Update core dependencies

pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>3.2.12</version>
+        <version>3.4.1</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
     <groupId>org.fairdatapoint</groupId>
@@ -55,15 +55,15 @@
         <rdf-resolver.version>0.2.0</rdf-resolver.version>
 
         <!-- Core -->
-        <springdoc.version>2.5.0</springdoc.version>
-        <postgresql.version>42.7.3</postgresql.version>
-        <rdf4j.version>4.3.12</rdf4j.version>
+        <springdoc.version>2.8.3</springdoc.version>
+        <postgresql.version>42.7.5</postgresql.version>
+        <rdf4j.version>5.1.0</rdf4j.version>
         <jwt.version>0.12.6</jwt.version>
-        <lombok.version>1.18.32</lombok.version>
-        <hypersistence.version>3.7.6</hypersistence.version>
+        <lombok.version>1.18.36</lombok.version>
+        <hypersistence.version>3.9.0</hypersistence.version>
 
         <!-- Test -->
-        <httpclient5.version>5.3.1</httpclient5.version>
+        <httpclient5.version>5.4.1</httpclient5.version>
 
         <!-- Plugins -->
         <plugin.license.version>4.5</plugin.license.version>
@@ -199,6 +199,10 @@
             <groupId>org.flywaydb</groupId>
             <artifactId>flyway-core</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.flywaydb</groupId>
+            <artifactId>flyway-database-postgresql</artifactId>
+        </dependency>
         <dependency>
             <groupId>io.hypersistence</groupId>
             <artifactId>hypersistence-utils-hibernate-63</artifactId>

src/main/java/org/fairdatapoint/api/controller/settings/SettingsDefaults.java

@@ -30,7 +30,6 @@
 import org.springframework.stereotype.Component;
 
 import java.util.List;
-import java.util.UUID;
 
 @Component
 @RequiredArgsConstructor
@@ -61,14 +60,14 @@ public Settings defaultSettings() {
     public List<SettingsMetric> defaultMetrics(Settings settings) {
         return List.of(
                 SettingsMetric.builder()
-                        .uuid(UUID.randomUUID())
+                        .uuid(null)
                         .metricUri("https://purl.org/fair-metrics/FM_F1A")
                         .resourceUri("https://www.ietf.org/rfc/rfc3986.txt")
                         .settings(settings)
                         .orderPriority(1)
                         .build(),
                 SettingsMetric.builder()
-                        .uuid(UUID.randomUUID())
+                        .uuid(null)
                         .metricUri("https://purl.org/fair-metrics/FM_A1.1")
                         .resourceUri("https://www.wikidata.org/wiki/Q8777")
                         .settings(settings)

src/main/java/org/fairdatapoint/entity/schema/MetadataSchema.java

@@ -42,14 +42,17 @@
 @SuperBuilder
 public class MetadataSchema extends BaseEntityCustomUUID {
 
-    @OneToMany(fetch = FetchType.LAZY, mappedBy = "schema")
+    @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL,
+            orphanRemoval = true, mappedBy = "schema")
     private List<MetadataSchemaVersion> versions;
 
     @OrderBy("orderPriority")
-    @OneToMany(mappedBy = "extendedMetadataSchema", fetch = FetchType.LAZY)
+    @OneToMany(mappedBy = "extendedMetadataSchema", cascade = CascadeType.ALL,
+            orphanRemoval = true, fetch = FetchType.LAZY)
     private List<MetadataSchemaExtension> extensions;
 
     @OrderBy("orderPriority")
-    @OneToMany(mappedBy = "usedMetadataSchema", fetch = FetchType.LAZY)
+    @OneToMany(mappedBy = "usedMetadataSchema", cascade = CascadeType.ALL,
+            orphanRemoval = true, fetch = FetchType.LAZY)
     private List<MetadataSchemaUsage> usages;
 }

src/main/java/org/fairdatapoint/entity/schema/MetadataSchemaVersion.java

@@ -52,11 +52,11 @@ public class MetadataSchemaVersion extends BaseEntityCustomUUID {
     @JoinColumn(name = "metadata_schema_id", nullable = false)
     private MetadataSchema schema;
 
-    @OneToOne(fetch = FetchType.LAZY)
+    @OneToOne(fetch = FetchType.LAZY, cascade = CascadeType.PERSIST)
     @JoinColumn(name = "previous_version_id", nullable = false)
     private MetadataSchemaVersion previousVersion;
 
-    @OneToOne(fetch = FetchType.LAZY, mappedBy = "previousVersion")
+    @OneToOne(cascade = CascadeType.PERSIST, mappedBy = "previousVersion")
     private MetadataSchemaVersion nextVersion;
 
