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<?xml version="1.0" encoding="UTF-8"?>
<!--
Licensed to the Apache Software Foundation (ASF) under one
or more contributor license agreements. See the NOTICE file
distributed with this work for additional information
regarding copyright ownership. The ASF licenses this file
to you under the Apache License, Version 2.0 (the
"License"); you may not use this file except in compliance
with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, either express or implied. See the License for the
specific language governing permissions and limitations
under the License.
-->
<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>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
<version>7.0.0-SNAPSHOT</version>
<packaging>pom</packaging>
<name>Apache cTAKES</name>
<url>http://ctakes.apache.org</url>
<inceptionYear>2012</inceptionYear>
<scm>
<!-- In child modules, Maven will append ${artifactId} to the following URLs -->
<connection>scm:git:https://github.com/apache/ctakes</connection>
<developerConnection>scm:git:https://github.com/apache/ctakes</developerConnection>
<url>https://github.com/apache/ctakes/tree/main</url>
</scm>
<issueManagement>
<system>GitHub</system>
<url>https://github.com/apache/ctakes/issues</url>
</issueManagement>
<!-- <ciManagement>-->
<!-- <system>jenkins</system>-->
<!-- <url>https://builds.apache.org/job/ctakes-trunk/</url>-->
<!-- </ciManagement>-->
<mailingLists>
<mailingList>
<name>Apache cTAKES Users</name>
<subscribe>user-subscribe@ctakes.apache.org</subscribe>
<unsubscribe>user-unsubscribe@ctakes.apache.org</unsubscribe>
<post>user@ctakes.apache.org</post>
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-user/</archive>
</mailingList>
<mailingList>
<name>Apache cTAKES Developers</name>
<subscribe>dev-subscribe@ctakes.apache.org</subscribe>
<unsubscribe>dev-unsubscribe@ctakes.apache.org</unsubscribe>
<post>dev@ctakes.apache.org</post>
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-dev/</archive>
</mailingList>
<mailingList>
<name>Apache cTAKES Commits</name>
<subscribe>commits-subscribe@ctakes.apache.org</subscribe>
<unsubscribe>commits-unsubscribe@ctakes.apache.org</unsubscribe>
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-commits/</archive>
</mailingList>
<mailingList>
<name>Apache cTAKES Notifications</name>
<subscribe>notifications-subscribe@ctakes.apache.org</subscribe>
<unsubscribe>notifications-unsubscribe@ctakes.apache.org</unsubscribe>
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-notifications/</archive>
</mailingList>
</mailingLists>
<properties>
<!-- dependencies -->
<activemq.version>6.1.2</activemq.version>
<ant.version>1.10.11</ant.version>
<antlr.version>2.7.7</antlr.version>
<ant-contrib.version>1.0b3</ant-contrib.version>
<args4j.version>2.37</args4j.version>
<artemis.version>2.36.0</artemis.version>
<aspectj.version>1.7.3</aspectj.version>
<backport-util.version>3.1</backport-util.version>
<cglib.version>2.2.2</cglib.version>
<checksum-maven-plugin.version>1.11</checksum-maven-plugin.version>
<classgraph.version>4.8.90</classgraph.version>
<clearnlp.version>1.3.1</clearnlp.version>
<!-- Clearnlp 1.4.2 is missing AbstractMPAnalyzer -->
<!-- <clearnlp.version>1.4.2</clearnlp.version>-->
<!-- Clearnlp in com.clearnlp is completely rewritten. We cannot use it without a lot of changes and tests. -->
<!-- <clearnlp.version>2.0.2</clearnlp.version>-->
<!-- Even after that, clearnlp was replaced by nlp4j https://emorynlp.github.io/nlp4j/ -->
<!-- nlp4j is still 8 years old and has known vulnerabilities. -->
<cleartk.version>3.0.0</cleartk.version>
<commons-beanutils.version>1.9.4</commons-beanutils.version>
<commons-cli.version>1.2</commons-cli.version>
<commons-collections.version>3.2.2</commons-collections.version>
<commons-collections4.version>4.4</commons-collections4.version>
<commons-dbcp.version>1.4</commons-dbcp.version>
<commons-el.version>1.0</commons-el.version>
<commons-io.version>2.2</commons-io.version>
<commons-jxpath.version>1.3</commons-jxpath.version>
<commons-io.version>2.7</commons-io.version>
<commons-lang.version>2.6</commons-lang.version>
<commons-pool.version>1.5.4</commons-pool.version>
<ctakesresources.version>4.0.0</ctakesresources.version>
<ctakes-models.version>5.0.0</ctakes-models.version>
<cxf.version>2.7.8</cxf.version>
<diffutils.version>1.3.0</diffutils.version>
<dom4j.version>2.1.4</dom4j.version>
<ehcache.version>2.4.6</ehcache.version>
<exec-maven-plugin.version>1.2.1</exec-maven-plugin.version>
<findstruct.version>0.0.1</findstruct.version>
<glassfish-javax-el.version>3.0.0</glassfish-javax-el.version>
<glassfish-web.version>2.2.1-b05</glassfish-web.version>
<gson.version>2.8.9</gson.version>
<guava.version>33.2.1-jre</guava.version>
<hapi.fhir.version>6.6.0</hapi.fhir.version>
<hapi.fhir.dstu3.version>6.3.18</hapi.fhir.dstu3.version>
<hibernate.version>5.4.24.Final</hibernate.version>
<!-- <hsqldb.version>2.3.4</hsqldb.version>-->
<hsqldb.version>2.7.3</hsqldb.version>
<httpclient.version>5.3.1</httpclient.version>
