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>5.0</version>
	</parent>  

   <groupId>net.sourceforge.ondex</groupId>
   <artifactId>ondex-full</artifactId>
   <version>7.0.2-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-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.

     As usually, this is a super-pom that define a lot of things used by the many components that Ondex
     is made of. The current Maven module arrangement was reviewed in 2017 and later years (by Marco Brandizi), with
     the aim of splitting things between what is most used for Knetminer, optional components and components to
     simply archive as legacy. In a few cases, this splitting isn't so sharp, due to existing dependencies that are
     difficult to disentangle. 
   </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>

	 <properties>
		 <java.version>17</java.version>
		 <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
						
		 <lucene.version>6.6.0</lucene.version>
			
		 <!-- Used by neo4j-related components -->
		 <rdf2neo.version>5.1</rdf2neo.version>  
			
		 <slf4j.version>2.0.9</slf4j.version>
			
     <jena.version>4.9.0</jena.version>
     
     <!-- This is used when we want to override rdf-common -->
     <!-- rdfutils.version>xxx</rdfutils.version -->

	 </properties>

   <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>
         </plugin>
         <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-source-plugin</artifactId>
         </plugin>
         
      </plugins>

      <pluginManagement>
         <plugins>
         		<plugin>
			       	<groupId>org.apache.maven.plugins</groupId>
			       	<artifactId>maven-dependency-plugin</artifactId>
         		</plugin>
         		
            <plugin>
               <groupId>org.apache.maven.plugins</groupId>
               <artifactId>maven-compiler-plugin</artifactId>
               <configuration>
                  <source>${java.version}</source>
                  <target>${java.version}</target>
                  <showWarnings>true</showWarnings>
                  <showDeprecation>true</showDeprecation>
                  <encoding>UTF-8</encoding>
               </configuration>
            </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>
            

            <!-- 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>
		        
		        <plugin>
	            <groupId>org.apache.maven.plugins</groupId>
	            <artifactId>maven-javadoc-plugin</artifactId>
	            <configuration>
	               <stylesheet>maven</stylesheet>
	            </configuration>
		        </plugin>
		        						
						<plugin>
						  <groupId>org.apache.maven.plugins</groupId>
						  <artifactId>maven-surefire-plugin</artifactId>
						  
						  <configuration>
								 <!-- Used to be forkMode = always, which is now deprecated -->
								 <forkCount>1</forkCount>
								 <reuseForks>false</reuseForks>
								 						     
						     <forkedProcessTimeoutInSeconds>700</forkedProcessTimeoutInSeconds>
						     <argLine>-XX:MaxRAM=4G -Dondex.dir=${basedir}/data -Dfile.encoding=UTF-8</argLine>
						     <excludes>
						        <exclude>net/sourceforge/ondex/apps/*</exclude>
						     </excludes>
						     <failIfNoTests>false</failIfNoTests>
						     <enableAssertions>true</enableAssertions>
						     <redirectTestOutputToFile>false</redirectTestOutputToFile>
						     <useFile>false</useFile>
             		 <trimStackTrace>false</trimStackTrace>        
								 <properties>
								   <property>
									   <!-- Prints out spaces and test name before/after every test method and automatically -->
										 <name>listener</name>
										 <value>uk.ac.ebi.utils.test.junit.TestOutputDecorator</value>
									 </property>
								 </properties>
						  </configuration>
						  <dependencies>
								<dependency>
						  		<groupId>uk.ac.ebi</groupId>
						  		<artifactId>jutils</artifactId>
		  						<version>${jutils.version}</version>
								</dependency>
						  </dependencies>
						</plugin>
						
						<plugin>
							<groupId>org.apache.maven.plugins</groupId>
							<artifactId>maven-failsafe-plugin</artifactId>
							<configuration>
								<trimStackTrace>false</trimStackTrace>
								<argLine>-XX:MaxRAM=4G -Dondex.dir=${basedir}/data -Dfile.encoding=UTF-8</argLine>
							</configuration>
							<executions>
								<execution>
									<phase>integration-test</phase>
									<goals><goal>integration-test</goal></goals>
								</execution>
						    <execution>
					        <id>verify</id>
					        <phase>verify</phase>
					        <goals><goal>verify</goal></goals>
						    </execution>
							</executions>
						</plugin>
						
						
					  <!-- 
							A small plug-in that starts Neo4j. 
					  -->
		        <plugin>
					    <groupId>com.github.harti2006</groupId>
						  <artifactId>neo4j-server-maven-plugin</artifactId>
		        </plugin>
		        
						<plugin>
							<groupId>org.apache.maven.plugins</groupId>
							<artifactId>maven-project-info-reports-plugin</artifactId>
							<version>3.4.5</version>
						</plugin>
						
						<plugin>
						  <groupId>org.codehaus.mojo</groupId>
						  <artifactId>taglist-maven-plugin</artifactId>
						  <version>3.0</version>
						</plugin>

