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<!--
~ Copyright (c) 2016 BMD Software and University of Aveiro.
~
~ Neji is a flexible and powerful platform for biomedical information extraction from text.
~
~ This project is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
~ To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
~
~ This project is a free software, you are free to copy, distribute, change and transmit it.
~ However, you may not use it for commercial purposes.
~
~ It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
~ without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-->
<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>pt.ua.tm</groupId>
<artifactId>neji</artifactId>
<version>2.0.2</version>
<packaging>jar</packaging>
<name>neji</name>
<url>http://maven.apache.org</url>
<!--
Repositories used to fetch project dependencies
-->
<repositories>
<!-- UA.PT Bioinformatics Maven Repository -->
<repository>
<id>bioinformatics-all</id>
<name>Bioinformatics Nexus (All)</name>
<url>http://bioinformatics.ua.pt/maven/content/groups/public</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
<!--
Artifact deployment configuration (project redistribution)
-->
<distributionManagement>
<!-- Versioned releases are published to the releases repository -->
<repository>
<id>bioinformatics-releases</id>
<name>Bioinformatics Nexus (Internal Releases)</name>
<url>http://bioinformatics.ua.pt/maven/content/repositories/releases</url>
</repository>
<!-- Snapshot releases are published to the snapshots repository -->
<snapshotRepository>
<id>bioinformatics-snapshots</id>
<name>Bioinformatics Nexus (Internal Snapshots)</name>
<url>http://bioinformatics.ua.pt/maven/content/repositories/snapshots</url>
</snapshotRepository>
</distributionManagement>
<!--
Repositories used to fetch maven plugins used by the project
-->
<pluginRepositories>
<!-- UA.PT Bioinformatics Maven Repository -->
<pluginRepository>
<id>bioinformatics-all</id>
<name>Bioinformatics Nexus (Plugins)</name>
<url>http://bioinformatics.ua.pt/maven/content/groups/public</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</pluginRepository>
<pluginRepository>
<id>onejar-maven-plugin.googlecode.com</id>
<url>http://onejar-maven-plugin.googlecode.com/svn/mavenrepo</url>
</pluginRepository>
</pluginRepositories>
<!--
Project properties (can be reused anywhere in the pom like this: ${prop.name})
-->
<properties>
<!-- Java version we use and depend on -->
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<!-- Compiler options -->
<maven.compiler.optimize>true</maven.compiler.optimize>
<maven.compiler.showDeprecations>true</maven.compiler.showDeprecations>
<!-- Explicitly set the source and output encoding to prevent Maven warnings -->
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<targetJdk>1.8</targetJdk>
<mainClass>pt.ua.tm.neji.cli.Main</mainClass>
</properties>
<!--
Project build configuration
-->
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
<resource>
<directory>src/main/resources/webapp</directory>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<optimize>${maven.compiler.optimize}</optimize>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2.1</version>
<executions>
<execution>
<id>cli</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>${mainClass}</mainClass>
</manifest>
<manifestEntries>
<Class-Path>.</Class-Path>
</manifestEntries>
</archive>
<finalName>${project.build.finalName}</finalName>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.7</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.2.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9</version>
<configuration>
<excludePackageNames>*.internal,*.example</excludePackageNames>
<doclet>org.jboss.apiviz.APIviz</doclet>
<docfilessubdirs>true</docfilessubdirs>
<docletArtifact>
<groupId>org.jboss.apiviz</groupId>
<artifactId>apiviz</artifactId>
<version>1.3.2.GA</version>
</docletArtifact>
<useStandardDocletOptions>true</useStandardDocletOptions>
<overview>${basedir}/src/javadoc/overview.html</overview>
<doctitle>Neji API Reference (${project.version})</doctitle>
<windowtitle>Neji API Reference (${project.version})</windowtitle>
<detectJavaApiLink>true</detectJavaApiLink>
<additionalparam>
-link http://docs.oracle.com/javase/7/docs/api/
-link http://docs.oracle.com/javaee/6/api/
-link http://www.slf4j.org/apidocs/
-link http://commons.apache.org/logging/commons-logging-1.1.1/apidocs/
-link http://logging.apache.org/log4j/1.2/apidocs/
-group "Core" pt.ua.tm.neji.core*
-group "Modules"
