First release

.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path=".apt_generated">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.gitignore

+/.apt_generated/
+/target/

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Limsi-SourceExtractor</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.springframework.ide.eclipse.core.springbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+		<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
+		<nature>org.springframework.ide.eclipse.core.springnature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+		<nature>org.eclipse.wst.jsdt.core.jsNature</nature>
+	</natures>
+</projectDescription>

.settings/.jsdtscope

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry excluding="**/bower_components/*|**/node_modules/*|**/*.min.js" kind="src" path="src/main/webapp"/>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.WebProject">
+		<attributes>
+			<attribute name="hide" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.baseBrowserLibrary"/>
+	<classpathentry kind="output" path=""/>
+</classpath>

.settings/org.eclipse.core.resources.prefs

+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding/<project>=UTF-8

.settings/org.eclipse.jdt.apt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.apt.aptEnabled=true

.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.processAnnotations=enabled
+org.eclipse.jdt.core.compiler.source=1.8

.settings/org.eclipse.m2e.core.prefs

+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

.settings/org.eclipse.wst.common.component

+<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
+    <wb-module deploy-name="limsiSourceExtractor">
+        <wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
+        <wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
+        <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
+        <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
+        <wb-resource deploy-path="/WEB-INF/classes" source-path="/.apt_generated"/>
+        <property name="java-output-path" value="/Limsi-SourceExtractor/target/classes"/>
+        <property name="context-root" value="limsiSourceExtractor"/>
+    </wb-module>
+</project-modules>

.settings/org.eclipse.wst.common.project.facet.core.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <fixed facet="wst.jsdt.web"/>
+  <installed facet="java" version="1.8"/>
+  <installed facet="jst.web" version="3.1"/>
+  <installed facet="wst.jsdt.web" version="1.0"/>
+</faceted-project>

.settings/org.eclipse.wst.jsdt.ui.superType.container

+org.eclipse.wst.jsdt.launching.baseBrowserLibrary
\ No newline at end of file

.settings/org.eclipse.wst.jsdt.ui.superType.name

+Window
\ No newline at end of file

.settings/org.eclipse.wst.validation.prefs

+disabled=06target
+eclipse.preferences.version=1

Readme.md

+# Limsi-SourceExtractor
+
+## Abstract
+
+This is a code refactoring of Limsi's source extractor program in order to expose source extraction as a web service.
+This is a Spring Boot application deployed in a Docker image. 
+
+## Project requirement
+This is a Java/Spring boot project. All dependencies are setup in a Maven pom.
+On Macos X or Windows workstation, Docker should be install [https://www.docker.com/docker-toolbox](https://www.docker.com/docker-toolbox)
+
++ Java Oracle JDK8 [http://www.oracle.com/technetwork/java/javase/downloads/index.html](http://www.oracle.com/technetwork/java/javase/downloads/index.html)
++ Apache Maven [https://maven.apache.org/download.cgi](https://maven.apache.org/download.cgi)
++ Docker [https://www.docker.com/docker-toolbox](https://www.docker.com/docker-toolbox)
+
+
+
+## Run and Build project
+### Run localy
++ Change `application.yml` in `PROJECT_HOME/Limsi-SourceExtractor/src/test/configuration` with local lib and resources path (change PROJECT_HOME). Required absolute path.
+
+    resource: 
+     #Directory containing the librairies and models
+     lib: PROJECT_HOME/Limsi-SourceExtractor/lib
+     #Directory containing the language-dependent resources
+     resources: PROJECT_HOME/Limsi-SourceExtractor/resources
+
++ `mvn clean install`
++ Goto to `target` directory
++ Run in a terminal `java -Dspring.config.location=../src/test/configuration/ -jar limsiSourceExtractor.jar` 
+
+If running from IDE (eclipse), VM argument `java -Dspring.config.location=src/test/configuration/` must be added in the "Run configuration".
+
+#### Troubleshooting
++ Application do not find `lib` and `resources` path at startup:
+ 
+	=> check that application.yml set the correct path for lib and resources
+	=> -Dspring.configuration path should end with /
+	
+#### Bug
++ Service stop on MacosX during extraction with wapiti's message `error: invalid model format` (This is not happening running inside eclipse ...)
+
+### Run with Docker
+####Use default resources
+Models and resources are embedded by default in the docker image.
++ Build docker image `mvn clean package docker:build`
++ Start default image `docker run -p 8080:8080 -t limsi-source-extractor`
+
+####Custom resources/lib
+Build image can be used with new traing set. In this case it is possible to overwrite default model configuration.
+
+In the docker image volumes have been setup to mount new resources.
++ `lib` folder should be mount to `/configuration/lib`
++ `resources` folder should be mount to `/configuration/resources`
++ Configuration file from PROJECT_HOME/Limsi-SourceExtractor/configuration/ that define `application.yml`  whith docker Volumes must be use.
+
++ Run docker image with mount resources:
+
+    docker run -p 8080:8080 -v /PROJECT_HOME/Limsi-SourceExtractor/configuration:/configuration -v /PROJECT_HOME/Limsi-SourceExtractor/lib:/configuration/lib -v /PROJECT_HOME/Limsi-SourceExtractor/resources:/configuration/resources -t limsi-source-extractor
+
+#### Docker cheat sheet
+
++ List images `docker images`
++ List containers `docker ps -a`
++ Stop container `docker stop <container_name>`
++ Start container `docker start <container_name>`
++ Remove stop containers `docker rm $(docker ps -a -q)`
++ Remove image `docker rmi <image_name>`
++ Load image from file `docker load < image_file.tar`
++ Export image `docker export > image_file.tar`
+
+## Test
+HTTP GET http://localhost:8080/sourceExtractor/
+
+    =>HTTP 200 "Greetings from Spring Boot!"
+    
+HTTP POST http://localhost:8080/sourceExtractor/extractNewsML
+Charset text/xml
+
+    curl -XPOST -H "Content-Type: text/xml" -d @afp.com-20150123T153420Z-TX-PAR-SZS52.xml http://localhost:8080/sourceExtractor/extractNewsML
+
+

