This is an automated email from the ASF dual-hosted git repository.
seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
The following commit(s) were added to refs/heads/main by this push:
new c2cac6e ctakes-web-rest docker uses actual ctakes pom, not a local
copy. Git instead of svn, mv not copy, RUN && Renamed profiles moved web-rest
profile declaration to main pom web-rest start_rest.sh use umls key instead of
username and password
c2cac6e is described below
commit c2cac6e4606c89701ec8d650cef753a74d281620
Author: Sean Finan <[email protected]>
AuthorDate: Mon Dec 26 13:43:13 2022 -0500
ctakes-web-rest docker uses actual ctakes pom, not a local copy. Git
instead of svn, mv not copy, RUN &&
Renamed profiles
moved web-rest profile declaration to main pom
web-rest start_rest.sh use umls key instead of username and password
---
ctakes-distribution/pom.xml | 4 +-
ctakes-user-resources/pom.xml | 11 +-
ctakes-web-rest/docker/Dockerfile | 24 +-
ctakes-web-rest/docker/pom.xml | 1095 ----------------------------------
ctakes-web-rest/docker/start_rest.sh | 13 +-
ctakes-web-rest/pom.xml | 57 --
ctakes-ytex-web/pom.xml | 3 +-
pom.xml | 59 +-
8 files changed, 70 insertions(+), 1196 deletions(-)
diff --git a/ctakes-distribution/pom.xml b/ctakes-distribution/pom.xml
index 53ca24a..fb4ccd4 100644
--- a/ctakes-distribution/pom.xml
+++ b/ctakes-distribution/pom.xml
@@ -163,10 +163,10 @@
<profiles>
<profile>
<!-- Because I got tired of building multiple zips when all
I wanted were jars. -->
- <id>no-build-zips</id>
+ <id>no-zips-build</id>
</profile>
<profile>
- <id>zips</id>
+ <id>zips-build</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
diff --git a/ctakes-user-resources/pom.xml b/ctakes-user-resources/pom.xml
index b69bf15..b3dc4a3 100644
--- a/ctakes-user-resources/pom.xml
+++ b/ctakes-user-resources/pom.xml
@@ -24,9 +24,8 @@
<artifactId>ctakes-user-resources</artifactId>
<name>Apache cTAKES user resources</name>
<description>For external projects to utilize user resources, e.g.
piper files and bsv definitions.</description>
-<!-- This is not a normal module. There should not be code or resources in
this module. -->
-<!-- This module, in conjunction with the main ctakes pom, creates a
ctakes-user-resources jar that can be -->
-<!-- a dependency for other projects. -->
+<!-- This is not a normal module. There should not be main code or main
resources in this module. -->
+<!-- This module creates a ctakes-user-resources jar that can be a
dependency for other projects. -->
<!-- Follow me here ... -->
<!-- 1. We want to place user resources ( pipers, regex bsvs, stop words,
etc.) in separate modules. -->
<!-- 2. For editable 'runtime' dev flexibility we want said resources in
the resources/ directory upon compile. -->
@@ -146,12 +145,6 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-ytex-uima</artifactId>
</dependency>
- <!-- <dependency>-->
- <!-- <groupId>org.apache.ctakes</groupId>-->
- <!--
<artifactId>ctakes-ytex-web</artifactId>-->
- <!-- <version>${project.version}</version>-->
- <!-- <classifier>classes</classifier>-->
- <!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-gui</artifactId>
diff --git a/ctakes-web-rest/docker/Dockerfile
b/ctakes-web-rest/docker/Dockerfile
index 1f7946a..2525bb4 100644
--- a/ctakes-web-rest/docker/Dockerfile
+++ b/ctakes-web-rest/docker/Dockerfile
@@ -1,33 +1,33 @@
FROM openjdk:8-alpine
-RUN apk update && apk add ca-certificates openssl wget unzip subversion maven
+RUN apk update && \
+ apk add --no-cache git openssh 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
+RUN wget
http://mirror.cc.columbia.edu/pub/software/apache/tomcat/tomcat-9/v9.0.14/bin/apache-tomcat-9.0.14.zip
&& \
+ 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
+RUN git clone https://github.com/apache/ctakes.git
## 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/
+RUN mkdir -p /ctakes/resources/org/apache/ctakes/dictionary/lookup/fast/ && \
+ wget -q -O dict.zip
https://downloads.sourceforge.net/project/ctakesresources/sno_rx_16ab.zip && \
+ 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
+# There is a profile to skip the building of zip distributables and
another to build the web-rest war.
