/** getXml. */ @Get public void getXml() { ExperimentService ss = BeanFactory.getExperimentServiceBean(); Experiment experiment = (Experiment) testIfNull(ss.findBySWAccession(Integer.parseInt(getId()))); Hibernate3DtoCopier copier = new Hibernate3DtoCopier(); JaxbObject<Experiment> jaxbTool = new JaxbObject<Experiment>(); Experiment dto = copier.hibernate2dto(Experiment.class, experiment); if (fields.contains("attributes")) { Set<ExperimentAttribute> eas = experiment.getExperimentAttributes(); if (eas != null && !eas.isEmpty()) { Set<ExperimentAttribute> newEas = new TreeSet<ExperimentAttribute>(); for (ExperimentAttribute ea : eas) { newEas.add(copier.hibernate2dto(ExperimentAttribute.class, ea)); } dto.setExperimentAttributes(newEas); } } Document line = XmlTools.marshalToDocument(jaxbTool, dto); getResponse().setEntity(XmlTools.getRepresentation(line)); }
/** {@inheritDoc} */ @Override @Put public Representation put(Representation entity) { authenticate(); Representation representation = null; Experiment newObj = null; JaxbObject<Experiment> jo = new JaxbObject<Experiment>(); try { String text = entity.getText(); newObj = (Experiment) XmlTools.unMarshal(jo, new Experiment(), text); } catch (SAXException ex) { ex.printStackTrace(); throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex); } catch (IOException e) { e.printStackTrace(); throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e); } try { ExperimentService service = BeanFactory.getExperimentServiceBean(); Experiment exp = (Experiment) testIfNull(service.findByID(newObj.getExperimentId())); exp.givesPermission(registration); // simple types String title = newObj.getTitle(); String name = newObj.getName(); String desc = newObj.getDescription(); String alias = newObj.getAlias(); String accession = newObj.getAccession(); String status = newObj.getStatus(); String centerName = newObj.getCenterName(); String sequencerSpace = newObj.getSequenceSpace(); String baseCaller = newObj.getBaseCaller(); String qualityScorer = newObj.getQualityScorer(); Integer qualityNumberLevels = newObj.getQualityNumberOfLevels(); Integer qualityMultiplier = newObj.getQualityMultiplier(); Long expectedNumberSpots = newObj.getExpectedNumberSpots(); Long expectedNumberReads = newObj.getExpectedNumberReads(); // foreign keys Study study = newObj.getStudy(); Registration owner = newObj.getOwner(); // sets Set<ExperimentAttribute> expAttributes = newObj.getExperimentAttributes(); if (title != null) { exp.setTitle(title); } if (name != null) { exp.setName(name); } if (desc != null) { exp.setDescription(desc); } if (alias != null) { exp.setAlias(alias); } if (accession != null) { exp.setAccession(accession); } if (status != null) { exp.setStatus(status); } if (centerName != null) { exp.setCenterName(centerName); } if (sequencerSpace != null) { exp.setSequenceSpace(sequencerSpace); } if (baseCaller != null) { exp.setBaseCaller(baseCaller); } if (qualityScorer != null) { exp.setQualityScorer(qualityScorer); } if (qualityNumberLevels != null) { exp.setQualityNumberOfLevels(qualityNumberLevels); } if (qualityMultiplier != null) { exp.setQualityMultiplier(qualityMultiplier); } if (expectedNumberSpots != null) { exp.setExpectedNumberSpots(expectedNumberSpots); } if (expectedNumberReads != null) { exp.setExpectedNumberReads(expectedNumberReads); } if (study != null) { StudyService ss = BeanFactory.getStudyServiceBean(); Study newStudy = ss.findByID(study.getStudyId()); if (newStudy != null && newStudy.givesPermission(registration)) { exp.setStudy(newStudy); } else if (newStudy == null) { Log.info("Could not be found " + study); } } if (owner != null) { RegistrationService rs = BeanFactory.getRegistrationServiceBean(); Registration newReg = rs.findByEmailAddress(owner.getEmailAddress()); if (newReg != null) { exp.setOwner(newReg); } else { Log.info("Could not be found " + owner); } } else if (exp.getOwner() == null) { exp.setOwner(registration); } if (null != expAttributes) { exp.getExperimentAttributes().clear(); for (ExperimentAttribute ea : expAttributes) { ea.setExperiment(exp); exp.getExperimentAttributes().add(ea); } } service.update(registration, exp); Hibernate3DtoCopier copier = new Hibernate3DtoCopier(); Experiment detachedLane = copier.hibernate2dto(Experiment.class, exp); Document line = XmlTools.marshalToDocument(jo, detachedLane); representation = XmlTools.getRepresentation(line); getResponse().setEntity(representation); getResponse() .setLocationRef( getRequest().getRootRef() + "/experiments/" + detachedLane.getSwAccession()); getResponse().setStatus(Status.SUCCESS_CREATED); } catch (SecurityException e) { getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage()); } catch (Exception e) { e.printStackTrace(); getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage()); } return representation; }