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>

    <name>SeqWare</name>
    <description>SeqWare Parent POM</description>
    <url>https://github.com/SeqWare/seqware</url>

    <prerequisites>
        <maven>3.3.2</maven>
    </prerequisites>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
        <!-- use for filtering of web service context files and related -->
        <seqware_meta_db_name>test_seqware_meta_db</seqware_meta_db_name>
        <seqware_meta_db_port>5432</seqware_meta_db_port>
        <seqware_meta_db_password>seqware</seqware_meta_db_password>
        <seqware_meta_db_user>seqware</seqware_meta_db_user>
        <seqware_meta_db_host>localhost</seqware_meta_db_host>

        <!-- while merging com.amazonaws.services.s3.transfer.MultipleFileUpload , I couldn't compile without setting a version here -->
        <aws-java-sdk.version>1.11.15</aws-java-sdk.version>
        <jackson.version>2.4.4</jackson.version>
        <spring.version>4.2.6.RELEASE</spring.version>
        <hibernate.version>5.1.0.Final</hibernate.version>
        <hibernate.jpa.version>1.0.0.Final</hibernate.jpa.version>
        <hibernate-validator.version>5.2.4.Final</hibernate-validator.version>
        <hamcrest.version>1.3</hamcrest.version>
        <beanlib.version>5.0.2beta</beanlib.version>
        <commons-lang.version>2.6</commons-lang.version>
        <commons-compress.version>1.2</commons-compress.version>
        <commons-cli.version>1.2</commons-cli.version>
        <commons-exec.version>1.3</commons-exec.version>
        <postgresql.version>9.4-1201-jdbc41</postgresql.version>
        <guava.version>19.0</guava.version>
        <restlet.version>2.3.7</restlet.version>
        <opencsv.version>2.3</opencsv.version>
        <maven-assembly-plugin.version>2.6</maven-assembly-plugin.version>
        <jetty-maven-plugin.version>6.1.26</jetty-maven-plugin.version>
        <github.url>scm:git:git@github.com:SeqWare/seqware.git</github.url>
        <maven-jar-plugin.version>2.6</maven-jar-plugin.version>
        <maven-clean-plugin.version>3.0.0</maven-clean-plugin.version>
        <maven-surefire-plugin.version>2.19.1</maven-surefire-plugin.version>
        <maven-failsafe-plugin.version>2.19.1</maven-failsafe-plugin.version>
        <maven-war-plugin.version>2.6</maven-war-plugin.version>
        <maven-compiler-plugin.version>3.5.1</maven-compiler-plugin.version>
        <maven-install-plugin.version>2.5.2</maven-install-plugin.version>
        <maven-deploy-plugin.version>2.8.2</maven-deploy-plugin.version>
        <maven-site-plugin.version>3.5.1</maven-site-plugin.version>
        <maven-versions-plugin.version>2.2</maven-versions-plugin.version>
        <maven-resources-plugin.version>2.7</maven-resources-plugin.version>
        <maven-antrun-plugin.version>1.8</maven-antrun-plugin.version>
        <maven-project-info-reports-plugin.version>2.9</maven-project-info-reports-plugin.version>
        <maven-release-plugin.version>2.5.3</maven-release-plugin.version>
        <maven-build-helper-plugin.version>1.10</maven-build-helper-plugin.version>
        <mockito.version>1.10.19</mockito.version>
        <powermock.version>1.6.5</powermock.version>
        <findbugs.version>3.0.3</findbugs.version>
        <maven-pmd-plugin.version>3.6</maven-pmd-plugin.version>
        <slf4j.version>1.7.21</slf4j.version>
        <old-jersey.version>1.19.1</old-jersey.version>

        <skipITs>true</skipITs>
        <!-- Needs to be set for memory issues, but must be overrideable from the command line for Bionimbus for unknown reasons -->
        <maven.compiler.fork>true</maven.compiler.fork>
        <main.basedir>${project.basedir}</main.basedir>
    </properties>

