private Cosmic getCosmic(Document clinical) { String mutationID = (String) clinical.get("mutationID"); String primarySite = (String) clinical.get("primarySite"); String siteSubtype = (String) clinical.get("siteSubtype"); String primaryHistology = (String) clinical.get("primaryHistology"); String histologySubtype = (String) clinical.get("histologySubtype"); String sampleSource = (String) clinical.get("sampleSource"); String tumourOrigin = (String) clinical.get("tumourOrigin"); String geneName = (String) clinical.get("geneName"); String mutationSomaticStatus = (String) clinical.get("mutationSomaticStatus"); return new Cosmic(mutationID, primarySite, siteSubtype, primaryHistology, histologySubtype, sampleSource, tumourOrigin, geneName, mutationSomaticStatus); }
private Cosmic getCosmic(Document clinical) { String mutationID = (String) clinical.get("mutationID"); String primarySite = (String) clinical.get("primarySite"); String siteSubtype = (String) clinical.get("siteSubtype"); String primaryHistology = (String) clinical.get("primaryHistology"); String histologySubtype = (String) clinical.get("histologySubtype"); String sampleSource = (String) clinical.get("sampleSource"); String tumourOrigin = (String) clinical.get("tumourOrigin"); String geneName = (String) clinical.get("geneName"); String mutationSomaticStatus = (String) clinical.get("mutationSomaticStatus"); return new Cosmic(mutationID, primarySite, siteSubtype, primaryHistology, histologySubtype, sampleSource, tumourOrigin, geneName, mutationSomaticStatus); }
case "CM": Cosmic cosmic = new Cosmic(); cosmic.setMutationId(fields[1]); cosmic.setPrimaryHistology(fields[2]);
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)); }
@Override public Cosmic build() { try { Cosmic record = new Cosmic(); record.mutationId = fieldSetFlags()[0] ? this.mutationId : (java.lang.String) defaultValue(fields()[0]); record.primarySite = fieldSetFlags()[1] ? this.primarySite : (java.lang.String) defaultValue(fields()[1]); record.siteSubtype = fieldSetFlags()[2] ? this.siteSubtype : (java.lang.String) defaultValue(fields()[2]); record.primaryHistology = fieldSetFlags()[3] ? this.primaryHistology : (java.lang.String) defaultValue(fields()[3]); record.histologySubtype = fieldSetFlags()[4] ? this.histologySubtype : (java.lang.String) defaultValue(fields()[4]); record.sampleSource = fieldSetFlags()[5] ? this.sampleSource : (java.lang.String) defaultValue(fields()[5]); record.tumourOrigin = fieldSetFlags()[6] ? this.tumourOrigin : (java.lang.String) defaultValue(fields()[6]); record.geneName = fieldSetFlags()[7] ? this.geneName : (java.lang.String) defaultValue(fields()[7]); record.mutationSomaticStatus = fieldSetFlags()[8] ? this.mutationSomaticStatus : (java.lang.String) defaultValue(fields()[8]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }