Refactor project file structure

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

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.actuator;
 
 import io.micrometer.common.KeyValue;
 import io.micrometer.core.instrument.MeterRegistry;

src/main/java/org/fairdatateam/fairdatapoint/service/actuator/AppInfoContributor.java → src/main/java/org/fairdatateam/fairdatapoint/actuator/AppInfoContributor.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.service.actuator;
+package org.fairdatateam.fairdatapoint.actuator;
 
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.actuate.info.Info;

src/main/java/org/fairdatateam/fairdatapoint/config/AsyncConfig.java → src/main/java/org/fairdatateam/fairdatapoint/common/config/AsyncConfig.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.common.config;
 
 import org.fairdatateam.fairdatapoint.Profiles;
 import org.springframework.context.annotation.Configuration;

src/main/java/org/fairdatateam/fairdatapoint/config/CacheConfig.java → src/main/java/org/fairdatateam/fairdatapoint/common/config/CacheConfig.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.common.config;
 
 import org.springframework.cache.annotation.EnableCaching;
 import org.springframework.cache.concurrent.ConcurrentMapCacheManager;
@@ -29,7 +29,7 @@
 
 import java.util.List;
 
-import static org.fairdatateam.fairdatapoint.config.AclConfig.ACL_CACHE;
+import static org.fairdatateam.fairdatapoint.security.acl.AclConfig.ACL_CACHE;
 
 @Configuration
 @EnableCaching

src/main/java/org/fairdatateam/fairdatapoint/config/ConverterConfig.java → src/main/java/org/fairdatateam/fairdatapoint/common/config/ConverterConfig.java

@@ -25,10 +25,10 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.common.config;
 
-import org.fairdatateam.fairdatapoint.api.converter.ErrorConverter;
-import org.fairdatateam.fairdatapoint.api.converter.RdfConverter;
+import org.fairdatateam.fairdatapoint.common.error.ErrorConverter;
+import org.fairdatateam.fairdatapoint.rdf.RdfConverter;
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;

src/main/java/org/fairdatateam/fairdatapoint/config/properties/InstanceProperties.java → src/main/java/org/fairdatateam/fairdatapoint/common/config/InstanceProperties.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config.properties;
+package org.fairdatateam.fairdatapoint.common.config;
 
 import lombok.AllArgsConstructor;
 import lombok.Getter;

src/main/java/org/fairdatateam/fairdatapoint/config/MongoConfig.java → src/main/java/org/fairdatateam/fairdatapoint/common/config/MongoConfig.java

@@ -20,15 +20,15 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.common.config;
 
 import io.mongock.api.config.LegacyMigration;
 import io.mongock.driver.mongodb.springdata.v4.SpringDataMongoV4Driver;
 import io.mongock.runner.springboot.MongockSpringboot;
 import io.mongock.runner.springboot.base.MongockInitializingBeanRunner;
-import org.fairdatateam.fairdatapoint.service.resource.ResourceDefinitionCache;
-import org.fairdatateam.fairdatapoint.service.resource.ResourceDefinitionTargetClassesCache;
-import org.fairdatateam.fairdatapoint.service.settings.SettingsCache;
+import org.fairdatateam.fairdatapoint.resource.ResourceDefinitionCache;
+import org.fairdatateam.fairdatapoint.resource.ResourceDefinitionTargetClassesCache;
+import org.fairdatateam.fairdatapoint.settings.SettingsCache;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
@@ -64,9 +64,7 @@ public MongockInitializingBeanRunner mongockApplicationRunner(
     ) {
         return MongockSpringboot.builder()
                 .setDriver(SpringDataMongoV4Driver.withDefaultLock(mongoTemplate))
-                .addMigrationScanPackage(
-                        "org.fairdatateam.fairdatapoint.database.mongo.migration.production"
-                )
+                .addMigrationScanPackage("org.fairdatateam.fairdatapoint.migration.mongodb.production")
                 .setSpringContext(springContext)
                 .setLegacyMigration(new LegacyMigration("dbchangelog"))
                 .addDependency(ResourceDefinitionCache.class, resourceDefinitionCache)

src/main/java/org/fairdatateam/fairdatapoint/config/PropertyConfig.java → src/main/java/org/fairdatateam/fairdatapoint/common/config/PropertyConfig.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.common.config;
 
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;

