<?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>

    <parent>
        <groupId>uk.ac.ebi.ddi.arrayexpress</groupId>
        <artifactId>arrayexpress-reader</artifactId>
        <version>0.1</version>
    </parent>

    <artifactId>arrayexpress-cli</artifactId>
    <version>0.2.2</version>


    <name>arrayexpress-cli</name>
    <description>Read and create the ebe files from MetabolomeWorbench submissions</description>

    <properties>
       <!-- slf4j dependency -->
        <rome.version>1.0</rome.version>
    </properties>

    <dependencies>

        <!--Spring-->
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-web</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-test</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context-support</artifactId>
        </dependency>

        <!-- logging dependencies -->
        <!-- logging dependencies -->
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>jcl-over-slf4j</artifactId>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-core</artifactId>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
        </dependency>

        <!--jUnit-->
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
        </dependency>

        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
        </dependency>

        <!-- jaxb dependencies-->
        <dependency>
            <groupId>com.sun.xml.bind</groupId>
            <artifactId>jaxb-impl</artifactId>
        </dependency>
        <dependency>
            <groupId>com.sun.xml.bind</groupId>
            <artifactId>jaxb-xjc</artifactId>
        </dependency>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-lang3</artifactId>
        </dependency>

        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
        </dependency>

        <dependency>
            <groupId>uk.ac.ebi.ddi.arrayexpress.readers</groupId>
            <artifactId>experiments-reader</artifactId>
            <version>1.1</version>
        </dependency>

        <dependency>
            <groupId>uk.ac.ebi.ddi.arrayexpress.readers</groupId>
            <artifactId>protocols-reader</artifactId>
            <version>1.1</version>
        </dependency>

        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
        </dependency>

        <dependency>
            <groupId>uk.ac.ebi.ddi</groupId>
            <artifactId>ddi-validator</artifactId>
            <version>1.0</version>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <!-- you can use this plugin to generate the unimod object model from
                     the schema and binding files specified below. Note: this will
                     need an explicit maven goal call, since it is not integrated
                     into the standard mvn life cycle. The goal to use is:
                     org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.6.3:generate

                     NOTE: the code generation may overwrite existing classes, so care
                           should be taken with files that were manually modified.
                 -->
                <groupId>org.jvnet.jaxb2.maven2</groupId>
                <artifactId>maven-jaxb2-plugin</artifactId>
                <version>0.7.3</version>

                <configuration>
                    <extension>true</extension>
                    <schemaDirectory>src/main/resources</schemaDirectory>
                    <schemaIncludes>
                        <include>experiments.xsd</include>
                    </schemaIncludes>
                    <bindingDirectory>src/main/resources</bindingDirectory>
                    <bindingIncludes>
                        <include>bindings.xjb</include>
                        <!--<include>pride-unimod-bindings.xjb</include>-->
                    </bindingIncludes>
                    <generateDirectory>src/main/java2</generateDirectory>
                    <removeOldOutput>false</removeOldOutput>
                    <forceRegenerate>true</forceRegenerate>
                    <verbose>true</verbose>
                    <args>
                        <arg>-no-header</arg>
                    </args>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-checkstyle-plugin</artifactId>
                <version>${maven.checkstyle.version}</version>
                <executions>
                    <execution>
                        <id>checkstyle</id>
                        <phase>validate</phase>
                        <goals>
                            <goal>check</goal>
                        </goals>
                        <configuration>
                            <failOnViolation>true</failOnViolation>
                            <consoleOutput>true</consoleOutput>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
</project>
