SCRUM-4771 Refactor validation code

src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java

@@ -19,7 +19,7 @@ private VocabularyConstants() {
 	public static final String AGM_RELATION_VOCABULARY = "agm_relation";
 	public static final String AGM_STR_RELATION_VOCABULARY_TERM_SET = "agm_str_relation";
 	public static final String AGM_ALLELE_RELATION_VOCABULARY_TERM_SET = "agm_allele_relation";
-	public static final String AGM_ALLELE_ASSOCIATION_VOCABULARY = "agm_allele_association_geno_terms";
+	public static final String AGM_ALLELE_GENOTYPE_TERMS_VOCABULARY = "agm_allele_association_geno_terms";
 	public static final String AGM_AGM_RELATION_VOCABULARY_TERM_SET = "agm_agm_relation";
 
 	public static final String PHENOTYPE_RELATION_VOCABULARY = "phenotype_relation";

src/main/java/org/alliancegenome/curation_api/dao/slotAnnotations/constructSlotAnnotations/ConstructComponentSlotAnnotationDAO.java

@@ -1,27 +1,14 @@
 package org.alliancegenome.curation_api.dao.slotAnnotations.constructSlotAnnotations;
 
-import org.alliancegenome.curation_api.dao.NoteDAO;
 import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
 import org.alliancegenome.curation_api.model.entities.slotAnnotations.constructSlotAnnotations.ConstructComponentSlotAnnotation;
 
 import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.inject.Inject;
-import jakarta.persistence.Query;
 
 @ApplicationScoped
 public class ConstructComponentSlotAnnotationDAO extends BaseSQLDAO<ConstructComponentSlotAnnotation> {
 
-	@Inject
-	NoteDAO noteDAO;
-
 	protected ConstructComponentSlotAnnotationDAO() {
 		super(ConstructComponentSlotAnnotation.class);
 	}
-
-	public void deleteAttachedNote(Long id) {
-		Query jpqlQuery = entityManager.createNativeQuery("DELETE FROM slotannotation_note WHERE relatednotes_id = '" + id + "'");
-		jpqlQuery.executeUpdate();
-
-		noteDAO.remove(id);
-	}
 }

src/main/java/org/alliancegenome/curation_api/model/entities/slotAnnotations/constructSlotAnnotations/ConstructComponentSlotAnnotation.java

@@ -25,6 +25,7 @@
 import com.fasterxml.jackson.annotation.JsonBackReference;
 import com.fasterxml.jackson.annotation.JsonView;
 
+import jakarta.persistence.CascadeType;
 import jakarta.persistence.Entity;
 import jakarta.persistence.Index;
 import jakarta.persistence.JoinColumn;
@@ -73,9 +74,12 @@ public class ConstructComponentSlotAnnotation extends SlotAnnotation {
 	@EqualsAndHashCode.Include
 	protected String taxonText;
 
-	@IndexedEmbedded(includeDepth = 1)
+	@IndexedEmbedded(includePaths = {"freeText", "noteType.name", "references.curie",
+			"references.primaryCrossReferenceCurie", "freeText_keyword", "noteType.name_keyword", "references.curie_keyword",
+			"references.primaryCrossReferenceCurie_keyword"
+	})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
-	@OneToMany
+	@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
 	@JsonView({ View.FieldsAndLists.class, View.ConstructView.class })
 	@JoinTable(
 		joinColumns = @JoinColumn(name = "slotannotation_id"),

src/main/java/org/alliancegenome/curation_api/services/ConstructService.java

@@ -147,6 +147,9 @@ public Long getIdByModID(String modID) {
 	}
 
 	public Construct getShallowEntity(Long id) {
+		if (id == null) {
+			return null;
+		}
 		return constructDAO.getShallowEntity(Construct.class, id);
 	}
 }

src/main/java/org/alliancegenome/curation_api/services/GenomicEntityService.java

@@ -55,6 +55,9 @@ public Long getIdByModID(String modID) {
 	}
 
 	public GenomicEntity getShallowEntity(Long id) {
+		if (id == null) {
+			return null;
+		}
 		return genomicEntityDAO.getShallowEntity(GenomicEntity.class, id);
 	}
 }

src/main/java/org/alliancegenome/curation_api/services/associations/SequenceTargetingReagentGeneAssociationService.java

