SCRUM-4667 remove agmAgmObjectAssociation

alliance-genome · Jan 24, 2025 · fd8620d · fd8620d
1 parent a6769dc
commit fd8620d
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Showing 3 changed files with 39 additions and 62 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
@@ -105,16 +105,4 @@ public class AffectedGenomicModel extends GenomicEntity {
 	@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
 	private List<AgmAgmAssociation> agmAgmAssociations;
 
-	@IndexedEmbedded(includePaths = {
-		"agmAgmAssociationObject.name",
-		"agmAgmAssociationObject.name_keyword",
-		"agmAgmAssociationObject.synonyms",
-		"agmAgmAssociationObject.synonyms_keyword",
-		"agmAgmAssociationObject.secondaryIdentifiers",
-		"agmAgmAssociationObject.secondaryIdentifiers_keyword"
-	})
-	@OneToMany(mappedBy = "agmAgmAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
-	@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
-	private List<AgmAgmAssociation> agmAgmObjectAssociations;
-
 }
diff --git a/...ncegenome/curation_api/model/entities/associations/agmAssociations/AgmAgmAssociation.java b/...ncegenome/curation_api/model/entities/associations/agmAssociations/AgmAgmAssociation.java
@@ -46,7 +46,7 @@ public class AgmAgmAssociation extends Association {
 		"primaryExternalId", "perimaryExternalId_keyword", "modInternalId", "modInternalId_keyword"})
 	@ManyToOne
 	@JsonView({View.FieldsOnly.class})
-	@JsonIgnoreProperties({"agmAgmAssociations", "agmAgmObjectAssociations", "agmSequenceTargetingReagentAssociations"})
+	@JsonIgnoreProperties({"agmAgmAssociations", "agmSequenceTargetingReagentAssociations"})
 	@Fetch(FetchMode.JOIN)
 	private AffectedGenomicModel agmAssociationSubject;
 
@@ -60,6 +60,6 @@ public class AgmAgmAssociation extends Association {
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
 	@JsonView({View.FieldsOnly.class})
-	@JsonIgnoreProperties({"agmAgmAssociations", "agmAgmObjectAssociations", "agmSequenceTargetingReagentAssociations"})
+	@JsonIgnoreProperties({"agmAgmAssociations", "agmSequenceTargetingReagentAssociations"})
 	private AffectedGenomicModel agmAgmAssociationObject;
 }
diff --git a/src/test/java/org/alliancegenome/curation_api/AgmAgmAssociationBulkUploadITCase.java b/src/test/java/org/alliancegenome/curation_api/AgmAgmAssociationBulkUploadITCase.java
@@ -13,7 +13,8 @@
 
 import java.time.OffsetDateTime;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.is;
 
 
 @QuarkusIntegrationTest
@@ -23,19 +24,19 @@
 @DisplayName("1001 - AffectedGenomicModel AffectedGenomicModel Associations bulk upload")
 @Order(1001)
 public class AgmAgmAssociationBulkUploadITCase extends BaseITCase {
-	
+
 	private AffectedGenomicModel agmSubject;
 	private AffectedGenomicModel agmObject;
-	private String agmSubjectCurie = "AMGTEST:AffectedGenomicModel0010";
-	private String agmObjectCurie = "AMGTEST:AffectedGenomicModel0020";
-	private String relationName = "has_parental_population";
+	private static final String agmSubjectCurie = "AMGTEST:AffectedGenomicModel0010";
+	private static final String agmObjectCurie = "AMGTEST:AffectedGenomicModel0020";
+	private static final String relationName = "has_parental_population";
 
 	@BeforeEach
 	public void init() {
 		RestAssured.config = RestAssuredConfig.config()
-				.httpClient(HttpClientConfig.httpClientConfig()
-					.setParam("http.socket.timeout", 60000)
-					.setParam("http.connection.timeout", 60000));
+			.httpClient(HttpClientConfig.httpClientConfig()
+				.setParam("http.socket.timeout", 60000)
+				.setParam("http.connection.timeout", 60000));
 	}
 
 	private final String agmAgmAssociationBulkPostEndpoint = "/api/agmagmassociation/bulk/ZFIN/associationFile";
@@ -48,84 +49,72 @@ private void loadRequiredEntities() {
 		agmSubject = createAffectedGenomicModel(agmSubjectCurie, "test name subject", "NCBITaxon:7955", "fish", false, dataProvider);
 		agmObject = createAffectedGenomicModel(agmObjectCurie, "test name object", "NCBITaxon:7955", "fish", false, dataProvider);
 	}
-	
+
 	@Test
 	@Order(1)
 	public void agmAgmAssociationBulkUploadCheckFields() throws Exception {
 		loadRequiredEntities();
-		
+
 		checkSuccessfulBulkLoad(agmAgmAssociationBulkPostEndpoint, agmAgmAssociationTestFilePath + "AF_01_all_fields.json");
-	
+
 		RestAssured.given().
 			when().
 			get(agmAgmAssociationGetEndpoint + "?agmSubjectId=" + agmSubject.getId() + "&relationName=" + relationName + "&agmObjectId=" + agmObject.getId()).
 			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)).
 			body("entity.createdBy.uniqueId", is("AGMTEST:Person0001")).
 			body("entity.updatedBy.uniqueId", is("AGMTEST:Person0002")).
 			body("entity.dateCreated", is(OffsetDateTime.parse("2022-03-09T22:10:12+00:00").toString())).
 			body("entity.dateUpdated", is(OffsetDateTime.parse("2022-03-10T22:10:12+00:00").toString()));
-		
+
 		RestAssured.given().
 			when().
 			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")));
-
-		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")));
+			body("entity.agmAgmAssociations[0].agmAssociationSubject.primaryExternalId", is(agmSubjectCurie));
 	}
 
+	@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()).
-				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)).
-				body("entity.createdBy.uniqueId", is("AGMTEST:Person0001")).
-				body("entity.updatedBy.uniqueId", is("AGMTEST:Person0002")).
-				body("entity.dateCreated", is(OffsetDateTime.parse("2022-03-09T22:10:12+00:00").toString())).
-				body("entity.dateUpdated", is(OffsetDateTime.parse("2022-03-10T22:10:12+00:00").toString()));
+			when().
+			get(agmAgmAssociationGetEndpoint + "?agmSubjectId=" + agmSubject.getId() + "&relationName=" + relationName + "&agmObjectId=" + agmObject.getId()).
+			then().
+			statusCode(200).
+			body("entity.relation.name", is(relationName)).
+			body("entity.agmAssociationSubject.primaryExternalId", is(agmSubjectCurie)).
+			body("entity.internal", is(true)).
+			body("entity.obsolete", is(true)).
+			body("entity.createdBy.uniqueId", is("AGMTEST:Person0001")).
+			body("entity.updatedBy.uniqueId", is("AGMTEST:Person0002")).
+			body("entity.dateCreated", is(OffsetDateTime.parse("2022-03-09T22:10:12+00:00").toString())).
+			body("entity.dateUpdated", is(OffsetDateTime.parse("2022-03-10T22:10:12+00:00").toString()));
 
 
 		RestAssured.given().
-				when().
-				get(agmGetEndpoint + agmSubjectCurie).
-				then().
-				statusCode(200).
-				body("entity.agmSequenceTargetingReagentAssociations", hasSize(1));
+			when().
+			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));
+			when().
+			get(agmGetEndpoint + agmObjectCurie).
+			then().
+			statusCode(200).
+			body("entity.agmSequenceTargetingReagentAssociations", hasSize(1));
 	}
 
 	@Test