@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; } }
private VariantTraitAssociation parseClinicalData(Document clinicalData) { if (clinicalData != null) { int size = 0; VariantTraitAssociation variantTraitAssociation = new VariantTraitAssociation(); List cosmicDBList = (List) clinicalData.get(CLINICAL_COSMIC_FIELD); if (cosmicDBList != null) { variantTraitAssociation.setCosmic(cosmicList); variantTraitAssociation.setGwas(gwasList); variantTraitAssociation.setClinvar(clinvarList);
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 "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 "gwas": 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(",")));
@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"); }
VariantTraitAssociation variantTraitAssociation = new VariantTraitAssociation(); variantTraitAssociation.setClinvar(clinVarList); variantTraitAssociation.setCosmic(cosmicList);
private VariantTraitAssociation convertToVariantTraitAssociation(List<EvidenceEntry> traitAssociation) { List<ClinVar> clinvarList = new ArrayList<>(); List<Cosmic> cosmicList = new ArrayList<>(traitAssociation.size()); for (EvidenceEntry evidenceEntry : traitAssociation) { switch (evidenceEntry.getSource().getName()) { case CLINVAR: clinvarList.add(parseClinvar(evidenceEntry)); break; case COSMIC: cosmicList.add(parseCosmic(evidenceEntry)); break; default: break; } } return new VariantTraitAssociation(clinvarList, null, cosmicList); }
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 "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 "gwas": 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(",")));
private VariantTraitAssociation convertToVariantTraitAssociation(List<EvidenceEntry> traitAssociation) { List<ClinVar> clinvarList = new ArrayList<>(); List<Cosmic> cosmicList = new ArrayList<>(traitAssociation.size()); for (EvidenceEntry evidenceEntry : traitAssociation) { switch (evidenceEntry.getSource().getName()) { case CLINVAR: clinvarList.add(parseClinvar(evidenceEntry)); break; case COSMIC: cosmicList.add(parseCosmic(evidenceEntry)); break; default: break; } } return new VariantTraitAssociation(clinvarList, null, cosmicList); }
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)
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());
@Override public VariantTraitAssociation build() { try { VariantTraitAssociation record = new VariantTraitAssociation(); record.clinvar = fieldSetFlags()[0] ? this.clinvar : (java.util.List<org.opencb.biodata.models.variant.avro.ClinVar>) defaultValue(fields()[0]); record.gwas = fieldSetFlags()[1] ? this.gwas : (java.util.List<org.opencb.biodata.models.variant.avro.Gwas>) defaultValue(fields()[1]); record.cosmic = fieldSetFlags()[2] ? this.cosmic : (java.util.List<org.opencb.biodata.models.variant.avro.Cosmic>) defaultValue(fields()[2]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
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());