@@ -18,7 +18,7 @@
 import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.response.SearchResponse;
 import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
-import org.alliancegenome.curation_api.services.validation.associations.SequenceTargetingReagentGeneAssociationFmsDTOValidator;
+import org.alliancegenome.curation_api.services.validation.dto.fms.SequenceTargetingReagentGeneAssociationFmsDTOValidator;
 
 import jakarta.annotation.PostConstruct;
 import jakarta.enterprise.context.RequestScoped;

src/main/java/org/alliancegenome/curation_api/services/helpers/UniqueIdentifierHelper.java

@@ -30,12 +30,14 @@ public static void setObsoleteAndInternal(DiseaseAnnotationDTO dto, AuditedObjec
 		annotation.setInternal(dto.getInternal() != null && dto.getInternal());
 	}
 
-	public static <E extends AnnotationDTO, F extends Annotation> String setAnnotationID(E annotationDTO, F annotation, String uniqueId) {
+	public static <E extends AnnotationDTO, F extends Annotation> String setAnnotationIdentifiers(E annotationDTO, F annotation, String uniqueId) {
 		if (StringUtils.isNotBlank(annotationDTO.getPrimaryExternalId())) {
 			annotation.setPrimaryExternalId(annotationDTO.getPrimaryExternalId());
+			annotation.setModInternalId(null);
 			return annotationDTO.getPrimaryExternalId();
 		} else if (StringUtils.isNotBlank(annotationDTO.getModInternalId())) {
 			annotation.setModInternalId(annotationDTO.getModInternalId());
+			annotation.setPrimaryExternalId(null);
 			return annotationDTO.getModInternalId();
 		} else {
 			return uniqueId;
@@ -60,12 +62,14 @@ public static void setObsoleteAndInternal(SubmittedObjectDTO dto, SubmittedObjec
 		submittedObject.setInternal(dto.getInternal() != null && dto.getInternal());
 	}
 
-	public static <E extends SubmittedObjectDTO, F extends SubmittedObject> String setAnnotationID(E submittedObjectDTO, F submittedObject, String uniqueId) {
+	public static <E extends SubmittedObjectDTO, F extends SubmittedObject> String setSubmittedObjectIdentifiers(E submittedObjectDTO, F submittedObject, String uniqueId) {
 		if (StringUtils.isNotBlank(submittedObjectDTO.getPrimaryExternalId())) {
 			submittedObject.setPrimaryExternalId(submittedObjectDTO.getPrimaryExternalId());
+			submittedObject.setModInternalId(null);
 			return submittedObjectDTO.getPrimaryExternalId();
 		} else if (StringUtils.isNotBlank(submittedObjectDTO.getModInternalId())) {
 			submittedObject.setModInternalId(submittedObjectDTO.getModInternalId());
+			submittedObject.setPrimaryExternalId(null);
 			return submittedObjectDTO.getModInternalId();
 		} else {
 			return uniqueId;

src/main/java/org/alliancegenome/curation_api/services/validation/AGMDiseaseAnnotationValidator.java

@@ -1,10 +1,7 @@
 package org.alliancegenome.curation_api.services.validation;
 
-import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
 
-import org.alliancegenome.curation_api.constants.ValidationConstants;
 import org.alliancegenome.curation_api.constants.VocabularyConstants;
 import org.alliancegenome.curation_api.dao.AGMDiseaseAnnotationDAO;
 import org.alliancegenome.curation_api.dao.AffectedGenomicModelDAO;
@@ -16,9 +13,6 @@
 import org.alliancegenome.curation_api.model.entities.Gene;
 import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
 import org.alliancegenome.curation_api.response.ObjectResponse;
-import org.alliancegenome.curation_api.services.VocabularyTermService;
-import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.lang3.ObjectUtils;
 
 import jakarta.enterprise.context.RequestScoped;
 import jakarta.inject.Inject;
@@ -30,8 +24,6 @@ public class AGMDiseaseAnnotationValidator extends DiseaseAnnotationValidator {
 
