pom.xml 47.02 KiB
<?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>uk.ac.sanger</groupId>
<artifactId>artemis</artifactId>
<version>18.0.0-RC1</version>
<name>Artemis</name>
<description>Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.</description>
<inceptionYear>1998</inceptionYear>
<!-- GitHub repo connection -->
<scm>
<connection>scm:https://github.com/sanger-pathogens/Artemis.git</connection>
<url>https://github.com/sanger-pathogens/Artemis</url>
<developerConnection>scm:https://github.com/sanger-pathogens/Artemis.git</developerConnection>
<tag>HEAD</tag>
</scm>
<organization>
<name>Sanger Institute</name>
<url>http://www.sanger.ac.uk/</url>
</organization>
<url>http://sanger-pathogens.github.io/Artemis/</url>
<developers>
<developer>
<id>kp11</id>
<name>Kevin Pepper</name>
<email>artemis-help@sanger.ac.uk</email>
<url>http://www.sanger.ac.uk/science/tools/artemis</url>
<organization>Sanger Institute</organization>
<organizationUrl>http://www.sanger.ac.uk/</organizationUrl>
<roles>
<role>developer</role>
</roles>
<timezone>GB/London</timezone>
</developer>
</developers>
<licenses>
<license>
<name>The GNU General Public License, Version 3, June 2007</name>
<url>https://raw.githubusercontent.com/sanger-pathogens/Artemis/master/LICENSE</url>
</license>
</licenses>
<issueManagement>
<system>Github</system>
<url>https://github.com/sanger-pathogens/Artemis/issues</url>
</issueManagement>
<mailingLists>
<mailingList>
<name>Artemis support email address</name>
<post>artemis-help@sanger.ac.uk</post>
</mailingList>
</mailingLists>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<ignore.test.failures>true</ignore.test.failures>
<version.file>${project.basedir}/etc/versions</version.file>
<copyright.text>2018 Wellcome Trust Sanger Institute</copyright.text>
<!-- Properties passed into Maven on command line -->
<emboss.installation.root>${env.EMBOSS_ROOT}</emboss.installation.root>
<!-- Application names -->
<artemis.application.name>Artemis</artemis.application.name>
<artemis.chado.application.name>${artemis.application.name} (CHADO)</artemis.chado.application.name>
<act.application.name>ACT</act.application.name>
<act.chado.application.name>${act.application.name} (CHADO)</act.chado.application.name>
<dnaplotter.application.name>Circular-Plot</dnaplotter.application.name>
<bamview.application.name>BamView</bamview.application.name>
<!-- Deployable jar names -->
<artemis.jar.name>artemis.jar</artemis.jar.name>
<act.jar.name>act.jar</act.jar.name>
<bamview.jar.name>bamview.jar</bamview.jar.name>
<dnaplotter.jar.name>dnaplotter.jar</dnaplotter.jar.name>
<!-- Main classes -->
<artemis.main.class>uk.ac.sanger.artemis.components.ArtemisMain</artemis.main.class>
<act.main.class>uk.ac.sanger.artemis.components.ActMain</act.main.class>
<bamview.main.class>uk.ac.sanger.artemis.components.alignment.BamView</bamview.main.class>
<dnaplotter.main.class>uk.ac.sanger.artemis.circular.DNADraw</dnaplotter.main.class>
<!-- Java version-->
<java.compatibility.major.version>9</java.compatibility.major.version>
<bundler.jdk.path>/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk</bundler.jdk.path>
<osx.bundler.jar>${project.basedir}/maven-lib/appbundler-1.0ea.jar</osx.bundler.jar>
<osx.bundler.volume>Artemis_Tools</osx.bundler.volume>
<osx.bundler.chado.volume>Artemis_Tools_Chado</osx.bundler.chado.volume>
<!-- Evosuite properties-->
<targetFolder>src/test/evosuite</targetFolder>
<evosuite.runtime.version>1.0.6</evosuite.runtime.version>
<evosuite.plugin.version>1.0.6</evosuite.plugin.version>
<!-- Assembly folders -->
<windows.assembly.folder>artemis</windows.assembly.folder>
<unix.assembly.folder>artemis</unix.assembly.folder>
<osx.assembly.folder>artemis</osx.assembly.folder>
<!-- Release deliverable folder -->
<release.artifact.folder>${project.build.directory}/release-artifacts</release.artifact.folder>
<windows.release.folder>${release.artifact.folder}/windows-release</windows.release.folder>
<osx.app.folder>${release.artifact.folder}/mac-osx-release</osx.app.folder>
<osx.app.chado.folder>${release.artifact.folder}/mac-osx-chado-release</osx.app.chado.folder>
<unix.release.folder>${release.artifact.folder}/unix-release</unix.release.folder>
<!-- Release file names -->
<unix.release.filename>artemis-unix-release-${project.version}</unix.release.filename>
<windows.release.filename>artemis-windows-release-${project.version}</windows.release.filename>
<osx.release.filename>artemis-macosx-release-${project.version}</osx.release.filename>
