CE-5288- Upgraded springboot version to 4.0.7 (DRAFT)

pom.xml

@@ -5,8 +5,9 @@
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
-		<version>3.5.15</version>
-		<relativePath/> <!-- lookup parent from repository -->
+		<version>4.0.7</version>
+		<relativePath/>
+		<!-- lookup parent from repository -->
 	</parent>
 	<groupId>gov.epa.ccte.api</groupId>
 	<artifactId>hazard</artifactId>
@@ -15,19 +16,18 @@
 	<description>project for hazard data</description>
 	<properties>
 		<java.version>17</java.version>
-		<testcontainers.version>1.17.6</testcontainers.version>
-		<lombok.version>1.18.30</lombok.version>
-		<mapstruct.version>1.5.3.Final</mapstruct.version>
-		<sentry.version>8.18.0</sentry.version>
+		<lombok.version>1.18.46</lombok.version>
+		<mapstruct.version>1.6.3</mapstruct.version>
+		<sentry.version>8.49.0</sentry.version>
 	</properties>
 
 	<distributionManagement>
-        	<repository>
-            		<id>github</id>
-            		<name>GitHub OWNER Apache Maven Packages</name>
-            		<url>https://maven.pkg.github.com/USEPA/ccte-api-hazard</url>
-        	</repository>
-    	</distributionManagement>
+		<repository>
+			<id>github</id>
+			<name>GitHub OWNER Apache Maven Packages</name>
+			<url>https://maven.pkg.github.com/USEPA/ccte-api-hazard</url>
+		</repository>
+	</distributionManagement>
 
 	<dependencies>
 
@@ -38,7 +38,7 @@
 
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
-			<artifactId>spring-boot-starter-web</artifactId>
+			<artifactId>spring-boot-starter-webmvc</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
@@ -67,6 +67,11 @@
 			<artifactId>lombok</artifactId>
 			<optional>true</optional>
 		</dependency>
+		<dependency>
+			<groupId>org.projectlombok</groupId>
+			<artifactId>lombok-mapstruct-binding</artifactId>
+			<version>0.2.0</version>
+		</dependency>
 		<!--		&lt;!&ndash; Exception handler - ref https://www.baeldung.com/problem-spring-web &ndash;&gt;-->
 		<!--		<dependency>-->
 		<!--			<groupId>org.zalando</groupId>-->
@@ -84,11 +89,11 @@
 			<artifactId>commons-lang3</artifactId>
 		</dependency>
 		<!-- Swagger/OpenAPI doc -->
-   		<dependency>
-      		<groupId>org.springdoc</groupId>
-      		<artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
-      		<version>2.8.8</version>
-   		</dependency>
+		<dependency>
+			<groupId>org.springdoc</groupId>
+			<artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
+			<version>3.0.3</version>
+		</dependency>
 		<!-- https://mvnrepository.com/artifact/io.pivotal.cfenv/java-cfenv-boot -->
 		<dependency>
 			<groupId>io.pivotal.cfenv</groupId>
@@ -98,13 +103,13 @@
 		<dependency>
 			<groupId>org.mapstruct</groupId>
 			<artifactId>mapstruct</artifactId>
-			<version>1.5.3.Final</version>
+			<version>1.6.3</version>
 		</dependency>
 		<dependency>
-            <groupId>io.sentry</groupId>
-            <artifactId>sentry-spring-boot-starter-jakarta</artifactId>
-            <version>${sentry.version}</version>
-        </dependency>
+			<groupId>io.sentry</groupId>
+			<artifactId>sentry-spring-boot-4-starter</artifactId>
+			<version>${sentry.version}</version>
+		</dependency>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-configuration-processor</artifactId>
@@ -117,23 +122,13 @@
 			<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>junit-jupiter</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.testcontainers</groupId>
-			<artifactId>postgresql</artifactId>
+			<groupId>com.h2database</groupId>
+			<artifactId>h2</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.h2database</groupId>
-			<artifactId>h2</artifactId>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-data-jpa-test</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -142,9 +137,9 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.fasterxml.jackson.datatype</groupId>
-			<artifactId>jackson-datatype-hibernate6</artifactId>
-			<version>2.15.2</version>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-webmvc-test</artifactId>
+			<scope>test</scope>
 		</dependency>
 	</dependencies>
 
@@ -160,8 +155,8 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
 				<configuration>
-					<source>${java.version}</source> <!-- or higher, depending on your project -->
-					<target>${java.version}</target> <!-- or higher, depending on your project -->
+					<!-- or higher, depending on your project -->
+					<!-- or higher, depending on your project -->
 					<annotationProcessorPaths>
 						<path>
 							<groupId>org.projectlombok</groupId>
@@ -178,13 +173,19 @@
 							<artifactId>spring-boot-configuration-processor</artifactId>
 							<version>${project.parent.version}</version>
 						</path>
+						<path>
+							<groupId>org.projectlombok</groupId>
+							<artifactId>lombok-mapstruct-binding</artifactId>
+							<version>0.2.0</version>
+						</path>
 					</annotationProcessorPaths>
 					<compilerArgs>
 						<arg>-Amapstruct.suppressGeneratorTimestamp=true</arg>
 						<arg>-Amapstruct.defaultComponentModel=spring</arg>
 					</compilerArgs>
+					<release>${java.version}</release>
 				</configuration>
 			</plugin>
 		</plugins>
 	</build>
-</project>
+</project>

