private ClinVar parseClinvar(EvidenceEntry evidenceEntry) { String clinicalSignificance = getAdditionalProperty(evidenceEntry, CLINICAL_SIGNIFICANCE_IN_SOURCE_FILE); List<String> traitList = null; if (evidenceEntry.getHeritableTraits() != null) { traitList = evidenceEntry .getHeritableTraits() .stream() .map((heritableTrait) -> heritableTrait.getTrait()) .collect(Collectors.toList()); } List<String> geneNameList = null; if (evidenceEntry.getGenomicFeatures() != null) { geneNameList = evidenceEntry .getGenomicFeatures() .stream() .map((genomicFeature) -> genomicFeature.getXrefs().get(SYMBOL)) .collect(Collectors.toList()); } String reviewStatus = getAdditionalProperty(evidenceEntry, REVIEW_STATUS_IN_SOURCE_FILE); return new ClinVar(evidenceEntry.getId(), clinicalSignificance, traitList, geneNameList, reviewStatus); }
private ClinVar parseClinvar(EvidenceEntry evidenceEntry) { String clinicalSignificance = getAdditionalProperty(evidenceEntry, CLINICAL_SIGNIFICANCE_IN_SOURCE_FILE); List<String> traitList = null; if (evidenceEntry.getHeritableTraits() != null) { traitList = evidenceEntry .getHeritableTraits() .stream() .map((heritableTrait) -> heritableTrait.getTrait()) .collect(Collectors.toList()); } List<String> geneNameList = null; if (evidenceEntry.getGenomicFeatures() != null) { geneNameList = evidenceEntry .getGenomicFeatures() .stream() .map((genomicFeature) -> genomicFeature.getXrefs().get(SYMBOL)) .collect(Collectors.toList()); } String reviewStatus = getAdditionalProperty(evidenceEntry, REVIEW_STATUS_IN_SOURCE_FILE); return new ClinVar(evidenceEntry.getId(), clinicalSignificance, traitList, geneNameList, reviewStatus); }
private Cosmic parseCosmic(EvidenceEntry evidenceEntry) { String primarySite = null; String siteSubtype = null; String primaryHistology = null; String histologySubtype = null; String sampleSource = null; String tumourOrigin = null; if (evidenceEntry.getSomaticInformation() != null) { primarySite = evidenceEntry.getSomaticInformation().getPrimarySite(); siteSubtype = evidenceEntry.getSomaticInformation().getSiteSubtype(); primaryHistology = evidenceEntry.getSomaticInformation().getPrimaryHistology(); histologySubtype = evidenceEntry.getSomaticInformation().getHistologySubtype(); sampleSource = evidenceEntry.getSomaticInformation().getSampleSource(); tumourOrigin = evidenceEntry.getSomaticInformation().getTumourOrigin(); } return new Cosmic(evidenceEntry.getId(), primarySite, siteSubtype, primaryHistology, histologySubtype, sampleSource, tumourOrigin, parseGeneName(evidenceEntry), getAdditionalProperty(evidenceEntry, MUTATION_SOMATIC_STATUS_IN_SOURCE_FILE)); }
private Cosmic parseCosmic(EvidenceEntry evidenceEntry) { String primarySite = null; String siteSubtype = null; String primaryHistology = null; String histologySubtype = null; String sampleSource = null; String tumourOrigin = null; if (evidenceEntry.getSomaticInformation() != null) { primarySite = evidenceEntry.getSomaticInformation().getPrimarySite(); siteSubtype = evidenceEntry.getSomaticInformation().getSiteSubtype(); primaryHistology = evidenceEntry.getSomaticInformation().getPrimaryHistology(); histologySubtype = evidenceEntry.getSomaticInformation().getHistologySubtype(); sampleSource = evidenceEntry.getSomaticInformation().getSampleSource(); tumourOrigin = evidenceEntry.getSomaticInformation().getTumourOrigin(); } return new Cosmic(evidenceEntry.getId(), primarySite, siteSubtype, primaryHistology, histologySubtype, sampleSource, tumourOrigin, parseGeneName(evidenceEntry), getAdditionalProperty(evidenceEntry, MUTATION_SOMATIC_STATUS_IN_SOURCE_FILE)); }