configuration/application.yml

+server:
+ context-path: /sourceExtractor
+ 
+resource: 
+ #Directory containing the librairies and models
+ #lib: /Users/bertrand/Documents/eclipse-workspace/afp-asrael/Limsi-SourceExtractor/lib
+ lib: /configuration/lib
+ #Directory containing the language-dependent resources
+ resources: /configuration/resources
+ #Directory containing trained data
+ data: /home/xtannier/Recherche/SourceExtractor
+
+logging:
+  level:
+    fr.limsi.sourceExtractor: info 
\ No newline at end of file

pom.xml

+<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>Limsi-SourceExtractor</groupId>
+	<artifactId>Limsi-SourceExtractor</artifactId>
+	<version>0.0.1-SNAPSHOT</version>
+	<!-- <packaging>war</packaging> -->
+	<parent>
+		<groupId>org.springframework.boot</groupId>
+		<artifactId>spring-boot-starter-parent</artifactId>
+		<version>1.5.2.RELEASE</version>
+	</parent>
+	<name>LimsiSourceExtractor</name>
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+	</properties>
+	<build>
+		<finalName>limsiSourceExtractor</finalName>
+		<resources>
+			<resource>
+				<directory>src/main/resources</directory>
+			</resource>
+		</resources>
+		<plugins>
+			<plugin>
+				<groupId>org.springframework.boot</groupId>
+				<artifactId>spring-boot-maven-plugin</artifactId>
+				<configuration>
+					<includeSystemScope>true</includeSystemScope>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>com.spotify</groupId>
+				<artifactId>docker-maven-plugin</artifactId>
+				<version>1.0.0</version>
+				<configuration>
+					<imageName>limsi-source-extractor</imageName>
+					<dockerDirectory>src/main/docker</dockerDirectory>
+					<resources>
+						<resource>
+							<targetPath>/</targetPath>
+							<directory>${project.build.directory}</directory>
+							<include>${project.build.finalName}.jar</include>
+						</resource>
+						<resource>
+							<targetPath>/</targetPath>
+							<directory>${project.basedir}</directory>
+							<includes>
+								<include>lib/**/*</include>
+								<include>resources/**/*</include>
+							</includes>
+							<excludes>
+								<exclude>lib/jar/**/*</exclude>
+								<exclude>**/.*</exclude>
+							</excludes>
+						</resource>
+					</resources>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+	<dependencies>
+		<dependency>
+			<groupId>edu.stanford.nlp</groupId>
+			<artifactId>stanford-corenlp</artifactId>
+			<version>3.7.0</version>
+			<exclusions>
+				<exclusion>
+					<groupId>com.io7m.xom</groupId>
+					<artifactId>xom</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.maltparser</groupId>
+			<artifactId>maltparser</artifactId>
+			<version>1.9.0</version>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+			<version>21.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.grobid</groupId>
+			<artifactId>grobid-core</artifactId>
+			<version>0.4.1</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-log4j12</artifactId>
+				</exclusion>
+				<exclusion></exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>edu.stanford.nlp</groupId>
+			<artifactId>stanford-french-corenlp-2016-01-14-models</artifactId>
+			<version>3.7.0</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jar/stanford-french-corenlp-2016-01-14-models.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>fr.limsi.wapiti</groupId>
+			<artifactId>wapiti-win</artifactId>
+			<version>1.5.0</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jar/wapiti-1.5.0-win.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>net.sf</groupId>
+			<artifactId>hfst</artifactId>
+			<version>1.0</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jar/hfst-ol.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.5</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-lang3</artifactId>
+			<version>3.4</version>
+		</dependency>
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+			<version>1.3.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-collections4</artifactId>
+			<version>4.1</version>
+		</dependency>
+		<!-- Dépendances couche de service -->
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-configuration-processor</artifactId>
+			<optional>true</optional>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-tomcat</artifactId>
+			<scope>provided</scope>
+		</dependency>
+		<!-- <dependency> -->
+		<!-- <groupId>org.springframework.boot</groupId> -->
+		<!-- <artifactId>spring-boot-starter-actuator</artifactId> -->
+		<!-- </dependency> -->
+	</dependencies>
+</project>
\ No newline at end of file

