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)); }
return false; if (evidenceEntry1.getSomaticInformation() != null ? !evidenceEntry1.getSomaticInformation().equals(evidenceEntry2.getSomaticInformation()) : evidenceEntry2.getSomaticInformation() != null) { return false;
evidenceEntry.setBibliography(Collections.emptyList()); if (evidenceEntry.getSomaticInformation() != null) { if (evidenceEntry.getSomaticInformation().getSampleSource() == null) { evidenceEntry.getSomaticInformation().setSampleSource(""); if (evidenceEntry.getSomaticInformation().getTumourOrigin() == null) { evidenceEntry.getSomaticInformation().setTumourOrigin("");
evidenceEntry.setBibliography(Collections.emptyList()); if (evidenceEntry.getSomaticInformation() != null) { if (evidenceEntry.getSomaticInformation().getSampleSource() == null) { evidenceEntry.getSomaticInformation().setSampleSource(""); if (evidenceEntry.getSomaticInformation().getTumourOrigin() == null) { evidenceEntry.getSomaticInformation().setTumourOrigin("");