<?xml version="1.0" encoding="ISO-8859-1"?>
<!--
    CRUK-CI Genologics REST API Java Client.
    Copyright (C) 2013 Cancer Research UK Cambridge Institute.

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

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

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-->

<project xmlns="http://maven.apache.org/POM/4.0.0"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

    <modelVersion>4.0.0</modelVersion>

    <groupId>org.cruk.genologics</groupId>
    <artifactId>clarity-client</artifactId>
    <packaging>jar</packaging>
    <version>2.24.9</version>

    <name>CRUK-CI Genologics API Client</name>

    <description>
        A Java client for working with Genologics' REST API.
    </description>

    <url>http://crukci-bioinformatics.github.io/clarityclient</url>

    <inceptionYear>2013</inceptionYear>

    <scm>
        <connection>scm:git:https://github.com/crukci-bioinformatics/clarityclient</connection>
        <developerConnection>scm:git:ssh://git@github.com/crukci-bioinformatics/clarityclient</developerConnection>
        <url>https://github.com/crukci-bioinformatics/clarityclient</url>
    </scm>

    <issueManagement>
        <system>GitHub</system>
        <url>https://github.com/crukci-bioinformatics/clarityclient/issues</url>
    </issueManagement>

    <organization>
        <name>Cancer Research UK Cambridge Institute</name>
        <url>http://www.cruk.cam.ac.uk</url>
    </organization>

    <developers>
        <developer>
            <name>Richard Bowers</name>
            <email>richard.bowers@cruk.cam.ac.uk</email>
            <organization>Cancer Research UK Cambridge Institute</organization>
            <roles>
                <role>Author</role>
                <role>Lead Developer</role>
            </roles>
        </developer>
    </developers>

    <licenses>
        <license>
            <name>GNU General Public License, version 3.0</name>
            <url>http://www.gnu.org/licenses/gpl-3.0.txt</url>
            <distribution>repo</distribution>
        </license>
        <license>
            <name>GNU Lesser General Public License, version 3.0</name>
            <url>http://www.gnu.org/licenses/lgpl-3.0.txt</url>
            <distribution>repo</distribution>
        </license>
    </licenses>

    <properties>
        <dependency.locations.enabled>false</dependency.locations.enabled>
        <spring.version>4.3.19.RELEASE</spring.version>
        <aspectj.version>1.8.13</aspectj.version>
        <slf4j.version>1.7.25</slf4j.version>
        <jaxb.version>2.2.11</jaxb.version>
    </properties>

    <pluginRepositories>
        <pluginRepository>
            <id>mulesoft</id>
            <url>https://repository-master.mulesoft.org/nexus/content/groups/public</url>
            <layout>default</layout>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
            <releases>
                <enabled>true</enabled>
            </releases>
        </pluginRepository>
    </pluginRepositories>

    <repositories>
        <repository>
            <id>mulesoft</id>
            <url>https://repository-master.mulesoft.org/nexus/content/groups/public</url>
            <layout>default</layout>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
            <releases>
                <enabled>true</enabled>
            </releases>
        </repository>
    </repositories>

    <distributionManagement>
        <downloadUrl>https://github.com/crukci-bioinformatics/clarityclient/archive/master.zip</downloadUrl>
        <site>
            <id>github</id>
            <name>GitHub Pages</name>
            <url>ssh://git@github.com/crukci-bioinformatics/clarityclient</url>
        </site>
        <repository>
            <id>crukci-bioinformatics</id>
            <url>scpexe://comp-httpdev001.cri.camres.org/var/www/html/bioinformatics/maven</url>
        </repository>
        <snapshotRepository>
            <id>bioinformatics</id>
            <url>scpexe://internal-bioinformatics.cruk.cam.ac.uk/var/www/html/maven</url>
        </snapshotRepository>
    </distributionManagement>

    <build>
        <extensions>
            <extension>
                <groupId>org.apache.maven.wagon</groupId>
                <artifactId>wagon-ssh</artifactId>
                <version>2.6</version>
            </extension>
            <extension>
                <groupId>org.apache.maven.wagon</groupId>
                <artifactId>wagon-ssh-external</artifactId>
                <version>2.6</version>
            </extension>
        </extensions>

