Here are the examples of the java api net.sf.beanlib.hibernate3.Hibernate3DtoCopier.hibernate2dto() taken from open source projects. By voting up you can indicate which examples are most useful and appropriate.
67 Examples
19
View Complete Implementation : WorkflowRunIdFilesResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* hello.
* </p>
*
* @param wrSWA
* a int.
* @return a {@link java.util.List} object.
* @throws java.sql.SQLException
* if any.
*/
public List<File> hello(int wrSWA) throws SQLException {
WorkflowRunService wrs = BeanFactory.getWorkflowRunServiceBean();
List<File> files = (List<File>) testIfNull(wrs.findFiles(wrSWA));
List<File> dtoFiles = new ArrayList<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
for (File file : files) {
dtoFiles.add(copier.hibernate2dto(File.clreplaced, file));
}
return dtoFiles;
}
16
View Complete Implementation : LibrarySourceResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
LibrarySourceService ss = BeanFactory.getLibrarySourceServiceBean();
logger.debug("registration: " + registration);
List<LibrarySource> objects = (List<LibrarySource>) testIfNull(ss.list());
logger.debug("library_sources: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<LibrarySourceList> jaxbTool = new JaxbObject<>();
LibrarySourceList list = new LibrarySourceList();
list.setList(new ArrayList());
for (LibrarySource obj : objects) {
LibrarySource dto = copier.hibernate2dto(LibrarySource.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
16
View Complete Implementation : PlatformResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
PlatformService ss = BeanFactory.getPlatformServiceBean();
logger.debug("registration: " + registration);
List<Platform> objects = (List<Platform>) testIfNull(ss.list());
logger.debug("platforms: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<PlatformList> jaxbTool = new JaxbObject<>();
PlatformList list = new PlatformList();
list.setList(new ArrayList());
for (Platform obj : objects) {
Platform dto = copier.hibernate2dto(Platform.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
16
View Complete Implementation : ExperimentSpotDesignResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
ExperimentSpotDesignService ss = BeanFactory.getExperimentSpotDesignServiceBean();
logger.debug("registration: " + registration);
List<ExperimentSpotDesign> objects = (List<ExperimentSpotDesign>) testIfNull(ss.list());
logger.debug("experiment spot designs: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<ExperimentSpotDesignList> jaxbTool = new JaxbObject<>();
ExperimentSpotDesignList list = new ExperimentSpotDesignList();
list.setList(new ArrayList());
for (ExperimentSpotDesign obj : objects) {
ExperimentSpotDesign dto = copier.hibernate2dto(ExperimentSpotDesign.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
15
View Complete Implementation : WorkflowRunIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* {@inheritDoc}
*
* @return
*/
@Override
public Representation put(Representation enreplacedy) {
Representation toreturn = null;
if (enreplacedy.getMediaType().equals(MediaType.APPLICATION_XML)) {
WorkflowRun newWR = null;
JaxbObject<WorkflowRun> jo = new JaxbObject<>();
try {
String text = enreplacedy.getText();
Log.debug(text);
newWR = (WorkflowRun) XmlTools.unMarshal(jo, new WorkflowRun(), text);
} catch (SAXException | IOException ex) {
Log.fatal(ex, ex);
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
}
try {
WorkflowRun wr = updateWorkflowRun(newWR);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, copier.hibernate2dto(wr));
toreturn = XmlTools.getRepresentation(line);
getResponse().setEnreplacedy(toreturn);
getResponse().setLocationRef(getRequest().getRootRef() + "/workflowruns/" + newWR.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e);
} catch (SQLException ex) {
Log.fatal(ex, ex);
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
} catch (Exception e) {
Log.error(e, e);
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e);
} finally {
try {
enreplacedy.exhaust();
} catch (IOException ex) {
Log.fatal(ex, ex);
throw new ResourceException(Status.SERVER_ERROR_INTERNAL, ex);
}
enreplacedy.release();
DBAccess.close();
}
} else {
throw new ResourceException(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE);
}
return toreturn;
}
15
View Complete Implementation : LibrarySelectionResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
LibrarySelectionService ss = BeanFactory.getLibrarySelectionServiceBean();
logger.debug("registration: " + registration);
List<LibrarySelection> objects = (List<LibrarySelection>) testIfNull(ss.list());