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

@@ -20,11 +20,11 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.common.config;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
-import org.fairdatateam.fairdatapoint.api.converter.ErrorConverter;
-import org.fairdatateam.fairdatapoint.api.converter.RdfConverter;
+import org.fairdatateam.fairdatapoint.common.error.ErrorConverter;
+import org.fairdatateam.fairdatapoint.rdf.RdfConverter;
 import org.jspecify.annotations.NonNull;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;

src/main/java/org/fairdatateam/fairdatapoint/config/WorkerConfig.java → src/main/java/org/fairdatateam/fairdatapoint/common/config/WorkerConfig.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.config;
+package org.fairdatateam.fairdatapoint.common.config;
 
 import org.springframework.context.annotation.Configuration;
 import org.springframework.scheduling.annotation.EnableScheduling;

src/main/java/org/fairdatateam/fairdatapoint/api/converter/ErrorConverter.java → src/main/java/org/fairdatateam/fairdatapoint/common/error/ErrorConverter.java

@@ -25,9 +25,8 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-package org.fairdatateam.fairdatapoint.api.converter;
+package org.fairdatateam.fairdatapoint.common.error;
 
-import org.fairdatateam.fairdatapoint.api.dto.error.ErrorDTO;
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.springframework.http.HttpInputMessage;
 import org.springframework.http.HttpOutputMessage;

src/main/java/org/fairdatateam/fairdatapoint/api/dto/error/ErrorDTO.java → src/main/java/org/fairdatateam/fairdatapoint/common/error/ErrorDTO.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.api.dto.error;
+package org.fairdatateam.fairdatapoint.common.error;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;

src/main/java/org/fairdatateam/fairdatapoint/api/controller/exception/ExceptionControllerAdvice.java → src/main/java/org/fairdatateam/fairdatapoint/common/error/ExceptionControllerAdvice.java

@@ -25,17 +25,16 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-package org.fairdatateam.fairdatapoint.api.controller.exception;
+package org.fairdatateam.fairdatapoint.common.error;
 
 import io.swagger.v3.oas.annotations.media.Content;
 import io.swagger.v3.oas.annotations.media.Schema;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import jakarta.validation.ConstraintViolationException;
 import lombok.extern.slf4j.Slf4j;
-import org.fairdatateam.fairdatapoint.api.dto.error.ErrorDTO;
-import org.fairdatateam.fairdatapoint.entity.exception.*;
-import org.fairdatateam.fairdatapoint.entity.index.exception.AbstractIndexException;
-import org.fairdatateam.fairdatapoint.service.metadata.exception.MetadataServiceException;
+import org.fairdatateam.fairdatapoint.index.exception.AbstractIndexException;
+import org.fairdatateam.fairdatapoint.rdf.RdfValidationException;
+import org.fairdatateam.fairdatapoint.rdf.metadata.MetadataServiceException;
 import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.query.MalformedQueryException;
@@ -57,8 +56,8 @@
 import java.util.Map;
 
 import static java.lang.String.format;
-import static org.fairdatateam.fairdatapoint.util.RdfIOUtil.getWriterConfig;
-import static org.fairdatateam.fairdatapoint.util.ValueFactoryHelper.i;
+import static org.fairdatateam.fairdatapoint.rdf.RdfIOUtil.getWriterConfig;
+import static org.fairdatateam.fairdatapoint.common.util.ValueFactoryHelper.i;
 
 @ControllerAdvice
 @Slf4j

src/main/java/org/fairdatateam/fairdatapoint/entity/exception/ForbiddenException.java → src/main/java/org/fairdatateam/fairdatapoint/common/error/ForbiddenException.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.entity.exception;
+package org.fairdatateam.fairdatapoint.common.error;
 
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ResponseStatus;

src/main/java/org/fairdatateam/fairdatapoint/entity/exception/ResourceNotFoundException.java → src/main/java/org/fairdatateam/fairdatapoint/common/error/ResourceNotFoundException.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.entity.exception;
+package org.fairdatateam.fairdatapoint.common.error;
 
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ResponseStatus;

src/main/java/org/fairdatateam/fairdatapoint/entity/exception/UnauthorizedException.java → src/main/java/org/fairdatateam/fairdatapoint/common/error/UnauthorizedException.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.entity.exception;
+package org.fairdatateam.fairdatapoint.common.error;
 
