Merge pull request #1748 from alliance-genome/SCRUM-4447

SCRUM-4447 Add gene/phenotypes xrefs
alliance-genome · Dec 5, 2024 · de97af9 · de97af9
2 parents 4037159 + fcf17ed
commit de97af9
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Showing 7 changed files with 99 additions and 5 deletions.
diff --git a/src/main/java/org/alliancegenome/curation_api/services/CrossReferenceService.java b/src/main/java/org/alliancegenome/curation_api/services/CrossReferenceService.java
@@ -62,6 +62,11 @@ public List<CrossReference> getMergedFmsXrefList(List<CrossReferenceFmsDTO> fmsC
 
 	@Transactional
 	public List<CrossReference> getUpdatedXrefList(List<CrossReference> incomingXrefs, List<CrossReference> existingXrefs) {
+		return getUpdatedXrefList(incomingXrefs, existingXrefs, false);
+	}
+
+	@Transactional
+	public List<CrossReference> getUpdatedXrefList(List<CrossReference> incomingXrefs, List<CrossReference> existingXrefs, Boolean keepAllExisting) {
 		Map<String, CrossReference> existingXrefMap = new HashMap<>();
 		if (CollectionUtils.isNotEmpty(existingXrefs)) {
 			for (CrossReference existingXref : existingXrefs) {
@@ -71,6 +76,11 @@ public List<CrossReference> getUpdatedXrefList(List<CrossReference> incomingXref
 
 		List<CrossReference> finalXrefs = new ArrayList<>();
 		List<String> addedXrefUniqueIds = new ArrayList<>();
+
+		if (keepAllExisting && CollectionUtils.isNotEmpty(existingXrefs)) {
+			incomingXrefs.addAll(existingXrefs);
+		}
+
 		if (CollectionUtils.isNotEmpty(incomingXrefs)) {
 			for (CrossReference incomingXref : incomingXrefs) {
 				String incomingXrefUniqueId = getCrossReferenceUniqueId(incomingXref);

diff --git a/src/main/java/org/alliancegenome/curation_api/services/PhenotypeAnnotationService.java b/src/main/java/org/alliancegenome/curation_api/services/PhenotypeAnnotationService.java
@@ -91,6 +91,7 @@ protected <D extends BaseSQLDAO<?>> List<Long> getAnnotationIdsByDataProvider(D
 		return annotationIds;
 	}
 
+	@Transactional
 	public Long upsertPrimaryAnnotation(PhenotypeFmsDTO dto, BackendBulkDataProvider dataProvider) throws ValidationException {
 		if (StringUtils.isBlank(dto.getObjectId())) {
 			throw new ObjectValidationException(dto, "objectId - " + ValidationConstants.REQUIRED_MESSAGE);

diff --git a/...cegenome/curation_api/services/helpers/annotations/GenePhenotypeAnnotationXrefHelper.java b/...cegenome/curation_api/services/helpers/annotations/GenePhenotypeAnnotationXrefHelper.java
@@ -0,0 +1,59 @@
+package org.alliancegenome.curation_api.services.helpers.annotations;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+
+import org.alliancegenome.curation_api.dao.GeneDAO;
+import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.curation_api.model.entities.ResourceDescriptorPage;
+import org.alliancegenome.curation_api.services.CrossReferenceService;
+import org.alliancegenome.curation_api.services.ResourceDescriptorPageService;
+
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
+
+@RequestScoped
+public class GenePhenotypeAnnotationXrefHelper {
+
+	@Inject ResourceDescriptorPageService rdpService;
+	@Inject CrossReferenceService xrefService;
+	@Inject GeneDAO geneDAO;
+
+	@Transactional
+	public Gene addGenePhenotypeCrossReference(BackendBulkDataProvider dataProvider, Gene gene) {
+
+		if (Objects.equals("HUMAN", dataProvider.name()) || gene.getIdentifier().startsWith("HGNC:")) {
+			return gene;
+		}
+
+		CrossReference xref = new CrossReference();
+
+		String[] geneCurieParts = gene.getIdentifier().split(":");
+		String prefix = geneCurieParts[0];
+		String pageName = Objects.equals("MGI", prefix) ? "gene_phenotypes_impc" : "gene/phenotypes";
+
+		ResourceDescriptorPage rdp = rdpService.getPageForResourceDescriptor(prefix, pageName);
+		xref.setDisplayName(prefix);
+		xref.setReferencedCurie(gene.getIdentifier());
+		xref.setResourceDescriptorPage(rdp);
+
+		List<CrossReference> updatedXrefs = xrefService.getUpdatedXrefList(List.of(xref), gene.getCrossReferences());
+
+		if (gene.getCrossReferences() != null) {
+			gene.getCrossReferences().clear();
+		}
+		if (updatedXrefs != null) {
+			if (gene.getCrossReferences() == null) {
+				gene.setCrossReferences(new ArrayList<>());
+			}
+			gene.getCrossReferences().addAll(updatedXrefs);
+		}
+
+		return geneDAO.persist(gene);
+	}
+
+}
diff --git a/...enome/curation_api/services/validation/dto/fms/AGMPhenotypeAnnotationFmsDTOValidator.java b/...enome/curation_api/services/validation/dto/fms/AGMPhenotypeAnnotationFmsDTOValidator.java
@@ -21,6 +21,7 @@
 import org.alliancegenome.curation_api.services.GenomicEntityService;
 import org.alliancegenome.curation_api.services.PhenotypeAnnotationService;
 import org.alliancegenome.curation_api.services.helpers.annotations.AnnotationUniqueIdHelper;
+import org.alliancegenome.curation_api.services.helpers.annotations.GenePhenotypeAnnotationXrefHelper;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 
@@ -33,6 +34,7 @@ public class AGMPhenotypeAnnotationFmsDTOValidator extends PhenotypeAnnotationFm
 	@Inject AGMPhenotypeAnnotationDAO agmPhenotypeAnnotationDAO;
 	@Inject GenomicEntityService genomicEntityService;
 	@Inject PhenotypeAnnotationService phenotypeAnnotationService;
+	@Inject GenePhenotypeAnnotationXrefHelper xrefHelper;
 
