</packaging>

  <name>MedSavant - Parent POM</name>
  <description>MedSavant is a search engine for genetic variants </description>
  <url>http://www.genomesavant.com/p/medsavant/</url>
  <inceptionYear>2011</inceptionYear>

  <licenses>
    <license>
      <name>LGPL 2.1</name>
      <url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html</url>
      <distribution>repo</distribution>
    </license>
  </licenses>

  <scm>
    <connection>scm:git:git://github.com/compbio-UofT/medsavant.git</connection>
    <developerConnection>scm:git:git@github.com:compbio-UofT/medsavant.git</developerConnection>
    <url>https://github.com/compbio-UofT/medsavant.git/tree/master/</url>
    <tag>HEAD</tag>
  </scm>

  <organization>
    <name>University of Toronto, Computational Biology Lab</name>
    <url>http://compbio.cs.toronto.edu/</url>
  </organization>

  <distributionManagement>
    <site>
      <id>nexus.cs.toronto.edu</id>
      <url>dav:http://nexus.cs.toronto.edu/nexus/content/sites/site/${project.groupId}/${project.artifactId}/${project.version}</url>
    </site>
    <repository>
      <id>nexus.cs.toronto.edu</id>
      <name>Maven2 Remote Repository for Releases</name>
      <url>http://nexus.cs.toronto.edu/nexus/content/repositories/releases</url>
    </repository>
    <snapshotRepository>
      <id>nexus.cs.toronto.edu</id>
      <name>Maven2 Development Repository for Snapshots</name>
      <url>http://nexus.cs.toronto.edu/nexus/content/repositories/snapshots</url>
    </snapshotRepository>
  </distributionManagement>

  <repositories>
    <repository>
      <id>uoft-releases</id>
      <name>UofT Releases repository</name>
      <url>http://nexus.cs.toronto.edu/nexus/content/repositories/releases/</url>
      <releases>
        <enabled>true</enabled>
        <checksumPolicy>fail</checksumPolicy>
      </releases>
      <snapshots>
        <enabled>false</enabled>
        <checksumPolicy>fail</checksumPolicy>
      </snapshots>
    </repository>
    <repository>
      <id>uoft-snapshots</id>
      <name>UofT Releases repository</name>
      <url>http://nexus.cs.toronto.edu/nexus/content/repositories/snapshots/</url>
      <releases>
        <enabled>false</enabled>
        <checksumPolicy>fail</checksumPolicy>
      </releases>
      <snapshots>
        <checksumPolicy>fail</checksumPolicy>
      </snapshots>
    </repository>
    <repository>
      <id>uoft-externals</id>
      <name>UofT external repositories mirror</name>
      <url>http://nexus.cs.toronto.edu/nexus/content/groups/public/</url>
      <releases>
        <enabled>true</enabled>
      </releases>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
    </repository>
  </repositories>
  <pluginRepositories>
    <pluginRepository>
      <id>uoft-externals</id>
      <name>UofT external repositories mirror</name>
      <url>http://nexus.cs.toronto.edu/nexus/content/groups/public/</url>
      <releases>
        <enabled>true</enabled>
      </releases>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
    </pluginRepository>
  </pluginRepositories>

  <properties>
    <enforcer.skip>false</enforcer.skip>
    <checkstyle.skip>false</checkstyle.skip>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <jide.version>3.5.6</jide.version>
    <savant.version>2.0.5</savant.version>
  </properties>

  <dependencyManagement>
    <dependencies>
      <!-- Apache Commons -->
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-lang3</artifactId>
        <version>3.1</version>
      </dependency>
      <!-- Everybody logs -->
      <dependency>
        <groupId>commons-logging</groupId>
        <artifactId>commons-logging</artifactId>
        <version>1.1.3</version>
      </dependency>
    </dependencies>
  </dependencyManagement>

  <build>
    <defaultGoal>install</defaultGoal>

    <extensions>
      <!-- Enables uploading releases to Nexus -->
      <extension>
        <groupId>org.apache.maven.wagon</groupId>
        <artifactId>wagon-webdav-jackrabbit</artifactId>
        <version>2.2</version>
      </extension>
    </extensions>

    <plugins>
      <!-- Show compiler warnings -->
      <plugin>
        <artifactId>maven-compiler-plugin</artifactId>
        <configuration>
          <compilerArgument>-Xlint:none</compilerArgument>
          <showWarnings>true</showWarnings>
          <showDeprecation>true</showDeprecation>
        </configuration>
      </plugin>