    <scm>
        <connection>${github.url}</connection>
        <developerConnection>${github.url}</developerConnection>
        <url>${github.url}</url>
    </scm>
    <distributionManagement>
        <repository>
            <id>wrench.res.oicr.on.ca</id>
            <name>wrench.res.oicr.on.ca-releases</name>
            <url>http://seqwaremaven.oicr.on.ca/artifactory/seqware-release</url>
            <uniqueVersion>false</uniqueVersion>
        </repository>
    </distributionManagement>

    <artifactId>seqware</artifactId>
    <packaging>pom</packaging>
    <groupId>com.github.seqware</groupId>
    <version>1.2.0-alpha.1-SNAPSHOT</version>

    <repositories>
        <repository>
            <id>seqware.sourceforge.net</id>
            <name>SeqWare Maven Repository</name>
            <url>http://seqwaremaven.oicr.on.ca/artifactory/seqware-release</url>
            <releases>
                <enabled>true</enabled>
            </releases>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
        </repository>
        <repository>
            <id>snapshot.seqware.sourceforge.net</id>
            <name>SeqWare Snapshot Maven Repository</name>
            <url>http://seqwaremaven.oicr.on.ca/artifactory/seqware-snapshot</url>
            <releases>
                <enabled>false</enabled>
            </releases>
            <snapshots>
                <enabled>true</enabled>
            </snapshots>
        </repository>
        <repository>
            <id>dependencies.seqware.sourceforge.net</id>
            <name>SeqWare Dependencies Maven Repository</name>
            <url>http://seqwaremaven.oicr.on.ca/artifactory/seqware-dependencies</url>
            <releases>
                <enabled>true</enabled>
            </releases>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
        </repository>
        <repository>
            <id>org.codehaus.plexus</id>
            <name>Plexus</name>
            <url>http://repo1.maven.org/maven2/org/codehaus/plexus/</url>
        </repository>
        <!-- Breaks install because of missing files        <repository>
            <id>ibiblio.org</id>
            <name>Maven Mirror</name>
            <url>http://mirrors.ibiblio.org/pub/mirrors/maven2</url>
        </repository> -->
        <repository>
            <id>maven-restlet</id>
            <name>Public online Restlet repository</name>
            <url>http://maven.restlet.org/</url>
        </repository>
        <repository>
            <id>apache-releases</id>
            <name>Apache Releases repository</name>
            <url>https://repository.apache.org/content/repositories/releases/</url>
        </repository>
        <repository>
            <id>cloudera</id>
            <url>https://repository.cloudera.com/artifactory/cloudera-repos/</url>
        </repository>
        <repository>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
            <id>jcenter</id>
            <name>bintray</name>
            <url>http://jcenter.bintray.com</url>
        </repository>
    </repositories>

    <modules>
        <module>seqware-meta-db</module>
        <module>seqware-common</module>
        <module>seqware-pipeline</module>
        <module>seqware-admin-webservice</module>
        <module>seqware-ext-admin-testing</module>
        <module>seqware-webservice</module>
        <module>seqware-archetypes/seqware-archetype-decider</module>
        <module>seqware-archetypes/seqware-archetype-java-workflow</module>
        <module>seqware-archetypes/seqware-archetype-module</module>
        <module>seqware-distribution</module>
        <module>seqware-ext-testing</module>
        <module>seqware-sanity-check</module>
    </modules>


    <licenses>
        <license>
            <name>GNU General Public License (GPLv3)</name>
            <url>http://www.gnu.org/licenses/gpl-3.0.html</url>
        </license>
    </licenses>

    <organization>
        <name>SeqWare</name>
        <url>https://github.com/SeqWare</url>
    </organization>

