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<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>${skip.artifact.creation}</skipAssembly>
</configuration>
<!-- ============================= Sign executable jar files ============================ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jarsigner-plugin</artifactId>
<version>1.4</version>
<executions>
<execution>
<id>sign-non-unix-jars</id>
<phase>package</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<skip>${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>${signer-keystore-password}</keypass>
<removeExistingSignatures>true</removeExistingSignatures>
<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
</configuration>
</execution>
<execution>
<id>sign-unix-jars</id>
<phase>package</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<skip>${jarsigner.skip}</skip>
<verbose>false</verbose>
<processMainArtifact>false</processMainArtifact>
<processAttachedArtifacts>false</processAttachedArtifacts>
<archiveDirectory>target/unix-jars</archiveDirectory>
<keystore>${signer-keystore-path}</keystore>
<storetype>${signer-keystore-type}</storetype>
<alias>${signer-keystore-alias}</alias>
<storepass>${signer-keystore-password}</storepass>
<keypass>${signer-keystore-password}</keypass>
<removeExistingSignatures>true</removeExistingSignatures>
<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
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</plugin>
<!-- ========================== Create release zips ============================ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>create-unix-release</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<outputDirectory>${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>
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<!-- 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>${evosuite.plugin.version}</version>
<executions>
<execution>
<id>create-evosuite-tests</id>
<goals>
<goal>prepare</goal>
</goals>
<phase>process-test-classes</phase>
</execution>
</executions>
<configuration>
<extraArgs>-Dsearch_budget=90 -Dconsider_main_methods=false -Duse_separate_classloader=false</extraArgs>
</configuration>
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<!--
Deploy artifacts to a GitHub release - run manually using:
mvn github-release:release
-->
<!-- plugin>
<groupId>de.jutzig</groupId>
<artifactId>github-release-plugin</artifactId>
<version>1.2.0</version>
<inherited>false</inherited>
<configuration>
<description>See ChangeLog for details</description>
<releaseName>Release v${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>
<failOnError>false</failOnError>
<quiet>true</quiet>
<excludePackageNames>org.*</excludePackageNames>
<excludes>**/*Test.java, **/*_scaffolding*.java</excludes>
<reportSets>
<reportSet>
<reports>
<report>javadoc-no-fork</report>
<report>test-javadoc-no-fork</report>
</reports>
</reportSet>
</reportSets>
</plugin>
</plugins>
</reporting>
<!-- ========================== Profile section =================================-->
<profiles>
<!-- The configuration of the default development profile -->
<profile>
<id>dev</id>
<!-- The development profile is active by default and does not run any tests -->
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<properties>
<evosuite.exclude.filter>**/*_ESTest*</evosuite.exclude.filter>
<skip.artifact.creation>true</skip.artifact.creation>
<skip.coverage.reporting>true</skip.coverage.reporting>
<skip.javadoc>true</skip.javadoc>
<build.profile.id>dev</build.profile.id>
</properties>
</profile>
<profile>
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<properties>
<skip.tests>false</skip.tests>
<evosuite.exclude.filter>**/*_ESTest*</evosuite.exclude.filter>
<skip.artifact.creation>false</skip.artifact.creation>
<skip.coverage.reporting>false</skip.coverage.reporting>
<build.profile.id>release</build.profile.id>
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<build>
<plugins>
<!--
Package jar files into OSX .apps and create dmg images.