 	@Inject AGMDiseaseAnnotationDAO agmDiseaseAnnotationDAO;
 
-	@Inject VocabularyTermService vocabularyTermService;
-
 	@Inject AlleleDAO alleleDAO;
 
 	private String errorMessage;
@@ -67,22 +59,22 @@ public AGMDiseaseAnnotation validateAnnotationCreate(AGMDiseaseAnnotation uiEnti
 
 	public AGMDiseaseAnnotation validateAnnotation(AGMDiseaseAnnotation uiEntity, AGMDiseaseAnnotation dbEntity) {
 
-		AffectedGenomicModel subject = validateSubject(uiEntity, dbEntity);
+		AffectedGenomicModel subject = validateRequiredEntity(affectedGenomicModelDAO, "diseaseAnnotationSubject", uiEntity.getDiseaseAnnotationSubject(), dbEntity.getDiseaseAnnotationSubject());
 		dbEntity.setDiseaseAnnotationSubject(subject);
 
-		Gene inferredGene = validateInferredGene(uiEntity, dbEntity);
+		Gene inferredGene = validateEntity(geneDAO, "inferredGene", uiEntity.getInferredGene(), dbEntity.getInferredGene());
 		dbEntity.setInferredGene(inferredGene);
 
-		List<Gene> assertedGenes = validateAssertedGenes(uiEntity, dbEntity);
+		List<Gene> assertedGenes = validateEntities(geneDAO, "assertedGenes", uiEntity.getAssertedGenes(), dbEntity.getAssertedGenes());
 		dbEntity.setAssertedGenes(assertedGenes);
 
-		Allele inferredAllele = validateInferredAllele(uiEntity, dbEntity);
+		Allele inferredAllele = validateEntity(alleleDAO, "inferredAllele", uiEntity.getInferredAllele(), dbEntity.getInferredAllele());
 		dbEntity.setInferredAllele(inferredAllele);
 
-		Allele assertedAllele = validateAssertedAllele(uiEntity, dbEntity);
+		Allele assertedAllele = validateEntity(alleleDAO, "assertedAllele", uiEntity.getAssertedAllele(), dbEntity.getAssertedAllele());
 		dbEntity.setAssertedAllele(assertedAllele);
 
-		VocabularyTerm relation = validateDiseaseRelation(uiEntity, dbEntity);
+		VocabularyTerm relation = validateRequiredTermInVocabularyTermSet("relation", VocabularyConstants.AGM_DISEASE_RELATION_VOCABULARY_TERM_SET, uiEntity.getRelation(), dbEntity.getRelation());
 		dbEntity.setRelation(relation);
 
 		dbEntity = (AGMDiseaseAnnotation) validateCommonDiseaseAnnotationFields(uiEntity, dbEntity);
@@ -94,146 +86,4 @@ public AGMDiseaseAnnotation validateAnnotation(AGMDiseaseAnnotation uiEntity, AG
 
