List of usage examples for javax.xml.bind JAXBIntrospector getElementName
public abstract QName getElementName(Object jaxbElement);
Get xml element qname for jaxbElement.
From source file:gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.BiospecimenMetaDataProcessor.java
private void getExaminationMetaData(final Patient patient, final BiospecimenMetaData patientMetaData, final Map<String, BiospecimenMetaData> biospecimenMetaDataByUUIDORBarcode, final JAXBIntrospector jaxbIntrospector, final Archive archive) throws ProcessorException, UUIDException { if (patient.getExaminations() != null) { List<Examination> examinations = patient.getExaminations().getExamination(); if (examinations != null) { // Get examination meta-data for the patient for (final Examination examination : examinations) { BiospecimenMetaData examinationMetaData = BiospecimenMetaData.newInstance(patientMetaData); final String uuid = JAXBUtil.getJAXBObjectValue(examination.getBcrExaminationUuid()); examinationMetaData.setBarcode(examination.getBcrExaminationBarcode().getValue()); setUUID(examinationMetaData, uuid, archive); examinationMetaData.setUuidType(jaxbIntrospector.getElementName(examination).getLocalPart()); biospecimenMetaDataByUUIDORBarcode .put((uuid == null || uuid.isEmpty()) ? examinationMetaData.getBarcode() : examinationMetaData.getUuid(), examinationMetaData); }//from w w w.j a v a 2 s .co m } } }
From source file:gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.BiospecimenMetaDataProcessor.java
private void getSlideMetaData(final Portion portion, final BiospecimenMetaData portionMetaData, final Map<String, BiospecimenMetaData> biospecimenMetaDataByUUIDORBarcode, final JAXBIntrospector jaxbIntrospector, final Archive archive) throws UUIDException, ProcessorException { if (portion.getSlides() != null) { List<Slide> slides = portion.getSlides().getSlide(); if (slides != null) { // Get slide meta-data for the sample for (final Slide slide : slides) { BiospecimenMetaData slideMetaData = BiospecimenMetaData.newInstance(portionMetaData); final String uuid = JAXBUtil.getJAXBObjectValue(slide.getBcrSlideUuid()); String slideBarcode = slide.getBcrSlideBarcode().getValue(); slideMetaData.setBarcode(slideBarcode); slideMetaData.setSlide(getSlideForBarcode(slideBarcode)); setUUID(slideMetaData, uuid, archive); slideMetaData.setUuidType(jaxbIntrospector.getElementName(slide).getLocalPart()); slideMetaData.setSlideLayer(slide.getSectionLocation().getValue().toLowerCase()); biospecimenMetaDataByUUIDORBarcode.put( (uuid == null || uuid.isEmpty()) ? slideMetaData.getBarcode() : slideMetaData.getUuid(), slideMetaData);//from www.j a v a2 s . com logger.info("BiospecimenMetaDataProcessor: Processed slide with UUID " + slideMetaData.getUuid() + " and parent " + slideMetaData.getParentUUID()); } } } }
From source file:gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.BiospecimenMetaDataProcessor.java
private void getShipmentPortionMetaData(final Sample sample, final BiospecimenMetaData sampleMetaData, final Map<String, BiospecimenMetaData> biospecimenMetaDataByUUIDORBarcode, final JAXBIntrospector jaxbIntrospector, final Archive archive) throws ProcessorException, UUIDException { if (sample.getPortions() != null) { List<ShipmentPortion> shipmentPortions = sample.getPortions().getShipmentPortion(); if (shipmentPortions != null) { // Get shipment portion meta-data for the sample for (final ShipmentPortion shipmentPortion : shipmentPortions) { BiospecimenMetaData shipmentPortionMetaData = BiospecimenMetaData.newInstance(sampleMetaData); final String uuid = JAXBUtil.getJAXBObjectValue(shipmentPortion.getBcrShipmentPortionUuid()); shipmentPortionMetaData/* w ww .j a v a 2s . co m*/ .setBarcode(shipmentPortion.getShipmentPortionBcrAliquotBarcode().getValue()); setUUID(shipmentPortionMetaData, uuid, archive); shipmentPortionMetaData .setUuidType(jaxbIntrospector.getElementName(shipmentPortion).getLocalPart()); shipmentPortionMetaData.setPortionId(shipmentPortion.getPortionNumber().getValue().toString()); shipmentPortionMetaData.setPlateId(shipmentPortion.getPlateId().getValue()); shipmentPortionMetaData.setReceivingCenter(shipmentPortion.getCenterId().getValue()); shipmentPortionMetaData.setCenterCode(shipmentPortion.getCenterId().getValue()); biospecimenMetaDataByUUIDORBarcode .put((uuid == null || uuid.isEmpty()) ? shipmentPortionMetaData.getBarcode() : shipmentPortionMetaData.getUuid(), shipmentPortionMetaData); } } } }
From source file:gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.BiospecimenMetaDataProcessor.java
