First Commit

.gitignore

+#
+# Project specific excludes
+#
+
+tomcat
+
+#
+# Default excludes
+#
+
+# Binaries
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+*.war
+*.ear
+*.sar
+*.class
+
+# Maven 
+target/
+
+# IntelliJ project files 
+*.iml
+*.iws
+*.ipr
+.idea/
+
+# eclipse project file
+.settings/
+.classpath
+.project
+
+# NetBeans specific
+nbproject/private/
+build/
+nbbuild/
+dist/
+nbdist/
+nbactions.xml
+nb-configuration.xml
+
+
+# OS
+.DS_Store
+
+# Misc
+*.swp
+release.properties
+pom.xml.releaseBackup
+pom.xml.tag
+
+#custom
+pos/
+

Dockerfile

+FROM alpine:3.9
+WORKDIR /usr/local/share/ades_relation
+
+ARG	ADES_RELATION_VERSION=1.0
+COPY	docker-build.sh /usr/local/bin/docker-build.sh
+COPY	src src
+COPY	pom.xml .
+
+RUN mkdir logs
+RUN chmod u=rwx,g=rwx,o=r /usr/local/share/ades_relation -R
+
+RUN	docker-build.sh ${ADES_RELATION_VERSION}
+

README.md

+ades-relation-extraction
+========================
+
+<b>Relation Extraction for Preclinical Adverse Drug Effect text-mining Project</b>   
+
+========================
+
+Internal project. Specific for the preclinical adverse Drug effect text-mining pipeline.  
+
+It uses the nlp-gate-generic-component; and contains specific jape rules for the relation extraction of the treatment-related findings. 
+
+This project it uses gate formated documents as input and output.  
+
+The most important information is that this project is only usefull inside the preclinical adverse drug effect pipeline.
+
+The main objective is to extract the relations between the entities and retrieve the treatment-related findings of the toxicology reports.
+
+========================
+
+
+
+		
+		

docker-build.old.sh

+#!/bin/sh
+
+BASEDIR=/usr/local
+ADES_RELATION_EXTRACTION_HOME="${BASEDIR}/share/ades_relation_extraction/"
+
+ADES_RELATION_EXTRACTION_VERSION=1.0
+
+# Exit on error
+set -e
+
+if [ $# -ge 1 ] ; then
+	ADES_RELATION_EXTRACTION_VERSION="$1"
+fi
+
+if [ -f /etc/alpine-release ] ; then
+	# Installing OpenJDK 8
+	apk add --update openjdk8-jre
+	
+	# dict tagger development dependencies
+	apk add openjdk8 git maven
+else
+	# Runtime dependencies
+	apt-get update
+	apt-get install openjdk-8-jre
+	
+	# The development dependencies
+	apt-get install openjdk-8-jdk git maven
+fi
+
+git clone --depth 1 https://github.com/inab/docker-textmining-tools.git nlp_gate_generic_component
+cd nlp_gate_generic_component
+git filter-branch --prune-empty --subdirectory-filter nlp-gate-generic-component HEAD
+mvn clean install -DskipTests
+cd ..
+#rename jar
+mv nlp_gate_generic_component/target/nlp-gate-generic-component-0.0.1-SNAPSHOT-jar-with-dependencies.jar nlp-gate-generic-component-${ADES_RELATION_EXTRACTION_VERSION}.jar
+
+cat > /usr/local/bin/ades-relation-extraction <<EOF
+#!/bin/sh
+exec java \$JAVA_OPTS -jar "${ADES_RELATION_EXTRACTION_HOME}/nlp-gate-generic-component-${ADES_RELATION_EXTRACTION_VERSION}.jar" -workdir "${ADES_RELATION_EXTRACTION_HOME}" -j jape_rules/main.jape "\$@" 
+EOF
+chmod +x /usr/local/bin/ades-relation-extraction
+
+#delete target, do not delete for now because it has the jape rules inside
+#rm -R nlp_generic_annotation
+
+#add bash for nextflow
+apk add bash
+
+if [ -f /etc/alpine-release ] ; then
+	# Removing not needed tools
+	apk del openjdk8 git maven
+	rm -rf /var/cache/apk/*
+else
+	apt-get remove openjdk-8-jdk git maven
+	rm -rf /var/cache/dpkg
+fi
+

