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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>
<groupId>org.contentmine</groupId>
<artifactId>ami3</artifactId>
<version>2021.09.27_15.49-NEXT-SNAPSHOT</version>
<packaging>jar</packaging>
<name>ami3</name>
<description>A Java tool for turning scientific literature into semantic form</description>
<!-- Note: the parent POM causes problems for the maven-release-plugin: it has hg (mercurial) configured as SCM, preventing us from using git... -->
<!-- <parent>-->
<!-- <groupId>org.contentmine</groupId>-->
<!-- <artifactId>cm-parent</artifactId>-->
<!-- <version>7.1.0</version>-->
<!-- </parent>-->
<developers>
<developer>
<id>pm286</id>
<name>Peter Murray-Rust</name>
</developer>
</developers>
<inceptionYear>1994-2020</inceptionYear>
<scm>
<connection>scm:git:https://github.com/petermr/ami3.git</connection>
<developerConnection>scm:git:https://github.com/petermr/ami3.git</developerConnection>
</scm>
<properties>
<!-- if this is uncommented the tests are all skipped
<skipTests>true</skipTests>
-->
<!-- maybe uncomment this generally? -->
<!--
<skipITs>true</skipITs>
-->
<!-- java version -->
<java.version>8</java.version> <!-- not used? -->
<java.source.version>${java.version}</java.source.version>
<java.target.version>${java.version}</java.target.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<!-- dependencies -->
<boofcv-all.version>0.33.1</boofcv-all.version>
<boofcv-core.version>0.35</boofcv-core.version>
<boofcv-swing.version>0.32</boofcv-swing.version>
<boofcv-visualize.version>0.26</boofcv-visualize.version>
<commons-io.version>2.6</commons-io.version>
<commons-lang3.version>3.10</commons-lang3.version>
<commons-math.version>2.2</commons-math.version>
<commons-csv.version>1.8</commons-csv.version>
<com.google.code.gson.version>2.3.1</com.google.code.gson.version>
<ejml-all.version>0.39</ejml-all.version>
<gson.version>2.8.6</gson.version>
<guava.version>29.0-jre</guava.version>
<htmlunit.version>2.42.0</htmlunit.version>
<imgscalr-lib.version>4.2</imgscalr-lib.version>
<jai-imageio-core.version>1.4.0</jai-imageio-core.version>
<javax.media.version>1.1.3</javax.media.version>
<javax.ws.rs.version>2.1.1</javax.ws.rs.version>
<jbrowser.version>1.1.1</jbrowser.version>
<joda-time.version>2.10.5</joda-time.version>
<json-path.version>2.4.0</json-path.version>
<jsoup.version>1.13.1</jsoup.version>
<jtidy.version>4aug2000r7-dev</jtidy.version>
<jbig2-imageio.version>3.0.3</jbig2-imageio.version>
<json-path.version>2.4.0</json-path.version>
<jsoup.version>1.13.1</jsoup.version>
<junit.version>4.13</junit.version>
<junit5.version>5.6.2</junit5.version>
<lucene.version>8.5.1</lucene.version>
<!-- is this necessary? -->
<!-- <lucene-query.version>4.0.0-BETA</lucene-query.version> -->
<log4j.version>2.17.1</log4j.version>
<pdf2dom.version>1.9</pdf2dom.version>
<pdfbox2.version>2.0.19</pdfbox2.version>
<pdfbox-tools.version>2.0.19</pdfbox-tools.version>
<picocli.version>4.5.0</picocli.version>
<picocli.jansi.graalvm.version>1.2.0</picocli.jansi.graalvm.version>
<resteasy.client>4.5.3.Final</resteasy.client>
<Saxon-HE.version>10.0</Saxon-HE.version>
<selenium-java.version>4.0.0-alpha-5</selenium-java.version>
<system-rules.version>1.19.0</system-rules.version>
<tagsoup.version>1.2.1</tagsoup.version>
<univocity.version>2.8.4</univocity.version>
<xom.version>1.3.4</xom.version>
<xml-apis.version>2.0.2</xml-apis.version>
<xmlunit.version>1.6</xmlunit.version>
<!-- maven plugin versions -->
<appassembler-maven-plugin.version>1.8.1</appassembler-maven-plugin.version>
<depgraph-maven-plugin.version>2.0.1</depgraph-maven-plugin.version>
<maven-assembly-plugin.version>2.4</maven-assembly-plugin.version>
<maven-compiler-plugin.version>3.8.1</maven-compiler-plugin.version>
<maven-deploy-plugin.version>3.0.0-M1</maven-deploy-plugin.version>
<maven-failsafe-plugin.version>2.22.0</maven-failsafe-plugin.version>
<maven-jar-plugin.version>2.1</maven-jar-plugin.version>
<maven-scm-plugin.version>1.11.2</maven-scm-plugin.version>