<icefaces.version>2.0.2</icefaces.version>
<jackson.version>2.17.2</jackson.version>
<jackson-core-asl.version>1.9.13</jackson-core-asl.version>
<jackson-databind.version>2.17.2</jackson-databind.version>
<jakarta-activation.version>2.0.1</jakarta-activation.version>
<javassist.version>3.15.0-GA</javassist.version>
<javax.annotation.version>1.3.2</javax.annotation.version>
<jaxb.version>2.3.1</jaxb.version>
<jaxb-runtime.version>4.0.5</jaxb-runtime.version>
<jaxb-xjc.version>4.0.5</jaxb-xjc.version>
<jaxb2-maven-plugin.version>3.1.0</jaxb2-maven-plugin.version>
<jaxws-ri.version>4.0.2</jaxws-ri.version>
<jaxws-api.version>2.3.1</jaxws-api.version>
<jcasgen-maven-plugin.version>3.5.0</jcasgen-maven-plugin.version>
<jchronic.version>0.2.8</jchronic.version>
<jdom.version>2.0.6.1</jdom.version>
<jetty.version>12.0.8</jetty.version>
<jetty-runner.version>11.0.20</jetty-runner.version>
<jetty-maven.version>11.0.20</jetty-maven.version>
<jetty-jsp.version>9.2.30.v20200428</jetty-jsp.version>
<jewelcli.version>0.8.9</jewelcli.version>
<jsf-api.version>2.1.3</jsf-api.version>
<jsf-impl.version>2.1.3</jsf-impl.version>
<jsr107cache.version>1.0</jsr107cache.version>
<junit.version>4.13.1</junit.version>
<jwi.version>2.2.3</jwi.version>
<libsvm.version>3.31</libsvm.version>
<log4j.version>2.23.1</log4j.version>
<lucene-analyzers.version>8.11.3</lucene-analyzers.version>
<lucene-core.version>9.11.1</lucene-core.version>
<lucene-queries.version>9.11.1</lucene-queries.version>
<lucene-queryparser.version>9.11.1</lucene-queryparser.version>
<apache-rat-plugin.version>0.15</apache-rat-plugin.version>
<properties-maven-plugin.version>1.1.0</properties-maven-plugin.version>
<maven-antrun-plugin.version>3.1.0</maven-antrun-plugin.version>
<maven-assembly-plugin.version>3.7.1</maven-assembly-plugin.version>
<maven-clean-plugin.version>3.3.2</maven-clean-plugin.version>
<maven-compiler-plugin.version>3.13.0</maven-compiler-plugin.version>
<maven-dependency-plugin.version>3.6.1</maven-dependency-plugin.version>
<maven-deploy-plugin.version>3.1.1</maven-deploy-plugin.version>
<maven-failsafe-plugin.version>3.2.3</maven-failsafe-plugin.version>
<maven-gpg-plugin.version>3.0.1</maven-gpg-plugin.version>
<maven-help-plugin.version>3.4.1</maven-help-plugin.version>
<maven-install-plugin.version>3.1.1</maven-install-plugin.version>
<maven-jar-plugin.version>3.3.0</maven-jar-plugin.version>
<maven-javadoc-plugin.version>3.6.3</maven-javadoc-plugin.version>
<maven-license-plugin.version>1.9.0</maven-license-plugin.version>
<maven-remote-resources-plugin.version>3.1.0</maven-remote-resources-plugin.version>
<maven-resources-plugin.version>3.3.1</maven-resources-plugin.version>
<maven-site-plugin.version>4.0.0-M13</maven-site-plugin.version>
<maven-source-plugin.version>3.3.0</maven-source-plugin.version>
<maven-surefire-plugin.version>3.2.3</maven-surefire-plugin.version>
<maven-war-plugin.version>3.4.0</maven-war-plugin.version>
<mysql-connector.version>8.0.28</mysql-connector.version>
<openaifsm.version>0.0.1</openaifsm.version>
<opennlp.version>2.3.3</opennlp.version>
<!-- opennlp-maxent depends upon opennlp 1.5.3 The project looks like it hasn't changed in a while. -->
<opennlp.maxent.version>3.0.3</opennlp.maxent.version>
<protobuf.version>4.27.2</protobuf.version>
<scala-library.version>2.13.14</scala-library.version>
<scala-tools.version>0.4.0</scala-tools.version>
<servlet-jsp-api.version>2.2</servlet-jsp-api.version>
<servlet-jstl.version>1.2</servlet-jstl.version>
<slf4j.version>2.0.13</slf4j.version>
<log4j-slf4j2.version>2.23.1</log4j-slf4j2.version>
<solr.version>3.5.0</solr.version>
<spring.version>5.3.20</spring.version>
<spring-aop.version>6.1.11</spring-aop.version>
<spring-context.version>6.1.11</spring-context.version>
<spring-core.version>6.1.11</spring-core.version>
<spring-jdbc.version>6.1.11</spring-jdbc.version>
<spring-orm.version>6.1.11</spring-orm.version>
<spring-web.version>6.1.11</spring-web.version>
<sqlwrapper.version>0.0.1</sqlwrapper.version>
<timenorm.version>1.0.5</timenorm.version>
<uimafit.version>3.5.0</uimafit.version>
<uimaj.version>3.5.0</uimaj.version>
<weka.version>3.6.10</weka.version>
<xerces.version>2.12.2</xerces.version>
<xml-apis.version>1.4.01</xml-apis.version>
<xmlunit.version>1.4</xmlunit.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.build.timestamp.format>yyyy-MM-dd HH:mm</maven.build.timestamp.format>
</properties>
<parent>
<groupId>org.apache</groupId>
<artifactId>apache</artifactId>
<version>13</version>
</parent>
<modules>
<module>ctakes-gui</module>
<module>ctakes-fhir</module>
<module>ctakes-utils</module>
<module>ctakes-core</module>
<module>ctakes-type-system</module>
<module>ctakes-pos-tagger</module>
<module>ctakes-chunker</module>
<module>ctakes-preprocessor</module>
<module>ctakes-dictionary-lookup</module>
<module>ctakes-context-tokenizer</module>
<module>ctakes-lvg</module>
<module>ctakes-ne-contexts</module>
<module>ctakes-constituency-parser</module>
<module>ctakes-coreference</module>
<module>ctakes-drug-ner</module>