    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>commons-logging</groupId>
                <artifactId>commons-logging</artifactId>
                <version>1.1.3</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-lang3</artifactId>
                <version>3.4</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-api</artifactId>
                <version>${slf4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-log4j12</artifactId>
                <version>${slf4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>jul-to-slf4j</artifactId>
                <version>${slf4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>jcl-over-slf4j</artifactId>
                <version>${slf4j.version}</version>
            </dependency>
            <dependency>
                <groupId>log4j</groupId>
                <artifactId>log4j</artifactId>
                <version>1.2.17</version>
            </dependency>
            <dependency>
                <groupId>net.sf.jopt-simple</groupId>
                <artifactId>jopt-simple</artifactId>
                <version>5.0.1</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-collections4</artifactId>
                <version>4.1</version>
            </dependency>
            <dependency>
                <groupId>commons-collections</groupId>
                <artifactId>commons-collections</artifactId>
                <version>3.2.1</version>
            </dependency>
            <dependency>
                <groupId>commons-digester</groupId>
                <artifactId>commons-digester</artifactId>
                <version>1.8</version>
            </dependency>
            <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-compress -->
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-compress</artifactId>
                <version>1.12</version>
            </dependency>
            <dependency>
                <groupId>commons-dbutils</groupId>
                <artifactId>commons-dbutils</artifactId>
                <version>1.6</version>
            </dependency>
            <dependency>
                <groupId>commons-io</groupId>
                <artifactId>commons-io</artifactId>
                <version>2.5</version>
            </dependency>
            <dependency>
                <groupId>org.netbeans.api</groupId>
                <artifactId>org-openide-util-lookup</artifactId>
                <version>RELEASE80</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-exec</artifactId>
                <version>${commons-exec.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.tomcat</groupId>
                <artifactId>tomcat-dbcp</artifactId>
                <version>7.0.50</version>
            </dependency>
            <!-- while moving to HubFlow, the combination of HubFlow and maven:prepare is causing problems.
            release:update-versions seems to have an easier time with versions defined here -->
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-meta-db</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-common</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-pipeline</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-webservice</artifactId>
                <version>${project.version}</version>
                <type>war</type>
            </dependency>
            <dependency>
                <groupId>org.apache.zookeeper</groupId>
                <artifactId>zookeeper</artifactId>
                <version>3.4.6</version>
            </dependency>
            <dependency>
                <groupId>org.mortbay.jetty</groupId>
                <artifactId>jetty-util</artifactId>
                <version>6.1.26.cloudera.4</version>
            </dependency>
            <dependency>
                <groupId>org.apache.hadoop</groupId>
                <artifactId>hadoop-common</artifactId>
                <version>2.6.0-cdh5.4.4</version>
            </dependency>
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-portal</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-ext-testing</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-ext-admin-testing</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>com.github.seqware</groupId>
                <artifactId>seqware-distribution</artifactId>
                <version>${project.version}</version>
            </dependency>

            <!-- Amazon Web Services SDK dependencies -->
            <dependency>
                <groupId>com.amazonaws</groupId>
                <artifactId>aws-java-sdk</artifactId>
                <version>${aws-java-sdk.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.codehaus.jackson</groupId>
                        <artifactId>jackson-core-asl</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>commons-logging</groupId>
                        <artifactId>commons-logging</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.httpcomponents</groupId>
                        <artifactId>httpclient</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>com.fasterxml.jackson.core</groupId>
                        <artifactId>jackson-core</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>com.fasterxml.jackson.core</groupId>
                        <artifactId>jackson-annotations</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>com.amazonaws</groupId>
                <artifactId>aws-java-sdk-core</artifactId>
                <version>${aws-java-sdk.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.codehaus.jackson</groupId>
                        <artifactId>jackson-core-asl</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>commons-logging</groupId>
                        <artifactId>commons-logging</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.apache.httpcomponents</groupId>
                        <artifactId>httpclient</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>com.fasterxml.jackson.core</groupId>
                        <artifactId>jackson-core</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>com.fasterxml.jackson.core</groupId>
                        <artifactId>jackson-annotations</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>com.fasterxml.jackson.core</groupId>
                        <artifactId>jackson-databind</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>

            <!-- enforce for dependencies but replaced by com.fasterxml.jackson in our code -->
            <dependency>
                <groupId>org.codehaus.jackson</groupId>
                <artifactId>jackson-mapper-asl</artifactId>
                <version>1.9.13</version>
            </dependency>
            <dependency>
                <groupId>org.codehaus.jackson</groupId>
                <artifactId>jackson-core-asl</artifactId>
                <version>1.9.13</version>
            </dependency>

