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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>org.lifs-tools</groupId>
<artifactId>lifs-goslin-webapp</artifactId>
<version>2.2.1-SNAPSHOT</version>
<packaging>jar</packaging>
<description>Grammar of Succinct Lipid Nomenclature - Webapplication and REST service for parsing, validation and normalization of lipid names.</description>
<name>LIFS Goslin webapp.</name>
<url>https://github.com/lifs-tool/goslin-webapp</url>
<licenses>
<license>
<name>The Apache License, Version 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<name>Nils Hoffmann</name>
<email>[email protected]</email>
<organization>Center For Biotechnology</organization>
<organizationUrl>https://cebitec.uni-bielefeld.de</organizationUrl>
<roles>
<role>developer</role>
</roles>
<timezone>Europe/Berlin</timezone>
</developer>
</developers>
<scm>
<connection>scm:git:ssh://github.com:lifs-tools/goslin-webapp.git</connection>
<developerConnection>scm:git:ssh://github.com:lifs-tools/goslin-webapp.git</developerConnection>
<url>https://github.com/lifs-tools/goslin-webapp</url>
</scm>
<issueManagement>
<system>GitHub</system>
<url>https://github.com/lifs-tools/goslin-webapp/issues</url>
</issueManagement>
<organization>
<name>Lipidomics Informatics for Life Sciences</name>
<url>https://lifs-tools.org</url>
</organization>
<inceptionYear>2019</inceptionYear>
<distributionManagement>
<repository>
<id>artifactory-releases</id>
<name>lifstools-release-local</name>
<url>https://m.lifs-tools.org/artifactory/lifs-libs-release-local</url>
</repository>
<snapshotRepository>
<id>artifactory-snapshots</id>
<name>lifstools-snapshot-local</name>
<url>https://m.lifs-tools.org/artifactory/lifs-libs-snapshot-local</url>
</snapshotRepository>
</distributionManagement>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<!-- for spring boot -->
<java.version>17</java.version>
<application.version.number>${project.version}</application.version.number>
<docker.image.prefix>docker.lifs-tools.org/lifs</docker.image.prefix>
<docker.base.image>eclipse-temurin</docker.base.image>
<docker.base.image.version>17-jdk-alpine</docker.base.image.version>
<skip.docker>true</skip.docker>
<app.port>8083</app.port>
<jackson.version>2.18.1</jackson.version>
<spring.boot.version>3.3.5</spring.boot.version>
<springfox.version>3.0.0</springfox.version>
<lifs.webapps.common.version>1.1.4</lifs.webapps.common.version>
<jgoslin.version>2.2.1</jgoslin.version>
<jacoco.version>0.8.10</jacoco.version>
<assembly.dir>${project.artifactId}</assembly.dir>
<app.name>goslin</app.name>
<contextPath>/goslin</contextPath>
<start-class>org.lifstools.jgoslin.webapp.Application</start-class>
<spring.profiles.active></spring.profiles.active>
<!-- tracking info -->
<ga.id>10</ga.id>
<ga.url>https://lifs-tools.org/matomo/matomo.php</ga.url>
<ga.app.url>https://apps.lifs-tools.org/goslin</ga.app.url>
<!-- tool info -->
<tool.title>JGoslin</tool.title>
<tool.description></tool.description>
<tool.author>Nils Hoffmann, Dominik Kopczynski</tool.author>
<tool.license>Apache License v2</tool.license>
<tool.licenseUrl>https://www.apache.org/licenses/LICENSE-2.0</tool.licenseUrl>
<tool.version>${jgoslin.version}</tool.version>
<tool.contact>https://github.com/lifs-tools/jgoslin/issues</tool.contact>
<tool.url>https://github.com/lifs-tools/jgoslin</tool.url>
<!-- timestamp -->
<timestamp>${maven.build.timestamp}</timestamp>
<maven.build.timestamp.format>yyyy-MM-dd HH:mm</maven.build.timestamp.format>
</properties>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.lifs-tools</groupId>
<artifactId>lifs-webapps-common</artifactId>
<version>${lifs.webapps.common.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- HTTP client: jersey-client -->
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-multipart</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-json-jackson</artifactId>
<version>${jersey.version}</version>
</dependency>
<!-- JSON processing: jackson -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.14.2</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-joda</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-csv</artifactId>
<version>${jackson.version}</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>${jodatime.version}</version>
</dependency>
<!-- Base64 encoding that works in both JVM and Android -->
<dependency>
<groupId>com.brsanthu</groupId>
<artifactId>migbase64</artifactId>
<version>${migbase.version}</version>
</dependency>
<dependency>
<groupId>io.github.swagger2markup</groupId>
<artifactId>swagger2markup</artifactId>
<version>${swagger2markup.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.lifs-tools</groupId>
<artifactId>lifs-webapps-common</artifactId>
<version>${lifs.webapps.common.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf.extras</groupId>
<artifactId>thymeleaf-extras-springsecurity5</artifactId>
</dependency>
<dependency>
<groupId>org.keycloak</groupId>
<artifactId>keycloak-spring-boot-starter</artifactId>
<version>15.1.1</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-validation</artifactId>
</dependency>
<!--SpringFox dependencies -->
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-boot-starter</artifactId>
<version>${springfox.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-devtools</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-websocket</artifactId>
</dependency>
<!-- webjars -->
<dependency>
<groupId>org.webjars</groupId>
<artifactId>webjars-locator-core</artifactId>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>jquery</artifactId>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<version>${spring.boot.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.lifs-tools</groupId>
<artifactId>jgoslin-parsers</artifactId>
<version>${jgoslin.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>4.4</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
<type>jar</type>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<type>jar</type>
<version>32.0.0-jre</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-csv</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
