public EvidenceEntry fromCosmic(Cosmic cosmic) {
EvidenceSource evidenceSource = new EvidenceSource(COSMIC, null, null);
List<GenomicFeature> genomicFeatures;
if (cosmic.getGeneName() != null) {
genomicFeatures = Collections.singletonList(
new GenomicFeature(FeatureTypes.gene, null, Collections.singletonMap(SYMBOL, cosmic.getGeneName())));
} else {
genomicFeatures = null;
}
SomaticInformation somaticInformation = new SomaticInformation(
cosmic.getPrimarySite(),
cosmic.getSiteSubtype(),
cosmic.getPrimaryHistology(),
cosmic.getHistologySubtype(),
cosmic.getTumourOrigin(),
cosmic.getSampleSource());
List<Property> additionalProperties = null;
if (StringUtils.isNotEmpty(cosmic.getMutationSomaticStatus())) {
additionalProperties = Collections.singletonList(
new Property(null, MUTATION_SOMATIC_STATUS_IN_SOURCE_FILE, cosmic.getMutationSomaticStatus()));
}
return new EvidenceEntry(
evidenceSource, Collections.emptyList(),
somaticInformation, null,
cosmic.getMutationId(), null, null, Collections.emptyList(),
genomicFeatures, null, null, null, null, EthnicCategory.Z, null, null, null,
additionalProperties, Collections.emptyList());
}