pom.xml

<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
         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>uk.ac.ebi.phenotype</groupId>
    <artifactId>PhenotypeArchive</artifactId>
    <version>2.2.3</version>
    <packaging>war</packaging>
    <name>EBI Phenotype Archive</name>
    <description>EBI Phenotype Archive Project</description>


    <distributionManagement>
        <repository>
            <id>deployment</id>
            <name>Internal Releases</name>
            <url>http://ves-ebi-d9.ebi.ac.uk:8080/nexus/content/repositories/releases/</url>
        </repository>
        <snapshotRepository>
            <id>deployment</id>
            <name>Internal Snapshot</name>
            <url>http://ves-ebi-d9.ebi.ac.uk:8080/nexus/content/repositories/snapshots/</url>
        </snapshotRepository>
    </distributionManagement>

    <properties>
        <maven.compiler.target>1.7</maven.compiler.target>
        <maven.compiler.source>1.7</maven.compiler.source>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <spring.version>3.1.4.RELEASE</spring.version>
        <slf4j.version>1.7.7</slf4j.version>
        <java.version>1.7</java.version>
        <junit.version>4.11</junit.version>
        <hibernate.show_sql>true</hibernate.show_sql>
        <hibernate.dialect>org.hibernate.dialect.MySQLDialect</hibernate.dialect>
        <hibernate.version>3.6.10.Final</hibernate.version>
        <servlet.api.version>2.3</servlet.api.version>

        <selenium.version>2.41.0</selenium.version>
        <selenium-firefox.version>2.44.0</selenium-firefox.version>
        <seleniumUrl>http://mi-selenium-win.windows.ebi.ac.uk:4444/wd/hub</seleniumUrl>

        <baseUrl>http://localhost:8080/phenotype-archive</baseUrl>

        <!-- The solrUrl bypasses the proxy at mousephenotype.org and goes directly
            to EBI servers for performance -->
        <solrUrl>http://wwwdev.ebi.ac.uk/mi/impc/dev/solr</solrUrl>
        <internalSolrUrl>http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr</internalSolrUrl>
        <!-- internalSolrUrl>http://wwwdev.ebi.ac.uk/mi/impc/dev/solr</internalSolrUrl-->
        <buildIndexesSolrUrl>http://ves-ebi-d0.ebi.ac.uk:8090/build_indexes</buildIndexesSolrUrl>
        <preqcXmlfile>
            /nfs/web-hx/webadmin/tomcat/bases/mouseinformatics/solr_home_phenotypes_test/datafiles/PhenotypeCallSummary.xml
        </preqcXmlfile>
        <human2mouseFile>
            /nfs/web-hx/webadmin/tomcat/bases/mouseinformatics/solr_home_phenotypes_test/datafiles/HMD_HumanPhenotype.rpt
        </human2mouseFile>
        <drupalBaseUrl>https://dev.mousephenotype.org</drupalBaseUrl>
        <mediaBaseUrl>https://dev.mousephenotype.org/data/media</mediaBaseUrl>
        <impcMediaBaseUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
        <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
        <googleAnalytics></googleAnalytics>
        <liveSite>false</liveSite>
        <ebi.distrib.repository>http://ves-ebi-d9.ebi.ac.uk:8080/nexus/content/groups/public</ebi.distrib.repository>
        <phenodigm.solrserver>http://solrclouddev.sanger.ac.uk/solr/phenodigm</phenodigm.solrserver>
        <imits.solrserver>http://ikmc.vm.bytemark.co.uk:8983/solr/allele2</imits.solrserver>
        <datasourcesConfig>devDatasourcesConfig.properties</datasourcesConfig>
    </properties>

    <dependencies>

        <!--  orace jdbc driver -->
        <dependency>
            <groupId>com.oracle</groupId>
            <artifactId>ojdbc6</artifactId>
            <version>11.2.0</version>
        </dependency>

        <dependency>
            <groupId>net.sf.opencsv</groupId>
            <artifactId>opencsv</artifactId>
            <version>2.3</version>
        </dependency>

        <!--Phenodigm disease pages dependencies -->
        <dependency>
            <groupId>uk.ac.sanger</groupId>
            <artifactId>phenodigm2-core</artifactId>
            <version>1.5.0</version>
        </dependency>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math3</artifactId>
            <version>3.0</version>
        </dependency>

