/**
* asDto.
*
* @param sample a {@link net.sourceforge.seqware.common.model.Sample} object.
* @return a {@link net.sourceforge.seqware.webservice.dto.LibraryDto} object.
*/
public static LibraryDto asDto(Sample sample) {
DateTimeFormatter dateTimeFormatter = ISODateTimeFormat.dateTimeNoMillis();
LibraryDto dto = new LibraryDto();
dto.setName(sample.getName());
dto.setDescription(sample.getDescription());
dto.setCreateTimeStamp(dateTimeFormatter.print(sample.getCreateTimestamp().getTime()));
dto.setUpdateTimeStamp(dateTimeFormatter.print(sample.getUpdateTimestamp().getTime()));
dto.setOwner(Dtos.asDto(sample.getOwner()));
dto.setOrganism(Dtos.atDto(sample.getOrganism()));
return dto;
}
/** getXml. */
@Get
public void getXml() {
authenticate();
JaxbObject<Lane> jaxbTool = new JaxbObject<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
SampleService ss = BeanFactory.getSampleServiceBean();
Sample sample = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<Sample>[] createCollectionPropertyNames =
CollectionPropertyName.createCollectionPropertyNames(
Sample.class, new String[] {"sampleAttributes"});
Sample dto =
copier.hibernate2dto(
Sample.class, sample, new Class<?>[] {}, createCollectionPropertyNames);
if (fields.contains("lanes")) {
SortedSet<Lane> lanes = sample.getLanes();
if (lanes != null) {
SortedSet<Lane> copiedLanes = new TreeSet<>();
for (Lane lane : lanes) {
copiedLanes.add(copier.hibernate2dto(Lane.class, lane));
}
dto.setLanes(copiedLanes);
} else {
Log.info("Could not be found: lanes");
}
}
if (fields.contains("ius")) {
SortedSet<IUS> ius = sample.getIUS();
if (ius != null) {
SortedSet<IUS> copiedIUS = new TreeSet<>();
for (IUS i : ius) {
copiedIUS.add(copier.hibernate2dto(IUS.class, i));
}
dto.setIUS(copiedIUS);
}
{
Log.info("Could not be found : ius");
}
}
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;
}
/**
* {@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;
}