vibe
Used in:
components
- OverviewOverview
- VersionsVersions
- DependentsDependents
- DependenciesDependencies
<dependency>
<groupId>org.molgenis</groupId>
<artifactId>vibe</artifactId>
<version>5.2.0</version>
</dependency><?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>org.molgenis</groupId>
<artifactId>vibe</artifactId>
<version>5.2.0</version>
<packaging>pom</packaging>
<!-- More Project Information -->
<name>VIBE</name>
<description>
A tool to generate prioritized genes using phenotype information.
</description>
<url>https://github.com/molgenis/vibe</url>
<licenses>
<license>
<name>GNU Lesser General Public License, Version 3.0</name>
<url>http://www.gnu.org/licenses/lgpl-3.0.txt</url>
</license>
</licenses>
<scm>
<connection>
scm:git:https://${env.GITHUB_USER}:${env.GITHUB_TOKEN}@github.com/molgenis/vibe.git
</connection>
<url>https://github.com/molgenis/vibe</url>
<tag>vibe-5.2.0</tag>
</scm>
<developers>
<developer>
<name>MOLGENIS development team</name>
<email>molgenis@gmail.com</email>
<organization>
University Medical Centre Groningen, System Genetics, Genomics Coordination Centre
</organization>
<organizationUrl>http://www.molgenis.org</organizationUrl>
</developer>
</developers>
<issueManagement>
<system>GitHub</system>
<url>https://github.com/molgenis/vibe/issues</url>
</issueManagement>
<properties>
<!-- vibe database information (requirement: vibe-database.version <= project.version) -->
<vibe-database.version>5.1.0</vibe-database.version>
<vibe-database.archive>vibe-${vibe-database.version}-hdt.tar.gz</vibe-database.archive>
<vibe-database.download>https://downloads.molgeniscloud.org/downloads/vibe/${vibe-database.archive}</vibe-database.download>
<!-- used hpo.owl github tag -->
<hpo-owl.tag>v2019-11-08</hpo-owl.tag>
<hpo-owl.download>https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/${hpo-owl.tag}/hp.owl</hpo-owl.download>
<!-- fix for: https://maven.apache.org/general.html#encoding-warning -->
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<!-- authentication for release scm plugin -->
<project.scm.id>github</project.scm.id>
<!-- defines java version of code -->
<java.version>1.8</java.version>
<!-- artifact publish properties -->
<sonatype.id>sonatype-nexus-staging</sonatype.id>
<!-- sonar configuration -->
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
<sonar.organization>molgenis</sonar.organization>
<sonar.github.repository>molgenis/vibe</sonar.github.repository>
<sonar.dynamicAnalysis>reuseReports</sonar.dynamicAnalysis>
<sonar.java.codeCoveragePlugin>jacoco</sonar.java.codeCoveragePlugin>
<sonar.coverage.jacoco.xmlReportPaths>${jacoco.merged-test.outputDir}/jacoco.xml</sonar.coverage.jacoco.xmlReportPaths>
<!-- jacoco configuration -->
<jacoco.unit-test.destFile>${jacoco.merged-test.fileSetDir}/jacoco-unit-tests.exec</jacoco.unit-test.destFile>
<jacoco.unit-test.dataFile>${jacoco.unit-test.destFile}</jacoco.unit-test.dataFile>
<jacoco.unit-test.outputDir>${project.reporting.outputDirectory}/jacoco-unit-test-coverage-report</jacoco.unit-test.outputDir>
<jacoco.integration-test.destFile>${jacoco.merged-test.fileSetDir}/jacoco-integration-tests.exec</jacoco.integration-test.destFile>
<jacoco.integration-test.dataFile>${jacoco.integration-test.destFile}</jacoco.integration-test.dataFile>
<jacoco.integration-test.outputDir>${project.reporting.outputDirectory}/jacoco-integration-test-coverage-report</jacoco.integration-test.outputDir>
<jacoco.merged-test.fileSetDir>${project.build.directory}/jacoco-output</jacoco.merged-test.fileSetDir>
<jacoco.merged-test.destFile>${jacoco.merged-test.fileSetDir}/jacoco-merged-tests.exec</jacoco.merged-test.destFile>
<jacoco.merged-test.dataFile>${jacoco.merged-test.destFile}</jacoco.merged-test.dataFile>
<jacoco.merged-test.outputDir>${project.reporting.outputDirectory}/jacoco-merged-test-coverage-report</jacoco.merged-test.outputDir>
<!-- plugin versions -->
<maven-compiler-plugin.version>3.8.1</maven-compiler-plugin.version>
<maven-jar-plugin.version>3.2.0</maven-jar-plugin.version>
<maven-dependency-plugin.version>3.1.1</maven-dependency-plugin.version>
<maven-shade-plugin.version>3.2.1</maven-shade-plugin.version>
<dockerfile-maven-plugin.version>1.4.10</dockerfile-maven-plugin.version>
<checksum-maven-plugin.version>1.8</checksum-maven-plugin.version>
<maven-surefire-plugin.version>2.22.2</maven-surefire-plugin.version>
<maven-failsafe-plugin.version>2.22.2</maven-failsafe-plugin.version>
<sonar-maven-plugin.version>3.5.0.1254</sonar-maven-plugin.version>
<jacoco-maven-plugin.version>0.8.2</jacoco-maven-plugin.version>
<nexus-staging-maven-plugin.version>1.6.8</nexus-staging-maven-plugin.version>
<maven-release-plugin.version>2.5.3</maven-release-plugin.version>
<pgp-maven-plugin.version>1.1</pgp-maven-plugin.version>
<!-- dependency versions -->
<slf4j-nop.version>1.7.29</slf4j-nop.version>
<apache-jena-libs.version>3.13.1</apache-jena-libs.version>
<rdfhdt.version>2.1.2</rdfhdt.version>
<commons-cli.version>1.4</commons-cli.version>
<gson.version>2.8.6</gson.version>
<junit-jupiter.version>5.6.0</junit-jupiter.version>
<mockito.version>3.7.7</mockito.version>
</properties>
<distributionManagement>
<snapshotRepository>
<id>${sonatype.id}</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
<repository>
<id>${sonatype.id}</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
</distributionManagement>
<!-- Profiles to override default configuration (can be triggered manually using "-P<id>") -->
<profiles>
<!-- Jenkins release specific configuration -->
<profile>
<id>jenkins_release</id>
<build>
<pluginManagement>
<plugins>
<plugin>
<!-- sign in a non-interactive way -->
<groupId>org.kohsuke</groupId>
<artifactId>pgp-maven-plugin</artifactId>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>install</phase> <!-- deploy -> install -->