        <dependency>
            <groupId>se.jiderhamn</groupId>
            <artifactId>classloader-leak-prevention</artifactId>
            <version>[1.0,2.0)</version>
            <exclusions>
                <!-- Exclude el-api as it's provided by tomcat -->
                <exclusion>
                    <groupId>javax.el</groupId>
                    <artifactId>el-api</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math</artifactId>
            <version>2.0</version>
        </dependency>

        <dependency>
            <groupId>com.googlecode.htmlcompressor</groupId>
            <artifactId>htmlcompressor</artifactId>
            <version>1.4</version>
        </dependency>

        <dependency>
            <groupId>com.samaxes.maven</groupId>
            <artifactId>minify-maven-plugin</artifactId>
            <version>1.7</version>
        </dependency>

        <!-- Maven's transitive dependency mechanism will take care of all required
            jars -->
        <dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi-ooxml</artifactId>
            <version>3.8</version>
            <exclusions>
                <!-- Exclude xml-apis as it's provided by tomcat -->
                <exclusion>
                    <groupId>xml-apis</groupId>
                    <artifactId>xml-apis</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <artifactId>solr-solrj</artifactId>
            <groupId>org.apache.solr</groupId>
            <version>4.9.0</version>
        </dependency>

        <dependency>
            <groupId>mysql</groupId>
            <artifactId>mysql-connector-java</artifactId>
            <version>5.1.21</version>
        </dependency>

        <!-- servlet API is provided by the container -->
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>servlet-api</artifactId>
            <version>${servlet.api.version}</version>
            <scope>provided</scope>
        </dependency>

        <!-- Bean Validation Dependencies -->

        <dependency>
            <groupId>javax.validation</groupId>
            <artifactId>validation-api</artifactId>
            <version>1.0.0.GA</version>
            <scope>compile</scope>
        </dependency>

        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-validator</artifactId>
            <version>4.0.0.GA</version>
            <scope>compile</scope>
        </dependency>

        <!-- JPA Persistence Dependencies -->

        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-entitymanager</artifactId>
            <version>${hibernate.version}</version>
            <scope>compile</scope>
        </dependency>

        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-core</artifactId>
            <version>${hibernate.version}</version>
            <scope>compile</scope>
                        <exclusions>
                <!-- Exclude Commons Logging in favor of SLF4j -->
                <exclusion>
                    <groupId>commons-collections</groupId>
                    <artifactId>commons-collections</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>org.hibernate.javax.persistence</groupId>
            <artifactId>hibernate-jpa-2.0-api</artifactId>
            <version>1.0.1.Final</version>
            <scope>compile</scope>
        </dependency>

        <!-- JSON Dependencies -->
        <dependency>
            <groupId>net.sf.json-lib</groupId>
            <artifactId>json-lib</artifactId>
            <version>2.2.3</version>
        </dependency>

        <dependency>
            <groupId>org.codehaus.jackson</groupId>
            <artifactId>jackson-jaxrs</artifactId>
            <version>1.9.3</version>
            <scope>compile</scope>
        </dependency>

        <!-- Spring Dependencies -->

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context</artifactId>
            <version>${spring.version}</version>
            <exclusions>
                <!-- Exclude Commons Logging in favor of SLF4j -->
                <exclusion>
                    <groupId>commons-logging</groupId>
                    <artifactId>commons-logging</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-webmvc</artifactId>
            <version>${spring.version}</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-orm</artifactId>
            <version>${spring.version}</version>
            <type>jar</type>
            <scope>compile</scope>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context-support</artifactId>
            <version>${spring.version}</version>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-oxm</artifactId>
            <version>${spring.version}</version>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-test</artifactId>
            <version>${spring.version}</version>
            <type>jar</type>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-aop</artifactId>
            <version>${spring.version}</version>
        </dependency>

		<!-- Apache Commons Upload -->
        <dependency>
           <groupId>commons-fileupload</groupId>
           <artifactId>commons-fileupload</artifactId>
           <version>1.2.2</version>
        </dependency>

        <!-- Apache Commons Upload -->
        <dependency>
           <groupId>commons-io</groupId>
           <artifactId>commons-io</artifactId>
           <version>1.3.2</version>
        </dependency>

        <!-- DB Dependencies -->

        <dependency>
            <groupId>commons-dbcp</groupId>
            <artifactId>commons-dbcp</artifactId>
            <version>20030825.184428</version>
            <type>jar</type>
            <scope>compile</scope>
        </dependency>
        <dependency>
            <groupId>commons-pool</groupId>
            <artifactId>commons-pool</artifactId>
            <version>20030825.183949</version>
            <type>jar</type>
            <scope>compile</scope>
        </dependency>

