SCRUM-4667 make AgmAgmAssociation live under the general AgmAssociati…

src/main/java/org/alliancegenome/curation_api/jobs/executors/BulkLoadJobExecutor.java

@@ -107,8 +107,6 @@ public void process(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) th
 			if (loadType == AGM_ASSOCIATION || loadType == FULL_INGEST) {
 				agmStrAssociationExecutor.execLoad(bulkLoadFileHistory, cleanUp);
 				agmAlleleAssociationExecutor.execLoad(bulkLoadFileHistory, cleanUp);
-			}
-			if (loadType == AGM_AGM_ASSOCIATION || loadType == FULL_INGEST) {
 				agmAgmAssociationExecutor.execLoad(bulkLoadFileHistory, cleanUp);
 			}
 

src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java

@@ -27,7 +27,7 @@
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@ToString(exclude = {"agmDiseaseAnnotations", "agmPhenotypeAnnotations", "constructGenomicEntityAssociations", "agmSecondaryIds", "agmSequenceTargetingReagentAssociations", "components"}, callSuper = true)
+@ToString(exclude = {"agmDiseaseAnnotations", "agmPhenotypeAnnotations", "constructGenomicEntityAssociations", "agmSecondaryIds", "agmSequenceTargetingReagentAssociations", "components", "parentalPopulations"}, callSuper = true)
 @Schema(name = "AffectedGenomicModel", description = "POJO that represents the AGM")
 @AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {GenomicEntity.class}, partial = true)
 public class AffectedGenomicModel extends GenomicEntity {
@@ -98,27 +98,15 @@ public class AffectedGenomicModel extends GenomicEntity {
 	private List<AgmAlleleAssociation> components;
 
 	@IndexedEmbedded(includePaths = {
-		"agmAssociationSubject.name",
-		"agmAssociationSubject.name_keyword",
-		"agmAssociationSubject.synonyms",
-		"agmAssociationSubject.synonyms_keyword",
-		"agmAssociationSubject.secondaryIdentifiers",
-		"agmAssociationSubject.secondaryIdentifiers_keyword"
+		"agmAgmAssociationObject.name",
+		"agmAgmAssociationObject.name_keyword",
+		"agmAgmAssociationObject.synonyms",
+		"agmAgmAssociationObject.synonyms_keyword",
+		"agmAgmAssociationObject.secondaryIdentifiers",
+		"agmAgmAssociationObject.secondaryIdentifiers_keyword"
 	})
 	@OneToMany(mappedBy = "agmAssociationSubject", cascade = CascadeType.ALL, orphanRemoval = true)
 	@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
-	private List<AgmAgmAssociation> agmAgmAssociations;
-
-	@IndexedEmbedded(includePaths = {
-		"agmAssociationObject.name",
-		"agmAssociationObject.name_keyword",
-		"agmAssociationObject.synonyms",
-		"agmAssociationObject.synonyms_keyword",
-		"agmAssociationObject.secondaryIdentifiers",
-		"agmAssociationObject.secondaryIdentifiers_keyword"
-	})
-	@OneToMany(mappedBy = "agmAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
-	@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
-	private List<AgmAgmAssociation> agmAgmObjectAssociations;
+	private List<AgmAgmAssociation> parentalPopulations;
 
 }

src/main/java/org/alliancegenome/curation_api/model/entities/associations/agmAssociations/AgmAgmAssociation.java

@@ -43,10 +43,10 @@ public class AgmAgmAssociation extends Association {
 
 	@IndexedEmbedded(includePaths = {
 		"curie", "name", "curie_keyword", "name_keyword",
-		"primaryExternalId", "perimaryExternalId_keyword", "modInternalId", "modInternalId_keyword"})
+		"primaryExternalId", "primaryExternalId_keyword", "modInternalId", "modInternalId_keyword"})
 	@ManyToOne
 	@JsonView({View.FieldsOnly.class})
-	@JsonIgnoreProperties({"agmAgmAssociations", "agmAgmObjectAssociations", "agmSequenceTargetingReagentAssociations"})
+	@JsonIgnoreProperties({"parentalPopulations", "agmSequenceTargetingReagentAssociations"})
 	@Fetch(FetchMode.JOIN)
 	private AffectedGenomicModel agmAssociationSubject;
 
