pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<!--
    Licensed to the Apache Software Foundation (ASF) under one or more
    contributor license agreements.  See the NOTICE file distributed with
    this work for additional information regarding copyright ownership.
    The ASF licenses this file to You under the Apache License, Version 2.0
    (the "License"); you may not use this file except in compliance with
    the License.  You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

    Unless required by applicable law or agreed to in writing, software
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.
-->
<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>com.google.cloud.genomics</groupId>
  <artifactId>cba</artifactId>
  <version>v1</version>

  <packaging>jar</packaging>

  <properties>
    <beam.version>2.8.0</beam.version>
    <google.dataflow.version>2.1.0</google.dataflow.version>
    <bigquery.version>v2-rev383-1.23.0</bigquery.version>
    <google-clients.version>1.24.1</google-clients.version>
    <guava.version>[30.0-jre,)</guava.version>
    <hamcrest.version>1.3</hamcrest.version>
    <jackson.version>2.8.9</jackson.version>
    <joda.version>2.4</joda.version>
    <junit.version>4.13.1</junit.version>
    <maven-compiler-plugin.version>3.6.1</maven-compiler-plugin.version>
    <maven-exec-plugin.version>1.4.0</maven-exec-plugin.version>
    <maven-jar-plugin.version>3.0.2</maven-jar-plugin.version>
    <maven-shade-plugin.version>3.0.0</maven-shade-plugin.version>
    <pubsub.version>v1-rev10-1.22.0</pubsub.version>
    <slf4j.version>1.7.14</slf4j.version>
    <spark.version>1.6.3</spark.version>
    <surefire-plugin.version>2.20</surefire-plugin.version>
  </properties>

  <repositories>
    <repository>
      <id>apache.snapshots</id>
      <name>Apache Development Snapshot Repository</name>
      <url>https://repository.apache.org/content/repositories/snapshots/</url>
      <releases>
        <enabled>false</enabled>
      </releases>
      <snapshots>
        <enabled>true</enabled>
      </snapshots>
    </repository>
  </repositories>

  <build>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>${maven-compiler-plugin.version}</version>
        <configuration>
          <source>1.7</source>
          <target>1.7</target>
        </configuration>
      </plugin>

      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>${surefire-plugin.version}</version>
        <configuration>
          <parallel>all</parallel>
          <threadCount>4</threadCount>
          <redirectTestOutputToFile>true</redirectTestOutputToFile>
        </configuration>
        <dependencies>
          <dependency>
            <groupId>org.apache.maven.surefire</groupId>
            <artifactId>surefire-junit47</artifactId>
            <version>${surefire-plugin.version}</version>
          </dependency>
        </dependencies>
      </plugin>

      <!-- Ensure that the Maven jar plugin runs before the Maven
        shade plugin by listing the plugin higher within the file. -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-jar-plugin</artifactId>
        <version>${maven-jar-plugin.version}</version>
      </plugin>

      <!--
        Configures `mvn package` to produce a bundled jar ("fat jar") for runners
        that require this for job submission to a cluster.
      -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-shade-plugin</artifactId>
        <version>${maven-shade-plugin.version}</version>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
            <configuration>
              <finalName>${project.artifactId}-bundled-${project.version}</finalName>
              <filters>
                <filter>
                  <artifact>*:*</artifact>
                  <excludes>
                    <exclude>META-INF/LICENSE</exclude>
                    <exclude>META-INF/*.SF</exclude>
                    <exclude>META-INF/*.DSA</exclude>
                    <exclude>META-INF/*.RSA</exclude>
                  </excludes>
                </filter>
              </filters>
              <transformers>
                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
              </transformers>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>

    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>exec-maven-plugin</artifactId>
          <version>${maven-exec-plugin.version}</version>
          <configuration>
            <cleanupDaemonThreads>false</cleanupDaemonThreads>
          </configuration>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>

