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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>
<groupId>edu.ucdavis.fiehnlab.mona</groupId>
<artifactId>mona</artifactId>
<version>2.6.3-SNAPSHOT</version>
<name>mona</name>
<packaging>pom</packaging>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.6.3</version>
<relativePath/>
</parent>
<properties>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
<encoding>UTF-8</encoding>
<scala.version>2.13</scala.version>
<scala.minor.version>6</scala.minor.version>
<java.version>17</java.version>
<jackson.version>2.13.1</jackson.version>
</properties>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>javax.el</groupId>
<artifactId>javax.el-api</artifactId>
<version>3.0.0</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.module/jackson-module-scala_2.11 -->
<dependency>
<groupId>com.fasterxml.jackson.module</groupId>
<artifactId>jackson-module-scala_2.13</artifactId>
<version>${jackson.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-core -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.jayway.restassured</groupId>
<artifactId>rest-assured</artifactId>
<version>2.8.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.mangofactory</groupId>
<artifactId>swagger-springmvc</artifactId>
<version>1.0.2</version>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-actor_2.13</artifactId>
<version>2.6.17</version>
</dependency>
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-java8-compat_2.13</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>io.spray</groupId>
<artifactId>spray-client_2.13</artifactId>
<version>1.3.5</version>
</dependency>
<dependency>
<groupId>io.spray</groupId>
<artifactId>spray-json_2.13</artifactId>
<version>1.3.5</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>2.10.0</version>
</dependency>
<dependency>
<groupId>org.springframework.cloud</groupId>
<artifactId>spring-cloud-dependencies</artifactId>
<version>2021.0.3</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>edu.ucdavis.fiehnlab.utilities</groupId>
<artifactId>compress</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.typesafe.scala-logging/scala-logging_2.11 -->
<dependency>
<groupId>com.typesafe.scala-logging</groupId>
<artifactId>scala-logging_${scala.version}</artifactId>
<version>3.9.4</version>
</dependency>
</dependencies>
</dependencyManagement>
<!-- our default stack to be used in the fiehnlab -->
<profiles>
<!--scala support for compiling of tests-->
<profile>
<id>scala-test</id>
<activation>
<file>
<exists>src/test/scala</exists>
</file>
</activation>
<dependencies>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}.${scala.minor.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.scalatest/scalatest_2.11 -->
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.version}</artifactId>
<version>3.2.9</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatestplus</groupId>
<artifactId>scalacheck-1-15_2.13</artifactId>
<version>3.2.9.0</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/org.scala-lang.modules/scala-parser-combinators -->
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-parser-combinators_2.13</artifactId>
<version>2.1.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.scala-lang.modules/scala-xml -->
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-xml_2.13</artifactId>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-parallel-collections_2.13</artifactId>
<version>0.2.0</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.7.0</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/scala</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.7.0</version>
<executions>
<execution>
<id>scala-compile</id>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}.${scala.minor.version}</scalaVersion>
<jvmArgs>
<jvmArg>-Xms64m</jvmArg>
<jvmArg>-Xmx8192m</jvmArg>
<jvmArg>-XX:+UseParallelGC</jvmArg>
<jvmArg>-XX:ReservedCodeCacheSize=2G</jvmArg>
<jvmArg>-XX:+UseCodeCacheFlushing</jvmArg>
<jvmArg>--add-opens=java.base/sun.nio.ch=ALL-UNNAMED</jvmArg>
<jvmArg>--add-opens java.base/java.lang=ALL-UNNAMED</jvmArg>
</jvmArgs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.12.4</version>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>scalatest.txt</filereports>
<parallel>false</parallel>
<forkMode>once</forkMode>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<!-- support to compile scala files -->
<profile>
<id>scala</id>
<activation>
<file>
<exists>src/main/scala</exists>
</file>
</activation>
<dependencies>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}.${scala.minor.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.scalatest/scalatest_2.11 -->
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.version}</artifactId>
<version>3.2.9</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-parallel-collections_2.13</artifactId>
<version>0.2.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.scala-lang.modules/scala-parser-combinators -->
