/**
* asDto.
*
* @param from a {@link net.sourceforge.seqware.common.model.Registration} object.
* @return a {@link net.sourceforge.seqware.webservice.dto.OwnerDto} object.
*/
public static OwnerDto asDto(Registration from) {
OwnerDto dto = new OwnerDto();
dto.setEmail(from.getEmailAddress());
dto.setFirstName(from.getFirstName());
dto.setLastName(from.getLastName());
dto.setInstitution(from.getInstitution());
return dto;
}
/**
* {@inheritDoc}
*
* @return
* @throws java.lang.Exception
*/
@Override
protected ModelAndView handleRequestInternal(
HttpServletRequest request, HttpServletResponse response) throws Exception {
Registration registration = Security.getRegistration(request);
if (registration == null) return new ModelAndView("redirect:/login.htm");
WorkflowRun workflowRun = getRequestedWorkflowRun(request);
if (workflowRun != null) {
Integer ownerId = workflowRun.getOwner().getRegistrationId();
Integer registrationId = registration.getRegistrationId();
if (registrationId.equals(ownerId)) {
if (workflowRun.getStatus() != WorkflowRunStatus.completed) {
workflowRun.setStatus(WorkflowRunStatus.cancelled);
getWorkflowRunService().update(workflowRun);
}
}
}
return null;
}
/**
* {@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;
}