<module>ctakes-side-effect</module>
<module>ctakes-smoking-status</module>
<module>ctakes-dependency-parser</module>
<module>ctakes-relation-extractor</module>
<module>ctakes-mastif-zoner</module>
<module>ctakes-assertion</module>
<module>ctakes-assertion-zoner</module>
<module>ctakes-temporal</module>
<module>ctakes-clinical-pipeline</module>
<module>ctakes-distribution</module>
<module>ctakes-regression-test</module>
<module>ctakes-template-filler</module>
<module>ctakes-examples</module>
<module>ctakes-ytex</module>
<module>ctakes-ytex-uima</module>
<module>ctakes-dictionary-lookup-fast</module>
<module>ctakes-dockhand</module>
<module>ctakes-tiny-rest</module>
<module>ctakes-pbj</module>
<module>ctakes-user-resources</module>
</modules>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>${ant.version}</version>
</dependency>
<dependency>
<groupId>ant-contrib</groupId>
<artifactId>ant-contrib</artifactId>
<version>${ant-contrib.version}</version>
<exclusions>
<exclusion>
<artifactId>ant</artifactId>
<groupId>ant</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant-launcher</artifactId>
<version>${ant.version}</version>
</dependency>
<dependency>
<groupId>antlr</groupId>
<artifactId>antlr</artifactId>
<version>${antlr.version}</version>
</dependency>
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjweaver</artifactId>
<version>${aspectj.version}</version>
</dependency>
<dependency>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
<version>${javax.annotation.version}</version>
</dependency>
<dependency>
<groupId>com.googlecode.java-diff-utils</groupId>
<artifactId>diffutils</artifactId>
<version>${diffutils.version}</version>
</dependency>
<dependency>
<groupId>org.dom4j</groupId>
<artifactId>dom4j</artifactId>
<version>${dom4j.version}</version>
</dependency>
<dependency>
<groupId>org.apache.activemq</groupId>
<artifactId>activemq-all</artifactId>
<version>${activemq.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.activemq</groupId>
<artifactId>artemis-jms-client</artifactId>
<version>${artemis.version}</version>
</dependency>
<dependency>
<groupId>io.github.classgraph</groupId>
<artifactId>classgraph</artifactId>
<version>${classgraph.version}</version>
</dependency>
<!-- hapi-fhir-structures-dstu3 is required to actually write a dstu3 json file -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${hapi.fhir.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.dstu3</artifactId>
<version>${hapi.fhir.dstu3.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${gson.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents.client5</groupId>
<artifactId>httpclient5</artifactId>
<version>${httpclient.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version>
</dependency>
<dependency>
<groupId>net.sf.ehcache</groupId>
<artifactId>ehcache-core</artifactId>
<version>${ehcache.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-ehcache</artifactId>
<version>${hibernate.version}</version>
<exclusions>
<exclusion>
<groupId>net.sf.ehcache</groupId>
<artifactId>ehcache-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>${javassist.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>edu.mit</groupId>
<artifactId>jwi</artifactId>
<version>${jwi.version}</version>
</dependency>
<!-- Possible Logging types and versions. This does not add the jars to a cTAKES installation. -->
<!-- cTAKES uses slf4j to 'log'. bom (Bill of Materials) pom is only a list of possible jars+. -->
<!-- The slf4j dependency is declared in uimaj-core, used (first) by cTAKES Common Type System. -->
<!-- To use a logging "provider", e.g. log4j, see https://www.slf4j.org/manual.html#swapping -->
<!-- cTAKES code does not directly use log4j 1. However, it has some older dependencies that do. -->
<!-- log4j-1.2-api, the "log4j bridge" is a facade that forwards lo4j 1 method calls to log4j 2. -->
<!-- slf4j provides a similar bridge. https://www.slf4j.org/legacy.html#log4j-over-slf4j -->
<!-- The slf4j bom should contain the latest version of log4j-over-slf4j, so we don't declare it. -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-bom</artifactId>
<version>${slf4j.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<!-- log4j 2 version, just in case it is what a user wants. Use at runtime, not during compilation.-->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j2-impl</artifactId>
<version>${log4j-slf4j2.version}</version>
<!-- <scope>runtime</scope>-->
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j.version}</version>
<!-- <scope>runtime</scope>-->
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j.version}</version>
<!-- <scope>runtime</scope>-->
</dependency>
<!-- <dependency>-->
<!-- <groupId>xml-apis</groupId>-->
<!-- <artifactId>xml-apis</artifactId>-->
<!-- <version>${xml-apis.version}</version>-->
<!-- </dependency>-->
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>${xerces.version}</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.jdom</groupId>
<artifactId>jdom2</artifactId>
<version>${jdom.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-core</artifactId>