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-parser-combinators_2.13</artifactId>
<version>2.1.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.scala-lang.modules/scala-xml -->
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-xml_2.13</artifactId>
<version>2.0.1</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.7.0</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/scala</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.7.0</version>
<executions>
<execution>
<id>scala-compile</id>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}.${scala.minor.version}</scalaVersion>
<jvmArgs>
<jvmArg>-Xms64m</jvmArg>
<jvmArg>-Xmx1024m</jvmArg>
<jvmArg>-XX:+UseParallelGC</jvmArg>
<jvmArg>-XX:ReservedCodeCacheSize=4G</jvmArg>
</jvmArgs>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<!-- test jar -->
<profile>
<id>test-jar</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.2</version>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
<phase>test-compile</phase>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<!-- java doc jar -->
<profile>
<id>doc-jar</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<!-- source jar -->
<profile>
<id>source-jar</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<!-- this profile is building a docker image for us, which can be a standalone or deployed in a docker-compose file -->
<profile>
<id>docker</id>
<!-- will activate if you have a .docker file in your project directory-->
<activation>
<file>
<exists>.docker</exists>
</file>
</activation>
<properties>
<docker.registry>public.ecr.aws/fiehnlab</docker.registry>
<docker.baseImage>amazoncorretto:17.0.6</docker.baseImage>
<docker.imagePrefix>mona</docker.imagePrefix>
<docker.imageName>${docker.imagePrefix}-${project.name}</docker.imageName>
<docker.imagePath>${docker.registry}/${docker.imageName}</docker.imagePath>
<docker.expose>8080</docker.expose>
<docker.jvm>-Xmx2048m</docker.jvm>
<docker.tag>test</docker.tag>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<phase>compile</phase>
<id>download-remote-resources</id>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
<get src="https://raw.githubusercontent.com/vishnubob/wait-for-it/master/wait-for-it.sh"
dest="${project.build.directory}"/>
<chmod file="${project.build.directory}/wait-for-it.sh" perm="777"/>
</target>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<executions>
<execution>
<id>repackage</id>
<goals>
<goal>repackage</goal>
</goals>
<configuration>
<classifier>exec</classifier>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.spotify</groupId>
<artifactId>docker-maven-plugin</artifactId>
<version>1.2.2</version>
<configuration>
<imageName>${docker.registry}/${docker.imageName}</imageName>
<baseImage>${docker.baseImage}</baseImage>
<entryPoint>["java","${docker.jvm}", "-jar", "/${project.build.finalName}.jar"]</entryPoint>
<exposes>
<expose>${docker.expose}</expose>
</exposes>
<!-- copy the service's jar file from target into the root directory of the image -->
<resources>
<resource>
<targetPath>/</targetPath>
<directory>${project.build.directory}</directory>
<include>${project.build.finalName}-exec.jar</include>
<include>wait-for-it.sh</include>
</resource>
</resources>
<forceTags>true</forceTags>
<imageTags>
<imageTag>${project.version}</imageTag>
<imageTag>${docker.tag}</imageTag>
</imageTags>
<runs>
<run>mv /${project.build.finalName}-exec.jar /${project.build.finalName}.jar</run>
<run>chmod 777 /wait-for-it.sh</run>
</runs>
</configuration>
<executions>
<execution>
<phase>install</phase>
<goals>
<goal>build</goal>
</goals>
</execution>
<execution>
<id>push-image-version</id>
<phase>deploy</phase>
<goals>
<goal>push</goal>
</goals>
<configuration>
<imageName>${docker.registry}/${docker.imageName}:${project.version}</imageName>
</configuration>
</execution>
<execution>
<id>push-image-latest</id>
<phase>deploy</phase>
<goals>
<goal>push</goal>
</goals>
<configuration>
<imageName>${docker.registry}/${docker.imageName}:${docker.tag}</imageName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<distributionManagement>
<repository>
<id>releases</id>
<name>Fiehnlab Releases</name>
<url>http://gose.fiehnlab.ucdavis.edu:55000/content/repositories/releases/</url>
</repository>
<snapshotRepository>
<id>snapshots</id>
<name>Fiehnlab Snapshots</name>
<url>http://gose.fiehnlab.ucdavis.edu:55000/content/repositories/snapshots/</url>
</snapshotRepository>
</distributionManagement>
<repositories>
<repository>
<id>spring-releases</id>
<url>https://repo.spring.io/libs-release</url>
</repository>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>true</enabled>
</releases>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>spring-releases</id>
<url>https://repo.spring.io/libs-release</url>
</pluginRepository>
</pluginRepositories>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>${maven.compiler.source}</source>
<target>${maven.compiler.target}</target>
</configuration>
</plugin>
</plugins>
</build>
</project>