logger.debug("library_selections: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<LibrarySelectionList> jaxbTool = new JaxbObject<>();
LibrarySelectionList list = new LibrarySelectionList();
list.setList(new ArrayList());
for (LibrarySelection obj : objects) {
LibrarySelection dto = copier.hibernate2dto(LibrarySelection.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
15
View Complete Implementation : ExperimentSpotDesignReadSpecResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
ExperimentSpotDesignReadSpecService ss = BeanFactory.getExperimentSpotDesignReadSpecServiceBean();
logger.debug("registration: " + registration);
List<ExperimentSpotDesignReadSpec> objects = (List<ExperimentSpotDesignReadSpec>) testIfNull(ss.list());
logger.debug("experiment spot design read specs: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<ExperimentSpotDesignReadSpecList> jaxbTool = new JaxbObject<>();
ExperimentSpotDesignReadSpecList list = new ExperimentSpotDesignReadSpecList();
list.setList(new ArrayList());
for (ExperimentSpotDesignReadSpec obj : objects) {
ExperimentSpotDesignReadSpec dto = copier.hibernate2dto(ExperimentSpotDesignReadSpec.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
15
View Complete Implementation : WorkflowParamValueResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
WorkflowParamValueService ss = BeanFactory.getWorkflowParamValueServiceBean();
Doreplacedent line;
if (queryValues.get("id") != null) {
WorkflowParamValue wp = ((WorkflowParamValue) testIfNull(ss.findByID(parseClientInt(queryValues.get("id")))));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<WorkflowParamValue> jaxbTool = new JaxbObject<>();
WorkflowParamValue dto = copier.hibernate2dto(WorkflowParamValue.clreplaced, wp);
line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
} else {
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<WorkflowParamValueList> jaxbTool = new JaxbObject<>();
WorkflowParamValueList list = new WorkflowParamValueList();
List<WorkflowParamValue> wpvs = (List<WorkflowParamValue>) testIfNull(ss.list());
for (WorkflowParamValue wpv : wpvs) {
list.add(copier.hibernate2dto(WorkflowParamValue.clreplaced, wpv));
}
line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
}
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
14
View Complete Implementation : OrganismResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
OrganismService ss = BeanFactory.getOrganismServiceBean();
logger.debug("registration: " + registration);
List<Organism> objects = (List<Organism>) testIfNull(ss.list());
logger.debug("organisms: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<OrganismList> jaxbTool = new JaxbObject<>();
OrganismList list = new OrganismList();
list.setList(new ArrayList());
for (Organism obj : objects) {
Organism dto = copier.hibernate2dto(Organism.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
14
View Complete Implementation : WorkflowResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
private Doreplacedent detachWorkflow(Workflow workflow) {
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Workflow> jaxbTool = new JaxbObject<>();
Workflow dto = copier.hibernate2dto(Workflow.clreplaced, workflow);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
return line;
}
13
View Complete Implementation : ExperimentIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
ExperimentService ss = BeanFactory.getExperimentServiceBean();
Experiment experiment = testIfNull(ss.findBySWAccession(getId()));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Experiment> jaxbTool = new JaxbObject<>();
CollectionPropertyName<Experiment>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(Experiment.clreplaced, new String[] { "experimentAttributes" });
Experiment dto = copier.hibernate2dto(Experiment.clreplaced, experiment, new Clreplaced<?>[] { ExperimentSpotDesign.clreplaced, ExperimentLibraryDesign.clreplaced, ExperimentAttribute.clreplaced }, createCollectionPropertyNames);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
13
View Complete Implementation : ExperimentLibraryDesignResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
ExperimentLibraryDesignService ss = BeanFactory.getExperimentLibraryDesignServiceBean();
logger.debug("registration: " + registration);
List<ExperimentLibraryDesign> objects = (List<ExperimentLibraryDesign>) testIfNull(ss.list());
logger.debug("experiment library designs: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<ExperimentLibraryDesignList> jaxbTool = new JaxbObject<>();
ExperimentLibraryDesignList list = new ExperimentLibraryDesignList();
list.setList(new ArrayList());
