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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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<packaging>pom</packaging>
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools</artifactId>
<version>5.0.0-SNAPSHOT</version>
<name>Paxtools</name>
<description>Paxtools is a Java library that allows software to read, write, analyze and manipulate BioPAX models.
Paxtools provide a consistent, fully implemented, validating BioPAX API that significantly reduces development
time of oftware that require programmatic access to BioPAX. Paxtools is modular, lightweight and platform
independent to be easily embedded into applications.
</description>
<url>https://biopax.github.io/Paxtools</url>
<organization>
<name>BioPAX</name>
<url>http://www.biopax.org</url>
</organization>
<modules>
<module>paxtools-core</module>
<module>gsea-converter</module>
<module>psimi-converter</module>
<module>sbgn-converter</module>
<module>paxtools-console</module>
<module>paxtools-query</module>
<module>paxtools-trove</module>
<module>paxtools-archetype</module>
<module>json-converter</module>
<module>paxtools-search</module>
<module>pattern</module>
<module>normalizer</module>
</modules>
<properties>
<java.version>1.6</java.version>
<github.global.server>github</github.global.server>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<junit.version>4.10</junit.version>
<slf4j.version>1.7.7</slf4j.version>
<logback.version>1.1.2</logback.version>
<commons-lang.version>2.6</commons-lang.version>
<collections-generic.version>4.01</collections-generic.version>
<maven.version.range>[3.0,4)</maven.version.range>
<maven-compiler-plugin.version>3.3</maven-compiler-plugin.version>
<maven-war-plugin.version>2.6</maven-war-plugin.version>
<maven-resources-plugin>2.7</maven-resources-plugin>
<maven-release-plugin.version>2.5.1</maven-release-plugin.version>
<wagon-ssh.version>2.8</wagon-ssh.version>
<wagon-scm.version>2.8</wagon-scm.version>
<maven-surefire-plugin.version>2.18.1</maven-surefire-plugin.version>
<maven-jar-plugin.version>2.6</maven-jar-plugin.version>
<maven-source-plugin.version>2.4</maven-source-plugin.version>
<maven-site-plugin.version>3.4</maven-site-plugin.version>
<maven-javadoc-plugin.version>2.10.2</maven-javadoc-plugin.version>
<maven-jxr-plugin.version>2.5</maven-jxr-plugin.version>
<maven-project-info-reports-plugin.version>2.8</maven-project-info-reports-plugin.version>
<maven-deploy-plugin.version>2.8.2</maven-deploy-plugin.version>
<maven-gpg-plugin.version>1.6</maven-gpg-plugin.version>
<nexus-staging-maven-plugin.version>1.6.5</nexus-staging-maven-plugin.version>
<doxia-integration-tools.version>1.6</doxia-integration-tools.version>
<maven-enforcer-plugin>1.4</maven-enforcer-plugin>
<!--<site-maven-plugin.version>0.12</site-maven-plugin.version>-->
<!--<github.host>github.com</github.host>-->
<!--<github.server.id>github</github.server.id> -->
<!--<github.site.path>${project.version}</github.site.path>-->
</properties>
<developers>
<developer>
<id>emekdemir</id>
<name>Emek Demir</name>
<organization>CBIO MSKCC</organization>
<roles>
<role>architect</role>
<role>developer</role>
</roles>
</developer>
<developer>
<id>rodche</id>
<name>Igor Rodchenkov</name>
<organization>University of Toronto</organization>
<roles>
<role>developer</role>
</roles>
</developer>
<developer>
<id>ozgunbabur</id>
<name>Ozgun Babur</name>
<organization>CBIO MSKCC</organization>
<roles>
<role>developer</role>
</roles>
</developer>
<developer>
<id>kenichirofukuda</id>
<name>Ken-Ichiro Fukuda</name>
<organization />
<roles>
<role>developer</role>
</roles>
</developer>
<developer>
<id>armanaksoy</id>
<name>B. Arman Aksoy</name>
<organization>CBIO MSKCC</organization>
<roles>
<role>developer</role>
</roles>
</developer>
<developer>
<id>benjamingross</id>
<name>Benjamin Gross</name>
<organization>CBIO MSKCC</organization>
<roles>
<role>developer</role>
</roles>
</developer>
</developers>
<mailingLists>
<mailingList>
<name>BioPAX Discussion Group</name>
<post>[email protected]</post>
</mailingList>
</mailingLists>
<licenses>
<license>
<name>LGPL 2.0 license</name>
<url>http://www.gnu.org/licenses/lgpl-2.0.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<issueManagement>
<system>GitHub Issues</system>
<url>https://github.com/BioPAX/Paxtools/issues</url>
</issueManagement>
<ciManagement>
<system>Travis CI</system>
<url>https://travis-ci.org/BioPAX/Paxtools</url>
</ciManagement>
<profiles>
<profile>
<!-- It's auto-enabled during mvn release:perform;