 		return dbEntity;
 	}
-
-	private AffectedGenomicModel validateSubject(AGMDiseaseAnnotation uiEntity, AGMDiseaseAnnotation dbEntity) {
-		String field = "diseaseAnnotationSubject";
-		if (ObjectUtils.isEmpty(uiEntity.getDiseaseAnnotationSubject())) {
-			addMessageResponse(field, ValidationConstants.REQUIRED_MESSAGE);
-			return null;
-		}
-
-		AffectedGenomicModel subjectEntity = null;
-		if (uiEntity.getDiseaseAnnotationSubject().getId() != null) {
-			subjectEntity = affectedGenomicModelDAO.find(uiEntity.getDiseaseAnnotationSubject().getId());
-		}
-		if (subjectEntity == null) {
-			addMessageResponse(field, ValidationConstants.INVALID_MESSAGE);
-			return null;
-		}
-
-		if (subjectEntity.getObsolete() && (dbEntity.getDiseaseAnnotationSubject() == null || !subjectEntity.getId().equals(dbEntity.getDiseaseAnnotationSubject().getId()))) {
-			addMessageResponse(field, ValidationConstants.OBSOLETE_MESSAGE);
-			return null;
-		}
-
-		return subjectEntity;
-
-	}
-
-	private Gene validateInferredGene(AGMDiseaseAnnotation uiEntity, AGMDiseaseAnnotation dbEntity) {
-		if (uiEntity.getInferredGene() == null) {
-			return null;
-		}
-
-		Gene inferredGene = null;
-		if (uiEntity.getInferredGene().getId() != null) {
-			inferredGene = geneDAO.find(uiEntity.getInferredGene().getId());
-		}
-		if (inferredGene == null) {
-			addMessageResponse("inferredGene", ValidationConstants.INVALID_MESSAGE);
-			return null;
-		}
-
-		if (inferredGene.getObsolete() && (dbEntity.getInferredGene() == null || !inferredGene.getId().equals(dbEntity.getInferredGene().getId()))) {
-			addMessageResponse("inferredGene", ValidationConstants.OBSOLETE_MESSAGE);
-			return null;
-		}
-
-		return inferredGene;
-	}
-
-	private List<Gene> validateAssertedGenes(AGMDiseaseAnnotation uiEntity, AGMDiseaseAnnotation dbEntity) {
-		if (CollectionUtils.isEmpty(uiEntity.getAssertedGenes())) {
-			return null;
-		}
-
-		List<Gene> assertedGenes = new ArrayList<Gene>();
-		List<Long> previousIds = new ArrayList<Long>();
-		if (CollectionUtils.isNotEmpty(dbEntity.getAssertedGenes())) {
-			previousIds = dbEntity.getAssertedGenes().stream().map(Gene::getId).collect(Collectors.toList());
-		}
-		for (Gene gene : uiEntity.getAssertedGenes()) {
-			Gene assertedGene = null;
-			if (gene.getId() != null) {
-				assertedGene = geneDAO.find(gene.getId());
-			}
-			if (assertedGene == null) {
-				addMessageResponse("assertedGenes", ValidationConstants.INVALID_MESSAGE);
-				return null;
-			}
-			if (assertedGene.getObsolete() && !previousIds.contains(assertedGene.getId())) {
-				addMessageResponse("assertedGenes", ValidationConstants.OBSOLETE_MESSAGE);
-				return null;
-			}
-			assertedGenes.add(assertedGene);
-		}
-
-		return assertedGenes;
-	}
-
-	private Allele validateInferredAllele(AGMDiseaseAnnotation uiEntity, AGMDiseaseAnnotation dbEntity) {
-		if (uiEntity.getInferredAllele() == null) {
-			return null;
-		}
-
-		Allele inferredAllele = null;
-		if (uiEntity.getInferredAllele().getId() != null) {
-			inferredAllele = alleleDAO.find(uiEntity.getInferredAllele().getId());
-		}
-		if (inferredAllele == null) {
-			addMessageResponse("inferredAllele", ValidationConstants.INVALID_MESSAGE);
-			return null;
-		}
-
-		if (inferredAllele.getObsolete() && (dbEntity.getInferredAllele() == null || !inferredAllele.getId().equals(dbEntity.getInferredAllele().getId()))) {
-			addMessageResponse("inferredAllele", ValidationConstants.OBSOLETE_MESSAGE);
-			return null;
-		}
-
-		return inferredAllele;
-	}
-
-	private Allele validateAssertedAllele(AGMDiseaseAnnotation uiEntity, AGMDiseaseAnnotation dbEntity) {
-		if (uiEntity.getAssertedAllele() == null) {
-			return null;
-		}
-
-		Allele assertedAllele = null;
-		if (uiEntity.getAssertedAllele().getId() != null) {
-			assertedAllele = alleleDAO.find(uiEntity.getAssertedAllele().getId());
-		}
-		if (assertedAllele == null) {
-			addMessageResponse("assertedAllele", ValidationConstants.INVALID_MESSAGE);
-			return null;
-		}
-
-		if (assertedAllele.getObsolete() && (dbEntity.getAssertedAllele() == null || !assertedAllele.getId().equals(dbEntity.getAssertedAllele().getId()))) {
-			addMessageResponse("assertedAllele", ValidationConstants.OBSOLETE_MESSAGE);
-			return null;
-		}
-
-		return assertedAllele;
-	}
-
-	private VocabularyTerm validateDiseaseRelation(AGMDiseaseAnnotation uiEntity, AGMDiseaseAnnotation dbEntity) {
-		String field = "relation";
-		if (uiEntity.getRelation() == null) {
-			addMessageResponse(field, ValidationConstants.REQUIRED_MESSAGE);
-			return null;
-		}
-
-		VocabularyTerm relation = vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.AGM_DISEASE_RELATION_VOCABULARY_TERM_SET, uiEntity.getRelation().getName()).getEntity();
-
-		if (relation == null) {
-			addMessageResponse(field, ValidationConstants.INVALID_MESSAGE);
-			return null;
-		}
-
-		if (relation.getObsolete() && (dbEntity.getRelation() == null || !relation.getName().equals(dbEntity.getRelation().getName()))) {
-			addMessageResponse(field, ValidationConstants.OBSOLETE_MESSAGE);
-			return null;
-		}
-
-		return relation;
-	}
 }