/** * Extracts biospecimen meta-data from a clinical XML file and returns a list of {@link BiospecimenMetaData} * objects. Each object represents a single XML meta-data element. * * @param xmlFile - the XML file to extract biospecimen meta-data from * @param qcContext - qcContext//from ww w. ja va2 s .c o m * @return a list of {@link BiospecimenMetaData} objects, with each object representing a single meta-data element * @throws UUIDException if an error occurs while attempting to generate a UUID for a specific meta-data * element when not provided in the XML * @throws ProcessorException if errors occur while attempting extract meta-data */ protected List<BiospecimenMetaData> handleBiospecimenMetaData(final File xmlFile, final QcContext qcContext) throws UUIDException, ProcessorException { logger.debug("starting handleBiospecimenMetadata"); final Archive archive = qcContext.getArchive(); // Unmarshal the XML file into a JAXB generated object TcgaBcr tcgaBcr; UnmarshalResult unmarshalResult; JAXBIntrospector jaxbIntrospector; try { unmarshalResult = JAXBUtil.unmarshal(xmlFile, TcgaBcr.class, true, false); tcgaBcr = (TcgaBcr) unmarshalResult.getJaxbObject(); jaxbIntrospector = JAXBUtil.getJAXBIntrospector(TcgaBcr.class); logger.debug("JAXB Unmarshalling of BiospecimenMetadata done"); } catch (Exception e) { logger.info(e); throw new ProcessorException(e.getMessage()); } Map<String, BiospecimenMetaData> biospecimenMetaDataByUUIDORBarcode; List<BiospecimenMetaData> biospecimenMetaData = null; if (tcgaBcr != null) { final Patient patient = tcgaBcr.getPatient(); if (patient != null) { biospecimenMetaDataByUUIDORBarcode = new LinkedHashMap<String, BiospecimenMetaData>(); final BiospecimenMetaData patientMetaData = new BiospecimenMetaData(); final String uuid = JAXBUtil.getJAXBObjectValue(patient.getBcrPatientUuid()); patientMetaData.setBarcode(patient.getBcrPatientBarcode().getValue()); setUUID(patientMetaData, uuid, archive); patientMetaData.setUuidType(jaxbIntrospector.getElementName(patient).getLocalPart()); patientMetaData.setBcr(archive.getTheCenter().getCenterId().toString()); patientMetaData.setBatch(archive.getSerialIndex()); patientMetaData.setDisease(archive.getTheTumor().getTumorName()); patientMetaData.setParticipantId(patient.getPatientId().getValue()); patientMetaData.setTissueSourceSite(patient.getTissueSourceSite().getValue()); biospecimenMetaDataByUUIDORBarcode.put( (uuid == null || uuid.isEmpty()) ? patientMetaData.getBarcode() : patientMetaData.getUuid(), patientMetaData); logger.debug("Patient metadata done"); // Get the transform of JAXB object into a list of meta-data entity objects getSampleMetaData(patient, patientMetaData, biospecimenMetaDataByUUIDORBarcode, jaxbIntrospector, archive); logger.debug("Sample metadata done"); getDrugMetaData(patient, patientMetaData, biospecimenMetaDataByUUIDORBarcode, jaxbIntrospector, archive); logger.debug("Drug metadata done"); getRadiationMetaData(patient, patientMetaData, biospecimenMetaDataByUUIDORBarcode, jaxbIntrospector, archive); logger.debug("Radiation metadata done"); getExaminationMetaData(patient, patientMetaData, biospecimenMetaDataByUUIDORBarcode, jaxbIntrospector, archive); logger.debug("Examination metadata done"); getSurgeryMetaData(patient, patientMetaData, biospecimenMetaDataByUUIDORBarcode, jaxbIntrospector, archive); logger.debug("Surgery metadata done"); biospecimenMetaData = new ArrayList<BiospecimenMetaData>( biospecimenMetaDataByUUIDORBarcode.values()); // Persist the meta-data if (!biospecimenMetaDataByUUIDORBarcode.isEmpty()) { // Get the existing meta data from the data base and warn the user if the meta data is changed. final Map<String, BiospecimenMetaData> existingBiospecimenMetaData = uuidHierarchyQueries .getMetaData(new ArrayList<String>(biospecimenMetaDataByUUIDORBarcode.keySet())); logger.debug("Get existing metadata: " + existingBiospecimenMetaData); logger.debug("Persisting metadata starting"); uuidHierarchyQueries.persistUUIDHierarchy(biospecimenMetaData); logger.debug("Persisting metadata done"); final List<BiospecimenMetaData> updatedMetaData = new ArrayList<BiospecimenMetaData>(); // get the updatedMetadata for (final String existingUUIDOrBarcode : existingBiospecimenMetaData.keySet()) { updatedMetaData.add(biospecimenMetaDataByUUIDORBarcode.get(existingUUIDOrBarcode)); } // remove the metadata that are not changed updatedMetaData.removeAll(existingBiospecimenMetaData.values()); if (updatedMetaData.size() > 0) { final StringBuffer warning = new StringBuffer(); for (final BiospecimenMetaData metaData : updatedMetaData) { warning.append("Meta data was updated: "); // get the existing meta data. Key can be either uuid or barcode BiospecimenMetaData existingMetaData = existingBiospecimenMetaData .get(metaData.getUuid()); existingMetaData = (existingMetaData == null) ? existingBiospecimenMetaData.get(metaData.getBarcode()) : existingMetaData; warning.append(existingMetaData.getMetaDataString()).append("-->") .append(metaData.getMetaDataString()); qcContext.addWarning(warning.toString()); warning.delete(0, warning.length()); } } } } processControls(tcgaBcr); } return biospecimenMetaData; }