pom.xml

<?xml version="1.0"?>
<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>edu.ucsb.nceas</groupId>
  <artifactId>metadig-engine</artifactId>
  <version>3.0.2</version>
  <packaging>jar</packaging>
  <name>metadig-engine</name>
  <description>MetaDIG library for running metadata quality tests</description>
  <url>https://github.com/NCEAS/metadig-engine</url>
  <properties>
    <bookkeeper.version>0.1.0-SNAPSHOT</bookkeeper.version>
    <jackson.version>2.15.2</jackson.version>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <d1_libclient_java.version>2.3.1</d1_libclient_java.version>
    <renjin.version>0.8.2567</renjin.version>
    <jython.version>2.7.3</jython.version>
    <gson.version>2.10.1</gson.version>
    <json-path.version>2.8.0</json-path.version>
    <moxy.version>2.7.0</moxy.version>
    <log4j.version>2.23.0</log4j.version>
    <d1_cn_index_processor_version>2.3.15</d1_cn_index_processor_version>
    <d1_cn_index_common_version>2.3.2</d1_cn_index_common_version>
    <!-- Have to use a very old version of Spring in order to stay compatible with d1_cn_index_processor -->
    <!-- <spring.version>4.3.8.RELEASE</spring.version> -->
    <spring.version>5.3.22</spring.version>
    <!-- <docker.registry>docker.io</docker.registry> -->
    <docker.repo>metadig</docker.repo>
    <docker.tag>2.5.0</docker.tag>
    <modules.test.includes>**/*Test.java</modules.test.includes>
    <modules.test.excludes>**/LTERSuiteTest.java</modules.test.excludes>
    <maven.wagon.version>3.5.3</maven.wagon.version>
  </properties>
  <scm>
    <url>https://github.com/NCEAS/metadig-engine.git</url>
  </scm>
  <organization>
    <name>National Center for Ecological Analysis and Synthesis, UC Santa Barbara</name>
    <url>http://nceas.ucsb.edu</url>
  </organization>
  <dependencies>

    <!-- https://mvnrepository.com/artifact/org.quartz-scheduler/quartz -->
    <!--<dependency>-->
    <!--<groupId>org.quartz-scheduler</groupId>-->
    <!--<artifactId>quartz</artifactId>-->
    <!--<version>2.3.2</version>-->
    <!--</dependency>-->
    <dependency>
      <groupId>com.fasterxml.jackson.core</groupId>
      <artifactId>jackson-databind</artifactId>
      <version>${jackson.version}</version>
    </dependency>
    <dependency>
      <groupId>org.renjin</groupId>
      <artifactId>renjin-script-engine</artifactId>
      <version>${renjin.version}</version>
      <exclusions>
        <exclusion>
          <groupId>org.apache.httpcomponents</groupId>
          <artifactId>httpclient</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <!-- https://mvnrepository.com/artifact/org.python/jython-standalone -->
    <dependency>
      <groupId>black.ninia</groupId>
      <artifactId>jep</artifactId>
      <version>4.1.1</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/junit/junit -->
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.13.2</version>
      <type>jar</type>
      <scope>test</scope>
    </dependency>
    <!-- http://mvnrepository.com/artifact/com.google.code.gson/gson -->
    <dependency>
      <groupId>com.google.code.gson</groupId>
      <artifactId>gson</artifactId>
      <version>${gson.version}</version>
    </dependency>
    <dependency>
      <groupId>com.jayway.jsonpath</groupId>
      <artifactId>json-path</artifactId>
      <version>${json-path.version}</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/net.minidev/json-smart -->
    <dependency>
      <groupId>net.minidev</groupId>
      <artifactId>json-smart</artifactId>
      <version>2.5.0</version>
    </dependency>
    <!-- http://mvnrepository.com/artifact/commons-io/commons-io -->
    <dependency>
      <groupId>commons-io</groupId>
      <artifactId>commons-io</artifactId>
      <version>2.15.1</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-csv</artifactId>
      <version>1.10.0</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-configuration2</artifactId>
      <version>2.9.0</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/commons-beanutils/commons-beanutils -->
    <dependency>
      <groupId>commons-beanutils</groupId>
      <artifactId>commons-beanutils</artifactId>
      <version>1.9.4</version>
    </dependency>
    <!-- http://mvnrepository.com/artifact/org.eclipse.persistence/org.eclipse.persistence.moxy -->
    <dependency>
      <groupId>org.eclipse.persistence</groupId>
      <artifactId>org.eclipse.persistence.moxy</artifactId>
      <version>${moxy.version}</version>
