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EVA-4117 Project upgrade to java-21 and spring 3.4.13 #136

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db27a8d
Project upgrade to java-21 and spring 3.4.13
nitin-ebi Jun 26, 2026
76d6d92
Project upgrade to java-21 and spring 3.4.13
nitin-ebi Jun 26, 2026
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28 changes: 0 additions & 28 deletions .github/workflows/maven.yml
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32 changes: 32 additions & 0 deletions .github/workflows/run-tests.yml
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@@ -0,0 +1,32 @@
name: Run tests

on:
push:
branches: [ master, java21 ]
pull_request:
branches: [ master, java21 ]

jobs:
build:
runs-on: ubuntu-latest

permissions:
contents: read

strategy:
matrix:
java-version: [ 21 ]

steps:
- name: Checkout
uses: actions/checkout@v4

- name: Setup Java 21
uses: actions/setup-java@v4
with:
distribution: temurin
java-version: ${{ matrix.java-version }}
cache: maven

- name: Run Maven tests
run: mvn -B clean test
143 changes: 44 additions & 99 deletions pom.xml
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@@ -1,160 +1,105 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
~ Copyright 2020 EMBL - European Bioinformatics Institute
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->

<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.7.18</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>

<groupId>uk.ac.ebi.eva</groupId>
<artifactId>contig-alias</artifactId>
<version>0.1.12-SNAPSHOT</version>
<version>${revision}</version>
<name>contig-alias</name>
<description>Service to provide synonyms of chromosome/contig identifiers</description>
<packaging>war</packaging>

<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.4.13</version>
</parent>

<properties>
<java.version>8</java.version>
<testcontainers.version>1.17.6</testcontainers.version>
<revision>0.1.12-SNAPSHOT</revision>
<java.version>21</java.version>
</properties>

<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>

<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
</exclusion>
</exclusions>
</dependency>

<!-- https://mvnrepository.com/artifact/commons-net/commons-net -->
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.10.0</version>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>

<!-- Embedded H2 database for testing and CI testing -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<scope>runtime</scope>
<version>2.2.220</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>

<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
<artifactId>spring-boot-starter-hateoas</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
<artifactId>spring-boot-starter-aop</artifactId>
</dependency>

<!-- https://mvnrepository.com/artifact/org.springframework.security/spring-security-test -->
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-test</artifactId>
<scope>test</scope>
<groupId>org.springframework.retry</groupId>
<artifactId>spring-retry</artifactId>
</dependency>

<dependency>
<groupId>org.springdoc</groupId>
<artifactId>springdoc-openapi-ui</artifactId>
<version>1.7.0</version>
<artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
<version>2.8.17</version>
</dependency>

<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<scope>runtime</scope>
</dependency>

<!-- https://search.maven.org/artifact/org.springframework.boot/spring-boot-starter-hateoas -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-hateoas</artifactId>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.10.0</version>
</dependency>

<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-aop -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-aop</artifactId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>

<!-- https://mvnrepository.com/artifact/org.springframework.retry/spring-retry -->
<dependency>
<groupId>org.springframework.retry</groupId>
<artifactId>spring-retry</artifactId>
<version>1.3.1</version>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-test</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-testcontainers</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>postgresql</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers-bom</artifactId>
<version>${testcontainers.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>

<build>
<finalName>${project.artifactId}-${project.version}-${git.commit.id.abbrev}</finalName>
<finalName>${project.artifactId}-${revision}-${git.commit.id.abbrev}</finalName>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
Expand All @@ -168,9 +113,9 @@
</executions>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.2.5</version>
<groupId>io.github.git-commit-id</groupId>
<artifactId>git-commit-id-maven-plugin</artifactId>
<version>9.0.1</version>
<configuration>
<includeOnlyProperties>
<includeOnlyProperty>^git.tags$</includeOnlyProperty>
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4 changes: 2 additions & 2 deletions ...ac/ebi/eva/contigalias/controller/authentication/CustomBasicAuthenticationEntryPoint.java
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Expand Up @@ -16,12 +16,12 @@

package uk.ac.ebi.eva.contigalias.controller.authentication;

import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.springframework.security.core.AuthenticationException;
import org.springframework.security.web.authentication.www.BasicAuthenticationEntryPoint;
import org.springframework.stereotype.Component;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.io.PrintWriter;

