Merge pull request #1777 from alliance-genome/SCRUM-4654

Add synonyms to variant

src/main/cliapp/src/containers/variantsPage/VariantsTable.js

@@ -23,6 +23,7 @@ import { OntologyTermTemplate } from '../../components/Templates/OntologyTermTem
 import { CountDialogTemplate } from '../../components/Templates/dialog/CountDialogTemplate';
 import { BooleanTemplate } from '../../components/Templates/BooleanTemplate';
 import { IdTemplate } from '../../components/Templates/IdTemplate';
+import { StringListTemplate } from '../../components/Templates/StringListTemplate';
 
 import { useGetTableData } from '../../service/useGetTableData';
 import { useGetUserSettings } from '../../service/useGetUserSettings';
@@ -226,6 +227,13 @@ export const VariantsTable = () => {
 			filterConfig: FILTER_CONFIGS.sourceGeneralConsequenceFilterConfig,
 			editor: (props) => <SourceGeneralConsequenceTableEditor rowProps={props} errorMessagesRef={errorMessagesRef} />,
 		},
+		{
+			field: 'synonyms',
+			header: 'Synonyms',
+			sortable: true,
+			filterConfig: FILTER_CONFIGS.synonymsFilterConfig,
+			body: (rowData) => <StringListTemplate list={rowData.synonyms} />,
+		},
 		{
 			field: 'dataProvider.sourceOrganization.abbreviation',
 			header: 'Data Provider',

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

@@ -10,14 +10,20 @@
 import org.alliancegenome.curation_api.view.View;
 import org.hibernate.annotations.Fetch;
 import org.hibernate.annotations.FetchMode;
+import org.hibernate.search.engine.backend.types.Aggregable;
+import org.hibernate.search.engine.backend.types.Searchable;
+import org.hibernate.search.engine.backend.types.Sortable;
 import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
 
 import com.fasterxml.jackson.annotation.JsonView;
 
 import jakarta.persistence.CascadeType;
+import jakarta.persistence.ElementCollection;
 import jakarta.persistence.Entity;
 import jakarta.persistence.Index;
 import jakarta.persistence.JoinTable;
@@ -33,7 +39,7 @@
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
 @ToString(exclude = { "curatedVariantGenomicLocations", "alleleVariantAssociations" }, callSuper = true)
-@AGRCurationSchemaVersion(min = "1.10.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class })
+@AGRCurationSchemaVersion(min = "2.9.1", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class })
 @Table(indexes = {
 		@Index(name = "variant_varianttype_index", columnList = "varianttype_id"),
 		@Index(name = "variant_variantstatus_index", columnList = "variantstatus_id"),
@@ -89,4 +95,11 @@ public class Variant extends GenomicEntity {
 	@JsonView({ View.FieldsAndLists.class, View.VariantDetailView.class })
 	private List<AlleleVariantAssociation> alleleVariantAssociations;
 
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "synonyms_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ElementCollection
+	@JoinTable(indexes = @Index(name = "variant_synonyms_variant_index", columnList = "variant_id"))
+	@JsonView({ View.FieldsAndLists.class, View.VariantView.class })
+	private List<String> synonyms;
 }

src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/VariantFmsDTO.java

@@ -23,4 +23,5 @@ public class VariantFmsDTO extends BaseDTO {
 	private List<VariantNoteFmsDTO> notes;
 	private List<PublicationRefFmsDTO> references;
 	private List<CrossReferenceFmsDTO> crossReferences;
+	private List<String> synonyms;
 }

