Upgrade/upgrade to java 17

Dockerfile

@@ -1,21 +1,21 @@
-FROM maven:3.6.1-jdk-11 as MAVEN
+FROM maven:3.9.6-eclipse-temurin-17-alpine as MAVEN
 
 COPY . /fta-fmea
 WORKDIR /fta-fmea/ontology-generator
 RUN mvn clean install
 
-FROM gradle:6.4-jdk11 as GRADLE
+FROM gradle:8.4-jdk17-alpine as GRADLE
 COPY . /fta-fmea
 WORKDIR /fta-fmea
 
 COPY --from=MAVEN /fta-fmea/src/main/generated/cz/cvut/kbss/analysis/util/Vocabulary.java \
                    ./src/main/generated/cz/cvut/kbss/analysis/util/Vocabulary.java
 
-RUN ./gradlew clean war
+RUN ./gradlew clean bootJar
 
-FROM tomcat:8-jdk11
+FROM eclipse-temurin:17-jdk-alpine as runtime
 
-COPY --from=GRADLE /fta-fmea/build/libs/fta-fmea-*.war /usr/local/tomcat/webapps/fta-fmea.war
+COPY --from=GRADLE /fta-fmea/build/libs/fta-fmea-*.jar /fta-fmea.jar
 
 EXPOSE 8080
-CMD ["catalina.sh", "run"]
+CMD ["java", "-jar", "/fta-fmea.jar"]

build.gradle

@@ -8,7 +8,7 @@ buildscript {
 }
 
 plugins {
-    id 'org.springframework.boot' version '2.7.17'
+    id 'org.springframework.boot' version '3.1.5'
     id 'io.spring.dependency-management' version '1.1.3'
     id 'io.freefair.aspectj.post-compile-weaving' version '8.4'
     id 'java'
@@ -19,8 +19,8 @@ group = 'cz.cvut.kbss.analysis'
 version = '0.0.1-SNAPSHOT'
 
 compileJava {
-    sourceCompatibility = '11'
-    targetCompatibility = '11'
+    sourceCompatibility = '17'
+    targetCompatibility = '17'
 }
 
 repositories {
@@ -49,10 +49,12 @@ dependencies {
     implementation 'com.fasterxml:classmate:1.5.0'
     implementation 'com.opencsv:opencsv:5.3'
 
-    implementation 'org.projectlombok:lombok:1.18.12'
-    annotationProcessor 'org.projectlombok:lombok:1.18.12'
+    implementation 'org.projectlombok:lombok:1.18.30'
+    annotationProcessor 'org.projectlombok:lombok:1.18.30'
     providedRuntime 'org.springframework.boot:spring-boot-starter-tomcat'
 
+    providedRuntime 'jakarta.servlet:jakarta.servlet-api'
+
     implementation 'javax.xml.bind:jaxb-api:2.3.1' // needed for java 17
 
     aspect 'cz.cvut.kbss.jopa:jopa-impl:1.1.4'

ontology-generator/pom.xml

@@ -20,7 +20,7 @@
                 <!-- Generate entity classes from OWL integrity constraints -->
                 <groupId>cz.cvut.kbss.jopa</groupId>
                 <artifactId>jopa-maven-plugin</artifactId>
-                <version>0.14.7</version>
+                <version>1.1.4</version>
                 <configuration>
                     <package>cz.cvut.kbss.analysis.util</package>
                     <!--Generate Vocabulary into Gradle project dirs-->

src/main/java/cz/cvut/kbss/analysis/config/JacksonConfig.java

@@ -4,6 +4,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import cz.cvut.kbss.jsonld.ConfigParam;
 import cz.cvut.kbss.jsonld.jackson.JsonLdModule;
+import cz.cvut.kbss.jsonld.jackson.serialization.SerializationConstants;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
@@ -16,6 +17,7 @@ public ObjectMapper objectMapper() {
         mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
         JsonLdModule m = new JsonLdModule();
         m.configure(ConfigParam.SCAN_PACKAGE, "cz.cvut.kbss.analysis");
+        m.configure(SerializationConstants.FORM, SerializationConstants.FORM_COMPACT_WITH_CONTEXT);
         mapper.registerModule(m);
         return mapper;
     }

src/main/java/cz/cvut/kbss/analysis/config/SecurityConfig.java

@@ -3,23 +3,29 @@
 import cz.cvut.kbss.analysis.security.JwtConfigurer;
 import cz.cvut.kbss.analysis.service.JwtTokenProvider;
 import cz.cvut.kbss.analysis.service.security.SecurityUtils;
+import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.security.authentication.AuthenticationManager;
-import org.springframework.security.config.annotation.method.configuration.EnableGlobalMethodSecurity;
+import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
+import org.springframework.security.config.annotation.method.configuration.EnableMethodSecurity;
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
-import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
+import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
 import org.springframework.security.config.http.SessionCreationPolicy;
+import org.springframework.security.web.SecurityFilterChain;
+import org.springframework.security.web.util.matcher.AntPathRequestMatcher;
 import org.springframework.web.cors.CorsConfiguration;
 import org.springframework.web.cors.CorsConfigurationSource;
 import org.springframework.web.cors.UrlBasedCorsConfigurationSource;
 
 import java.util.Arrays;
 