    </dependency>
    <!-- D1 libclient -->
    <dependency>
      <groupId>org.dataone</groupId>
      <artifactId>d1_libclient_java</artifactId>
      <version>${d1_libclient_java.version}</version>
      <type>jar</type>
      <exclusions>
        <exclusion>
          <groupId>org.apache.httpcomponents</groupId>
          <artifactId>httpclient-cache</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-api</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-core</artifactId>
        </exclusion>
        <exclusion><groupId>org.javassist</groupId>
          <artifactId>javassist</artifactId>
        </exclusion>
        <exclusion>
          <groupId>javax.xml.bind</groupId>
           <artifactId>jaxb-api</artifactId>
       </exclusion>
        </exclusions>
    </dependency>
    <!-- https://mvnrepository.com/artifact/com.rabbitmq/amqp-client -->
    <dependency>
      <groupId>com.rabbitmq</groupId>
      <artifactId>amqp-client</artifactId>
      <version>5.18.0</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/joda-time/joda-time -->
    <dependency>
      <groupId>joda-time</groupId>
      <artifactId>joda-time</artifactId>
      <version>2.12.5</version>
    </dependency>
    <dependency>
      <groupId>org.apache.solr</groupId>
      <artifactId>solr-solrj</artifactId>
      <version>8.11.1</version>
      <exclusions>
        <exclusion>
          <groupId>junit</groupId>
          <artifactId>junit</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.slf4j</groupId>
          <artifactId>slf4j-jdk</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.slf4j</groupId>
          <artifactId>slf4j-api</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.apache.solr</groupId>
      <artifactId>solr-core</artifactId>
      <version>9.4.1</version>
      <exclusions>
        <exclusion>
          <groupId>org.slf4j</groupId>
          <artifactId>slf4j-jdk14</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-api</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-core</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-slf4j-impl</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-web</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.logging.log4j</groupId>
          <artifactId>log4j-1.2-api</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.slf4j</groupId>
          <artifactId>slf4j-api</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-log4j12</artifactId>
      <version>1.7.33</version>
      <exclusions>
        <exclusion>
          <groupId>log4j</groupId>
          <artifactId>log4j</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-1.2-api</artifactId>
      <version>${log4j.version}</version>
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-core</artifactId>
      <version>${log4j.version}</version>
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-jcl</artifactId>
      <version>${log4j.version}</version>
    </dependency>
    <dependency>
      <groupId>commons-logging</groupId>
      <artifactId>commons-logging</artifactId>
      <version>1.3.0</version>
      <exclusions>
        <exclusion>
          <groupId>log4j</groupId>
          <artifactId>log4j</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <!-- httpclient 4.5.5 is needed by solrj 7.2.1 but the solrj pom only loads
       httpclient 4.5.3, so this dependency is included here. If this version is not included,
       then trying to create an HttpSolrClient causes an unchecked Exception. -->
    <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpclient -->
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpclient</artifactId>
      <version>4.5.14</version>
    </dependency>
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpclient-cache</artifactId>
      <version>4.5.5</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-context-support</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.dataone</groupId>
      <artifactId>d1_cn_index_processor</artifactId>
      <version>${d1_cn_index_processor_version}</version>
      <type>jar</type>
      <exclusions>
        <exclusion>
          <groupId>com.hp.hpl.jena</groupId>
          <artifactId>jena</artifactId>
        </exclusion>
        <exclusion>
          <groupId>xml-apis</groupId>
          <artifactId>xml-apis</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.solr</groupId>
          <artifactId>solr-solrj</artifactId>
        </exclusion>
        <exclusion>
