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Posted to commits@ctakes.apache.org by tm...@apache.org on 2019/01/23 21:47:03 UTC
svn commit: r1851986 - in /ctakes/trunk/ctakes-web-rest/docker: ./
Default.piper Dockerfile customDictionary.xml pom.xml start_rest.sh
Author: tmill
Date: Wed Jan 23 21:47:02 2019
New Revision: 1851986
URL: http://svn.apache.org/viewvc?rev=1851986&view=rev
Log:
Merge branch 'rest-docker'
Added:
ctakes/trunk/ctakes-web-rest/docker/
ctakes/trunk/ctakes-web-rest/docker/Default.piper
ctakes/trunk/ctakes-web-rest/docker/Dockerfile
ctakes/trunk/ctakes-web-rest/docker/customDictionary.xml
ctakes/trunk/ctakes-web-rest/docker/pom.xml
ctakes/trunk/ctakes-web-rest/docker/start_rest.sh (with props)
Added: ctakes/trunk/ctakes-web-rest/docker/Default.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/Default.piper?rev=1851986&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/docker/Default.piper (added)
+++ ctakes/trunk/ctakes-web-rest/docker/Default.piper Wed Jan 23 21:47:02 2019
@@ -0,0 +1,20 @@
+// Commands and parameters to create a default plaintext document processing pipeline with UMLS lookup
+
+// set the thread count
+threads 3
+
+// Load a simple token processing pipeline from another pipeline file
+load pipers/TsDefaultTokenizerPipeline
+
+// Add non-core annotators
+add ContextDependentTokenizerAnnotator
+addDescription POSTagger
+
+// Add Chunkers
+load pipers/TsChunkerSubPipe
+
+// Default fast dictionary lookup
+load pipers/TsDictionarySubPipe
+
+// Add Cleartk Entity Attribute annotators
+//load pipers/TsAttributeCleartkSubPipe
Added: ctakes/trunk/ctakes-web-rest/docker/Dockerfile
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/Dockerfile?rev=1851986&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/docker/Dockerfile (added)
+++ ctakes/trunk/ctakes-web-rest/docker/Dockerfile Wed Jan 23 21:47:02 2019
@@ -0,0 +1,41 @@
+FROM openjdk:8-alpine
+
+RUN apk update && apk add ca-certificates openssl wget unzip subversion maven
+
+## Download apache-tomcat and extract:
+RUN wget http://mirror.cc.columbia.edu/pub/software/apache/tomcat/tomcat-9/v9.0.14/bin/apache-tomcat-9.0.14.zip
+RUN unzip apache-tomcat-9.0.14.zip
+
+## Check out version of ctakes with best working web-rest module
+## Then compile with maven
+RUN svn co https://svn.apache.org/repos/asf/ctakes/trunk@1850060 ctakes
+
+## Copy hsql dictionary descriptor into right location
+RUN wget -q -O dict.zip https://downloads.sourceforge.net/project/ctakesresources/sno_rx_16ab.zip
+RUN mkdir -p /ctakes/resources/org/apache/ctakes/dictionary/lookup/fast/
+RUN unzip -o dict.zip -d /ctakes/resources/org/apache/ctakes/dictionary/lookup/fast/
+
+COPY customDictionary.xml /ctakes/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/
+COPY pom.xml /ctakes
+
+# This version of the default piper comments out a memory-intensive negation module. If you need to run
+# negation detection, then comment out this line.
+COPY Default.piper /ctakes/ctakes-web-rest/src/main/resources/pipers/
+
+WORKDIR /ctakes
+RUN mvn compile -DskipTests
+RUN mvn install -pl '!ctakes-distribution' -DskipTests
+
+WORKDIR /
+RUN cp /ctakes/ctakes-web-rest/target/ctakes-web-rest.war /apache-tomcat-9.0.14/webapps/
+
+ENV TOMCAT_HOME=/apache-tomcat-9.0.14
+ENV CTAKES_HOME=/ctakes
+
+EXPOSE 8080
+
+
+WORKDIR $TOMCAT_HOME
+RUN chmod u+x bin/*.sh
+
+CMD bin/catalina.sh run
Added: ctakes/trunk/ctakes-web-rest/docker/customDictionary.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/customDictionary.xml?rev=1851986&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/docker/customDictionary.xml (added)
+++ ctakes/trunk/ctakes-web-rest/docker/customDictionary.xml Wed Jan 23 21:47:02 2019
@@ -0,0 +1,94 @@
+<?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.
