ctakes-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From tm...@apache.org
Subject svn commit: r1851986 - in /ctakes/trunk/ctakes-web-rest/docker: ./ Default.piper Dockerfile customDictionary.xml pom.xml start_rest.sh
Date Wed, 23 Jan 2019 21:47:03 GMT
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 = *



Mime
View raw message