        <pluginManagement>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-compiler-plugin</artifactId>
                    <version>3.6.1</version>
                    <configuration>
                        <source>1.6</source>
                        <target>1.6</target>
                        <encoding>UTF-8</encoding>
                        <compilerArgs>
                            <arg>-Xlint:all</arg>
                            <arg>-XDignore.symbol.file</arg>
                        </compilerArgs>
                        <fork>true</fork>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-resources-plugin</artifactId>
                    <version>3.0.2</version>
                    <configuration>
                        <encoding>UTF-8</encoding>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-jar-plugin</artifactId>
                    <version>3.0.2</version>
                    <configuration>
                        <archive>
                            <index>true</index>
                            <manifest>
                                <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                                <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                            </manifest>
                        </archive>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-assembly-plugin</artifactId>
                    <version>3.0.0</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-dependency-plugin</artifactId>
                    <version>3.0.0</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-source-plugin</artifactId>
                    <version>3.0.1</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-surefire-plugin</artifactId>
                    <version>2.19.1</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-shade-plugin</artifactId>
                    <version>2.4.3</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-site-plugin</artifactId>
                    <version>3.6</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-toolchains-plugin</artifactId>
                    <version>1.1</version>
                </plugin>
                <plugin>
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>jaxb2-maven-plugin</artifactId>
                    <version>1.5</version>
                </plugin>
                <plugin>
                    <groupId>com.github.github</groupId>
                    <artifactId>site-maven-plugin</artifactId>
                    <version>0.9</version>
                </plugin>
                <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-toolchains-plugin</artifactId>
                                        <versionRange>[1.0,)</versionRange>
                                        <goals>
                                            <goal>toolchain</goal>
                                        </goals>
                                    </pluginExecutionFilter>
                                    <action>
                                        <ignore/>
                                    </action>
                                </pluginExecution>
                            </pluginExecutions>
                        </lifecycleMappingMetadata>
                    </configuration>
                </plugin>
            </plugins>
        </pluginManagement>

        <plugins>
<!--
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>jaxb2-maven-plugin</artifactId>
                <executions>
                    <execution>
                        <id>generation</id>
                        <phase>generate-sources</phase>
                        <goals>
                            <goal>xjc</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <verbose>false</verbose>
                    <quiet>false</quiet>
                    <clearOutputDir>false</clearOutputDir>
                    <extension>true</extension>
                    <arguments>-no-header</arguments>
                </configuration>
            </plugin>
-->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <configuration>
                    <systemPropertyVariables>
                        <!-- Additional Java 6 certificates -->
                        <javax.net.ssl.trustStore>${basedir}/java6-cacerts</javax.net.ssl.trustStore>
                        <javax.net.ssl.trustStorePassword>changeit</javax.net.ssl.trustStorePassword>
                  </systemPropertyVariables>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-toolchains-plugin</artifactId>
                <configuration>
                    <toolchains>
                        <jdk>
                            <version>1.6</version>
                            <vendor>sun</vendor>
                        </jdk>
                    </toolchains>
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>toolchain</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <executions>
                    <execution>
                        <id>attach-sources</id>
                        <phase>verify</phase>
                        <goals>
                            <goal>jar-no-fork</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <!-- Seems that the configuration of this needs to be in the "reports"
                     section when run as part of the site plugin, but needs to be here
                     when run directly from the Javadoc plugin.
                 -->
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <version>2.10.4</version>
                <configuration>
                    <overview>${project.build.sourceDirectory}/overview.html</overview>
                    <source>1.6</source>
                    <encoding>UTF-8</encoding>
                    <breakiterator>true</breakiterator>
                    <serialwarn>false</serialwarn>
                    <show>protected</show>
                    <links>
                        <link>https://www.slf4j.org/apidocs/</link>
                        <link>https://docs.spring.io/spring/docs/4.3.x/javadoc-api/</link>
                        <link>https://docs.spring.io/spring-integration/docs/4.3.x/api/</link>
                        <link>http://hc.apache.org/httpcomponents-client-4.5.x/httpclient/apidocs/</link>
                        <link>http://hc.apache.org/httpcomponents-core-ga/httpcore/apidocs/</link>
                        <link>https://eclipse.org/aspectj/doc/released/runtime-api/</link>
                        <link>https://eclipse.org/aspectj/doc/released/aspectj5rt-api/</link>
                        <link>http://ehcache.org/apidocs/2.6.9/</link>
                    </links>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-site-plugin</artifactId>
                <configuration>
                    <skipDeploy>true</skipDeploy>
                </configuration>
            </plugin>
            <plugin>
                <groupId>com.github.github</groupId>
                <artifactId>site-maven-plugin</artifactId>
                <executions>
                    <execution>
                        <goals>
                            <goal>site</goal>
                        </goals>
                        <phase>site-deploy</phase>
                    </execution>
                </executions>
                <configuration>
                    <server>github</server>
                    <message>Rebuild of the clarityclient site for ${project.version}.</message>
                    <branch>gh-pages</branch>
                    <merge>false</merge>
                </configuration>
            </plugin>
        </plugins>