+-->
+
+<!-- New format for the .xml lookup specification. Uses table name and value type/class for Concept Factories. -->
+<lookupSpecification>
+ <dictionaries>
+ <dictionary>
+ <name>sno_rx_16abTerms</name>
+ <implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary</implementationName>
+ <properties>
+ <!-- urls for hsqldb memory connections must be file types in hsql 1.8.
+ These file urls must be either absolute path or relative to current working directory.
+ They cannot be based upon the classpath.
+ Though JdbcConnectionFactory will attempt to "find" a db based upon the parent dir of the url
+ for the sake of ide ease-of-use, the user should be aware of these hsql limitations.
+ -->
+ <property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
+ <property key="jdbcUrl" value="jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
+ <property key="jdbcUser" value="sa"/>
+ <property key="jdbcPass" value=""/>
+ <property key="rareWordTable" value="cui_terms"/>
+ <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
+ <property key="umlsVendor" value="NLM-6515182895"/>
+ <property key="umlsUser" value="CHANGEME"/>
+ <property key="umlsPass" value="CHANGEME"/>
+ </properties>
+ </dictionary>
+ </dictionaries>
+
+ <conceptFactories>
+ <conceptFactory>
+ <name>sno_rx_16abConcepts</name>
+ <implementationName>org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory</implementationName>
+ <properties>
+ <property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
+ <property key="jdbcUrl" value="jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
+ <property key="jdbcUser" value="sa"/>
+ <property key="jdbcPass" value=""/>
+ <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
+ <property key="umlsVendor" value="NLM-6515182895"/>
+ <property key="umlsUser" value="CHANGEME"/>
+ <property key="umlsPass" value="CHANGEME"/>
+ <property key="tuiTable" value="tui"/>
+ <property key="prefTermTable" value="prefTerm"/>
+ <!-- Optional tables for optional term info.
+ Uncommenting these lines alone may not persist term information;
+ persistence depends upon the TermConsumer. -->
+ <property key="rxnormTable" value="long"/>
+ <property key="snomedct_usTable" value="long"/>
+ </properties>
+ </conceptFactory>
+ </conceptFactories>
+
+ <!-- Defines what terms and concepts will be used -->
+ <dictionaryConceptPairs>
+ <dictionaryConceptPair>
+ <name>sno_rx_16abPair</name>
+ <dictionaryName>sno_rx_16abTerms</dictionaryName>
+ <conceptFactoryName>sno_rx_16abConcepts</conceptFactoryName>
+ </dictionaryConceptPair>
+ </dictionaryConceptPairs>
+
+ <!-- DefaultTermConsumer will persist all spans.
+ PrecisionTermConsumer will only persist only the longest overlapping span of any semantic group.