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
</profile>
</profiles>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<pluginManagement>
<plugins>
<!-- define java version -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven-compiler-plugin.version}</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
<compilerArguments>
<Xlint />
</compilerArguments>
</configuration>
</plugin>
<!-- create skinny jar -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>${maven-jar-plugin.version}</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>
true
</addDefaultImplementationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<!-- checksum creation -->
<plugin>
<groupId>net.nicoulaj.maven.plugins</groupId>
<artifactId>checksum-maven-plugin</artifactId>
<version>${checksum-maven-plugin.version}</version>
<executions>
<execution>
<goals>
<goal>artifacts</goal>
</goals>
</execution>
</executions>
<configuration>
<algorithms>
<!-- see: https://en.wikipedia.org/wiki/Secure_Hash_Algorithms -->
<algorithm>MD5</algorithm>
<algorithm>SHA-256</algorithm>
<algorithm>SHA-512</algorithm>
<algorithm>SHA3-512</algorithm>
</algorithms>
<!-- dir for individual files -->
<individualFilesOutputDirectory>checksums</individualFilesOutputDirectory>
</configuration>
</plugin>
<!-- unit testing -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
</plugin>
<!-- integration testing -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${maven-failsafe-plugin.version}</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- integrates SonarQube -->
<plugin>
<groupId>org.sonarsource.scanner.maven</groupId>
<artifactId>sonar-maven-plugin</artifactId>
<version>${sonar-maven-plugin.version}</version>
</plugin>
<!-- JAva COde COverage -->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco-maven-plugin.version}</version>
<executions>
<!-- unit tests -->
<execution>
<id>pre-unit-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<destFile>${jacoco.unit-test.destFile}</destFile>
</configuration>
</execution>
<execution>
<id>post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<dataFile>${jacoco.unit-test.dataFile}</dataFile>
<outputDirectory>${jacoco.unit-test.outputDir}</outputDirectory>
</configuration>
</execution>
<!-- integration tests -->
<execution>
<id>pre-integration-test</id>
<phase>pre-integration-test</phase>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<destFile>${jacoco.integration-test.destFile}</destFile>
</configuration>
</execution>
<execution>
<id>post-integration-test</id>
<phase>post-integration-test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<dataFile>${jacoco.integration-test.dataFile}</dataFile>
<outputDirectory>${jacoco.integration-test.outputDir}</outputDirectory>
</configuration>
</execution>
<!-- tests combined -->
<execution>
<id>merge-unit-and-integration</id>
<phase>post-integration-test</phase>
<goals>
<goal>merge</goal>
</goals>
<configuration>
<fileSets>
<fileSet>
<directory>${jacoco.merged-test.fileSetDir}</directory>
<includes>
<include>*.exec</include>
</includes>
</fileSet>
</fileSets>
<destFile>${jacoco.merged-test.destFile}</destFile>
</configuration>
</execution>
<execution>
<id>create-merged-report</id>
<phase>post-integration-test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<dataFile>${jacoco.merged-test.dataFile}</dataFile>
<outputDirectory>${jacoco.merged-test.outputDir}</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<!-- deploy to sonatype nexus -->
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>${nexus-staging-maven-plugin.version}</version>
<extensions>true</extensions>
<configuration>
<serverId>${sonatype.id}</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<!-- closing the repo in the build fails miserably with a connection reset error -->
<skipStagingRepositoryClose>true</skipStagingRepositoryClose>
</configuration>
</plugin>
<!-- plugin for releasing -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>${maven-release-plugin.version}</version>
<configuration>
<autoVersionSubmodules>true</autoVersionSubmodules>
<scmCommentPrefix>[ci skip] [maven-release-plugin]${line.separator}</scmCommentPrefix>
</configuration>
</plugin>
<!-- sign artifacts -->
<plugin>
<!-- sign in a non-interactive way -->
<groupId>org.kohsuke</groupId>
<artifactId>pgp-maven-plugin</artifactId>
<version>${pgp-maven-plugin.version}</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>deploy</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- deploy to sonatype nexus -->
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
</plugin>
<!-- sign artifacts -->
<plugin>
<!-- sign in a non-interactive way -->
<groupId>org.kohsuke</groupId>
<artifactId>pgp-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
<dependencyManagement>
<dependencies>
<!-- Disables 'SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".' warnings, see: https://www.slf4j.org/codes.html#StaticLoggerBinder -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-nop</artifactId>
<version>${slf4j-nop.version}</version>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>${apache-jena-libs.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
</exclusions>
<type>pom</type>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons-cli.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${gson.version}</version>
</dependency>
<dependency>
<groupId>org.molgenis</groupId>
<artifactId>vibe-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>${junit-jupiter.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit-jupiter.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<version>${junit-jupiter.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
</dependencyManagement>
<modules>
<module>vibe-core</module>
<module>vibe-cli</module>
</modules>
</project>