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pom.xml
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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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<properties>
<project.version>2.8-RELEASE</project.version>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<bundle.dir>${project.build.directory}/bundles</bundle.dir>
<bundle.dir.ubuntu>${bundle.dir}/Gigwa_V${project.version}-Ubuntu</bundle.dir.ubuntu>
<bundle.dir.osx>${bundle.dir}/Gigwa_V${project.version}-OSX</bundle.dir.osx>
<bundle.dir.windows>${bundle.dir}/Gigwa_V${project.version}-Windows</bundle.dir.windows>
<path.to.ubuntu.jre>/home/sempere/Bureau/projects/gigwa/bundle_jre/zulu17.40.19-ca-jre17.0.6-linux_x64.tar.gz</path.to.ubuntu.jre>
<path.to.osx.jre>/home/sempere/Bureau/projects/gigwa/bundle_jre/zulu17.40.19-ca-jre17.0.6-macosx_x64.tar.gz</path.to.osx.jre>
<path.to.windows.jre>/home/sempere/Bureau/projects/gigwa/bundle_jre/zulu17.40.19-ca-jre17.0.6-win_x64.tar.gz</path.to.windows.jre>
<!-- ubuntu https://cdn.azul.com/zulu/bin/zulu17.40.19-ca-jre17.0.6-linux_x64.tar.gz -->
<!-- macos https://cdn.azul.com/zulu/bin/zulu17.40.19-ca-jre17.0.6-macosx_x64.tar.gz -->
<!-- win https://cdn.azul.com/zulu/bin/zulu17.40.19-ca-jre17.0.6-win_x64.tar.gz -->
<tomcat.version>9.0.64</tomcat.version>
<mongodb.linux.file>linux-x86_64-ubuntu1804-4.2.25</mongodb.linux.file>
<mongodb.windows.file>win32-x86_64-2012plus-4.2.25</mongodb.windows.file>
<mongodb.osx.file>macos-x86_64-4.2.25</mongodb.osx.file>
<mongodb.osx.folder>macos-x86_64-4.2.25</mongodb.osx.folder> <!-- for some reason the OSX folder name differs from the archive name -->
</properties>
<groupId>fr.cirad</groupId>
<artifactId>Gigwa2</artifactId>
<version>${project.version}</version>
<packaging>war</packaging>
<name>Gigwa</name>
<dependencies>
<dependency>
<groupId>fr.cirad</groupId>
<artifactId>role_manager</artifactId>
<version>1.3.7-RELEASE</version>
</dependency>
<dependency>
<groupId>fr.cirad</groupId>
<artifactId>Mgdb2BrapiImpl</artifactId>
<version>1.1.7-RELEASE</version>
</dependency>
<dependency>
<groupId>fr.cirad</groupId>
<artifactId>Mgdb2BrapiV2Impl</artifactId>
<version>2.0.7-RELEASE</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.auth0</groupId>
<artifactId>java-jwt</artifactId>
<version>3.19.0</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>8.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>fr.cirad</groupId>
<artifactId>Gigwa2ServiceImpl</artifactId>
<version>2.8-RELEASE</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
<exclusion>
<groupId>org.ga4gh</groupId>
<artifactId>ga4gh-schemas</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-oas</artifactId>
<version>3.0.0</version>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger-ui</artifactId>
<version>3.0.0</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.1.2</version>
</dependency>
<dependency>
<groupId>taglibs</groupId>
<artifactId>standard</artifactId>
<version>1.1.2</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-taglibs</artifactId>
<version>5.6.10</version>
<exclusions>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
</exclusion>
<exclusion>
<artifactId>spring-aop</artifactId>
<groupId>org.springframework</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-cas</artifactId>
<version>5.6.10</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springmodules</groupId>
<artifactId>spring-modules-validation</artifactId>
<version>0.8</version>
<exclusions>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring</artifactId>
</exclusion>
<exclusion>
<groupId>commons-validator</groupId>
<artifactId>commons-validator</artifactId>
</exclusion>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
<exclusion>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
</exclusion>
<exclusion>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.13.4.1</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>2.13.4</version>
</dependency>
<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>1.4</version>
<exclusions>
<exclusion>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.github.jmchilton.blend4j</groupId>
<artifactId>blend4j</artifactId>
<version>0.2.0</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</exclusion>
<exclusion>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
