pom.xml

<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>5.0.1-SNAPSHOT</version>
	</parent>  

	<artifactId>app-common</artifactId>
	<name>app-common - KnetMiner App top/common POM container</name>
	<version>5.7-SNAPSHOT</version>
	<description>
		KnetMiner is a platform for fast candidate gene discovery using data mining techniques.
		See http://github.com/Rothamsted/knetminer/wiki for technical details.
	</description>
	<url>http://knetminer.org/</url>
	<packaging>pom</packaging>

	<organization>
		<name>Rothamsted Research</name>
		<url>http://www.rothamsted.ac.uk/</url>
	</organization>

	<licenses>
		<license>
			<name>GNU GPL</name>
			<url>http://www.gnu.org/licenses/gpl.html</url>
		</license>
	</licenses>

	<modules>
    <module>client-base</module>
    <module>server-base</module>
    <module>server-datasource-api</module>
    <module>server-datasource-ondexlocal</module>
    <module>server-ondex</module>
    <module>aratiny</module>
    <module>knetminer-initializer</module>
    <module>knetminer-initializer-cli</module>
	</modules>

	<properties>
		
		<!-- 
			This is the default dir where Knetminer looks for its configuration (ie, config.xml, as defined
		  in web.xml). 
		  
		  This default works under the Docker instance. It's not hard-wired for the case you want to build
		  the WS WAR for another environment. As you can see in web.xml, this default can also be 
		  overridden by the Java property (-D) knetminer.api.configFilePath, to be passed at runtime
		  (eg, to your Tomcat's JVM).
		-->
		<knetminer.defaultConfigDir>/root/knetminer-dataset/config</knetminer.defaultConfigDir>
		<!-- A different one is used for the neo4j profile -->
		<knetminer.testConfigFileName>test-cfg.yml</knetminer.testConfigFileName>		
		
		<!-- 
		  Several of these properties can be overriden by instance-specific Maven profiles.
		  Here, we give values suitable for maven tests (eg, in aratiny).
		  
		  See https://github.com/Rothamsted/knetminer/wiki/3.-Deploying-KnetMiner-with-Docker
		  
		  TODO: Update docs
		  
		  
		  ***** WARNING ****
		   
		  NEVER EVER USE Maven properties for production configurations (eg, Docker)!
		  
		  While we used to do it in the past, now these values are used for Maven interpolation during
		  Maven builds ONLY (and to make different builds, eg, for testing or for Docker. 
		  
		  Once a distro file has been built via Maven using these values (eg, a .war, the Docker 
		  image using that .war), then that file has NO REFERENCE to these POM properties.
		  Therefore, you CAN'T change them from here (without rebuilding everything, which is 
		  STRONGLY discouraged practice).
		
		  Configuration values for knetminer is done via YAML files (see TODO). Some sub-component
		  still needs Java system properties (eg, the Neo4j traverser). In such cases, you can use
		  "systemProperties" in the YAML configuration (see documentation and existing examples).
		 -->
		
		<!--
			In most cases, probably you'll be fine with the overriding provided below, in the 'docker' profile.
			For aratiny, we need this non-common value since it's difficult to rename a downloaded test file. 
		-->
		<knetminer.oxlFile>${project.build.directory}/dependency/poaceae-sample.oxl</knetminer.oxlFile>
								
		<knetminer.api.httpPort>9090</knetminer.api.httpPort>
		<knetminer.api.url>http://localhost:${knetminer.api.httpPort}/ws/aratiny</knetminer.api.url>


		<!--
			These shouldn't need to be changed (apart from development purposes).
		-->
		
		<!-- 
			=========> WARNING! <=========
			
			Unless you need to repeat a version more times (eg, a group of modules produced by the same developer that have 
			their versions aligned), IT IS ABSOLUTELY FORBIDDEN to set a plug-in or dependency version in a property and use
			it later ONLY ONCE, or doing it for the sole purpose of inserting that dependency in multiple submodules. 
			MAVEN HAS PLUG-IN AND MODULE MANAGEMENT SECTIONS FOR THIS PURPOSE. USE MAVEN PROPERLY! 