<version>${lucene-core.version}</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>org.apache.lucene</groupId>-->
<!-- <artifactId>lucene-contrib</artifactId>-->
<!-- <version>4.0.0</version>-->
<!-- </dependency>-->
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-queries</artifactId>
<version>${lucene-queries.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-queryparser</artifactId>
<version>${lucene-queryparser.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-common</artifactId>
<version>${lucene-analyzers.version}</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>${jaxb.version}</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>${jaxb.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>${jaxb-runtime.version}</version>
</dependency>
<dependency>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
<version>${jakarta-activation.version}</version>
</dependency>
<!-- Jackson -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson-databind.version}</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
<version>${jackson-core-asl.version}</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>${jackson-mapper.version}</version>
</dependency>
<!-- Scala -->
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala-library.version}</version>
</dependency>
<dependency>
<groupId>org.scala-tools.sbinary</groupId>
<artifactId>sbinary_2.9.0</artifactId>
<version>${scala-tools.version}</version>
</dependency>
<!-- Apache UIMA -->
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
<version>${uimaj.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-cpe</artifactId>
<version>${uimaj.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-document-annotation</artifactId>
<version>${uimaj.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-tools</artifactId>
<version>${uimaj.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimafit-core</artifactId>
<version>${uimafit.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimafit-cpe</artifactId>
<version>${uimafit.version}</version>
</dependency>
<dependency>
<groupId>org.apache.opennlp</groupId>
<artifactId>opennlp-tools</artifactId>
<version>${opennlp.version}</version>
</dependency>
<dependency>
<groupId>org.apache.opennlp</groupId>
<artifactId>opennlp-uima</artifactId>
<version>${opennlp.version}</version>
</dependency>
<dependency>
<groupId>org.apache.opennlp</groupId>
<artifactId>opennlp-maxent</artifactId>
<version>${opennlp.maxent.version}</version>
</dependency>
<dependency>
<groupId>tw.edu.ntu.csie</groupId>
<artifactId>libsvm</artifactId>
<version>${libsvm.version}</version>
</dependency>
<dependency>
<groupId>cglib</groupId>
<artifactId>cglib</artifactId>
<version>${cglib.version}</version>
</dependency>
<!-- import a consistent set of versions for all ClearTK modules -->
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk</artifactId>
<version>${cleartk.version}</version>
<type>pom</type>
<scope>import</scope>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-crfsuite</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.ivy</groupId>
<artifactId>ivy</artifactId>
</exclusion>
<exclusion>
<groupId>org.codehaus.plexus</groupId>
<artifactId>plexus-utils</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-libsvm</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-mallet</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.beanshell</groupId>
<artifactId>bsh</artifactId>
</exclusion>
<exclusion>
<groupId>org.jdom</groupId>
<artifactId>jdom-legacy</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-timeml</artifactId>
<version>${cleartk.version}</version>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-type-system</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-util</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-opennlp-maxent</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-eval</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-svmlight</artifactId>
<version>${cleartk.version}</version>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-tksvmlight</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-ml-liblinear</artifactId>
<version>${cleartk.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.clulab</groupId>
<artifactId>timenorm_2.13</artifactId>
<version>${timenorm.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.rubiconproject.oss</groupId>
<artifactId>jchronic</artifactId>
<version>${jchronic.version}</version>
</dependency>
<dependency>
<groupId>org.hsqldb</groupId>
<artifactId>hsqldb</artifactId>
<version>${hsqldb.version}</version>
</dependency>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
<version>${args4j.version}</version>
</dependency>
<dependency>
<groupId>com.lexicalscope.jewelcli</groupId>
<artifactId>jewelcli</artifactId>
<version>${jewelcli.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>${commons-collections4.version}</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>${commons-collections.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>${commons-beanutils.version}</version>