        <dependency>
            <groupId>commons-net</groupId>
            <artifactId>commons-net</artifactId>
            <version>3.1</version>
            <type>jar</type>
            <scope>compile</scope>
        </dependency>

        <!-- A Java library for parsing command line options -->
        <dependency>
            <groupId>net.sf.jopt-simple</groupId>
            <artifactId>jopt-simple</artifactId>
            <version>4.8</version>
        </dependency>

        <!-- HTTP components Dependencies -->

        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpcore</artifactId>
            <version>4.3</version>
        </dependency>

        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
            <version>4.3.1</version>
        </dependency>

        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpmime</artifactId>
            <version>4.3.1</version>
        </dependency>

        <dependency>
            <groupId>org.apache.james</groupId>
            <artifactId>apache-mime4j</artifactId>
            <version>0.5</version>
            <exclusions>
                <exclusion>
                    <groupId>commons-logging</groupId>
                    <artifactId>commons-logging</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>commons-logging</groupId>
            <artifactId>commons-logging</artifactId>
            <version>1.1.1</version>
            <exclusions>
                <!-- Exclude servlet api -->
                <exclusion>
                    <groupId>javax.servlet</groupId>
                    <artifactId>servlet-api</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>wsdl4j</groupId>
            <artifactId>wsdl4j</artifactId>
            <version>1.6.2</version>
        </dependency>

        <dependency>
            <groupId>org.apache.ws.commons.schema</groupId>
            <artifactId>XmlSchema</artifactId>
            <version>1.3.2</version>
        </dependency>

        <dependency>
            <groupId>commons-discovery</groupId>
            <artifactId>commons-discovery</artifactId>
            <version>0.4</version>
            <exclusions>
                <exclusion>
                    <groupId>commons-logging</groupId>
                    <artifactId>commons-logging</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>javax.xml</groupId>
            <artifactId>jaxrpc-api</artifactId>
            <version>1.1</version>
        </dependency>

        <!-- View Dependencies -->
        <dependency>
            <groupId>jstl</groupId>
            <artifactId>jstl</artifactId>
            <version>1.2</version>
            <scope>compile</scope>
        </dependency>


        <!-- Test Dependencies -->
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>${junit.version}</version>
            <scope>test</scope>
        </dependency>

        <!-- logging -->
        <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>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-log4j12</artifactId>
            <version>${slf4j.version}</version>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.17</version>
            <exclusions>
                <exclusion>
                    <groupId>com.sun.jdmk</groupId>
                    <artifactId>jmxtools</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>com.sun.jmx</groupId>
                    <artifactId>jmxri</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>javax.jms</groupId>
                    <artifactId>jms</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <!-- Selenium dependencies -->
        <dependency>
            <groupId>org.seleniumhq.selenium</groupId>
            <artifactId>selenium-java</artifactId>
            <version>${selenium.version}</version>
        </dependency>
        <dependency>
            <groupId>org.seleniumhq.selenium</groupId>
            <artifactId>selenium-firefox-driver</artifactId>
            <version>${selenium-firefox.version}</version>
        </dependency>
        <dependency>
            <groupId>org.seleniumhq.selenium</groupId>
            <artifactId>selenium-chrome-driver</artifactId>
            <version>${selenium.version}</version>
        </dependency>
        <dependency>
            <groupId>org.seleniumhq.selenium</groupId>
            <artifactId>selenium-safari-driver</artifactId>
            <version>${selenium.version}</version>
        </dependency>
        <dependency>
            <groupId>org.seleniumhq.selenium</groupId>
            <artifactId>selenium-ie-driver</artifactId>
            <version>${selenium.version}</version>
        </dependency>

        <dependency>
            <groupId>net.sf.alchim</groupId>
            <artifactId>yuicompressor-maven-plugin</artifactId>
            <version>0.7.1</version>
        </dependency>

        <dependency>
            <groupId>com.google.code</groupId>
            <artifactId>sitemapgen4j</artifactId>
            <version>1.0.1</version>
        </dependency>


    </dependencies>

    <repositories>
        <!-- JBoss Repository used for Java EE 6 pieces -->
        <repository>
            <id>repository.jboss.org</id>
            <name>JBoss Repository</name>
            <url>http://repository.jboss.org/nexus/content/groups/public-jboss/</url>
        </repository>

        <repository>
            <id>org.springframework.maven.milestone</id>
            <name>Spring Maven Milestone Repository</name>
            <url>http://maven.springframework.org/milestone</url>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
        </repository>
    </repositories>