            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-annotations</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->
            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-databind</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-core</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.dataformat</groupId>
                <artifactId>jackson-dataformat-yaml</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>org.yaml</groupId>
                <artifactId>snakeyaml</artifactId>
                <version>1.17</version>
            </dependency>

            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-core</artifactId>
                <version>${spring.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>commons-logging</groupId>
                        <artifactId>commons-logging</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-web</artifactId>
                <version>${spring.version}</version>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-beans</artifactId>
                <version>${spring.version}</version>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-context</artifactId>
                <version>${spring.version}</version>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-aop</artifactId>
                <version>${spring.version}</version>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-context-support</artifactId>
                <version>${spring.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>${spring.version}</version>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-struts</artifactId>
                <version>${spring.version}</version>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-test</artifactId>
                <version>${spring.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-webmvc</artifactId>
                <version>${spring.version}</version>
            </dependency>

            <dependency>
                <groupId>org.hibernate</groupId>
                <artifactId>hibernate-entitymanager</artifactId>
                <version>${hibernate.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>cglib</groupId>
                        <artifactId>cglib</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <artifactId>hibernate-core</artifactId>
                <groupId>org.hibernate</groupId>
                <version>${hibernate.version}</version>
            </dependency>
            <dependency>
                <groupId>org.hibernate.javax.persistence</groupId>
                <artifactId>hibernate-jpa-2.1-api</artifactId>
                <version>${hibernate.jpa.version}</version>
            </dependency>
            <dependency>
                <groupId>org.hibernate</groupId>
                <artifactId>hibernate-validator</artifactId>
                <version>${hibernate-validator.version}</version>
            </dependency>
            <dependency>
                <groupId>org.hamcrest</groupId>
                <artifactId>hamcrest-all</artifactId>
                <version>${hamcrest.version}</version>
                <scope>test</scope>
            </dependency>

            <dependency>
                <groupId>javax.validation</groupId>
                <artifactId>validation-api</artifactId>
                <version>1.1.0.Final</version>
                <type>jar</type>
            </dependency>
            <dependency>
                <groupId>net.sf.beanlib</groupId>
                <artifactId>beanlib-hibernate</artifactId>
                <version>${beanlib.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.hibernate</groupId>
                        <artifactId>hibernate</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.springframework</groupId>
                        <artifactId>spring</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>net.sf.beanlib</groupId>
                <artifactId>beanlib</artifactId>
                <version>${beanlib.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>commons-lang</groupId>
                        <artifactId>commons-lang</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>cglib</groupId>
                        <artifactId>cglib</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>xstream</groupId>
                        <artifactId>xstream</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>


            <dependency>
                <groupId>commons-lang</groupId>
                <artifactId>commons-lang</artifactId>
                <version>${commons-lang.version}</version>
            </dependency>

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

            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.xstream</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.jackson</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.codehaus.woodstox</groupId>
                <artifactId>stax2-api</artifactId>
                <version>3.1.4</version>
            </dependency>
            <dependency>
                <groupId>xml-apis</groupId>
                <artifactId>xml-apis</artifactId>
                <version>1.4.01</version>
            </dependency>
            <dependency>
                <groupId>stax</groupId>
                <artifactId>stax-api</artifactId>
                <version>1.0.1</version>
            </dependency>
            <dependency>
                <groupId>org.javassist</groupId>
                <artifactId>javassist</artifactId>
                <version>3.20.0-GA</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml</groupId>
                <artifactId>classmate</artifactId>
                <version>1.3.0</version>
            </dependency>
            <dependency>
                <groupId>org.jboss.logging</groupId>
                <artifactId>jboss-logging</artifactId>
                <version>3.3.0.Final</version>
            </dependency>

            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.xml</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.net</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.fileupload</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.servlet</artifactId>
                <version>${restlet.version}</version>
            </dependency>

            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.wadl</artifactId>
                <version>${restlet.version}</version>
            </dependency>

