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/maven-v4_0_0.xsd">
   <modelVersion>4.0.0</modelVersion>

	<parent>
	  <groupId>uk.ac.rothamsted.knetminer</groupId>
	  <artifactId>knetminer-common</artifactId>
	  <version>1.0</version>
	</parent>  

   <groupId>net.sourceforge.ondex</groupId>
   <artifactId>ondex-full</artifactId>
   <version>3.0.1-SNAPSHOT</version>
   <packaging>pom</packaging>

   <name>ONDEX POM for Full Build</name>

   <modules>
      <module>ondex-base</module>
      <module>ondex-opt</module>
      <module>ondex-desktop</module>
      <module>ondex-doc</module>
      <module>ondex-knet-builder</module>
   </modules>

   <licenses>
      <license>
         <name>GNU GPL</name>
         <url>http://www.gnu.org/licenses/gpl.html</url>
      </license>
   </licenses>
   <description>
     ONDEX enables data from diverse biological data sets to be linked, integrated and visualised through
     graph analysis techniques.

     This is a super-pom that... TODO
    </description>
   <url>http://www.ondex.org/</url>

   <ciManagement>
      <system>jenkins</system>
      <url>http://ondex.rothamsted.ac.uk/build</url>
   </ciManagement>

   <organization>
      <name>ONDEX</name>
      <url>https://github.com/Rothamsted/ondex-knet-builder</url>
   </organization>

   <scm>
      <connection>scm:git:https://github.com/Rothamsted/ondex-full.git</connection>
      <url>https://github.com/Rothamsted/ondex-full</url>
   </scm>

   <distributionManagement>
      <site>
         <id>Ondex_site</id>
         <url>file:///var/www/html/ondex</url>
      </site>
   </distributionManagement>

   <build>
      <plugins>
         <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-compiler-plugin</artifactId>
         </plugin>
         <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-surefire-plugin</artifactId>
            <version>${maven.surefire.plugin.version}</version>
            <configuration>
               <forkMode>always</forkMode>
               <forkedProcessTimeoutInSeconds>700</forkedProcessTimeoutInSeconds>
               <argLine>-Xms1G -Xmx1G -Dondex.dir=${basedir}/data</argLine>
               <excludes>
                  <exclude>net/sourceforge/ondex/apps/*</exclude>
               </excludes>
               <failIfNoTests>false</failIfNoTests>
               <enableAssertions>true</enableAssertions>
               <redirectTestOutputToFile>false</redirectTestOutputToFile>
               <!--testFailureIgnore>true</testFailureIgnore -->
               <useFile>false</useFile>
            </configuration>
         </plugin>
         <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-source-plugin</artifactId>
            <version>${maven.source.plugin.version}</version>
            <executions>
               <execution>
                  <id>attach-sources</id>
                  <phase>verify</phase>
                  <goals>
                     <goal>jar-no-fork</goal>
                  </goals>
               </execution>
            </executions>
         </plugin>
         <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-release-plugin</artifactId>
            <configuration>
               <preparationGoals>clean verify install</preparationGoals>
            </configuration>
         </plugin>
      </plugins>

