Merge pull request #136 from TheJacksonLaboratory/feature/spring6

Feature/spring6
TheJacksonLaboratory · Jul 19, 2024 · 5146345 · 5146345
2 parents 4376039 + b521c3a
commit 5146345
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diff --git a/build.gradle b/build.gradle
@@ -1,6 +1,6 @@
 plugins {
-	id 'org.springframework.boot' version '2.2.4.RELEASE'
-	id 'io.spring.dependency-management' version '1.0.9.RELEASE'
+	id 'org.springframework.boot' version '3.2.3'
+	id 'io.spring.dependency-management' version '1.1.4'
 	id 'java'
 	id 'war'
 	id 'groovy'
@@ -10,8 +10,9 @@ plugins {
 }
 
 group = 'org.monarchinitiative.poet'
-version = '1.1.0'
-sourceCompatibility = '11'
+version = '1.1.1'
+sourceCompatibility = 17
+targetCompatibility = 17
 
 configurations {
 	jaxb
@@ -37,7 +38,7 @@ task genJaxb {
 				produces(dir: sourcesDir, includes: "**/*.java")
 			}
 
-			javac(destdir: classesDir, source: 1.8, target: 1.8, debug: true,
+			javac(destdir: classesDir, source: 17, target: 17, debug: true,
 					debugLevel: "lines,vars,source",
 					classpath: configurations.jaxb.asPath) {
 				src(path: sourcesDir)
@@ -69,29 +70,28 @@ dependencies {
 	implementation 'org.springframework.security:spring-security-config'
 	implementation 'org.springframework.boot:spring-boot-starter-security'
 	implementation group: 'org.monarchinitiative.phenol', name: 'phenol-core', version: '2.0.0'
-	implementation 'org.mariadb.jdbc:mariadb-java-client:2.7.4'
+	implementation 'mysql:mysql-connector-java:8.0.33'
 	implementation 'org.monarchinitiative.phenol:phenol-annotations:2.0.0'
 	implementation 'org.monarchinitiative.phenol:phenol-io:2.0.0'
 	implementation 'org.apache.commons:commons-csv:1.9.0'
 	implementation 'org.springframework.ws:spring-ws-core'
 	implementation 'org.apache.commons:commons-text:1.10.0'
-	// For Java 11:
 	implementation 'org.glassfish.jaxb:jaxb-runtime'
 	implementation(files(genJaxb.classesDir).builtBy(genJaxb))
 	implementation('org.springframework.boot:spring-boot-starter-web-services') {
 		exclude group: 'org.springframework.boot', module: 'spring-boot-starter-tomcat'
 	}
+	implementation 'org.springframework.boot:spring-boot-starter-validation:3.2.3'
 
-	jaxb "com.sun.xml.bind:jaxb-xjc:2.1.7"
+	jaxb "com.sun.xml.bind:jaxb-xjc:4.0.4"
 
 	testRuntimeOnly 'com.h2database:h2'
 	providedRuntime 'org.springframework.boot:spring-boot-starter-tomcat'
-	testImplementation('org.springframework.boot:spring-boot-starter-test') {
-		exclude group: 'org.junit.vintage', module: 'junit-vintage-engine'
-	}
-	testImplementation group: 'org.spockframework', name: 'spock-core', version: '1.3-groovy-2.4'
-	testImplementation group: 'org.spockframework', name: 'spock-spring', version: '1.3-groovy-2.4'
-	testImplementation 'org.springframework.security:spring-security-test:4.2.3.RELEASE'
+	testImplementation 'org.springframework.boot:spring-boot-starter-test'
+	testImplementation 'org.codehaus.groovy:groovy-all:3.0.22'
+	testImplementation group: 'org.spockframework', name: 'spock-core', version: '2.3-groovy-3.0'
+	testImplementation group: 'org.spockframework', name: 'spock-spring', version: '2.3-groovy-3.0'
+	testImplementation 'org.springframework.security:spring-security-test:6.3.1'
 }
 
