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); }
evidenceEntry.setSubmissions(Collections.emptyList()); if (evidenceEntry.getHeritableTraits() == null) { evidenceEntry.setHeritableTraits(Collections.emptyList());
evidenceEntry.setSubmissions(Collections.emptyList()); if (evidenceEntry.getHeritableTraits() == null) { evidenceEntry.setHeritableTraits(Collections.emptyList()); } else { for (HeritableTrait heritableTrait : evidenceEntry.getHeritableTraits()) { if (heritableTrait.getInheritanceMode() == null) { heritableTrait.setInheritanceMode(ModeOfInheritance.unknown);
evidenceEntry.setSubmissions(Collections.emptyList()); if (evidenceEntry.getHeritableTraits() == null) { evidenceEntry.setHeritableTraits(Collections.emptyList()); } else { for (HeritableTrait heritableTrait : evidenceEntry.getHeritableTraits()) { if (heritableTrait.getInheritanceMode() == null) { heritableTrait.setInheritanceMode(ModeOfInheritance.unknown);