      <!-- To define the producer version in your parent POM -->      
      <pluginManagement>
         <plugins>
            <plugin>
               <groupId>org.apache.maven.plugins</groupId>
               <artifactId>maven-compiler-plugin</artifactId>
               <version>${maven.compiler.plugin.version}</version>
               <configuration>
                  <source>${java.version}</source>
                  <target>${java.version}</target>
                  <showWarnings>true</showWarnings>
                  <showDeprecation>true</showDeprecation>
                  <maxmem>4096m</maxmem>
                  <encoding>UTF-8</encoding>
                  <fork>true</fork>
               </configuration>
            </plugin>
            <plugin>
               <groupId>org.codehaus.mojo</groupId>
               <artifactId>jaxb2-maven-plugin</artifactId>
               <version>${mojo.jaxb2.maven.plugin.version}</version>
               <executions>
                  <execution>
                     <id>jaxb2-xjc</id>
                     <phase>generate-sources</phase>
                     <goals>
                        <goal>xjc</goal>
                     </goals>
                  </execution>
               </executions>
            </plugin>
            <!-- Needed for newer Eclipse versions with m2e integrated -->
            <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-dependency-plugin</artifactId>
                              <versionRange>[2.0,)</versionRange>
                              <goals>
                                 <goal>copy-dependencies</goal>
                                 <goal>unpack</goal>
                              </goals>
                           </pluginExecutionFilter>
                           <action>
                              <ignore/>
                           </action>
                        </pluginExecution>
                        <pluginExecution>
                           <pluginExecutionFilter>
                              <groupId>org.apache.maven.plugins</groupId>
                              <artifactId>maven-javadoc-plugin</artifactId>
                              <versionRange>[2.6,)</versionRange>
                              <goals>
                                 <goal>javadoc</goal>
                              </goals>
                           </pluginExecutionFilter>
                           <action>
                              <ignore/>
                           </action>
                        </pluginExecution>
                        <pluginExecution>
                           <pluginExecutionFilter>
                              <groupId>org.apache.cxf</groupId>
                              <artifactId>cxf-java2ws-plugin</artifactId>
                              <versionRange>[2.2,)</versionRange>
                              <goals>
                                 <goal>java2ws</goal>
                              </goals>
                           </pluginExecutionFilter>
                           <action>
                              <ignore/>
                           </action>
                        </pluginExecution>
                        <pluginExecution>
                           <pluginExecutionFilter>
                              <groupId>org.apache.cxf</groupId>
                              <artifactId>cxf-codegen-plugin</artifactId>
                              <versionRange>[2.2,)</versionRange>
                              <goals>
                                 <goal>generate-sources</goal>
                              </goals>
                           </pluginExecutionFilter>
                           <action>
                              <ignore/>
                           </action>
                        </pluginExecution>
                     </pluginExecutions>
                  </lifecycleMappingMetadata>
               </configuration>
            </plugin>
            <!-- Cleans up things that are usualy left around on the main module folder, not in target/ -->
		        <plugin>
		          <artifactId>maven-clean-plugin</artifactId>
		          <configuration>
		            <filesets>
		              <fileset>
		                <directory>${basedir}</directory>
		                <includes>
		                  <include>ondex.log</include>
		                  <include>velocity.log</include>
		                  <include>uninstall.log</include>
		                </includes>
		              </fileset>
		            </filesets>
		          </configuration>
		        </plugin>
		        
					  <!-- 
							A small plug-in that starts Neo4j. 
							
							1.0.1 is the official version that integrated our improvements at
							at https://github.com/Rothamsted/neo4j-server-maven-plugin 
					  -->
		        <plugin>
					    <groupId>com.github.harti2006</groupId>
						  <artifactId>neo4j-server-maven-plugin</artifactId>
						  <version>1.1</version>
							<configuration>
								<version>${neo4j.server.version}</version>
								<port>${neo4j.server.httpPort}</port>
								<boltPort>${neo4j.server.boltPort}</boltPort>
								<deleteDb>true</deleteDb>
								<serverReadyAttempts>120</serverReadyAttempts>
							</configuration>
							<executions>
								<execution>
									<id>start-neo4j-server</id>
									<goals><goal>start</goal></goals>
								</execution>
								<execution>
									<id>stop-neo4j-server</id>
									<goals><goal>stop</goal></goals>
								</execution>
							</executions>		        
		        </plugin>
         </plugins>
      </pluginManagement>