src/main/java/gov/epa/ccte/api/hazard/HazardApplication.java

@@ -7,7 +7,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.boot.autoconfigure.web.servlet.error.ErrorMvcAutoConfiguration;
+import org.springframework.boot.webmvc.autoconfigure.error.ErrorMvcAutoConfiguration;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.core.env.Environment;
@@ -79,11 +79,18 @@ private static void logApplicationStartup(Environment env) {
 			log.warn("The host name could not be determined, using `localhost` as fallback");
 		}
 		log.info(
-				"\n----------------------------------------------------------\n\t" +
-						"Application '{}' is running! Access URLs:\n\t" +
-						"Local: \t\t{}://localhost:{}{}\n\t" +
-						"External: \t{}://{}:{}{}\n\t" +
-						"Profile(s): \t{}\n----------------------------------------------------------",
+				"""
+
+                ----------------------------------------------------------
+                \t\
+                Application '{}' is running! Access URLs:
+                \t\
+                Local: \t\t{}://localhost:{}{}
+                \t\
+                External: \t{}://{}:{}{}
+                \t\
+                Profile(s): \t{}
+                ----------------------------------------------------------""",
 				env.getProperty("spring.application.name"),
 				protocol,
 				serverPort,
@@ -100,8 +107,12 @@ private static void logApplicationStartup(Environment env) {
 			configServerStatus = "Not found or not setup for this application";
 		}
 		log.info(
-				"\n----------------------------------------------------------\n\t" +
-						"Config Server: \t{}\n----------------------------------------------------------",
+				"""
+
+                ----------------------------------------------------------
+                \t\
+                Config Server: \t{}
+                ----------------------------------------------------------""",
 				configServerStatus
 		);
 	}

src/main/java/gov/epa/ccte/api/hazard/config/JacksonConfiguration.java

@@ -1,33 +1,9 @@
 package gov.epa.ccte.api.hazard.config;
 
-import com.fasterxml.jackson.datatype.hibernate6.Hibernate6Module;
-import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
 @Configuration
 public class JacksonConfiguration {
-
-    /**
-     * Support for Java date and time API.
-     * @return the corresponding Jackson module.
-     */
-    @Bean
-    public JavaTimeModule javaTimeModule() {
-        return new JavaTimeModule();
-    }
-
-    @Bean
-    public Jdk8Module jdk8TimeModule() {
-        return new Jdk8Module();
-    }
-
-    /*
-     * Support for Hibernate types in Jackson.
-     */
-    @Bean
-    public Hibernate6Module hibernate6Module() {
-        return new Hibernate6Module();
-    }
-}
+    // Intentionally empty: Hibernate Jackson module wiring is disabled until
+    // dependency versions are aligned with Spring Boot 4.x.
+}

src/main/java/gov/epa/ccte/api/hazard/config/SpringDataRestCustomization.java

@@ -1,6 +1,7 @@
 package gov.epa.ccte.api.hazard.config;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import tools.jackson.databind.ObjectMapper;
+import tools.jackson.databind.cfg.MapperBuilder;
 import gov.epa.ccte.api.hazard.config.converter.StringToImageFormatConverter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.convert.support.ConfigurableConversionService;
@@ -49,8 +50,8 @@ public void configureHttpMessageConverters(List<HttpMessageConverter<?>> message
     }
 
     @Override
-    public void configureJacksonObjectMapper(ObjectMapper objectMapper) {
-        RepositoryRestConfigurer.super.configureJacksonObjectMapper(objectMapper);
+    public void configureJacksonObjectMapper(MapperBuilder<? extends ObjectMapper, ? extends MapperBuilder<?, ?>> objectMapperBuilder) {
+        RepositoryRestConfigurer.super.configureJacksonObjectMapper(objectMapperBuilder);
     }
 
     @Override
@@ -62,4 +63,4 @@ public AuditableBeanWrapperFactory customizeAuditableBeanWrapperFactory(Auditabl
     public LinkCollector customizeLinkCollector(LinkCollector collector) {
         return RepositoryRestConfigurer.super.customizeLinkCollector(collector);
     }
-}
+}

src/main/java/gov/epa/ccte/api/hazard/repository/AdmeRepository.java

@@ -3,7 +3,7 @@
 import java.util.List;
 
 import org.springframework.data.jpa.repository.JpaRepository;
-import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.jpa.repository.NativeQuery;
 import org.springframework.data.repository.query.Param;
 import org.springframework.data.rest.core.annotation.RepositoryRestResource;
 import org.springframework.transaction.annotation.Transactional;
@@ -18,7 +18,7 @@ public interface AdmeRepository extends JpaRepository<Adme, Integer>{
     @Transactional(readOnly = true)
     <T>List<T> findByDtxsid(String dtxsid, Class<T> type);
 