src/main/java/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java

@@ -132,6 +132,27 @@ public Long validateVariant(VariantFmsDTO dto, List<Long> idsAdded, BackendBulkD
 			}
 		}
 		variant.setSourceGeneralConsequence(consequence);
+
+		if (CollectionUtils.isNotEmpty(dto.getSynonyms())) {
+			List<String> existingSynonyms = variant.getSynonyms();
+			if (CollectionUtils.isEmpty(existingSynonyms)) {
+				existingSynonyms = new ArrayList<>();
+			}
+			// remove synonyms that are no longer in the submitted file
+			List<String> toBeRemoved = existingSynonyms.stream()
+				.filter(synonym -> !dto.getSynonyms().contains(synonym))
+				.toList();
+			existingSynonyms.removeIf(toBeRemoved::contains);
+			// add missing synonyms
+			final List<String> synonymStrings = existingSynonyms;
+			List<String> toBeAdded = dto.getSynonyms().stream()
+				.filter(synonym -> !synonymStrings.contains(synonym))
+				.toList();
+			existingSynonyms.addAll(toBeAdded);
+			variant.setSynonyms(existingSynonyms);
+		} else {
+			variant.setSynonyms(null);
+		}
 
 		List<CrossReference> validatedXrefs = new ArrayList<>();
 		if (CollectionUtils.isNotEmpty(dto.getCrossReferences())) {

src/main/resources/db/migration/v0.38.0.23__variant_synonyms.sql

@@ -0,0 +1,8 @@
+CREATE TABLE variant_synonyms (
+    variant_id bigint,
+    synonyms text
+);
+
+CREATE INDEX variant_synonyms_variant_index ON variant_synonyms USING btree (variant_id);
+
+ALTER TABLE variant_synonyms ADD CONSTRAINT variant_synonyms_variant_id_fk FOREIGN KEY (variant_id) REFERENCES variant (id);

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

@@ -4,6 +4,7 @@
 import static org.hamcrest.Matchers.is;
 
 import java.util.HashMap;
+import java.util.List;
 
 import org.alliancegenome.curation_api.base.BaseITCase;
 import org.alliancegenome.curation_api.constants.VocabularyConstants;
@@ -91,6 +92,7 @@ public void variantFmsBulkUpload() throws Exception {
 			body("entity.taxon.curie", is("NCBITaxon:6239")).
 			body("entity.dataProvider.sourceOrganization.abbreviation", is("WB")).
 			body("entity.variantType.curie", is("SO:1000002")).
+			body("entity.synonyms", is(List.of("Syn 1", "Syn 2"))).
 			body("entity.sourceGeneralConsequence.curie", is("SO:0001587")).
 			body("entity.curatedVariantGenomicLocations", hasSize(1)).
 			body("entity.curatedVariantGenomicLocations[0].hgvs", is("NC_003279.8:g.1A>T")).
@@ -132,6 +134,7 @@ public void variantFmsBulkUploadUpdate() throws Exception {
 			body("entity.taxon.curie", is("NCBITaxon:6239")).
 			body("entity.dataProvider.sourceOrganization.abbreviation", is("WB")).
 			body("entity.variantType.curie", is("SO:1000008")).
+			body("entity.synonyms", is(List.of("Syn 3", "Syn 4"))).
 			body("entity.sourceGeneralConsequence.curie", is("SO:0001578")).
 			body("entity.curatedVariantGenomicLocations", hasSize(1)).
 			body("entity.curatedVariantGenomicLocations[0].hgvs", is("NC_003279.8:g.1A>T")).
@@ -195,7 +198,7 @@ public void variantFmsBulkUploadEmptyRequiredFields() throws Exception {
 	}
 
 	@Test
-	@Order(3)
+	@Order(5)
 	public void variantFmsBulkUploadInvalidFields() throws Exception {
 		HashMap<String, HashMap<String, Integer>> params = new HashMap<>();
 		params.put("Entities", createCountParams(1, 1, 0, 0));

src/test/resources/bulk/fms/10_variant/AF_01_all_fields.json

@@ -42,6 +42,9 @@
 					"homepage"
 				]
 			}
+		],
+		"synonyms" : [
+		  "Syn 1","Syn 2"
 		]
 	}
 ]

src/test/resources/bulk/fms/10_variant/UD_01_update_variant.json

@@ -35,6 +35,9 @@
 				]
 			}
 		],
+		"synonyms" : [
+		  "Syn 3","Syn 4"
+		],
 		"crossReferences": [
 			{
 				"id": "TEST:WBVar00252637",