 def profile = 'development'
@@ -129,6 +129,7 @@ task test_release(){
 
 test {
 	systemProperty 'spring.profiles.active', 'test'
+	useJUnitPlatform()
 }
 
 jacocoTestReport {

diff --git a/src/main/java/org/monarchinitiative/poet/PoetConfiguration.java b/src/main/java/org/monarchinitiative/poet/PoetConfiguration.java
@@ -7,55 +7,44 @@
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.core.io.Resource;
 import org.springframework.oxm.jaxb.Jaxb2Marshaller;
-import org.springframework.web.servlet.config.annotation.CorsRegistry;
-import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry;
-import org.springframework.web.servlet.config.annotation.ViewControllerRegistry;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
+import org.springframework.util.AntPathMatcher;
+import org.springframework.web.servlet.config.annotation.*;
 import org.springframework.web.servlet.resource.PathResourceResolver;
+import org.springframework.web.util.UrlPathHelper;
+import org.springframework.web.util.pattern.PathPatternParser;
 import org.springframework.ws.client.core.WebServiceTemplate;
 
 import java.io.IOException;
 
 @Configuration
-public class PoetConfiguration {
+@EnableWebMvc
+public class PoetConfiguration implements WebMvcConfigurer {
 
-    @Autowired
-    private Environment env;
-
-    @Bean
-    public WebMvcConfigurer corsConfigurer() {
-        return new WebMvcConfigurer() {
-            @Override
-            public void addCorsMappings(CorsRegistry registry) {
-                registry.addMapping("/**/*");
-            }
-
-            @Override
-            public void addResourceHandlers(ResourceHandlerRegistry registry) {
-                registry.addResourceHandler(env.getProperty("api.client").split(","))
-                        .addResourceLocations("classpath:/static/")
-                        .resourceChain(true)
-                        .addResolver(new PathResourceResolver() {
-                            @Override
-                            protected Resource getResource(String resourcePath, Resource location) throws IOException {
-                                Resource requestedResource = location.createRelative(resourcePath);
-                                return requestedResource.exists() && requestedResource.isReadable() ?
-                                        requestedResource : new ClassPathResource("/static/index.html");
-                            }
-                        });
-                registry.setOrder(Integer.MAX_VALUE);
-            }
+    @Override
+    public void addCorsMappings(CorsRegistry registry) {
+        registry.addMapping("/**")
+                .allowedOrigins("*")
+                .allowedMethods("GET","POST", "PUT", "DELETE", "OPTIONS", "HEAD");
+    }
 
-            @Override
-            public void addViewControllers(ViewControllerRegistry registry) {
-                registry.addViewController("/{spring:(?!assets)\\w+}")
-                        .setViewName("forward:/");
-                registry.addViewController("/**/{spring:\\w+}")
-                        .setViewName("forward:/");
-                registry.addViewController("/{spring:(?!assets)\\w+}/**{spring:?!(\\.js|\\.css)$}")
-                        .setViewName("forward:/");
-            }
-        };
+    @Override
+    public void addResourceHandlers(ResourceHandlerRegistry registry) {
+        registry.addResourceHandler("/*")
+                .addResourceLocations("classpath:/static/")
+                .resourceChain(true)
+                .addResolver(new PathResourceResolver() {
+                    @Override
+                    protected Resource getResource(String resourcePath, Resource location) throws IOException {
+                        if (resourcePath.startsWith("/api/")) {
+                            return null; // Return null to indicate not found
+                        } else {
+                            Resource requestedResource = location.createRelative(resourcePath);
+                            return requestedResource.exists() && requestedResource.isReadable() ?
+                                    requestedResource : new ClassPathResource("/static/index.html");
+                        }
+                    }
+                });
+        registry.setOrder(Integer.MAX_VALUE);
     }
 
     @Bean

diff --git a/src/main/java/org/monarchinitiative/poet/controller/DiseaseController.java b/src/main/java/org/monarchinitiative/poet/controller/DiseaseController.java
@@ -25,7 +25,7 @@
  */
 @CrossOrigin
 @RestController
-@RequestMapping(value = "${api.version}/entity/disease/")
+@RequestMapping(value = "${api.version}/entity/disease")
 public class DiseaseController {
     private final EntityService entityService;
     private final StatisticsService statisticsService;

diff --git a/src/main/java/org/monarchinitiative/poet/controller/ExportController.java b/src/main/java/org/monarchinitiative/poet/controller/ExportController.java
@@ -7,12 +7,12 @@
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
 @CrossOrigin
 @RestController
-@RequestMapping(value = "${api.version}/export/")
+@RequestMapping(value = "${api.version}/export")
 public class ExportController {
     private final ExportService exportService;
 

