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/maven-v4_0_0.xsd">

  <modelVersion>4.0.0</modelVersion>
  <groupId>org.biopax.validator</groupId>
  <artifactId>parent</artifactId>
  <version>6.0.1-SNAPSHOT</version>
  <packaging>pom</packaging>

  <modules>
    <module>validator-core</module>
    <module>obo-fetcher</module>
    <module>biopax-validator</module>
    <module>biopax-validator-web</module>
    <module>biopax-validator-client</module>
    <module>distr</module>
  </modules>

  <name>Parent</name>
  <description>The BioPAX Validator Project (including a general-purpose
    object model validation and error reporting API core, OBO ontologies manager,
    MIRIAM registry access (to resolve bio db names and identifiers), hundreds
    BioPAX Level3 rules, settings, and the console and web applications)</description>

  <inceptionYear>2008</inceptionYear>

  <organization>
    <name>BioPAX.org</name>
    <url>http://www.biopax.org</url>
  </organization>

  <url>https://biopax.github.io/validator</url>

  <mailingLists>
    <mailingList>
      <name>BioPAX Discussion Group</name>
      <post>biopax-discuss@googlegroups.com</post>
    </mailingList>
  </mailingLists>

  <licenses>
    <license>
      <name>MIT</name>
      <url>https://raw.githubusercontent.com/BioPAX/validator/master/LICENSE</url>
    </license>
  </licenses>

  <issueManagement>
    <system>GitHub Issues</system>
    <url>https://github.com/BioPAX/validator/issues</url>
  </issueManagement>

  <ciManagement>
    <system>GitHub</system>
    <url>https://github.com/BioPAX/Validator/actions/workflows/maven.yml</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>
            <version>1.6.13</version>
            <extensions>true</extensions>
            <configuration>
              <serverId>ossrh</serverId>
              <nexusUrl>https://oss.sonatype.org/</nexusUrl>
            </configuration>
          </plugin>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-source-plugin</artifactId>
            <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-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>
            <version>3.1.0</version>
            <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/validator.git</connection>
    <developerConnection>scm:git:git@github.com:BioPAX/validator.git</developerConnection>
    <url>https://github.com/BioPAX/validator/tree/master</url>
    <tag>HEAD</tag>
  </scm>

  <distributionManagement>
    <site>
      <!-- do:
        mvn site site:stage -DstagingDirectory=/tmp/path (absolute path!)
         - then manually copy the site and push to the gh-pages branch. -->
      <id>github</id>
      <name>BioPAX Validator Maven site</name>
      <url>https://biopax.github.io/validator/${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/validator/</downloadUrl>
  </distributionManagement>

  <developers>
    <developer>
      <id>rodche</id>
      <name>Igor Rodchenkov</name>
      <organization>University of Toronto</organization>
      <roles>
        <role>architect</role>
        <role>developer</role>
      </roles>
    </developer>
    <developer>
      <name>Gary Bader</name>
      <organization>University of Toronto</organization>
      <roles>
        <role>leader</role>
      </roles>
    </developer>
    <developer>
      <id>emekdemir</id>
      <name>Emek Demir</name>
      <organization>CBIO MSKCC</organization>
      <roles>
        <role>architect</role>
      </roles>
    </developer>
  </developers>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
    <github.global.server>github</github.global.server>
    <spring-framework.version>6.1.5</spring-framework.version>
    <slf4j.version>2.0.11</slf4j.version>
    <agent>${settings.localRepository}/org/springframework/spring-instrument/${spring-framework.version}/spring-instrument-${spring-framework.version}.jar</agent>
    <paxtools.version>6.0.1-SNAPSHOT</paxtools.version>
    <license.licenseName>MIT</license.licenseName>
    <jvm.options>-Xmx3g -Dfile.encoding=UTF-8 -ea --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED</jvm.options>
  </properties>