						
            <!-- 
            	This is needed by Eclipse, to in which build life cycle phase a plug-in is
            	triggered. It won't hurt you if you don't use Eclipse.
            -->
            <plugin>
               <groupId>org.eclipse.m2e</groupId>
               <artifactId>lifecycle-mapping</artifactId>
               <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>						
         </plugins>
      </pluginManagement>
      
   </build>

   
   <profiles>
   </profiles>

	 <repositories>
			<repository>
				<id>knetminer-repo</id>
				<name>Rothamsted Maven Repo</name>
				<url>https://knetminer.com/artifactory/repository/maven-public/</url>
			  <snapshots><enabled>true</enabled></snapshots>
			  <releases><enabled>true</enabled></releases>
			</repository>
						                 
	 </repositories>
	 
   <dependencyManagement>
     <dependencies>

       <dependency>
          <groupId>log4j</groupId>
          <artifactId>log4j</artifactId>
          <version>1.2.17</version>
          <scope>provided</scope>
       </dependency>
        
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>slf4j-log4j12</artifactId>
				<version>${slf4j.version}</version>
			</dependency>

			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>log4j-over-slf4j</artifactId>
				<version>${slf4j.version}</version>
			</dependency>
			
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>jcl-over-slf4j</artifactId>
				<version>${slf4j.version}</version>
			</dependency>
			
			
			<!-- Newer modules that are stand-alone command lines use this logger -->
      <dependency>
        <groupId>ch.qos.logback</groupId>
        <artifactId>logback-classic</artifactId>
        <version>1.4.11</version>
      </dependency>
			
			<!-- Since JDK 11, we need this as a separate lib -->
			<dependency>
			  <groupId>jakarta.xml.bind</groupId>
			  <artifactId>jakarta.xml.bind-api</artifactId>
			  <version>4.0.1</version>
			</dependency>
			<!--
			  This should be the implementation of jakarta.xml.bind-api
			  (https://stackoverflow.com/a/72151763/529286) 
			-->
			<dependency>
				<groupId>com.sun.xml.bind</groupId>
			  <artifactId>jaxb-impl</artifactId>
			  <version>4.0.4</version>
			</dependency>

			<!-- Spring annotations that were supported JDK<11 -->
			<dependency>             
        <groupId>javax.annotation</groupId>
        <artifactId>javax.annotation-api</artifactId>
        <version>1.3.2</version>
			</dependency>  
			<dependency>             
        <groupId>javax.annotation</groupId>
        <artifactId>jsr250-api</artifactId>
        <version>1.3.2</version>
			</dependency>  
                
      <dependency>
        <groupId>com.thoughtworks.xstream</groupId>
        <artifactId>xstream</artifactId>
        <version>1.4.20</version>
      </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>4.4</version>
			</dependency>
										
      <dependency>
       <groupId>net.sourceforge.jexcelapi</groupId>
       <artifactId>jxl</artifactId>
       <version>2.6.12</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>


			<!-- 
				The lib with main components in one bundle only.
				
				TODO: this is used in the scripting module only, more recent modules (eg, RDF exporter, Neo4j exporter)
				link these in their own way.
			-->
			<dependency>
    		<groupId>org.apache.jena</groupId>
				<artifactId>apache-jena-libs</artifactId>
		    <version>${jena.version}</version>
				<type>pom</type>		    
			</dependency>

			<dependency>
				<groupId>org.apache.jena</groupId>
				<artifactId>jena-osgi</artifactId>
		    <version>${jena.version}</version>
			</dependency>		  


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

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

			<dependency>
				<groupId>uk.ac.rothamsted.kg</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>
         <exclusions>
         	 <!-- It shouldn't be necessary and causes problems to Eclipse 
         			 (javax.xml.stream referred by two modules) -->
         	 <exclusion>
         		 <groupId>javax.xml.stream</groupId>
         		 <artifactId>stax-api</artifactId>
         	 </exclusion>
         </exclusions>
      </dependency>
      <dependency>
        <groupId>org.codehaus.woodstox</groupId>
        <artifactId>stax2-api</artifactId>
        <version>4.2.2</version>
      </dependency>
			<dependency>
				<groupId>org.apache.cxf</groupId>
			  <artifactId>cxf-wstx-msv-validation</artifactId>
				<!-- was 2.2.6 First that works is 2.2.11, 2.2 is the last on Central -->
			  <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>5.8</version>
			</dependency>
			
			<dependency>
				<groupId>xerces</groupId>
				<artifactId>xercesImpl</artifactId>
				<version>2.12.2</version>
			</dependency>
			
      <dependency>
        <groupId>com.googlecode.json-simple</groupId>
        <artifactId>json-simple</artifactId>
        <version>1.1.1</version>
      </dependency>
      
      <dependency>
				<groupId>org.jsoup</groupId>
				<artifactId>jsoup</artifactId>
				<version>1.16.2</version>
      </dependency>
      
      <!-- TODO: would be good to replace all the uses of this with picocli, at the moment we use both -->
			<dependency>
				<groupId>commons-cli</groupId>
				<artifactId>commons-cli</artifactId>
				<version>1.6.0</version>
			</dependency>			
			
    </dependencies>
	</dependencyManagement>
</project>