          <groupId>postgresql</groupId>
          <artifactId>postgresql</artifactId>
        </exclusion>
        <exclusion>
          <groupId>commons-beanutils</groupId>
          <artifactId>commons-beanutils</artifactId>
        </exclusion>
        <exclusion>
          <groupId>com.rabbitmq</groupId>
          <artifactId>amqp-client</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.slf4j</groupId>
          <artifactId>slf4j-log4j12</artifactId>
        </exclusion>
        <exclusion>
          <groupId>com.hp.hpl.jena</groupId>
          <artifactId>jena</artifactId>
        </exclusion>
        <exclusion>
          <groupId>xml-apis</groupId>
          <artifactId>xml-apis</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.apache.httpcomponents</groupId>
          <artifactId>httpclient</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.slf4j</groupId>
          <artifactId>slf4j-api</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.springframework</groupId>
          <artifactId>spring-context-support</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <!-- https://mvnrepository.com/artifact/org.json/json -->
    <dependency>
      <groupId>org.json</groupId>
      <artifactId>json</artifactId>
      <version>20230618</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
    <dependency>
      <groupId>org.postgresql</groupId>
      <artifactId>postgresql</artifactId>
      <version>42.7.2</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpcore -->
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpcore</artifactId>
      <version>4.4.16</version>
    </dependency>
    <dependency>
      <groupId>org.dataone</groupId>
      <artifactId>bookkeeper-client</artifactId>
      <version>${bookkeeper.version}</version>
      <exclusions>
        <exclusion>
          <groupId>io.dropwizard</groupId>
          <artifactId>dropwizard-core</artifactId>
        </exclusion>
        <exclusion>
          <groupId>io.dropwizard</groupId>
          <artifactId>dropwizard-json-logging</artifactId>
        </exclusion>
        <exclusion>
          <groupId>io.dropwizard</groupId>
          <artifactId>dropwizard-testing</artifactId>
        </exclusion>
        <exclusion>
          <groupId>io.dropwizard</groupId>
          <artifactId>dropwizard-jdbi3</artifactId>
        </exclusion>
        <exclusion>
          <groupId>io.dropwizard</groupId>
          <artifactId>dropwizard-auth</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.postgresql</groupId>
          <artifactId>postgresql</artifactId>
        </exclusion>
        <exclusion>
          <groupId>com.opentable.components</groupId>
          <artifactId>otj-pg-embedded</artifactId>
        </exclusion>
        <exclusion>
          <groupId>com.opentable.components</groupId>
          <artifactId>otj-pg-embedded</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.flywaydb</groupId>
          <artifactId>flyway-maven-plugin</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.mockito</groupId>
          <artifactId>mockito-core</artifactId>
        </exclusion>
        <exclusion>
          <groupId>org.dataone</groupId>
          <artifactId>d1_libclient_java</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
   <!-- API, java.xml.bind module -->
   <dependency>
      <groupId>jakarta.xml.bind</groupId>
      <artifactId>jakarta.xml.bind-api</artifactId>
      <version>2.3.2</version>
    </dependency>
  </dependencies>
  <repositories>
    <repository>
      <id>bedatadriven</id>
      <name>bedatadriven public repo</name>
      <url>https://nexus.bedatadriven.com/content/groups/public/</url>
    </repository>
    <repository>
      <id>dataone.org</id>
      <name>DataONE Maven repo</name>
      <url>https://maven.dataone.org/</url>
    </repository>
  </repositories>
  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>true</filtering>
      </resource>
    </resources>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>3.8.1</version>
        <configuration>
          <source>17</source>
          <target>17</target>
        </configuration>
      </plugin>
      <!-- Include all dependencies using a 'shade' jar so that the
        MetaDIG Controller and Worker can be run directly from this
        jar file. This allows deployment either in the MetaDIG web
        app (which runs the Controller, or as a command line task
        (which is how the Worker is run). 