			Violating this rule might condemn you to an afterlife in the Hell of Developers, where the damned are forced 
			to give IT support to biologists who are still using Windows XP.      
		-->
			
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<java.version>17</java.version>

		<ondex.version>7.0.1</ondex.version>
		<knetminer.backend.version>4.0.1</knetminer.backend.version>

		<!-- TODO: realign with the rest -->
		<jutils.version>14.1-SNAPSHOT</jutils.version>				

		<!-- We define these using the Jetty properties, so that they can be overridden from the 
		     command line -->
		<jetty.http.port>8080</jetty.http.port>
		<jetty.http.stopPort>8081</jetty.http.stopPort>
		
	</properties>


	<scm>
		<connection>scm:git:https://github.com/Rothamsted/knetminer</connection>
		<developerConnection>scm:git:https://github.com/Rothamsted/knetminer</developerConnection>
		<url>https://github.com/Rothamsted/knetminer</url>
	</scm>

	<ciManagement>
		<system>GitHub Actions</system>
		<url>https://github.com/Rothamsted/knetminer/actions</url>
	</ciManagement>
  
	<build>
		<pluginManagement>
			<plugins>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-war-plugin</artifactId>
					<version>3.4.0</version>
				</plugin>
			
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-surefire-plugin</artifactId>
					<configuration>
						<!-- TODO: remove, the default reuseForks=true and forkCount=1 should be the same-->
						<!-- <forkMode>always</forkMode> -->
						<forkedProcessTimeoutInSeconds>900</forkedProcessTimeoutInSeconds>
						<argLine>-Xms4G -Xmx4G</argLine>
						<failIfNoTests>false</failIfNoTests>
						<enableAssertions>true</enableAssertions>
						<redirectTestOutputToFile>false</redirectTestOutputToFile>
						<useFile>false</useFile>
					</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>
				
				<plugin>
				  <groupId>org.eclipse.jetty</groupId>
				  <artifactId>jetty-maven-plugin</artifactId>
			    <version>11.0.19</version>
				  <executions>
				  	<execution>
				  		<id>start</id>
				  		<phase>pre-integration-test</phase>
				  		<goals><goal>start</goal></goals>
				  	</execution>
				  	<execution>
				  		<id>stop</id>
				  		<phase>post-integration-test</phase>
				  		<goals><goal>stop</goal></goals>
				  	</execution>
				  </executions>
				  <configuration>
				    <scan>10</scan>
		        <!-- This is defined in the properties section -->
		        <!-- httpConnector>
		          <port>8080</port>
		        </httpConnector -->			    
				    <webApp>
				      <contextPath>/</contextPath>
							<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
				    </webApp>
				    <!-- Again, this is in the properties above -->
				    <!--stopPort>8081</stopPort -->
				    <stopKey>araTinyJetty</stopKey>
				    <stopWait>10</stopWait>

						<systemProperties>
							<!-- 
								This is the absolute value of the current projet's 'target/'.
								It's used by provisional code taking mockup data from this dir.							
							-->
							<maven.target>${project.build.directory}</maven.target>
						</systemProperties>			      
				    
				  </configuration>
				</plugin>

				<plugin>
					<groupId>org.codehaus.mojo</groupId>
					<artifactId>properties-maven-plugin</artifactId>
					<version>1.2.1</version>
					<executions>
						<execution>
							<goals>
								<goal>set-system-properties</goal>
							</goals>
							<configuration>
								<properties>
									<property>
										<!-- 
											WS scanning sometimes times out with the default (#551) 
											TODO: Is still needed with recent Jetty? Does it need a new
											variable name?
										-->
										<name>org.eclipse.jetty.annotations.maxWait</name>
										<value>600</value>
									</property>
								</properties>
							</configuration>
						</execution>
					</executions>
				</plugin>

			</plugins>		
		</pluginManagement>
	</build>


	<profiles>
		
		<profile>
			<id>docker</id>
			<activation><activeByDefault>false</activeByDefault></activation>
			<properties>
								
				<knetminer.api.httpPort>8080</knetminer.api.httpPort>
				
				<!-- It's just this, so that our Tomcat can append the right prefix automatically -->
				<knetminer.api.url>/ws/aratiny</knetminer.api.url>

			</properties>
				
		</profile>

	</profiles>

	<repositories>
	  <repository>
	  	<!-- This is needed to let Maven find the parent POM -->
			<id>knetminer-repo</id>
			<name>Knetminer Unified Repository</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>uk.ac.rothamsted.knetminer</groupId>
				<artifactId>server-datasource-ondexlocal</artifactId>
				<version>${project.version}</version>
				<exclusions>
					<!-- Removes the old log4j and requires a replacement with log4j-1.2-api (listed below) -->
					<exclusion>
						<groupId>log4j</groupId>
						<artifactId>log4j</artifactId>
					</exclusion>
				</exclusions>
			</dependency>
			