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ResponseStatus;

src/main/java/org/fairdatateam/fairdatapoint/entity/exception/ValidationException.java → src/main/java/org/fairdatateam/fairdatapoint/common/error/ValidationException.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.entity.exception;
+package org.fairdatateam.fairdatapoint.common.error;
 
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ResponseStatus;

src/main/java/org/fairdatateam/fairdatapoint/util/HttpUtil.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/HttpUtil.java

@@ -20,11 +20,11 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.util;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import jakarta.servlet.http.HttpServletRequest;
 import lombok.extern.slf4j.Slf4j;
-import org.fairdatateam.fairdatapoint.entity.exception.ValidationException;
+import org.fairdatateam.fairdatapoint.common.error.ValidationException;
 import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.springframework.http.HttpHeaders;
@@ -36,7 +36,7 @@
 import static java.lang.String.format;
 import static java.util.Optional.of;
 import static java.util.Optional.ofNullable;
-import static org.fairdatateam.fairdatapoint.util.ValueFactoryHelper.i;
+import static org.fairdatateam.fairdatapoint.common.util.ValueFactoryHelper.i;
 
 @Slf4j
 public class HttpUtil {

src/main/java/org/fairdatateam/fairdatapoint/api/validator/IriValidator.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/IriValidator.java

@@ -20,12 +20,12 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.api.validator;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import jakarta.validation.ConstraintValidator;
 import jakarta.validation.ConstraintValidatorContext;
 
-import static org.fairdatateam.fairdatapoint.util.ValueFactoryHelper.i;
+import static org.fairdatateam.fairdatapoint.common.util.ValueFactoryHelper.i;
 
 public class IriValidator implements ConstraintValidator<ValidIri, String> {
 

src/main/java/org/fairdatateam/fairdatapoint/util/KnownUUIDs.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/KnownUUIDs.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.util;
+package org.fairdatateam.fairdatapoint.common.util;
 
 public class KnownUUIDs {
 

src/main/java/org/fairdatateam/fairdatapoint/entity/schema/SemVer.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/SemVer.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.entity.schema;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import lombok.*;
 

src/main/java/org/fairdatateam/fairdatapoint/api/validator/SemVerValidator.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/SemVerValidator.java

@@ -20,11 +20,10 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.api.validator;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import jakarta.validation.ConstraintValidator;
 import jakarta.validation.ConstraintValidatorContext;
-import org.fairdatateam.fairdatapoint.entity.schema.SemVer;
 
 public class SemVerValidator implements ConstraintValidator<ValidSemVer, String> {
 

src/main/java/org/fairdatateam/fairdatapoint/util/ResourceReader.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/SpringResourceReader.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.util;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import com.google.common.base.Charsets;
 import com.google.common.io.Resources;
@@ -37,7 +37,11 @@
 import static java.lang.String.format;
 import static java.nio.charset.StandardCharsets.UTF_8;
 
-public class ResourceReader {
+/**
+ * Loads <a href="https://docs.spring.io/spring-framework/reference/core/resources.html">Spring Resources</a>.
+ * Beware: This has nothing to do with the concept of an FDP "Resource".
+ */
+public class SpringResourceReader {
 
     public static String loadResource(String name) {
         return loadResource(getResource(name));

src/main/java/org/fairdatateam/fairdatapoint/util/ThrowingFunction.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/ThrowingFunction.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.util;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import java.util.function.Function;
 

src/main/java/org/fairdatateam/fairdatapoint/api/validator/ValidIri.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/ValidIri.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.api.validator;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import jakarta.validation.Constraint;
 import jakarta.validation.Payload;

src/main/java/org/fairdatateam/fairdatapoint/api/validator/ValidSemVer.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/ValidSemVer.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.api.validator;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import jakarta.validation.Constraint;
 import jakarta.validation.Payload;

src/main/java/org/fairdatateam/fairdatapoint/util/ValidationUtil.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/ValidationUtil.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.util;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import org.springframework.validation.BeanPropertyBindingResult;
 import org.springframework.validation.BindException;

src/main/java/org/fairdatateam/fairdatapoint/util/ValueFactoryHelper.java → src/main/java/org/fairdatateam/fairdatapoint/common/util/ValueFactoryHelper.java

@@ -20,7 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package org.fairdatateam.fairdatapoint.util;
+package org.fairdatateam.fairdatapoint.common.util;
 
 import org.eclipse.rdf4j.model.*;
 import org.eclipse.rdf4j.model.impl.SimpleValueFactory;