</exclusion>
<exclusion>
<groupId>org.mortbay.jetty</groupId>
<artifactId>servlet-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
</exclusion>
<exclusion>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<repositories>
<repository>
<id>REDHAT_GA</id>
<url>https://maven.repository.redhat.com/ga/</url>
</repository>
<repository>
<id>central</id>
<url>http://central.maven.org/maven2/</url>
</repository>
<repository>
<id>sonatype</id>
<url>https://oss.sonatype.org/content/repositories/releases/</url>
</repository>
</repositories>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>del-target-dir</id>
<phase>validate</phase>
<goals>
<goal>clean</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.9.0</version>
<configuration>
<source>17</source>
<target>17</target>
<compilerArguments>
<endorseddirs>${endorsed.dir}</endorseddirs>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.3.2</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
<archive>
<manifestEntries>
<Implementation-version>${project.version}</Implementation-version>
</manifestEntries>
<manifestFile>src/main/resources/MANIFEST.MF</manifestFile>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<outputDirectory>${endorsed.dir}</outputDirectory>
<silent>true</silent>
<artifactItems>
<artifactItem>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>8.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>exec-maven-plugin</artifactId>
<version>1.6.0</version>
<groupId>org.codehaus.mojo</groupId>
<executions>
<!-- decompress war to directory -->
<execution>
<id>unwar</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>unzip</executable>
<workingDirectory>${project.build.directory}</workingDirectory>
<arguments>
<argument>-uo</argument>
<argument>${project.build.finalName}.war</argument>
<argument>-d</argument>
<argument>gigwa</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>update-docker-compose-image-version</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>sed</executable>
<arguments>
<argument>-i</argument>
<argument>-E</argument>
<argument>s/(image: guilhemsempere\/gigwa.*)/image: guilhemsempere\/gigwa:${project.version}/g</argument>
<argument>${project.basedir}/docker-compose.yml</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>update-bundle-linux-project-version</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>sed</executable>
<arguments>
<argument>-i</argument>
<argument>-E</argument>
<argument>s/(project_version=.*)/project_version="${project.version}"/g</argument>
<argument>${project.basedir}/misc/linux_bundle.sh</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>update-bundle-macos-project-version</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>sed</executable>
<arguments>
<argument>-i</argument>
<argument>-E</argument>
<argument>s/(project_version=.*)/project_version="${project.version}"/g</argument>
<argument>${project.basedir}/misc/macos_bundle.command</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>update-bundle-windows-project-version</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>sed</executable>
<arguments>
<argument>-i</argument>
<argument>-E</argument>
<argument>s/(\$project_version =.*)/$project_version = "${project.version}"/g</argument>
<argument>${project.basedir}/misc/win_bundle.ps1</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>update-manifest-version</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>sed</executable>
<arguments>
<argument>-i</argument>
<argument>-E</argument>
<argument>s/Implementation-version:.*/Implementation-version: ${project.version}/g</argument>
<argument>${project.basedir}/src/main/webapp/META-INF/MANIFEST.MF</argument>
</arguments>
</configuration>
</execution>
</executions>
</plugin>
<!-- MUST remain here although empty, bundle build will fail otherwise
(making Maven respect an execution order is a nightmare!) -->
<plugin>
<groupId>com.coderplus.maven.plugins</groupId>
<artifactId>copy-rename-maven-plugin</artifactId>
<version>1.0.1</version>
<executions>
</executions>
</plugin>
<plugin>
<artifactId>exec-maven-plugin</artifactId>
<version>1.6.0</version>
<groupId>org.codehaus.mojo</groupId>
<executions>
<!-- make log4j write to file and change DEBUG levels to INFO -->
<execution>
<id>update-log4j-config</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>sed</executable>
