SCRUM-4657: fixes after review

alliance-genome · Jan 10, 2025 · 657fe72 · 657fe72
1 parent e029a5b
commit 657fe72
Show file tree

Hide file tree

Showing 4 changed files with 58 additions and 3 deletions.
diff --git a/...a/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java b/...a/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java
@@ -188,6 +188,8 @@ public Long validateVariant(VariantFmsDTO dto, List<Long> idsAdded, BackendBulkD
 				}
 				variant.getReferences().addAll(validatedReferences);
 			}
+		} else {
+			variant.setReferences(null);
 		}
 
 		if (variant.getRelatedNotes() != null) {

diff --git a/src/test/java/org/alliancegenome/curation_api/VariantFmsITCase.java b/src/test/java/org/alliancegenome/curation_api/VariantFmsITCase.java
@@ -54,6 +54,7 @@ public void init() {
 	private final String reference = "AGRKB:000000001";
 	private final String reference2 = "AGRKB:000000021";
 	private final String pubmedId = "PMID:25920554";
+	private final String updatedPubmedId = "PMID:009";
 
 	private void loadRequiredEntities() throws Exception {
 		createSoTerm("SO:1000002", "substitution", false);
@@ -155,8 +156,8 @@ public void variantFmsBulkUploadUpdate() throws Exception {
 			body("entity.crossReferences", hasSize(1)).
 			body("entity.crossReferences[0].referencedCurie", is("TEST:WBVar00252637")).
 			body("entity.crossReferences[0].displayName", is("TEST:WBVar00252637")).
-			body("entity.crossReferences[0].resourceDescriptorPage.name", is("homepage"));
-
+			body("entity.crossReferences[0].resourceDescriptorPage.name", is("homepage")).
+			body("entity.references[0].crossReferences[0].referencedCurie", is(updatedPubmedId));
 	}
 
 	@Test
@@ -207,6 +208,7 @@ public void variantFmsBulkUploadInvalidFields() throws Exception {
 		checkBulkLoadRecordCounts(variantFmsBulkPostEndpoint, variantFmsTestFilePath + "IV_01_invalid_type.json", params);
 		checkBulkLoadRecordCounts(variantFmsBulkPostEndpoint, variantFmsTestFilePath + "IV_02_invalid_type_for_fms_submissions.json", params);
 		checkBulkLoadRecordCounts(variantFmsBulkPostEndpoint, variantFmsTestFilePath + "IV_03_invalid_consequence.json", params);
+		checkBulkLoadRecordCounts(variantFmsBulkPostEndpoint, variantFmsTestFilePath + "IV_06_invalid_reference.json", params);
 
 		params.put("Entities", createCountParams(1, 0, 1, 0));
 		params.put("Associations", createCountParams(1, 0, 1, 0));

diff --git a/src/test/resources/bulk/fms/10_variant/IV_06_invalid_reference.json b/src/test/resources/bulk/fms/10_variant/IV_06_invalid_reference.json
@@ -0,0 +1,51 @@
+[
+	{
+		"alleleId": "WB:AlleleWithVar1",
+		"sequenceOfReferenceAccessionNumber": "RefSeq:NC_003279.8",
+		"start": 1,
+		"end": 1000,
+		"genomicReferenceSequence": "A",
+		"genomicVariantSequence": "T",
+		"type": "SO:1000002",
+		"consequence": "SO:0001587",
+		"references": [
+			{
+				"publicationId": "PMID:unknown",
+				"crossReference": {
+					"id": "WB:WBPaper00042242",
+					"pages": [
+						"reference"
+					]
+				}
+			}
+		],
+		"notes": [
+			{
+				"note": "This is a test note.",
+				"references": [
+					{
+						"publicationId": "PMID:25920550",
+						"crossReference": {
+							"id": "WB:WBPaper00042241",
+							"pages": [
+								"reference"
+							]
+						}
+					}
+				]
+			}
+		],
+		"crossReferences": [
+			{
+				"id": "TEST:WBVar00252636",
+				"pages": [
+					"homepage"
+				]
+			}
+		],
+		"synonyms" : [
+			"Syn 1","Syn 2"
+		]
+	}
+]
+
diff --git a/src/test/resources/bulk/fms/10_variant/UD_01_update_variant.json b/src/test/resources/bulk/fms/10_variant/UD_01_update_variant.json
@@ -10,7 +10,7 @@
 		"consequence": "SO:0001578",
 		"references": [
 			{
-				"publicationId": "PMID:25920554",
+				"publicationId": "PMID:009",
 				"crossReference": {
 					"id": "WB:WBPaper00042242",
 					"pages": [