<!-- There is a vulnerability in commons-collections, but we can't exclude it. -->
<!-- <exclusions>-->
<!-- <exclusion>-->
<!-- <groupId>commons-collections</groupId>-->
<!-- <artifactId>commons-collections</artifactId>-->
<!-- </exclusion>-->
<!-- </exclusions>-->
</dependency>
<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
<version>${commons-dbcp.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons-cli.version}</version>
</dependency>
<dependency>
<groupId>commons-jxpath</groupId>
<artifactId>commons-jxpath</artifactId>
<version>${commons-jxpath.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-commons-csv</artifactId>
<version>${solr.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-aop</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${spring-context.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>${spring-core.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring-web.version}</version>
</dependency>
<dependency>
<groupId>edu.mit.findstruct</groupId>
<artifactId>structmulti</artifactId>
<version>${findstruct.version}</version>
</dependency>
<dependency>
<groupId>edu.mit.findstruct</groupId>
<artifactId>findstructapi</artifactId>
<version>${findstruct.version}</version>
</dependency>
<dependency>
<groupId>com.googlecode.armbrust-file-utils</groupId>
<artifactId>sqlwrapper</artifactId>
<version>${sqlwrapper.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.openai</groupId>
<artifactId>openaifsm</artifactId>
<version>${openaifsm.version}</version>
</dependency>
<dependency>
<groupId>gov.nih.nlm.nls.lvg</groupId>
<artifactId>lvgdist</artifactId>
<version>2016.0</version>
</dependency>
<dependency>
<groupId>com.googlecode.clearnlp</groupId>
<artifactId>clearnlp</artifactId>
<version>${clearnlp.version}</version>
<exclusions>
<exclusion>
<!-- Exclude log4j v1 -->
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- cTAKES module versions -->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-gui</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-fhir</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-examples</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-utils</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-template-filler</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-core-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-preprocessor</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-pos-tagger</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-pos-tagger-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-chunker</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-chunker-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-lvg</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-context-tokenizer</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-clinical-pipeline</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-ne-contexts</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-mastif-zoner</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-assertion</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-assertion-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-assertion-zoner</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-constituency-parser</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-constituency-parser-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-coreference</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-coreference-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-drug-ner</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-side-effect</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-side-effect-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-smoking-status</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-smoking-status-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dependency-parser</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dependency-parser-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dependency-parser-models-clear</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-relation-extractor</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-relation-extractor-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-temporal</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-temporal-models</artifactId>
<version>${ctakes-models.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-ytex</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-ytex-uima</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-distribution</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dockhand</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-tiny-rest</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-user-resources</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-pbj</artifactId>
<version>${project.version}</version>
</dependency>
<!-- cTAKES dictionary Resources -->
<dependency>
<groupId>net.sourceforge.ctakesresources</groupId>
<artifactId>ctakes-resources-lvg2008</artifactId>