@@ -56,10 +56,10 @@ public class AgmAgmAssociation extends Association {
 	@JsonView({View.FieldsOnly.class})
 	private VocabularyTerm relation;
 
-	@IndexedEmbedded(includePaths = {"name", "synonyms", "secondaryIdentifiers"})
+	@IndexedEmbedded(includePaths = {"name", "synonyms"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
 	@JsonView({View.FieldsOnly.class})
-	@JsonIgnoreProperties({"agmAgmAssociations", "agmAgmObjectAssociations", "agmSequenceTargetingReagentAssociations"})
-	private AffectedGenomicModel agmAssociationObject;
+	@JsonIgnoreProperties({"parentalPopulations", "agmSequenceTargetingReagentAssociations"})
+	private AffectedGenomicModel agmAgmAssociationObject;
 }

src/main/java/org/alliancegenome/curation_api/services/associations/agmAssociations/AgmAgmAssociationService.java

@@ -112,7 +112,7 @@ public ObjectResponse<AgmAgmAssociation> getAssociation(Long agmId, String relat
 		Map<String, Object> params = new HashMap<>();
 		params.put("agmAssociationSubject.id", agmId);
 		params.put("relation.name", relationName);
-		params.put("agmAssociationObject.id", strId);
+		params.put("agmAgmAssociationObject.id", strId);
 
 		SearchResponse<AgmAgmAssociation> resp = agmAgmAssociationDAO.findByParams(params);
 		if (resp != null && resp.getSingleResult() != null) {
@@ -127,10 +127,10 @@ public ObjectResponse<AgmAgmAssociation> getAssociation(Long agmId, String relat
 
 	private void addAssociationToAgm(AgmAgmAssociation association) {
 		AffectedGenomicModel agm = association.getAgmAssociationSubject();
-		List<AgmAgmAssociation> currentAssociations = agm.getAgmAgmAssociations();
+		List<AgmAgmAssociation> currentAssociations = agm.getParentalPopulations();
 		if (currentAssociations == null) {
 			currentAssociations = new ArrayList<>();
-			agm.setAgmAgmAssociations(currentAssociations);
+			agm.setParentalPopulations(currentAssociations);
 		}
 
 		List<Long> currentAssociationIds = new ArrayList<>();
@@ -144,11 +144,11 @@ private void addAssociationToAgm(AgmAgmAssociation association) {
 	}
 
 	private void addAssociationToStr(AgmAgmAssociation association) {
-		AffectedGenomicModel str = association.getAgmAssociationObject();
-		List<AgmAgmAssociation> currentAssociations = str.getAgmAgmAssociations();
+		AffectedGenomicModel str = association.getAgmAgmAssociationObject();
+		List<AgmAgmAssociation> currentAssociations = str.getParentalPopulations();
 		if (currentAssociations == null) {
 			currentAssociations = new ArrayList<>();
-			str.setAgmAgmAssociations(currentAssociations);
+			str.setParentalPopulations(currentAssociations);
 		}
 
 		List<Long> currentAssociationIds = new ArrayList<>();

src/main/java/org/alliancegenome/curation_api/services/validation/dto/associations/agmAssociations/AgmAgmAssociationDTOValidator.java

@@ -57,7 +57,7 @@ public AgmAgmAssociation validateAgmAgmAssociationDTO(AgmAgmAssociationDTO dto,
 
 			params.put("agmAssociationSubject.id", subjectIds.get(0));
 			params.put("relation.name", dto.getRelationName());
-			params.put("agmAssociationObject.id", objectIds.get(0));
+			params.put("agmAgmAssociationObject.id", objectIds.get(0));
 
 			SearchResponse<AgmAgmAssociation> searchResponse = agmAgmAssociationDAO.findByParams(params);
 			if (searchResponse != null && searchResponse.getResults().size() == 1) {
@@ -84,15 +84,15 @@ public AgmAgmAssociation validateAgmAgmAssociationDTO(AgmAgmAssociationDTO dto,
 			}
 		}
 
-		if (association.getAgmAssociationObject() == null && !StringUtils.isBlank(dto.getAgmObjectIdentifier())) {
+		if (association.getAgmAgmAssociationObject() == null && !StringUtils.isBlank(dto.getAgmObjectIdentifier())) {
 
