Changes in IT

alliance-genome · Dec 12, 2024 · 0a90c85 · 0a90c85
1 parent 73b0e5f
commit 0a90c85
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Showing 2 changed files with 25 additions and 16 deletions.
diff --git a/src/test/java/org/alliancegenome/curation_api/GeneBulkUploadITCase.java b/src/test/java/org/alliancegenome/curation_api/GeneBulkUploadITCase.java
@@ -6,9 +6,13 @@
 import static org.hamcrest.Matchers.not;
 
 import java.time.OffsetDateTime;
+import java.util.List;
 
 import org.alliancegenome.curation_api.base.BaseITCase;
+import org.alliancegenome.curation_api.constants.VocabularyConstants;
 import org.alliancegenome.curation_api.model.entities.ResourceDescriptor;
+import org.alliancegenome.curation_api.model.entities.Vocabulary;
+import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
 import org.alliancegenome.curation_api.resources.TestContainerResource;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.DisplayName;
@@ -48,6 +52,8 @@ public void init() {
 	private String requiredDataProvider2 = "RGD";
 	private String soTerm = "SO:0001217";
 	private String soTerm2 = "SO:0000336";
+	private String noteType = "comment";
+	private VocabularyTerm noteTypeVocabTerm;
 
 	private final String geneBulkPostEndpoint = "/api/gene/bulk/WB/genes";
 	private final String geneBulkPostEndpointRGD = "/api/gene/bulk/RGD/genes";
@@ -64,6 +70,9 @@ private void loadRequiredEntities() throws Exception {
 		createResourceDescriptorPage("homepage2", "http://test2.org", rd2);
 		createSoTerm(soTerm, "protein_coding_gene", false);
 		createSoTerm(soTerm2, "pseudogene", false);
+		Vocabulary noteTypeVocab = getVocabulary("note_type");
+		noteTypeVocabTerm = createVocabularyTerm(noteTypeVocab, noteType, false);
+		createVocabularyTermSet(VocabularyConstants.GENE_NOTE_TYPES_VOCABULARY_TERM_SET, noteTypeVocab, List.of(noteTypeVocabTerm));
 	}
 
 	@Test
@@ -161,8 +170,7 @@ public void geneBulkUploadCheckFields() throws Exception {
 			body("entity.relatedNotes[0].dateUpdated", is(OffsetDateTime.parse("2022-03-10T22:10:12Z").toString())).
 			body("entity.relatedNotes[0].dateCreated", is(OffsetDateTime.parse("2022-03-09T22:10:12Z").toString())).
 			body("entity.relatedNotes[0].freeText", is("Test note")).
-			body("entity.relatedNotes[0].noteType.name", is("comment")).
-			body("entity.relatedNotes[0].references[0].curie", is(requiredReference));
+			body("entity.relatedNotes[0].noteType.name", is(noteType));
 	}
 
 	@Test
@@ -251,15 +259,14 @@ public void geneBulkUploadUpdateFields() throws Exception {
 			body("entity.crossReferences[0].resourceDescriptorPage.name", is("homepage2")).
 			body("entity.geneType.curie", is(soTerm2)).
 			body("entity.relatedNotes", hasSize(1)).
-			body("entity.relatedNotes[0].internal", is(true)).
-			body("entity.relatedNotes[0].obsolete", is(false)).
-			body("entity.relatedNotes[0].updatedBy.uniqueId", is("DATEST:Person0001")).
-			body("entity.relatedNotes[0].createdBy.uniqueId", is("DATEST:Person0002")).
-			body("entity.relatedNotes[0].dateUpdated", is(OffsetDateTime.parse("2022-03-20T22:10:12Z").toString())).
-			body("entity.relatedNotes[0].dateCreated", is(OffsetDateTime.parse("2022-03-19T22:10:12Z").toString())).
+			body("entity.relatedNotes[0].internal", is(false)).
+			body("entity.relatedNotes[0].obsolete", is(true)).
+			body("entity.relatedNotes[0].updatedBy.uniqueId", is("DATEST:Person0002")).
+			body("entity.relatedNotes[0].createdBy.uniqueId", is("DATEST:Person0001")).
+			body("entity.relatedNotes[0].dateUpdated", is(OffsetDateTime.parse("2022-03-10T22:10:12Z").toString())).
+			body("entity.relatedNotes[0].dateCreated", is(OffsetDateTime.parse("2022-03-09T22:10:12Z").toString())).
 			body("entity.relatedNotes[0].freeText", is("Test note")).
-			body("entity.relatedNotes[0].noteType.name", is("indel_verification")).
-			body("entity.relatedNotes[0].references[0].curie", is(requiredReference2));
+			body("entity.relatedNotes[0].noteType.name", is(noteType));
 	}
 
 	@Test

diff --git a/src/test/resources/bulk/01_gene/UD_01_update_all_except_default_fields.json b/src/test/resources/bulk/01_gene/UD_01_update_all_except_default_fields.json
@@ -81,13 +81,15 @@
     "note_dtos": [
       {
         "free_text": "Test note",
-        "note_type_name": "indel_verification",
-        "created_by_curie": "DATEST:Person0002",
-        "updated_by_curie": "DATEST:Person0001",
-        "date_created": "2022-03-19T22:10:12+00:00",
-        "date_updated": "2022-03-20T22:10:12+00:00",
+        "note_type_name": "comment",
+        "internal": false,
+        "obsolete": true,
+        "created_by_curie": "DATEST:Person0001",
+        "updated_by_curie": "DATEST:Person0002",
+        "date_created": "2022-03-09T22:10:12+00:00",
+        "date_updated": "2022-03-10T22:10:12+00:00",
         "evidence_curies": [
-          "PMID:25920551"
+          "PMID:25920550"
         ]
       }
     ],