Merge pull request #1490 from alliance-genome/SCRUM-3711_refactor.2

Refactor to remove some classes SCRUM-3711.2

src/main/java/org/alliancegenome/curation_api/controllers/base/BaseAnnotationDTOCrudController.java

@@ -3,13 +3,13 @@
 import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
 import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
 import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
-import org.alliancegenome.curation_api.interfaces.base.BaseDTOCrudControllerInterface;
+import org.alliancegenome.curation_api.interfaces.base.BaseUpsertControllerInterface;
 import org.alliancegenome.curation_api.model.entities.Annotation;
 import org.alliancegenome.curation_api.model.ingest.dto.AnnotationDTO;
 import org.alliancegenome.curation_api.services.base.BaseAnnotationDTOCrudService;
 
 public abstract class BaseAnnotationDTOCrudController<S extends BaseAnnotationDTOCrudService<E, T, D>, E extends Annotation, T extends AnnotationDTO, D extends BaseSQLDAO<E>> extends BaseEntityCrudController<S, E, D>
-	implements BaseDTOCrudControllerInterface<E, T> {
+	implements BaseUpsertControllerInterface<E, T> {
 
 	protected abstract void init();
 
@@ -21,7 +21,7 @@ protected void setService(S service) {
 	}
 
 	public E upsert(T dto) throws ObjectUpdateException {
-		return upsert(dto, null);
+		return service.upsert(dto);
 	}
 
 	public E upsert(T dto, BackendBulkDataProvider dataProvider) throws ObjectUpdateException {

src/main/java/org/alliancegenome/curation_api/controllers/base/BaseDocumentController.java

@@ -4,13 +4,12 @@
 
 import org.alliancegenome.curation_api.dao.base.BaseDocumentDAO;
 import org.alliancegenome.curation_api.document.base.BaseDocument;
-import org.alliancegenome.curation_api.interfaces.base.BaseIdDocumentInterface;
+import org.alliancegenome.curation_api.interfaces.base.BaseSearchControllerInterface;
 import org.alliancegenome.curation_api.model.input.Pagination;
-import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.response.SearchResponse;
 import org.alliancegenome.curation_api.services.base.BaseDocumentService;
 
-public abstract class BaseDocumentController<S extends BaseDocumentService<E, D>, E extends BaseDocument, D extends BaseDocumentDAO<E>> implements BaseIdDocumentInterface<E> {
+public abstract class BaseDocumentController<S extends BaseDocumentService<E, D>, E extends BaseDocument, D extends BaseDocumentDAO<E>> implements BaseSearchControllerInterface<E> {
 
 	private BaseDocumentService<E, D> service;
 
@@ -20,10 +19,6 @@ protected void setService(S service) {
 
 	protected abstract void init();
 
-	public ObjectResponse<E> get(String curie) {
-		return service.get(curie);
-	}
-
 	public SearchResponse<E> search(Integer page, Integer limit, HashMap<String, Object> params) {
 		if (params == null)
 			params = new HashMap<String, Object>();

src/main/java/org/alliancegenome/curation_api/controllers/base/BaseEntityCrudController.java

@@ -5,14 +5,14 @@
 
 import org.alliancegenome.curation_api.dao.base.BaseEntityDAO;
 import org.alliancegenome.curation_api.interfaces.base.BaseIdCrudInterface;
-import org.alliancegenome.curation_api.model.entities.base.BaseEntity;
+import org.alliancegenome.curation_api.model.entities.base.AuditedObject;
 import org.alliancegenome.curation_api.model.input.Pagination;
 import org.alliancegenome.curation_api.response.ObjectListResponse;
 import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.response.SearchResponse;
 import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
 
-public abstract class BaseEntityCrudController<S extends BaseEntityCrudService<E, D>, E extends BaseEntity, D extends BaseEntityDAO<E>> implements BaseIdCrudInterface<E> {
+public abstract class BaseEntityCrudController<S extends BaseEntityCrudService<E, D>, E extends AuditedObject, D extends BaseEntityDAO<E>> implements BaseIdCrudInterface<E> {
 
 	protected BaseEntityCrudService<E, D> service;
 
@@ -30,16 +30,24 @@ public ObjectListResponse<E> create(List<E> entities) {
 		return service.create(entities);
 	}
 