    <build>
        <finalName>phenotype-archive</finalName>
        <pluginManagement>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-surefire-plugin</artifactId>
                    <version>2.15</version>
                    <configuration>
                        <skipTests>true</skipTests>
                        <testFailureIgnore>true</testFailureIgnore>
                        <excludes>
                            <exclude>**PageTest.java</exclude>
                            <exclude>**/org/mousephenotype/www/**</exclude>
                        </excludes>
                    </configuration>
                </plugin>

                <plugin>
                    <groupId>com.samaxes.maven</groupId>
                    <artifactId>minify-maven-plugin</artifactId>
                    <version>1.7</version>
                </plugin>

            </plugins>
        </pluginManagement>

        <plugins>

            <!-- Facilitates downloading source and javadoc in Eclipse -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-eclipse-plugin</artifactId>
                <version>2.8</version>
                <configuration>
                    <wtpversion>2.0</wtpversion>
                    <downloadSources>true</downloadSources>
                    <downloadJavadocs>true</downloadJavadocs>
                </configuration>
            </plugin>

            <!-- minify JS and CSS -->

            <plugin>
                <groupId>com.samaxes.maven</groupId>
                <artifactId>minify-maven-plugin</artifactId>
                <!-- <version>1.7</version> -->
                <executions>
                    <execution>
                        <id>default-minify</id>
                        <!-- process-resources won't work -->
                        <phase>process-resources</phase>
                        <!-- phase>process-resources</phase -->
                        <configuration>
                            <charset>utf-8</charset>
                            <jsEngine>yui</jsEngine>
                            <debug>true</debug>
                            <webappSourceDir>${basedir}/WebContent/resources/</webappSourceDir>
                            <webappTargetDir>${basedir}/WebContent/resources/</webappTargetDir>
                            <cssSourceDir>css</cssSourceDir>
                            <cssSourceFiles>
                                <cssSourceFile>searchAndFacet.css</cssSourceFile>
                                <cssSourceFile>vendor/DataTables-1.9.4/jquery.dataTables.css</cssSourceFile>
                                <cssSourceFile>vendor/DataTables-1.9.4/customDataTable.css</cssSourceFile>
                                <!-- catch all for us -->
                                <cssSourceFile>custom.css</cssSourceFile>
                            </cssSourceFiles>
                            <cssFinalFile>style.css</cssFinalFile>
                            <jsSourceDir>js</jsSourceDir>
                            <jsSourceFiles>
                                <jsSourceFile>documentationConfig.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/homepage_seach_button_enter.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/searchAndFacetConfig.js</jsSourceFile>
                                <jsSourceFile>vendor/DataTables-1.9.4/jquery.dataTables.js</jsSourceFile>
                                <jsSourceFile>vendor/DataTables-1.9.4/core.filter.js</jsSourceFile>
                                <jsSourceFile>vendor/DataTables-1.9.4/TableTools.min.js</jsSourceFile>
                                <jsSourceFile>utils/tools.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/geneFacetWidget.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/mpFacetWidget.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/maFacetWidget.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/pipelineFacetWidget.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/imagesFacetWidget.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/diseaseFacetWidget.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/search.js</jsSourceFile>
                                <jsSourceFile>searchAndFacet/searchAndFacet_primer.js</jsSourceFile>
                            </jsSourceFiles>
                            <jsFinalFile>script.js</jsFinalFile>
                        </configuration>
                        <goals>
                            <goal>minify</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-war-plugin</artifactId>
                <!-- 2.2 => 2.0.1 -->
                <version>2.2</version>
                <executions>
                    <!-- added for making the replace plugin run in the exploded phase -->
                    <execution>
                        <id>prepare-war</id>
                        <phase>prepare-package</phase>
                        <goals>
                            <goal>exploded</goal>
                        </goals>
                    </execution>
                </executions>

                <configuration>

                    <!-- Overiddes default Maven configuration for Admin Tools -->
                    <warSourceDirectory>WebContent</warSourceDirectory>

                    <!-- excluded because these resources are minified -->
                    <warSourceExcludes>
                        <!-- **/bootstrap.min.css ,**/bootstrap-responsive.min.css -->
                        **/vendor/DataTables-1.9.4/jquery.dataTables.css
                        ,**/vendor/DataTables-1.9.4/customDataTable.css
                        <!-- **/searchAndFacet.css ,**/searchAndFacet/searchAndFacetConfig.js
                            ,**/vendor/DataTables-1.9.4/jquery.dataTables.js ,**/vendor/DataTables-1.9.4/core.filter.js
                            ,**/vendor/DataTables-1.9.4/TableTools.min.js ,**/utils/tools.js ,**/searchAndFacet/geneFacetWidget.js
                            ,**/searchAndFacet/mpFacetWidget.js ,**/searchAndFacet/pipelineFacetWidget.js
                            ,**/searchAndFacet/imagesFacetWidget.js ,**/searchAndFacet/search.js ,**/searchAndFacet/searchAndFacet_primer.js -->
                    </warSourceExcludes>