  <build>
    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.11.0</version>
          <configuration>
            <release>17</release>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>versions-maven-plugin</artifactId>
          <version>2.16.0</version>
          <configuration>
            <generateBackupPoms>false</generateBackupPoms>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-jar-plugin</artifactId>
          <version>3.1.0</version>
          <executions>
            <execution>
              <goals>
                <goal>test-jar</goal>
              </goals>
            </execution>
          </executions>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-source-plugin</artifactId>
          <version>3.3.0</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-site-plugin</artifactId>
          <version>3.12.1</version>
          <executions>
            <execution>
              <id>attach-descriptor</id>
              <goals>
                <goal>attach-descriptor</goal>
              </goals>
            </execution>
          </executions>
          <configuration>
            <skipDeploy>true</skipDeploy>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-release-plugin</artifactId>
          <version>3.0.1</version>
          <configuration>
            <goals>deploy site-deploy</goals>
            <autoVersionSubmodules>true</autoVersionSubmodules>
            <useReleaseProfile>false</useReleaseProfile>
            <releaseProfiles>sonatype-release</releaseProfiles>
            <tagNameFormat>v@{project.version}</tagNameFormat>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-resources-plugin</artifactId>
          <version>3.3.1</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>jaxb2-maven-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <version>3.5.0</version>
          <configuration>
            <doclint>none</doclint>
            <failOnError>false</failOnError>
            <excludePackageNames>org.biopax.validator.jaxb:org.biopax.validator.api.beans:org.biopax.validator.impl:org.biopax.validator.rules:net.biomodels.*</excludePackageNames>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-surefire-plugin</artifactId>
          <version>3.1.2</version>
          <configuration>
            <argLine>${jvm.options}</argLine>
            <runOrder>alphabetical</runOrder>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-failsafe-plugin</artifactId>
          <version>3.1.2</version>
          <configuration>
            <argLine>${jvm.options} -javaagent:${agent}</argLine>
            <runOrder>alphabetical</runOrder>
            <useSystemClassLoader>false</useSystemClassLoader>
          </configuration>
        </plugin>
      </plugins>
    </pluginManagement>

    <extensions>
      <extension>
        <groupId>org.apache.maven.wagon</groupId>
        <artifactId>wagon-ssh</artifactId>
        <version>2.10</version>
      </extension>
      <extension>
        <groupId>org.apache.maven.wagon</groupId>
        <artifactId>wagon-scm</artifactId>
        <version>2.10</version>
      </extension>
      <extension>
        <groupId>org.apache.maven.doxia</groupId>
        <artifactId>doxia-integration-tools</artifactId>
        <version>1.11.1</version>
      </extension>
    </extensions>

    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-source-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-release-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-site-plugin</artifactId>
        <configuration>
          <skipDeploy>true</skipDeploy>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-failsafe-plugin</artifactId>
        <executions>
          <execution>
            <id>verify</id>
            <goals>
              <goal>integration-test</goal>
              <goal>verify</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>

  <repositories>
    <repository>
      <id>ossrh</id>
      <name>OSSRH Repository</name>
      <url>https://oss.sonatype.org/content/groups/public/</url>
    </repository>
    <repository>
      <id>ebi-repo</id>
      <name>The EBI internal repository</name>
      <url>https://www.ebi.ac.uk/~maven/m2repo</url>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
    </repository>
    <repository>
      <id>intact.nexus</id>
      <name>IntAct Nexus</name>
      <url>https://www.ebi.ac.uk/intact/maven/nexus/content/groups/public/</url>
    </repository>
  </repositories>