pt.ua.tm.neji.reader*:pt.ua.tm.neji.writer*:pt.ua.tm.neji.nlp*:pt.ua.tm.neji.dictionary*:pt.ua.tm.neji.ml*:pt.ua.tm.neji.misc*:pt.ua.tm.neji.entity*:pt.ua.tm.neji.sentence*:pt.ua.tm.neji.statistics*
-group "Tools and Helpers"
pt.ua.tm.neji.annotator*:pt.ua.tm.neji.sentencesplitter*:pt.ua.tm.neji.normalization*:pt.ua.tm.neji.disambiguator*
-group "Context" pt.ua.tm.neji.context*
-group "CLI" pt.ua.tm.neji.cli*
-group "Batch" pt.ua.tm.neji.batch*
-group "Support" pt.ua.tm.neji.exception*:pt.ua.tm.neji.util*
-sourceclasspath ${project.build.outputDirectory}
<!---nopackagediagram-->
</additionalparam>
<encoding>UTF-8</encoding>
<locale>en_US</locale>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<argLine>-Dfile.encoding=UTF-8</argLine>
<argLine>-Xmx4G</argLine>
<forkMode>always</forkMode>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.2</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>${project.build.finalName}-server</finalName>
<transformers>
<!--use transformer to handle merge of META-INF/services - see http://java.net/jira/browse/JERSEY-440?focusedCommentId=14822&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#action_14822-->
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>pt.ua.tm.neji.web.cli.WebMain</Main-Class>
</manifestEntries>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
</transformers>
<filters>
<!--filter to address "Invalid signature file" issue - see http://stackoverflow.com/a/6743609/589215-->
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<!--
Dependencies
-->
<dependencies>
<dependency>
<groupId>bioc</groupId>
<artifactId>bioc</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>com.aliasi</groupId>
<artifactId>lingpipe</artifactId>
<version>4.1.0</version>
</dependency>
<!-- Text parsing -->
<dependency>
<groupId>monq</groupId>
<artifactId>monq</artifactId>
<version>1.1.1</version>
</dependency>
<!-- Machine Learning -->
<dependency>
<groupId>cc.mallet</groupId>
<artifactId>mallet</artifactId>
<version>2.0.7.1</version>
</dependency>
<!-- Linguistic features -->
<dependency>
<groupId>org.apache.opennlp</groupId>
<artifactId>opennlp-tools</artifactId>
<version>1.5.3</version>
</dependency>
<!-- Useful already implemented features -->
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>3.2.1</version>
<type>jar</type>
</dependency>
<!-- Dictionary Matching -->
<dependency>
<groupId>uk.ac.man</groupId>
<artifactId>linnaeus</artifactId>
<version>2.0</version>
</dependency>
<!-- Graph support-->
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht</artifactId>
<version>0.8.3</version>
</dependency>
<!-- JSON generation -->
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.2.2</version>
</dependency>
<!-- Logging -->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.6.2</version>
</dependency>
<!-- JUnit-->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.1</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.7</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<version>1.7.3</version>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>0.9.9-RC1</version>
</dependency>
<!--LVG-->
<dependency>
<groupId>gov.nih.nlm.nls.lvg</groupId>
<artifactId>lvgdist</artifactId>
<version>2015</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<version>8.0.0.RC0</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-jsp-2.1</artifactId>
<version>7.5.4.v20111024</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.0.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.mortbay.jetty</groupId>
<artifactId>jsp-2.1-glassfish</artifactId>
<version>2.1.v20100127</version>
</dependency>
<dependency>
<groupId>com.sun.jersey</groupId>
<artifactId>jersey-server</artifactId>
<version>1.9</version>
</dependency>
<dependency>
<groupId>com.sun.jersey</groupId>
<artifactId>jersey-client</artifactId>
<version>1.9</version>
</dependency>
<dependency>
<groupId>com.sun.jersey</groupId>
<artifactId>jersey-json</artifactId>
<version>1.9</version>
</dependency>
<dependency>
<groupId>com.sun.jersey.contribs</groupId>
<artifactId>jersey-multipart</artifactId>
<version>1.9</version>
<exclusions>
<exclusion>
<groupId>org.jvnet</groupId>
<artifactId>mimepull</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.jvnet.mimepull</groupId>
<artifactId>mimepull</artifactId>
<version>1.9</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>4.4.4</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.1</version>
</dependency>
<!-- SQLite -->
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>3.8.10.1</version>
</dependency>
<!-- Apache Ant Core -->
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>1.10.1</version>
</dependency>
</dependencies>
</project>