                    <webResources>
                        <resource>
                            <directory>${basedir}/WebContent/WEB-INF</directory>
                            <filtering>true</filtering>
                            <targetPath>WEB-INF</targetPath>
                            <includes>
                                <include>**/web.xml</include>
                                <include>**/app-config.xml</include>
                                <include>**/test-config.xml</include>
                                <include>**/index-app-config.xml</include>
                                <include>**/views/404.jsp</include>
                                <include>**/views/identifierError.jsp</include>
                            </includes>
                        </resource>
                    </webResources>

                    <archive>
                        <addMavenDescriptor>true</addMavenDescriptor>
                        <manifest>
                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                        </manifest>
                    </archive>

                </configuration>
            </plugin>

            <!-- Ensures we are compiling at 1.7 level -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.3.2</version>
                <configuration>
                    <source>${java.version}</source>
                    <target>${java.version}</target>
                    <excludes>
                        <exclude>${project.basedir}/src/test/java/**/*.java</exclude>
                    </excludes>
                </configuration>
            </plugin>
        </plugins>
    </build>

    <profiles>

        <profile>
            <id>datamodel</id>

            <properties>
                <envClassifier>datamodel</envClassifier>
            </properties>

            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>true</skipTests>
                            <excludes>
                                <exclude>**PageTest.java</exclude>
                                <exclude>**/org/mousephenotype/www/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>
                    <plugin>
                        <artifactId>maven-jar-plugin</artifactId>
                        <version>2.4</version>
                        <executions>
                            <execution>
                                <id>make-jar</id>
                                <phase>compile</phase>
                                <goals>
                                    <goal>jar</goal>
                                </goals>
                            </execution>
                        </executions>
                        <configuration>

                            <classifier>datamodel</classifier>
                            <includes>
                                <include>**/bean/*</include>
                                <include>**/dao/*</include>
                                <include>**/pojo/*</include>
                                <include>**/phenotype/data/imits/*</include>
                                <include>**/phenotype/util/*</include>
                                <include>**/phenotype/imaging/**</include>
                                <include>**/data/europhenome/*</include>
                                <include>**/data/cda/*</include>
                                <include>**/data/impress/*</include>
                                <include>**/chart/**</include>
                                <include>**/stats/**</include>
                                <include>**/service/**</include>
                                <include>**/service/dto/**</include>
                                <include>**/phenotype/error/**</include>
                                <include>**/generic/util/*</include>
                                <include>**/web/util/*</include>
                                <include>**/enumeration/*</include>
                            </includes>
                        </configuration>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-install-plugin</artifactId>
                        <version>2.5.1</version>
                        <executions>
                            <execution>
                                <id>install-jar</id>
                                <phase>install</phase>
                                <goals>
                                    <goal>install-file</goal>
                                </goals>
                                <configuration>
                                    <generatePom>true</generatePom>
                                    <packaging>jar</packaging>
                                    <artifactId>${project.artifactId}</artifactId>
                                    <groupId>${project.groupId}</groupId>
                                    <version>${project.version}</version>
                                    <file>${project.build.directory}/${project.build.finalName}-datamodel.jar</file>
                                </configuration>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>

        <profile>
            <id>development</id>

            <!-- Internal development uses the default POM properties -->
            <properties>
                <baseUrl>/data</baseUrl>
                <internalSolrUrl>http://localhost:8090/mi/impc/dev/solr</internalSolrUrl>
                <liveSite>false</liveSite>
            </properties>

            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>false</skipTests>
                            <excludes>
                                <exclude>**PageTest.java</exclude>
                                <exclude>**/org/mousephenotype/www/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>

                </plugins>
            </build>
        </profile>

        <profile>
            <id>test</id>

            <!-- Internal development uses the default POM properties -->
            <properties>
                <baseUrl>/data</baseUrl>
                <internalSolrUrl>http://localhost:8090/mi/impc/dev/solr</internalSolrUrl>
                <liveSite>false</liveSite>
            </properties>