 	public AGMPhenotypeAnnotation validatePrimaryAnnotation(AffectedGenomicModel subject, PhenotypeFmsDTO dto, BackendBulkDataProvider dataProvider) throws ObjectValidationException {
 
@@ -104,15 +106,16 @@ public List<AGMPhenotypeAnnotation> validateInferredOrAssertedEntities(AffectedG
 			if (inferredOrAssertedEntity == null) {
 				apaResponse.addErrorMessage("objectId", ValidationConstants.INVALID_MESSAGE + " (" + dto.getObjectId() + ")");
 			} else if (inferredOrAssertedEntity instanceof Gene) {
+				Gene inferredOrAssertedGene = xrefHelper.addGenePhenotypeCrossReference(dataProvider, (Gene) inferredOrAssertedEntity);
 				for (AGMPhenotypeAnnotation primaryAnnotation : primaryAnnotations) {
 					if (dataProvider.hasInferredGenePhenotypeAnnotations) {
-						primaryAnnotation.setInferredGene((Gene) inferredOrAssertedEntity);
+						primaryAnnotation.setInferredGene(inferredOrAssertedGene);
 					} else if (dataProvider.hasAssertedGenePhenotypeAnnotations) {
 						List<Gene> assertedGenes = primaryAnnotation.getAssertedGenes();
 						if (assertedGenes == null) {
 							assertedGenes = new ArrayList<>();
 						}
-						assertedGenes.add((Gene) inferredOrAssertedEntity);
+						assertedGenes.add(inferredOrAssertedGene);
 						primaryAnnotation.setAssertedGenes(assertedGenes);
 					} else {
 						apaResponse.addErrorMessage("objectId", ValidationConstants.INVALID_MESSAGE + " (" + dto.getObjectId() + ")");

diff --git a/...me/curation_api/services/validation/dto/fms/AllelePhenotypeAnnotationFmsDTOValidator.java b/...me/curation_api/services/validation/dto/fms/AllelePhenotypeAnnotationFmsDTOValidator.java
@@ -20,6 +20,7 @@
 import org.alliancegenome.curation_api.services.GenomicEntityService;
 import org.alliancegenome.curation_api.services.PhenotypeAnnotationService;
 import org.alliancegenome.curation_api.services.helpers.annotations.AnnotationUniqueIdHelper;
+import org.alliancegenome.curation_api.services.helpers.annotations.GenePhenotypeAnnotationXrefHelper;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 
@@ -32,6 +33,7 @@ public class AllelePhenotypeAnnotationFmsDTOValidator extends PhenotypeAnnotatio
 	@Inject AllelePhenotypeAnnotationDAO allelePhenotypeAnnotationDAO;
 	@Inject GenomicEntityService genomicEntityService;
 	@Inject PhenotypeAnnotationService phenotypeAnnotationService;
+	@Inject GenePhenotypeAnnotationXrefHelper xrefHelper;
 
 	public AllelePhenotypeAnnotation validatePrimaryAnnotation(Allele subject, PhenotypeFmsDTO dto, BackendBulkDataProvider dataProvider) throws ObjectValidationException {
 
