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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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.reactome.server.graph</groupId>
<artifactId>graph-importer</artifactId>
<packaging>jar</packaging>
<version>1.1.0</version>
<name>GraphImporter</name>
<description>
The Graph Importer is a executable jar file to convert data taken form the Reactome MySQL Database to a Neo4j Graph Database.
For more information visit the reactome github repository.
</description>
<organization>
<name>The European Bioinformatics Institute</name>
<url>http://www.ebi.ac.uk/</url>
</organization>
<developers>
<developer>
<id>fkorn</id>
<name>Florian Korninger</name>
<email>fkorn@ebi.ac.uk</email>
<organization>http://www.ebi.ac.uk/</organization>
</developer>
<developer>
<id>fabregat</id>
<name>Antonio Fabregat</name>
<email>fabregat@ebi.ac.uk</email>
<organization>http://www.ebi.ac.uk/</organization>
</developer>
</developers>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<reactome.graph.core>1.1.20-SNAPSHOT</reactome.graph.core>
<reactome.base>1.2.20</reactome.base>
<neo4j.version>3.4.12</neo4j.version>
<interactor-core>1.0.15-SNAPSHOT</interactor-core>
<json.version>20090211</json.version>
</properties>
<dependencies>
<!--Graph core dependency, needed for accessing the model-->
<dependency>
<groupId>org.reactome.server.graph</groupId>
<artifactId>graph-core</artifactId>
<version>${reactome.graph.core}</version>
</dependency>
<!--Reactome-base for MYSQL Adapter-->
<dependency>
<groupId>org.reactome.base</groupId>
<artifactId>reactome-base</artifactId>
<version>${reactome.base}</version>
</dependency>
<!--Neo4j batch importer-->
<dependency>
<groupId>org.neo4j</groupId>
<artifactId>neo4j-kernel</artifactId>
<version>${neo4j.version}</version>
</dependency>
<dependency>
<groupId>org.neo4j</groupId>
<artifactId>neo4j-lucene-index</artifactId>
<version>${neo4j.version}</version>
</dependency>
<!--Jasp console reader-->
<dependency>
<groupId>com.martiansoftware</groupId>
<artifactId>jsap</artifactId>
<version>2.1</version>
</dependency>
<!--Org json importer-->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>${json.version}</version>
</dependency>
<!-- SQLite JDBC -->
<dependency>
<groupId>org.reactome.server.interactors</groupId>
<artifactId>interactor-core</artifactId>
<version>${interactor-core}</version>
</dependency>
<!--Logback classic-->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.1.10</version>
</dependency>
<!-- Mysql connector -->
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.47</version>
</dependency>
</dependencies>
<repositories>
<!--EBI repository-->
<repository>
<id>nexus-ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<!-- EBI SNAPSHOT repository -->
<repository>
<id>nexus-ebi-snapshot-repo</id>
<name>The EBI internal snapshot repository</name>
<url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
<build>
<finalName>${project.name}</finalName>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.5.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<archive>
<manifest>
<mainClass>org.reactome.server.graph.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<!--Concatenate all versions of org.neo4j.kernel.impl.api.scan.NativeLabelScanStoreExtension from different jars with the same name-->
<!--<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
<transformer
implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/spring.handlers</resource>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/spring.schemas</resource>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>org.reactome.server.graph.Main</Main-Class>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>-->
</plugins>
</build>
</project>