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pom.xml
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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>uk.ac.ebi.pride.utilities</groupId>
<artifactId>ms-data-core-api</artifactId>
<version>2.0.31-SNAPSHOT</version>
<name>Open-source Data Model for computational proteomics</name>
<url>http://github.com/PRIDE-Utilities/ms-data-core-api</url>
<description>Open-source java library to handle different file format standards for proteomics. Specially
ms-data-core-api is good for MetaData representation.
</description>
<parent>
<groupId>uk.ac.ebi.pride.architectural</groupId>
<artifactId>pride-core</artifactId>
<version>1.0.1</version>
</parent>
<developers>
<developer>
<id>Yasset Perez-Riverol</id>
<name>Yasset Perez-Riverol</name>
<url>http://computationalproteomic.blogspot.co.uk/</url>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
<organizationUrl>http://www.ebi.ac.uk/pride</organizationUrl>
<roles>
<role>developer</role>
<role>architect</role>
</roles>
<timezone>0</timezone>
</developer>
<developer>
<id>ntoro</id>
<name>Noemi del Toro Ayllón</name>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
<organizationUrl>http://www.ebi.ac.uk/pride</organizationUrl>
<roles>
<role>developer</role>
<role>tester</role>
</roles>
<timezone>0</timezone>
</developer>
<developer>
<id>tobias</id>
<name>Tobias Ternent</name>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
<organizationUrl>http://www.ebi.ac.uk/pride</organizationUrl>
<roles>
<role>developer</role>
<role>tester</role>
</roles>
<timezone>0</timezone>
</developer>
<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>Suresh Hewapathirana</id>
<name>Suresh Chanaka Hewapathirana</name>
<organization>Proteomics Services Team, EMBL-European Bioinformatics Institute</organization>
<organizationUrl>http://www.ebi.ac.uk/pride</organizationUrl>
<roles>
<role>developer</role>
<role>tester</role>
</roles>
<timezone>Europe/London</timezone>
</developer>
</developers>
<contributors>
<contributor>
<name>Rui Wang</name>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
<organizationUrl>http://www.ebi.ac.uk/pride</organizationUrl>
</contributor>
</contributors>
<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>
<assembly.dir>${project.name}-${project.version}</assembly.dir>
<json.version>20090211</json.version>
<commonscode.version>1.7</commonscode.version>
<c3p0.version>0.9.1.2</c3p0.version>
<uk.ac.ebi.jmzidml-jmzidentml.version>1.2.11</uk.ac.ebi.jmzidml-jmzidentml.version>
<uk.ac.ebi.jmzml-jmzml.version>1.7.11</uk.ac.ebi.jmzml-jmzml.version>
<xmlschemavalidator.version>2.1</xmlschemavalidator.version>
<uk.ac.ebi.pride-jmztab-modular-model.version>3.0.8</uk.ac.ebi.pride-jmztab-modular-model.version>
<uk.ac.ebi.pride-jmztab-modular-util.version>3.0.8</uk.ac.ebi.pride-jmztab-modular-util.version>
<uk.ac.ebi.pride-jmztab-modular-converters.version>3.0.8</uk.ac.ebi.pride-jmztab-modular-converters.version>
<uk.ac.ebi.pride.tools-jmzreader.version>2.0.6</uk.ac.ebi.pride.tools-jmzreader.version>
<jnetCDF.version>0.0.2</jnetCDF.version>
<uk.ac.ebi.pride.jaxb-pride-jaxb.version>1.0.22</uk.ac.ebi.pride.jaxb-pride-jaxb.version>
<uk.ac.ebi.pride.utilities-pride-utilities.version>2.0.18</uk.ac.ebi.pride.utilities-pride-utilities.version>
<uk.ac.ebi.pride.utilities-pride-mod.version>2.1.9</uk.ac.ebi.pride.utilities-pride-mod.version>
<commons-cli.version>1.3.1</commons-cli.version>
</properties>
<dependencies>
<dependency>
<groupId>uk.ac.ebi.pride.architectural</groupId>
<artifactId>pride-tdd</artifactId>
<type>pom</type>
<version>${uk.ac.ebi.pride.architectural-pride-tdd.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.architectural</groupId>
<artifactId>pride-logging</artifactId>
<type>pom</type>
<version>${uk.ac.ebi.pride.architectural-pride-logging.version}</version>
</dependency>
<!-- mzML dependencies -->
<dependency>
<groupId>uk.ac.ebi.jmzml</groupId>
<artifactId>jmzml</artifactId>
<version>${uk.ac.ebi.jmzml-jmzml.version}</version>
</dependency>
<!-- End -->
<!-- netCDF dependencies -->
<dependency>
<groupId>uk.ac.ebi.pride.utilities</groupId>
<artifactId>netCDF-parser</artifactId>
<version>${jnetCDF.version}</version>
<exclusions>
<exclusion>
<groupId>lennart</groupId>
<artifactId>lmjunit</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- End -->
<!-- mzIdentML File dependencies -->
<dependency>
<groupId>uk.ac.ebi.jmzidml</groupId>
<artifactId>jmzidentml</artifactId>
<version>${uk.ac.ebi.jmzidml-jmzidentml.version}</version>
</dependency>
<!-- End -->
<!-- Validator xml -->
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>xmlSchemaValidator</artifactId>
<version>${xmlschemavalidator.version}</version>
</dependency>
<!-- End -->
<!-- mzTab dependencies -->
<dependency>
<groupId>uk.ac.ebi.pride</groupId>
<artifactId>jmztab-modular-model</artifactId>
<version>${uk.ac.ebi.pride-jmztab-modular-model.version}</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride</groupId>