-	public ObjectResponse<E> get(Long id) {
-		return service.get(id);
+	public ObjectResponse<E> getById(Long id) {
+		return service.getById(id);
+	}
+
+	public ObjectResponse<E> getByCurie(String curie) {
+		return service.getByCurie(curie);
 	}
 
 	public ObjectResponse<E> update(E entity) {
 		return service.update(entity);
 	}
 
-	public ObjectResponse<E> delete(Long id) {
-		return service.delete(id);
+	public ObjectResponse<E> deleteByCurie(String curie) {
+		return service.deleteByCurie(curie);
+	}
+
+	public ObjectResponse<E> deleteById(Long id) {
+		return service.deleteById(id);
 	}
 
 	public SearchResponse<E> findByField(String field, String value) {

src/main/java/org/alliancegenome/curation_api/controllers/base/BaseOntologyTermController.java

@@ -10,7 +10,7 @@
 import org.alliancegenome.curation_api.services.helpers.GenericOntologyLoadHelper;
 import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
 
-public abstract class BaseOntologyTermController<S extends BaseOntologyTermService<E, D>, E extends OntologyTerm, D extends BaseEntityDAO<E>> extends CurieObjectCrudController<S, E, BaseEntityDAO<E>> {
+public abstract class BaseOntologyTermController<S extends BaseOntologyTermService<E, D>, E extends OntologyTerm, D extends BaseEntityDAO<E>> extends BaseEntityCrudController<S, E, BaseEntityDAO<E>> {
 
 	private GenericOntologyLoadHelper<E> loader;
 

src/main/java/org/alliancegenome/curation_api/controllers/base/SubmittedObjectCrudController.java

@@ -3,13 +3,17 @@
 import org.alliancegenome.curation_api.dao.base.BaseEntityDAO;
 import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
 import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
-import org.alliancegenome.curation_api.interfaces.base.SubmittedObjectCrudInterface;
+import org.alliancegenome.curation_api.interfaces.base.BaseUpsertControllerInterface;
+import org.alliancegenome.curation_api.interfaces.base.BaseSubmittedObjectCrudInterface;
 import org.alliancegenome.curation_api.model.entities.base.SubmittedObject;
 import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
 import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.services.base.SubmittedObjectCrudService;
 
-public abstract class SubmittedObjectCrudController<S extends SubmittedObjectCrudService<E, T, D>, E extends SubmittedObject, T extends BaseDTO, D extends BaseEntityDAO<E>> extends CurieObjectCrudController<S, E, D> implements SubmittedObjectCrudInterface<E> {
+public abstract class SubmittedObjectCrudController<S extends SubmittedObjectCrudService<E, T, D>, E extends SubmittedObject, T extends BaseDTO, D extends BaseEntityDAO<E>> extends BaseEntityCrudController<S, E, D> implements 
+	BaseSubmittedObjectCrudInterface<E>,
+	BaseUpsertControllerInterface<E, T> 
+{
 
 	protected SubmittedObjectCrudService<E, T, D> service;
 
@@ -18,22 +22,20 @@ protected void setService(S service) {
 		this.service = service;
 	}
 
-	@Override
-	public ObjectResponse<E> get(String identifierString) {
-		return service.get(identifierString);
-	}
-
-	@Override
-	public ObjectResponse<E> delete(String identifierString) {
-		return service.delete(identifierString);
-	}
-
 	public E upsert(T dto) throws ObjectUpdateException {
-		return upsert(dto, null);
+		return service.upsert(dto);
 	}
 
 	public E upsert(T dto, BackendBulkDataProvider dataProvider) throws ObjectUpdateException {
 		return service.upsert(dto, dataProvider);
 	}
 
+	public ObjectResponse<E> getByIdentifier(String identifierString) {
+		return service.getByIdentifier(identifierString);
+	}
+
+	public ObjectResponse<E> deleteByIdentifier(String identifierString) {
+		return service.deleteByIdentifier(identifierString);
+	}
+
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/AGMDiseaseAnnotationCrudController.java

@@ -34,7 +34,8 @@ public APIResponse updateAgmDiseaseAnnotations(String dataProvider, List<AGMDise
 		return agmDiseaseAnnotationExecutor.runLoad(dataProvider, annotations);
 	}
 
-	public ObjectResponse<AGMDiseaseAnnotation> get(String identifierString) {
-		return agmDiseaseAnnotationService.get(identifierString);
+	public ObjectResponse<AGMDiseaseAnnotation> getByIdentifier(String identifierString) {
+		return agmDiseaseAnnotationService.getByIdentifier(identifierString);
 	}
+
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/AGMPhenotypeAnnotationCrudController.java