<version>${ctakesresources.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.ctakesresources</groupId>
<artifactId>ctakes-resources-orangebook-hsqldb</artifactId>
<version>${ctakesresources.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.ctakesresources</groupId>
<artifactId>ctakes-resources-rxnorm-hsqldb-2011ab</artifactId>
<version>${ctakesresources.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.ctakesresources</groupId>
<artifactId>ctakes-resources-sno_rx</artifactId>
<version>${ctakesresources.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.ctakesresources</groupId>
<artifactId>ctakes-resources-umls2011ab</artifactId>
<version>${ctakesresources.version}</version>
</dependency>
<dependency>
<groupId>xmlunit</groupId>
<artifactId>xmlunit</artifactId>
<version>${xmlunit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.nicoulaj.maven.plugins</groupId>
<artifactId>checksum-maven-plugin</artifactId>
<version>${checksum-maven-plugin.version}</version>
<exclusions>
<exclusion>
<groupId>org.bouncycastle</groupId>
<artifactId>bcprov-jdk15on</artifactId>
</exclusion>
<exclusion>
<groupId>org.codehaus.plexus</groupId>
<artifactId>plexus-utils</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>nz.ac.waikato.cms.weka</groupId>
<artifactId>weka-stable</artifactId>
<version>${weka.version}</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
<version>${protobuf.version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysql-connector.version}</version>
<exclusions>
<exclusion>
<!-- Exclude protobuf v3 -->
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
</dependencyManagement>
<repositories>
<repository>
<id>apache.snapshots</id>
<name>Apache Development Snapshot Repository</name>
<url>https://repository.apache.org/content/groups/snapshots/</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
<resource>
<directory>src/user/resources</directory>
</resource>
<resource>
<directory>src/user/config</directory>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>${maven-resources-plugin.version}</version>
<executions>
<execution>
<!-- Copy resources that should be user-editable for testing without requiring recompiling. -->
<!-- This makes it much easier for developers to find resources. -->
<!-- Permanent edits must still be made in src/main/resources -->
<id>copy-user-resources</id>
<phase>compile</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<resources>
<resource>
<directory>src/user/resources</directory>
</resource>
</resources>
<outputDirectory>${project.basedir}/../resources</outputDirectory>
</configuration>
</execution>
<execution>
<!-- Copy config that should be user-editable for testing without requiring recompiling. -->
<!-- This makes it much easier for developers to find configuration files. -->
<!-- Permanent edits must still be made in src/main/resources -->
<id>copy-user-config</id>
<phase>compile</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<resources>
<resource>
<directory>src/user/config</directory>
</resource>
</resources>
<outputDirectory>${project.basedir}/../config</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.mycila.maven-license-plugin</groupId>
<artifactId>maven-license-plugin</artifactId>
<version>${maven-license-plugin.version}</version>
<configuration>
<header>ctakes-distribution/src/main/config/license_header.txt</header>
<excludes>
<!-- We're disabling .txt files for now because some Annotators may
not be able to handle standard comments in text files. This may break name
values pairs such as stopWords.txt -->
<exclude>**.txt</exclude>
</excludes>
<useDefaultMapping>false</useDefaultMapping>
<quiet>false</quiet>
<failIfMissing>false</failIfMissing>
<mapping>
<java>JAVADOC_STYLE</java>
<groovy>JAVADOC_STYLE</groovy>
<js>JAVADOC_STYLE</js>
<css>JAVADOC_STYLE</css>
<xml>XML_STYLE</xml>
<dtd>XML_STYLE</dtd>
<xsd>XML_STYLE</xsd>
<html>XML_STYLE</html>
<htm>XML_STYLE</htm>
<xsl>XML_STYLE</xsl>
<fml>XML_STYLE</fml>
<apt>DOUBLETILDE_STYLE</apt>
<properties>SCRIPT_STYLE</properties>
<sh>SCRIPT_STYLE</sh>
<!-- <txt>TEXT</txt> -->
<bat>BATCH</bat>
<cmd>BATCH</cmd>
<sql>DOUBLEDASHES_STYLE</sql>
<jsp>DYNASCRIPT_STYLE</jsp>
<ftl>FTL</ftl>
<xhtml>XML_STYLE</xhtml>
<vm>SHARPSTAR_STYLE</vm>
<jspx>XML_STYLE</jspx>
</mapping>
<properties>
<owner>Apache Software Foundation</owner>
<year>${project.inceptionYear}</year>
<email>dev@ctakes.apache.org</email>
</properties>
<strictCheck>true</strictCheck>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>${maven-assembly-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-help-plugin</artifactId>
<version>${maven-help-plugin.version}</version>
<executions>
<execution>
<id>show-profiles</id>
<phase>compile</phase>
<goals>
<goal>active-profiles</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.nicoulaj.maven.plugins</groupId>
<artifactId>checksum-maven-plugin</artifactId>
<version>${checksum-maven-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>${maven-clean-plugin.version}</version>
<configuration>
<filesets>
<!-- Clean up the resources directory so that mvn compile regenerates with any changes.