            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>false</skipTests>
                            <excludes>
                                <exclude>**PageTest.java</exclude>
                                <exclude>**/org/mousephenotype/www/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>

        <profile>
            <id>external-dev</id>

            <properties>
                <baseUrl>/data</baseUrl>
                <solrUrl>https://wwwdev.ebi.ac.uk/mi/impc/dev/solr</solrUrl>
                <internalSolrUrl>http://localhost:8090/mi/impc/dev/solr</internalSolrUrl>
                <drupalBaseUrl>https://dev.mousephenotype.org</drupalBaseUrl>
                <mediaBaseUrl>https://dev.mousephenotype.org/data/media</mediaBaseUrl>
                <impcMediaBaseUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
                <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
                <liveSite>false</liveSite>
            </properties>


            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>true</skipTests>
                            <excludes>
                                <exclude>**PageTest.java</exclude>
                                <exclude>**/org/mousephenotype/www/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>

                </plugins>
            </build>

        </profile>

        <profile>
            <id>dev-web-tests</id>

            <properties>
                <baseUrl>http://ves-ebi-d0:8080/mi/impc/dev/phenotype-archive</baseUrl>
                <solrUrl>https://wwwdev.ebi.ac.uk/mi/impc/dev/solr</solrUrl>
                <internalSolrUrl>http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr</internalSolrUrl>
                <drupalBaseUrl>https://dev.mousephenotype.org</drupalBaseUrl>
                <mediaBaseUrl>https://dev.mousephenotype.org/data/media</mediaBaseUrl>
                <impcMediaBaseUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
                <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
                <seleniumUrl>http://mi-selenium-mac.windows.ebi.ac.uk:4444/wd/hub</seleniumUrl>
                <datasourcesConfig>devDatasourcesConfig.properties</datasourcesConfig>
                <liveSite>false</liveSite>
            </properties>

            <build>
                <resources>
                    <resource>
                        <directory>src/test/resources</directory>
                        <targetPath>${basedir}/target/test-classes</targetPath>
                        <includes>
                            <include>**/test-config.xml</include>
                        </includes>
                        <filtering>true</filtering>
                    </resource>
                </resources>
                <pluginManagement>
                    <plugins>
                        <plugin>
                            <groupId>org.apache.maven.plugins</groupId>
                            <artifactId>maven-surefire-plugin</artifactId>
                            <version>2.4.2</version>
                            <configuration>
                                <skipTests>false</skipTests>
                                <testFailureIgnore>true</testFailureIgnore>
                                <includes>
                                    <include>**PageTest.java</include>
                                    <include>**/org/mousephenotype/www/**</include>
                                </includes>
                                <excludes>
                                    <exclude></exclude>
                                </excludes>
                            </configuration>
                        </plugin>
                    </plugins>
                </pluginManagement>
            </build>
        </profile>

        <profile>
            <id>beta-web-tests</id>

            <properties>
                <baseUrl>http://beta.mousephenotype.org/data</baseUrl>
                <solrUrl>https://www.ebi.ac.uk/mi/impc/beta/solr</solrUrl>
                <internalSolrUrl>https://www.ebi.ac.uk/mi/impc/beta/solr</internalSolrUrl>
                <drupalBaseUrl>https://beta.mousephenotype.org</drupalBaseUrl>
                <mediaBaseUrl>https://beta.mousephenotype.org/data/media</mediaBaseUrl>
                <impcMediaBaseUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
                <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
                <seleniumUrl>http://mi-selenium-mac.windows.ebi.ac.uk:4444/wd/hub</seleniumUrl>
                <datasourcesConfig>betaDatasourcesConfig.properties</datasourcesConfig>
                <liveSite>false</liveSite>
            </properties>

            <build>
                <resources>
                    <resource>
                        <directory>src/test/resources</directory>
                        <targetPath>${basedir}/target/test-classes</targetPath>
                        <includes>
                            <include>**/test-config.xml</include>
                        </includes>
                        <filtering>true</filtering>
                    </resource>
                </resources>
                <pluginManagement>
                    <plugins>
                        <plugin>
                            <groupId>org.apache.maven.plugins</groupId>
                            <artifactId>maven-surefire-plugin</artifactId>
                            <version>2.4.2</version>
                            <configuration>
                                <skipTests>false</skipTests>
                                <testFailureIgnore>true</testFailureIgnore>
                                <includes>
                                    <include>**PageTest.java</include>
                                    <include>**/org/mousephenotype/www/**</include>
                                </includes>
                                <excludes>
                                    <exclude></exclude>
                                </excludes>
                            </configuration>
                        </plugin>
                    </plugins>
                </pluginManagement>
            </build>
        </profile>