   </build>

	 <properties>
		<java.version>1.8</java.version>
		<ondex.version>${project.version}</ondex.version>
		<target.dir>target</target.dir>
		<!--Plugin Properties -->
		<!-- was 2.2.6 First that works is 2.2.11 -->
		<cxf.version>2.2.11</cxf.version>
		<!-- 
		  TODO: this is the last version known to work, except for the fact it creates directories with the wrong
		  permissions. 
		 -->
		<maven.assembly.plugin.version>2.2-beta-5</maven.assembly.plugin.version>
		<maven.compiler.plugin.version>2.1</maven.compiler.plugin.version>
		<maven.dependency.plugin.version>3.0.0</maven.dependency.plugin.version>
		<maven.failsafe.plugin.version>2.6</maven.failsafe.plugin.version>
		<maven.jar.plugin.version>2.3</maven.jar.plugin.version>
		<maven.javadoc.plugin.version>2.6.1</maven.javadoc.plugin.version>
		<maven.pmd.plugin.version>2.4</maven.pmd.plugin.version>
		<maven.project.info.reports.plugin.version>2.1.2</maven.project.info.reports.plugin.version>
		<maven.scm.plugin.version>1.2</maven.scm.plugin.version>
		<maven.source.plugin.version>2.1.2</maven.source.plugin.version>
		<maven.surefire.plugin.version>2.4.3</maven.surefire.plugin.version>
		<maven.surefire.report.plugin.version>2.4</maven.surefire.report.plugin.version>
		<mojo.axistools.maven.plugin.version>1.3</mojo.axistools.maven.plugin.version>
		<mojo.cobertura.maven.plugin.version>2.4</mojo.cobertura.maven.plugin.version>
		<mojo.taglist.maven.plugin.version>2.4</mojo.taglist.maven.plugin.version>
		<mojo.jaxb2.maven.plugin.version>1.3</mojo.jaxb2.maven.plugin.version>
		<mojo.nsis.maven.plugin.version>1.0-ONDEX</mojo.nsis.maven.plugin.version>
		<!-- Dependecies not yet used but ready -->
		<apache.log4j.version>1.2.15</apache.log4j.version>
		<collections.generic.version>4.01</collections.generic.version>
		<org.biopax.paxtools.version>20101113</org.biopax.paxtools.version>
		<com.hp.hpl.jena.version>2.5.7</com.hp.hpl.jena.version>
		<com.thoughtworks.xstream.version>1.3.1</com.thoughtworks.xstream.version>
		<javax.management.jmxri>1.2.1</javax.management.jmxri>
		<jexcelapi.jxl.version>2.6.10</jexcelapi.jxl.version>
		<junit.version>4.7</junit.version>
		<mysql.connector.java.version>5.1.6</mysql.connector.java.version>
		<jutils.version>9.1</jutils.version>
		<rdfutils.version>2.1.1</rdfutils.version>		
		<lucene.version>6.6.0</lucene.version>
		<spring.version>4.3.6.RELEASE</spring.version>
		
		<!-- Used by neo4j-related components -->
		<neo4j.server.version>3.5.12</neo4j.server.version>
		<neo4j.server.boltPort>17690</neo4j.server.boltPort>
		<neo4j.server.httpPort>17490</neo4j.server.httpPort>
		<rdf2neo.version>1.0.1</rdf2neo.version>  

   </properties>


   <profiles>
      <profile>
         <id>eclipse-folders</id>
         <properties>
            <target.dir>target-eclipse</target.dir>
         </properties>
      </profile>
      <profile>
         <id>with-report</id>
         <build>
            <plugins><!-- test code coverage -->
               <plugin>
                  <groupId>org.codehaus.mojo</groupId>
                  <artifactId>cobertura-maven-plugin</artifactId>
                  <version>2.4</version>
                  <configuration>
                     <formats>
                        <format>xml</format>
                        <format>html</format>
                     </formats>
                  </configuration>
                  <executions>
                     <execution>
                        <id>cobertura-copertura</id>
                        <phase>package</phase>
                        <goals>
                           <goal>cobertura</goal>
                        </goals>
                     </execution>
                     <execution>
                        <id>cobertura-clean</id>
                        <phase>clean</phase>
                        <goals>
                           <goal>clean</goal>
                        </goals>
                     </execution>
                  </executions>
               </plugin>
            </plugins>
         </build>
      </profile>
      
			<profile>
				<id>deploy-brandizi</id>
				<activation><activeByDefault>false</activeByDefault></activation>
				
				<distributionManagement>
			
			    <snapshotRepository>
			    	<id>marcobrandizi.info</id>
						<url>http://www.marcobrandizi.info:8081/artifactory/maven</url>
			    </snapshotRepository>
			
			    <repository>
			    	<id>marcobrandizi.info</id>
						<url>http://www.marcobrandizi.info:8081/artifactory/maven</url>
			    </repository>
					
				</distributionManagement>	
			
			</profile>
			
		<!-- TODO: testing the new repo, needs to be moved into the defaults -->
		<profile>
			<id>knetminer-repo</id>
			<activation><activeByDefault>false</activeByDefault></activation>
			
			<distributionManagement>
			  <repository>
					<id>knetminer-releases</id>
					<name>Internal Releases</name>
					<url>http://babvs58.rothamsted.ac.uk:8081/nexus/repository/maven-releases/</url>
			  </repository>
			  <snapshotRepository>
					<id>knetminer-snapshots</id>
					<name>Internal Snapshots</name>
					<url>http://babvs58.rothamsted.ac.uk:8081/nexus/repository/maven-snapshots/</url>
			  </snapshotRepository>
			</distributionManagement>				
		</profile>
					     
   </profiles>

	 <repositories>
			<repository>
				<id>knetminer-repo</id>
				<name>Rothamsted Maven Repo</name>
				<url>https://knetminer.org/artifactory/repository/maven-public/</url>
			  <snapshots><enabled>true</enabled></snapshots>
			</repository>
	 
