Hi Gandhi,
The setting were out-of-the-box. Tried both the trunk branches for both
github and svn.
pom.xml is attached.
Thanks!
On Mon, Sep 30, 2019 at 9:53 AM gandhi rajan <gandhiraja...@gmail.com>
wrote:
> Hi Greg, Can you check you pom.xml and see if you have enabled any
> sonarqube related profile Iin build?
>
> On Sunday, September 29, 2019, Greg Silverman <g...@umn.edu> wrote:
>
> > Trying to do the maven build and getting the following error: "You're not
> > authorized to execute any SonarQube analysis. Please contact your
> SonarQube
> > administrator."
> >
> > Please advise. I'm under a pretty tight time line to get these files
> > processed.
> >
> > Thanks!
> >
> > Greg--
> >
> >
> > On Sun, Sep 29, 2019 at 10:56 AM Greg Silverman <g...@umn.edu> wrote:
> >
> > > Never mind! I see I have to build from source.
> > >
> > > Greg--
> > >
> > > On Sun, Sep 29, 2019 at 10:44 AM Greg Silverman <g...@umn.edu> wrote:
> > >
> > >> Hi Sean,
> > >> I just ran another set of notes through cTAKES and noticed the
> following
> > >> error:
> > >>
> > >> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy
> HH:mm:ss}
> > >> %5p %c{1} - %m%n].
> > >> log4j: Adding appender named [consoleAppender] to category [root].
> > >> 29 Sep 2019 15:31:21 ERROR PiperFileReader - Piper File not found:
> > >> WindowedAttributeCleartkSubPipe
> > >>
> > >> Is something missing? This is how my DefaultFastPipeline.piper file
> > looks
> > >> (NB: I also tried load WindowedAttributeCleartkSubPipe.piper, with
> > similar
> > >> results)
> > >>
> > >> // Commands and parameters to create a default plaintext document
> > >> processing pipeline with UMLS lookup
> > >>
> > >> // Load a simple token processing pipeline from another pipeline file
> > >> load DefaultTokenizerPipeline.piper
> > >>
> > >> // Add non-core annotators
> > >> add ContextDependentTokenizerAnnotator
> > >> addDescription POSTagger
> > >>
> > >> // Add Chunkers
> > >> load ChunkerSubPipe.piper
> > >>
> > >> // Default fast dictionary lookup
> > >> add DefaultJCasTermAnnotator
> > >>
> > >> // Add Cleartk Entity Attribute annotators
> > >> // see https://issues.apache.org/jira/browse/CTAKES-449
> > >> //load AttributeCleartkSubPipe.piper
> > >> load WindowedAttributeCleartkSubPipe
> > >>
> > >>
> > >> All files seem to have been processed fine, but wondering if something
> > >> was missed, due to the error. If so, how do I construct the
> > >> WindowedAttributeCleartkSubPipe.piper file?
> > >>
> > >> Thanks very much in advance!
> > >>
> > >> Greg--
> > >>
> > >>
> > >> On Tue, Sep 24, 2019 at 7:27 PM Greg Silverman <g...@umn.edu> wrote:
> > >>
> > >>> Sweet! That was definitely it! It's flying now (granted, our files
> are
> > >>> not in the > 1 mb realm, like it the jira issue - just in the nnn.kb
> > realm,
> > >>> but still!).
> > >>>
> > >>> Mahalo nui loa!
> > >>>
> > >>>
> > >>>
> > >>> On Tue, Sep 24, 2019 at 6:29 PM Finan, Sean <
> > >>> sean.fi...@childrens.harvard.edu> wrote:
> > >>>
> > >>>> Hi Greg,
> > >>>>
> > >>>> Check your log to see what component is taking all the time.
> > >>>>
> > >>>> There is a known problem with the cleartk assertion annotators:
> > >>>>
> > >>>> https://issues.apache.org/jira/browse/CTAKES-449
> > >>>>
> > >>>> A partial fix was made in the "windowed" sub-package of
> > >>>> ctakes-assertion: org.apache.ctakes.assertion.
> > medfacts.cleartk.windowed.
> > >>>>
> > >>>> Each of the normal assertion engines has a replacement in the
> windowed
> > >>>> package.
