Upgrade to spring-boot 4

pom.xml

@@ -5,7 +5,8 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>3.5.15</version>
+        <version>4.1.0</version>
+        <!-- spring-boot managed dependencies: https://docs.spring.io/spring-boot/appendix/dependency-versions/coordinates.html -->
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
     <groupId>org.fairdatateam</groupId>
@@ -54,12 +55,12 @@
         <maven.compiler.target>21</maven.compiler.target>
 
         <!-- Project related -->
-        <spring-rdf-migration.version>2.0.0</spring-rdf-migration.version>
-        <rdf-resource-resolver.version>0.2.0</rdf-resource-resolver.version>
-        <spring-security-acl-mongodb.version>6.0.4</spring-security-acl-mongodb.version>
+        <spring-rdf-migration.version>2.0.1</spring-rdf-migration.version>
+        <rdf-resource-resolver.version>0.2.2</rdf-resource-resolver.version>
+        <spring-security-acl-mongodb.version>6.0.5</spring-security-acl-mongodb.version>
 
         <!-- Core -->
-        <springdoc-openapi-starter-webmvc-ui.version>2.8.16</springdoc-openapi-starter-webmvc-ui.version>
+        <springdoc-openapi-starter-webmvc-ui.version>3.0.3</springdoc-openapi-starter-webmvc-ui.version>
         <mongock-bom.version>5.5.1</mongock-bom.version>
         <rdf4j-runtime.version>5.3.1</rdf4j-runtime.version>
         <jjwt-api.version>0.13.0</jjwt-api.version>
@@ -127,9 +128,10 @@
         <!-- ////////////////// -->
         <!--   Spring           -->
         <!-- ////////////////// -->
+
         <dependency>
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-web</artifactId>
+            <artifactId>spring-boot-starter-actuator</artifactId>
             <exclusions>
                 <exclusion>
                     <!-- excluded because we're using spring-boot-starter-log4j2 instead (see spring-boot logging docs) -->
@@ -140,40 +142,75 @@
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-security</artifactId>
+            <artifactId>spring-boot-starter-aspectj</artifactId>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-log4j2</artifactId>
+            <artifactId>spring-boot-starter-jackson</artifactId>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-configuration-processor</artifactId>
+            <artifactId>spring-boot-starter-log4j2</artifactId>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-mongodb</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.springframework.security</groupId>
-            <artifactId>spring-security-acl</artifactId>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-data-mongodb-test</artifactId>
+            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-actuator</artifactId>
+            <artifactId>spring-boot-starter-restclient</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-restclient-test</artifactId>
+            <scope>test</scope>
         </dependency>
         <dependency>
+            <!-- https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-4.0-Migration-Guide#testresttemplate-failures -->
+            <!-- todo: remove in favor of restclient, see #897 -->
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-aop</artifactId>
+            <artifactId>spring-boot-resttestclient</artifactId>
+            <scope>test</scope>
         </dependency>
         <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-security</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-security-test</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <!-- with transitive dependency on hibernate-validator -->
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-validation</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-validation-test</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-webmvc</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-webmvc-test</artifactId>
+            <scope>test</scope>
+        </dependency>
 
         <!-- ////////////////// -->
         <!--   Mongock          -->
         <!-- ////////////////// -->
+
+        <!-- mongock versions are managed via mongock-bom -->
         <dependency>
             <groupId>io.mongock</groupId>
             <artifactId>mongock-springboot</artifactId>
@@ -182,10 +219,6 @@
             <groupId>io.mongock</groupId>
             <artifactId>mongodb-springdata-v4-driver</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.springframework.data</groupId>
-            <artifactId>spring-data-mongodb</artifactId>
-        </dependency>
 
         <!-- ////////////////// -->
         <!--   Core             -->
@@ -238,30 +271,19 @@
             <groupId>org.projectlombok</groupId>
             <artifactId>lombok</artifactId>
         </dependency>
-
-        <!-- ////////////////// -->
-        <!--   Test             -->
-        <!-- ////////////////// -->
         <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-test</artifactId>
-            <scope>test</scope>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.vaadin.external.google</groupId>
-                    <artifactId>android-json</artifactId>
-                </exclusion>
-            </exclusions>
+            <groupId>org.apache.httpcomponents.client5</groupId>
+            <artifactId>httpclient5</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.springframework.security</groupId>
-            <artifactId>spring-security-test</artifactId>
-            <scope>test</scope>
+            <groupId>jakarta.servlet</groupId>
+            <artifactId>jakarta.servlet-api</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.apache.httpcomponents.client5</groupId>
-            <artifactId>httpclient5</artifactId>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
         </dependency>
+
     </dependencies>
 
     <build>

src/main/java/org/fairdatateam/fairdatapoint/api/dto/schema/MetadataSchemaDraftDTO.java

@@ -22,14 +22,14 @@
  */
 package org.fairdatateam.fairdatapoint.api.dto.schema;
 