      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-enforcer-plugin</artifactId>
        <!-- Lock down plugin version for build reproducibility -->
        <version>1.1</version>
        <executions>
          <!-- Check that all Maven plugins have versions defined -->
          <execution>
            <id>enforce-plugins</id>
            <goals>
              <goal>enforce</goal>
            </goals>
            <configuration>
              <rules>
                <requirePluginVersions>
                  <message>Best Practice is to always define plugin versions!</message>
                  <banLatest>false</banLatest>
                  <banRelease>false</banRelease>
                  <banSnapshots>false</banSnapshots>
                </requirePluginVersions>
              </rules>
            </configuration>
          </execution>
        </executions>
        <configuration>
          <skip>${enforcer.skip}</skip>
        </configuration>
      </plugin>
    </plugins>
    <pluginManagement>
      <plugins>
        <!-- Apply checkstyle rules and fail the build in case of errors. The checkstyle config
             files are taken from the build-tools JAR module.-->
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-checkstyle-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.9.1</version>
          <dependencies>
            <dependency>
              <groupId>edu.toronto.cs</groupId>
              <artifactId>common-verification-resources</artifactId>
              <version>1.0</version>
            </dependency>
          </dependencies>
          <configuration>
            <consoleOutput>true</consoleOutput>
            <!-- We use this to disable checkstyle when the clover profile is executed since there's a
                 conflict between checkstyle and clover. Namely the clovered code doesn't pass our
                 checkstyle rules -->
            <skip>${checkstyle.skip}</skip>
            <configLocation>checkstyle.xml</configLocation>
          </configuration>
          <executions>
            <execution>
              <goals>
                <goal>check</goal>
              </goals>
            </execution>
          </executions>
        </plugin>
        <!-- Check license headers and fail the build if they're missing or not matching the defined format -->
        <plugin>
          <groupId>com.mycila.maven-license-plugin</groupId>
          <artifactId>maven-license-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>1.9.0</version>
          <configuration>
            <skip>${license.skip}</skip>
            <header>license.txt</header>
            <strictCheck>true</strictCheck>
            <headerDefinitions>
              <!-- Our style for XML headers isn't standard so we need to define it in a custom manner.
                   See xwiki-commons-tool-validation-resources module -->
              <headerDefinition>license-apache-xml-definition.xml</headerDefinition>
              <headerDefinition>license-apache-script-definition.xml</headerDefinition>
              <headerDefinition>license-apache-batch-definition.xml</headerDefinition>
            </headerDefinitions>
            <!-- Our Java and XML styles aren't the default so we need to change the mapping -->
            <mapping>
              <java>SLASHSTAR_STYLE</java>
              <aj>SLASHSTAR_STYLE</aj>
            </mapping>
            <!-- We're only interested in checking our sources and our POMs -->
            <includes>
              <include>src/**</include>
              <include>pom.xml</include>
            </includes>
          </configuration>
          <!-- Add a dependency since this is where the maven-license-plugin plugin will find the license.txt file -->
          <dependencies>
            <dependency>
              <groupId>edu.toronto.cs</groupId>
              <artifactId>common-verification-resources</artifactId>
              <version>1.0</version>
            </dependency>
          </dependencies>
          <executions>
            <execution>
              <goals>
                <goal>check</goal>
              </goals>
            </execution>
          </executions>
        </plugin>
        <!-- Run the exec plugin on the final jar, not on individual classes,
             since we require the MANIFEST file to be present (that is where the version is defined) -->
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>exec-maven-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>1.2.1</version>
          <executions>
            <execution>
              <id>default-cli</id>
              <phase>install</phase>
              <goals>
                <goal>exec</goal>
              </goals>
              <configuration>
                <executable>java</executable>
                <arguments>
                  <argument>-Xmx4G</argument>
                  <argument>-jar</argument>
                  <argument>${project.build.directory}/${project.build.finalName}.jar</argument>
                  <classpath/>
                </arguments>
              </configuration>
            </execution>
          </executions>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-resources-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.6</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-remote-resources-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>1.3</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-release-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.4</version>
          <configuration>
            <!-- By default the release plugin will execute the "clean" and "verify" goals but won't perform an
                 "install". This is causing problems since several modules will fail to build during release:prepare.
                 See http://tinyurl.com/354vwe for more details. Thus we're forcing the execution of the "install"
                 goal. -->
            <preparationGoals>clean install</preparationGoals>
            <!-- Avoid site generation during the release:perform to speed up release process -->
            <goals>deploy</goals>
            <mavenExecutorId>forked-path</mavenExecutorId>
            <autoVersionSubmodules>true</autoVersionSubmodules>
            <localCheckout>true</localCheckout>