      -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-shade-plugin</artifactId>
        <version>3.5.1</version>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
            <configuration>
              <filters>
                <filter>
                  <artifact>*:*</artifact>
                  <excludes>
                    <exclude>META-INF/*.SF</exclude>
                    <exclude>META-INF/*.DSA</exclude>
                    <exclude>META-INF/*.RSA</exclude>
                    <exclude>META-INF/</exclude>
                  </excludes>
                </filter>
              </filters>
              <!-- Exclude javax.servlet.http.HttpServlet" from the jar so that
                            we can determine when we are running in a servlet enviromnet. This class will be
                            provided by the servlet container distribution when running as a sevlet
                            -->
              <artifactSet>
                <excludes>
                  <exclude>javax.servlet:*</exclude>
                </excludes>
              </artifactSet>
              <transformers>
                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                  <manifestEntries>
                    <Main-Class>edu.ucsb.nceas.mdqengine.Controller</Main-Class>
                    <Build-Number>1</Build-Number>
                  </manifestEntries>
                  <manifestEntries>
                    <Main-Class>edu.ucsb.nceas.mdqengine.Worker</Main-Class>
                    <Build-Number>1</Build-Number>
                  </manifestEntries>
                  <manifestEntries>
                    <Main-Class>edu.ucsb.nceas.mdqengine.MDQEngine</Main-Class>
                    <Build-Number>1</Build-Number>
                  </manifestEntries>
                </transformer>
              </transformers>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-antrun-plugin</artifactId>
        <version>3.1.0</version>
        <executions>
          <execution>
            <id>copy-jar-file</id>
            <phase>package</phase>
            <goals>
              <goal>run</goal>
            </goals>
            <configuration>
              <!-- Copy files needed by the local environments of the Docker containers -->
              <target name="copy files">
                <copy file="${project.build.directory}/metadig-engine-${project.version}.jar" tofile="${project.basedir}/Docker/metadig-worker/metadig-engine.jar"/>
                <copy file="${project.build.directory}/metadig-engine-${project.version}.jar" tofile="${project.basedir}/Docker/metadig-scheduler/metadig-engine.jar"/>
                <copy file="${project.build.directory}/metadig-engine-${project.version}.jar" tofile="${project.basedir}/Docker/metadig-scorer/metadig-engine.jar"/>
                <copy file="${project.build.directory}/classes/solr/application-context-mdq.xml" tofile="${project.basedir}/Docker/metadig-worker/solr/application-context-mdq.xml"/>
                <copy file="${project.build.directory}/classes/solr/application-context-systemmeta-200.xml" tofile="${project.basedir}/Docker/metadig-worker/solr/application-context-systemmeta-200.xml"/>
                <copy file="${project.build.directory}/classes/solr/metadig-index-processor-context.xml" tofile="${project.basedir}/Docker/metadig-worker/solr/metadig-index-processor-context.xml"/>
                <copy file="${project.build.directory}/classes/solr/application-context-mdq.xml" tofile="${project.basedir}/Docker/metadig-scorer/solr/application-context-mdq.xml"/>
                <copy file="${project.build.directory}/classes/solr/application-context-systemmeta-200.xml" tofile="${project.basedir}/Docker/metadig-scorer/solr/application-context-systemmeta-200.xml"/>
                <copy file="${project.build.directory}/classes/solr/metadig-index-processor-context.xml" tofile="${project.basedir}/Docker/metadig-scorer/solr/metadig-index-processor-context.xml"/>
              </target>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>3.2.5</version>
        <configuration>
          <excludes>
            <exclude>${modules.test.excludes}</exclude>
            <exclude>**/*IT.java</exclude>
          </excludes>
          <includes>
            <include>${modules.test.includes}</include>
          </includes>
        </configuration>
        <executions>
          <execution>
            <id>integration-test</id>
            <goals>
              <goal>test</goal>
            </goals>
            <phase>integration-test</phase>
            <configuration>
              <excludes>
                <exclude>none</exclude>
              </excludes>
              <includes>
                <include>**/*IT.java</include>
              </includes>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
    <extensions>
            <extension>
                <groupId>org.apache.maven.wagon</groupId>
                <artifactId>wagon-ssh</artifactId>
                <version>${maven.wagon.version}</version>
            </extension>
    </extensions>
  </build>
  <distributionManagement>
        <repository>
            <uniqueVersion>false</uniqueVersion>
            <id>maven.dataone.org</id>
            <name>DataONE</name>
            <url>scp://maven.dataone.org/var/www/maven</url>
            <layout>default</layout>
        </repository>
  </distributionManagement>
</project>