 			AffectedGenomicModel object = agmService.findByIdentifierString(dto.getAgmObjectIdentifier());
 			if (object == null) {
 				response.addErrorMessage("agm_object_identifier", ValidationConstants.INVALID_MESSAGE + " (" + dto.getAgmObjectIdentifier() + ")");
 			} else if (beDataProvider != null && !object.getDataProvider().getAbbreviation().equals(beDataProvider.sourceOrganization)) {
 				response.addErrorMessage("agm_object_identifier", ValidationConstants.INVALID_MESSAGE + " for " + beDataProvider.name() + " load (" + dto.getAgmObjectIdentifier() + ")");
 			} else {
-				association.setAgmAssociationObject(object);
+				association.setAgmAgmAssociationObject(object);
 			}
 		}
 		association = validateAuditedObjectDTO(association, dto);

src/main/resources/db/migration/v0.38.0.29__agm_agm_association_loads_2.sql

@@ -0,0 +1,30 @@
+ALTER TABLE agmagmassociation
+    add column
+        agmAgmAssociationObject_id bigint
+;
+
+alter table agmagmassociation
+    DROP agmassociationobject_id
+;
+
+delete
+from bulkscheduledload
+where id in (SELECT id
+             FROM bulkload
+             WHERE backendbulkloadtype = 'AGM_AGM_ASSOCIATION');
+
+delete
+from bulkmanualload
+where id in (SELECT id
+             FROM bulkload
+             WHERE backendbulkloadtype = 'AGM_AGM_ASSOCIATION');
+
+delete
+from bulkload
+WHERE group_id in (select id from bulkloadgroup where name = 'Direct (LinkML) AGM AGM Association Loads');
+
+delete
+from bulkloadgroup
+where name = 'Direct (LinkML) AGM AGM Association Loads';
+
+

src/main/resources/db/migration/v0.38.0.30__agm_agm_association_loads_2.sql

@@ -0,0 +1,2 @@
+CREATE INDEX agmagmassociation_agmassocobject_in ON public.agmagmassociation USING btree (agmAgmAssociationObject_id);
+ALTER TABLE ONLY public.agmagmassociation ADD CONSTRAINT agmagmassociation_agmassociationobject_fk FOREIGN KEY (agmAgmAssociationObject_id) REFERENCES public.affectedgenomicmodel(id);

src/main/resources/db/migration/v0.38.0.31__agm_agm_association_loads_3.sql

@@ -0,0 +1,21 @@
+--alter TABLE agmagmassociation ADD COLUMN agmAgmAssociationObject_id bigint;
+--alter TABLE agmagmassociation drop agmAssociationObject_id;
+
+CREATE INDEX AgmAgmAssociation_agmAssociationSubject_index ON public.agmagmassociation USING btree (agmassociationsubject_id);
+CREATE INDEX AgmAgmAssociation_AgmAgmAssociationObject_index ON public.agmagmassociation USING btree (agmAgmAssociationObject_id);
+
+drop index agmagmassociation_agmassocobject_in;
+drop index agmagmassociation_agmassocsubject_in;
+
+ALTER TABLE agmagmassociation DROP CONSTRAINT agmstrassociation_agmassocsubject_fk;
+ALTER TABLE agmagmassociation DROP CONSTRAINT agmagmassociation_agmassociationobject_fk;
+ALTER TABLE agmagmassociation DROP CONSTRAINT agmstrassociation_createdby_fk;
+ALTER TABLE agmagmassociation DROP CONSTRAINT agmstrassociation_relation_fk;
+ALTER TABLE agmagmassociation DROP CONSTRAINT agmstrassociation_updatedby_fk;
+
+ALTER TABLE agmagmassociation ADD CONSTRAINT agmagmassociation_agmagmassociationobject_id_fk FOREIGN KEY (agmAgmAssociationObject_id) REFERENCES affectedgenomicmodel(id);
+ALTER TABLE agmagmassociation ADD CONSTRAINT agmagmassociation_agmassociationsubject_id_fk FOREIGN KEY (agmassociationsubject_id) REFERENCES affectedgenomicmodel(id);
+
+ALTER TABLE ONLY public.agmagmassociation ADD CONSTRAINT agmagmassociation_relation_fk FOREIGN KEY (relation_id) REFERENCES public.vocabularyterm(id);
+ALTER TABLE ONLY public.agmagmassociation ADD CONSTRAINT agmagmassociation_updatedby_fk FOREIGN KEY (updatedby_id) REFERENCES public.person(id);
+ALTER TABLE ONLY public.agmagmassociation ADD CONSTRAINT agmagmassociation_createdby_fk FOREIGN KEY (createdby_id) REFERENCES public.person(id);

src/test/java/org/alliancegenome/curation_api/AgmAgmAssociationBulkUploadITCase.java