<osx.chado.release.filename>artemis-macosx-chado-release-${project.version}</osx.chado.release.filename>
<!-- Mac OS application JVM options -->
<postgres.command.line.arg>-Djdbc.drivers=org.postgresql.Driver</postgres.command.line.arg>
<maxheap.command.line.arg>-mx2g</maxheap.command.line.arg>
<initialheap.command.line.arg>-ms128m</initialheap.command.line.arg>
<noverify.command.line.arg>-noverify</noverify.command.line.arg>
<unixenv.command.line.arg>-Dartemis.environment=UNIX</unixenv.command.line.arg>
<macosx.menuname.command.line.arg>-Dcom.apple.mrj.application.apple.menu.about.name</macosx.menuname.command.line.arg>
<macosx.dock.command.line.arg>-Xdock:name</macosx.dock.command.line.arg>
<macosx.use.menubar.arg>-Dapple.laf.useScreenMenuBar=true</macosx.use.menubar.arg>
<chado.command.line.arg>-Dchado="localhost:5432/databasename?username"</chado.command.line.arg>
<ibatis.command.line.arg>-Dibatis</ibatis.command.line.arg>
<sangeroptions.command.line.arg>-Dsanger_options=yes</sangeroptions.command.line.arg>
<blackbelt.command.line.arg>-Dblack_belt_mode=false</blackbelt.command.line.arg>
<!-- Surefire unit test plugin parameters --> <unit.test.timeout.ms>8000</unit.test.timeout.ms>
<surefire.num.forks>1</surefire.num.forks>
<default.tests.surefireArgLine>-Xmx4g ${noverify.command.line.arg} ${postgres.command.line.arg} -DEMBOSS_ROOT=${emboss.installation.root} --illegal-access=warn</default.tests.surefireArgLine>
<surefireArgLine>${default.tests.surefireArgLine} -Dtimeout=${unit.test.timeout.ms} -Duse_separate_classloader=false</surefireArgLine>
<!-- Files to exclude from the build, e.g. Mac resource files. -->
<default.file.excludes>**/log4j*.xml META-INF/* **/.DS_Store **/._*</default.file.excludes>
<!-- Etc files to exclude from the build. -->
<etc.file.excludes>*.seq *.fasta *.embl *.tab *.crunch *.genbank</etc.file.excludes>
<!-- Images -->
<artemis.icons.path>${project.basedir}/icons</artemis.icons.path>
<artemis.images.path>${project.basedir}/images</artemis.images.path>
<!-- Default build flag settings -->
<skip.tests>false</skip.tests>
<evosuite.exclude.filter>**/*_ESTest*</evosuite.exclude.filter>
<jarsigner.skip>true</jarsigner.skip>
<skip.artifact.creation>true</skip.artifact.creation>
<skip.coverage.reporting>true</skip.coverage.reporting>
<skip.javadoc>true</skip.javadoc>
</properties>
<dependencies>
<!-- Start of BATIK Jars -->
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-codec -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-codec</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-dom -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-dom</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-ext -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-ext</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-svggen -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-svggen</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-util -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-util</artifactId>
<version>1.9.1</version>
</dependency>
<!-- End of BATIK Jars -->
<!-- Start of IBATIS jars -->
<!-- https://mvnrepository.com/artifact/com.ibatis/ibatis (local legacy jar) -->
<dependency>
<groupId>com.ibatis</groupId>
<artifactId>ibatis</artifactId>
<version>2.3.4.726</version> </dependency>
<!-- This is now out of date but is used by the ibatis jar-->
<!-- https://mvnrepository.com/artifact/cglib/cglib-nodep -->
<dependency>
<groupId>cglib</groupId>
<artifactId>cglib-nodep</artifactId>
<version>2.2</version>
</dependency>
<!-- This is now out of date - the package name has changed and so updating will mean many changes -->
<!-- https://mvnrepository.com/artifact/log4j/log4j -->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<!-- End of IBATIS jars (local) -->
<dependency>
<groupId>com.sshtools</groupId>
<artifactId>j2ssh-core</artifactId>
<version>0.2.9</version>
</dependency>
<!-- Latest commons logging from 2014! -->
<!-- https://mvnrepository.com/artifact/commons-logging/commons-logging -->
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.2</version>
</dependency>
<!-- End of J2SSH jars (local) -->
<dependency>
<groupId>org.emboss</groupId>
<artifactId>jemboss</artifactId>
<version>1.0</version>
</dependency>
<!-- Very out of date, but using the latest v3 will not compile atm -->
<!-- https://mvnrepository.com/artifact/commons-lang/commons-lang -->
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-net/commons-net -->