			<!-- The new backend, based on Neo4j -->
			<dependency>
				<groupId>uk.ac.rothamsted.knetminer.backend</groupId>
				<artifactId>cypher-client</artifactId>
				<version>${knetminer.backend.version}</version>
				<exclusions>
					<exclusion>
						<groupId>org.slf4j</groupId>
						<artifactId>log4j-over-slf4j</artifactId>
					</exclusion>
				</exclusions>
			</dependency>
					
			<dependency>
				<groupId>jakarta.servlet</groupId>
				<artifactId>jakarta.servlet-api</artifactId>
				<version>6.0.0</version>
			</dependency>
			<dependency>
				<groupId>org.glassfish.web</groupId>
				<artifactId>jakarta.servlet.jsp.jstl</artifactId>
				<version>3.0.1</version>
			</dependency>

	    <dependency>
	      <groupId>net.sourceforge.ondex.core</groupId>
	      <artifactId>tools</artifactId>
	      <version>${ondex.version}</version>
	    </dependency>

			<dependency>
				<groupId>net.sourceforge.ondex.core</groupId>
				<artifactId>workflow-api</artifactId>
				<version>${ondex.version}</version>
				<exclusions>
					<exclusion>
						<groupId>org.slf4j</groupId>
						<artifactId>slf4j-log4j12</artifactId>
					</exclusion>
				</exclusions>
			</dependency>
			<dependency>
				<groupId>net.sourceforge.ondex.core</groupId>
				<artifactId>memory</artifactId>
				<version>${ondex.version}</version>
			</dependency>
			<dependency>
				<groupId>net.sourceforge.ondex.core</groupId>
				<artifactId>lucene</artifactId>
				<version>${ondex.version}</version>
			</dependency>
			<dependency>
				<groupId>net.sourceforge.ondex.modules</groupId>
				<artifactId>generic</artifactId>
				<version>${ondex.version}</version>
			</dependency>
			<dependency>
				<groupId>net.sourceforge.ondex.modules</groupId>
				<artifactId>oxl</artifactId>
				<version>${ondex.version}</version>
			</dependency>
			<dependency>
				<groupId>net.sourceforge.ondex.modules</groupId>
				<artifactId>cyjs_json</artifactId>
				<version>${ondex.version}</version>
			</dependency>

			<dependency>
				<groupId>org.apache.lucene</groupId>
				<artifactId>lucene-analyzers-common</artifactId>
				<version>6.6.0</version>
			</dependency>

			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-api</artifactId>
				<version>${log4j.version}</version>
			</dependency>
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-core</artifactId>
				<version>${log4j.version}</version>
			</dependency>
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-jcl</artifactId>
				<version>${log4j.version}</version>
			</dependency>
			<!-- slf4j 2 needs this bridge -->
			<dependency>
			  <groupId>org.apache.logging.log4j</groupId>
			  <artifactId>log4j-slf4j2-impl</artifactId>
				<version>${log4j.version}</version>
			</dependency>			
			<dependency>
			 	<groupId>org.apache.logging.log4j</groupId>
			 	<artifactId>log4j-slf4j-impl</artifactId>
				<version>${log4j.version}</version>
				<exclusions>
					<exclusion>
						<!-- We use our own -->
						<groupId>org.slf4j</groupId>
						<artifactId>slf4j-api</artifactId>
					</exclusion>
				</exclusions>
			</dependency>
			<!-- 
				The old log4j v1.2 can be replaced by this, but only if the dependant is written well-enough.
				(https://logging.apache.org/log4j/2.x/manual/migration.html)
			 -->
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-1.2-api</artifactId>
				<version>${log4j.version}</version>
			</dependency>
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-web</artifactId>
				<version>${log4j.version}</version>
			</dependency>
			<dependency>
				<groupId>junit</groupId>
				<artifactId>junit</artifactId>
				<version>4.13.2</version>
			</dependency>

			<dependency>
				<groupId>org.apache.httpcomponents</groupId>
				<artifactId>httpclient</artifactId>
				<version>4.5.14</version>
				<exclusions>
					<exclusion>
						<groupId>commons-logging</groupId>
					  <artifactId>commons-logging</artifactId>
					</exclusion>			
				</exclusions>
			</dependency>
			
			<!-- Needed in Java >= 11 -->	  
			<dependency>
				<groupId>javax.annotation</groupId>
				<artifactId>javax.annotation-api</artifactId>
				<version>1.3.2</version>
			</dependency>
			
		</dependencies>
	</dependencyManagement>

</project>