+ SemanticCleanupTermConsumer works as Precision** but also removes signs/sympoms contained within disease/disorder,
+ and (just in case) removes any s/s and d/d that are also (exactly) anatomical sites. -->
+ <rareWordConsumer>
+ <name>Term Consumer</name>
+ <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>-->
+ <implementationName>org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer</implementationName>
+ <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer</implementationName>-->
+ <properties>
+ <!-- Depending upon the consumer, the value of codingScheme may or may not be used. With the packaged consumers,
+ codingScheme is a default value used only for cuis that do not have secondary codes (snomed, rxnorm, etc.) -->
+ <property key="codingScheme" value="sno_rx_16ab"/>
+ </properties>
+ </rareWordConsumer>
+
+</lookupSpecification>
Added: ctakes/trunk/ctakes-web-rest/docker/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/pom.xml?rev=1851986&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/docker/pom.xml (added)
+++ ctakes/trunk/ctakes-web-rest/docker/pom.xml Wed Jan 23 21:47:02 2019
@@ -0,0 +1,1151 @@
+<?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>4.0.1-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:svn:https://svn.apache.org/repos/asf/ctakes/trunk</connection>
+ <developerConnection>scm:svn:https://svn.apache.org/repos/asf/ctakes/trunk</developerConnection>
+ <url>https://svn.apache.org/repos/asf/ctakes/trunk</url>
+ </scm>
+ <issueManagement>
+ <system>jira</system>
+ <url>https://issues.apache.org/jira/browse/ctakes</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 -->
+ <ant.version>1.9.2</ant.version>
+ <antlr.version>2.7.7</antlr.version>
+ <ant-contrib.version>1.0b3</ant-contrib.version>
+ <aspectj.version>1.7.3</aspectj.version>
+ <backport-util.version>3.1</backport-util.version>
+ <cglib.version>2.2.2</cglib.version>
+ <cleartk.version>2.0.0</cleartk.version>
+ <commons-beanutils.version>1.8.3</commons-beanutils.version>
+ <commons-cli.version>1.2</commons-cli.version>
+ <commons-collections.version>3.2.1</commons-collections.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-lang.version>2.6</commons-lang.version>
+ <commons-logging-api.version>1.1</commons-logging-api.version>
+ <commons-logging.version>1.1.1</commons-logging.version>
+ <commons-pool.version>1.5.4</commons-pool.version>
+ <ctakesresources.version>4.0.0</ctakesresources.version>
+ <cxf.version>2.7.8</cxf.version>
+ <diffutils.version>1.3.0</diffutils.version>
+ <dom4j.version>1.6.1</dom4j.version>
+ <ehcache.version>2.4.6</ehcache.version>
+ <exec-maven-plugin.version>1.2.1</exec-maven-plugin.version>
+ <fast-classpath-scanner.version>2.0.18</fast-classpath-scanner.version>
+ <glassfish-web.version>2.2</glassfish-web.version>
+ <hibernate.version>4.2.6.Final</hibernate.version>
+ <hsqldb.version>2.3.4</hsqldb.version>
+ <icefaces.version>2.0.2</icefaces.version>
+ <jackson.version>1.5.0</jackson.version>
+ <javassist.version>3.15.0-GA</javassist.version>
+ <jaxb.version>2.2.5</jaxb.version>
+ <jaxb2-maven-plugin.version>1.6</jaxb2-maven-plugin.version>
+ <jchronic.version>0.2.6</jchronic.version>
+ <jetty.version>9.1.0.M0</jetty.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>4.11</junit.version>
+ <jwi.version>2.2.3</jwi.version>
+ <mastif.version>1.4</mastif.version>
+ <maven-antrun-plugin.version>1.6</maven-antrun-plugin.version>
+ <maven-assembly-plugin.version>2.4</maven-assembly-plugin.version>
+ <maven-failsafe-plugin.version>2.20.1</maven-failsafe-plugin.version>
+ <maven-surefire-plugin.version>2.12.1</maven-surefire-plugin.version>
+ <maven-war-plugin.version>2.4</maven-war-plugin.version>
+ <mysql-connector.version>5.1.26</mysql-connector.version>
+ <scala-library.version>2.11.7</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>1.6.1</slf4j.version>
+ <solr.version>3.5.0</solr.version>
+ <spring.version>4.3.12.RELEASE</spring.version>
+ <uimafit.version>2.4.0</uimafit.version>
+ <uimaj.version>2.10.2</uimaj.version>
+ <timenorm.version>0.9.5</timenorm.version>
+ <weka.version>3.6.10</weka.version>
+ <xmlunit.version>1.4</xmlunit.version>
+ <!-- project specific conventions -->
+ <maven.compiler.source>1.8</maven.compiler.source>
+ <maven.compiler.target>1.8</maven.compiler.target>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ </properties>
+
+ <parent>
+ <groupId>org.apache</groupId>
+ <artifactId>apache</artifactId>
+ <version>13</version>
+ </parent>
+
+ <modules>
+ <module>ctakes-gui</module>
+ <module>ctakes-gui-res</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-assertion</module>
+ <module>ctakes-assertion-zoner</module>
+ <module>ctakes-temporal</module>
+ <module>ctakes-clinical-pipeline</module>
+ <module>ctakes-clinical-pipeline-res</module>
+ <module>ctakes-distribution</module>
+ <module>ctakes-regression-test</module>
+ <module>ctakes-assertion-res</module>
+ <module>ctakes-chunker-res</module>
+ <module>ctakes-constituency-parser-res</module>
+ <module>ctakes-core-res</module>
+ <module>ctakes-coreference-res</module>