+RUN mvn package -P no-zips-build,web-rest-build -DskipTests
WORKDIR /
-RUN cp /ctakes/ctakes-web-rest/target/ctakes-web-rest.war
/apache-tomcat-9.0.14/webapps/
+RUN mv /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
diff --git a/ctakes-web-rest/docker/pom.xml b/ctakes-web-rest/docker/pom.xml
deleted file mode 100644
index 110c1f3..0000000
--- a/ctakes-web-rest/docker/pom.xml
+++ /dev/null
@@ -1,1095 +0,0 @@
-<?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>5.0.0-SNAPSHOT</version>
- <packaging>pom</packaging>
- <name>Apache cTAKES</name>
- <url>http://ctakes.apache.org</url>
- <inceptionYear>2012</inceptionYear>
- <scm>
- <!-- In child modules, Maven will append ${artifactId} to the
following
- URLs -->
-
<connection>scm: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>[email protected]</subscribe>
-
<unsubscribe>[email protected]</unsubscribe>
- <post>[email protected]</post>
-
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-user/</archive>
- </mailingList>
-
- <mailingList>
- <name>Apache cTAKES Developers</name>
- <subscribe>[email protected]</subscribe>
-
<unsubscribe>[email protected]</unsubscribe>
- <post>[email protected]</post>
-
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-dev/</archive>
- </mailingList>
-
- <mailingList>
- <name>Apache cTAKES Commits</name>
-
<subscribe>[email protected]</subscribe>
-
<unsubscribe>[email protected]</unsubscribe>
-
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-commits/</archive>
- </mailingList>
-
- <mailingList>
- <name>Apache cTAKES Notifications</name>
-
<subscribe>[email protected]</subscribe>
-
<unsubscribe>[email protected]</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-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-distribution</module>
- <module>ctakes-regression-test</module>
- <module>ctakes-assertion-models</module>
- <module>ctakes-chunker-models</module>
- <module>ctakes-constituency-parser-models</module>
- <module>ctakes-core-models</module>
- <module>ctakes-coreference-models</module>
- <module>ctakes-dependency-parser-models</module>
-<!-- <module>ctakes-dependency-parser-models-clear</module>-->
- <module>ctakes-pos-tagger-models</module>
- <module>ctakes-relation-extractor-models</module>
- <module>ctakes-side-effect-models</module>
- <module>ctakes-smoking-status-models</module>
- <module>ctakes-temporal-models</module>
- <module>ctakes-template-filler</module>
- <module>ctakes-examples</module>
- <module>ctakes-ytex</module>
- <module>ctakes-ytex-uima</module>
- <module>ctakes-ytex-web</module>
- <module>ctakes-dictionary-lookup-fast</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-fhir</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-examples</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-utils</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core-models</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
-
<artifactId>ctakes-dictionary-lookup</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
-
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-preprocessor</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-pos-tagger</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
-
<artifactId>ctakes-pos-tagger-models</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-chunker</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-chunker-models</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-context-tokenizer
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-clinical-pipeline
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-ne-contexts
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-assertion
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-assertion-models
- </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-constituency-parser
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-constituency-parser-models
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-coreference
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-coreference-models
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-drug-ner
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-side-effect
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-side-effect-models
- </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-models