        <resources>
            <resource>
                <directory>${project.basedir}/src/main/resources</directory>
                <targetPath>${project.build.outputDirectory}</targetPath>
            </resource>
            <resource>
                <directory>${project.basedir}/src/test/resources</directory>
                <targetPath>${project.build.testOutputDirectory}</targetPath>
            </resource>
            <resource>
                <directory>${project.basedir}</directory>
                <targetPath>META-INF</targetPath>
                <includes>
                    <include>LICENSE*</include>
                </includes>
            </resource>
        </resources>
    </build>

    <reporting>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-project-info-reports-plugin</artifactId>
                <version>2.9</version>
                <configuration>
                    <reportSets>
                        <reportSet>
                            <reports>
                                <report>dependencies</report>
                                <report>scm</report>
                            </reports>
                        </reportSet>
                    </reportSets>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-report-plugin</artifactId>
                <version>2.19.1</version>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <configuration>
                    <overview>${project.build.sourceDirectory}/overview.html</overview>
                    <source>1.6</source>
                    <encoding>UTF-8</encoding>
                    <breakiterator>true</breakiterator>
                    <serialwarn>false</serialwarn>
                    <show>protected</show>
                    <links>
                        <link>https://www.slf4j.org/apidocs/</link>
                        <link>https://docs.spring.io/spring/docs/4.3.x/javadoc-api/</link>
                        <link>https://docs.spring.io/spring-integration/docs/4.3.x/api/</link>
                        <link>http://hc.apache.org/httpcomponents-client-4.5.x/httpclient/apidocs/</link>
                        <link>http://hc.apache.org/httpcomponents-core-ga/httpcore/apidocs/</link>
                        <link>https://eclipse.org/aspectj/doc/released/runtime-api/</link>
                        <link>https://eclipse.org/aspectj/doc/released/aspectj5rt-api/</link>
                        <link>http://ehcache.org/apidocs/2.6.9/</link>
                    </links>
                </configuration>
                <reportSets>
                    <reportSet>
                        <id>default</id>
                        <reports>
                            <report>javadoc</report>
                        </reports>
                    </reportSet>
                </reportSets>
            </plugin>
        </plugins>
    </reporting>

    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>commons-beanutils</groupId>
                <artifactId>commons-beanutils</artifactId>
                <version>1.9.3</version>
                <exclusions>
                    <exclusion>
                        <groupId>commons-logging</groupId>
                        <artifactId>commons-logging</artifactId>
                    </exclusion>
                    <exclusion>
                        <groupId>commons-collections</groupId>
                        <artifactId>commons-collections</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>commons-codec</groupId>
                <artifactId>commons-codec</artifactId>
                <version>1.11</version>
            </dependency>
            <dependency>
                <groupId>commons-collections</groupId>
                <artifactId>commons-collections</artifactId>
                <version>3.2.2</version>
            </dependency>
            <dependency>
                <groupId>commons-io</groupId>
                <artifactId>commons-io</artifactId>
                <version>2.4</version>
            </dependency>
            <dependency>
                <groupId>commons-net</groupId>
                <artifactId>commons-net</artifactId>
                <version>3.4</version>
            </dependency>
            <dependency>
                <groupId>commons-lang</groupId>
                <artifactId>commons-lang</artifactId>
                <version>2.6</version>
            </dependency>

            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-lang3</artifactId>
                <version>3.4</version>
            </dependency>
            <dependency>
                <groupId>org.apache.httpcomponents</groupId>
                <artifactId>httpclient</artifactId>
                <version>4.5.4</version>
                <exclusions>
                    <exclusion>
                        <groupId>commons-logging</groupId>
                        <artifactId>commons-logging</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>

            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-api</artifactId>
                <version>${slf4j.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>jcl-over-slf4j</artifactId>
                <version>${slf4j.version}</version>
            </dependency>

