diff --git a/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java b/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java index aa5576c8c..e7030ecb6 100644 --- a/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java +++ b/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java @@ -7,7 +7,7 @@ import org.alliancegenome.core.translators.tdf.DownloadHeader; import org.alliancegenome.curation_api.model.entities.ExperimentalCondition; import org.alliancegenome.curation_api.model.entities.*; -import org.alliancegenome.curation_api.model.entities.base.CurieAuditedObject; +import org.alliancegenome.curation_api.model.entities.base.SubmittedObject; import org.alliancegenome.neo4j.entity.DiseaseAnnotation; import org.alliancegenome.neo4j.entity.PrimaryAnnotatedEntity; import org.alliancegenome.neo4j.entity.node.CrossReference; @@ -193,13 +193,13 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance row.setMainEntitySymbol(subjectSymbol); // needs better generics or have subject attribute on the parent class (DiseaseAnnotation) if (primaryAnnotation instanceof AGMDiseaseAnnotation pAnnotation) { - row.setGeneticEntityID(pAnnotation.getSubject().getCurie()); - row.setGeneticEntityName(pAnnotation.getSubject().getName()); - row.setGeneticEntityType(pAnnotation.getSubject().getSubtype().getName()); + row.setGeneticEntityID(pAnnotation.getDiseaseAnnotationSubject().getIdentifier()); + row.setGeneticEntityName(pAnnotation.getDiseaseAnnotationSubject().getName()); + row.setGeneticEntityType(pAnnotation.getDiseaseAnnotationSubject().getSubtype().getName()); List assertedGenes = pAnnotation.getAssertedGenes(); if (CollectionUtils.isNotEmpty(assertedGenes)) { row.setAssertedGeneID(assertedGenes.stream().filter(gene -> !gene.getCurie().equals(subjectCurie)) - .map(CurieAuditedObject::getCurie).collect(Collectors.joining("|"))); + .map(SubmittedObject::getIdentifier).collect(Collectors.joining("|"))); row.setAssertedGeneName(assertedGenes.stream().filter(gene -> !gene.getCurie().equals(subjectCurie)) .map(gene -> gene.getGeneSymbol().getDisplayText()).collect(Collectors.joining("|"))); } @@ -211,8 +211,8 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance row.setGeneticEntityType("gene"); } else { if (primaryAnnotation instanceof GeneDiseaseAnnotation pAnnotation) { - row.setGeneticEntityID(pAnnotation.getSubject().getCurie()); - row.setGeneticEntityName(pAnnotation.getSubject().getGeneSymbol().getDisplayText()); + row.setGeneticEntityID(pAnnotation.getDiseaseAnnotationSubject().getIdentifier()); + row.setGeneticEntityName(pAnnotation.getDiseaseAnnotationSubject().getGeneSymbol().getDisplayText()); if (pAnnotation.getSgdStrainBackground() != null) { row.setStrainBackgroundID(pAnnotation.getSgdStrainBackground().getCurie()); row.setStrainBackgroundName(pAnnotation.getSgdStrainBackground().getName()); @@ -220,8 +220,8 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance row.setGeneticEntityType("gene"); } if (primaryAnnotation instanceof AlleleDiseaseAnnotation pAnnotation) { - row.setGeneticEntityID(pAnnotation.getSubject().getCurie()); - row.setGeneticEntityName(pAnnotation.getSubject().getAlleleSymbol().getDisplayText()); + row.setGeneticEntityID(pAnnotation.getDiseaseAnnotationSubject().getIdentifier()); + row.setGeneticEntityName(pAnnotation.getDiseaseAnnotationSubject().getAlleleSymbol().getDisplayText()); row.setGeneticEntityType("Allele"); } } @@ -245,7 +245,7 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance row.setDateAssigned(primaryAnnotation.getDateCreated().toString()); } if (CollectionUtils.isNotEmpty(primaryAnnotation.getWith())) { - row.setBasedOnID(primaryAnnotation.getWith().stream().map(CurieAuditedObject::getCurie).collect(Collectors.joining("|"))); + row.setBasedOnID(primaryAnnotation.getWith().stream().map(SubmittedObject::getIdentifier).collect(Collectors.joining("|"))); row.setBasedOnName(primaryAnnotation.getWith().stream().map(gene -> gene.getGeneSymbol().getDisplayText()).collect(Collectors.joining("|"))); } if (primaryAnnotation.getGeneticSex() != null) { @@ -272,7 +272,7 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance } List diseaseGeneticModifiers = primaryAnnotation.getDiseaseGeneticModifiers(); if (CollectionUtils.isNotEmpty(diseaseGeneticModifiers)) { - row.setDiseaseGeneticModifierID(diseaseGeneticModifiers.stream().map(CurieAuditedObject::getCurie).collect(Collectors.joining("|"))); + row.setDiseaseGeneticModifierID(diseaseGeneticModifiers.stream().map(SubmittedObject::getIdentifier).collect(Collectors.joining("|"))); StringJoiner joiner = new StringJoiner("|"); diseaseGeneticModifiers.forEach(entity -> { if (entity instanceof org.alliancegenome.curation_api.model.entities.Gene gene) { diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java index 0205ac553..3fa29681a 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java @@ -6,7 +6,7 @@ import org.alliancegenome.api.entity.AlleleDiseaseAnnotationDocument; import org.alliancegenome.api.entity.GeneDiseaseAnnotationDocument; import org.alliancegenome.curation_api.model.entities.*; -import org.alliancegenome.curation_api.model.entities.base.CurieAuditedObject; +import org.alliancegenome.curation_api.model.entities.base.SubmittedObject; import org.alliancegenome.curation_api.model.entities.ontology.DOTerm; import org.alliancegenome.curation_api.model.entities.ontology.ECOTerm; import org.alliancegenome.curation_api.model.entities.ontology.OntologyTerm; @@ -120,7 +120,7 @@ private List createGeneDiseaseAnnotationViaOrthol // Group By: // Disease, association type, Disease qualifiers, BasedOn Gene List (names), Map>>>> groupedByAnnotations = diseaseAnnotations.stream() - .collect(groupingBy(DiseaseAnnotation::getObject, + .collect(groupingBy(DiseaseAnnotation::getDiseaseAnnotationObject, groupingBy(DiseaseAnnotation::getRelation, groupingBy(diseaseAnnotation -> { List terms = diseaseAnnotation.getDiseaseQualifiers(); @@ -148,7 +148,7 @@ private List createGeneDiseaseAnnotationViaOrthol String generatedRelationString = getGeneratedRelationString(gdad.getRelation().getName(), diseaseAnnotation.getNegated()); gdad.setGeneratedRelationString(generatedRelationString); gdad.setObject(diseaseTerm); - gdad.setParentSlimIDs(closureMap.get(diseaseAnnotation.getObject().getCurie())); + gdad.setParentSlimIDs(closureMap.get(diseaseAnnotation.getDiseaseAnnotationObject().getCurie())); // create distinct and sorted list of ECOTerm objects Set ecoTerms = diseaseAnnotations1.stream().map(DiseaseAnnotation::getEvidenceCodes).flatMap(Collection::stream).collect(Collectors.toSet()); @@ -163,7 +163,7 @@ private List createGeneDiseaseAnnotationViaOrthol // create distinct list of basedOn Genes Set basedOnGenes = diseaseAnnotations1.stream().map(DiseaseAnnotation::getWith).flatMap(Collection::stream).collect(Collectors.toSet()); - List ids = basedOnGenes.stream().map(CurieAuditedObject::getCurie).toList(); + List ids = basedOnGenes.stream().map(SubmittedObject::getIdentifier).toList(); gdad.setBasedOnGenes(new ArrayList<>(basedOnGenes)); gdad.addReference(diseaseAnnotation.getSingleReference()); @@ -207,7 +207,7 @@ private List createGeneDiseaseAnnotationDocuments addCreatedDiseaseAnnotationsImplicatedToMap(generatedAnnotation, gene); } - String key = relation.getName() + "_" + da.getObject().getName() + "_" + da.getNegated(); + String key = relation.getName() + "_" + da.getDiseaseAnnotationObject().getName() + "_" + da.getNegated(); if (da.getDiseaseQualifiers() != null) { key += "_" + da.getDiseaseQualifiers().stream().map(VocabularyTerm::getName).sorted().collect(Collectors.joining("_")); @@ -227,8 +227,8 @@ private List createGeneDiseaseAnnotationDocuments gdad.setRelation(relation); String generatedRelationString = getGeneratedRelationString(gdad.getRelation().getName(), da.getNegated()); gdad.setGeneratedRelationString(generatedRelationString); - gdad.setObject(da.getObject()); - gdad.setParentSlimIDs(closureMap.get(da.getObject().getCurie())); + gdad.setObject(da.getDiseaseAnnotationObject()); + gdad.setParentSlimIDs(closureMap.get(da.getDiseaseAnnotationObject().getCurie())); lookup.put(key, gdad); } @@ -273,15 +273,15 @@ private DiseaseAnnotation createImplicatedDA(DiseaseAnnotation da) { DiseaseAnnotation implicatedDA = null; if (da instanceof AGMDiseaseAnnotation agmAnnotation) { AGMDiseaseAnnotation agmAnno = new AGMDiseaseAnnotation(); - agmAnno.setSubject(agmAnnotation.getSubject()); + agmAnno.setDiseaseAnnotationSubject(agmAnnotation.getDiseaseAnnotationSubject()); implicatedDA = agmAnno; } else if (da instanceof AlleleDiseaseAnnotation alleleAnno) { AlleleDiseaseAnnotation alleleDA = new AlleleDiseaseAnnotation(); - alleleDA.setSubject(alleleAnno.getSubject()); + alleleDA.setDiseaseAnnotationSubject(alleleAnno.getDiseaseAnnotationSubject()); implicatedDA = alleleDA; } implicatedDA.setRelation(da.getRelation()); - implicatedDA.setObject(da.getObject()); + implicatedDA.setDiseaseAnnotationObject(da.getDiseaseAnnotationObject()); implicatedDA.setDiseaseQualifiers(da.getDiseaseQualifiers()); implicatedDA.setDiseaseQualifiers(da.getDiseaseQualifiers()); implicatedDA.setSingleReference(da.getSingleReference()); @@ -327,7 +327,7 @@ private List createAlleleDiseaseAnnotationDocum relation = da.getRelation(); } - String key = relation.getName() + "_" + da.getObject().getName() + "_" + da.getNegated(); + String key = relation.getName() + "_" + da.getDiseaseAnnotationObject().getName() + "_" + da.getNegated(); AlleleDiseaseAnnotationDocument adad = lookup.get(key); if (adad == null) { @@ -338,7 +338,7 @@ private List createAlleleDiseaseAnnotationDocum adad.setRelation(relation); String generatedRelationString = getGeneratedRelationString(relation.getName(), da.getNegated()); adad.setGeneratedRelationString(generatedRelationString); - adad.setObject(da.getObject()); + adad.setObject(da.getDiseaseAnnotationObject()); lookup.put(key, adad); } adad.setEvidenceCodes(da.getEvidenceCodes()); @@ -346,7 +346,7 @@ private List createAlleleDiseaseAnnotationDocum Set diseaseQualifiers = da.getDiseaseQualifiers().stream().map(term -> term.getName().replace("_", " ")).collect(Collectors.toSet()); adad.setDiseaseQualifiers(diseaseQualifiers); } - adad.setParentSlimIDs(closureMap.get(da.getObject().getCurie())); + adad.setParentSlimIDs(closureMap.get(da.getDiseaseAnnotationObject().getCurie())); // gdad.setDataProvider(da.getDataProvider()); adad.addReference(da.getSingleReference()); @@ -375,7 +375,7 @@ private List createAGMDiseaseAnnotationDocuments() HashMap lookup = new HashMap<>(); for (DiseaseAnnotation da : entry.getValue().getRight()) { - String key = da.getRelation().getName() + "_" + da.getObject().getName() + "_" + da.getNegated(); + String key = da.getRelation().getName() + "_" + da.getDiseaseAnnotationObject().getName() + "_" + da.getNegated(); AGMDiseaseAnnotationDocument adad = lookup.get(key); if (adad == null) { @@ -384,7 +384,7 @@ private List createAGMDiseaseAnnotationDocuments() adad.setSpeciesOrder(order); adad.setSubject(entry.getValue().getLeft()); adad.setRelation(da.getRelation()); - adad.setObject(da.getObject()); + adad.setObject(da.getDiseaseAnnotationObject()); lookup.put(key, adad); } adad.setEvidenceCodes(da.getEvidenceCodes()); @@ -407,7 +407,7 @@ private void indexGenes() { private void addDiseaseAnnotationsToLGlobalMap(List geneDiseaseAnnotations) { log.info("Filtered Genes: " + geneDiseaseAnnotations.size()); for (GeneDiseaseAnnotation da : geneDiseaseAnnotations) { - Gene gene = da.getSubject(); + Gene gene = da.getDiseaseAnnotationSubject(); Pair> pair = geneMap.computeIfAbsent(gene.getCurie(), geneCurie -> Pair.of(gene, new ArrayList<>())); pair.getRight().add(da); } @@ -423,7 +423,7 @@ private void indexAlleles() { List alleleDiseaseAnnotations = alleleService.getFiltered(); log.info("Filtered Alleles: " + alleleDiseaseAnnotations.size()); for (AlleleDiseaseAnnotation da : alleleDiseaseAnnotations) { - Allele allele = da.getSubject(); + Allele allele = da.getDiseaseAnnotationSubject(); Pair> allelePair = alleleMap.computeIfAbsent(allele.getCurie(), alleleCurie -> Pair.of(allele, new ArrayList<>())); allelePair.getRight().add(da); @@ -458,7 +458,7 @@ private void indexAGMs() { log.info("Filtered AGMs: " + agmDiseaseAnnotations.size()); for (AGMDiseaseAnnotation da : agmDiseaseAnnotations) { - AffectedGenomicModel genomicModel = da.getSubject(); + AffectedGenomicModel genomicModel = da.getDiseaseAnnotationSubject(); Pair> allelePair = agmMap.computeIfAbsent(genomicModel.getCurie(), agmCurie -> Pair.of(genomicModel, new ArrayList<>())); allelePair.getRight().add(da); diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java index 425c66edc..5be8c633b 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java @@ -110,17 +110,17 @@ public Map> getOrthologousGeneDiseaseAnnotations(M DiseaseAnnotation gda = null; if (focusDiseaseAnnotation instanceof AGMDiseaseAnnotation agmda) { AGMDiseaseAnnotation da = new AGMDiseaseAnnotation(); - da.setSubject(agmda.getSubject()); + da.setDiseaseAnnotationSubject(agmda.getDiseaseAnnotationSubject()); gda = da; } if (focusDiseaseAnnotation instanceof AlleleDiseaseAnnotation ada) { AlleleDiseaseAnnotation da = new AlleleDiseaseAnnotation(); - da.setSubject(ada.getSubject()); + da.setDiseaseAnnotationSubject(ada.getDiseaseAnnotationSubject()); gda = da; } if (focusDiseaseAnnotation instanceof GeneDiseaseAnnotation gdann) { GeneDiseaseAnnotation da = new GeneDiseaseAnnotation(); - da.setSubject(gdann.getSubject()); + da.setDiseaseAnnotationSubject(gdann.getDiseaseAnnotationSubject()); gda = da; } @@ -136,7 +136,7 @@ public Map> getOrthologousGeneDiseaseAnnotations(M gda.setDataProvider(dataProvider); gda.setWith(List.of(geneGeneOrthology.getSubjectGene())); gda.setSingleReference(allianceReference); - gda.setObject(focusDiseaseAnnotation.getObject()); + gda.setDiseaseAnnotationObject(focusDiseaseAnnotation.getDiseaseAnnotationObject()); gda.setEvidenceCodes(List.of(ecoTermIEA)); gda.setDiseaseQualifiers(focusDiseaseAnnotation.getDiseaseQualifiers()); List geneAnnotations = newDAMap.computeIfAbsent(orthologousGene, k -> new ArrayList<>()); @@ -149,7 +149,7 @@ public Map> getOrthologousGeneDiseaseAnnotations(M // consolidating DAs: // by: disease, relation and disease qualifier newDAMap.forEach((gene, diseaseAnnotations) -> { - Map>>> groupedDAs = diseaseAnnotations.stream().collect(groupingBy(da1 -> da1.getObject().getCurie(), + Map>>> groupedDAs = diseaseAnnotations.stream().collect(groupingBy(da1 -> da1.getDiseaseAnnotationObject().getCurie(), groupingBy(da -> da.getRelation().getName(), groupingBy(da -> { List diseaseQualifiers = da.getDiseaseQualifiers(); // allow for grouping by missing based-on genes diff --git a/pom.xml b/pom.xml index 95fe83386..67b9e2652 100644 --- a/pom.xml +++ b/pom.xml @@ -30,7 +30,7 @@ quarkus-bom io.quarkus.platform ${quarkus.version} - v0.30.0 + v0.31.0