<artifactId>jmztab-modular-util</artifactId>
<version>${uk.ac.ebi.pride-jmztab-modular-util.version}</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride</groupId>
<artifactId>jmztab-modular-converters</artifactId>
<version>${uk.ac.ebi.pride-jmztab-modular-converters.version}</version>
<exclusions>
<exclusion>
<groupId>uk.ac.ebi.pride.jaxb</groupId>
<artifactId>pride-jaxb</artifactId>
</exclusion>
<exclusion>
<groupId>uk.ac.ebi.pride.utilities</groupId>
<artifactId>pride-utilities</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- End -->
<!-- pride mod dependency -->
<dependency>
<groupId>uk.ac.ebi.pride.utilities</groupId>
<artifactId>pride-mod</artifactId>
<version>${uk.ac.ebi.pride.utilities-pride-mod.version}</version>
</dependency>
<!-- End -->
<!-- Begin of the jmzReader Dependencies. MzML and Pride XML files will be parse
with jaxb and jmzml directly in order to keep more matadata -->
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>jmzreader</artifactId>
<version>${uk.ac.ebi.pride.tools-jmzreader.version}</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commonscode.version}</version>
</dependency>
<!-- PRIDE XML dependency -->
<dependency>
<groupId>uk.ac.ebi.pride.jaxb</groupId>
<artifactId>pride-jaxb</artifactId>
<version>${uk.ac.ebi.pride.jaxb-pride-jaxb.version}</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.utilities</groupId>
<artifactId>pride-utilities</artifactId>
<version>${uk.ac.ebi.pride.utilities-pride-utilities.version}</version>
</dependency>
<!-- Dependencies related with CommandLine-->
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons-cli.version}</version>
</dependency>
<!--<!– pride.archive repo –>-->
<!--<dependency>-->
<!--<groupId>uk.ac.ebi.pride.archive</groupId>-->
<!--<artifactId>archive-repo</artifactId>-->
<!--<version>${archive.repo.version}</version>-->
<!--<exclusions>-->
<!--<exclusion>-->
<!--<groupId>ch.qos.logback</groupId>-->
<!--<artifactId>logback-classic</artifactId>-->
<!--</exclusion>-->
<!--<exclusion>-->
<!--<groupId>ch.qos.logback</groupId>-->
<!--<artifactId>logback-core</artifactId>-->
<!--</exclusion>-->
<!--<exclusion>-->
<!--<groupId>org.slf4j</groupId>-->
<!--<artifactId>slf4j-log4j12</artifactId>-->
<!--</exclusion>-->
<!--<exclusion>-->
<!--<groupId>org.slf4j</groupId>-->
<!--<artifactId>slf4j-api</artifactId>-->
<!--</exclusion>-->
<!--</exclusions>-->
<!--<scope>provided</scope>-->
<!--</dependency>-->
<!-- For File handling -->
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>r05</version>
</dependency>
<!-- Java version of Redis -->
<dependency>
<groupId>redis.clients</groupId>
<artifactId>jedis</artifactId>
<version>2.9.0</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<!-- Java Performance Monitoring Library -->
<dependency>
<groupId>com.jamonapi</groupId>
<artifactId>jamon</artifactId>
<version>2.81</version>
<scope>test</scope>
</dependency>
<!-- Lombok -->
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.16.20</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.8</version>
<configuration>
<outputDirectory>${basedir}/lib</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<excludeTransitive>false</excludeTransitive>
<artifactItems />
</configuration>
</plugin>
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.4</version>
<configuration>
<skip>true</skip>
<skipDeploy>true</skipDeploy>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.6</version>
<configuration>
<archive>
<manifest>
<!-- Adds the classpath to the created manifest -->
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<!-- Configures the main class of the application -->
<mainClass>uk.ac.ebi.pride.utilities.data.exporters.MzTabConverterTool</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>${project.basedir}/assembly.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<repositories>
<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 -->
<repository>
<id>pst-snapshots</id>
<name>EBI Nexus Snapshots Repository</name>
<url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
</repository>
<repository>
<id>springsource-repo</id>
<name>SpringSource Repository</name>
<url>http://repo.springsource.org/release</url>
</repository>
<repository>
<id>JBoss</id>
<name>JBoss repository</name>
<url>https://repository.jboss.org/nexus/content/repositories/releases/</url>
</repository>
</repositories>
<!-- Plugin Repositories -->
<pluginRepositories>
<pluginRepository>
<id>maven2-repository.dev.java.net</id>
<url>http://download.java.net/maven/2</url>
</pluginRepository>
</pluginRepositories>
<!-- Overwrites the previous repositories-->
<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>
<!--scm git config-->
<scm>
<connection>scm:git:https://github.com/PRIDE-Utilities/ms-data-core-api.git</connection>
<developerConnection>scm:git:https://github.com/PRIDE-Utilities/ms-data-core-api.git</developerConnection>
<url>https://github.com/PRIDE-Utilities/ms-data-core-api.git</url>
<tag>HEAD</tag>
</scm>
</project>