<maven-surefire-plugin.version>2.12.4</maven-surefire-plugin.version>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven-compiler-plugin.version}</version>
<configuration>
<source>${java.source.version}</source>
<target>${java.target.version}</target>
<annotationProcessorPaths>
<path>
<groupId>info.picocli</groupId>
<artifactId>picocli-codegen</artifactId>
<version>${picocli.version}</version>
</path>
</annotationProcessorPaths>
<compilerArgs>
<arg>-Aproject=${project.groupId}/${project.artifactId}</arg>
</compilerArgs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<configuration>
<forkCount>3</forkCount>
<reuseForks>true</reuseForks>
<argLine>-Xmx1024m -XX:MaxPermSize=256m</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${maven-failsafe-plugin.version}</version>
<configuration>
<skipITs>${skipITs}</skipITs>
</configuration>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<source>1.8</source>
<useStandardDocletOptions>false</useStandardDocletOptions>
<doclint>none</doclint>
</configuration>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
<configuration>
<failOnError>false</failOnError>
<additionalparam>-Xdoclint:none</additionalparam>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
<version>${appassembler-maven-plugin.version}</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>assemble</goal>
</goals>
</execution>
</executions>
<configuration>
<programs>
<!-- TOOLS -->
<program>
<mainClass>org.contentmine.ami.tools.AMI</mainClass>
<!-- description: lists AMI commands (ami-*) -->
<id>ami</id>
</program>
<program>
<mainClass>org.contentmine.ami.tools.AMIDict</mainClass>
<!-- description: lists AMIDict commands (ami-*) -->
<id>amidict</id>
</program>
<!-- Legacy tools. TODO remove? -->
<program>
<mainClass>org.contentmine.ami.AMIProcessor</mainClass>
<!-- description: lists AMI commands (ami-*) -->
<id>ami-all</id>
</program>
<program>
<mainClass>org.contentmine.ami.plugins.EntityAnalyzer</mainClass>
<!-- description: -->
<id>ami-frequencies</id>
</program>
<program>
<mainClass>org.contentmine.ami.plugins.gene.GenePlugin</mainClass>
<!-- description: -->
<id>ami-gene</id>
</program>
<program>
<mainClass>org.contentmine.ami.plugins.identifier.IdentifierPlugin</mainClass>
<!-- description: -->
<id>ami-identifier</id>
</program>
<program>
<mainClass>org.contentmine.ami.plugins.regex.RegexPlugin</mainClass>
<!-- description: -->
<id>ami-regex</id>
</program>
<program>
<mainClass>org.contentmine.ami.plugins.sequence.SequencePlugin</mainClass>
<!-- description: -->
<id>ami-sequence</id>
</program>
<program>
<mainClass>org.contentmine.ami.plugins.species.SpeciesPlugin</mainClass>
<!-- description: -->
<id>ami-species</id>
</program>
<program>
<mainClass>org.xmlcml.cproject.PMan</mainClass>
<id>pman</id>
</program>
</programs>
<!-- Prevent long directories -->
<repositoryLayout>flat</repositoryLayout>
<!-- short names for Windows -->
<useWildcardClassPath>true</useWildcardClassPath>
</configuration>
</plugin>
<plugin>
<groupId>com.github.ferstl</groupId>
<artifactId>depgraph-maven-plugin</artifactId>
<version>${depgraph-maven-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>${maven-jar-plugin.version}</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>org.contentmine.ami.tools.AMI</mainClass>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<!-- Create distribution archives from the result of appassembler. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>${maven-assembly-plugin.version}</version>
<configuration>
<descriptors>
<descriptor>src/assembly/distribution.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- to enable `mvn deploy` to publish packages -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>${maven-deploy-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-scm-plugin</artifactId>
<version>${maven-scm-plugin.version}</version>
<configuration>
<!-- <tag>${project.artifactId}-${project.version}</tag>-->
<tag>v${project.version}</tag>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
<version>${Saxon-HE.version}</version>
</dependency>
<!-- to avoid Xerces Hell?
