/** 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;
}