            <!-- Include a specific reference implementation of JAXB as the ones included -->
            <!-- in the JREs do not have all the features used by the work flow code.     -->
            <dependency>
                <groupId>javax.xml.bind</groupId>
                <artifactId>jaxb-api</artifactId>
                <version>${jaxb.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jaxb</groupId>
                <artifactId>jaxb-core</artifactId>
                <version>${jaxb.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jaxb</groupId>
                <artifactId>jaxb-runtime</artifactId>
                <version>${jaxb.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jaxb</groupId>
                <artifactId>txw2</artifactId>
                <version>${jaxb.version}</version>
            </dependency>

            <dependency>
                <groupId>aopalliance</groupId>
                <artifactId>aopalliance</artifactId>
                <version>1.0</version>
            </dependency>
            <dependency>
                <groupId>org.aspectj</groupId>
                <artifactId>aspectjrt</artifactId>
                <version>${aspectj.version}</version>
            </dependency>
            <dependency>
                <groupId>org.aspectj</groupId>
                <artifactId>aspectjweaver</artifactId>
                <version>${aspectj.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.xmlbeans</groupId>
                <artifactId>xmlbeans</artifactId>
                <version>2.6.0</version>
            </dependency>

            <!-- This is the Spring "Bill of Materials". -->
            <!-- See http://docs.spring.io/autorepo/docs/spring-security/4.1.0.RC1/reference/htmlsingle/#maven-bom -->
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-framework-bom</artifactId>
                <version>${spring.version}</version>
                <type>pom</type>
                <scope>import</scope>
            </dependency>
            <dependency>
                <groupId>org.springframework</groupId>
                <artifactId>spring-core</artifactId>
                <version>${spring.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>commons-logging</groupId>
                        <artifactId>commons-logging</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>org.springframework.integration</groupId>
                <artifactId>spring-integration-sftp</artifactId>
                <version>${spring.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>com.jcraft</groupId>
                        <artifactId>jsch</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
        </dependencies>
    </dependencyManagement>

    <dependencies>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>jcl-over-slf4j</artifactId>
            <scope>runtime</scope>
        </dependency>

        <dependency>
            <groupId>commons-beanutils</groupId>
            <artifactId>commons-beanutils</artifactId>
        </dependency>
        <dependency>
            <groupId>commons-collections</groupId>
            <artifactId>commons-collections</artifactId>
            <scope>runtime</scope>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-lang3</artifactId>
        </dependency>

        <dependency>
            <groupId>javax.xml.bind</groupId>
            <artifactId>jaxb-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jaxb</groupId>
            <artifactId>jaxb-runtime</artifactId>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jaxb</groupId>
            <artifactId>txw2</artifactId>
        </dependency>

        <dependency>
            <groupId>org.aspectj</groupId>
            <artifactId>aspectjrt</artifactId>
        </dependency>
        <dependency>
            <groupId>org.aspectj</groupId>
            <artifactId>aspectjweaver</artifactId>
            <scope>runtime</scope>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-aop</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context-support</artifactId>
            <scope>runtime</scope>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-core</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-oxm</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-web</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework.integration</groupId>
            <artifactId>spring-integration-sftp</artifactId>
        </dependency>

        <dependency>
            <groupId>com.jcraft</groupId>
            <artifactId>jsch</artifactId>
            <version>0.1.54</version>
        </dependency>

        <!-- If, in future, caching is annotation driven.
        <dependency>
            <groupId>com.googlecode.ehcache-spring-annotations</groupId>
            <artifactId>ehcache-spring-annotations</artifactId>
            <version>1.2.0</version>
            <exclusions>
                <exclusion>
                    <groupId>net.sf.ehcache</groupId>
                    <artifactId>ehcache-core</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        -->
        <dependency>
            <groupId>net.sf.ehcache</groupId>
            <artifactId>ehcache-core</artifactId>
            <version>2.6.11</version>
        </dependency>

        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-log4j12</artifactId>
            <version>${slf4j.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.12</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.easymock</groupId>
            <artifactId>easymock</artifactId>
            <version>3.4</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>xmlunit</groupId>
            <artifactId>xmlunit</artifactId>
            <version>1.6</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.bouncycastle</groupId>
            <artifactId>bcprov-jdk15on</artifactId>
            <version>1.54</version>
            <scope>test</scope>
        </dependency>
    </dependencies>
</project>