  <profiles>
    <profile>
      <id>direct-runner</id>
      <activation>
        <activeByDefault>true</activeByDefault>
      </activation>
      <!-- Makes the DirectRunner available when running a pipeline. -->
      <dependencies>
        <dependency>
          <groupId>org.apache.beam</groupId>
          <artifactId>beam-runners-direct-java</artifactId>
          <version>${beam.version}</version>
          <scope>runtime</scope>
        </dependency>
      </dependencies>
    </profile>

    <profile>
      <id>apex-runner</id>
      <!-- Makes the ApexRunner available when running a pipeline. -->
      <dependencies>
        <dependency>
          <groupId>org.apache.beam</groupId>
          <artifactId>beam-runners-apex</artifactId>
          <version>${beam.version}</version>
          <scope>runtime</scope>
        </dependency>
      </dependencies>
    </profile>

    <profile>
      <id>dataflow-runner</id>
      <!-- Makes the DataflowRunner available when running a pipeline. -->
      <dependencies>
        <dependency>
          <groupId>org.apache.beam</groupId>
          <artifactId>beam-runners-google-cloud-dataflow-java</artifactId>
          <version>${beam.version}</version>
          <scope>runtime</scope>
        </dependency>
      </dependencies>
    </profile>

    <profile>
      <id>flink-runner</id>
      <!-- Makes the FlinkRunner available when running a pipeline. -->
      <dependencies>
        <dependency>
          <groupId>org.apache.beam</groupId>
          <artifactId>beam-runners-flink_2.10</artifactId>
          <version>${beam.version}</version>
          <scope>runtime</scope>
        </dependency>
      </dependencies>
    </profile>

    <profile>
      <id>spark-runner</id>
      <!-- Makes the SparkRunner available when running a pipeline. Additionally,
           overrides some Spark dependencies to Beam-compatible versions. -->
      <dependencies>
        <dependency>
          <groupId>org.apache.beam</groupId>
          <artifactId>beam-runners-spark</artifactId>
          <version>${beam.version}</version>
          <scope>runtime</scope>
        </dependency>
        <dependency>
          <groupId>org.apache.beam</groupId>
          <artifactId>beam-sdks-java-io-hadoop-file-system</artifactId>
          <version>${beam.version}</version>
          <scope>runtime</scope>
        </dependency>
        <dependency>
          <groupId>org.apache.spark</groupId>
          <artifactId>spark-streaming_2.10</artifactId>
          <version>${spark.version}</version>
          <scope>runtime</scope>
          <exclusions>
            <exclusion>
              <groupId>org.slf4j</groupId>
              <artifactId>jul-to-slf4j</artifactId>
            </exclusion>
          </exclusions>
        </dependency>
        <dependency>
          <groupId>com.fasterxml.jackson.module</groupId>
          <artifactId>jackson-module-scala_2.10</artifactId>
          <version>${jackson.version}</version>
          <scope>runtime</scope>
        </dependency>
      </dependencies>
    </profile>
  </profiles>

  <dependencies>
    <!-- Adds a dependency on the Beam SDK. -->
    <dependency>
      <groupId>org.apache.beam</groupId>
      <artifactId>beam-sdks-java-core</artifactId>
      <version>${beam.version}</version>
    </dependency>
        <dependency>
            <groupId>com.google.cloud</groupId>
            <artifactId>google-cloud-bigquery</artifactId>
            <version>0.21.1-beta</version>
	</dependency>
        <dependency>
          <groupId>com.google.apis</groupId>
          <artifactId>google-api-services-bigquery</artifactId>
          <version>v2-rev354-1.24.1</version>
        </dependency>


    <dependency>
      <groupId>org.apache.beam</groupId>
      <artifactId>beam-runners-google-cloud-dataflow-java</artifactId>
      <version>${google.dataflow.version}</version>
    </dependency>

    <dependency>
      <groupId>com.google.cloud.dataflow</groupId>
      <artifactId>google-cloud-dataflow-java-sdk-all</artifactId>
      <version>${google.dataflow.version}</version>
    </dependency>
 

