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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>
<parent>
<groupId>org.sonatype.oss</groupId>
<artifactId>oss-parent</artifactId>
<version>7</version>
</parent>
<groupId>org.molgenis</groupId>
<artifactId>molgenis</artifactId>
<version>1.19.0-SNAPSHOT</version>
<packaging>pom</packaging>
<!-- More Project Information -->
<name>Molgenis</name>
<description>
MOLGENIS is a collaborative open source project on a mission to generate great software infrastructure for life
science research
</description>
<url>http://www.molgenis.org</url>
<licenses>
<license>
<name>GNU Library or Lesser General Public License (LGPL)</name>
</license>
</licenses>
<scm>
<connection>scm:git:git://github.com/molgenis/molgenis.git</connection>
<url>https://github.com/molgenis/molgenis</url>
</scm>
<developers />
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<slf4j.version>1.7.12</slf4j.version>
<logback.version>1.1.3</logback.version>
<spring.version>4.1.8.RELEASE</spring.version>
<spring.security.version>4.0.3.RELEASE</spring.security.version>
<mysql.connector.java.version>5.1.28</mysql.connector.java.version>
<hibernate.validator.version>4.2.0.Final</hibernate.validator.version>
<httpclient.version>4.5.1</httpclient.version>
<google.guava.version>16.0.1</google.guava.version>
<maven.build.timestamp.format>yyyy-MM-dd HH:mm z</maven.build.timestamp.format>
<molgenis.build.timestamp>${maven.build.timestamp}</molgenis.build.timestamp>
</properties>
<build>
<!-- include *.ftl in src folder -->
<resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**/*.ftl</include>
</includes>
</resource>
<resource>
<directory>${project.basedir}/src/main/resources</directory>
<excludes>
<exclude>**molgenis.properties</exclude>
<exclude>**git.properties</exclude>
</excludes>
</resource>
</resources>
<pluginManagement>
<plugins>
<!-- use java 1.8 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.2</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<compilerArguments>
<Xlint />
</compilerArguments>
</configuration>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.4</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
<!--
Exclude JCL and LOG4J since all logging should go through SLF4J.
Note that we're excluding log4j-<version>.jar but keeping log4j-over-slf4j-<version>.jar
-->
<packagingExcludes>WEB-INF/lib/commons-logging-*.jar,%regex[WEB-INF/lib/log4j-(?!over-slf4j).*.jar]</packagingExcludes>
</configuration>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<mainClass>test.App</mainClass>
<addDefaultImplementationEntries>
true
</addDefaultImplementationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.6</version>
<executions>
<!-- copy generated resources to target folder -->
<execution>
<id>copy-generated-resources</id>
<phase>process-classes</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.outputDirectory}</outputDirectory>
<resources>
<resource>
<directory>target/generated-resources</directory>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
<!--
Copying the das server config to the war ROOT
the uk.ac.ebi.mydas.controller.MydasServlet cannot find the file if
its placed in the normal WEB-INF/classes folder
-->
<execution>
<id>copy-resources</id>
<phase>validate</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>target/${project.name}-${project.version}</outputDirectory>
<resources>
<resource>
<directory>src/main/resources/</directory>
<includes>
<include>MydasServerConfig.xml</include>
</includes>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!-- specify java 8 compatible plugin version -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.1</version>
<configuration>
<additionalparam>-Xdoclint:none</additionalparam>
</configuration>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>jaxb2-maven-plugin</artifactId>
<version>1.5</version>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.jvnet.jax-ws-commons</groupId>
<artifactId>jaxws-maven-plugin</artifactId>
<version>2.1</version>
</plugin>
<!-- configure molgenis generator execution -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.7</version>
<executions>
<execution>
<id>generate-sources</id>
<phase>generate-sources</phase>
<configuration>
<tasks>
<path id="generate-classpath">
<path refid="maven.compile.classpath" />
<pathelement path="${project.basedir}/src/main/resources" />
</path>