+import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import jakarta.validation.constraints.NotBlank;
 import jakarta.validation.constraints.NotNull;
 import lombok.*;
 
 import java.util.List;
 
-@NoArgsConstructor
 @AllArgsConstructor
 @Getter
 @Setter
@@ -47,7 +47,7 @@ public class MetadataSchemaDraftDTO {
     @NotNull
     private String description;
 
-    private boolean abstractSchema;
+    private Boolean abstractSchema;
 
     @NotNull
     private String definition;
@@ -63,4 +63,13 @@ public class MetadataSchemaDraftDTO {
 
     @JsonInclude(JsonInclude.Include.ALWAYS)
     private String lastVersion;
+
+    /**
+     * No-args constructor explicitly marked as default for JSON creation.
+     * See <a href="https://github.com/FasterXML/jackson/wiki/Jackson-Release-3.0#jackson-databind">
+     * FasterXML/jackson-databind#5318</a> for more info.
+     */
+    @JsonCreator
+    public MetadataSchemaDraftDTO() {
+    }
 }

src/main/java/org/fairdatateam/fairdatapoint/api/filter/JwtTokenFilter.java

@@ -22,7 +22,6 @@
  */
 package org.fairdatateam.fairdatapoint.api.filter;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
 import jakarta.servlet.FilterChain;
 import jakarta.servlet.ServletException;
 import jakarta.servlet.http.HttpServletRequest;
@@ -38,6 +37,7 @@
 import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.stereotype.Component;
 import org.springframework.web.filter.OncePerRequestFilter;
+import tools.jackson.databind.json.JsonMapper;
 
 import java.io.IOException;
 
@@ -53,7 +53,7 @@ public class JwtTokenFilter extends OncePerRequestFilter {
     private ApiKeyService apiKeyService;
 
     @Autowired
-    private ObjectMapper objectMapper;
+    private JsonMapper jsonMapper;
 
     @Override
     public void doFilterInternal(
@@ -69,7 +69,7 @@ public void doFilterInternal(
             response.setStatus(HttpServletResponse.SC_UNAUTHORIZED);
             response.setContentType(MediaType.APPLICATION_JSON.toString());
             final ErrorDTO error = new ErrorDTO(HttpStatus.UNAUTHORIZED, "You have to be log in");
-            objectMapper.writeValue(response.getWriter(), error);
+            jsonMapper.writeValue(response.getWriter(), error);
         }
     }
 

src/main/java/org/fairdatateam/fairdatapoint/config/ActuatorMetricsConfig.java

@@ -26,7 +26,7 @@
 import io.micrometer.core.instrument.MeterRegistry;
 import io.micrometer.core.instrument.config.MeterFilter;
 import lombok.extern.slf4j.Slf4j;
-import org.springframework.boot.actuate.autoconfigure.metrics.MeterRegistryCustomizer;
+import org.springframework.boot.micrometer.metrics.autoconfigure.MeterRegistryCustomizer;
 import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;

src/main/java/org/fairdatateam/fairdatapoint/config/HttpClientConfig.java

@@ -22,7 +22,7 @@
  */
 package org.fairdatateam.fairdatapoint.config;
 
-import org.springframework.boot.web.client.RestTemplateBuilder;
+import org.springframework.boot.restclient.RestTemplateBuilder;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.web.client.RestClient;
@@ -45,9 +45,8 @@ public class HttpClientConfig {
     @Bean
     public RestTemplate restTemplate(RestTemplateBuilder restTemplateBuilder) {
         return restTemplateBuilder
-                // todo: these are deprecated, but we should replace RestTemplate by RestClient anyway
-                .setConnectTimeout(TIMEOUT)
-                .setReadTimeout(TIMEOUT)
+                .connectTimeout(TIMEOUT)
+                .readTimeout(TIMEOUT)
                 .build();
     }
 

src/main/java/org/fairdatateam/fairdatapoint/config/SecurityConfig.java

@@ -23,7 +23,7 @@
 package org.fairdatateam.fairdatapoint.config;
 
 import org.fairdatateam.fairdatapoint.api.filter.FilterConfigurer;
-import org.springframework.boot.actuate.autoconfigure.security.servlet.EndpointRequest;
+import org.springframework.boot.security.autoconfigure.actuate.web.servlet.EndpointRequest;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.http.HttpMethod;

src/main/java/org/fairdatateam/fairdatapoint/config/WebMvcConfig.java

@@ -22,48 +22,58 @@
  */
 package org.fairdatateam.fairdatapoint.config;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.annotation.JsonInclude;
 import org.fairdatateam.fairdatapoint.api.converter.ErrorConverter;
 import org.fairdatateam.fairdatapoint.api.converter.RdfConverter;
-import org.springframework.beans.factory.annotation.Autowired;
+import org.jspecify.annotations.NonNull;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.converter.ByteArrayHttpMessageConverter;
-import org.springframework.http.converter.HttpMessageConverter;
+import org.springframework.http.converter.HttpMessageConverters;
 import org.springframework.http.converter.StringHttpMessageConverter;
-import org.springframework.http.converter.json.MappingJackson2HttpMessageConverter;
+import org.springframework.http.converter.json.JacksonJsonHttpMessageConverter;
 import org.springframework.web.servlet.config.annotation.ContentNegotiationConfigurer;
 import org.springframework.web.servlet.config.annotation.CorsRegistry;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
 import org.springframework.web.servlet.view.InternalResourceViewResolver;
+import tools.jackson.databind.DeserializationFeature;
+import tools.jackson.databind.json.JsonMapper;
 
 import java.util.List;
 