NOTE1: artemis_sqlmap is already included in the original jar
NOTE2: The skip flag does not work on this plugin so it needs to be added into the profile [hack]
-->
<plugin>
<groupId>sh.tak.appbundler</groupId>
<artifactId>appbundle-maven-plugin</artifactId>
<version>1.1.0</version>
<executions>
<execution>
<id>create-artemis-osx-app</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>${skip.artifact.creation}</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${artemis.application.name}</bundleName>
<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${artemis.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/artemis.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${artemis.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${artemis.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
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<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
<execution>
<id>create-act-osx-app</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>false</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${act.application.name}</bundleName>
<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${act.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/act.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${act.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${act.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
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<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
<execution>
<id>create-dnaplotter-osx-app</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>false</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${dnaplotter.application.name}</bundleName>
<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${dnaplotter.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/dnaplotter.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${dnaplotter.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${dnaplotter.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
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<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
<!-- The last execution also creates the disk image file... -->
<execution>
<id>create-bamview-osx-app</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>false</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.folder}</buildDirectory>
<generateDiskImageFile>true</generateDiskImageFile>
<diskImageFile>${osx.app.folder}/${osx.release.filename}.dmg</diskImageFile>
<bundleName>${bamview.application.name}</bundleName>
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<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${bamview.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/bamview.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${bamview.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${bamview.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
<!-- Package CHADO version of toolkit -->
<execution>
<id>create-artemis-osx-app-CHADO</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>${skip.artifact.creation}</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.chado.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${artemis.application.name} (CHADO)</bundleName>
<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${artemis.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/artemis.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${postgres.command.line.arg}</jvmOption>
<jvmOption>${chado.command.line.arg}</jvmOption>
<jvmOption>${ibatis.command.line.arg}</jvmOption>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${artemis.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${artemis.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
<execution>
<id>create-act-osx-app-CHADO</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>false</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.chado.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${act.application.name} (CHADO)</bundleName>
<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${act.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/act.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${postgres.command.line.arg}</jvmOption>
<jvmOption>${chado.command.line.arg}</jvmOption>
<jvmOption>${ibatis.command.line.arg}</jvmOption>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${act.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${act.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
<execution>
<id>create-dnaplotter-osx-app-CHADO</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>false</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.chado.folder}</buildDirectory>
<generateDiskImageFile>false</generateDiskImageFile>
<bundleName>${dnaplotter.application.name}</bundleName>
<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${dnaplotter.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/dnaplotter.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${dnaplotter.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${dnaplotter.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
<!-- The last execution also creates the disk image file... -->
<execution>
<id>create-bamview-osx-app-CHADO</id>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
<configuration>
<skip>false</skip>
<version>${project.version}</version>
<buildDirectory>${osx.app.chado.folder}</buildDirectory>
<generateDiskImageFile>true</generateDiskImageFile>
<diskImageFile>${osx.app.chado.folder}/${osx.chado.release.filename}.dmg</diskImageFile>
<bundleName>${bamview.application.name}</bundleName>
<jrePath>${osx.jdk.path}</jrePath>
<mainClass>${bamview.main.class}</mainClass>
<iconFile>${project.build.directory}/icons/bamview.icns</iconFile>
<jvmVersion>${java.target.version}</jvmVersion>
<jvmOptions>
<jvmOption>${maxheap.command.line.arg}</jvmOption>
<jvmOption>${initialheap.command.line.arg}</jvmOption>
<jvmOption>${noverify.command.line.arg}</jvmOption>
<jvmOption>${unixenv.command.line.arg}</jvmOption>
<jvmOption>${macosx.menuname.command.line.arg}=${bamview.application.name}</jvmOption>
<jvmOption>${macosx.dock.command.line.arg}=${bamview.application.name}</jvmOption>
<jvmOption>${sangeroptions.command.line.arg}</jvmOption>
<jvmOption>${j2ssh.command.line.arg}</jvmOption>
</jvmOptions>
<additionalBundledClasspathResources>
<fileSet>
<directory>${project.build.directory}/icons</directory>
<includes>
<include>Readme.txt</include>
</includes>
</fileSet>
</additionalBundledClasspathResources>
</configuration>
</execution>
</executions>
<!-- Release profile: Creates the site HTML reports. -->
<id>site</id>
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<properties>
<skip.tests>false</skip.tests>
<evosuite.exclude.filter></evosuite.exclude.filter>
<jarsigner.skip>true</jarsigner.skip>
<skip.artifact.creation>true</skip.artifact.creation>
<skip.coverage.reporting>false</skip.coverage.reporting>
<skip.javadoc>false</skip.javadoc>
<build.profile.id>site</build.profile.id>
</properties>