@@ -23,7 +23,7 @@ protected void init() {
 		setService(agmPhenotypeAnnotationService);
 	}
 
-	public ObjectResponse<AGMPhenotypeAnnotation> get(String identifierString) {
-		return agmPhenotypeAnnotationService.get(identifierString);
+	public ObjectResponse<AGMPhenotypeAnnotation> getByIdentifier(String identifierString) {
+		return agmPhenotypeAnnotationService.getByIdentifier(identifierString);
 	}
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/AlleleDiseaseAnnotationCrudController.java

@@ -35,7 +35,8 @@ public APIResponse updateAlleleDiseaseAnnotations(String dataProvider, List<Alle
 		return alleleDiseaseAnnotationExecutor.runLoad(dataProvider, annotations);
 	}
 
-	public ObjectResponse<AlleleDiseaseAnnotation> get(String identifierString) {
-		return alleleDiseaseAnnotationService.get(identifierString);
+	public ObjectResponse<AlleleDiseaseAnnotation> getByIdentifier(String identifierString) {
+		return alleleDiseaseAnnotationService.getByIdentifier(identifierString);
 	}
+
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/AllelePhenotypeAnnotationCrudController.java

@@ -23,7 +23,7 @@ protected void init() {
 		setService(allelePhenotypeAnnotationService);
 	}
 
-	public ObjectResponse<AllelePhenotypeAnnotation> get(String identifierString) {
-		return allelePhenotypeAnnotationService.get(identifierString);
+	public ObjectResponse<AllelePhenotypeAnnotation> getByIdentifier(String identifierString) {
+		return allelePhenotypeAnnotationService.getByIdentifier(identifierString);
 	}
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/ConstructCrudController.java

@@ -16,8 +16,7 @@
 import jakarta.inject.Inject;
 
 @RequestScoped
-public class ConstructCrudController extends SubmittedObjectCrudController<ConstructService, Construct, ConstructDTO, ConstructDAO>
-	implements ConstructCrudInterface {
+public class ConstructCrudController extends SubmittedObjectCrudController<ConstructService, Construct, ConstructDTO, ConstructDAO> implements ConstructCrudInterface {
 
 	@Inject
 	ConstructService constructService;
@@ -34,4 +33,6 @@ protected void init() {
 	public APIResponse updateConstructs(String dataProvider, List<ConstructDTO> annotations) {
 		return constructExecutor.runLoad(dataProvider, annotations);
 	}
+
+
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/DiseaseAnnotationCrudController.java

@@ -23,7 +23,7 @@ protected void init() {
 		setService(diseaseAnnotationService);
 	}
 
-	public ObjectResponse<DiseaseAnnotation> get(String identifierString) {
-		return diseaseAnnotationService.get(identifierString);
+	public ObjectResponse<DiseaseAnnotation> getByIdentifier(String identifierString) {
+		return diseaseAnnotationService.getByIdentifier(identifierString);
 	}
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneDiseaseAnnotationCrudController.java

@@ -35,7 +35,7 @@ public APIResponse updateGeneDiseaseAnnotations(String dataProvider, List<GeneDi
 		return geneDiseaseAnnotationExecutor.runLoad(dataProvider, annotations);
 	}
 
-	public ObjectResponse<GeneDiseaseAnnotation> get(String identifierString) {
-		return geneDiseaseAnnotationService.get(identifierString);
+	public ObjectResponse<GeneDiseaseAnnotation> getByIdentifier(String identifierString) {
+		return geneDiseaseAnnotationService.getByIdentifier(identifierString);
 	}
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneGeneticInteractionCrudController.java

@@ -31,11 +31,12 @@ protected void init() {
 		setService(geneGeneticInteractionService);
 	}
 
-	public ObjectResponse<GeneGeneticInteraction> get(String identifierString) {
-		return geneGeneticInteractionService.get(identifierString);
+	public ObjectResponse<GeneGeneticInteraction> getByIdentifier(String identifierString) {
+		return geneGeneticInteractionService.getByIdentifier(identifierString);
 	}
 
 	public APIResponse updateInteractions(List<PsiMiTabDTO> interactionData) {
 		return geneGeneticInteractionExecutor.runLoad(interactionData);
 	}
+
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneInteractionCrudController.java