            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.json</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.jaxb</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.protobuf</artifactId>
                <version>2.1-R2</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.slf4j</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.httpclient</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.ext.jsslutils</artifactId>
                <version>${restlet.version}</version>
            </dependency>
            <dependency>
                <groupId>javax.xml.bind</groupId>
                <artifactId>jaxb-api</artifactId>
                <version>2.2.2</version>
            </dependency>
            <dependency>
                <groupId>org.restlet.jee</groupId>
                <artifactId>org.restlet.test</artifactId>
                <version>${restlet.version}</version>
                <exclusions>
                    <!-- Excluded since they rely on maven 2 specific code that prevents maven 3 from being used. -->
                    <exclusion>
                        <groupId>org.restlet.jee</groupId>
                        <artifactId>org.restlet.ext.lucene</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.restlet.jee</groupId>
                        <artifactId>org.restlet.ext.jibx</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>commons-codec</groupId>
                        <artifactId>commons-codec</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>commons-logging</groupId>
                        <artifactId>commons-logging</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>net.sf.opencsv</groupId>
                <artifactId>opencsv</artifactId>
                <version>${opencsv.version}</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey</groupId>
                <artifactId>jersey-json</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey.contribs</groupId>
                <artifactId>jersey-moxy</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey.glassfish.v3.osgi</groupId>
                <artifactId>jersey-gf-server</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey</groupId>
                <artifactId>jersey-client</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey</groupId>
                <artifactId>jersey-grizzly</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey.glassfish.v3.osgi</groupId>
                <artifactId>jersey-gf-statsproviders</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.hk2.external</groupId>
                <artifactId>asm-all-repackaged</artifactId>
                <version>1.1.15</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey.glassfish.v3.osgi</groupId>
                <artifactId>jersey-gf-servlet</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.codehaus.jettison</groupId>
                <artifactId>jettison</artifactId>
                <version>1.3.5</version>
            </dependency>
            <dependency>
                <groupId>org.jvnet.mimepull</groupId>
                <artifactId>mimepull</artifactId>
                <version>1.9.3</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey.contribs</groupId>
                <artifactId>jersey-multipart</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>com.sun.jersey</groupId>
                <artifactId>jersey-core</artifactId>
                <version>${old-jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>4.12</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.powermock</groupId>
                <artifactId>powermock-core</artifactId>
                <version>${powermock.version}</version>
            </dependency>
            <dependency>
                <groupId>org.powermock</groupId>
                <artifactId>powermock-module-junit4</artifactId>
                <version>${powermock.version}</version>
            </dependency>
            <dependency>
                <groupId>org.powermock</groupId>
                <artifactId>powermock-api-mockito</artifactId>
                <version>${powermock.version}</version>
            </dependency>
            <dependency>
                <groupId>org.powermock</groupId>
                <artifactId>powermock-api-easymock</artifactId>
                <version>${powermock.version}</version>
            </dependency>
            <dependency>
                <groupId>org.objenesis</groupId>
                <artifactId>objenesis</artifactId>
                <version>2.2</version>
            </dependency>
            <dependency>
                <groupId>org.mockito</groupId>
                <artifactId>mockito-all</artifactId>
                <version>${mockito.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.objenesis</groupId>
                        <artifactId>objenesis</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.hamcrest</groupId>
                        <artifactId>hamcrest-core</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.mockito</groupId>
                <artifactId>mockito-core</artifactId>
                <version>${mockito.version}</version>
                <scope>test</scope>
                <exclusions>
                    <exclusion>
                        <groupId>org.hamcrest</groupId>
                        <artifactId>hamcrest-core</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.easymock</groupId>
                <artifactId>easymock</artifactId>
                <version>3.2</version>
                <exclusions>
                    <exclusion>
                        <groupId>org.objenesis</groupId>
                        <artifactId>objenesis</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>org.hamcrest</groupId>
                        <artifactId>hamcrest-core</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>com.google.code.gson</groupId>
                <artifactId>gson</artifactId>
                <version>2.7</version>
            </dependency>
            <dependency>
                <groupId>joda-time</groupId>
                <artifactId>joda-time</artifactId>
                <version>2.9.3</version>
            </dependency>
            <dependency>
                <groupId>com.github.stefanbirkner</groupId>
                <artifactId>system-rules</artifactId>
                <version>1.16.0</version>
                <exclusions>
                    <exclusion>
                        <groupId>junit</groupId>
                        <artifactId>junit-dep</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>