	 		<!-- TODO: remove Includes releases and a couple of others 
      <repository>
         <id>ondex-repo</id>
         <name>Ondex Repository</name>
         <url>http://ondex.rothamsted.ac.uk/nexus/content/groups/public</url>
         <releases><enabled>true</enabled></releases>
         <snapshots><enabled>false</enabled></snapshots>
      </repository>
      <repository>
         <id>ondex-snapshots</id>
         <name>Ondex Repository for Snapshots</name>
         <url>http://ondex.rothamsted.ac.uk/nexus/content/groups/public-snapshots</url>
         <releases><enabled>false</enabled></releases>
         <snapshots><enabled>true</enabled></snapshots>
      </repository>

			<repository>
				<id>marcobrandizi.info</id>
				<url>http://www.marcobrandizi.info:8081/artifactory/maven</url>
				<releases><enabled>true</enabled></releases>
				<snapshots><enabled>true</enabled></snapshots>
			</repository>
			
			<repository>
			  <id>EBIBioSamples-GH-repo</id>
			  <url>https://raw.githubusercontent.com/EBIBioSamples/EBIBioSamples.github.io/maven-repo</url>
			  <snapshots><enabled>true</enabled></snapshots>
			</repository -->
			          
			<repository>
				<id>spring-plugins</id>
				<url>https://repo.spring.io/plugins-release/</url>
			</repository>       
	 </repositories>

   <pluginRepositories>

			<!-- TODO: Remove Includes releases and a couple of others 
      <pluginRepository>
         <id>ondex-repo</id>
         <name>Ondex Repository</name>
         <url>http://ondex.rothamsted.ac.uk/nexus/content/groups/public</url>
         <releases><enabled>true</enabled></releases>
         <snapshots><enabled>false</enabled></snapshots>
      </pluginRepository>
      <pluginRepository>
         <id>ondex-snapshots</id>
         <name>Ondex Repository for Snapshots</name>
         <url>http://ondex.rothamsted.ac.uk/nexus/content/groups/public-snapshots</url>
         <releases><enabled>false</enabled></releases>
         <snapshots><enabled>true</enabled></snapshots>
      </pluginRepository -->

      <!-- TODO:remove? pluginRepository>
      	<id>sonatype-releases</id>
      	<url>https://oss.sonatype.org/content/repositories/releases</url>
      </pluginRepository -->
        
   </pluginRepositories>

   <dependencies>
      <dependency>
         <groupId>junit</groupId>
         <artifactId>junit</artifactId>
         <scope>test</scope>
      </dependency>
      <dependency>
         <groupId>log4j</groupId>
         <artifactId>log4j</artifactId>
         <scope>provided</scope>
      </dependency>
   </dependencies>

   <dependencyManagement>
     <dependencies>

	     <dependency>
	        <groupId>junit</groupId>
	        <artifactId>junit</artifactId>
	        <version>4.11</version>
	        <scope>test</scope>
	     </dependency>

       <dependency>
          <groupId>log4j</groupId>
          <artifactId>log4j</artifactId>
          <version>1.2.17</version>
          <type>jar</type>
       </dependency>
        
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>slf4j-log4j12</artifactId>
				<version>1.7.25</version>
			</dependency>

			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>log4j-over-slf4j</artifactId>
				<version>1.7.25</version>
			</dependency>
			
			<!-- Newer modules that are stand-alone command lines use this logger -->
      <dependency>
        <groupId>ch.qos.logback</groupId>
        <artifactId>logback-classic</artifactId>
        <version>1.2.3</version>
      </dependency>
			
			<dependency>
			  <groupId>com.sun.xml.bind</groupId>
			  <artifactId>jaxb-impl</artifactId>
			  <version>2.3.0</version>
			</dependency>         

			<dependency>
				<groupId>org.glassfish.jaxb</groupId>
				<artifactId>jaxb-core</artifactId>
				<version>2.3.0</version>
			</dependency>

      <dependency>
        <groupId>com.hp.hpl.jena</groupId>
        <artifactId>jena</artifactId>
        <version>2.5.7</version>
        <scope>compile</scope>
      </dependency>

      <dependency>
       <groupId>net.sourceforge.collections</groupId>
       <artifactId>collections-generic</artifactId>
       <version>4.01</version>
      </dependency>

