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

	<groupId>readbiomed</groupId>
	<artifactId>readbiomed-pathogen-annotator</artifactId>
	<version>0.1.0-SNAPSHOT</version>

	<properties>
		<maven.compiler.source>1.8</maven.compiler.source>
		<maven.compiler.target>1.8</maven.compiler.target>
		<cleartk.version>2.0.0</cleartk.version>
	</properties>
	<build>
		<plugins>
			<!--<plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-compiler-plugin</artifactId> 
				<configuration> <source>11</source> <target>11</target> </configuration> 
				</plugin> -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.8.1</version>
				<!-- annotationProcessorPaths requires maven-compiler-plugin version 
					3.5 or higher <version>${maven-compiler-plugin-version}</version> -->
				<configuration>
					<annotationProcessorPaths>
						<path>
							<groupId>info.picocli</groupId>
							<artifactId>picocli-codegen</artifactId>
							<version>4.6.1</version>
						</path>
					</annotationProcessorPaths>
					<compilerArgs>
						<arg>-Aproject=${project.groupId}/${project.artifactId}</arg>
					</compilerArgs>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.apache.uima</groupId>
				<artifactId>jcasgen-maven-plugin</artifactId>
				<version>2.5.0</version>  <!-- change this to the latest version -->
				<executions>
					<execution>
						<goals>
							<goal>generate</goal>
						</goals>
						<configuration>
							<typeSystemIncludes>
								<typeSystemInclude>src/main/resources/readbiomed/document/TypeSystem.xml</typeSystemInclude>
								<typeSystemInclude>src/main/resources/readbiomed/annotators/dictionary/utils/ConceptMapperTypes.xml</typeSystemInclude>
							</typeSystemIncludes>
							<typeSystemExcludes>
							</typeSystemExcludes>
							<limitToProject>false</limitToProject>
						</configuration>
					</execution>
				</executions>
			</plugin>
			<plugin>
				<groupId>org.codehaus.mojo</groupId>
				<artifactId>build-helper-maven-plugin</artifactId>
				<version>1.8</version>
				<executions>
					<execution>
						<id>add-source</id>
						<phase>generate-sources</phase>
						<goals>
							<goal>add-source</goal>
						</goals>
						<configuration>
							<sources>
								<source>${project.build.directory}/generated-sources/java/</source>
							</sources>
						</configuration>
					</execution>
				</executions>
			</plugin>
		</plugins>
	</build>
	<repositories>
		<repository>
			<id>bionlp-sourceforge</id>
			<url>http://svn.code.sf.net/p/bionlp/code/repo/</url>
		</repository>
	</repositories>

	<dependencies>
		<dependency>
			<groupId>info.picocli</groupId>
			<artifactId>picocli</artifactId>
			<version>4.6.1</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-lang3</artifactId>
			<version>3.12.0</version>
		</dependency>
		<dependency>
			<groupId>org.apache.uima</groupId>
			<artifactId>uimafit-core</artifactId>
			<version>2.5.0</version>
		</dependency>
		<dependency>
			<groupId>org.apache.uima</groupId>
			<artifactId>ConceptMapper</artifactId>
			<version>2.10.2</version>
		</dependency>
		<dependency>
			<groupId>org.cleartk</groupId>
			<artifactId>cleartk-token</artifactId>
			<version>${cleartk.version}</version>
		</dependency>
		<dependency>
			<groupId>org.cleartk</groupId>
			<artifactId>cleartk-util</artifactId>
			<version>${cleartk.version}</version>
		</dependency>
		<dependency>
			<groupId>org.cleartk</groupId>
			<artifactId>cleartk-ml</artifactId>
			<version>${cleartk.version}</version>
		</dependency>
		<dependency>
			<groupId>org.cleartk</groupId>
			<artifactId>cleartk-corpus</artifactId>
			<version>${cleartk.version}</version>
		</dependency>
		<dependency>
			<groupId>org.cleartk</groupId>
			<artifactId>cleartk-ml-libsvm</artifactId>
			<version>${cleartk.version}</version>
		</dependency>
		<dependency>
			<groupId>org.cleartk</groupId>
			<artifactId>cleartk-opennlp-tools</artifactId>
			<version>${cleartk.version}</version>
		</dependency>
		<dependency>
			<groupId>readbiomed</groupId>
			<artifactId>readbiomed-ncbi-pathogen-dataset-generation</artifactId>
			<version>0.0.1-SNAPSHOT</version>
		</dependency>
		<dependency>
			<groupId>edu.ucdenver.ccp</groupId>
			<artifactId>nlp-pipelines-conceptmapper</artifactId>
			<version>0.5.4</version>
			<exclusions>
				<exclusion>
					<groupId>stax</groupId>
					<artifactId>stax-api</artifactId>
				</exclusion>
			</exclusions>
		</dependency>
		<dependency>
			<groupId>au.com.nicta.csp</groupId>
			<artifactId>MTIMLExtension</artifactId>
			<version>0.0.1-SNAPSHOT</version>
		</dependency>
	</dependencies>
</project>