docker-build.sh

+#!/bin/sh
+
+BASEDIR=/usr/local
+ADES_RELATION_HOME="${BASEDIR}/share/ades_relation/"
+
+ADES_RELATION_VERSION=1.0
+
+# Exit on error
+set -e
+
+if [ $# -ge 1 ] ; then
+	ADES_RELATION_VERSION="$1"
+fi
+
+if [ -f /etc/alpine-release ] ; then
+	# Installing OpenJDK 8
+	apk add --update openjdk8-jre
+	
+	# dict tagger development dependencies
+	apk add openjdk8 git maven
+else
+	# Runtime dependencies
+	apt-get update
+	apt-get install openjdk-8-jre
+	
+	# The development dependencies
+	apt-get install openjdk-8-jdk git maven
+fi
+
+mvn clean install -DskipTests
+
+#rename jar
+mv target/ades-relation-extraction-0.0.1-SNAPSHOT-jar-with-dependencies.jar ades-relation-extraction-${ADES_RELATION_VERSION}.jar
+
+cat > /usr/local/bin/ades-relation-extraction <<EOF
+#!/bin/sh
+exec java \$JAVA_OPTS -jar "${ADES_RELATION_HOME}/ades-relation-extraction-${ADES_RELATION_VERSION}.jar" -workdir "${ADES_RELATION_HOME}" "\$@"
+EOF
+chmod +x /usr/local/bin/ades-relation-extraction
+
+#delete target
+rm -R target src pom.xml
+
+#add bash for nextflow
+apk add bash
+
+if [ -f /etc/alpine-release ] ; then
+	# Removing not needed tools
+	apk del openjdk8 git maven
+	rm -rf /var/cache/apk/*
+else
+	apt-get remove openjdk-8-jdk git maven
+	rm -rf /var/cache/dpkg
+fi
+

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>es.bsc.inb.nlp</groupId>
+  <artifactId>ades-relation-extraction</artifactId>
+  <version>0.0.1-SNAPSHOT</version>
+  <packaging>jar</packaging>
+
+  <name>ades-relation-extraction</name>
+  <url>http://maven.apache.org</url>
+
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.target>1.8</maven.compiler.target>
+  </properties>
+
+  <dependencies>
+      	<dependency>
+			<groupId>uk.ac.gate</groupId>
+			<artifactId>gate-core</artifactId>
+			<version>8.5.1</version>
+		</dependency>
+		
+		<dependency>
+			<groupId>org.apache.maven.plugins</groupId>
+			<artifactId>maven-assembly-plugin</artifactId>
+			<version>3.1.0</version>
+		</dependency>
+		<dependency>
+		    <groupId>commons-cli</groupId>
+		    <artifactId>commons-cli</artifactId>
+		    <version>1.4</version>
+		</dependency>
+
+  </dependencies>
+  
+  <build>
+		<plugins>
+			<plugin>
+			    <groupId>org.apache.maven.plugins</groupId>
+			    <artifactId>maven-assembly-plugin</artifactId>
+			    <executions>
+			        <execution>
+			            <phase>package</phase>
+			            <goals>
+			                <goal>single</goal>
+			            </goals>
+			            <configuration>
+			                <archive>
+			                <manifest>
+			                    <mainClass>
+			                        es.bsc.inb.ades.relation.extraction.main.App
+			                    </mainClass>
+			                </manifest>
+			                </archive>
+			                <descriptorRefs>
+			                    <descriptorRef>jar-with-dependencies</descriptorRef>
+			                </descriptorRefs>
+			            </configuration>
+			        </execution>
+			    </executions>
+			</plugin>
+		</plugins>
+	</build>
+  
+</project>

src/main/java/es/bsc/inb/ades/relation/extraction/model/Finding.java

+package es.bsc.inb.ades.relation.extraction.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import gate.Annotation;
+
+public class Finding implements Cloneable{  
+	
+	private Integer id;
+	
+	private List<Annotation> annotations;
+	
+	public Finding(Integer id) {
+		this.id = id;
+		this.annotations = new ArrayList<Annotation>();
+	}
+
+	public Integer getId() {
+		return id;
+	}
+
+	public void setId(Integer id) {
+		this.id = id;
+	}
+
+	public List<Annotation> getAnnotations() {
+		return annotations;
+	}
+
+	public void setAnnotations(List<Annotation> annotations) {
+		this.annotations = annotations;
+	}
+
+	public void addAnnotation(Annotation finding) {
+		annotations.add(finding);
+	}
+	
+	public Finding clone() {
+		try {
+			return (Finding)super.clone();
+		} catch (CloneNotSupportedException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return null;
+	}
+
+}