+ <module>ctakes-dependency-parser-res</module>
+ <module>ctakes-dictionary-lookup-res</module>
+ <module>ctakes-lvg-res</module>
+ <module>ctakes-pos-tagger-res</module>
+ <module>ctakes-relation-extractor-res</module>
+ <module>ctakes-side-effect-res</module>
+ <module>ctakes-smoking-status-res</module>
+ <module>ctakes-temporal-res</module>
+ <module>ctakes-assertion-zoner-res</module>
+ <module>ctakes-drug-ner-res</module>
+ <module>ctakes-ne-contexts-res</module>
+ <module>ctakes-template-filler</module>
+ <module>ctakes-examples</module>
+ <module>ctakes-examples-res</module>
+ <module>ctakes-ytex-res</module>
+ <module>ctakes-ytex</module>
+ <module>ctakes-ytex-uima</module>
+ <module>ctakes-ytex-web</module>
+ <module>ctakes-dictionary-lookup-fast</module>
+ <module>ctakes-dictionary-lookup-fast-res</module>
+ <module>ctakes-web-rest</module>
+ </modules>
+ <dependencyManagement>
+ <dependencies>
+ <!-- cTAKES third party dependency versions -->
+ <!-- <dependency> <groupId>jama</groupId> <artifactId>jama</artifactId>
+ <version>1.0.2</version> </dependency> -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>1.2.17</version>
+ </dependency>
+ <!-- There is an xml=apis 2.0 in maven central, but it is pom only, therefore broken. -->
+ <dependency>
+ <groupId>xml-apis</groupId>
+ <artifactId>xml-apis</artifactId>
+ <version>1.4.01</version>
+ </dependency>
+ <dependency>
+ <groupId>xerces</groupId>
+ <artifactId>xercesImpl</artifactId>
+ <version>2.11.0</version>
+ </dependency>
+ <!-- TODO : Remove jdom and refactor code to jdom2 -->
+ <dependency>
+ <groupId>jdom</groupId>
+ <artifactId>jdom</artifactId>
+ <version>1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>jdom2</artifactId>
+ <version>2.0.6</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ <version>4.0.0</version>
+ </dependency>
+ <!--<dependency>-->
+ <!--<groupId>org.apache.lucene</groupId>-->
+ <!--<artifactId>lucene-parent</artifactId>-->
+ <!--<version>6.5.0</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>4.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-queryparser</artifactId>
+ <version>4.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-analyzers-common</artifactId>
+ <version>4.0.0</version>
+ </dependency>
+ <!-- TODO: remove unused dependency -->
+ <!-- dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-solr-grandparent</artifactId>
+ <version>4.0.0</version>
+ </dependency -->
+ <!-- TODO : update snowball -->
+ <!--<dependency>-->
+ <!--<groupId>org.apache.lucene</groupId>-->
+ <!--<artifactId>lucene-snowball</artifactId>-->
+ <!--<version>4.0.0</version>-->
+ <!--</dependency>-->
+ <!-- Jackson -->
+ <dependency>
+ <groupId>org.codehaus.jackson</groupId>
+ <artifactId>jackson-core-asl</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.codehaus.jackson</groupId>
+ <artifactId>jackson-mapper-asl</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
+ <!-- Mastif: Assertion Classificaiton System -->
+ <dependency>
+ <groupId>net.sf.mastif</groupId>
+ <artifactId>mastif-zoner</artifactId>
+ <version>${mastif.version}</version>
+ </dependency>
+ <!-- Scala -->
+ <dependency>
+ <groupId>org.scala-lang</groupId>
+ <artifactId>scala-library</artifactId>
+ <version>${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>${uimafit.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-tools</artifactId>
+ <version>1.7.2</version>
+ </dependency>
+ <!-- dependency is uima 2.3 -->
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-uima</artifactId>
+ <version>1.7.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-maxent</artifactId>
+ <version>3.0.3</version>
+ </dependency>
+ <!--<dependency>-->
+ <!--<groupId>org.apache.uima</groupId>-->
+ <!--<artifactId>uimaj-examples</artifactId>-->
+ <!--<version>2.9.0</version>-->
+ <!--</dependency>-->
+ <dependency>
+ <groupId>tw.edu.ntu.csie</groupId>
+ <artifactId>libsvm</artifactId>
+ <version>3.1</version>
+ </dependency>
+ <!-- import a consistent set of versions for all ClearTK modules -->
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk</artifactId>
+ <version>${cleartk.version}</version>
+ <type>pom</type>
+ <scope>import</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-ml-liblinear</artifactId>
+ <version>${cleartk.version}</version>
+ </dependency>
+ <!-- HSQL DB -->
+ <dependency>
+ <groupId>org.hsqldb</groupId>
+ <artifactId>hsqldb</artifactId>
+ <version>${hsqldb.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>args4j</groupId>
+ <artifactId>args4j</artifactId>
+ <version>2.0.16</version>
+ </dependency>
+ <dependency>
+ <groupId>com.lexicalscope.jewelcli</groupId>
+ <artifactId>jewelcli</artifactId>
+ <version>0.8.3</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.2</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>${commons-lang.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-cli</groupId>
+ <artifactId>commons-cli</artifactId>
+ <version>${commons-cli.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ <version>10.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.carrotsearch</groupId>
+ <artifactId>hppc</artifactId>