    <!-- Adds a dependency on the Beam Google Cloud Platform IO module. -->
    <dependency>
      <groupId>org.apache.beam</groupId>
      <artifactId>beam-sdks-java-io-google-cloud-platform</artifactId>
      <version>${beam.version}</version>
    </dependency>

    <!-- Dependencies below this line are specific dependencies needed by the examples code. -->
    <dependency>
      <groupId>com.google.api-client</groupId>
      <artifactId>google-api-client</artifactId>
      <version>${google-clients.version}</version>
      <exclusions>
        <!-- Exclude an old version of guava that is being pulled
             in by a transitive dependency of google-api-client -->
        <exclusion>
          <groupId>com.google.guava</groupId>
          <artifactId>guava-jdk5</artifactId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>com.google.apis</groupId>
      <artifactId>google-api-services-bigquery</artifactId>
      <version>${bigquery.version}</version>
      <exclusions>
        <!-- Exclude an old version of guava that is being pulled
             in by a transitive dependency of google-api-client -->
        <exclusion>
          <groupId>com.google.guava</groupId>
          <artifactId>guava-jdk5</artifactId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>com.google.http-client</groupId>
      <artifactId>google-http-client</artifactId>
      <version>${google-clients.version}</version>
      <exclusions>
        <!-- Exclude an old version of guava that is being pulled
             in by a transitive dependency of google-api-client -->
        <exclusion>
          <groupId>com.google.guava</groupId>
          <artifactId>guava-jdk5</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    
    <dependency>
      <groupId>com.google.apis</groupId>
      <artifactId>google-api-services-pubsub</artifactId>
      <version>${pubsub.version}</version>
      <exclusions>
        <!-- Exclude an old version of guava that is being pulled
             in by a transitive dependency of google-api-client -->
        <exclusion>
          <groupId>com.google.guava</groupId>
          <artifactId>guava-jdk5</artifactId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>joda-time</groupId>
      <artifactId>joda-time</artifactId>
      <version>${joda.version}</version>
    </dependency>

    <dependency>
      <groupId>com.google.guava</groupId>
      <artifactId>guava</artifactId>
      <version>${guava.version}</version>
    </dependency>

    <!-- Add slf4j API frontend binding with JUL backend -->
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-api</artifactId>
      <version>${slf4j.version}</version>
    </dependency>

    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-jdk14</artifactId>
      <version>${slf4j.version}</version>
      <!-- When loaded at runtime this will wire up slf4j to the JUL backend -->
      <scope>runtime</scope>
    </dependency>

    <!-- Hamcrest and JUnit are required dependencies of PAssert,
         which is used in the main code of DebuggingWordCount example. -->
    <dependency>
      <groupId>org.hamcrest</groupId>
      <artifactId>hamcrest-all</artifactId>
      <version>${hamcrest.version}</version>
    </dependency>

    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>${junit.version}</version>
    </dependency>

  <dependency>
      <groupId>com.google.cloud.genomics</groupId>
      <artifactId>google-genomics-utils</artifactId>
      <version>v1-0.9</version>
      <exclusions>
        <!-- Exclude an old version of guava which is being pulled
             in by a transitive dependency google-api-client. -->
        <exclusion>
          <groupId>com.google.guava</groupId>
          <artifactId>guava-jdk5</artifactId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>com.google.cloud.genomics</groupId>
      <artifactId>google-genomics-dataflow</artifactId>
      <version>LATEST</version>
    </dependency>

     <dependency>
    	<groupId>org.apache.beam</groupId>
    	<artifactId>beam-sdks-java-extensions-sorter</artifactId>
    	<version>2.3.0</version>
    </dependency>

    <!-- The DirectRunner is needed for unit tests. -->
    <dependency>
      <groupId>org.apache.beam</groupId>
      <artifactId>beam-runners-direct-java</artifactId>
      <version>${beam.version}</version>
      <scope>test</scope>
    </dependency>
  </dependencies>
</project>