 @Configuration
-@EnableGlobalMethodSecurity(prePostEnabled = true)
-public class SecurityConfig extends WebSecurityConfigurerAdapter {
+@EnableWebSecurity
+@Slf4j
+@EnableMethodSecurity(prePostEnabled = true)
+public class SecurityConfig {
 
     private final JwtTokenProvider jwtTokenProvider;
     private final SecurityUtils securityUtils;
@@ -31,13 +37,13 @@ public SecurityConfig(JwtTokenProvider jwtTokenProvider, SecurityUtils securityU
     }
 
     @Bean
-    @Override
-    public AuthenticationManager authenticationManagerBean() throws Exception {
-        return super.authenticationManagerBean();
+    public AuthenticationManager buildAuthenticationManager(HttpSecurity http) throws Exception {
+        final AuthenticationManagerBuilder ab = http.getSharedObject(AuthenticationManagerBuilder.class);
+        return ab.build();
     }
 
-    @Bean
-    CorsConfigurationSource corsConfigurationSource() {
+    protected CorsConfigurationSource corsConfigurationSource() {
+
         UrlBasedCorsConfigurationSource source = new UrlBasedCorsConfigurationSource();
 
         CorsConfiguration corsConfiguration = new CorsConfiguration();
@@ -49,20 +55,22 @@ CorsConfigurationSource corsConfigurationSource() {
         return source;
     }
 
-    @Override
-    protected void configure(HttpSecurity http) throws Exception {
+
+    @Bean
+    public SecurityFilterChain filterChain(HttpSecurity http) throws Exception {
+        log.debug("Using internal security mechanisms.");
+        final AuthenticationManager authManager = buildAuthenticationManager(http);
         http
-                .cors()
-                .and()
-                .httpBasic().disable()
-                .csrf().disable()
-                .sessionManagement().sessionCreationPolicy(SessionCreationPolicy.STATELESS)
-                .and()
-                .authorizeRequests()
-                .antMatchers("/auth/register").permitAll()
-                .antMatchers("/auth/signin").permitAll()
-                .anyRequest().authenticated()
-                .and()
+//                .requestMatcher(r -> false)
+                .cors(auth -> auth.configurationSource(corsConfigurationSource()))
+                .httpBasic(basic -> basic.disable())
+                .csrf(csrf -> csrf.disable())
+                .sessionManagement(sessionManagement -> sessionManagement.sessionCreationPolicy(SessionCreationPolicy.STATELESS))
+                .authorizeHttpRequests(auth -> auth
+                        .requestMatchers(AntPathRequestMatcher.antMatcher("/auth/register")).permitAll()
+                        .requestMatchers(AntPathRequestMatcher.antMatcher("/auth/signin")).permitAll()
+                        .anyRequest().authenticated())
                 .apply(new JwtConfigurer(jwtTokenProvider, securityUtils));
+        return http.build();
     }
 }

src/main/java/cz/cvut/kbss/analysis/controller/FailureModesTableController.java

@@ -14,7 +14,7 @@
 import org.springframework.http.MediaType;
 import org.springframework.web.bind.annotation.*;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.net.URI;
 import java.util.List;
 

src/main/java/cz/cvut/kbss/analysis/controller/util/RestExceptionHandler.java

@@ -4,6 +4,7 @@
 import cz.cvut.kbss.analysis.exception.EntityNotFoundException;
 import cz.cvut.kbss.analysis.exception.LogicViolationException;
 import cz.cvut.kbss.analysis.exception.ValidationException;
+import jakarta.servlet.http.HttpServletRequest;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.context.support.DefaultMessageSourceResolvable;
 import org.springframework.http.HttpStatus;
@@ -12,9 +13,6 @@
 import org.springframework.web.bind.annotation.ResponseStatus;
 import org.springframework.web.bind.annotation.RestControllerAdvice;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
 import java.util.stream.Collectors;
 
 @RestControllerAdvice

src/main/java/cz/cvut/kbss/analysis/model/Behavior.java

@@ -6,7 +6,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotEmpty;
 
 import java.util.HashSet;
 import java.util.Set;

src/main/java/cz/cvut/kbss/analysis/model/Component.java

@@ -5,7 +5,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotEmpty;
 import java.net.URI;
 import java.util.HashSet;
 import java.util.Objects;

src/main/java/cz/cvut/kbss/analysis/model/FailureModesRow.java

@@ -6,7 +6,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.NotNull;
+import jakarta.validation.constraints.NotNull;
 import java.net.URI;
 import java.util.Objects;
 import java.util.Set;

src/main/java/cz/cvut/kbss/analysis/model/FailureModesTable.java

@@ -6,7 +6,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotEmpty;
 import java.util.HashSet;
 import java.util.Objects;
 import java.util.Set;
@@ -21,10 +21,10 @@ public class FailureModesTable extends AbstractEntity {
     @OWLDataProperty(iri = Vocabulary.s_p_hasName)
     private String name;
 