+ <version>0.4.1</version>
+ </dependency>
+ <!-- org.springframework -->
+ <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>${spring.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-context-support</artifactId>
+ <version>${spring.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-core</artifactId>
+ <version>${spring.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-jdbc</artifactId>
+ <version>${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>${spring.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.mit.findstruct</groupId>
+ <artifactId>structmulti</artifactId>
+ <version>0.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.mit.findstruct</groupId>
+ <artifactId>findstructapi</artifactId>
+ <version>0.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>com.googlecode.armbrust-file-utils</groupId>
+ <artifactId>sqlwrapper</artifactId>
+ <version>0.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.openai</groupId>
+ <artifactId>openaifsm</artifactId>
+ <version>0.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>gov.nih.nlm.nls.lvg</groupId>
+ <artifactId>lvgdist</artifactId>
+ <version>2016.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.googlecode.clearnlp</groupId>
+ <artifactId>clearnlp</artifactId>
+ <version>1.3.1</version>
+ </dependency>
+ <!-- cTAKES module versions -->
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-gui</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-gui-res</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>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-examples-res</artifactId>
+ <version>${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-core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core-res</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup-res</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup-fast</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup-fast-res</artifactId>
+ <version>${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-res</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker-res</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-lvg</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-lvg-res</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>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-clinical-pipeline-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-ne-contexts
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-ne-contexts-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-assertion
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-assertion-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-zoner</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-zoner-res</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-constituency-parser
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-constituency-parser-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-coreference
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-coreference-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-drug-ner
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-drug-ner-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-side-effect
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-side-effect-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-smoking-status
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-smoking-status-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-dependency-parser
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-dependency-parser-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-relation-extractor
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-relation-extractor-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-temporal
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-temporal-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-ytex-res
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-ytex
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-ytex-uima</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-ytex-web</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>
+ ctakes-distribution
+ </artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <!-- cTAKES Resources -->
+ <dependency>
+ <groupId>net.sourceforge.ctakesresources</groupId>
+ <artifactId>ctakes-resources-lvg2008</artifactId>
+ <version>${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>
+ <!-- XML Unit -->
+ <dependency>
+ <groupId>xmlunit</groupId>
+ <artifactId>xmlunit</artifactId>
+ <version>${xmlunit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
+ <build>
+ <!-- It's good practice to explicitly declare versions for all plugins -->
+ <pluginManagement>
+ <plugins>
+ <!-- TODO: remove dependency upon Apache Ant -->
+ <plugin>
+ <artifactId>maven-antrun-plugin</artifactId>
+ <version>${maven-antrun-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <groupId>com.mycila.maven-license-plugin</groupId>
+ <artifactId>maven-license-plugin</artifactId>
+ <version>1.9.0</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>${project.inceptionYear}</year>