            <!-- security updates -->
            <dependency>
                <groupId>commons-beanutils</groupId>
                <artifactId>commons-beanutils</artifactId>
                <version>1.9.2</version>
            </dependency>

            <dependency>
                <groupId>asm</groupId>
                <artifactId>asm</artifactId>
                <version>3.3.1</version>
            </dependency>

            <!-- explicitly define dependency to version 0.8.11 -->
            <dependency>
                <groupId>org.raml</groupId>
                <artifactId>raml-parser</artifactId>
                <version>0.8.14</version>
            </dependency>

            <!-- https://mvnrepository.com/artifact/com.google.code.findbugs/jsr305 -->
            <dependency>
                <groupId>com.google.code.findbugs</groupId>
                <artifactId>jsr305</artifactId>
                <version>3.0.0</version>
            </dependency>

        </dependencies>
    </dependencyManagement>

    <build>
        <pluginManagement>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-scm-publish-plugin</artifactId>
                    <version>1.1</version>
                    <configuration>
                        <pubScmUrl>scm:git:ssh://git@github.com/SeqWare/unstable.seqware.io.git</pubScmUrl>
                        <content>${project.build.directory}/site/</content>
                        <tryUpdate>true</tryUpdate>
                        <skipDeletedFiles>true</skipDeletedFiles>
                        <scmBranch>gh-pages</scmBranch>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-failsafe-plugin</artifactId>
                    <version>${maven-failsafe-plugin.version}</version>
                </plugin>
                <plugin>
                    <artifactId>maven-assembly-plugin</artifactId>
                    <version>${maven-assembly-plugin.version}</version>
                </plugin>