@@ -24,7 +24,7 @@ protected void init() {
 		setService(geneInteractionService);
 	}
 
-	public ObjectResponse<GeneInteraction> get(String identifierString) {
-		return geneInteractionService.get(identifierString);
+	public ObjectResponse<GeneInteraction> getByIdentifier(String identifierString) {
+		return geneInteractionService.getByIdentifer(identifierString);
 	}
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/GeneMolecularInteractionCrudController.java

@@ -31,8 +31,8 @@ protected void init() {
 		setService(geneMolecularInteractionService);
 	}
 
-	public ObjectResponse<GeneMolecularInteraction> get(String identifierString) {
-		return geneMolecularInteractionService.get(identifierString);
+	public ObjectResponse<GeneMolecularInteraction> getByIdentifier(String identifierString) {
+		return geneMolecularInteractionService.getByIdentifier(identifierString);
 	}
 
 	public APIResponse updateInteractions(List<PsiMiTabDTO> interactionData) {

src/main/java/org/alliancegenome/curation_api/controllers/crud/GenePhenotypeAnnotationCrudController.java

@@ -23,7 +23,7 @@ protected void init() {
 		setService(genePhenotypeAnnotationService);
 	}
 
-	public ObjectResponse<GenePhenotypeAnnotation> get(String identifierString) {
-		return genePhenotypeAnnotationService.get(identifierString);
+	public ObjectResponse<GenePhenotypeAnnotation> getByIdentifier(String identifierString) {
+		return genePhenotypeAnnotationService.getByIdentifier(identifierString);
 	}
 }

src/main/java/org/alliancegenome/curation_api/controllers/crud/InformationContentEntityCrudController.java

@@ -1,6 +1,6 @@
 package org.alliancegenome.curation_api.controllers.crud;
 
-import org.alliancegenome.curation_api.controllers.base.CurieObjectCrudController;
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
 import org.alliancegenome.curation_api.dao.InformationContentEntityDAO;
 import org.alliancegenome.curation_api.interfaces.crud.InformationContentEntityCrudInterface;
 import org.alliancegenome.curation_api.model.entities.InformationContentEntity;
@@ -11,7 +11,7 @@
 import jakarta.inject.Inject;
 
 @RequestScoped
-public class InformationContentEntityCrudController extends CurieObjectCrudController<InformationContentEntityService, InformationContentEntity, InformationContentEntityDAO>
+public class InformationContentEntityCrudController extends BaseEntityCrudController<InformationContentEntityService, InformationContentEntity, InformationContentEntityDAO>
 	implements InformationContentEntityCrudInterface {
 
 	@Inject

src/main/java/org/alliancegenome/curation_api/controllers/crud/MoleculeCrudController.java

@@ -1,6 +1,6 @@
 package org.alliancegenome.curation_api.controllers.crud;
 
-import org.alliancegenome.curation_api.controllers.base.CurieObjectCrudController;
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
 import org.alliancegenome.curation_api.dao.MoleculeDAO;
 import org.alliancegenome.curation_api.interfaces.crud.MoleculeCrudInterface;
 import org.alliancegenome.curation_api.jobs.executors.MoleculeExecutor;
@@ -16,7 +16,7 @@
 import jakarta.inject.Inject;
 
 @RequestScoped
-public class MoleculeCrudController extends CurieObjectCrudController<MoleculeService, Molecule, MoleculeDAO> implements MoleculeCrudInterface {
+public class MoleculeCrudController extends BaseEntityCrudController<MoleculeService, Molecule, MoleculeDAO> implements MoleculeCrudInterface {
 
 	@Inject
 	MoleculeService moleculeService;

src/main/java/org/alliancegenome/curation_api/controllers/crud/PhenotypeAnnotationCrudController.java

@@ -30,8 +30,8 @@ protected void init() {
 		setService(phenotypeAnnotationService);
 	}
 
-	public ObjectResponse<PhenotypeAnnotation> get(String identifierString) {
-		return phenotypeAnnotationService.get(identifierString);
+	public ObjectResponse<PhenotypeAnnotation> getByIdentifier(String identifierString) {
+		return phenotypeAnnotationService.getByIdentifier(identifierString);
 	}
 
 	public APIResponse updatePhenotypeAnnotations(String dataProvider, List<PhenotypeFmsDTO> annotations) {