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">
  <modelVersion>4.0.0</modelVersion>

  <groupId>de.charite.compbio</groupId>
  <artifactId>ontologizer-parent</artifactId>
  <version>2.1-SNAPSHOT</version>
  <packaging>pom</packaging>
  <name>Ontologizer - Parent project</name>

  <prerequisites>
    <maven>3.0</maven>
  </prerequisites>

  <scm>
    <connection>scm:git:git://github.com/phenotips/ontologizer.git</connection>
    <developerConnection>scm:git:git@github.com:phenotips/ontologizer.git</developerConnection>
    <url>https://github.com/phenotips/ontologizer.git/tree/master/</url>
    <tag>HEAD</tag>
  </scm>

  <distributionManagement>
    <repository>
      <id>nexus.phenotips.org</id>
      <name>Maven2 Remote Repository for Releases</name>
      <url>https://nexus.phenotips.org/nexus/content/repositories/releases</url>
    </repository>
    <snapshotRepository>
      <id>nexus.phenotips.org</id>
      <name>Maven2 Development Repository for Snapshots</name>
      <url>https://nexus.phenotips.org/nexus/content/repositories/snapshots</url>
    </snapshotRepository>
  </distributionManagement>

  <repositories>
    <repository>
      <id>phenotips-releases</id>
      <name>PhenoTips Releases repository</name>
      <url>https://nexus.phenotips.org/nexus/content/repositories/releases/</url>
      <releases>
        <enabled>true</enabled>
        <checksumPolicy>fail</checksumPolicy>
      </releases>
      <snapshots>
        <enabled>false</enabled>
        <checksumPolicy>fail</checksumPolicy>
      </snapshots>
    </repository>
    <repository>
      <id>phenotips-snapshots</id>
      <name>PhenoTips Snapshots repository</name>
      <url>https://nexus.phenotips.org/nexus/content/repositories/snapshots/</url>
      <releases>
        <enabled>false</enabled>
        <checksumPolicy>fail</checksumPolicy>
      </releases>
      <snapshots>
        <enabled>true</enabled>
        <checksumPolicy>fail</checksumPolicy>
      </snapshots>
    </repository>
    <repository>
      <id>phenotips-externals</id>
      <name>PhenoTips external repositories mirror</name>
      <url>https://nexus.phenotips.org/nexus/content/groups/public/</url>
      <releases>
        <enabled>true</enabled>
      </releases>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
    </repository>
  </repositories>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
  </properties>

  <build>
    <defaultGoal>install</defaultGoal>
    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-resources-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.0.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-remote-resources-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>1.5</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-release-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.5.3</version>
          <configuration>
            <!-- 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>3.0.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-source-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.0.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-plugin-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.5</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-install-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.5.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.7.0</version>
          <configuration>
            <!-- Show compiler warnings -->
            <compilerArgument>-Xlint:all</compilerArgument>
            <showWarnings>true</showWarnings>
            <showDeprecation>true</showDeprecation>
            <!-- Java 1.7 is required -->
            <source>1.7</source>
            <target>1.7</target>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-surefire-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.20.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-jar-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.0.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-assembly-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-dependency-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.0.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-deploy-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>2.8.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-gpg-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>1.6</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <!-- Lock down plugin version for build reproducibility -->
          <version>3.0.0</version>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>

  <profiles>
    <profile>
      <!-- Profile used when the release plugin executes. We want javadocs and source jars to be released
           + ensure we sign files using GPG. -->
      <id>release</id>
      <activation>
        <property>
          <!-- This property is automatically defined by the Maven release plugin when executing
               a release. Thus this profile will be automatically enabled when releasing -->
          <name>performRelease</name>
          <value>true</value>
        </property>
      </activation>
      <build>
        <plugins>
          <plugin>
            <!-- Generate a jar with the source code -->
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-source-plugin</artifactId>
            <executions>
              <execution>
                <id>attach-sources</id>
                <goals>
                  <goal>jar</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
          <plugin>
            <!-- Generate a jar with the HTML javadoc -->
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-javadoc-plugin</artifactId>
            <executions>
              <execution>
                <id>attach-javadocs</id>
                <goals>
                  <goal>jar</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
          <plugin>
            <!-- Sign the uploaded artifacts with the GPG key of the releaser -->
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-gpg-plugin</artifactId>
            <executions>
              <execution>
                <id>sign-artifacts</id>
                <phase>verify</phase>
                <goals>
                  <goal>sign</goal>
                </goals>
                <configuration>
                  <useAgent>true</useAgent>
                </configuration>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>

  <modules>
    <module>core</module>
    <module>svd</module>
    <module>tests</module>
    <module>gui</module>
    <module>cmdline</module>
    <module>benchmark</module>
  </modules>
</project>