for (ExperimentLibraryDesign obj : objects) {
ExperimentLibraryDesign dto = copier.hibernate2dto(ExperimentLibraryDesign.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
13
View Complete Implementation : LibraryStrategyResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
LibraryStrategyService ss = BeanFactory.getLibraryStrategyServiceBean();
logger.debug("registration: " + registration);
List<LibraryStrategy> objects = (List<LibraryStrategy>) testIfNull(ss.list());
logger.debug("library_strategies: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<LibraryStrategyList> jaxbTool = new JaxbObject<>();
LibraryStrategyList list = new LibraryStrategyList();
list.setList(new ArrayList());
for (LibraryStrategy obj : objects) {
LibraryStrategy dto = copier.hibernate2dto(LibraryStrategy.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
13
View Complete Implementation : StudyTypeResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
StudyTypeService ss = BeanFactory.getStudyTypeServiceBean();
logger.debug("registration: " + registration);
List<StudyType> objects = (List<StudyType>) testIfNull(ss.list());
logger.debug("study_types: " + objects.size() + " " + objects);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<StudyTypeList> jaxbTool = new JaxbObject<>();
StudyTypeList list = new StudyTypeList();
list.setList(new ArrayList());
for (StudyType obj : objects) {
StudyType dto = copier.hibernate2dto(StudyType.clreplaced, obj);
list.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
12
View Complete Implementation : RootSampleResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject jaxbTool;
for (String key : queryValues.keySet()) {
Log.debug("key: " + key + " -> " + queryValues.get(key));
}
SampleService ss = BeanFactory.getSampleServiceBean();
jaxbTool = new JaxbObject<>();
List<Sample> samples = (List<Sample>) testIfNull(ss.list());
SampleList eList = new SampleList();
eList.setList(new ArrayList());
for (Sample sample : samples) {
if (sample.getParents().isEmpty()) {
Sample dto = copier.hibernate2dto(Sample.clreplaced, sample);
eList.add(dto);
}
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
12
View Complete Implementation : WorkflowRunIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<WorkflowRun> jaxbTool = new JaxbObject<>();
WorkflowRunService ss = BeanFactory.getWorkflowRunServiceBean();
WorkflowRun workflowRun = getWorkflowRun(ss);
// specify that we want the input file set to be copied along, if this works, we should clean up the manual copying below
CollectionPropertyName<WorkflowRun>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(WorkflowRun.clreplaced, new String[] { "inputFileAccessions", "workflowRunAttributes" });
WorkflowRun dto = copier.hibernate2dto(WorkflowRun.clreplaced, workflowRun, ArrayUtils.EMPTY_CLreplaced_ARRAY, createCollectionPropertyNames);
// Log.debug("getXML() Workflow run contains " + workflowRun.getInputFileAccessions().size() + " input files");
// dto.setInputFileAccessions(workflowRun.getInputFileAccessions());
if (fields.contains("lanes")) {
SortedSet<Lane> lanes = workflowRun.getLanes();
if (lanes != null) {
SortedSet<Lane> copiedLanes = new TreeSet<>();
for (Lane lane : lanes) {
copiedLanes.add(copier.hibernate2dto(Lane.clreplaced, lane));
}
dto.setLanes(copiedLanes);
} else {
Log.info("Could not be found: lanes");
}
}
if (fields.contains("ius")) {
SortedSet<IUS> iuses = workflowRun.getIus();
if (iuses != null) {
SortedSet<IUS> copiedIUS = new TreeSet<>();
for (IUS i : iuses) {
copiedIUS.add(copier.hibernate2dto(IUS.clreplaced, i));
}
dto.setIus(copiedIUS);
} else {
Log.info("Could not be found: ius");
}
}
if (fields.contains("processes")) {
SortedSet<Processing> procs = workflowRun.getProcessings();
if (procs != null) {
SortedSet<Processing> copiedPs = new TreeSet<>();
for (Processing p : procs) {
copiedPs.add(copier.hibernate2dto(Processing.clreplaced, p));
}
dto.setProcessings(copiedPs);
} else {
Log.info("Could not be found: processings");
}
procs = workflowRun.getOffspringProcessings();
if (procs != null) {
SortedSet<Processing> copiedPs = new TreeSet<>();
for (Processing p : procs) {
copiedPs.add(copier.hibernate2dto(Processing.clreplaced, p));
}
dto.setOffspringProcessings(copiedPs);
} else {
Log.info("Could not be found: offspring processings");
}
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
12
View Complete Implementation : WorkflowRunIDWorkflowResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* {@inheritDoc}
*/
@Override
public void handle(Request request, Response response) {
authenticate(request.getChallengeResponse().getIdentifier());