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.6</version>
</dependency>
<!-- NOTE: IBatis is no longer supported and very out of date -->
<!-- Using the new postgres driver may cause issues - needs testing -->
<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>42.2.5</version>
</dependency>
<!-- Using latest version gives compilation errors! -->
<dependency>
<groupId>org.biojava</groupId> <artifactId>biojava</artifactId>
<version>1.6</version>
</dependency>
<!-- Start of Picard jars -->
<!-- https://mvnrepository.com/artifact/com.github.broadinstitute/picard -->
<!-- Latest as of 24th Sept 2018 -->
<!-- It contains two htsjdk fixes for CRAM index caching and the query mate issue -->
<dependency>
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
<version>2.18.14</version>
</dependency>
<!-- End of Picard jars -->
<!-- Testing only -->
<!-- https://mvnrepository.com/artifact/junit/junit -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.evosuite</groupId>
<artifactId>evosuite-standalone-runtime</artifactId>
<version>${evosuite.runtime.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-nop</artifactId>
<version>1.7.25</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/org.mockito/mockito-core -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>2.23.0</version>
<scope>test</scope>
</dependency>
<!-- End of testing only -->
<!-- Redundant dependencies..... -->
<!-- Latest version as of 2005 -->
<!-- https://mvnrepository.com/artifact/jakarta-regexp/jakarta-regexp -->
<!-- dependency>
<groupId>jakarta-regexp</groupId>
<artifactId>jakarta-regexp</artifactId>
<version>1.4</version>
</dependency-->
<!-- https://mvnrepository.com/artifact/batik/batik-awt-util -->
<!-- dependency>
<groupId>batik</groupId>
<artifactId>batik-awt-util</artifactId>
<version>1.6-1</version>
</dependency-->
<!-- https://mvnrepository.com/artifact/batik/batik-xml -->
<!-- dependency>
<groupId>batik</groupId>
<artifactId>batik-xml</artifactId> <version>1.6-1</version>
</dependency-->
</dependencies>
<build>
<plugins>
<!-- =================== Evosuite needs at least Maven 3.1 ======================= -->
<plugin>
<inherited>true</inherited>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.3.1</version>
<executions>
<execution>
<id>enforce-maven-3</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>3.1</version>
</requireMavenVersion>
</rules>
<fail>true</fail>
</configuration>
</execution>
</executions>
</plugin>
<!-- ====================== Read signing related properties ======================= -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.0.0</version>
<executions>
<execution>
<id>load-external-properties</id>
<phase>initialize</phase>
<goals>
<goal>read-project-properties</goal>
</goals>
<configuration>
<!-- Build will not fail if properties file is not found, but signing will fail -->
<quiet>true</quiet>
<files>
<file>maven.properties</file>
</files>
</configuration>
</execution>
</executions>
</plugin>
<!-- ====================== Install essential old jars into the local Maven repo ======================= -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
<executions>
<execution>
<id>install-biojava-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals> <configuration>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>1.6</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/biojava.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-jemalign-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>org.emboss</groupId>
<artifactId>jemboss</artifactId>
<version>1.0</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/jemAlign.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-j2ssh-core-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>com.sshtools</groupId>
<artifactId>j2ssh-core</artifactId>
<version>0.2.9</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/j2ssh-core.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-ibatis-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>com.ibatis</groupId>
<artifactId>ibatis</artifactId>
<version>2.3.4.726</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/ibatis-2.3.4.726.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
</executions>
</plugin>
<!-- ========= Store release version number to the Artemis splash screen version file ======== -->
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>updating-software-version-number</id>
<phase>initialize</phase>
<goals>
<goal>run</goal>
</goals>
<configuration> <target>