-    @Query(value = """
+    @NativeQuery("""
 			SELECT
 			    adme.dtxsid,
 			    adme.measured,
@@ -49,7 +49,7 @@ public interface AdmeRepository extends JpaRepository<Adme, Integer>{
 			    adme.mv_ivive adme     					  					
 			WHERE
 			    adme.dtxsid = :dtxsid
-		""", nativeQuery = true)
+		""")
     	List<CcdADME> findByDtxsidWithLabelColumn(@Param("dtxsid")String dtxsid);
 
 }

src/main/java/gov/epa/ccte/api/hazard/repository/GenetoxDetailRepository.java

@@ -4,7 +4,7 @@
 import gov.epa.ccte.api.hazard.projection.CcdGenetoxDetail;
 
 import org.springframework.data.jpa.repository.JpaRepository;
-import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.jpa.repository.NativeQuery;
 import org.springframework.data.repository.query.Param;
 import org.springframework.data.rest.core.annotation.RepositoryRestResource;
 import org.springframework.transaction.annotation.Transactional;
@@ -19,7 +19,7 @@ public interface GenetoxDetailRepository extends JpaRepository<GenetoxDetail, In
 
     <T> List<T> findByDtxsidInOrderByDtxsidAsc(String[] dtxsids, Class<T> type);
 
-    @Query(value = """
+    @NativeQuery("""
 			SELECT
     			genetox.dtxsid,
 			    genetox.source, 
@@ -34,6 +34,6 @@ public interface GenetoxDetailRepository extends JpaRepository<GenetoxDetail, In
 			    toxval.mv_genetox_details genetox     					  					
 			WHERE
 			    genetox.dtxsid = :dtxsid
-		""", nativeQuery = true)
+		""")
     List<CcdGenetoxDetail> findByDtxsidWithConcatenatedColumn(@Param("dtxsid")String dtxsid);
 }

src/main/java/gov/epa/ccte/api/hazard/security/ApiKeyRequestFilter.java

@@ -1,6 +1,8 @@
 package gov.epa.ccte.api.hazard.security;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import tools.jackson.databind.ObjectMapper;
+import tools.jackson.databind.json.JsonMapper;
+
 import gov.epa.ccte.api.hazard.web.rest.error.AuthorizationProblem;
 import jakarta.servlet.FilterChain;
 import jakarta.servlet.ServletException;
@@ -28,7 +30,7 @@ public class ApiKeyRequestFilter extends GenericFilterBean {
 
     private final ConcurrentHashMap<UUID, String> keyStore;// = new ConcurrentHashMap();
     private final ConcurrentHashMap<String, String> approvedOriginStore;// = new ConcurrentHashMap();
-    private final ObjectMapper mapper = new ObjectMapper();
+    private final ObjectMapper mapper = new JsonMapper();
     private final String keyName;
 
     public ApiKeyRequestFilter(ConcurrentHashMap<UUID, String> keyStore,

src/main/java/gov/epa/ccte/api/hazard/web/rest/AdmeApi.java

@@ -4,9 +4,8 @@
 
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
 import gov.epa.ccte.api.hazard.domain.Adme;
@@ -40,7 +39,7 @@ public interface AdmeApi {
             @ApiResponse(responseCode = "200", description = "OK", content = @Content(mediaType = "application/json",
                     schema = @Schema(oneOf = { Adme.class, CcdADME.class}))),
     })
-    @RequestMapping(value = "hazard/adme-ivive/search/by-dtxsid/{dtxsid}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
+    @GetMapping(value = "hazard/adme-ivive/search/by-dtxsid/{dtxsid}", produces = MediaType.APPLICATION_JSON_VALUE)
     List<?> admeDataByDtxsid(@Parameter(required = true, description = "DSSTox Substance Identifier", example = "DTXSID7020182") 
     						@PathVariable("dtxsid") String dtxsid,
     						@Parameter(description = "Specifies if projection is used. Option: ccd-adme-data. " +

src/main/java/gov/epa/ccte/api/hazard/web/rest/AdmeResource.java

@@ -34,8 +34,8 @@ public List<?> admeDataByDtxsid(String dtxsid, String projection) {
         	default -> repository.findByDtxsid(dtxsid, Adme.class);
         };
 
-        if (result instanceof List<?>) {
-            return (List<?>) result;
+        if (result instanceof List<?> list) {
+            return list;
         } else if (result != null) {
             return List.of(result); 
         } else {

src/main/java/gov/epa/ccte/api/hazard/web/rest/GenetoxResource.java

@@ -71,8 +71,8 @@ public List<?> getGenetoxDetailsByDtxsid(String dtxsid, String projection) {
         	default -> detailRepository.findByDtxsidOrderBySourceAsc(dtxsid, CcdGenetoxDetail.class);
         };
 
-        if (result instanceof List<?>) {
-            return (List<?>) result;
+        if (result instanceof List<?> list) {
+            return list;
         } else if (result != null) {
             return List.of(result); 
         } else {