     @NotNull

src/main/java/org/fairdatapoint/service/apikey/ApiKeyMapper.java

@@ -27,8 +27,6 @@
 import org.fairdatapoint.entity.user.UserAccount;
 import org.springframework.stereotype.Component;
 
-import java.util.UUID;
-
 @Component
 public class ApiKeyMapper {
 
@@ -38,7 +36,7 @@ public ApiKeyDTO toDTO(ApiKey apiKey) {
 
     public ApiKey createApiKey(UserAccount userAccount, String token) {
         return ApiKey.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .token(token)
                 .userAccount(userAccount)
                 .build();

src/main/java/org/fairdatapoint/service/index/entry/IndexEntryService.java

@@ -243,7 +243,7 @@ public IndexEntry storeEntry(@Valid PingDTO pingDTO) {
         else {
             log.info("Storing new entry {}", clientUrl);
             entry = new IndexEntry();
-            entry.setUuid(UUID.randomUUID());
+            entry.setUuid(null);
             entry.setClientUrl(clientUrl);
             entry.setCreatedAt(Instant.now());
             if (settings.getAutoPermit()) {

src/main/java/org/fairdatapoint/service/resource/ResourceDefinitionMapper.java

@@ -29,14 +29,13 @@
 
 import java.time.Instant;
 import java.util.List;
-import java.util.UUID;
 
 @Service
 public class ResourceDefinitionMapper {
 
     public ResourceDefinition fromChangeDTO(ResourceDefinitionChangeDTO dto) {
         return ResourceDefinition.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .name(dto.getName())
                 .urlPrefix(dto.getUrlPrefix())
                 .build();
@@ -119,7 +118,7 @@ private ResourceDefinitionChildListViewMetadataDTO toChildMetadataDTO(ResourceDe
 
     public MetadataSchemaUsage toUsage(MetadataSchema schema, ResourceDefinition definition, int orderPriority) {
         return MetadataSchemaUsage.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .usedMetadataSchema(schema)
                 .resourceDefinition(definition)
                 .orderPriority(orderPriority)
@@ -130,7 +129,7 @@ public ResourceDefinitionLink toLink(
             ResourceDefinitionLinkDTO dto, ResourceDefinition definition, int orderPriority
     ) {
         return ResourceDefinitionLink.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .title(dto.getTitle())
                 .propertyUri(dto.getPropertyUri())
                 .resourceDefinition(definition)
@@ -144,7 +143,7 @@ public ResourceDefinitionChild toChild(
             ResourceDefinitionChildDTO dto, ResourceDefinition source, ResourceDefinition target, int orderPriority
     ) {
         return ResourceDefinitionChild.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .relationUri(dto.getRelationUri())
                 .title(dto.getListView().getTitle())
                 .tagsUri(dto.getListView().getTagsUri())
@@ -160,7 +159,7 @@ public ResourceDefinitionChildMetadata toChildMetadata(
             ResourceDefinitionChildListViewMetadataDTO dto, ResourceDefinitionChild child, int orderPriority
     ) {
         return ResourceDefinitionChildMetadata.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .title(dto.getTitle())
                 .propertyUri(dto.getPropertyUri())
                 .child(child)

src/main/java/org/fairdatapoint/service/schema/MetadataSchemaMapper.java

@@ -299,7 +299,7 @@ public MetadataSchemaExtension newExtension(
             MetadataSchemaVersion version, MetadataSchema metadataSchema, int orderPriority
     ) {
         return MetadataSchemaExtension.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .extendedMetadataSchema(metadataSchema)
                 .metadataSchemaVersion(version)
                 .orderPriority(orderPriority)

src/main/java/org/fairdatapoint/service/schema/MetadataSchemaService.java

@@ -160,15 +160,15 @@ public boolean deleteSchemaDraft(UUID uuid) {
             return false;
         }
         final MetadataSchemaVersion draft = oDraft.get();
-        final boolean isOnlyVersion = draft.getSchema().getVersions().size() == 1;
-        extensionRepository.deleteAll(draft.getExtensions());
-        versionRepository.delete(draft);
+        final boolean isOnlyVersion = versionRepository.getBySchemaUuid(draft.getSchema().getUuid()).size() == 1;
+        entityManager.clear();
 
         if (isOnlyVersion) {
-            usageRepository.deleteAll(draft.getSchema().getUsages());
-            extensionRepository.deleteAll(draft.getSchema().getExtensions());
             schemaRepository.delete(draft.getSchema());
         }
+        else {
+            versionRepository.delete(draft);
+        }
         return true;
     }
 