> > >>>>
> > >>>> If you are using a piper file that contains "load
> > >>>> AttributeCleartkSubPipe" as the Default clinical pipeline does, just
> > >>>> replace it with "load WindowedAttributeCleartkSubPipe".
> > >>>>
> > >>>> It isn't a full fix for the problem, and I don't know if it will
> make
> > >>>> your processing faster, but you can give it a try.
> > >>>>
> > >>>> Sean
> > >>>>
> > >>>> ________________________________________
> > >>>> From: Greg Silverman <g...@umn.edu>
> > >>>> Sent: Tuesday, September 24, 2019 6:47 PM
> > >>>> To: dev@ctakes.apache.org
> > >>>> Subject: Large files taking forever to process [EXTERNAL]
> > >>>>
> > >>>> Any suggestions on how to speed up processing large clinical text
> > notes
> > >>>> approaching 13K lines? This is a very old corpus culled from EPIC
> > notes
> > >>>> back in 2009. I thought about splitting the notes into smaller
> chunks,
> > >>>> but
> > >>>> then I would have to deal with the offsets when analyzing system
> > output
> > >>>> against manual annotations that had been done.
> > >>>>
> > >>>> As is, I've tried different garbage collection options (this seemed
> to
> > >>>> have
> > >>>> worked well with CLAMP on the same set of notes).
> > >>>>
> > >>>> TIA!
> > >>>>
> > >>>> Greg--
> > >>>>
> > >>>> --
> > >>>> Greg M. Silverman
> > >>>> Senior Systems Developer
> > >>>> NLP/IE <
> > >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__
> > healthinformatics.umn.edu_research_nlpie-2Dgroup&d=
> > DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=kVCVyGR2m-zb7CsPmrrCeBL1N-
> > 9Z6tXZOp869xqkcBQ&s=TEirYUPMXTOjZ1PoJMxTXt7M8I5axwQI9zzNrvLmGRo&e=
> > >>>> >
> > >>>> Department of Surgery
> > >>>> University of Minnesota
> > >>>> g...@umn.edu
> > >>>>
> > >>>> › evaluate-it.org ‹
> > >>>>
> > >>>
> > >>>
> > >>> --
> > >>> Greg M. Silverman
> > >>> Senior Systems Developer
> > >>> NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
> > >>> Department of Surgery
> > >>> University of Minnesota
> > >>> g...@umn.edu
> > >>>
> > >>> › evaluate-it.org ‹
> > >>>
> > >>
> > >>
> > >> --
> > >> Greg M. Silverman
> > >> Senior Systems Developer
> > >> NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
> > >> Department of Surgery
> > >> University of Minnesota
> > >> g...@umn.edu
> > >>
> > >> › evaluate-it.org ‹
> > >>
> > >
> > >
> > > --
> > > Greg M. Silverman
> > > Senior Systems Developer
> > > NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
> > > Department of Surgery
> > > University of Minnesota
> > > g...@umn.edu
> > >
> > > › evaluate-it.org ‹
> > >
> >
> >
> > --
> > Greg M. Silverman
> > Senior Systems Developer
> > NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
> > Department of Surgery
> > University of Minnesota
> > g...@umn.edu
> >
> > › evaluate-it.org ‹
> >
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
--
Greg M. Silverman
Senior Systems Developer
NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
g...@umn.edu
› evaluate-it.org ‹
<?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-subscr...@ctakes.apache.org</subscribe>
<unsubscribe>user-unsubscr...@ctakes.apache.org</unsubscribe>
<post>u...@ctakes.apache.org</post>
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-user/</archive>
</mailingList>
<mailingList>
<name>Apache cTAKES Developers</name>
<subscribe>dev-subscr...@ctakes.apache.org</subscribe>
<unsubscribe>dev-unsubscr...@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-subscr...@ctakes.apache.org</subscribe>
<unsubscribe>commits-unsubscr...@ctakes.apache.org</unsubscribe>
<archive>http://mail-archives.apache.org/mod_mbox/ctakes-commits/</archive>
</mailingList>
<mailingList>
<name>Apache cTAKES Notifications</name>
<subscribe>notifications-subscr...@ctakes.apache.org</subscribe>
<unsubscribe>notifications-unsubscr...@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>
</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>