        <profile>
            <id>external-test</id>

            <properties>
                <baseUrl>/data</baseUrl>
                <solrUrl>https://wwwdev.ebi.ac.uk/mi/impc/dev/solr</solrUrl>
                <internalSolrUrl>http://localhost:8090/mi/impc/dev/solr</internalSolrUrl>
                <drupalBaseUrl>https://test.mousephenotype.org</drupalBaseUrl>
                <mediaBaseUrl>https://dev.mousephenotype.org/data/media</mediaBaseUrl>
                <impcMediaBaseUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
                <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
                <liveSite>false</liveSite>
            </properties>


            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>true</skipTests>
                            <excludes>
                                <exclude>**/web/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>

                </plugins>
            </build>
        </profile>

        <profile>
            <id>external-user</id>

            <properties>
                <baseUrl>/data</baseUrl>
                <solrUrl>https://wwwdev.ebi.ac.uk/mi/impc/dev/solr</solrUrl>
                <internalSolrUrl>https://wwwdev.ebi.ac.uk/mi/impc/dev/solr</internalSolrUrl>
                <drupalBaseUrl>http://localhost:8084</drupalBaseUrl>
                <mediaBaseUrl>https://dev.mousephenotype.org/data/media</mediaBaseUrl>
                <impcMediaBaseUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
                <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
                <liveSite>false</liveSite>
            </properties>

            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>true</skipTests>
                            <excludes>
                                <exclude>**PageTest.java</exclude>
                                <exclude>**/org/mousephenotype/www/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>

        <profile>
            <id>external-beta</id>

            <properties>
                <baseUrl>/data</baseUrl>
                <drupalBaseUrl>https://beta.mousephenotype.org</drupalBaseUrl>
                <solrUrl>https://www.ebi.ac.uk/mi/impc/beta/solr</solrUrl>
                <internalSolrUrl>http://localhost:8090/mi/impc/beta/solr</internalSolrUrl>
                <buildIndexesSolrUrl>http://ves-ebi-d0.ebi.ac.uk:8090/build_indexes_beta</buildIndexesSolrUrl>
                <mediaBaseUrl>https://beta.mousephenotype.org/data/media</mediaBaseUrl>
                <impcMediaBaseUrl>//www.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
                <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
                <googleAnalytics>UA-33310077-1</googleAnalytics>
                <liveSite>false</liveSite>
            </properties>

            <build>
                <resources>
                    <resource>
                        <directory>src/test/resources</directory>
                        <filtering>true</filtering>
                    </resource>
                    <resource>
                        <directory>src/main/resources</directory>
                        <filtering>true</filtering>
                    </resource>
                </resources>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>true</skipTests>
                            <excludes>
                                <exclude>**PageTest.java</exclude>
                                <exclude>**/org/mousephenotype/www/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>
                    <!-- allows you to select derived on the target directory in eclipse
                        so we dont have it polluting search etc and then this stops the target being
                        overwritten and thus the setting reset all the time -->
                    <!-- http://stackoverflow.com/questions/283489/is-there-a-way-to-hide-maven-2-target-folder-in-eclipse-3 -->
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-clean-plugin</artifactId>
                        <version>2.5</version>
                        <configuration>
                            <excludeDefaultDirectories>true</excludeDefaultDirectories>
                            <filesets>
                                <!-- delete directories that will be generated when you start the
                                    develpment server/client in eclipse -->
                                <fileset>
                                    <directory>target</directory>
                                    <includes>
                                        <include>**/*</include>
                                    </includes>
                                </fileset>
                            </filesets>
                        </configuration>
                    </plugin>

                </plugins>
            </build>

        </profile>


        <profile>
            <id>live</id>

            <properties>
                <baseUrl>/data</baseUrl>
                <drupalBaseUrl>https://www.mousephenotype.org</drupalBaseUrl>
                <solrUrl>https://www.ebi.ac.uk/mi/impc/solr</solrUrl>
                <internalSolrUrl>http://localhost:8090/mi/impc/solr</internalSolrUrl>
                <buildIndexesSolrUrl>http://ves-ebi-d0.ebi.ac.uk:8090/build_indexes_live</buildIndexesSolrUrl>
                <phenodigm.solrserver>http://solrcloudlive.sanger.ac.uk/solr/phenodigm</phenodigm.solrserver>
                <mediaBaseUrl>https://www.mousephenotype.org/data/media</mediaBaseUrl>
                <impcMediaBaseUrl>//www.ebi.ac.uk/mi/media/omero/webgateway</impcMediaBaseUrl>
                <pdfThumbnailUrl>//wwwdev.ebi.ac.uk/mi/media/omero/webgateway/render_thumbnail/119501</pdfThumbnailUrl>
                <googleAnalytics>UA-23433997-1</googleAnalytics>
                <liveSite>true</liveSite>
            </properties>