Use individual ctakes modules.
Do not use universal ctakes/ alone as user may add their own module. -->
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/assertion</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/chunker</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/clinical</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/constituency</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/core</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/coreference</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/dependency</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/dictionary</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/examples</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/lvg</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/ne</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/pbj</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/pos</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/postagger</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/relation</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/sideeffect</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/smoking</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/temporal</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/apache/ctakes/utils</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/mitre/medfacts</directory>
</fileset>
<fileset>
<directory>${project.basedir}/../resources/org/mitre/medfacts</directory>
</fileset>
<!-- Remove any old error log. -->
<fileset>
<directory>${project.basedir}/..</directory>
<includes>cTAKES.error.log</includes>
</fileset>
</filesets>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven-compiler-plugin.version}</version>
<configuration>
<source>17</source>
<target>17</target>
<release>17</release>
<compilerArgument>-Xlint</compilerArgument>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>${maven-deploy-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>${maven-gpg-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>${maven-install-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-remote-resources-plugin</artifactId>
<version>${maven-remote-resources-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>${maven-antrun-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>${maven-jar-plugin.version}</version>
<configuration>
<includes>
<!-- Resources will be copied by the assembly
No need for it to be inside the jar
<include>**/*.class</include>
<include>**/types/*.xml</include>
<include>**/META-INF/**</include>
-->
</includes>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
</manifest>
<manifestEntries>
<Implementation-Build-Date>${maven.build.timestamp}</Implementation-Build-Date>
</manifestEntries>
</archive>
</configuration>
</plugin>
<!-- <plugin>-->
<!-- <artifactId>maven-javadoc-plugin</artifactId>-->
<!-- <version>${maven-javadoc-plugin.version}</version>-->
<!-- </plugin>-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>${maven-dependency-plugin.version}</version>
<executions>
<execution>
<id>analyze</id>
<goals>
<goal>analyze</goal>
</goals>
<phase>test-compile</phase>
<configuration>
<ignoredUnusedDeclaredDependencies>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-core-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-pos-tagger-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-chunker-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-constituency-parser-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-smoking-status-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-side-effect-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-dependency-parser-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-dependency-parser-models-clear</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-assertion-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-relation-extractor-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-temporal-models</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.apache.ctakes:ctakes-coreference-models</ignoredUnusedDeclaredDependency>
</ignoredUnusedDeclaredDependencies>
</configuration>
</execution>
<!-- There weren't great options for getting a logger that could be listened to while still forwarding. -->
<!-- This should prevent maven from unpacking the LoggerFactory that comes with slf4j. -->
<!-- We want to use our own LoggerFactory in ctakes-type-system. -->
<execution>
<id>unpack</id>
<phase>generate-sources</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<type>jar</type>
<overWrite>true</overWrite>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
<excludes>**/LoggerFactory.class</excludes>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>${maven-site-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>${maven-source-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${maven-failsafe-plugin.version}</version>
</plugin>
<!-- Maven expects tests to start or end with "Test", not "Tests", so
explicitly include files ending in "Tests" -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<configuration>
<includes>
<include>**/Test*.java</include>
<include>**/*Test.java</include>
<include>**/*Tests.java</include>
<include>**/*TestCase.java</include>
</includes>
<argLine>-Xmx3g</argLine>
<forkedProcessTimeoutInSeconds>900</forkedProcessTimeoutInSeconds>
<additionalClasspathElements>