<arguments>
<argument>-i</argument>
<argument>-E</argument>
<argument>s/ref ref="console"/ref ref="FILE"/g;s/priority value="DEBUG"/priority value="INFO"/g</argument>
<argument>target/gigwa/WEB-INF/classes/log4j.xml</argument>
</arguments>
</configuration>
</execution>
<!-- zip directory to create webapp package -->
<execution>
<id>zip-webapp</id>
<phase>pre-integration-test</phase> <!-- This should be in package phase but when it's there it executes before set-default-config -->
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>zip</executable>
<workingDirectory>${project.build.directory}</workingDirectory>
<arguments>
<argument>-u</argument>
<argument>-r</argument>
<argument>Gigwa_V${project.version}_Webapp.zip</argument>
<argument>gigwa</argument>
</arguments>
</configuration>
</execution>
<!-- copy updateGigwa scripts so users always get the latest version for their OS -->
<execution>
<id>copy-updateGigwa-scripts</id>
<phase>pre-integration-test</phase> <!-- This should be in package phase but when it's there it executes before set-default-config -->
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>zip</executable>
<workingDirectory>${project.build.directory}</workingDirectory>
<arguments>
<argument>-j</argument>
<argument>-u</argument>
<argument>Gigwa_V${project.version}_Webapp.zip</argument>
<argument>${project.basedir}/bundle_files/ubuntu/updateGigwa.sh</argument>
<argument>${project.basedir}/bundle_files/windows/updateGigwa.bat</argument>
<argument>${project.basedir}/bundle_files/osx/updateGigwa.command</argument>
<argument>target</argument>
</arguments>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<!-- This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself -->
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
</artifactId>
<versionRange>
[3.0.0,)
</versionRange>
<goals>
<goal>clean</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore></ignore>
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
<profiles>
<profile>
<id>bundles</id> <!-- Create bundles for Ubuntu, OSX and Windows -->
<build>
<plugins>
<plugin>
<groupId>com.googlecode.maven-download-plugin</groupId>
<artifactId>download-maven-plugin</artifactId>
<version>1.4.2</version>
<executions>
<!-- Download and unzip Tomcat -->
<execution>
<id>download-apache-tomcat-for-bundle-ubuntu</id>
<phase>initialize</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://archive.apache.org/dist/tomcat/tomcat-9/v${tomcat.version}/bin/apache-tomcat-${tomcat.version}.zip</url>
<unpack>true</unpack>
<outputDirectory>${bundle.dir.ubuntu}</outputDirectory>
</configuration>
</execution>
<execution>
<id>download-apache-tomcat-for-bundle-osx</id>
<phase>initialize</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://archive.apache.org/dist/tomcat/tomcat-9/v${tomcat.version}/bin/apache-tomcat-${tomcat.version}.zip</url>
<unpack>true</unpack>
<outputDirectory>${bundle.dir.osx}</outputDirectory>
</configuration>
</execution>
<execution>
<id>download-apache-tomcat-for-bundle-windows</id>
<phase>initialize</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://archive.apache.org/dist/tomcat/tomcat-9/v${tomcat.version}/bin/apache-tomcat-${tomcat.version}.zip</url>
<unpack>true</unpack>
<outputDirectory>${bundle.dir.windows}</outputDirectory>
</configuration>
</execution>
<!-- Download and unzip MongoDB -->
<execution>
<id>download-mongo-for-bundle-ubuntu</id>
<phase>initialize</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://fastdl.mongodb.org/linux/mongodb-${mongodb.linux.file}.tgz</url>
<unpack>true</unpack>
<outputDirectory>${bundle.dir.ubuntu}</outputDirectory>
</configuration>
</execution>
<execution>
<id>download-mongo-for-bundle-osx</id>
<phase>initialize</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://fastdl.mongodb.org/osx/mongodb-${mongodb.osx.file}.tgz</url>
<unpack>true</unpack>
<outputDirectory>${bundle.dir.osx}</outputDirectory>
</configuration>
</execution>
<execution>
<id>download-mongo-for-bundle-windows</id>
<phase>initialize</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>https://fastdl.mongodb.org/win32/mongodb-${mongodb.windows.file}.zip</url>
<unpack>true</unpack>
<outputDirectory>${bundle.dir.windows}</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.coderplus.maven.plugins</groupId>
<artifactId>copy-rename-maven-plugin</artifactId>