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59 changes: 37 additions & 22 deletions src/main/java/uk/ac/ebi/eva/contigalias/controller/authentication/SecurityConfiguration.java
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Expand Up @@ -18,17 +18,22 @@

import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
import org.springframework.security.config.annotation.web.builders.HttpSecurity;
import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
import org.springframework.security.config.annotation.web.configurers.AbstractHttpConfigurer;
import org.springframework.security.config.http.SessionCreationPolicy;
import org.springframework.security.core.userdetails.User;
import org.springframework.security.core.userdetails.UserDetailsService;
import org.springframework.security.crypto.bcrypt.BCryptPasswordEncoder;
import org.springframework.security.crypto.password.PasswordEncoder;
import org.springframework.security.provisioning.InMemoryUserDetailsManager;
import org.springframework.security.web.SecurityFilterChain;

@Configuration
@EnableWebSecurity
public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
public class SecurityConfiguration {

public static final String REALM = "EBI-REALM";

Expand All @@ -47,26 +52,36 @@ public SecurityConfiguration(CustomBasicAuthenticationEntryPoint customBasicAuth
this.customBasicAuthenticationEntryPoint = customBasicAuthenticationEntryPoint;
}

@Autowired
public void configureGlobalSecurity(AuthenticationManagerBuilder auth) throws Exception {
String encodedPassword = "{bcrypt}" + new BCryptPasswordEncoder().encode(PASSWORD_ADMIN);
auth.inMemoryAuthentication()
.withUser(USERNAME_ADMIN)
.password(encodedPassword)
.roles(ROLE_ADMIN);
@Bean
public PasswordEncoder passwordEncoder() {
return new BCryptPasswordEncoder();
}

@Bean
public UserDetailsService userDetailsService() {
return new InMemoryUserDetailsManager(
User.withUsername(USERNAME_ADMIN)
.password(passwordEncoder().encode(PASSWORD_ADMIN))
.roles(ROLE_ADMIN)
.build()
);
}

@Override
protected void configure(HttpSecurity http) throws Exception {
http.csrf().disable()
.authorizeRequests()
.antMatchers("/v1/assemblies/**", "/v1/chromosomes/**", "/v1/search/**").permitAll()
.antMatchers("/info", "/health").permitAll()
.antMatchers("/swagger-ui/**", "/v3/api-docs/**", "/swagger-ui.html").permitAll()
.antMatchers("/v1/admin/**").hasRole(ROLE_ADMIN)
.anyRequest().denyAll()
.and().httpBasic().realmName(REALM)
.authenticationEntryPoint(customBasicAuthenticationEntryPoint)
.and().sessionManagement().sessionCreationPolicy(SessionCreationPolicy.STATELESS);
@Bean
public SecurityFilterChain securityFilterChain(HttpSecurity http) throws Exception {
http.csrf(AbstractHttpConfigurer::disable)
.authorizeHttpRequests(auth -> auth
.requestMatchers("/v1/assemblies/**", "/v1/chromosomes/**", "/v1/search/**").permitAll()
.requestMatchers("/info", "/health").permitAll()
.requestMatchers("/swagger-ui/**", "/v3/api-docs/**", "/swagger-ui.html").permitAll()
.requestMatchers("/v1/admin/**").hasRole(ROLE_ADMIN)
.anyRequest().denyAll()
).httpBasic(basic -> basic.realmName(REALM)
.authenticationEntryPoint(customBasicAuthenticationEntryPoint)
).sessionManagement(session -> session
.sessionCreationPolicy(SessionCreationPolicy.STATELESS)
);

return http.build();
}
}
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