+ <email>dev@ctakes.apache.org</email>
+ </properties>
+ <strictCheck>true</strictCheck>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>${maven-assembly-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-clean-plugin</artifactId>
+ <version>2.4.1</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.4</version>
+ <configuration>
+ <source>1.8</source>
+ <target>1.8</target>
+ <compilerArgument>-Xlint</compilerArgument>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-deploy-plugin</artifactId>
+ <version>2.7</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-eclipse-plugin</artifactId>
+ <version>2.9</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-gpg-plugin</artifactId>
+ <version>1.4</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-install-plugin</artifactId>
+ <version>2.3.1</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.4</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>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.9</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-resources-plugin</artifactId>
+ <version>2.5</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>2.8</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-site-plugin</artifactId>
+ <version>3.1</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-source-plugin</artifactId>
+ <version>2.1.2</version>
+ </plugin>
+ <!-- Maven expects tests to start or end with "Test", not "Tests", so
+ explicitly include files ending in "Tests" -->
+ <plugin>
+ <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-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-assertion-zoner-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-chunker-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-clinical-pipeline-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-constituency-parser-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-core-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-coreference-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-dependency-parser-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-dictionary-lookup-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-drug-ner-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-lvg-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-ne-contexts-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-pos-tagger-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-relation-extractor-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-side-effect-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-smoking-status-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-temporal-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-ytex-res/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-dictionary-lookup-fast-res/src/main/resources</additionalClasspathElement>
+ </additionalClasspathElements>
+ </configuration>
+ </plugin>
+
+ <!-- apache-rat:check validate release -->
+ <plugin>
+ <groupId>org.apache.rat</groupId>
+ <artifactId>apache-rat-plugin</artifactId>
+ <configuration>
+ <excludes>
+ <!-- generated directories -->
+ <exclude>**/target/**/*</exclude>
+ <exclude>resources/**/*</exclude>
+ <!-- version control -->
+ <exclude>.git/**/*</exclude>
+ <exclude>.gitignore</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>2.8</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>[1.0.0,)</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>${uimaj.version}</version>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+ <profiles>
+ <profile>
+ <id>disable-java8-doclint</id>
+ <activation>
+ <jdk>[1.8,)</jdk>
+ </activation>
+ <properties>
+ <additionalparam>-Xdoclint:none</additionalparam>
+ </properties>
+ </profile>
+ <!-- START SNIPPET: release-profile -->
+ <!-- !IMPORTANT: Overrides the official org.apache:apache (parent pom) -->
+ <profile>
+ <id>apache-release</id>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>${maven-surefire-plugin.version}</version>
+ <configuration>
+ <environmentVariables>
+ <ctakes.umlsuser>CHANGE_ME</ctakes.umlsuser>
+ </environmentVariables>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+ <!-- END SNIPPET: release-profile -->
+ </profiles>
+</project>
Added: ctakes/trunk/ctakes-web-rest/docker/start_rest.sh
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/start_rest.sh?rev=1851986&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/docker/start_rest.sh (added)
+++ ctakes/trunk/ctakes-web-rest/docker/start_rest.sh Wed Jan 23 21:47:02 2019
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+## Make sure there are environment variables for umls username and password
+if [ -z $ctakes_umlsuser ] ; then
+ echo "Environment variable ctakes_umlsuser must be defined"
+ exit 1
+fi
+
+if [ -z $ctakes_umlspw ] ; then
+ echo "Environment variable ctakes_umlspw must be defined"
+ exit 1
+fi
+
+## Pass in environment variables
+docker run -p 8080:8080 -e ctakes_umlsuser -e ctakes_umlspw -d ctakes-web-rest
+
Propchange: ctakes/trunk/ctakes-web-rest/docker/start_rest.sh
------------------------------------------------------------------------------
svn:executable = *