pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xmlns="http://maven.apache.org/POM/4.0.0"
         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.tools</groupId>
    <artifactId>analysis-report</artifactId>
    <version>1.1.4</version>
    <packaging>jar</packaging>

    <properties>
        <java.version>1.8</java.version>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

        <graph.core.version>1.1.20</graph.core.version>
        <analysis.core.version>3.3.0</analysis.core.version>
        <diagram.exporter>1.3.12</diagram.exporter>
        <fireworks.exporter>1.1.4</fireworks.exporter>

        <jsap.version>2.1</jsap.version>
        <junit.version>4.12</junit.version>
        <itext.version>7.1.5</itext.version>
        <jsoup.version>1.11.2</jsoup.version>
        <logback.version>1.2.3</logback.version>
        <maven.jar.version>2.6</maven.jar.version>
        <jackson.version>2.9.2</jackson.version>
        <httpclient.version>4.5.4</httpclient.version>
    </properties>

    <dependencies>
        <!-- https://mvnrepository.com/artifact/com.martiansoftware/jsap -->
        <dependency>
            <groupId>com.martiansoftware</groupId>
            <artifactId>jsap</artifactId>
            <version>${jsap.version}</version>
        </dependency>

        <!-- https://mvnrepository.com/artifact/junit/junit -->
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>${junit.version}</version>
            <scope>test</scope>
        </dependency>

        <!-- https://mvnrepository.com/artifact/ch.qos.logback/logback-classic -->
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
            <version>${logback.version}</version>
        </dependency>

        <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpclient -->
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
            <version>${httpclient.version}</version>
        </dependency>

        <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-databind</artifactId>
            <version>${jackson.version}</version>
        </dependency>

        <dependency>
            <groupId>org.reactome.server.tools</groupId>
            <artifactId>analysis-core</artifactId>
            <version>${analysis.core.version}</version>
        </dependency>
        <!-- https://mvnrepository.com/artifact/org.jsoup/jsoup -->
        <dependency>
            <groupId>org.jsoup</groupId>
            <artifactId>jsoup</artifactId>
            <version>${jsoup.version}</version>
        </dependency>

        <!-- iText -->
        <dependency>
            <groupId>com.itextpdf</groupId>
            <artifactId>kernel</artifactId>
            <version>${itext.version}</version>
        </dependency>
        <dependency>
            <groupId>com.itextpdf</groupId>
            <artifactId>io</artifactId>
            <version>${itext.version}</version>
        </dependency>
        <dependency>
            <groupId>com.itextpdf</groupId>
            <artifactId>layout</artifactId>
            <version>${itext.version}</version>
        </dependency>
        <dependency>
            <groupId>com.itextpdf</groupId>
            <artifactId>hyph</artifactId>
            <version>${itext.version}</version>
        </dependency>
        <dependency>
            <groupId>net.sourceforge.cssparser</groupId>
            <artifactId>cssparser</artifactId>
            <version>0.9.25</version>
        </dependency>

        <!-- fireworks -->
        <dependency>
            <groupId>org.reactome.server.tools</groupId>
            <artifactId>fireworks-exporter</artifactId>
            <version>${fireworks.exporter}</version>
        </dependency>
        <!-- diagrams -->
        <dependency>
            <groupId>org.reactome.server.tools</groupId>
            <artifactId>diagram-exporter</artifactId>
            <version>${diagram.exporter}</version>
        </dependency>
        <!-- graph-core -->
        <dependency>
            <groupId>org.reactome.server.graph</groupId>
            <artifactId>graph-core</artifactId>
            <version>${graph.core.version}</version>
        </dependency>
        <dependency>
            <groupId>xml-security</groupId>
            <artifactId>xml-security</artifactId>
            <version>1.0.4</version>
        </dependency>
    </dependencies>

    <repositories>
        <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 repo -->
        <repository>
            <id>nexus-ebi-snapshot-repo</id>
            <name>The EBI internal snapshot repository</name>
            <url>
                http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots/
            </url>
            <releases>
                <enabled>false</enabled>
            </releases>
            <snapshots>
                <enabled>true</enabled>
            </snapshots>
        </repository>
    </repositories>

    <!--Configures the distribution to nexus repository -->
    <distributionManagement>
        <!-- EBI repo -->
        <repository>
            <id>pst-release</id>
            <name>EBI Nexus Repository</name>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
        </repository>
        <!-- EBI SNAPSHOT repo -->
        <snapshotRepository>
            <uniqueVersion>false</uniqueVersion>
            <id>pst-snapshots</id>
            <name>EBI Nexus Snapshots Repository</name>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
        </snapshotRepository>
    </distributionManagement>
    <!--This configuration is needed so that javadoc is included in maven site-->

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.7.0</version>
                <configuration>
                    <source>1.8</source>
                    <target>1.8</target>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-jar-plugin</artifactId>
                <version>${maven.jar.version}</version>
                <configuration>
                    <excludes>
                        <exclude>**/logback.xml</exclude>
                    </excludes>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.20.1</version>
                <configuration>
                    <useSystemClassLoader>true</useSystemClassLoader>
                    <forkMode>always</forkMode>
                    <test>*Test.java</test>

                    <!-- Configure the Neo4j database for testcase -->
                    <systemPropertyVariables>
                        <neo4j.host>${neo4j.host}</neo4j.host>
                        <neo4j.port>${neo4j.port}</neo4j.port>
                        <neo4j.user>${neo4j.user}</neo4j.user>
                        <neo4j.password>${neo4j.password}</neo4j.password>
                    </systemPropertyVariables>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>