diff --git a/src/main/java/org/monarchinitiative/poet/controller/SearchController.java b/src/main/java/org/monarchinitiative/poet/controller/SearchController.java
@@ -34,7 +34,7 @@ public SearchController(final SearchService searchService) {
      * @return a list of search response objects containing ids and names.
      * @since 0.5.0
      */
-    @GetMapping(value = "", headers = "Accept=application/json")
+    @GetMapping(value = "/", headers = "Accept=application/json")
     public List<SearchResponse> searchPublicationsAndDiseases(@RequestParam String query) {
         return searchService.searchDisease(query.trim());
     }

diff --git a/src/main/java/org/monarchinitiative/poet/controller/UserController.java b/src/main/java/org/monarchinitiative/poet/controller/UserController.java
@@ -42,15 +42,15 @@ public ResponseEntity<?> checkUser(Authentication authentication) {
         return ResponseEntity.notFound().build();
     }
 
-    @PostMapping(value = "", headers = "Accept=application/json")
+    @PostMapping(value = "/", headers = "Accept=application/json")
     public ResponseEntity<?> updateOrcid(Authentication authentication,
                                          @RequestParam(value = "orcid") String orcid){
         userService.setUserOrcId(authentication, orcid);
         return ResponseEntity.ok().build();
     }
 
     @JsonView(UserViews.Simple.class)
-    @GetMapping(value = "", headers = "Accept=application/json")
+    @GetMapping(value = "/", headers = "Accept=application/json")
     public User getUserDetails(Authentication authentication){
         return userService.getExistingUser(authentication);
     }

diff --git a/src/main/java/org/monarchinitiative/poet/controller/annotation/PhenotypeController.java b/src/main/java/org/monarchinitiative/poet/controller/annotation/PhenotypeController.java
@@ -1,6 +1,7 @@
 package org.monarchinitiative.poet.controller.annotation;
 
 import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.validation.Valid;
 import org.monarchinitiative.poet.model.entities.PhenotypeAnnotation;
 import org.monarchinitiative.poet.model.entities.User;
 import org.monarchinitiative.poet.model.requests.PhenotypeRequest;
@@ -12,7 +13,6 @@
 import org.springframework.security.core.Authentication;
 import org.springframework.web.bind.annotation.*;
 
-import javax.validation.Valid;
 import java.util.List;
 
 @CrossOrigin

diff --git a/src/main/java/org/monarchinitiative/poet/controller/annotation/TreatmentController.java b/src/main/java/org/monarchinitiative/poet/controller/annotation/TreatmentController.java
@@ -1,6 +1,7 @@
 package org.monarchinitiative.poet.controller.annotation;
 
 import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.validation.Valid;
 import org.monarchinitiative.poet.exceptions.AnnotationSourceException;
 import org.monarchinitiative.poet.model.entities.TreatmentAnnotation;
 import org.monarchinitiative.poet.model.entities.User;
@@ -12,8 +13,6 @@
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.core.Authentication;
 import org.springframework.web.bind.annotation.*;
-
-import javax.validation.Valid;
 import java.util.List;
 
 /**

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/Annotation.java b/src/main/java/org/monarchinitiative/poet/model/entities/Annotation.java
@@ -7,7 +7,7 @@
 import org.monarchinitiative.poet.views.AnnotationViews;
 import org.monarchinitiative.poet.views.UserActivityViews;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.time.LocalDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.List;

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/AnnotationSource.java b/src/main/java/org/monarchinitiative/poet/model/entities/AnnotationSource.java
@@ -4,7 +4,7 @@
 import org.monarchinitiative.poet.views.AnnotationViews;
 import org.monarchinitiative.poet.views.UserActivityViews;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Objects;
 
 @Entity

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/Disease.java b/src/main/java/org/monarchinitiative/poet/model/entities/Disease.java
@@ -7,7 +7,7 @@
 import org.monarchinitiative.poet.views.PublicationViews;
 import org.monarchinitiative.poet.views.UserActivityViews;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/Message.java b/src/main/java/org/monarchinitiative/poet/model/entities/Message.java
@@ -3,7 +3,7 @@
 import com.fasterxml.jackson.annotation.JsonView;
 import org.monarchinitiative.poet.views.AnnotationViews;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Entity
 public class Message {