- </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-models
- </artifactId>
- <version>${project.version}</version>
- </dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>-->
-<!-- ctakes-dependency-parser-models-clear-->
-<!-- </artifactId>-->
-<!-- <version>${project.version}</version>-->
-<!-- </dependency>-->
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-relation-extractor
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-relation-extractor-models
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-temporal
- </artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>
- ctakes-temporal-models
- </artifactId>
- <version>${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>[email protected]</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-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-chunker-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-constituency-parser-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-core-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-coreference-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-dependency-parser-models/src/main/resources</additionalClasspathElement>
-<!--
<additionalClasspathElement>ctakes-dependency-parser-models-clear/src/main/resources</additionalClasspathElement>-->
-
<additionalClasspathElement>ctakes-pos-tagger-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-relation-extractor-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-side-effect-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-smoking-status-models/src/main/resources</additionalClasspathElement>
-
<additionalClasspathElement>ctakes-temporal-models/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>
- <executions>
- <execution>
-
<goals><goal>generate</goal></goals>
- <configuration>
-
<typeSystemIncludes>
-
<typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>
-
</typeSystemIncludes>
-
<limitToProject>true</limitToProject>
- </configuration>
- </execution>
- </executions>
- </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>
diff --git a/ctakes-web-rest/docker/start_rest.sh
b/ctakes-web-rest/docker/start_rest.sh
index acf51fa..d4ae5a9 100644
--- a/ctakes-web-rest/docker/start_rest.sh
+++ b/ctakes-web-rest/docker/start_rest.sh
@@ -1,16 +1,11 @@
#!/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"
+## Make sure there is an environment variable for the umls passkey
+if [ -z $ctakes_umls_apikey ] ; then
+ echo "Environment variable ctakes_umls_apikey must be defined"
exit 1
fi
## Pass in environment variables
-docker run -p 8080:8080 -e ctakes_umlsuser -e ctakes_umlspw -d ctakes-web-rest
+docker run -p 8080:8080 -e ctakes_umls_apikey -d ctakes-web-rest
diff --git a/ctakes-web-rest/pom.xml b/ctakes-web-rest/pom.xml
index 5661519..73f8bc2 100644
--- a/ctakes-web-rest/pom.xml
+++ b/ctakes-web-rest/pom.xml
@@ -20,8 +20,6 @@
<jettyVersion>9.2.6.v20141205</jettyVersion>
</properties>
<dependencies>
-<!-- Can I just throw ctakes in here as the main module?? -->
- <!-- cTAKES module versions-->
<!-- TODO Exclusions. See the pom files in dockhand goal/rest/pom/ -->
<dependency>
<groupId>org.apache.ctakes</groupId>
@@ -38,11 +36,6 @@
<artifactId>ctakes-core</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-core-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup</artifactId>
@@ -63,21 +56,11 @@
<artifactId>ctakes-pos-tagger</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-pos-tagger-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-chunker</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-chunker-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-lvg</artifactId>
@@ -103,11 +86,6 @@
<artifactId>ctakes-assertion</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-assertion-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-assertion-zoner</artifactId>
@@ -118,21 +96,11 @@
<artifactId>ctakes-constituency-parser</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-constituency-parser-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-coreference</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-coreference-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-drug-ner</artifactId>
@@ -143,51 +111,26 @@