<echo file="${version.file}">Artemis Release ${project.version}${line.separator}ACT Release ${project.version}${line.separator}DNAPlotter Release ${project.version}${line.separator}BamView ${project.version}</echo>
</target>
</configuration>
</execution>
</executions>
</plugin>
<!-- ============================== Copy resources to build folder ======================== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
<executions>
<!-- Copy etc on to classpath -->
<execution>
<id>copy-property-files</id>
<phase>process-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.outputDirectory}/etc</outputDirectory>
<resources>
<resource>
<directory>${project.basedir}/etc</directory>
</resource>
</resources>
</configuration>
</execution>
<execution>
<id>copy-icons-folder</id>
<phase>process-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/icons</outputDirectory>
<resources>
<resource>
<directory>${artemis.icons.path}</directory>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!-- ===================================== Compile ========================================= -->
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<verbose>false</verbose>
<showWarnings>true</showWarnings>
<!-- We use the release option for Java 9+ -->
<release>${java.compatibility.major.version}</release>
</configuration>
</plugin>
<!-- ============================== Jar customisation ===================================== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.0</version>
<configuration> <archive>
<manifest>
<addClasspath>false</addClasspath>
</manifest>
<manifestEntries>
<Permissions>all-permissions</Permissions>
<Codebase>*</Codebase>
</manifestEntries>
</archive>
</configuration>
</plugin>
<!-- ========================= Required for Evosuite test running ========================-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<id>add-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>${targetFolder}</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<!-- ======================================= Surefire Unit tests ==========================================-->
<!-- Only currently runs default unit tests because of bug in Evosuite on Java 9+. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
<configuration>
<skipTests>${skip.tests}</skipTests>
<trimStackTrace>true</trimStackTrace>
<forkCount>${surefire.num.forks}</forkCount>
<reuseForks>false</reuseForks>
<testFailureIgnore>${ignore.test.failures}</testFailureIgnore>
<argLine>@{default.tests.surefireArgLine}</argLine>
<excludes>
<!-- Exclude Evosuite tests -->
<exclude>**/*ESTest*</exclude>
<!-- Exclude manual adhoc tests -->
<exclude>**/RunBlastAtNCBITest.*</exclude>
<exclude>**/TestIbatisDAO.*</exclude>
<exclude>**/TestJdbcDAO.*</exclude>
</excludes>
</configuration>
</plugin>
<!-- =================================== Run Jacoco coverage report ======================================-->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.1</version>
<configuration>
<skip>${skip.coverage.reporting}</skip>
</configuration>
<executions> <execution>
<id>pre-unit-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<output>file</output>
<!-- Sets the path to the file which contains the execution data. -->
<destFile>${project.build.directory}/jacoco-ut.exec</destFile>
<!-- Sets the name of the property containing the settings for JaCoCo
runtime agent. -->
<propertyName>surefireArgLine</propertyName>
</configuration>
</execution>
<!-- Ensures that the code coverage report for unit tests is created after
unit tests have been run. -->
<execution>
<id>post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<dataFile>${project.build.directory}/jacoco-ut.exec</dataFile>
<outputDirectory>${project.build.directory}/coverage-report</outputDirectory>
<excludes>
<exclude>org/**</exclude>
</excludes>
</configuration>
</execution>
</executions>
</plugin>
<!-- ============= Package the code and dependent jars into one executable jar for each applications ========= -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>package-win-artemis-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/win-jars/${artemis.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${artemis.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes> </filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-artemis-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${artemis.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${artemis.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-win-act-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/win-jars/${act.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${act.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers> <filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-act-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${act.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${act.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-win-dnaplotter-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals> <configuration>