  <dependencyManagement>
    <dependencies>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-lang3</artifactId>
        <version>3.12.0</version>
      </dependency>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-text</artifactId>
        <version>1.10.0</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>slf4j-api</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>log4j-over-slf4j</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>jcl-over-slf4j</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>jul-to-slf4j</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>ch.qos.logback</groupId>
        <artifactId>logback-classic</artifactId>
        <version>1.4.14</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-beans</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-context</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-context-support</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-core</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-test</artifactId>
        <scope>test</scope>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-oxm</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-tx</artifactId>
        <scope>runtime</scope>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-aop</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-aspects</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.springframework</groupId>
        <artifactId>spring-instrument</artifactId>
        <version>${spring-framework.version}</version>
      </dependency>
      <dependency>
        <groupId>org.aspectj</groupId>
        <artifactId>aspectjweaver</artifactId>
        <version>1.9.7</version>
      </dependency>
      <dependency>
        <groupId>org.aspectj</groupId>
        <artifactId>aspectjrt</artifactId>
        <version>1.9.19</version>
      </dependency>
      <dependency>
        <groupId>commons-beanutils</groupId>
        <artifactId>commons-beanutils</artifactId>
        <version>1.9.4</version>
      </dependency>
      <dependency>
        <groupId>commons-digester</groupId>
        <artifactId>commons-digester</artifactId>
        <version>2.1</version>
      </dependency>
      <dependency>
        <groupId>commons-collections</groupId>
        <artifactId>commons-collections</artifactId>
        <version>3.2.2</version>
      </dependency>
      <dependency>
        <groupId>commons-fileupload</groupId>
        <artifactId>commons-fileupload</artifactId>
        <version>1.5</version>
      </dependency>
      <dependency>
        <groupId>commons-io</groupId>
        <artifactId>commons-io</artifactId>
        <version>2.13.0</version>
      </dependency>
      <dependency>
        <groupId>javax.annotation</groupId>
        <artifactId>javax.annotation-api</artifactId>
        <version>1.3.2</version>
      </dependency>
      <dependency>
        <groupId>jakarta.xml.bind</groupId>
        <artifactId>jakarta.xml.bind-api</artifactId>
        <version>4.0.0</version>
      </dependency>
      <dependency>
        <groupId>com.sun.xml.bind</groupId>
        <artifactId>jaxb-impl</artifactId>
        <version>4.0.3</version>
        <scope>runtime</scope>
      </dependency>
      <dependency>
        <groupId>jakarta.activation</groupId>
        <artifactId>jakarta.activation-api</artifactId>
        <version>2.1.2</version>
      </dependency>
      <dependency>
        <groupId>org.junit</groupId>
        <artifactId>junit-bom</artifactId>
        <version>5.10.2</version>
        <type>pom</type>
        <scope>import</scope>
      </dependency>
    </dependencies>
  </dependencyManagement>

  <dependencies>
    <dependency>
      <groupId>javax.annotation</groupId>
      <artifactId>javax.annotation-api</artifactId>
    </dependency>
    <dependency>
      <groupId>jakarta.activation</groupId>
      <artifactId>jakarta.activation-api</artifactId>
    </dependency>
    <dependency>
      <groupId>org.junit.jupiter</groupId>
      <artifactId>junit-jupiter</artifactId>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-api</artifactId>
    </dependency>
    <dependency>
      <!-- one of obo-fetcher's deps uses log4j directly-->
      <groupId>org.slf4j</groupId>
      <artifactId>log4j-over-slf4j</artifactId>
      <scope>test</scope>
      <optional>true</optional>
    </dependency>
    <dependency>
      <!--  obo and httpcomponents use JCL -->
      <groupId>org.slf4j</groupId>
      <artifactId>jcl-over-slf4j</artifactId>
      <scope>test</scope>
      <optional>true</optional>
    </dependency>
    <dependency>
      <groupId>ch.qos.logback</groupId>
      <artifactId>logback-classic</artifactId>
      <scope>test</scope>
      <optional>true</optional>
    </dependency>
  </dependencies>

  <reporting>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-javadoc-plugin</artifactId>
        <configuration>
          <linksource>true</linksource>
          <notimestamp>true</notimestamp>
          <links combine.children="append">
            <link>http://download.oracle.com/javase/17/docs/api/</link>
          </links>
          <level>public</level>
          <failOnError>false</failOnError>
<!--          <doclint>none</doclint>-->
          <excludePackageNames>org.biopax.validator.jaxb:org.biopax.validator.api.beans:org.biopax.validator.impl:org.biopax.validator.rules:net.biomodels.*</excludePackageNames>
        </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>3.3.0</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>3.4.5</version>
        <configuration>
          <dependencyDetailsEnabled>false</dependencyDetailsEnabled>
        </configuration>
        <reportSets>
          <reportSet>
            <reports>
              <report>index</report>
              <report>summary</report>
              <report>modules</report>
              <report>dependencies</report>
              <report>dependency-info</report>
              <report>distribution-management</report>
              <report>issue-management</report>
              <report>licenses</report>
              <report>team</report>
              <report>mailing-lists</report>
              <report>scm</report>
            </reports>
          </reportSet>
        </reportSets>
      </plugin>
    </plugins>
  </reporting>
</project>