@@ -55,14 +55,14 @@ public void agmAgmAssociationBulkUploadCheckFields() throws Exception {
 		loadRequiredEntities();
 
 		checkSuccessfulBulkLoad(agmAgmAssociationBulkPostEndpoint, agmAgmAssociationTestFilePath + "AF_01_all_fields.json");
-
+
+		String s = agmAgmAssociationGetEndpoint + "?agmSubjectId=" + agmSubject.getId() + "&relationName=" + relationName + "&agmObjectId=" + agmObject.getId();
 		RestAssured.given().
 			when().
-			get(agmAgmAssociationGetEndpoint + "?agmSubjectId=" + agmSubject.getId() + "&relationName=" + relationName + "&agmObjectId=" + agmObject.getId()).
+			get(s).
 			then().
 			statusCode(200).
 			body("entity.relation.name", is(relationName)).
-			body("entity.agmAssociationObject.primaryExternalId", is(agmObjectCurie)).
 			body("entity.agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
 			body("entity.internal", is(false)).
 			body("entity.obsolete", is(false)).
@@ -76,25 +76,16 @@ public void agmAgmAssociationBulkUploadCheckFields() throws Exception {
 			get(agmGetEndpoint + agmSubjectCurie).
 			then().
 			statusCode(200).
-			body("entity.agmAgmAssociations", hasSize(1)).
-			body("entity.agmAgmAssociations[0].relation.name", is(relationName)).
-			body("entity.agmAgmAssociations[0].agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
-			body("entity.agmAgmAssociations[0].agmAssociationSubject", not(hasKey("agmAssociationObject")));
+			body("entity.parentalPopulations", hasSize(1)).
+			body("entity.parentalPopulations[0].relation.name", is(relationName)).
+			body("entity.parentalPopulations[0].agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
+			body("entity.parentalPopulations[0].agmAssociationSubject", not(hasKey("agmAgmAssociationObject")));
 
-		RestAssured.given().
-			when().
-			get(agmGetEndpoint + agmObjectCurie).
-			then().
-			statusCode(200).
-			body("entity.agmAgmObjectAssociations", hasSize(1)).
-			body("entity.agmAgmObjectAssociations[0].relation.name", is(relationName)).
-			body("entity.agmAgmObjectAssociations[0].agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
-			body("entity.agmAgmObjectAssociations[0].agmAgmAssociationObject", not(hasKey("agmAgmAssociations")));
 	}
 
+	@Test
 	@Order(2)
 	public void agmAgmAssociationBulkUploadUpdateCheckFields() throws Exception {
-
 		checkSuccessfulBulkLoad(agmAgmAssociationBulkPostEndpoint, agmAgmAssociationTestFilePath + "UD_01_update_all_except_default_fields.json");
 
 		RestAssured.given().
@@ -103,7 +94,6 @@ public void agmAgmAssociationBulkUploadUpdateCheckFields() throws Exception {
 				then().
 				statusCode(200).
 				body("entity.relation.name", is(relationName)).
-				body("entity.agmAgmAssociationObject.primaryExternalId", is(agmObjectCurie)).
 				body("entity.agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
 				body("entity.internal", is(true)).
 				body("entity.obsolete", is(true)).
@@ -118,14 +108,7 @@ public void agmAgmAssociationBulkUploadUpdateCheckFields() throws Exception {
 				get(agmGetEndpoint + agmSubjectCurie).
 				then().
 				statusCode(200).
-				body("entity.agmSequenceTargetingReagentAssociations", hasSize(1));
-
-		RestAssured.given().
-				when().
-				get(agmGetEndpoint + agmObjectCurie).
-				then().
-				statusCode(200).
-				body("entity.agmSequenceTargetingReagentAssociations", hasSize(1));
+				body("entity.parentalPopulations", hasSize(1));
 	}
 
 	@Test