                <plugin>
                    <groupId>org.apache.tomcat.maven</groupId>
                    <artifactId>tomcat7-maven-plugin</artifactId>
                    <version>2.2</version>
                    <configuration>
                        <port>8889</port>
                        <useNaming>true</useNaming>
                    </configuration>
                    <executions>
                        <execution>
                            <id>tomcat-run</id>
                            <goals>
                                <goal>run-war-only</goal>
                            </goals>
                            <phase>pre-integration-test</phase>
                            <configuration>
                                <fork>true</fork>
                                <skip>${skipITs}</skip>
                            </configuration>
                        </execution>
                        <execution>
                            <id>tomcat-shutdown</id>
                            <goals>
                                <goal>shutdown</goal>
                            </goals>
                            <configuration>
                                <skip>${skipITs}</skip>
                            </configuration>
                            <phase>post-integration-test</phase>
                        </execution>
                    </executions>
                </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-compiler-plugin</artifactId>
                    <version>${maven-compiler-plugin.version}</version>
                    <configuration>
                        <source>1.8</source>
                        <target>1.8</target>
                        <showDeprecation>true</showDeprecation>
                        <!-- added forkMode, the full GitHub mvn compile seems to blow up with an OutOfMemoryError -->
                        <!-- Moved forkMode setting to Properties section, so it can be overriden on command line -->
                    </configuration>
                    <!--
                    <dependencies>
                        <dependency>
                            <groupId>org.codehaus.plexus</groupId>
                            <artifactId>plexus-compiler-javac</artifactId>
                            <version>1.8.2</version>
                        </dependency>
                        <dependency>
                            <groupId>org.codehaus.plexus</groupId>
                            <artifactId>plexus-compiler-api</artifactId>
                            <version>1.8.2</version>
                        </dependency>
                    </dependencies>
                    -->
                </plugin>
                <plugin>
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>findbugs-maven-plugin</artifactId>
                    <version>${findbugs.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-release-plugin</artifactId>
                    <version>${maven-release-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>exec-maven-plugin</artifactId>
                    <version>1.5.0</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-pmd-plugin</artifactId>
                    <version>${maven-pmd-plugin.version}</version>
                    <configuration>
                        <targetJdk>1.8</targetJdk>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>versions-maven-plugin</artifactId>
                    <version>${maven-versions-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-jar-plugin</artifactId>
                    <version>${maven-jar-plugin.version}</version>
                    <inherited>true</inherited>
                    <configuration>
                        <archive>
                            <manifest>
                                <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                                <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                            </manifest>
                        </archive>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>cobertura-maven-plugin</artifactId>
                    <version>2.7</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-clean-plugin</artifactId>
                    <version>${maven-clean-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-deploy-plugin</artifactId>
                    <version>${maven-deploy-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-install-plugin</artifactId>
                    <version>${maven-install-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-site-plugin</artifactId>
                    <version>${maven-site-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-surefire-plugin</artifactId>
                    <version>${maven-surefire-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-resources-plugin</artifactId>
                    <version>${maven-resources-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-antrun-plugin</artifactId>
                    <version>${maven-antrun-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-project-info-reports-plugin</artifactId>
                    <version>${maven-project-info-reports-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>build-helper-maven-plugin</artifactId>
                    <version>${maven-build-helper-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-war-plugin</artifactId>
                    <version>${maven-war-plugin.version}</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-checkstyle-plugin</artifactId>
                    <version>2.17</version>
                    <configuration>
                        <configLocation>checkstyle.xml</configLocation>
                    </configuration>
                </plugin>
                <plugin>
                    <artifactId>maven-dependency-plugin</artifactId>
                    <version>2.10</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-enforcer-plugin</artifactId>
                    <version>1.4.1</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-source-plugin</artifactId>
                    <version>3.0.0</version>
                </plugin>
                <!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
                <plugin>
                    <groupId>org.eclipse.m2e</groupId>
                    <artifactId>lifecycle-mapping</artifactId>
                    <version>1.0.0</version>
                    <configuration>
                        <lifecycleMappingMetadata>
                            <pluginExecutions>
                                <pluginExecution>
                                    <pluginExecutionFilter>
                                        <groupId>
                                            org.apache.maven.plugins
                                        </groupId>
                                        <artifactId>
                                            maven-checkstyle-plugin
                                        </artifactId>
                                        <versionRange>
                                            [2.12.1,)
                                        </versionRange>
                                        <goals>
                                            <goal>check</goal>
                                        </goals>
                                    </pluginExecutionFilter>
                                    <action>
                                        <ignore/>
                                    </action>
                                </pluginExecution>
                                <pluginExecution>
                                    <pluginExecutionFilter>
                                        <groupId>
                                            org.apache.maven.plugins
                                        </groupId>
                                        <artifactId>
                                            maven-dependency-plugin
                                        </artifactId>
                                        <versionRange>
                                            [2.9,)
                                        </versionRange>
                                        <goals>
                                            <goal>
                                                copy-dependencies
                                            </goal>
                                        </goals>
                                    </pluginExecutionFilter>
                                    <action>
                                        <ignore/>
                                    </action>
                                </pluginExecution>
                                <pluginExecution>
                                    <pluginExecutionFilter>
                                        <groupId>
                                            org.apache.maven.plugins
                                        </groupId>
                                        <artifactId>
                                            maven-enforcer-plugin
                                        </artifactId>
                                        <versionRange>
                                            [1.3.1,)
                                        </versionRange>
                                        <goals>
                                            <goal>enforce</goal>
                                        </goals>
                                    </pluginExecutionFilter>
                                    <action>
                                        <ignore/>
                                    </action>
                                </pluginExecution>
                            </pluginExecutions>
                        </lifecycleMappingMetadata>
                    </configuration>
                </plugin>
            </plugins>
        </pluginManagement>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-enforcer-plugin</artifactId>
                <version>1.3.1</version>
                <executions>
                    <execution>
                        <id>enforce</id>
                        <configuration>
                            <rules>
                                <DependencyConvergence/>
                                <requirePluginVersions>
                                    <message>Best Practice is to always define plugin versions!</message>
                                </requirePluginVersions>
                                <requireReleaseDeps>
                                    <message>No Snapshots Allowed!</message>
                                    <failWhenParentIsSnapshot>false</failWhenParentIsSnapshot>
                                    <excludes>
                                        <exclude>com.github.seqware:*</exclude>
                                    </excludes>
                                </requireReleaseDeps>
                                <requireUpperBoundDeps/>
                            </rules>
                        </configuration>
                        <goals>
                            <goal>enforce</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>analyze</id>
                        <goals>
                            <goal>analyze-only</goal>
                        </goals>
                        <configuration>
                            <failOnWarning>true</failOnWarning>
                            <outputXML>true</outputXML>
                            <ignoreNonCompile>true</ignoreNonCompile>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jxr-plugin</artifactId>
                <version>2.3</version>
            </plugin>