            <build>
                <resources>
                    <resource>
                        <directory>src/test/resources</directory>
                        <targetPath>${basedir}/target/test-classes</targetPath>
                        <includes>
                            <include>**/test-config.xml</include>
                        </includes>
                        <filtering>true</filtering>
                    </resource>
                    <resource>
                        <directory>src/main/resources</directory>
                        <filtering>true</filtering>
                    </resource>
                </resources>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <version>2.4.2</version>
                        <configuration>
                            <skipTests>true</skipTests>
                            <excludes>
                                <exclude>**PageTest.java</exclude>
                                <exclude>**/org/mousephenotype/www/**</exclude>
                            </excludes>
                        </configuration>
                    </plugin>

                </plugins>
            </build>

        </profile>

        <profile>
            <id>eclipse-only</id>
            <activation>
                <property>
                    <name>m2e.version</name>
                </property>
            </activation>
            <build>
                <pluginManagement>
                    <plugins>
                        <plugin>
                            <groupId>org.eclipse.m2e</groupId>
                            <artifactId>lifecycle-mapping</artifactId>
                            <version>1.0.0</version>
                            <configuration>
                                <lifecycleMappingMetadata>
                                    <pluginExecutions>
                                        <pluginExecution>
                                            <pluginExecutionFilter>
                                                <groupId>org.codehaus.mojo</groupId>
                                                <artifactId>gwt-maven-plugin</artifactId>
                                                <versionRange>[2.4.0,)</versionRange>
                                                <goals>
                                                    <goal>resources</goal>
                                                    <goal>compile</goal>
                                                    <goal>i18n</goal>
                                                    <goal>generateAsync</goal>
                                                </goals>
                                            </pluginExecutionFilter>
                                            <action>
                                                <execute/>
                                            </action>
                                        </pluginExecution>
                                        <pluginExecution>
                                            <pluginExecutionFilter>
                                                <groupId>org.apache.maven.plugins</groupId>
                                                <artifactId>maven-war-plugin</artifactId>
                                                <!-- 2.1.1 copy the resources twice use 2.0.1 -->
                                                <versionRange>[2.0.1,)</versionRange>
                                                <goals>
                                                    <goal>exploded</goal>
                                                </goals>
                                            </pluginExecutionFilter>
                                            <action>
                                                <execute/>
                                            </action>
                                        </pluginExecution>

                                        <pluginExecution>
                                            <pluginExecutionFilter>
                                                <groupId>org.codehaus.mojo</groupId>
                                                <artifactId>build-helper-maven-plugin</artifactId>
                                                <versionRange>[1.7,)</versionRange>
                                                <goals>
                                                    <goal>add-source</goal>
                                                </goals>
                                            </pluginExecutionFilter>
                                            <action>
                                                <execute/>
                                            </action>
                                        </pluginExecution>

                                        <pluginExecution>
                                            <pluginExecutionFilter>
                                                <groupId>com.google.code.maven-replacer-plugin</groupId>
                                                <artifactId>replacer</artifactId>
                                                <versionRange>[1.5.2,)</versionRange>
                                                <goals>
                                                    <goal>replace</goal>
                                                </goals>
                                            </pluginExecutionFilter>
                                            <action>
                                                <execute/>
                                            </action>
                                        </pluginExecution>

                                        <pluginExecution>
                                            <pluginExecutionFilter>
                                                <groupId>com.samaxes.maven</groupId>
                                                <artifactId>minify-maven-plugin</artifactId>
                                                <versionRange>[1.0.0,)</versionRange>
                                                <goals>
                                                    <goal>minify</goal>
                                                </goals>
                                            </pluginExecutionFilter>
                                            <action>
                                                <execute>
                                                    <runOnIncremental>false</runOnIncremental>
                                                </execute>
                                            </action>
                                        </pluginExecution>

                                    </pluginExecutions>
                                </lifecycleMappingMetadata>
                            </configuration>
                        </plugin>
                    </plugins>
                </pluginManagement>
            </build>
        </profile>

    </profiles>

</project>