-    @OWLObjectProperty(iri = Vocabulary.s_p_isDerivedFrom, fetch = FetchType.EAGER)
+    @OWLObjectProperty(iri = Vocabulary.s_p_isDerivedFrom, fetch = FetchType.LAZY)
     private FaultTree faultTree;
 
-    @OWLObjectProperty(iri = Vocabulary.s_p_hasRow, cascade = CascadeType.ALL, fetch = FetchType.EAGER)
+    @OWLObjectProperty(iri = Vocabulary.s_p_hasRow, cascade = CascadeType.ALL, fetch = FetchType.LAZY)
     private Set<FailureModesRow> rows = new HashSet<>();
 
     @Override

src/main/java/cz/cvut/kbss/analysis/model/FaultEvent.java

@@ -6,8 +6,8 @@
 import cz.cvut.kbss.jopa.model.annotations.*;
 import lombok.Getter;
 import lombok.Setter;
-import javax.validation.constraints.NotEmpty;
-import javax.validation.constraints.NotNull;
+import jakarta.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotNull;
 import java.net.URI;
 import java.util.*;
 

src/main/java/cz/cvut/kbss/analysis/model/FaultTree.java

@@ -6,8 +6,8 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.NotEmpty;
-import javax.validation.constraints.NotNull;
+import jakarta.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotNull;
 import java.util.HashSet;
 import java.util.Objects;
 import java.util.Set;

src/main/java/cz/cvut/kbss/analysis/model/Mitigation.java

@@ -9,7 +9,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotEmpty;
 import java.util.Objects;
 
 @OWLClass(iri = Vocabulary.s_c_Mitigation)

src/main/java/cz/cvut/kbss/analysis/model/RiskPriorityNumber.java

@@ -8,8 +8,8 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.Max;
-import javax.validation.constraints.Min;
+import jakarta.validation.constraints.Max;
+import jakarta.validation.constraints.Min;
 import java.math.BigDecimal;
 import java.math.RoundingMode;
 import java.util.Objects;

src/main/java/cz/cvut/kbss/analysis/model/System.java

@@ -5,7 +5,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotEmpty;
 import java.util.HashSet;
 import java.util.Objects;
 import java.util.Set;

src/main/java/cz/cvut/kbss/analysis/model/User.java

@@ -11,7 +11,7 @@
 import org.springframework.security.core.authority.SimpleGrantedAuthority;
 import org.springframework.security.core.userdetails.UserDetails;
 
-import javax.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotEmpty;
 import java.util.*;
 
 import static java.util.stream.Collectors.toList;

src/main/java/cz/cvut/kbss/analysis/persistence/MainPersistenceFactory.java

@@ -4,15 +4,16 @@
 import cz.cvut.kbss.analysis.config.conf.RepositoryConf;
 import cz.cvut.kbss.jopa.Persistence;
 import cz.cvut.kbss.jopa.model.EntityManagerFactory;
+import cz.cvut.kbss.jopa.model.JOPAPersistenceProperties;
 import cz.cvut.kbss.jopa.model.JOPAPersistenceProvider;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
 
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -66,7 +67,7 @@ private void init() {
         properties.put(ONTOLOGY_PHYSICAL_URI_KEY, repositoryConf.getUrl());
         properties.put(DATA_SOURCE_CLASS, persistenceConf.getDriver());
         properties.put(LANG, persistenceConf.getLanguage());
-        properties.put(CACHE_ENABLED, "false");
+//        properties.put(CACHE_ENABLED, Boolean.FALSE.toString());
 
         if(repositoryConf.getUsername() != null && repositoryConf.getPassword() != null) {
             properties.put(DATA_SOURCE_USERNAME, repositoryConf.getUsername());

src/main/java/cz/cvut/kbss/analysis/security/JwtTokenFilter.java

@@ -10,12 +10,12 @@
 import org.springframework.security.web.header.HeaderWriterFilter;
 import org.springframework.web.filter.GenericFilterBean;
 
-import javax.servlet.FilterChain;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
 @Slf4j

src/main/java/cz/cvut/kbss/analysis/service/JwtTokenProvider.java

@@ -12,7 +12,7 @@
 import org.springframework.security.core.userdetails.UserDetailsService;
 import org.springframework.stereotype.Component;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.util.Date;
 import java.util.List;
 

src/test/java/cz/cvut/kbss/analysis/environment/TestPersistenceFactory.java

@@ -14,8 +14,8 @@
 import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.ContextConfiguration;
 
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
 import java.util.HashMap;
 import java.util.Map;
 

src/test/java/cz/cvut/kbss/analysis/service/validation/FaultEventValidatorTest.java

@@ -17,9 +17,6 @@
 import org.springframework.validation.BindingResult;
 import org.springframework.validation.beanvalidation.SpringValidatorAdapter;
 
-import javax.xml.validation.Validator;
-
-import static org.junit.jupiter.api.Assertions.assertThrows;
 
 class FaultEventValidatorTest {