/**
* {@inheritDoc}
*
* @return
*/
@Override
@Put
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
try {
JaxbObject<Sample> jo = new JaxbObject<>();
String text = entity.getText();
Sample o = null;
try {
o = (Sample) XmlTools.unMarshal(jo, new Sample(), text);
} catch (SAXException ex) {
throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY, ex);
}
SampleService service = BeanFactory.getSampleServiceBean();
Sample sample = testIfNull(service.findByID(o.getSampleId()));
sample.givesPermission(registration);
String anonymizedName = o.getAnonymizedName();
String individualName = o.getIndividualName();
Integer swAccession = o.getSwAccession();
String name = o.getName();
String title = o.getTitle();
String alias = o.getAlias();
String description = o.getDescription();
String type = o.getType();
String tags = o.getTags();
String adapters = o.getAdapters();
String regions = o.getRegions();
Integer expectedNumRuns = o.getExpectedNumRuns();
Integer expectedNumSpots = o.getExpectedNumSpots();
Integer expectedNumReads = o.getExpectedNumReads();
Boolean skip = o.getSkip();
Boolean isSelected = o.getIsSelected();
Boolean isHasFile = o.getIsHasFile();
Integer countFile = o.getCountFile();
if (null != anonymizedName) sample.setAnonymizedName(anonymizedName);
if (null != individualName) sample.setIndividualName(individualName);
if (null != swAccession) sample.setSwAccession(swAccession);
if (null != name) sample.setName(name);
if (null != title) sample.setTitle(title);
if (null != alias) sample.setAlias(alias);
if (null != description) sample.setDescription(description);
if (null != type) sample.setType(type);
if (null != tags) sample.setTags(tags);
if (null != adapters) sample.setAdapters(adapters);
if (null != regions) sample.setRegions(regions);
if (null != expectedNumRuns) sample.setExpectedNumRuns(expectedNumRuns);
if (null != expectedNumSpots) sample.setExpectedNumSpots(expectedNumSpots);
if (null != expectedNumReads) sample.setExpectedNumReads(expectedNumReads);
if (null != skip) sample.setSkip(skip);
if (null != isSelected) sample.setIsSelected(isSelected);
if (null != isHasFile) sample.setIsHasFile(isHasFile);
if (null != countFile) sample.setCountFile(countFile);
if (null != o.getSampleAttributes()) {
// SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
SampleIDResource.mergeAttributes(
sample.getSampleAttributes(), o.getSampleAttributes(), sample);
}
if (null != o.getParents()) {
SampleService ss = BeanFactory.getSampleServiceBean();
Set<Sample> parents = new HashSet<>(sample.getParents());
for (Sample s : o.getParents()) {
parents.add(ss.findByID(s.getSampleId()));
}
sample.setParents(parents);
}
if (null != o.getChildren()) {
SampleService ss = BeanFactory.getSampleServiceBean();
Set<Sample> children = new HashSet<>(sample.getChildren());
for (Sample s : o.getChildren()) {
children.add(ss.findByID(s.getSampleId()));
}
sample.setChildren(children);
}
service.update(sample);
// persist object
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Sample detachedSample = copier.hibernate2dto(Sample.class, sample);
Document line = XmlTools.marshalToDocument(jo, detachedSample);
getResponse().setEntity(XmlTools.getRepresentation(line));
getResponse()
.setLocationRef(
getRequest().getRootRef() + "/samples/" + detachedSample.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e);
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e);
}
return representation;
}