<java classname="org.molgenis.Molgenis" classpathref="generate-classpath" failonerror="true">
<arg value="molgenis.properties" />
<arg value="${project.build.directory}/generated-sources/molgenis" />
</java>
</tasks>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
<execution>
<id>generate-test-sources</id>
<phase>generate-test-sources</phase>
<configuration>
<tasks>
<path id="generate-classpath">
<path refid="maven.compile.classpath" />
<pathelement path="${project.basedir}/src/main/resources" />
</path>
<java classname="org.molgenis.Molgenis" classpathref="generate-classpath" failonerror="true">
<arg value="molgenis.properties" />
<arg value="${project.build.directory}/generated-test-sources/molgenis" />
<arg value="--generatetests" />
</java>
</tasks>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- configure setting sources/resources generated by the molgenis generator -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>reserve-network-port</id>
<goals>
<goal>reserve-network-port</goal>
</goals>
<phase>process-resources</phase>
<configuration>
<minPortNumber>8080</minPortNumber>
<portNames>
<portName>jetty.http.port</portName>
</portNames>
</configuration>
</execution>
<execution>
<id>minify-build-helper</id>
<phase>generate-resources</phase>
<goals>
<goal>add-resource</goal>
</goals>
<configuration>
<resources>
<resource>
<directory>target/generated-resources</directory>
</resource>
</resources>
</configuration>
</execution>
<execution>
<id>execution-molgenis-generator</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
<goal>add-resource</goal>
</goals>
<configuration>
<sources>
<source>target/generated-sources/molgenis/java</source>
</sources>
<resources>
<resource>
<directory>target/generated-sources/molgenis/java</directory>
</resource>
</resources>
</configuration>
</execution>
<execution>
<id>execution-molgenis-generator-tests</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
<goal>add-test-resource</goal>
</goals>
<configuration>
<sources>
<source>target/generated-test-sources/molgenis/java</source>
</sources>
<resources>
<resource>
<directory>target/generated-test-sources/molgenis/java</directory>
</resource>
</resources>
</configuration>
</execution>
<!-- add sources created by jaxb -->
<execution>
<id>execution-annotations</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>target/generated-sources/annotations</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.3</version>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.2.1</version>
</plugin>
<!-- specify plugin version -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.0-alpha-2</version>
</plugin>
<!-- Eclipse m2e mappings -->
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<versionRange>[1.7,)</versionRange>
<goals>
<goal>run</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<versionRange>[1.0.0,)</versionRange>
<goals>
<goal>enforce</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.jvnet.jax-ws-commons</groupId>
<artifactId>jaxws-maven-plugin</artifactId>
<versionRange>[2.1,)</versionRange>
<goals>
<goal>wsimport</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<versionRange>[1.0-alpha-2,)</versionRange>
<goals>
<goal>read-project-properties</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<versionRange>[1.8,)</versionRange>
<goals>
<goal>reserve-network-port</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<versionRange>[0.7,)</versionRange>
<goals>
<goal>prepare-agent</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
<!-- integration test plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.8.1</version>
<executions>
<execution>
<id>integration-test</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
<execution>
<id>verify</id>
<phase>verify</phase>
<goals>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- minify css/js -->
<plugin>
<groupId>com.samaxes.maven</groupId>
<artifactId>minify-maven-plugin</artifactId>
<version>1.7.4</version>
<executions>
<execution>
<id>default-minify</id>
<phase>generate-resources</phase>
<goals>
<goal>minify</goal>
</goals>
<configuration>
<charset>UTF-8</charset>
<webappSourceDir>${project.basedir}/src/main/resources</webappSourceDir>
<webappTargetDir>${project.build.directory}/generated-resources</webappTargetDir>
<cssSourceIncludes>
<cssSourceInclude>**/*.css</cssSourceInclude>
<cssSourceInclude>**/**/*.css</cssSourceInclude>
