/** getXml. */
@Get
public void getXml() {
JaxbObject<Lane> jaxbTool = new JaxbObject<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Lane dto;
authenticate();
LaneService ss = BeanFactory.getLaneServiceBean();
Lane lane = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<Lane>[] createCollectionPropertyNames =
CollectionPropertyName.createCollectionPropertyNames(
Lane.class, new String[] {"laneAttributes"});
dto =
copier.hibernate2dto(
Lane.class,
lane,
new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
createCollectionPropertyNames);
if (fields.contains("sequencerRun")) {
SequencerRun sr = lane.getSequencerRun();
if (sr != null) {
SequencerRun copySR = copier.hibernate2dto(SequencerRun.class, sr);
dto.setSequencerRun(copySR);
} else {
Log.info("Could not be found sequencer run");
}
}
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
@Put
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
Lane newLane = null;
JaxbObject<Lane> jo = new JaxbObject<>();
try {
String text = entity.getText();
newLane = (Lane) XmlTools.unMarshal(jo, new Lane(), text);
} catch (SAXException | IOException ex) {
ex.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
}
try {
LaneService fs = BeanFactory.getLaneServiceBean();
Lane lane = testIfNull(fs.findByID(newLane.getLaneId()));
lane.givesPermission(registration);
// simple types
String name = newLane.getName();
String desc = newLane.getDescription();
Integer laneIndex = newLane.getLaneIndex();
String cycleDescriptor = newLane.getCycleDescriptor();
Boolean skip = newLane.getSkip();
String tags = newLane.getTags();
String regions = newLane.getRegions();
// foreign keys
Sample sample = newLane.getSample();
Registration owner = newLane.getOwner();
Set<LaneAttribute> newAttributes = newLane.getLaneAttributes();
if (name != null) {
lane.setName(name);
}
if (desc != null) {
lane.setDescription(desc);
}
if (laneIndex != null) {
lane.setLaneIndex(laneIndex);
}
if (cycleDescriptor != null) {
lane.setCycleDescriptor(cycleDescriptor);
}
if (skip != null) {
lane.setSkip(skip);
}
if (tags != null) {
lane.setTags(tags);
}
if (regions != null) {
lane.setRegions(regions);
}
if (sample != null) {
SampleService ss = BeanFactory.getSampleServiceBean();
Sample newSample = ss.findByID(sample.getSampleId());
if (newSample != null && newSample.givesPermission(registration)) {
lane.setSample(newSample);
} else if (newSample == null) {
Log.info("Could not be found " + sample);
}
}
if (owner != null) {
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
if (newReg != null) {
lane.setOwner(newReg);
} else {
Log.info("Could not be found " + owner);
}
} else if (lane.getOwner() == null) {
lane.setOwner(registration);
}
if (newAttributes != null) {
// SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
LaneIDResource.mergeAttributes(lane.getLaneAttributes(), newAttributes, lane);
}
fs.update(registration, lane);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Lane detachedLane =
copier.hibernate2dto(
Lane.class,
lane,
new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
new CollectionPropertyName<?>[] {});
Document line = XmlTools.marshalToDocument(jo, detachedLane);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse()
.setLocationRef(getRequest().getRootRef() + "/lanes/" + 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;
}
