Description

<dependency>
    <groupId>org.geneontology</groupId>
    <artifactId>obographs</artifactId>
    <version>0.2.1</version>
</dependency>

<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>org.geneontology</groupId>
  <artifactId>obographs</artifactId>
  <version>0.2.1</version>
  <packaging>jar</packaging>
  <name>${project.groupId}:${project.artifactId}</name>
  <description>Reference implementation for Obo Graphs</description>
  <url>http://geneontology.org</url>
  <inceptionYear>2016</inceptionYear>
  <licenses>
    <license>
      <name>The BSD 3-Clause License</name>
      <url>https://opensource.org/licenses/BSD-3-Clause</url>
      <distribution>repo</distribution>
    </license>
  </licenses>
  <developers>
    <developer>
      <name>Chris Mungall</name>
      <email>cjmungall@lbl.gov</email>
      <organization>Gene Ontology</organization>
      <organizationUrl>http://geneontology.org</organizationUrl>
    </developer>
  </developers>
  <scm>
    <connection>scm:git:https://github.com/geneontology/obographs.git</connection>
    <developerConnection>scm:git:git@github.com:geneontology/obographs.git
    </developerConnection>
    <url>https://github.com/geneontology/obographs</url>
    <tag>HEAD</tag>
  </scm>
  <ciManagement>
    <system>Travis CI</system>
    <url>https://travis-ci.org/geneontology/obographs</url>
  </ciManagement>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <java.version>1.8</java.version>
    <owlapi.version>4.5.6</owlapi.version>
  </properties>

  <distributionManagement>
    <snapshotRepository>
      <id>ossrh</id>
      <url>https://oss.sonatype.org/content/repositories/snapshots</url>
    </snapshotRepository>
  </distributionManagement>

  <profiles>
    <profile>
      <id>doclint-java8-disable</id>
      <activation>
        <jdk>[1.8,)</jdk>
      </activation>
      <build>
        <plugins>
	  <!-- Build a bin/obographs.jar file with all dependencies -->
	  <plugin>
	    <groupId>org.apache.maven.plugins</groupId>
	    <artifactId>maven-assembly-plugin</artifactId>
	    <configuration>
	      <finalName>obographs</finalName>
	      <appendAssemblyId>false</appendAssemblyId>
	      <attach>false</attach>
	      <outputDirectory>./bin</outputDirectory>
	      <descriptorRefs>
		<descriptorRef>jar-with-dependencies</descriptorRef>
	      </descriptorRefs>
	      <archive>
		<manifest>
		  <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
		  <mainClass>org.geneontology.obographs.runner.RunEngine</mainClass>
		</manifest>
	      </archive>
	    </configuration>
	    <executions>
	      <execution>
		<id>make-assembly</id>
		<phase>package</phase>
		<goals>
		  <goal>single</goal>
		</goals>
	      </execution>
	    </executions>
	  </plugin>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-javadoc-plugin</artifactId>
            <configuration>
              <additionalparam>-Xdoclint:none</additionalparam>
            </configuration>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>

  <build>
    <plugins>
      <plugin>
        <groupId>org.sonatype.plugins</groupId>
        <artifactId>nexus-staging-maven-plugin</artifactId>
        <version>1.6.3</version>
        <extensions>true</extensions>
        <configuration>
          <serverId>ossrh</serverId>
          <nexusUrl>https://oss.sonatype.org/</nexusUrl>
          <autoReleaseAfterClose>true</autoReleaseAfterClose>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-gpg-plugin</artifactId>
        <version>1.5</version>
        <executions>
          <execution>
            <id>sign-artifacts</id>
            <phase>verify</phase>
            <goals>
              <goal>sign</goal>
            </goals>
            <configuration>
                <gpgArguments>
                    <arg>--pinentry-mode</arg>
                    <arg>loopback</arg>
                </gpgArguments>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>3.1</version>
        <configuration>
          <source>${java.version}</source>
          <target>${java.version}</target>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>2.19</version>
        <configuration>
          <excludes>
            <exclude>**/FooTest.java</exclude>
          </excludes>
        </configuration>
      </plugin>

      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-source-plugin</artifactId>
        <version>2.2.1</version>
        <executions>
          <execution>
            <id>attach-sources</id>
            <goals>
              <goal>jar-no-fork</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-javadoc-plugin</artifactId>
        <version>2.9.1</version>
          <configuration>
            <doclet>ch.raffael.doclets.pegdown.PegdownDoclet</doclet>
            <docletArtifact>
              <groupId>ch.raffael.pegdown-doclet</groupId>
              <artifactId>pegdown-doclet</artifactId>
              <version>1.1</version>
            </docletArtifact>
            <useStandardDocletOptions>true</useStandardDocletOptions>
          </configuration>
        <executions>
          <execution>
            <id>attach-javadocs</id>
            <goals>
              <goal>jar</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>

  <dependencies>
    <dependency>
      <groupId>net.sourceforge.owlapi</groupId>
      <artifactId>owlapi-distribution</artifactId>
      <version>${owlapi.version}</version>
    </dependency>
    <dependency>
      <groupId>com.google.guava</groupId>
      <artifactId>guava</artifactId>
      <version>19.0</version>
    </dependency>
    <dependency>
      <groupId>commons-io</groupId>
      <artifactId>commons-io</artifactId>
      <version>2.2</version>
    </dependency>
		<dependency>
			<groupId>com.io-informatics.oss</groupId>
			<artifactId>jackson-jsonld</artifactId>
			<version>0.0.5</version>
			<exclusions>
				<exclusion>
					<artifactId>jackson-annotations</artifactId>
					<groupId>com.fasterxml.jackson.core</groupId>
				</exclusion>
				<exclusion>
					<artifactId>jackson-core</artifactId>
					<groupId>com.fasterxml.jackson.core</groupId>
				</exclusion>
				<exclusion>
					<artifactId>jackson-databind</artifactId>
					<groupId>com.fasterxml.jackson.core</groupId>
				</exclusion>
			</exclusions>
		</dependency>
		<dependency>
			<groupId>com.fasterxml.jackson.dataformat</groupId>
			<artifactId>jackson-dataformat-yaml</artifactId>
			<version>2.5.4</version>
		</dependency>
		<dependency>
			<groupId>com.fasterxml.jackson.module</groupId>
			<artifactId>jackson-module-jsonSchema</artifactId>
			<version>2.7.2</version>
		</dependency>
		<dependency>
			<groupId>com.fasterxml.jackson.dataformat</groupId>
			<artifactId>jackson-dataformat-protobuf</artifactId>
			<version>2.7.2</version>
		</dependency>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.12</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.hamcrest</groupId>
      <artifactId>hamcrest-core</artifactId>
      <version>1.3</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>com.beust</groupId>
      <artifactId>jcommander</artifactId>
      <version>1.48</version>
    </dependency>
  </dependencies>
</project>