<?xml version="1.0" encoding="UTF-8"?>

<!--
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership.
 *
 * This is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2.1 of
 * the License, or (at your option) any later version.
 *
 * This software 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. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this software; if not, write to the Free
 * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
 * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
-->

<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>org.phenotips</groupId>
    <artifactId>clinical-text-analysis-extension</artifactId>
    <version>1.0-alpha-6</version>
  </parent>
  <artifactId>clinical-text-analysis-extension-biolark</artifactId>
  <name>PhenoTips - Clinical Text Analysis - Biolark implementation for the Java APIs</name>
  <dependencies>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-component-api</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-lang3</artifactId>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-bridge</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-distribution</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-model</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-oldcore</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-query-manager</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-context</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <dependency>
      <groupId>${project.groupId}</groupId>
      <artifactId>clinical-text-analysis-extension-api</artifactId>
      <version>${project.version}</version>
    </dependency>
    <dependency>
      <groupId>${project.groupId}</groupId>
      <artifactId>phenotips-constants</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>${project.groupId}</groupId>
      <artifactId>ontology-access-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>net.sf.json-lib</groupId>
      <artifactId>json-lib</artifactId>
      <classifier>jdk15</classifier>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-api</artifactId>
    </dependency>
    <!-- Test dependencies -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-test-component</artifactId>
      <version>${xwiki.version}</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>javax.servlet</groupId>
      <artifactId>servlet-api</artifactId>
    </dependency>
    <dependency>
      <groupId>org.mockito</groupId>
      <artifactId>mockito-all</artifactId>
      <version>1.10.8</version>
    </dependency>

    <!-- Biolark dependencies -->
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolark-commons</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolark-cr</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolark-input</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolark-input-pheno</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolark-search</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolark-ta</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolark-variants</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>biolemmatizer-core</artifactId>
      <classifier>with-dependencies</classifier>
      <version>1.1</version>
    </dependency>
    <dependency>
      <groupId>org.biolark</groupId>
      <artifactId>lvg2013dist</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>edu.mit</groupId>
      <artifactId>jwi</artifactId>
      <version>2.2.4</version>
    </dependency>
    <dependency>
      <groupId>uk.ac.shef.wit</groupId>
      <artifactId>simmetrics</artifactId>
      <version>1.6.2</version>
    </dependency>
    <dependency>
      <groupId>br.pro.lab</groupId>
      <artifactId>OpenJGraph</artifactId>
      <version>0.9.1</version>
    </dependency>
    <dependency>
      <groupId>nu.xom</groupId>
      <artifactId>xom</artifactId>
      <version>1.2.8</version>
    </dependency>
    <dependency>
      <groupId>org.beanshell</groupId>
      <artifactId>bsh</artifactId>
      <version>2.0b5</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-collections4</artifactId>
      <version>4.0</version>
    </dependency>
    <dependency>
      <groupId>commons-collections</groupId>
      <artifactId>commons-collections</artifactId>
      <version>3.2.1</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-compress</artifactId>
      <version>1.4.1</version>
    </dependency>
    <dependency>
      <groupId>com.google.code.gson</groupId>
      <artifactId>gson</artifactId>
      <version>2.2.2</version>
    </dependency>
    <dependency>
      <groupId>com.ibm.icu</groupId>
      <artifactId>icu4j</artifactId>
      <version>49.1</version>
    </dependency>
    <dependency>
      <groupId>com.ibm.icu</groupId>
      <artifactId>icu4j</artifactId>
      <version>51.1</version>
    </dependency>
    <dependency>
      <groupId>jdom</groupId>
      <artifactId>jdom</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>jgrapht</groupId>
      <artifactId>jgrapht</artifactId>
      <version>0.6.0</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>1.7.2</version>
    </dependency>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.7</version>
    </dependency>
    <dependency>
      <groupId>net.sf.jwordnet</groupId>
      <artifactId>jwnl</artifactId>
      <version>1.3.3</version>
    </dependency>
    <dependency>
      <groupId>log4j</groupId>
      <artifactId>log4j</artifactId>
      <version>1.2.17</version>
    </dependency>
    <dependency>
      <groupId>edu.stanford.nlp</groupId>
      <artifactId>stanford-corenlp</artifactId>
      <version>3.5.1</version>
    </dependency>
    <dependency>
      <groupId>cc.mallet</groupId>
      <artifactId>mallet</artifactId>
      <version>2.0.7</version>
    </dependency>
    <dependency>
      <groupId>xerces</groupId>
      <artifactId>xercesImpl</artifactId>
      <version>2.9.1</version>
    </dependency>
    <dependency>
      <groupId>com.googlecode.matrix-toolkits-java</groupId>
      <artifactId>mtj</artifactId>
      <version>0.9.14</version>
    </dependency>
    <dependency>
      <groupId>net.sourceforge.nekohtml</groupId>
      <artifactId>nekohtml</artifactId>
      <version>1.9.17</version>
    </dependency>
    <dependency>
      <groupId>net.sf.trove4j</groupId>
      <artifactId>trove4j</artifactId>
      <version>2.0.2</version>
    </dependency>
    <dependency>
      <groupId>net.lingala.zip4j</groupId>
      <artifactId>zip4j</artifactId>
      <version>1.3.2</version>
    </dependency>
  </dependencies>
  <properties>
    <coverage.instructionRatio>0.18</coverage.instructionRatio>
  </properties>
</project>