            <pushChanges>false</pushChanges>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-clean-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.5</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-source-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.1.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-plugin-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.9</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-install-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.4</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.5.1</version>
          <!-- Java 1.6 is required -->
          <configuration>
            <source>1.6</source>
            <target>1.6</target>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-surefire-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.12.3</version>
          <!-- Rule is to put tests in *Test classes -->
          <configuration>
            <includes>
              <include>**/*Test.class</include>
            </includes>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-jar-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.4</version>
          <configuration>
            <archive>
              <manifest>
                <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
              </manifest>
            </archive>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-assembly-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.3</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-dependency-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.5.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-war-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-deploy-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.7</version>
          <!-- We're deploying to Nexus using the WebDAV protocol -->
          <dependencies>
            <dependency>
              <groupId>org.apache.maven.wagon</groupId>
              <artifactId>wagon-webdav-jackrabbit</artifactId>
              <version>2.2</version>
            </dependency>
          </dependencies>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-project-info-reports-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.4</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>clirr-maven-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.5</version>
          <executions>
            <execution>
              <id>clirr-check</id>
              <goals>
                <goal>check</goal>
              </goals>
            </execution>
          </executions>
          <configuration>
            <comparisonVersion>${clirr.previous.version}</comparisonVersion>
            <skip>${clirr.skip}</skip>
            <excludes>
              <exclude>**/internal/**</exclude>
            </excludes>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-gpg-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>1.4</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.8.1</version>
          <configuration>
            <!-- Always exclude the internal package since it's not user-public -->
            <excludePackageNames>*.internal.*</excludePackageNames>
            <!-- Make sure javadoc has enough memory -->
            <maxmemory>300m</maxmemory>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-site-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.2</version>
          <!-- Site Plugin doesn’t automatically pull the Apache Wagon implementation -->
          <dependencies>
            <dependency>
              <groupId>org.apache.maven.wagon</groupId>
              <artifactId>wagon-webdav-jackrabbit</artifactId>
              <version>2.2</version>
            </dependency>
          </dependencies>
          <configuration>
            <reportPlugins>
              <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-project-info-reports-plugin</artifactId>
                <version>2.4</version>
                <configuration>
                  <!-- Since contacting the Maven Repositories can take a very long time, tell the plugin not to display
                       the repository locations of the dependencies in the report. -->
                  <dependencyLocationsEnabled>false</dependencyLocationsEnabled>
                </configuration>
                <reports>
                  <report>summary</report>
                  <report>index</report>
                  <report>dependencies</report>
                  <report>dependency-convergence</report>
                  <report>mailing-list</report>
                  <report>issue-tracking</report>
                  <report>scm</report>
                </reports>
              </plugin>
              <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <version>2.8</version>
                <configuration>
                  <!-- Always exclude the internal package since it's not user-public -->
                  <excludePackageNames>*.internal.*</excludePackageNames>
                  <!-- Make sure javadoc has enough memory -->
                  <maxmemory>300m</maxmemory>
                </configuration>
                <!-- Don't generate test javadoc -->
                <reports>
                  <report>javadoc</report>
                </reports>
              </plugin>
            </reportPlugins>
          </configuration>
        </plugin>
        <!-- Ignore/Execute plugin execution -->
        <plugin>
          <groupId>org.eclipse.m2e</groupId>
          <artifactId>lifecycle-mapping</artifactId>
          <version>1.0.0</version>
          <configuration>
            <lifecycleMappingMetadata>
              <pluginExecutions>
                <!-- copy-dependency plugin -->
                <pluginExecution>
                  <pluginExecutionFilter>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-dependency-plugin</artifactId>
                    <versionRange>[1.0.0,)</versionRange>
                    <goals>
                      <goal>copy-dependencies</goal>
                    </goals>
                  </pluginExecutionFilter>
                  <action>
                    <ignore/>
                  </action>
                </pluginExecution>
              </pluginExecutions>
            </lifecycleMappingMetadata>
          </configuration>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>

  <modules>
    <module>utilities</module>
    <module>MedSavantShared</module>
    <module>jannovar</module>
    <module>MedSavantServerEngine</module>
    <module>MedSavantClient</module>
    <module>MedSavantJSONClient</module>
    <module>distribution</module>
    <module>custom-libs/medsavant-component-fields</module>
    <module>custom-libs/medsavant-app-comm</module>
    <module>custom-libs/mfiume-component-transition</module>
  </modules>
</project>