http://stackoverflow.com/questions/17777821/maven-dependency-conflict-org-w3c-dom-elementtraversal
-->
<!--
<dependency>
<groupId>org.vafer</groupId>
<artifactId>jdeb</artifactId>
<version>${jdeb.version}</version>
<!- - Prevents jar bloat in final package - ->
<scope>provided</scope>
</dependency>
-->
<dependency>
<groupId>xmlunit</groupId>
<artifactId>xmlunit</artifactId>
<version>${xmlunit.version}</version>
</dependency>
<!-- https://stackoverflow.com/questions/62061712/examples-for-using-latest-version-of-lucene -->
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-core</artifactId>
<version>${lucene.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-icu</artifactId>
<version>${lucene.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-common</artifactId>
<version>${lucene.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.lucene/lucene-queryparser -->
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-queryparser</artifactId>
<version>${lucene.version}</version>
</dependency>
<!-- these may be useful -->
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-facet</artifactId>
<version>${lucene.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-suggest</artifactId>
<version>${lucene.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-highlighter</artifactId>
<version>${lucene.version}</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-demo</artifactId>
<version>${lucene.version}</version>
</dependency>
<dependency>
<!-- https://github.com/uniVocity/univocity-parsers // needed for JAX -->
<groupId>com.univocity</groupId>
<artifactId>univocity-parsers</artifactId>
<version>${univocity.version}</version>
<type>jar</type>
</dependency>
<!-- https://mvnrepository.com/artifact/javax.ws.rs/javax.ws.rs-api -->
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>javax.ws.rs-api</artifactId>
<version>${javax.ws.rs.version}</version>
</dependency>
<dependency>
<groupId>org.jboss.resteasy</groupId>
<artifactId>resteasy-client</artifactId>
<version>${resteasy.client}</version>
</dependency>
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
<version>${picocli.version}</version>
</dependency>
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli-jansi-graalvm</artifactId>
<version>${picocli.jansi.graalvm.version}</version>
</dependency>
<!--
<dependency>
<groupId>javax.media</groupId>
<artifactId>jai_core</artifactId>
<version>${javax.media.version}</version>
</dependency>
-->
<!-- https://mvnrepository.com/artifact/javax.media.jai/com.springsource.javax.media.jai.core -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<!--
<version>${junit5.version}</version>
-->
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit5.version}</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-params -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<version>${junit5.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-core</artifactId>
<!-- use 2.9.1 for Java 7 projects -->
<version>3.17.1</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/org.assertj/assertj-core -->
<!-- extends JUnit, see https://stefanbirkner.github.io/system-rules/ -->
<dependency>
<groupId>com.github.stefanbirkner</groupId>
<artifactId>system-rules</artifactId>
<version>${system-rules.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>com.github.jai-imageio</groupId>
<artifactId>jai-imageio-core</artifactId>
<version>${jai-imageio-core.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-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.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${commons-lang3.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
<version>${commons-math.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>${commons-csv.version}</version>
</dependency>
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>${joda-time.version}</version>
</dependency>
<dependency>
<groupId>xom</groupId>
<artifactId>xom</artifactId>
<version>${xom.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
<dependency>
<groupId>jtidy</groupId>
<artifactId>jtidy</artifactId>
<version>${jtidy.version}</version>
</dependency>
<dependency>
<groupId>org.ccil.cowan.tagsoup</groupId>
<artifactId>tagsoup</artifactId>
<version>${tagsoup.version}</version>
</dependency>
<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>${jsoup.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.htmlunit</groupId>
<artifactId>htmlunit</artifactId>
<version>${htmlunit.version}</version>
</dependency>
<dependency>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
<version>${xml-apis.version}</version>
</dependency>
<!-- this should not be necessary There seems to be a rogue version of
guava somewhere (http://stackoverflow.com/questions/28978277/guava-multisets-copyhighestcountfirst-method-suddenly-not-working) -->
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${gson.version}</version>
</dependency>
<!-- https://github.com/jayway/JsonPath/blob/master/README.md -->
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<version>${json-path.version}</version>
</dependency>
<!-- usePDFBox 2 from here -->
<dependency>
<groupId>org.apache.pdfbox</groupId>
<artifactId>pdfbox</artifactId>
<version>${pdfbox2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.pdfbox</groupId>
<artifactId>pdfbox-tools</artifactId>
<version>${pdfbox-tools.version}</version>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-java</artifactId>
<version>${selenium-java.version}</version>
</dependency>
<dependency>
<groupId>org.boofcv</groupId>
<artifactId>boofcv-core</artifactId>
<version>${boofcv-core.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.boofcv/visualize -->
<dependency>
<groupId>org.boofcv</groupId>
<artifactId>visualize</artifactId>
<version>${boofcv-visualize.version}</version>
</dependency>
<dependency>
<groupId>org.imgscalr</groupId>
<artifactId>imgscalr-lib</artifactId>
<version>${imgscalr-lib.version}</version>
</dependency>
<dependency>
<groupId>org.apache.pdfbox</groupId>
<artifactId>jbig2-imageio</artifactId>
<version>${jbig2-imageio.version}</version>
</dependency>
<dependency>
<groupId>net.sf.cssbox</groupId>
<artifactId>pdf2dom</artifactId>
<version>${pdf2dom.version}</version>
</dependency>
<dependency>
<groupId>org.ejml</groupId>
<artifactId>ejml-all</artifactId>
<version>${ejml-all.version}</version>
</dependency>
<dependency>
<groupId>com.machinepublishers</groupId>
<artifactId>jbrowserdriver</artifactId>
<version>${jbrowser.version}</version>
</dependency>
</dependencies>
<!-- <repositories>-->
<!-- <repository>-->
<!-- <id>cm-pom</id>-->
<!-- <url>https://raw.github.com/ContentMine/cm-pom/mvn-repo/</url>-->
<!-- <snapshots>-->
<!-- <enabled>true</enabled>-->
<!-- <updatePolicy>always</updatePolicy>-->
<!-- </snapshots>-->
<!-- </repository>-->
<!-- </repositories>-->
<!-- see https://docs.github.com/en/packages/using-github-packages-with-your-projects-ecosystem/configuring-apache-maven-for-use-with-github-packages -->
<distributionManagement>
<repository>
<id>github</id>
<name>GitHub petermr Apache Maven Packages</name>
<url>https://maven.pkg.github.com/petermr/ami3</url>
</repository>
</distributionManagement>
</project>