@@ -256,6 +256,7 @@ public boolean deleteVersion(UUID uuid, String version) {
         }
         // Validate and fix links
         final MetadataSchemaVersion schema = oSchema.get();
+        final boolean isOnlyVersion = versionRepository.getBySchemaUuid(schema.getSchema().getUuid()).size() == 1;
         if (schema.isLatest()) {
             if (schema.getPreviousVersion() == null) {
                 metadataSchemaValidator.validateNotUsed(schema.getSchema());
@@ -274,14 +275,15 @@ public boolean deleteVersion(UUID uuid, String version) {
             schema.getNextVersion().setPreviousVersion(schema.getPreviousVersion());
             versionRepository.save(schema.getNextVersion());
         }
+        entityManager.flush();
+        entityManager.clear();
 
-        final boolean isOnlyVersion = schema.getSchema().getVersions().size() == 1;
-        versionRepository.delete(schema);
         if (isOnlyVersion) {
-            usageRepository.deleteAll(schema.getSchema().getUsages());
-            extensionRepository.deleteAll(schema.getSchema().getExtensions());
             schemaRepository.delete(schema.getSchema());
         }
+        else {
+            versionRepository.delete(schema);
+        }
         return true;
     }
 
@@ -300,9 +302,6 @@ public boolean deleteSchemaFull(UUID uuid) {
             throw new ValidationException("You can't delete INTERNAL Shape");
         }
         // Delete
-        versionRepository.deleteAll(schema.getVersions());
-        extensionRepository.deleteAll(schema.getExtensions());
-        usageRepository.deleteAll(schema.getUsages());
         schemaRepository.delete(schema);
         entityManager.flush();
         // Update cache

src/main/java/org/fairdatapoint/service/search/query/SearchSavedQueryMapper.java

@@ -33,7 +33,6 @@
 
 import java.time.Instant;
 import java.util.Optional;
-import java.util.UUID;
 
 @Component
 @RequiredArgsConstructor
@@ -64,7 +63,7 @@ public SearchSavedQuery fromChangeDTO(
             SearchSavedQueryChangeDTO reqDto, UserAccount userAccount
     ) {
         return SearchSavedQuery.builder()
-                .uuid(UUID.randomUUID())
+                .uuid(null)
                 .name(reqDto.getName())
                 .description(reqDto.getDescription())
                 .type(reqDto.getType())

src/main/java/org/fairdatapoint/service/settings/SettingsService.java

@@ -123,9 +123,6 @@ private List<SettingsAutocompleteSource> updateSources(SettingsUpdateDTO dto, Se
 
     private List<SettingsSearchFilter> updateSearchFilters(SettingsUpdateDTO dto, Settings settings) {
         // Delete old
-        settings
-                .getSearchFilters()
-                .forEach(searchFilter -> searchFilterItemRepository.deleteAll(searchFilter.getItems()));
         searchFilterRepository.deleteAll(settings.getSearchFilters());
         // Add new
         final List<SettingsSearchFilter> searchFilters = new ArrayList<>();

src/main/java/org/fairdatapoint/service/user/UserMapper.java

@@ -28,8 +28,6 @@
 import org.springframework.security.crypto.password.PasswordEncoder;
 import org.springframework.stereotype.Component;
 
-import java.util.UUID;
-
 @Component
 @RequiredArgsConstructor
 public class UserMapper {
@@ -56,14 +54,14 @@ public UserSimpleDTO toSimpleDTO(UserAccount user) {
     }
 
     public UserAccount fromCreateDTO(UserCreateDTO dto) {
-        return
-                new UserAccount(
-                        UUID.randomUUID(),
-                        dto.getFirstName(),
-                        dto.getLastName(),
-                        dto.getEmail(),
-                        passwordEncoder.encode(dto.getPassword()),
-                        dto.getRole());
+        return UserAccount.builder()
+                .uuid(null)
+                .firstName(dto.getFirstName())
+                .lastName(dto.getLastName())
+                .email(dto.getEmail())
+                .passwordHash(passwordEncoder.encode(dto.getPassword()))
+                .role(dto.getRole())
+                .build();
     }
 
     public UserAccount fromChangeDTO(UserChangeDTO dto, UserAccount user) {

src/test/java/org/fairdatapoint/acceptance/index/entry/List_All_GET.java

@@ -33,6 +33,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.ParameterizedTypeReference;
 import org.springframework.http.*;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.util.UriComponentsBuilder;
 
 import java.net.URI;
@@ -90,7 +91,6 @@ public void res200_listFew() {
         indexEntryRepository.deleteAll();
         List<IndexEntry> entries = TestIndexEntryFixtures.entriesFew();
         indexEntryRepository.saveAll(entries);
-        int size = 9;
 
         // AND: prepare request
         RequestEntity<?> request = RequestEntity