if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getClinvar() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getClinvar().stream() .map(ClinVar::getTraits).flatMap(Collection::stream) .collect(Collectors.joining(","))); if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getCosmic() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getCosmic().stream() .map(Cosmic::getPrimarySite) .collect(Collectors.joining(","))); if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getGwas() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getGwas().stream() .map(Gwas::getTraits).flatMap(Collection::stream) .collect(Collectors.joining(",")));
if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getClinvar() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getClinvar().stream() .map(ClinVar::getTraits).flatMap(Collection::stream) .collect(Collectors.joining(","))); if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getCosmic() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getCosmic().stream() .map(Cosmic::getPrimarySite) .collect(Collectors.joining(","))); if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getGwas() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getGwas().stream() .map(Gwas::getTraits).flatMap(Collection::stream) .collect(Collectors.joining(",")));
if (variantAnnotation.getVariantTraitAssociation() != null && CollectionUtils.isEmpty(variantAnnotation.getTraitAssociation())) { List<EvidenceEntry> evidenceEntries = traitAssociationConverter.convert(variantAnnotation.getVariantTraitAssociation()); variantAnnotation.setTraitAssociation(evidenceEntries);
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); if (annotatorSet.contains("variation")) { destination.setId(origin.getId()); } if (annotatorSet.contains("consequenceType")) { destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); } if (annotatorSet.contains("conservation")) { destination.setConservation(origin.getConservation()); } // destination.setGeneExpression(origin.getGeneExpression()); // destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); if (annotatorSet.contains("populationFrequencies")) { destination.setPopulationFrequencies(origin.getPopulationFrequencies()); } // destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); if (annotatorSet.contains("clinical")) { destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); } if (annotatorSet.contains("functionalScore")) { destination.setFunctionalScore(origin.getFunctionalScore()); } }
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); if (annotatorSet.contains("variation")) { destination.setId(origin.getId()); } if (annotatorSet.contains("consequenceType")) { destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); } if (annotatorSet.contains("conservation")) { destination.setConservation(origin.getConservation()); } // destination.setGeneExpression(origin.getGeneExpression()); // destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); if (annotatorSet.contains("populationFrequencies")) { destination.setPopulationFrequencies(origin.getPopulationFrequencies()); } // destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); if (annotatorSet.contains("clinical")) { destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); } if (annotatorSet.contains("functionalScore")) { destination.setFunctionalScore(origin.getFunctionalScore()); } }
if (variantAnnotation.getVariantTraitAssociation() != null && CollectionUtils.isEmpty(variantAnnotation.getTraitAssociation())) { List<EvidenceEntry> evidenceEntries = evidenceEntryConverter.convert(variantAnnotation.getVariantTraitAssociation()); variantAnnotation.setTraitAssociation(evidenceEntries); if (variantAnnotation.getVariantTraitAssociation() != null) { if (variantAnnotation.getVariantTraitAssociation().getCosmic() != null) { for (Cosmic cosmic : variantAnnotation.getVariantTraitAssociation().getCosmic()) { addNotNull(xrefs, cosmic.getMutationId()); if (variantAnnotation.getVariantTraitAssociation().getClinvar() != null) { for (ClinVar clinVar : variantAnnotation.getVariantTraitAssociation().getClinvar()) { addNotNull(xrefs, clinVar.getAccession());
if (variantAnnotation.getVariantTraitAssociation() != null) { if (variantAnnotation.getVariantTraitAssociation().getClinvar() != null) { variantAnnotation.getVariantTraitAssociation().getClinvar() .forEach(cv -> { xrefs.add(cv.getAccession()); }); if (variantAnnotation.getVariantTraitAssociation().getCosmic() != null) { variantAnnotation.getVariantTraitAssociation().getCosmic() .forEach(cosmic -> { xrefs.add(cosmic.getMutationId());
@Test public void testConvertToDataModelType() throws Exception { DocumentToVariantAnnotationConverter documentToVariantAnnotationConverter = new DocumentToVariantAnnotationConverter(); VariantAnnotation convertedVariantAnnotation = documentToVariantAnnotationConverter.convertToDataModelType(dbObject); assertEquals(convertedVariantAnnotation.getConsequenceTypes().get(2).getProteinVariantAnnotation().getReference(), "CYS"); assertEquals(convertedVariantAnnotation.getVariantTraitAssociation().getCosmic().get(0).getPrimarySite(), "large_intestine"); }
if (annotation.getVariantTraitAssociation() != null) { if (annotation.getVariantTraitAssociation().getCosmic() != null) { for (Cosmic cosmic : annotation.getVariantTraitAssociation().getCosmic()) { if (cosmic.getSiteSubtype() == null) { cosmic.setSiteSubtype("");
if (annotation.getVariantTraitAssociation() != null) { if (annotation.getVariantTraitAssociation().getCosmic() != null) { for (Cosmic cosmic : annotation.getVariantTraitAssociation().getCosmic()) { if (cosmic.getSiteSubtype() == null) { cosmic.setSiteSubtype("");
if (variantAnnotation.getVariantTraitAssociation() != null) { putNotNull(clinicalDocument, CLINICAL_COSMIC_FIELD, generateClinicalDBList(variantAnnotation.getVariantTraitAssociation().getCosmic())); if (variantAnnotation.getVariantTraitAssociation().getCosmic() != null) { variantAnnotation.getVariantTraitAssociation().getCosmic() .stream() .map(Cosmic::getMutationId) generateClinicalDBList(variantAnnotation.getVariantTraitAssociation().getGwas())); putNotNull(clinicalDocument, CLINICAL_CLINVAR_FIELD, generateClinicalDBList(variantAnnotation.getVariantTraitAssociation().getClinvar())); if (variantAnnotation.getVariantTraitAssociation().getClinvar() != null) { variantAnnotation.getVariantTraitAssociation().getClinvar() .stream() .map(ClinVar::getAccession)
va.setTraitAssociation(traitAssociationConverter.convert(va.getVariantTraitAssociation()));
private void mergeAnnotation(VariantAnnotation destination, VariantAnnotation origin) { if (origin != null) { destination.setId(origin.getId()); destination.setChromosome(origin.getChromosome()); destination.setStart(origin.getStart()); destination.setReference(origin.getReference()); destination.setAlternate(origin.getAlternate()); destination.setDisplayConsequenceType(origin.getDisplayConsequenceType()); destination.setConsequenceTypes(origin.getConsequenceTypes()); destination.setConservation(origin.getConservation()); destination.setGeneExpression(origin.getGeneExpression()); destination.setGeneTraitAssociation(origin.getGeneTraitAssociation()); destination.setGeneDrugInteraction(origin.getGeneDrugInteraction()); destination.setVariantTraitAssociation(origin.getVariantTraitAssociation()); destination.setFunctionalScore(origin.getFunctionalScore()); } }