            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <inherited>false</inherited>
                <version>2.10.3</version>
                <configuration>
                    <notimestamp>true</notimestamp>
		    <additionalparam>-Xdoclint:none</additionalparam>
                </configuration>
                <executions>
                    <execution>
                        <inherited>false</inherited>
                        <phase>site-deploy</phase>
                        <goals>
                            <goal>aggregate</goal>
                            <goal>test-aggregate</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-scm-publish-plugin</artifactId>
                <inherited>false</inherited>
                <executions>
                    <execution>
                        <inherited>false</inherited>
                        <phase>site-deploy</phase>
                        <goals>
                            <goal>publish-scm</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <inherited>false</inherited>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-project-info-reports-plugin</artifactId>
                <configuration>
                    <dependencyDetailsEnabled>false</dependencyDetailsEnabled>
                    <dependencyLocationsEnabled>false</dependencyLocationsEnabled>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-site-plugin</artifactId>
                <configuration>
                    <skip>true</skip>
                    <skipDeploy>true</skipDeploy>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-checkstyle-plugin</artifactId>
                <configuration>
                    <enableFilesSummary>true</enableFilesSummary>
                    <enableRulesSummary>true</enableRulesSummary>
                </configuration>
                <executions>
                    <execution>
                        <phase>
                            compile
                        </phase>
                        <goals>
                            <goal>check</goal>
                        </goals>
                        <configuration>
                            <consoleOutput>true</consoleOutput>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>findbugs-maven-plugin</artifactId>
                <executions>
                    <execution>
                        <goals>
                            <goal>check</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <!-- let's try to get rid of the timeout issue on Jenkins -->
                    <timeout>3600000</timeout>
                    <xmlOutput>true</xmlOutput>
                    <threshold>High</threshold>
                    <excludeFilterFile>findbugs-exclude.xml</excludeFilterFile>
                </configuration>
            </plugin>
            <plugin>
                <groupId>com.versioneye</groupId>
                <artifactId>versioneye-maven-plugin</artifactId>
                <version>3.9.2</version>
                <configuration>
                    <updatePropertiesAfterCreate>false</updatePropertiesAfterCreate>
		    <projectId>576c09f20c0727001206e716</projectId>
                </configuration>
            </plugin>
        </plugins>
    </build>

    <reporting>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jxr-plugin</artifactId>
                <version>2.5</version>
            </plugin>
        </plugins>
    </reporting>

    <!-- BEGIN: Specific to mapping unit tests and covered code -->
    <profiles>
        <!-- Jenkins by default defines a property BUILD_NUMBER which is used to enable the profile. -->
        <profile>
            <id>jenkins</id>
            <activation>
                <property>
                    <name>env.BUILD_NUMBER</name>
                </property>
            </activation>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.codehaus.mojo</groupId>
                        <artifactId>cobertura-maven-plugin</artifactId>
                        <configuration>
                            <check/>
                            <aggregate>true</aggregate>
                            <formats>
                                <format>xml</format>
                            </formats>
                        </configuration>
                        <executions>
                            <execution>
                                <phase>verify</phase>
                                <goals>
                                    <goal>cobertura</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>
    <!-- END: Specific to mapping unit tests and covered code -->

</project>