<version>1.0.1</version>
<executions>
<execution> <!-- Give generic names to tomcat and mongodb directories -->
<id>rename-tomcat-and-mongodb-dirs</id>
<phase>generate-sources</phase>
<goals>
<goal>rename</goal>
</goals>
<configuration>
<fileSets>
<fileSet>
<sourceFile>${bundle.dir.ubuntu}/apache-tomcat-${tomcat.version}</sourceFile>
<destinationFile>${bundle.dir.ubuntu}/tomcat</destinationFile>
</fileSet>
<fileSet>
<sourceFile>${bundle.dir.osx}/apache-tomcat-${tomcat.version}</sourceFile>
<destinationFile>${bundle.dir.osx}/tomcat</destinationFile>
</fileSet>
<fileSet>
<sourceFile>${bundle.dir.windows}/apache-tomcat-${tomcat.version}</sourceFile>
<destinationFile>${bundle.dir.windows}/tomcat</destinationFile>
</fileSet>
<fileSet>
<sourceFile>${bundle.dir.ubuntu}/mongodb-${mongodb.linux.file}</sourceFile>
<destinationFile>${bundle.dir.ubuntu}/mongodb</destinationFile>
</fileSet>
<fileSet>
<sourceFile>${bundle.dir.osx}/mongodb-${mongodb.osx.folder}</sourceFile>
<destinationFile>${bundle.dir.osx}/mongodb</destinationFile>
</fileSet>
<fileSet>
<sourceFile>${bundle.dir.windows}/mongodb-${mongodb.windows.file}</sourceFile>
<destinationFile>${bundle.dir.windows}/mongodb</destinationFile>
</fileSet>
</fileSets>
</configuration>
</execution>
<execution> <!-- Add sample vcf (the one required for unit tests) -->
<id>copy-vcf-sample</id>
<phase>generate-sources</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<fileSets>
<fileSet>
<sourceFile>${project.basedir}/test/sample.vcf</sourceFile>
<destinationFile>${bundle.dir.ubuntu}/vcf/sample.vcf</destinationFile>
</fileSet>
<fileSet>
<sourceFile>${project.basedir}/test/sample.vcf</sourceFile>
<destinationFile>${bundle.dir.osx}/vcf/sample.vcf</destinationFile>
</fileSet>
<fileSet>
<sourceFile>${project.basedir}/test/sample.vcf</sourceFile>
<destinationFile>${bundle.dir.windows}/vcf/sample.vcf</destinationFile>
</fileSet>
</fileSets>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>exec-maven-plugin</artifactId>
<version>1.6.0</version>
<groupId>org.codehaus.mojo</groupId>
<executions>
<!-- Create setenv scripts to adjust tomcat memory usage -->
<execution>
<phase>pre-integration-test</phase>
<id>create-setenv-ubuntu</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>echo</executable>
<arguments>
<argument>-e</argument>
<argument>LC_ALL=</argument>
<argument>\nexport CATALINA_OPTS="$CATALINA_OPTS -Xms512m -Xmx2048m"</argument>
<argument>\nexport JAVA_OPTS="$JAVA_OPTS -Dlog4j2.formatMsgNoLookups=true"</argument>
</arguments>
<outputFile>${bundle.dir.ubuntu}/tomcat/bin/setenv.sh</outputFile>
</configuration>
</execution>
<execution>
<phase>pre-integration-test</phase>
<id>create-setenv-osx</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>echo</executable>
<arguments>
<argument>-e</argument>
<argument>export CATALINA_OPTS="$CATALINA_OPTS -Xms512m -Xmx2048m"</argument>
<argument>\nexport JAVA_OPTS="$JAVA_OPTS -Dlog4j2.formatMsgNoLookups=true"</argument>
</arguments>
<outputFile>${bundle.dir.osx}/tomcat/bin/setenv.sh</outputFile>
</configuration>
</execution>
<execution>
<phase>pre-integration-test</phase>
<id>create-setenv-windows</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>echo</executable>
<arguments>
<argument>-e</argument>
<argument>set "JAVA_OPTS=%JAVA_OPTS% -Xms512m -Xmx2048m"</argument>
<argument>\nset "JAVA_OPTS=%JAVA_OPTS% -Dlog4j2.formatMsgNoLookups=true"</argument>
</arguments>
<outputFile>${bundle.dir.windows}/tomcat/bin/setenv.bat</outputFile>
</configuration>
</execution>
<!-- Add all additional files to bundles (start/stop/update scripts, license, readme) -->
<execution>
<phase>pre-integration-test</phase>
<id>copy-scripts-ubuntu</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>bash</executable>
<arguments>
<argument>-c</argument>
<argument>cp ${project.basedir}/bundle_files/ubuntu/* ${bundle.dir.ubuntu}</argument>
</arguments>
</configuration>
</execution>
<execution>
<phase>pre-integration-test</phase>
<id>copy-scripts-osx</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>bash</executable>
<arguments>
<argument>-c</argument>
<argument>cp ${project.basedir}/bundle_files/osx/* ${bundle.dir.osx}</argument>
</arguments>
</configuration>
</execution>
<execution>
<phase>pre-integration-test</phase>
<id>copy-scripts-windows</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>bash</executable>