</cssSourceIncludes>
<cssSourceExcludes>
<!-- changes to excludes must be applied to molgenis-core-ui/src/main/resources/templates/resource-macros.ftl -->
<cssSourceExclude>**/*.min.css</cssSourceExclude>
<cssSourceExclude>**/*-min.css</cssSourceExclude>
<cssSourceExclude>**/**/*.min.css</cssSourceExclude>
<cssSourceExclude>**/**/*-min.css</cssSourceExclude>
</cssSourceExcludes>
<jsSourceIncludes>
<jsSourceInclude>**/*.js</jsSourceInclude>
</jsSourceIncludes>
<jsSourceExcludes>
<!-- changes to excludes must be applied to molgenis-core-ui/src/main/resources/templates/resource-macros.ftl -->
<jsSourceExclude>**/*.min.js</jsSourceExclude>
<cssSourceExclude>**/*-min.js</cssSourceExclude>
<jsSourceExclude>**/src-min-noconflict/**</jsSourceExclude>
</jsSourceExcludes>
<nosuffix>false</nosuffix>
<skipMerge>true</skipMerge>
<skipMinify>false</skipMinify>
<verbose>true</verbose>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
</plugin>
<plugin>
<!-- add minified resources to build path -->
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>minify-build-helper</id>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.2.201409121644</version>
<executions>
<execution>
<id>amend-unit-test-java-agent-option</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<argLine>${argLine}</argLine>
</configuration>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<!-- code coverage -->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.2.201409121644</version>
</plugin>
<!-- code analysis -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<xmlOutput>true</xmlOutput>
</configuration>
</plugin>
<!-- project reports -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.7</version>
<configuration>
<!-- improve report generation performance -->
<dependencyLocationsEnabled>false</dependencyLocationsEnabled>
<project.remoteArtifactRepositories>enonic</project.remoteArtifactRepositories>
</configuration>
</plugin>
</plugins>
</reporting>
<dependencyManagement>
<dependencies>
<!-- see http://docs.spring.io/spring-security/site/docs/3.2.x/reference/htmlsingle/#maven-bom -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-framework-bom</artifactId>
<version>${spring.version}</version>
<type>pom</type>
<scope>import</scope>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<!-- logging -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback.version}</version>
</dependency>
<!-- for third party dependencies that use log4j -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<!-- scope: test -->
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<scope>test</scope>
</dependency>
<!-- scope: provided -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.0.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysql.connector.java.version}</version>
<scope>provided</scope>
</dependency>
</dependencies>
<modules>
<module>molgenis-core</module>
<module>molgenis-core-ui</module>
<module>molgenis-ontology-core</module>
<module>molgenis-ontology</module>
<module>molgenis-das</module>
<module>molgenis-dataexplorer</module>
<module>molgenis-app</module>
<module>molgenis-security</module>
<module>molgenis-security-core</module>
<module>molgenis-data-annotators</module>
<module>molgenis-data-excel</module>
<module>molgenis-data-csv</module>
<module>molgenis-data-googlespreadsheet</module>
<module>molgenis-data</module>
<module>molgenis-data-system</module>
<module>molgenis-data-merge</module>
<module>molgenis-data-mysql</module>
<module>molgenis-data-vcf</module>
<module>molgenis-data-rest</module>
<module>molgenis-data-elasticsearch</module>
<module>molgenis-data-semanticsearch</module>
<module>molgenis-data-validation</module>
<module>molgenis-data-idcard</module>
<module>molgenis-python</module>
<module>molgenis-r</module>
<module>molgenis-charts</module>
<module>molgenis-js</module>
<module>molgenis-model-registry</module>
<module>molgenis-data-examples</module>
<module>molgenis-scripts</module>
<module>molgenis-scripts-core</module>
<module>molgenis-data-import</module>
<module>molgenis-data-mapper</module>
<module>molgenis-pathways</module>
<module>molgenis-data-rest-client</module>
<module>molgenis-data-migrate</module>
<module>molgenis-questionnaires</module>
<module>molgenis-file</module>
<module>molgenis-catalogue</module>
<module>molgenis-file-ingester</module>
<module>molgenis-integration-tests</module>
</modules>
</project>