src/main/java/org/alliancegenome/curation_api/services/validation/AffectedGenomicModelValidator.java

@@ -1,28 +1,23 @@
 package org.alliancegenome.curation_api.services.validation;
 
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.constants.ValidationConstants;
 import org.alliancegenome.curation_api.constants.VocabularyConstants;
 import org.alliancegenome.curation_api.dao.AffectedGenomicModelDAO;
-import org.alliancegenome.curation_api.dao.CrossReferenceDAO;
 import org.alliancegenome.curation_api.exceptions.ApiErrorException;
 import org.alliancegenome.curation_api.model.entities.AffectedGenomicModel;
 import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
 import org.alliancegenome.curation_api.response.ObjectResponse;
-import org.alliancegenome.curation_api.services.VocabularyTermService;
 import org.apache.commons.collections4.CollectionUtils;
 
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
 @RequestScoped
 public class AffectedGenomicModelValidator extends GenomicEntityValidator<AffectedGenomicModel> {
 
 	@Inject
 	AffectedGenomicModelDAO affectedGenomicModelDAO;
-	@Inject
-	VocabularyTermService vocabularyTermService;
-	@Inject
-	CrossReferenceDAO crossReferenceDAO;
-
+
 	private String errorMessage;
 
 	public AffectedGenomicModel validateAffectedGenomicModelUpdate(AffectedGenomicModel uiEntity) {
@@ -64,7 +59,7 @@ private AffectedGenomicModel validateAffectedGenomicModel(AffectedGenomicModel u
 		String name = handleStringField(uiEntity.getName());
 		dbEntity.setName(name);
 
-		VocabularyTerm subtype = validateSubtype(uiEntity, dbEntity);
+		VocabularyTerm subtype = validateRequiredTermInVocabulary("subtype", VocabularyConstants.AGM_SUBTYPE_VOCABULARY, uiEntity.getSubtype(), dbEntity.getSubtype());
 		dbEntity.setSubtype(subtype);
 
 		if (CollectionUtils.isNotEmpty(uiEntity.getSynonyms())) {
@@ -81,25 +76,4 @@ private AffectedGenomicModel validateAffectedGenomicModel(AffectedGenomicModel u
 		return dbEntity;
 	}
 
-	public VocabularyTerm validateSubtype(AffectedGenomicModel uiEntity, AffectedGenomicModel dbEntity) {
-		String field = "subtype";
-		if (uiEntity.getSubtype() == null) {
-			addMessageResponse(field, ValidationConstants.REQUIRED_MESSAGE);
-			return null;
-		}
-
-		VocabularyTerm subtype = vocabularyTermService.getTermInVocabulary(VocabularyConstants.AGM_SUBTYPE_VOCABULARY, uiEntity.getSubtype().getName()).getEntity();
-		if (subtype == null) {
-			addMessageResponse(field, ValidationConstants.INVALID_MESSAGE);
-			return null;
-		}
-
-		if (subtype.getObsolete() && (dbEntity.getSubtype() == null || !subtype.getName().equals(dbEntity.getSubtype().getName()))) {
-			addMessageResponse(field, ValidationConstants.OBSOLETE_MESSAGE);
-			return null;
-		}
-
-		return subtype;
-	}
-
 }