@Override public List<EvidenceEntry> convert(VariantTraitAssociation variantTraitAssociation) { if (variantTraitAssociation == null) { return null; } else { List<EvidenceEntry> evidenceEntries = new ArrayList<>(); if (variantTraitAssociation.getClinvar() != null) { for (ClinVar clinVar : variantTraitAssociation.getClinvar()) { EvidenceEntry evidenceEntry = fromClinVar(clinVar); evidenceEntries.add(evidenceEntry); } } if (variantTraitAssociation.getCosmic() != null) { for (Cosmic cosmic : variantTraitAssociation.getCosmic()) { EvidenceEntry evidenceEntry = fromCosmic(cosmic); evidenceEntries.add(evidenceEntry); } } return evidenceEntries; } }
case "clinvar": 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(",")));
case "clinvar": 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 (variantAnnotation.getVariantTraitAssociation().getClinvar() != null) { for (ClinVar clinVar : variantAnnotation.getVariantTraitAssociation().getClinvar()) { addNotNull(xrefs, clinVar.getAccession());
if (variantAnnotation.getVariantTraitAssociation().getClinvar() != null) { variantAnnotation.getVariantTraitAssociation().getClinvar() .forEach(cv -> { xrefs.add(cv.getAccession());
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)