@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 "cosmic": if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getCosmic() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getCosmic().stream() .map(Cosmic::getPrimarySite) .collect(Collectors.joining(",")));
case "cosmic": if (variant.getAnnotation().getVariantTraitAssociation() != null && variant.getAnnotation().getVariantTraitAssociation().getCosmic() != null) { stringBuilder.append(variant.getAnnotation().getVariantTraitAssociation().getCosmic().stream() .map(Cosmic::getPrimarySite) .collect(Collectors.joining(",")));
@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 (variantAnnotation.getVariantTraitAssociation() != null) { putNotNull(clinicalDocument, CLINICAL_COSMIC_FIELD, generateClinicalDBList(variantAnnotation.getVariantTraitAssociation().getCosmic())); if (variantAnnotation.getVariantTraitAssociation().getCosmic() != null) { variantAnnotation.getVariantTraitAssociation().getCosmic() .stream() .map(Cosmic::getMutationId)