resources/fr/AhmetAkerLemmatizer_ressources/dictionaries/fr/conjDic.txt

+car===car;
+quand===quand;
+parce que===parce que;parceque;
+pourquoi===pourquoi;pourquoy;
+néanmoins===néanmoins;
+soit===soit;
+tandis===tandis;
+d'où===d'où;
+puis===puis;
+cependant===cependant;
+quoique===quoique;quoiqu';
+aussi===aussi;
+et/ou===et/ou;
+ou===ou;
+&===&;
+or===or;
+mais===mais;
+alors===alors;
+comme===comme;
+si===si;
+non===non;
+sinon===sinon;
+afin===afin;
+lorsque===lorsque;lorsqu';
+pis===pis;
+ni===ni;
+et===et;
+pi===pi;
+puisque===puisque;puisqu';

resources/fr/AhmetAkerLemmatizer_ressources/dictionaries/fr/detDic.txt

+de===des;
+son===ses;
+ce===cet;
+de===de;
+son===leur;
+ledit===ledit;
+mon===ma;
+mon===mes;
+ton===ta;
+ton===ton;
+votre===vos;
+leur===leurs;
+le===les;
+mon===mon;
+votre===votre;
+son===son;
+un===un;
+notre===notre;
+notre===nos;
+le===l';
+le===le;
+son===sa;
+un===une;
+le===la;
+ce===ce;
+ton===tes;

resources/fr/AhmetAkerLemmatizer_ressources/dictionaries/fr/particlesDic.txt

+tu===tu;
+ne===ne;
+-ci===-ci;
+-là===-là;
+ô===ô;
+parce===parce;

resources/fr/AhmetAkerLemmatizer_ressources/dictionaries/fr/prepDic.txt

+voici===voici;
+depuis===depuis;
+avant===avant;
+ca===ca;
+jusqu'à===jusqu'à;
+vs===vs;
+selon===selon;
+par===par;
+de===de;
+sur===sur;
+excepté===excepté;
+pour===pour;
+par-delà===par-delà;
+entre===entre;
+derrière===derrière;
+jusque===jusque;jusques;
+circa===circa;
+lez===lez;
+devant===devant;
+après===après;
+parmi===parmi;
+auprès===auprès;
+sous===sous;
+s/===s/;
+avec===avec;
+sauf===sauf;
+au-delà===au-delà;
+durant===durant;
+ci-contre===ci-contre;
+dans===dans;
+hormis===hormis;
+dès===dès;
+à===à;
+contre===contre;
+au-dessus===au-dessus;
+concernant===concernant;
+au-dessous===au-dessous;
+moins===moins;
+pendant===pendant;
+dedans===dedans;
+sans===sans;
+devers===devers;
+malgré===malgré;
+vers===vers;
+en===en;
+ès===ès;
+autour===autour;
+dessous===dessous;

resources/fr/AhmetAkerLemmatizer_ressources/dictionaries/fr/pronounDic.txt

+lequel===lesquels;
+quelqu'un===quelqu'un;quelqu'une;
+celui===celuy;
+quiconque===quiconque;
+moi-même===moi-même;
+rien===rien;
+lequel===lequel;
+tel===tel;
+te===te;
+toi-même===toi-même;
+chacun===chacun;
+quel===quelles;
+elle===elles;
+cela===cela;
+vôtre===vôtre;
+lui===lui;
+quelque===quelque;
+leur===leur;leurs;
+votre===vostre;
+on===on;
+quoi===quoy;
+aucun===aucun;aucune;
+lui-même===lui-même;
+ceci===ceci;
+notre===nostre;
+mien===miens;
+moi===moi;
+certain===certains;
+ça===ça;
+se===se;
+celui-ci===celui-ci;
+nous-même===nous-mêmes;
+celui===celui;
+grand-chose===grand-chose;
+autrui===autrui;
+mien===mien;
+soi===soi;
+le===le;
+dont===dont;