<outputFile>target/win-jars/${dnaplotter.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${dnaplotter.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-dnaplotter-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${dnaplotter.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${dnaplotter.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes> <exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-win-bamview-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/win-jars/${bamview.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${bamview.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-bamview-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${bamview.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${bamview.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter> <artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
<configuration>
<skipAssembly>${skip.artifact.creation}</skipAssembly>
</configuration>
</plugin>
<!-- ============================= Sign executable jar files ============================ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jarsigner-plugin</artifactId>
<version>1.4</version>
<executions>
<execution>
<id>sign-win-jars</id>
<phase>package</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<skip>${jarsigner.skip}</skip>
<verbose>false</verbose>
<processMainArtifact>false</processMainArtifact>
<processAttachedArtifacts>false</processAttachedArtifacts>
<archiveDirectory>target/win-jars</archiveDirectory>
<keystore>${signer-keystore-path}</keystore>
<storetype>${signer-keystore-type}</storetype>
<alias>${signer-keystore-alias}</alias>
<storepass>${signer-keystore-password}</storepass>
<keypass>${signer-keystore-password}</keypass>
<removeExistingSignatures>true</removeExistingSignatures>
<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
</configuration>
</execution>
<execution>
<id>sign-default-jars</id>
<phase>package</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<skip>${jarsigner.skip}</skip>
<verbose>false</verbose>
<processMainArtifact>false</processMainArtifact>
<processAttachedArtifacts>false</processAttachedArtifacts>
<archiveDirectory>target/jars</archiveDirectory>
<keystore>${signer-keystore-path}</keystore> <storetype>${signer-keystore-type}</storetype>
<alias>${signer-keystore-alias}</alias>
<storepass>${signer-keystore-password}</storepass>
<keypass>${signer-keystore-password}</keypass>
<removeExistingSignatures>true</removeExistingSignatures>
<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
</configuration>
</execution>
</executions>
</plugin>
<!-- ========================== Create release zips ============================ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>create-unix-release</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<outputDirectory>${unix.release.folder}</outputDirectory>
<descriptors>
<descriptor>src/assembly/unix-release-assembly.xml</descriptor>
</descriptors>
<finalName>${unix.release.filename}</finalName>
</configuration>
</execution>
<execution>
<id>create-windows-release</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<outputDirectory>${windows.release.folder}</outputDirectory>
<descriptors>
<descriptor>src/assembly/windows-release-assembly.xml</descriptor>
</descriptors>
<finalName>${windows.release.filename}</finalName>
</configuration>
</execution>
</executions>
<configuration>
<skipAssembly>${skip.artifact.creation}</skipAssembly>
</configuration>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<!-- We need this next bit to get rid of a warning on the enforcer plugin in Eclipse -->
<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-enforcer-plugin</artifactId>
<versionRange>[1.3.1,)</versionRange>
<goals>
<goal>enforce</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
<!-- ============= Special task used on an ad-hoc basis to create EvoSuite tests ============ -->
<plugin>
<groupId>org.evosuite.plugins</groupId>
<artifactId>evosuite-maven-plugin</artifactId>
<version>${evosuite.plugin.version}</version>
<executions>