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/PhenotypeAnnotation.java b/src/main/java/org/monarchinitiative/poet/model/entities/PhenotypeAnnotation.java
@@ -5,8 +5,8 @@
 import org.monarchinitiative.poet.model.requests.PhenotypeRequest;
 import org.monarchinitiative.poet.views.AnnotationViews;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
+import jakarta.persistence.DiscriminatorValue;
+import jakarta.persistence.Entity;
 
 @Entity
 @DiscriminatorValue("phenotype")

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/Publication.java b/src/main/java/org/monarchinitiative/poet/model/entities/Publication.java
@@ -4,7 +4,7 @@
 import org.monarchinitiative.poet.views.AnnotationViews;
 import org.monarchinitiative.poet.views.PublicationViews;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/TreatmentAnnotation.java b/src/main/java/org/monarchinitiative/poet/model/entities/TreatmentAnnotation.java
@@ -7,10 +7,10 @@
 import org.monarchinitiative.poet.model.requests.TreatmentRequest;
 import org.monarchinitiative.poet.views.AnnotationViews;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
+import jakarta.persistence.DiscriminatorValue;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
 import javax.validation.constraints.NotNull;
 
 @Entity

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/User.java b/src/main/java/org/monarchinitiative/poet/model/entities/User.java
@@ -6,7 +6,7 @@
 import org.monarchinitiative.poet.views.UserActivityViews;
 import org.monarchinitiative.poet.views.UserViews;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Objects;
 
 @Entity

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/UserActivity.java b/src/main/java/org/monarchinitiative/poet/model/entities/UserActivity.java
@@ -4,7 +4,7 @@
 import org.monarchinitiative.poet.model.enumeration.CurationAction;
 import org.monarchinitiative.poet.views.UserActivityViews;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.time.LocalDateTime;
 import java.time.ZoneId;
 import java.util.Objects;

diff --git a/src/main/java/org/monarchinitiative/poet/model/entities/Version.java b/src/main/java/org/monarchinitiative/poet/model/entities/Version.java
@@ -1,6 +1,6 @@
 package org.monarchinitiative.poet.model.entities;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.time.LocalDateTime;
 @Entity
 public class Version {

diff --git a/src/main/java/org/monarchinitiative/poet/model/requests/PhenotypeRequest.java b/src/main/java/org/monarchinitiative/poet/model/requests/PhenotypeRequest.java
@@ -1,7 +1,7 @@
 package org.monarchinitiative.poet.model.requests;
 
-import javax.validation.constraints.NotNull;
-import javax.validation.constraints.Pattern;
+import jakarta.validation.constraints.NotNull;
+import jakarta.validation.constraints.Pattern;
 import java.util.Objects;
 
 /**

diff --git a/src/main/java/org/monarchinitiative/poet/model/requests/TreatmentRequest.java b/src/main/java/org/monarchinitiative/poet/model/requests/TreatmentRequest.java
@@ -1,7 +1,7 @@
 package org.monarchinitiative.poet.model.requests;
 
-import javax.validation.constraints.NotNull;
-import javax.validation.constraints.Pattern;
+import jakarta.validation.constraints.NotNull;
+import jakarta.validation.constraints.Pattern;
 import java.util.Objects;
 
 /**

diff --git a/src/main/java/org/monarchinitiative/poet/repository/UserActivityRepository.java b/src/main/java/org/monarchinitiative/poet/repository/UserActivityRepository.java
@@ -5,13 +5,14 @@
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.PagingAndSortingRepository;
 import org.springframework.data.repository.query.Param;
 
 import java.time.LocalDateTime;
 import java.util.Optional;
 
-public interface UserActivityRepository extends PagingAndSortingRepository<UserActivity, Long> {
+public interface UserActivityRepository extends CrudRepository<UserActivity, Long>, PagingAndSortingRepository<UserActivity, Long> {
     Page<UserActivity> findUserActivityByOwnerAuthId(String authId, Pageable pageable);
     Integer countAllByAnnotation_AnnotationTypeAndOwnerAuthId(String annotation_type, String authId);
     Page<UserActivity> findUserActivityByDateTimeAfter(LocalDateTime dateTime, Pageable pageable);