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>uk.ac.ebi.pride.archive</groupId>
    <artifactId>archive-px-xml-generator</artifactId>
    <version>1.0.34-SNAPSHOT</version>
    <packaging>jar</packaging>

    <parent>
        <groupId>uk.ac.ebi.pride.architectural</groupId>
        <artifactId>pride-core</artifactId>
        <version>1.0.3</version>
    </parent>

    <name>ProteomeXchange XML file generator for PRIDE Archive</name>
    <description>Java object model for writing, updating, reading, validating, and posting of ProteomeXchange XML
        messages.
    </description>
    <url>https://github.com/PRIDE-Archive/archive-px-xml-generator</url>

    <developers>
        <developer>
            <id>mbernal</id>
            <name>Manuel Bernal-Llinares</name>
            <organization>Proteomics Team, EMBL-European Bioinformatics Institute</organization>
            <organizationUrl>http://www.ebi.ac.uk/pride</organizationUrl>
            <roles>
                <role>developer</role>
            </roles>
            <timezone>Europe/London</timezone>
        </developer>
        <developer>
            <id>tobias</id>
            <name>Tobias Ternent</name>
            <email>tobias@ebi.ac.uk</email>
            <organization>European Bioinformatics Institute</organization>
        </developer>
        <developer>
            <id>sureshhewabi</id>
            <name>Suresh Hewapathirana</name>
            <organization>Proteomics Team, EMBL-European Bioinformatics Institute</organization>
            <organizationUrl>http://www.ebi.ac.uk/pride</organizationUrl>
            <timezone>Europe/London</timezone>
        </developer>
    </developers>

    <contributors>
        <contributor>
            <name>Florian Reisinger</name>
            <email>florian@ebi.ac.uk</email>
            <organization>European Bioinformatics Institute</organization>
        </contributor>
        <contributor>
            <name>Daniel Rios</name>
            <email>dani@ebi.ac.uk</email>
            <organization>European Bioinformatics Institute</organization>
        </contributor>
        <contributor>
            <name>Jose A. Dianes</name>
            <email>jdianes@ebi.ac.uk</email>
            <organization>European Bioinformatics Institute</organization>
        </contributor>
    </contributors>
    <organization>
        <name>European Bioinformatics Institute</name>
        <url>http://www.ebi.ac.uk</url>
    </organization>

    <properties>
        <!-- Logging capabilities -->
        <uk.ac.ebi.pride.architectural-pride-logging.version>1.0.0</uk.ac.ebi.pride.architectural-pride-logging.version>
        <!-- TDD -->
        <uk.ac.ebi.pride.architectural-pride-tdd.version>1.0.3</uk.ac.ebi.pride.architectural-pride-tdd.version>
        <uk.ac.ebi.pride.tools-xmlSchemaValidator.version>2.1</uk.ac.ebi.pride.tools-xmlSchemaValidator.version>
        <uk.ac.ebi.pride-px-submission-core.version>2.1.0-SNAPSHOT</uk.ac.ebi.pride-px-submission-core.version>
        <uk.ac.ebi.pride.pubmed-pubmed-id-fetcher.version>2.0.8-SNAPSHOT</uk.ac.ebi.pride.pubmed-pubmed-id-fetcher.version>
    </properties>

    <dependencies>
        <dependency>
            <groupId>uk.ac.ebi.pride</groupId>
            <artifactId>px-submission-core</artifactId>
            <version>${uk.ac.ebi.pride-px-submission-core.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>org.slf4j</groupId>
                    <artifactId>jcl-over-slf4j</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-lang3</artifactId>
            <version>3.5</version>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
            <version>2.5</version>
        </dependency>
        <dependency>
            <groupId>uk.ac.ebi.pride.pubmed</groupId>
            <artifactId>pubmed-id-fetcher</artifactId>
            <version>${uk.ac.ebi.pride.pubmed-pubmed-id-fetcher.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpmime</artifactId>
            <version>4.5.7</version>
        </dependency>
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpcore</artifactId>
            <version>4.4</version>
        </dependency>
        <!-- Used to work with the older excel file format - `.xls` -->
        <!-- https://mvnrepository.com/artifact/org.apache.poi/poi -->
        <dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi</artifactId>
            <version>3.17</version>
        </dependency>
        <!-- Used to work with the newer excel file format - `.xlsx` -->
        <!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
        <dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi-ooxml</artifactId>
            <version>3.17</version>
        </dependency>
        <dependency>
            <groupId>uk.ac.ebi.pride.tools</groupId>
            <artifactId>xmlSchemaValidator</artifactId>
            <version>${uk.ac.ebi.pride.tools-xmlSchemaValidator.version}</version>
        </dependency>
        <dependency>
            <groupId>uk.ac.ebi.pride.architectural</groupId>
            <artifactId>pride-logging</artifactId>
            <type>pom</type>
            <version>${uk.ac.ebi.pride.architectural-pride-logging.version}</version>
        </dependency>
        <dependency>
            <groupId>uk.ac.ebi.pride.architectural</groupId>
            <artifactId>pride-tdd</artifactId>
            <type>pom</type>
            <version>${uk.ac.ebi.pride.architectural-pride-tdd.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <!-- jsoup HTML parser library -->
            <groupId>org.jsoup</groupId>
            <artifactId>jsoup</artifactId>
            <version>1.15.3</version>
        </dependency>
    </dependencies>

    <build>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
            </resource>
        </resources>
        <plugins>
            <!-- maven-source-plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
            </plugin>

            <!-- maven-jaxb2-plugin (generate model classes from XML Schema file) -->
            <plugin>
                <!-- you can use this plugin to generate the jaxb 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>0.6.3</version>
                <configuration>
                    <extension>true</extension>
                    <schemaDirectory>src/main/resources</schemaDirectory>
                    <schemaIncludes>
                        <include>proteomeXchange-1.3.0.xsd</include>
                    </schemaIncludes>
                    <bindingDirectory>src/main/resources</bindingDirectory>
                    <bindingIncludes>
                        <include>px-bindings.xjb</include>
                    </bindingIncludes>
                    <generateDirectory>src/main/java</generateDirectory>
                    <removeOldOutput>false</removeOldOutput>
                    <forceRegenerate>true</forceRegenerate>
                    <verbose>true</verbose>
                    <args>
                        <arg>-no-header</arg>
                    </args>
                </configuration>
            </plugin>
        </plugins>
    </build>

    <!-- Repos and distribution -->
    <repositories>
        <repository>
            <id>nexus-ebi-release-repo</id>
            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
        </repository>
        <repository>
            <id>nexus-ebi-snapshot-repo</id>
            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/</url>
        </repository>
    </repositories>

    <distributionManagement>
        <!-- Deployment to EBI's release repository -->
        <repository>
            <id>pst-release</id>
            <name>EBI Nexus Repository</name>
            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
        </repository>
        <!-- Deployment to EBI's snapshot repository -->
        <snapshotRepository>
            <uniqueVersion>false</uniqueVersion>
            <id>pst-snapshots</id>
            <name>EBI Nexus Snapshots Repository</name>
            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
        </snapshotRepository>
    </distributionManagement>


    <scm>
        <connection>scm:git:https://github.com/PRIDE-Archive/archive-px-xml-generator.git</connection>
        <developerConnection>scm:git:https://github.com/PRIDE-Archive/archive-px-xml-generator.git</developerConnection>
        <url>https://github.com/PRIDE-Archive/archive-px-xml-generator</url>
        <tag>HEAD</tag>
    </scm>
</project>