if (annotation.getVariantTraitAssociation().getCosmic() != null) { for (Cosmic cosmic : annotation.getVariantTraitAssociation().getCosmic()) { if (cosmic.getSiteSubtype() == null) { cosmic.setSiteSubtype(""); if (cosmic.getSampleSource() == null) { cosmic.setSampleSource(""); if (cosmic.getTumourOrigin() == null) { cosmic.setTumourOrigin(""); if (cosmic.getHistologySubtype() == null) { cosmic.setHistologySubtype(""); if (cosmic.getPrimarySite() == null) { cosmic.setPrimarySite(""); if (cosmic.getPrimaryHistology() == null) { cosmic.setPrimaryHistology("");
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()); }
case "CM": Cosmic cosmic = new Cosmic(); cosmic.setMutationId(fields[1]); cosmic.setPrimaryHistology(fields[2]); cosmic.setHistologySubtype(fields[3]); cosmicList.add(cosmic); break;
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); }
variantAnnotation.getVariantTraitAssociation().getCosmic() .forEach(cosmic -> { xrefs.add(cosmic.getMutationId()); traits.add("CM" + FIELD_SEP + cosmic.getMutationId() + FIELD_SEP + cosmic.getPrimaryHistology() + FIELD_SEP + cosmic.getHistologySubtype()); });
@Test public void testConvertToDataModelType() throws Exception { DocumentToVariantAnnotationConverter documentToVariantAnnotationConverter = new DocumentToVariantAnnotationConverter(); VariantAnnotation convertedVariantAnnotation = documentToVariantAnnotationConverter.convertToDataModelType(dbObject); assertEquals(convertedVariantAnnotation.getConsequenceTypes().get(2).getProteinVariantAnnotation().getReference(), "CYS"); assertEquals(convertedVariantAnnotation.getVariantTraitAssociation().getCosmic().get(0).getPrimarySite(), "large_intestine"); }
if (variantAnnotation.getVariantTraitAssociation().getCosmic() != null) { for (Cosmic cosmic : variantAnnotation.getVariantTraitAssociation().getCosmic()) { addNotNull(xrefs, cosmic.getMutationId());
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); }
if (annotation.getVariantTraitAssociation().getCosmic() != null) { for (Cosmic cosmic : annotation.getVariantTraitAssociation().getCosmic()) { if (cosmic.getSiteSubtype() == null) { cosmic.setSiteSubtype(""); if (cosmic.getSampleSource() == null) { cosmic.setSampleSource(""); if (cosmic.getTumourOrigin() == null) { cosmic.setTumourOrigin(""); if (cosmic.getHistologySubtype() == null) { cosmic.setHistologySubtype(""); if (cosmic.getPrimarySite() == null) { cosmic.setPrimarySite(""); if (cosmic.getPrimaryHistology() == null) { cosmic.setPrimaryHistology("");
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); } } }