/** getXml. */
@Get
public void getXml() {
authenticate();
WorkflowService ss = BeanFactory.getWorkflowServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Workflow> jaxbTool = new JaxbObject<Workflow>();
Workflow workflow = (Workflow) testIfNull(ss.findBySWAccession(Integer.parseInt(getId())));
Workflow dto = copier.hibernate2dto(Workflow.class, workflow);
if (fields.contains("params")) {
SortedSet<WorkflowParam> wps = workflow.getWorkflowParams();
if (wps != null) {
SortedSet<WorkflowParam> copiedParams = new TreeSet<WorkflowParam>();
for (WorkflowParam param : workflow.getWorkflowParams()) {
copiedParams.add(copier.hibernate2dto(WorkflowParam.class, param));
}
dto.setWorkflowParams(copiedParams);
} else {
Log.info("Could not be found: workflow params");
}
}
if (fields.contains("attributes")) {
Set<WorkflowAttribute> was = workflow.getWorkflowAttributes();
if (was != null && !was.isEmpty()) {
Set<WorkflowAttribute> newwas = new TreeSet<WorkflowAttribute>();
for (WorkflowAttribute wa : was) {
newwas.add(copier.hibernate2dto(WorkflowAttribute.class, wa));
}
dto.setWorkflowAttributes(newwas);
}
}
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
/** 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));
}
/** 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));
}
/** 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}
*
* @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} */
@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;
}
/** {@inheritDoc} */
@Override
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
Workflow newWorkflow = null;
JaxbObject<Workflow> jo = new JaxbObject<Workflow>();
try {
String text = entity.getText();
newWorkflow = (Workflow) XmlTools.unMarshal(jo, new Workflow(), text);
} catch (SAXException ex) {
ex.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex.getMessage());
} catch (IOException e) {
e.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage());
}
try {
WorkflowService fs = BeanFactory.getWorkflowServiceBean();
Workflow workflow = (Workflow) testIfNull(fs.findByID(newWorkflow.getWorkflowId()));
workflow.givesPermission(registration);
// simple types
String name = newWorkflow.getName();
String desc = newWorkflow.getDescription();
String baseIniFile = newWorkflow.getBaseIniFile();
String command = newWorkflow.getCommand();
String cwd = newWorkflow.getCwd();
String host = newWorkflow.getHost();
String inputAlgorithm = newWorkflow.getInputAlgorithm();
String permanentBundleLocation = newWorkflow.getPermanentBundleLocation();
String seqwareVersion = newWorkflow.getSeqwareVersion();
String template = newWorkflow.getTemplate();
String username = newWorkflow.getUsername();
String version = newWorkflow.getVersion();
// foreign keys
Registration owner = newWorkflow.getOwner();
workflow.setName(name);
workflow.setDescription(desc);
workflow.setBaseIniFile(baseIniFile);
workflow.setCommand(command);
workflow.setCwd(cwd);
workflow.setHost(host);
workflow.setInputAlgorithm(inputAlgorithm);
workflow.setPermanentBundleLocation(permanentBundleLocation);
workflow.setSeqwareVersion(seqwareVersion);
workflow.setTemplate(template);
workflow.setUsername(username);
workflow.setVersion(version);
workflow.setUpdateTimestamp(new Date());
workflow.setWorkflowClass(newWorkflow.getWorkflowClass());
workflow.setWorkflowType(newWorkflow.getWorkflowType());
workflow.setWorkflowEngine(newWorkflow.getWorkflowEngine());
if (owner != null) {
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
if (newReg != null) {
workflow.setOwner(newReg);
} else {
Log.info("Could not be found: " + owner);
}
} else if (workflow.getOwner() == null) {
workflow.setOwner(registration);
}
if (newWorkflow.getWorkflowAttributes() != null) {
workflow.getWorkflowAttributes().clear();
for (WorkflowAttribute wfa : newWorkflow.getWorkflowAttributes()) {
wfa.setWorkflow(workflow);
workflow.getWorkflowAttributes().add(wfa);
}
}
fs.update(registration, workflow);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Workflow detachedWorkflow = copier.hibernate2dto(Workflow.class, workflow);
Document line = XmlTools.marshalToDocument(jo, detachedWorkflow);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse()
.setLocationRef(
getRequest().getRootRef() + "/workflows/" + detachedWorkflow.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;
}