@@ -102,15 +104,16 @@ public List<AllelePhenotypeAnnotation> validateInferredOrAssertedEntities(Allele
 			if (inferredOrAssertedEntity == null) {
 				apaResponse.addErrorMessage("objectId", ValidationConstants.INVALID_MESSAGE + " (" + dto.getObjectId() + ")");
 			} else if (inferredOrAssertedEntity instanceof Gene) {
+				Gene inferredOrAssertedGene = xrefHelper.addGenePhenotypeCrossReference(dataProvider, (Gene) inferredOrAssertedEntity);
 				for (AllelePhenotypeAnnotation primaryAnnotation : primaryAnnotations) {
 					if (dataProvider.hasInferredGenePhenotypeAnnotations) {
-						primaryAnnotation.setInferredGene((Gene) inferredOrAssertedEntity);
+						primaryAnnotation.setInferredGene(inferredOrAssertedGene);
 					} else if (dataProvider.hasAssertedGenePhenotypeAnnotations) {
 						List<Gene> assertedGenes = primaryAnnotation.getAssertedGenes();
 						if (assertedGenes == null) {
 							assertedGenes = new ArrayList<>();
 						}
-						assertedGenes.add((Gene) inferredOrAssertedEntity);
+						assertedGenes.add(inferredOrAssertedGene);
 						primaryAnnotation.setAssertedGenes(assertedGenes);
 					} else {
 						apaResponse.addErrorMessage("objectId", ValidationConstants.INVALID_MESSAGE + " (" + dto.getObjectId() + ")");

diff --git a/...nome/curation_api/services/validation/dto/fms/GenePhenotypeAnnotationFmsDTOValidator.java b/...nome/curation_api/services/validation/dto/fms/GenePhenotypeAnnotationFmsDTOValidator.java
@@ -13,17 +13,21 @@
 import org.alliancegenome.curation_api.services.GenomicEntityService;
 import org.alliancegenome.curation_api.services.PhenotypeAnnotationService;
 import org.alliancegenome.curation_api.services.helpers.annotations.AnnotationUniqueIdHelper;
+import org.alliancegenome.curation_api.services.helpers.annotations.GenePhenotypeAnnotationXrefHelper;
 
 import jakarta.enterprise.context.RequestScoped;
 import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
 
 @RequestScoped
 public class GenePhenotypeAnnotationFmsDTOValidator extends PhenotypeAnnotationFmsDTOValidator {
 
 	@Inject GenePhenotypeAnnotationDAO genePhenotypeAnnotationDAO;
 	@Inject GenomicEntityService genomicEntityService;
 	@Inject PhenotypeAnnotationService phenotypeAnnotationService;
-
+	@Inject GenePhenotypeAnnotationXrefHelper xrefHelper;
+
+	@Transactional
 	public GenePhenotypeAnnotation validatePrimaryAnnotation(Gene subject, PhenotypeFmsDTO dto, BackendBulkDataProvider dataProvider) throws ValidationException {
 
 		ObjectResponse<GenePhenotypeAnnotation> apaResponse = new ObjectResponse<GenePhenotypeAnnotation>();
@@ -41,6 +45,8 @@ public GenePhenotypeAnnotation validatePrimaryAnnotation(Gene subject, Phenotype
 			annotation = annotationSearch.getSingleResult();
 		}
 
+		subject = xrefHelper.addGenePhenotypeCrossReference(dataProvider, subject);
+
 		annotation.setUniqueId(uniqueId);
 		annotation.setSingleReference(reference);
 		annotation.setPhenotypeAnnotationSubject(subject);

diff --git a/src/test/java/org/alliancegenome/curation_api/PhenotypeAnnotationBulkUploadFmsITCase.java b/src/test/java/org/alliancegenome/curation_api/PhenotypeAnnotationBulkUploadFmsITCase.java
@@ -88,6 +88,8 @@ private void loadRequiredEntities() throws Exception {
 		createMpTerm(mpTerm, "Test PhenotypeTerm");
 		ResourceDescriptor rd = createResourceDescriptor("PMID");
 		createResourceDescriptorPage("default", "https://www.ncbi.nlm.nih.gov/pubmed/[%s]", rd);
+		ResourceDescriptor rd2 = createResourceDescriptor("PATEST");
+		createResourceDescriptorPage("gene/phenotypes", "https://xref_url_test/[%s]", rd2);
 	}
 
 	@Test
@@ -198,6 +200,16 @@ public void genePhenotypeAnnotationBulkUploadCheckFields() throws Exception {
 				.body("results[0].crossReference.displayName", is("PMID:25920554"))
 				.body("results[0].phenotypeTerms", hasSize(1))
 				.body("results[0].phenotypeTerms[0].curie", is(mpTerm));
+
+		RestAssured.given().when().get("/api/gene/" + gene).
+				then().
+				statusCode(200).
+				body("entity.modEntityId", is(gene)).
+				body("entity.crossReferences", hasSize(1)).
+				body("entity.crossReferences[0].displayName", is("PATEST")).
+				body("entity.crossReferences[0].referencedCurie", is(gene)).
+				body("entity.crossReferences[0].resourceDescriptorPage.name", is("gene/phenotypes")).
+				body("entity.crossReferences[0].resourceDescriptorPage.urlTemplate", is("https://xref_url_test/[%s]"));
 	}
 
 	@Test