</dependencies>
<build>
<resources>
<!-- filter only application*.properties files -->
<resource>
<directory>${project.basedir}/src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>application.properties</include>
<include>application-dev.properties</include>
<include>lifs.properties</include>
<include>tool.properties</include>
<include>tracking.properties</include>
</includes>
</resource>
<!-- pick up all other properties files -->
<resource>
<directory>${project.basedir}/src/main/resources</directory>
<filtering>false</filtering>
<excludes>
<exclude>application.properties</exclude>
<exclude>application-dev.properties</exclude>
<exclude>lifs.properties</exclude>
<exclude>tool.properties</exclude>
<exclude>tracking.properties</exclude>
</excludes>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.owasp</groupId>
<artifactId>dependency-check-maven</artifactId>
<version>8.4.3</version>
<configuration>
<cveValidForHours>12</cveValidForHours>
<failBuildOnCVSS>4</failBuildOnCVSS>
<skipProvidedScope>true</skipProvidedScope>
<skipRuntimeScope>true</skipRuntimeScope>
</configuration>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>3.2.1</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>create</goal>
</goals>
</execution>
</executions>
<configuration>
<doCheck>false</doCheck>
<doUpdate>false</doUpdate>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>3.1.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>3.1.3</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.8.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.3.0</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
</manifest>
<manifestEntries>
<Implementation-Build>${buildNumber}</Implementation-Build>
<Commit>${buildNumber}</Commit>
<Branch>${scmBranch}</Branch>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.5.0</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
<configuration>
<additionalparam>-Xdoclint:none</additionalparam>
</configuration>
</execution>
<execution>
<goals>
<goal>javadoc</goal>
</goals>
<phase>site</phase>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.11.0</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.1.2</version>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
<parallel>classes</parallel>
<threadCount>2</threadCount>
<trimStackTrace>false</trimStackTrace>
<workingDirectory>${project.build.directory}/surefire-files</workingDirectory>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.6.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.3.1</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<executions>
<execution>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<phase>prepare-package</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
<execution>
<id>post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<dataFile>target/jacoco.exec</dataFile>
<!-- Sets the output directory for the code coverage report. -->
<outputDirectory>target/jacoco-ut</outputDirectory>
</configuration>
</execution>
</executions>
<configuration>
<systemPropertyVariables>
<jacoco-agent.destfile>target/jacoco.exec</jacoco-agent.destfile>
</systemPropertyVariables>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<executable>true</executable>
<!--<mainClass>${start-class}</mainClass>-->
<!--<layout>ZIP</layout>-->
<profiles>
<profile>${spring.profiles.active}</profile>
</profiles>
</configuration>
<version>${spring.boot.version}</version>
<executions>
<execution>
<goals>
<goal>repackage</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.3.1</version>
<configuration>
<delimiters>
<delimiter>@</delimiter>
</delimiters>
<useDefaultDelimiters>false</useDefaultDelimiters>
</configuration>
</plugin>
<plugin>
<groupId>com.google.cloud.tools</groupId>
<artifactId>jib-maven-plugin</artifactId>
<version>3.3.2</version>
<configuration>
<from>
<image>${docker.base.image}:${docker.base.image.version}</image>
</from>
<to>
<image>${docker.image.prefix}/${project.artifactId}</image>
<tags>
<tag>${project.version}</tag>
<tag>latest</tag>
<!-- <tag>${project.version}${deploy.env}</tag> -->
</tags>
</to>
<container>
<jvmFlags>
<jvmFlag>-Djava.security.egd=file:/dev/./urandom</jvmFlag>
</jvmFlags>
<ports>
<port>${app.port}</port>
</ports>
<volumes>
<volume>/tmp</volume>
</volumes>
<!--<user>1000:1000</user>-->
<creationTime>USE_CURRENT_TIMESTAMP</creationTime>
</container>
<skip>true</skip>
<allowInsecureRegistries>false</allowInsecureRegistries>
</configuration>
</plugin>
</plugins>
</build>
<profiles>
<profile>
<id>dev</id>
<properties>
<spring.profiles.active>dev</spring.profiles.active>
</properties>
</profile>
<profile>
<id>release</id>
<build>
<plugins>
<!-- temporarily disabled due to huge numbers of false positives
<plugin>
<groupId>org.owasp</groupId>
<artifactId>dependency-check-maven</artifactId>
<configuration>
<cveValidForHours>12</cveValidForHours>
<failBuildOnCVSS>4</failBuildOnCVSS>
<skipProvidedScope>true</skipProvidedScope>
<skipRuntimeScope>true</skipRuntimeScope>
<suppressionFile>suppressions.xml</suppressionFile>
</configuration>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin> -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>docker</id>
<properties>
<skip.docker>false</skip.docker>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<executions>
<execution>
<id>repackage</id>
<goals>
<goal>repackage</goal>
</goals>
<configuration>
<skip>${skip.docker}</skip>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.google.cloud.tools</groupId>
<artifactId>jib-maven-plugin</artifactId>
<executions>
<execution>
<id>docker-push</id>
<phase>install</phase>
<goals>
<goal>build</goal>
</goals>
<configuration>
<skip>${skip.docker}</skip>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<repositories>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>artifactory-releases</id>
<name>lifstools-release</name>
<url>https://m.lifs-tools.org/artifactory/libs-release</url>
</repository>
<repository>
<snapshots />
<id>artifactory-snapshots</id>
<name>lifstools-snapshot</name>
<url>https://m.lifs-tools.org/artifactory/libs-snapshot</url>
</repository>
</repositories>
</project>