<arguments>
<argument>-c</argument>
<argument>cp ${project.basedir}/bundle_files/windows/* ${bundle.dir.windows}</argument>
</arguments>
</configuration>
</execution>
<!-- Create data and logs directories -->
<execution>
<phase>pre-integration-test</phase>
<id>add-empty-folders-ubuntu</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>mkdir</executable>
<arguments>
<argument>${bundle.dir.ubuntu}/data</argument>
<argument>${bundle.dir.ubuntu}/logs</argument>
</arguments>
</configuration>
</execution>
<execution>
<phase>pre-integration-test</phase>
<id>add-empty-folders-osx</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>mkdir</executable>
<arguments>
<argument>${bundle.dir.osx}/data</argument>
<argument>${bundle.dir.osx}/logs</argument>
</arguments>
</configuration>
</execution>
<execution>
<phase>pre-integration-test</phase>
<id>add-empty-folders-windows</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>mkdir</executable>
<arguments>
<argument>${bundle.dir.windows}/data</argument>
<argument>${bundle.dir.windows}/logs</argument>
</arguments>
</configuration>
</execution>
<!-- Add JRE to bundle (this is not downloaded but expected to be found at locations defined in variables at the top of the file) -->
<execution>
<id>add-jre-ubuntu</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>tar</executable>
<workingDirectory>${bundle.dir.ubuntu}/jre</workingDirectory>
<arguments>
<argument>xvzf</argument>
<argument>${path.to.ubuntu.jre}</argument>
<argument>--strip-components=1</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>add-jre-osx</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>tar</executable>
<workingDirectory>${bundle.dir.osx}/jre</workingDirectory>
<arguments>
<argument>xvzf</argument>
<argument>${path.to.osx.jre}</argument>
<argument>--strip-components=1</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>add-jre-windows</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>tar</executable>
<workingDirectory>${bundle.dir.windows}/jre</workingDirectory>
<arguments>
<argument>xvzf</argument>
<argument>${path.to.windows.jre}</argument>
<argument>--strip-components=1</argument>
</arguments>
</configuration>
</execution>
<!-- Delete Tomcat's examples webapp -->
<execution>
<id>rm-examples-webapp-ubuntu</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>rm</executable>
<arguments>
<argument>-rf</argument>
<argument>${bundle.dir.ubuntu}/tomcat/webapps/examples</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>rm-examples-webapp-osx</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>rm</executable>
<arguments>
<argument>-rf</argument>
<argument>${bundle.dir.osx}/tomcat/webapps/examples</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>rm-examples-webapp-windows</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>rm</executable>
<arguments>
<argument>-rf</argument>
<argument>${bundle.dir.windows}/tomcat/webapps/examples</argument>
</arguments>
</configuration>
</execution>
<!-- Copy gigwa webapp into Tomcat -->
<execution>
<id>copy-webapp-ubuntu</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>cp</executable>
<arguments>
<argument>-r</argument>
<argument>${project.build.directory}/gigwa</argument>
<argument>${bundle.dir.ubuntu}/tomcat/webapps/gigwa</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>copy-webapp-osx</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>cp</executable>
<arguments>
<argument>-r</argument>
<argument>${project.build.directory}/gigwa</argument>
<argument>${bundle.dir.osx}/tomcat/webapps/gigwa</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>copy-webapp-windows</id>
<phase>integration-test</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>cp</executable>
<arguments>
<argument>-r</argument>
<argument>${project.build.directory}/gigwa</argument>
<argument>${bundle.dir.windows}/tomcat/webapps/gigwa</argument>
</arguments>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.google.code.maven-replacer-plugin</groupId>
<artifactId>replacer</artifactId>
<version>1.5.3</version>
<executions>
<!-- Set port to 59395 instead of 8080 in server.xml -->
<execution>
<id>set-tomcat-ports-ubuntu</id>
<phase>post-integration-test</phase>
<goals>
<goal>replace</goal>
</goals>
<configuration>
<file>${bundle.dir.ubuntu}/tomcat/conf/server.xml</file>
<replacements>
<replacement>