			<dependency>
				<groupId>org.apache.commons</groupId>
			  <artifactId>commons-collections4</artifactId>
			  <version>4.1</version>
			</dependency>
				
			<dependency>
			  <groupId>com.google.guava</groupId>
			  <artifactId>guava</artifactId>
			  <version>20.0</version>
			</dependency>
			
      <dependency>
       <groupId>net.sourceforge.jexcelapi</groupId>
       <artifactId>jxl</artifactId>
       <version>2.6.10</version>
      </dependency>
         
			<dependency>
			  <groupId>org.apache.lucene</groupId>
			 <artifactId>lucene-core</artifactId>
			 <version>${lucene.version}</version>
			</dependency>
				 
			<dependency>
			  <groupId>org.apache.lucene</groupId>
			 <artifactId>lucene-queryparser</artifactId>
			 <version>${lucene.version}</version>
			</dependency>
				 
			<dependency>
				<groupId>org.apache.lucene</groupId>
				<artifactId>lucene-analyzers-common</artifactId>
				<version>${lucene.version}</version>
			</dependency>
				 
			<dependency>
				<!-- Cute utility that allows for quick handling of exceptions (eg, checked/unchecked wrapping) -->
				<groupId>com.machinezoo.noexception</groupId>
				<artifactId>noexception</artifactId>
				<version>1.3.2</version>
			</dependency>      
				
			<dependency>
			  <groupId>org.apache.commons</groupId>
			  <artifactId>commons-lang3</artifactId>
			  <version>3.5</version>
			</dependency>
			
			<dependency>
			  <groupId>commons-io</groupId>
			  <artifactId>commons-io</artifactId>
			  <version>2.5</version>
			</dependency>				
			     
			<dependency>
				<groupId>org.springframework</groupId>
				<artifactId>spring-core</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>
         
			<!-- Marco Brandizi: my personal toolset -->
			<dependency>
		  		<groupId>uk.ac.ebi</groupId>
		  		<artifactId>jutils</artifactId>
		  		<version>${jutils.version}</version>
			</dependency>
			<dependency>
		  		<groupId>uk.ac.ebi</groupId>
		  		<artifactId>jutils-io</artifactId>
		  		<version>${jutils.version}</version>
			</dependency>
				
			<!-- Utilities for RDF and the Jena RDF framework -->
	    <dependency>
	      <groupId>info.marcobrandizi</groupId>
	      <artifactId>rdfutils-core</artifactId>
	      <version>${rdfutils.version}</version>
	    </dependency>
			<dependency>
			  <groupId>info.marcobrandizi</groupId>
			  <artifactId>rdfutils-jena</artifactId>
	      <version>${rdfutils.version}</version>
			</dependency>

      <dependency>
         <groupId>com.sleepycat</groupId>
         <artifactId>je</artifactId>
         <version>4.0.92</version>
      </dependency>
        
			<dependency>
				<groupId>uk.ac.rothamsted.rdf.neo4j</groupId>
				<artifactId>rdf2neo</artifactId>
				<version>${rdf2neo.version}</version>
			</dependency>

			<dependency>
				<groupId>uk.ac.rothamsted.rdf.neo4j</groupId>
				<artifactId>rdf2neo-cli</artifactId>
				<version>${rdf2neo.version}</version>
			</dependency>

			<dependency>
				<groupId>uk.ac.rothamsted.neo4j</groupId>
				<artifactId>neo4j-utils</artifactId>
				<version>${rdf2neo.version}</version>
			</dependency>

			<!-- Stream parser, used by OXL and other big XML parsers -->
      <dependency>
         <groupId>org.codehaus.woodstox</groupId>
         <artifactId>woodstox-core-lgpl</artifactId>
         <version>4.0.11</version>
      </dependency>
      <dependency>
        <groupId>org.codehaus.woodstox</groupId>
        <artifactId>stax2-api</artifactId>
        <version>3.0.4</version>
      </dependency>
			<dependency>
				<groupId>org.apache.cxf</groupId>
			  <artifactId>cxf-wstx-msv-validation</artifactId>
			  <version>2.2</version>
			</dependency>
			<dependency>
				<groupId>org.apache.commons</groupId>
				<artifactId>commons-math3</artifactId>
				<version>3.6.1</version>
			</dependency>
			<dependency>
				<groupId>com.opencsv</groupId>
				<artifactId>opencsv</artifactId>
				<version>5.1</version>
			</dependency>
    </dependencies>
	</dependencyManagement>
</project>