SCRUM-4667 fix review suggestions

alliance-genome · Jan 24, 2025 · c831a30 · c831a30
1 parent a6769dc
commit c831a30
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Showing 6 changed files with 33 additions and 52 deletions.
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java b/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java
@@ -93,18 +93,6 @@ public class AffectedGenomicModel extends GenomicEntity {
 	@OneToMany(mappedBy = "agmAssociationSubject", cascade = CascadeType.ALL, orphanRemoval = true)
 	@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
 	private List<AgmAlleleAssociation> components;
-	@IndexedEmbedded(includePaths = {
-		"agmAssociationSubject.name",
-		"agmAssociationSubject.name_keyword",
-		"agmAssociationSubject.synonyms",
-		"agmAssociationSubject.synonyms_keyword",
-		"agmAssociationSubject.secondaryIdentifiers",
-		"agmAssociationSubject.secondaryIdentifiers_keyword"
-	})
-	@OneToMany(mappedBy = "agmAssociationSubject", cascade = CascadeType.ALL, orphanRemoval = true)
-	@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
-	private List<AgmAgmAssociation> agmAgmAssociations;
-
 	@IndexedEmbedded(includePaths = {
 		"agmAgmAssociationObject.name",
 		"agmAgmAssociationObject.name_keyword",
@@ -113,8 +101,8 @@ public class AffectedGenomicModel extends GenomicEntity {
 		"agmAgmAssociationObject.secondaryIdentifiers",
 		"agmAgmAssociationObject.secondaryIdentifiers_keyword"
 	})
-	@OneToMany(mappedBy = "agmAgmAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@OneToMany(mappedBy = "agmAssociationSubject", cascade = CascadeType.ALL, orphanRemoval = true)
 	@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
-	private List<AgmAgmAssociation> agmAgmObjectAssociations;
+	private List<AgmAgmAssociation> parentalPopulations;
 
 }
diff --git a/...ncegenome/curation_api/model/entities/associations/agmAssociations/AgmAgmAssociation.java b/...ncegenome/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"})
+	@JsonIgnoreProperties({"parentalPopulations", "agmSequenceTargetingReagentAssociations"})
 	private AffectedGenomicModel agmAgmAssociationObject;
 }
diff --git a/...cegenome/curation_api/services/associations/agmAssociations/AgmAgmAssociationService.java b/...cegenome/curation_api/services/associations/agmAssociations/AgmAgmAssociationService.java
@@ -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<>();
@@ -145,10 +145,10 @@ private void addAssociationToAgm(AgmAgmAssociation association) {
 
 	private void addAssociationToStr(AgmAgmAssociation association) {
 		AffectedGenomicModel str = association.getAgmAgmAssociationObject();
-		List<AgmAgmAssociation> currentAssociations = str.getAgmAgmAssociations();
+		List<AgmAgmAssociation> currentAssociations = str.getParentalPopulations();
 		if (currentAssociations == null) {
 			currentAssociations = new ArrayList<>();
-			str.setAgmAgmAssociations(currentAssociations);
+			str.setParentalPopulations(currentAssociations);
 		}
 
 		List<Long> currentAssociationIds = new ArrayList<>();

diff --git a/src/main/resources/db/migration/v0.38.0.30__agm_agm_association_loads_2.sql b/src/main/resources/db/migration/v0.38.0.30__agm_agm_association_loads_2.sql
@@ -0,0 +1,4 @@
+drop INDEX agmagmassociation_agmassocobject_in;
+ALTER TABLE public.agmagmassociation DROP CONSTRAINT agmstrassociation_agmassociationobject_fk;
+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);
diff --git a/src/test/java/org/alliancegenome/curation_api/AgmAgmAssociationBulkUploadITCase.java b/src/test/java/org/alliancegenome/curation_api/AgmAgmAssociationBulkUploadITCase.java
@@ -26,8 +26,12 @@ public class AgmAgmAssociationBulkUploadITCase extends BaseITCase {
 
 	private AffectedGenomicModel agmSubject;
 	private AffectedGenomicModel agmObject;
+	private AffectedGenomicModel agmSubject2;
+	private AffectedGenomicModel agmObject2;
 	private String agmSubjectCurie = "AMGTEST:AffectedGenomicModel0010";
 	private String agmObjectCurie = "AMGTEST:AffectedGenomicModel0020";
+	private String agmSubjectCurie2 = "AMGTEST:AffectedGenomicModel00102";
+	private String agmObjectCurie2 = "AMGTEST:AffectedGenomicModel00202";
 	private String relationName = "has_parental_population";
 
 	@BeforeEach
@@ -55,14 +59,15 @@ 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();
+		System.out.println(s);
 		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.agmAgmAssociationObject.primaryExternalId", is(agmObjectCurie)).
 			body("entity.agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
 			body("entity.internal", is(false)).
 			body("entity.obsolete", is(false)).
@@ -76,35 +81,26 @@ 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("agmAgmAssociationObject")));
+			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().
 				when().
-				get(agmAgmAssociationGetEndpoint + "?agmSubjectId=" + agmSubject.getId() + "&relationName=" + relationName + "&agmObjectId=" + agmObject.getId()).
+				get(agmAgmAssociationGetEndpoint + "?agmSubjectId=" + agmSubject2.getId() + "&relationName=" + relationName + "&agmObjectId=" + agmObject2.getId()).
 				then().
 				statusCode(200).
 				body("entity.relation.name", is(relationName)).
-				body("entity.agmAgmAssociationObject.primaryExternalId", is(agmObjectCurie)).
-				body("entity.agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
+				body("entity.agmAssociationSubject.primaryExternalId", is(agmSubjectCurie2)).
 				body("entity.internal", is(true)).
 				body("entity.obsolete", is(true)).
 				body("entity.createdBy.uniqueId", is("AGMTEST:Person0001")).
@@ -115,17 +111,10 @@ public void agmAgmAssociationBulkUploadUpdateCheckFields() throws Exception {
 
 		RestAssured.given().
 				when().
-				get(agmGetEndpoint + agmSubjectCurie).
-				then().
-				statusCode(200).
-				body("entity.agmSequenceTargetingReagentAssociations", hasSize(1));
-
-		RestAssured.given().
-				when().
-				get(agmGetEndpoint + agmObjectCurie).
+				get(agmGetEndpoint + agmSubjectCurie2).
 				then().
 				statusCode(200).
-				body("entity.agmSequenceTargetingReagentAssociations", hasSize(1));
+				body("entity.agmAgmAssociations", hasSize(1));
 	}
 
 	@Test

diff --git a/...est/resources/bulk/AGMA01_agm_agm_association/UD_01_update_all_except_default_fields.json b/...est/resources/bulk/AGMA01_agm_agm_association/UD_01_update_all_except_default_fields.json
@@ -1,8 +1,8 @@
 [
   {
-    "agm_subject_identifier": "AMGTEST:AffectedGenomicModel0010",
+    "agm_subject_identifier": "AMGTEST:AffectedGenomicModel00102",
     "relation_name": "has_parental_population",
-    "agm_object_identifier": "AMGTEST:AffectedGenomicModel0020",
+    "agm_object_identifier": "AMGTEST:AffectedGenomicModel00202",
     "internal": true,
     "obsolete": true,
     "created_by_curie": "AGMTEST:Person0001",