for manual releasing (not snapshots): mvn clean deploy -P sonatype-release
-->
<id>sonatype-release</id>
<build>
<plugins>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<!-- <autoReleaseAfterClose>true</autoReleaseAfterClose> -->
</configuration>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-gpg-plugin</artifactId>
<groupId>org.apache.maven.plugins</groupId>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<scm>
<connection>scm:git:git://github.com/BioPAX/Paxtools.git</connection>
<developerConnection>scm:git:[email protected]:BioPAX/Paxtools.git</developerConnection>
<url>https://github.com/BioPAX/Paxtools</url>
<tag>HEAD</tag>
</scm>
<distributionManagement>
<site>
<id>github</id>
<name>BioPAX/Paxtools Maven site</name>
<url>https://biopax.github.io/Paxtools/${project.version}</url>
</site>
<repository>
<id>ossrh</id>
<name>Nexus Release Repository</name>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
<snapshotRepository>
<id>ossrh</id>
<name>Sonatype Nexus Snapshots</name>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</snapshotRepository>
<downloadUrl>http://www.biopax.org/downloads/paxtools/</downloadUrl>
</distributionManagement>
<build>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven-compiler-plugin.version}</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>${maven-jar-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>${maven-source-plugin.version}</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>${maven-release-plugin.version}</version>
<configuration>
<goals>deploy site-deploy</goals>
<autoVersionSubmodules>true</autoVersionSubmodules>
<useReleaseProfile>false</useReleaseProfile>
<releaseProfiles>sonatype-release</releaseProfiles>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>${maven-javadoc-plugin.version}</version>
<configuration>
<excludePackageNames>org.biopax.validator.*</excludePackageNames>
<failOnError>false</failOnError>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jxr-plugin</artifactId>
<version>${maven-jxr-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>${maven-project-info-reports-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>${maven-site-plugin.version}</version>
<!--<configuration>-->
<!--<skipDeploy>true</skipDeploy>-->
<!--</configuration>-->
</plugin>
<plugin>
<groupId>com.github.github</groupId>
<artifactId>site-maven-plugin</artifactId>
<version>${site-maven-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>${nexus-staging-maven-plugin.version}</version>
</plugin>
<plugin>
<artifactId>maven-gpg-plugin</artifactId>
<groupId>org.apache.maven.plugins</groupId>
<version>${maven-gpg-plugin.version}</version>
</plugin>
</plugins>
</pluginManagement>
<extensions>
<extension>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-ssh</artifactId>
<version>${wagon-ssh.version}</version>
</extension>
<extension>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-scm</artifactId>
<version>${wagon-scm.version}</version>
</extension>
<extension>
<groupId>org.apache.maven.doxia</groupId>
<artifactId>doxia-integration-tools</artifactId>
<version>${doxia-integration-tools.version}</version>
</extension>
</extensions>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>${maven-enforcer-plugin}</version>
<executions>
<execution>
<id>enforce-banned-dependencies</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<bannedDependencies>
<searchTransitive>true</searchTransitive>
<excludes>
<exclude>javassist:javassist</exclude><!-- org.javassist is the new one -->
<exclude>commons-logging</exclude>
<exclude>aspectj:aspectj*</exclude> <!-- org.aspectj is the new one -->
<exclude>hsqldb:hsqldb</exclude> <!-- org.hsqldb is the new one -->
<exclude>org.springframework</exclude>
<exclude>com.sun.xml.bind</exclude>
<exclude>javax.xml.bind</exclude>
<exclude>net.sf.saxon</exclude>
<exclude>c3p0:c3p0</exclude> <!-- com.mchange:c3p0 is the new one -->
<exclude>org.apache.commons:com.springsource.org.apache.commons.logging</exclude>
<exclude>log4j:log4j</exclude>
</excludes>
</bannedDependencies>
<requireMavenVersion>
<version>${maven.version.range}</version>
</requireMavenVersion>
<requireJavaVersion>
<version>${java.version}</version>
</requireJavaVersion>
</rules>
<fail>true</fail>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<testFailureIgnore>false</testFailureIgnore>
<!-- enable assertions during the tests -->
<argLine>-ea</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
</plugin>
<!--<plugin>-->
<!--<groupId>com.github.github</groupId>-->
<!--<artifactId>site-maven-plugin</artifactId>-->
<!--<configuration>-->