<artifactId>ctakes-side-effect</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-side-effect-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-smoking-status</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-smoking-status-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dependency-parser</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-dependency-parser-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-relation-extractor</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-relation-extractor-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-temporal</artifactId>
<version>${ctakes.version}</version>
</dependency>
-<!-- <dependency>-->
-<!-- <groupId>org.apache.ctakes</groupId>-->
-<!-- <artifactId>ctakes-temporal-models</artifactId>-->
-<!-- <version>${ctakes.version}</version>-->
-<!-- </dependency>-->
<!-- ctakes-user-resources exists specifically for standalone products
like ctakes-web-rest -->
<dependency>
<groupId>org.apache.ctakes</groupId>
diff --git a/ctakes-ytex-web/pom.xml b/ctakes-ytex-web/pom.xml
index 0be17f2..9d278d9 100644
--- a/ctakes-ytex-web/pom.xml
+++ b/ctakes-ytex-web/pom.xml
@@ -195,7 +195,8 @@
</executions>
</plugin>
<plugin>
- <artifactId>maven-war-plugin</artifactId>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-war-plugin</artifactId>
<version>${maven-war-plugin.version}</version>
<configuration>
<attachClasses>true</attachClasses>
diff --git a/pom.xml b/pom.xml
index 6c6b8e9..1b27037 100644
--- a/pom.xml
+++ b/pom.xml
@@ -125,7 +125,7 @@
<maven-assembly-plugin.version>3.4.2</maven-assembly-plugin.version>
<maven-failsafe-plugin.version>2.20.1</maven-failsafe-plugin.version>
<maven-surefire-plugin.version>3.0.0-M7</maven-surefire-plugin.version>
- <maven-war-plugin.version>3.3.2</maven-war-plugin.version>
+ <maven-war-plugin.version>3.2.3</maven-war-plugin.version>
<maven-license-plugin.version>1.9.0</maven-license-plugin.version>
<maven-clean-plugin.version>3.2.0</maven-clean-plugin.version>
<maven-compiler-plugin.version>3.10.1</maven-compiler-plugin.version>
@@ -198,10 +198,9 @@
<module>ctakes-examples</module>
<module>ctakes-ytex</module>
<module>ctakes-ytex-uima</module>
- <!-- <module>ctakes-ytex-web</module>-->
<module>ctakes-dictionary-lookup-fast</module>
<module>ctakes-dockhand</module>
- <module>ctakes-tiny-rest</module>
+ <module>ctakes-tiny-rest</module>
<module>ctakes-user-resources</module>
</modules>
<dependencyManagement>
@@ -724,11 +723,6 @@
<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>
@@ -1096,6 +1090,50 @@
</pluginManagement>
</build>
<profiles>
+
+ <profile>
+ <!-- ctakes-web-rest contains a full copy of
ctakes in its target/WEB-INF/lib -->
+ <!-- and another full copy in
target/ctakes-web-rest.war -->
+ <!-- This requires over 1.75 GB of disk
space, in addition to extra build time. -->
+ <!-- We do not distribute the
ctakes-web-rest.war with the ctakes distributable, so why build it? -->
+ <!-- It can be built when wanted by enabling
this profile ( web-rest-build ). -->
+ <id>web-rest-build</id>
+ <modules>
+ <module>ctakes-web-rest</module>
+ </modules>
+ <dependencyManagement>
+ <dependencies>
+ <dependency>
+
<groupId>org.apache.ctakes</groupId>
+
<artifactId>ctakes-web-rest</artifactId>
+
<version>${project.version}</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
+ </profile>
+
+ <profile>
+ <!-- ctakes-ytex-web contains a full copy of
ctakes in its target/WEB-INF/lib -->
+ <!-- and another full copy in
target/ctakes-ytex-web.war -->
+ <!-- This requires over 1.75 GB of disk
space, in addition to extra build time. -->
+ <!-- We do not distribute the
ctakes-web-rest.war with the ctakes distributable, so why build it? -->
+ <!-- It can be built when wanted by enabling
this profile ( web-rest-build ). -->
+ <id>ytex-web-build</id>
+ <modules>
+ <module>ctakes-ytex-web</module>
+ </modules>
+ <dependencyManagement>
+ <dependencies>
+ <dependency>
+
<groupId>org.apache.ctakes</groupId>
+
<artifactId>ctakes-ytex-web</artifactId>
+
<version>${project.version}</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
+ </profile>
+
+
<profile>
<id>disable-java8-doclint</id>
<activation>
@@ -1105,11 +1143,10 @@
<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>
+ <build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@@ -1124,6 +1161,6 @@
</plugins>
</build>
</profile>
- <!-- END SNIPPET: release-profile -->
+
</profiles>
</project>