-import static com.fasterxml.jackson.annotation.JsonInclude.Include.NON_NULL;
-
 @Configuration
 public class WebMvcConfig implements WebMvcConfigurer {
 
-    @Autowired
-    private List<ErrorConverter> errorConverters;
+    private final List<ErrorConverter> errorConverters;
 
-    @Autowired
-    private List<RdfConverter> rdfConverters;
+    private final List<RdfConverter> rdfConverters;
 
+    /**
+     * Constructor (autowired)
+     */
+    public WebMvcConfig(List<ErrorConverter> errorConverters, List<RdfConverter> rdfConverters) {
+        this.errorConverters = errorConverters;
+        this.rdfConverters = rdfConverters;
+    }
+
+    /**
+     * Configures message converters. See
+     * <a href="https://docs.spring.io/spring-framework/reference/web/webmvc/mvc-config/message-converters.html">
+     * example in Spring docs</a>.
+     */
     @Override
-    public void configureMessageConverters(List<HttpMessageConverter<?>> converters) {
-        converters.add(new StringHttpMessageConverter());
-        converters.addAll(errorConverters);
-        converters.addAll(rdfConverters);
-        converters.add(new ByteArrayHttpMessageConverter());
-        converters.add(new MappingJackson2HttpMessageConverter(objectMapper()));
+    public void configureMessageConverters(HttpMessageConverters.@NonNull ServerBuilder builder) {
+        builder.withStringConverter(new StringHttpMessageConverter())
+                .withJsonConverter(new JacksonJsonHttpMessageConverter(jsonMapper()))
+                .addCustomConverter(new ByteArrayHttpMessageConverter());
+        errorConverters.forEach(builder::addCustomConverter);
+        rdfConverters.forEach(builder::addCustomConverter);
     }
 
     @Override
-    public void configureContentNegotiation(ContentNegotiationConfigurer configurer) {
+    public void configureContentNegotiation(@NonNull ContentNegotiationConfigurer configurer) {
         for (ErrorConverter converter : errorConverters) {
             converter.configureContentNegotiation(configurer);
         }
@@ -75,12 +85,15 @@ public void configureContentNegotiation(ContentNegotiationConfigurer configurer)
 
     @Bean
     @Primary
-    public ObjectMapper objectMapper() {
-        final ObjectMapper mapper = new ObjectMapper();
-        mapper.findAndRegisterModules();
-        mapper.setSerializationInclusion(NON_NULL);
-        mapper.disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES);
-        return mapper;
+    public JsonMapper jsonMapper() {
+        return JsonMapper.builder()
+                // https://javadoc.io/doc/com.fasterxml.jackson.core/jackson-databind/2.9.8/com/fasterxml/jackson/databind/ObjectMapper.html#findAndRegisterModules--
+                // https://github.com/FasterXML/jackson/blob/main/jackson3/MIGRATING_TO_JACKSON_3.md#objectmapper-serialization-inclusion-configuration
+                .changeDefaultPropertyInclusion(incl -> incl.withValueInclusion(JsonInclude.Include.NON_NULL))
+                .changeDefaultPropertyInclusion(incl -> incl.withContentInclusion(JsonInclude.Include.NON_NULL))
+                // https://github.com/FasterXML/jackson/blob/main/jackson3/MIGRATING_TO_JACKSON_3.md#objectmapper-visibility-configuration
+                .disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES)
+                .build();
     }
 
     @Bean

src/main/java/org/fairdatateam/fairdatapoint/database/rdf/repository/AbstractMetadataRepository.java

@@ -22,7 +22,6 @@
  */
 package org.fairdatateam.fairdatapoint.database.rdf.repository;
 
-import jakarta.annotation.Nullable;
 import lombok.extern.slf4j.Slf4j;
 import org.eclipse.rdf4j.common.iteration.Iterations;
 import org.eclipse.rdf4j.model.*;
@@ -32,6 +31,7 @@
 import org.eclipse.rdf4j.repository.Repository;
 import org.eclipse.rdf4j.repository.RepositoryConnection;
 import org.eclipse.rdf4j.repository.RepositoryException;
+import org.jspecify.annotations.Nullable;
 
 import java.util.*;