<!--<message>Creating site ${project.url} for ${project.artifactId}:${project.version}</message>-->
<!--<host>${github.host}</host>-->
<!--<server>${github.server.id}</server>-->
<!--<path>${github.site.path}</path>-->
<!--<merge>true</merge>-->
<!--<repositoryName>Paxtools</repositoryName>-->
<!--<repositoryOwner>BioPAX</repositoryOwner>-->
<!--</configuration>-->
<!--<executions>-->
<!--<execution>-->
<!--<id>github-site</id>-->
<!--<goals>-->
<!--<goal>site</goal>-->
<!--</goals>-->
<!--<phase>site-deploy</phase>-->
<!--</execution>-->
<!--</executions>-->
<!--</plugin>-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<executions>
<execution>
<id>attach-descriptor</id>
<goals>
<goal>attach-descriptor</goal>
</goals>
</execution>
</executions>
<configuration>
<skipDeploy>true</skipDeploy>
</configuration>
</plugin>
</plugins>
</build>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sourceforge.collections</groupId>
<artifactId>collections-generic</artifactId>
<version>${collections-generic.version}</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>${commons-lang.version}</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>1.9.12</version>
</dependency>
<dependency>
<groupId>com.hp.hpl.jena</groupId>
<artifactId>jena</artifactId>
<version>2.5.7</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${slf4j.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<version>${slf4j.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
<optional>true</optional>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<repositories>
<!-- we'd remove repos below if everything were on OSSRH and Maven Central... -->
<repository>
<id>ossrh</id>
<name>OSSRH Repository</name>
<url>https://oss.sonatype.org/content/groups/public/</url>
</repository>
<repository><!-- currently, it's only to get org.sbgn:libsbgn:0.2 -->
<id>biopax.releases</id>
<name>BioPAX.org Repository</name>
<url>http://www.biopax.org/m2repo/releases/</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<!--<repository><!– TODO: this repo's gone... –>-->
<!--<id>chilay-repo</id>-->
<!--<name>Repository for chilay project</name>-->
<!--<url>http://maven-repo.chilay.googlecode.com/hg/</url>-->
<!--<snapshots>-->
<!--<enabled>true</enabled>-->
<!--<updatePolicy>always</updatePolicy>-->
<!--</snapshots>-->
<!--</repository>-->
<repository><!-- currently, it's only to get org.sbgn:libsbgn:0.2 -->
<id>biopax.snapshots</id>
<name>BioPAX.org Repository</name>
<url>http://www.biopax.org/m2repo/snapshots/</url>
<releases>
<enabled>false</enabled>
</releases>
</repository>
</repositories>
<!-- the following is used both by Maven 3.x and 2.x -->
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>${maven-javadoc-plugin.version}</version>
<configuration>
<linksource>true</linksource>
<notimestamp>true</notimestamp>
<links combine.children="append">
<link>http://download.oracle.com/javase/7/docs/api/</link>
</links>
<level>public</level>
<!--<excludePackageNames>org.biopax.validator.*,net.biomodels.miriam</excludePackageNames>-->
<excludePackageNames>org.biopax.validator.*</excludePackageNames>
<failOnError>false</failOnError>
</configuration>
<reportSets>
<reportSet>
<id>default</id>
<reports>
<!-- no test-javadoc -->
<report>javadoc</report>
</reports>
</reportSet>
<reportSet>
<id>aggregate</id>
<inherited>false</inherited>
<reports>
<report>aggregate</report>
</reports>
</reportSet>
</reportSets>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jxr-plugin</artifactId>
<version>${maven-jxr-plugin.version}</version>
<reportSets>
<reportSet>
<id>aggregate</id>
<inherited>false</inherited>
<reports>
<report>aggregate</report>
</reports>
</reportSet>
</reportSets>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>${maven-project-info-reports-plugin.version}</version>
<configuration>
<dependencyDetailsEnabled>false</dependencyDetailsEnabled>
<dependencyLocationsEnabled>false</dependencyLocationsEnabled>
</configuration>
<reportSets>
<reportSet>
<reports>
<report>index</report>
<report>summary</report>
<report>modules</report>
<!-- <report>cim</report> -->
<report>dependencies</report>
<!-- <report>dependency-convergence</report> -->
<report>dependency-info</report>
<report>dependency-management</report>
<report>distribution-management</report>
<report>issue-tracking</report>
<report>license</report>
<!-- <report>plugin-management</report> -->
<!-- <report>plugins</report> -->
<report>project-team</report>
<report>mailing-list</report>
<report>scm</report>
</reports>
</reportSet>
</reportSets>
</plugin>
</plugins>
</reporting>
</project>