<additionalClasspathElement>ctakes-assertion-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-chunker-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-constituency-parser-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-core-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-coreference-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-dependency-parser-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-dependency-parser-model-clear/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-pos-tagger-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-relation-extractor-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-side-effect-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-smoking-status-model/src/main/resources
</additionalClasspathElement>
<additionalClasspathElement>ctakes-temporal-model/src/main/resources
</additionalClasspathElement>
</additionalClasspathElements>
</configuration>
</plugin>
<!-- apache-rat:check validate release -->
<plugin>
<groupId>org.apache.rat</groupId>
<artifactId>apache-rat-plugin</artifactId>
<version>${apache-rat-plugin.version}</version>
<configuration>
<excludes>
<!-- generated directories -->
<exclude>**/target/**/*</exclude>
<exclude>resources/**/*</exclude>
<!-- version control -->
<exclude>.git/**/*</exclude>
<exclude>.gitignore</exclude>
<exclude>.github/**/*</exclude>
<!-- Eclipse files -->
<exclude>**/.*</exclude>
<exclude>**/.settings/*</exclude>
<exclude>**/eclipse-classes/**/*</exclude>
<!-- IDEA IntelliJ files -->
<exclude>**/*.iml</exclude>
<exclude>**/*.ipr</exclude>
<exclude>**/*.iws</exclude>
<exclude>**/.idea/**/*</exclude>
<!-- File generated by maven-release-plugin -->
<exclude>release.properties</exclude>
<!-- Exclude bin/model resources -->
<!-- TODO: do not exclude resources. Rat should exclude binaries by default -->
<exclude>**/src/main/resources/**</exclude>
<exclude>**/src/test/resources/**</exclude>
<exclude>**/META-INF/org.uimafit/types.txt</exclude>
<exclude>**/MANIFEST.MF</exclude>
<!-- Exclude test data files -->
<exclude>**/data/test/**</exclude>
<exclude>**/data/**</exclude>
<exclude>**/output/**</exclude>
<exclude>**/sample_note.txt</exclude>
</excludes>
<numUnapprovedLicenses>0</numUnapprovedLicenses>
</configuration>
</plugin>
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<!--
This is needed to execute/unpack resources in m2e eclipse ide
Currently used in the ctakes-dictionary-lookup project
-->
<pluginExecutionFilter>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<versionRange>[${maven-dependency-plugin.version},)</versionRange>
<goals>
<goal>unpack-dependencies</goal>
</goals>
</pluginExecutionFilter>
<action>
<execute>
<runOnIncremental>true</runOnIncremental>
</execute>
</action>
</pluginExecution>
<pluginExecution>
<!--
Ignore the Maven remote resources plugin in Eclipse. We don't use it from Eclipse,
and it causes a warning if m2e is not configured to ignore it as below.
-->
<pluginExecutionFilter>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-remote-resources-plugin</artifactId>
<versionRange>[${maven-remote-resources-plugin.version},)</versionRange>
<goals>
<goal>process</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore/>
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
<!-- exec-maven-plugin -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>${exec-maven-plugin.version}</version>
<executions>
<execution>
<phase>compile</phase>
<goals>
<goal>java</goal>
</goals>
</execution>
</executions>
<configuration>
<executable>java</executable>
<includeProjectDependencies>true</includeProjectDependencies>
<includePluginDependencies>true</includePluginDependencies>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.uima</groupId>
<artifactId>jcasgen-maven-plugin</artifactId>
<version>${jcasgen-maven-plugin.version}</version>
<executions>
<execution>
<goals>
<goal>generate</goal>
</goals>
<configuration>
<typeSystemIncludes>
<typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/*.xml
</typeSystemInclude>
</typeSystemIncludes>
<limitToProject>true</limitToProject>
<!-- <limitToProject>false</limitToProject>-->
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
<profiles>
<profile>
<!-- ctakes-web-rest contains a full copy of ctakes in its target/WEB-INF/lib -->
<!-- and another full copy in target/ctakes-web-rest.war -->
<!-- This requires over 1.75 GB of disk space, in addition to extra build time. -->
<!-- We do not distribute the ctakes-web-rest.war with the ctakes distributable. -->
<!-- It can be built when wanted by enabling this profile ( web-rest-build ). -->
<id>web-rest-build</id>
<modules>
<module>ctakes-web-rest</module>
</modules>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-web-rest</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
</profile>
<profile>
<!-- ctakes-ytex-web contains a full copy of ctakes in its target/WEB-INF/lib -->
<!-- and another full copy in target/ctakes-ytex-web.war -->
<!-- This requires over 1.75 GB of disk space, in addition to extra build time. -->
<!-- We do not distribute the ctakes-ytex-web.war with the ctakes distributable. -->
<!-- It can be built when wanted by enabling this profile ( ytex-web-build ). -->
<id>ytex-web-build</id>
<modules>
<module>ctakes-ytex-web</module>
</modules>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-ytex-web</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
</profile>
<profile>
<id>disable-java8-doclint</id>
<activation>
<jdk>[1.8,)</jdk>
</activation>
<properties>
<additionalparam>-Xdoclint:none</additionalparam>
</properties>
</profile>
<!-- Disable this profile if you do not want to use log4j2 while running in IDEs etc. -->
<profile>
<id>use-log4j2</id>
<activation>
<property>
<name>!nolog4j</name>
</property>
</activation>
<dependencies>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j2-impl</artifactId>
<version>${log4j-slf4j2.version}</version>
<scope>runtime</scope>
</dependency>
</dependencies>
</profile>
</profiles>
</project>