<execution>
<id>create-evosuite-tests</id>
<goals>
<goal>prepare</goal>
</goals>
<phase>process-test-classes</phase>
</execution>
</executions>
<configuration>
<extraArgs>-Dsearch_budget=90 -Dconsider_main_methods=false -Duse_separate_classloader=false</extraArgs>
</configuration>
</plugin>
<!-- =========== Check for plugin updates ================== -->
<!-- Use: mvn versions:display-plugin-updates -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.7</version>
<configuration>
<generateBackupPoms>false</generateBackupPoms>
</configuration>
</plugin>
<!--
Deploy artifacts to a GitHub release - run manually using:
mvn github-release:release
-->
<!-- plugin>
<groupId>de.jutzig</groupId>
<artifactId>github-release-plugin</artifactId>
<version>1.2.0</version>
<inherited>false</inherited>
<configuration>
<description>See ChangeLog for details</description>
<releaseName>Release v${project.version}</releaseName>
<tag>v${project.version}</tag>
<draft>true</draft>
<artifact>${unix.release.folder}/${unix.release.filename}</artifact>
<fileSets>
<fileSet>
<includes>
<include>${osx.app.folder}/${osx.release.filename}.dmg</include>
<include>${windows.release.folder}/${windows.release.filename}</include>
<include>${project.basedir}/ChangeLog</include>
</includes> </fileSet>
</fileSets>
</configuration>
</plugin -->
</plugins>
</pluginManagement>
</build>
<reporting>
<plugins>
<!-- Javadoc -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<skip>${skip.javadoc}</skip>
<failOnError>false</failOnError>
<quiet>true</quiet>
<excludePackageNames>org.*</excludePackageNames>
<excludes>**/*Test.java, **/*_scaffolding*.java</excludes>
</configuration>
<reportSets>
<reportSet>
<reports>
<report>javadoc-no-fork</report>
<report>test-javadoc-no-fork</report>
</reports>
</reportSet>
</reportSets>
</plugin>
</plugins>
</reporting>
<!-- ========================== Profile section =================================-->
<profiles>
<profile>
<id>old-java8-profile-deprecated</id>
<!-- This profile runs all unit tests including Evosuite ones on Java 8. -->
<!-- Note however that some code changes will now be needed to compile on Java 8. -->
<activation>
<jdk>1.8</jdk>
</activation>
<properties>
<build.profile.id>java8-profile</build.profile.id>
</properties>
<build>
<plugins>
<!--
Compiling with Java 8 JDK... the compiler does not have the -release parameter,
so we fall back to source and target
-->
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<verbose>false</verbose>
<source>1.8</source>
<target>1.8</target>
</configuration> </plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
<configuration>
<skipTests>${skip.tests}</skipTests>
<trimStackTrace>true</trimStackTrace>
<forkCount>${surefire.num.forks}</forkCount>
<reuseForks>false</reuseForks>
<testFailureIgnore>${ignore.test.failures}</testFailureIgnore>
<argLine>@{surefireArgLine}</argLine>
<excludes>
<!-- Start of Evosuite excludes -->
<exclude>${evosuite.exclude.filter}</exclude>
<exclude>org/gmod/**</exclude>
<exclude>**/j2ssh/**</exclude>
<!-- End of Evosuite excludes -->
<!-- Exclude manual adhoc tests -->
<exclude>**/RunBlastAtNCBITest.*</exclude>
<exclude>**/TestIbatisDAO.*</exclude>
<exclude>**/TestJdbcDAO.*</exclude>
</excludes>
<!-- Required when running Evosuite tests along with normal tests -->
<properties>
<property>
<name>listener</name>
<value>org.evosuite.runtime.InitializingListener</value>
</property>
</properties>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>mac-osx-dmg-packaging</id>
<!--
App/dmg packaging that can only be run on a Mac.
-->
<activation>
<os>
<family>mac</family>
</os>
</activation>
<properties>
<build.profile.id>mac-osx-dmg-packaging</build.profile.id>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>build-macosx</id>
<phase>verify</phase>
<configuration>
<skip>${skip.artifact.creation}</skip>
<target>
<ant antfile="${project.basedir}/src/assembly/macosx-release-assembly.xml"> <target name="bundle-mac-osx"/>
<target name="bundle-mac-osx-chado"/>
</ant>
</target>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>release</id>
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<properties>
<skip.tests>false</skip.tests>
<evosuite.exclude.filter></evosuite.exclude.filter>
<jarsigner.skip>false</jarsigner.skip>
<skip.artifact.creation>false</skip.artifact.creation>
<skip.coverage.reporting>false</skip.coverage.reporting>
<skip.javadoc>false</skip.javadoc>
<build.profile.id>release</build.profile.id>
</properties>
</profile>
</profiles>
</project>