String id = request.getAttributes().get("workflowRunId").toString();
WorkflowRunService wrs = BeanFactory.getWorkflowRunServiceBean();
WorkflowRun run = (WorkflowRun) testIfNull(wrs.findBySWAccession(parseClientInt(id)));
Workflow w = run.getWorkflow();
JaxbObject<Workflow> jaxbTool = new JaxbObject<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Workflow wdto = copier.hibernate2dto(Workflow.clreplaced, w);
Doreplacedent doc = XmlTools.marshalToDoreplacedent(jaxbTool, wdto);
response.setEnreplacedy(XmlTools.getRepresentation(doc));
}
11
View Complete Implementation : FileIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
FileService ss = BeanFactory.getFileServiceBean();
File file = testIfNull(ss.findBySWAccession(getId()));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<File> jaxbTool = new JaxbObject<>();
CollectionPropertyName<File>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(File.clreplaced, new String[] { "fileAttributes" });
File dto = copier.hibernate2dto(File.clreplaced, file, new Clreplaced<?>[] {}, createCollectionPropertyNames);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
11
View Complete Implementation : IusResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*
* @throws java.io.IOException
* if any.
*/
@Get
public void getXml() throws IOException {
authenticate();
IUSService ss = BeanFactory.getIUSServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Doreplacedent line;
if (queryValues.get("id") != null) {
IUS p = (IUS) testIfNull(ss.findByID(parseClientInt(queryValues.get("id"))));
JaxbObject<IUS> jaxbTool = new JaxbObject<>();
IUS dto = copier.hibernate2dto(IUS.clreplaced, p);
line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
} else {
JaxbObject<IUSList> jaxbTool = new JaxbObject<>();
IUSList list = new IUSList();
List<IUS> iuses = (List<IUS>) testIfNull(ss.list());
for (IUS i : iuses) {
list.add(copier.hibernate2dto(IUS.clreplaced, i));
}
line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
}
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
11
View Complete Implementation : LaneIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@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.clreplaced, new String[] { "laneAttributes" });
dto = copier.hibernate2dto(Lane.clreplaced, lane, new Clreplaced<?>[] { LibraryStrategy.clreplaced, LibrarySource.clreplaced, LibrarySelection.clreplaced }, createCollectionPropertyNames);
if (fields.contains("sequencerRun")) {
SequencerRun sr = lane.getSequencerRun();
if (sr != null) {
SequencerRun copySR = copier.hibernate2dto(SequencerRun.clreplaced, sr);
dto.setSequencerRun(copySR);
} else {
Log.info("Could not be found sequencer run");
}
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
11
View Complete Implementation : LaneResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*
* @throws java.io.IOException
* if any.
*/
@Get
public void getXml() throws IOException {
authenticate();
LaneService ss = BeanFactory.getLaneServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Doreplacedent line;
if (queryValues.get("id") != null) {
JaxbObject<Lane> jaxbTool = new JaxbObject<>();
Lane p = (Lane) testIfNull(ss.findByID(parseClientInt(queryValues.get("id"))));
Lane dto = copier.hibernate2dto(Lane.clreplaced, p);
line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
} else {
JaxbObject<LaneList> jaxbTool = new JaxbObject<>();
LaneList list = new LaneList();
List<Lane> lanes = (List<Lane>) testIfNull(ss.list());
for (Lane l : lanes) {
list.add(copier.hibernate2dto(Lane.clreplaced, l));
}
line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
}
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
11
View Complete Implementation : SampleIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@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.clreplaced, new String[] { "sampleAttributes" });
Sample dto = copier.hibernate2dto(Sample.clreplaced, sample, new Clreplaced<?>[] {}, 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.clreplaced, 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.clreplaced, i));
}
dto.setIUS(copiedIUS);
}
{
Log.info("Could not be found : ius");
}
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
11
View Complete Implementation : StudyIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
StudyService ss = BeanFactory.getStudyServiceBean();
Study study = testIfNull(ss.findBySWAccession(getId()));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Study> jaxbTool = new JaxbObject<>();
CollectionPropertyName<Study>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(Study.clreplaced, new String[] { "studyAttributes" });
Study dto = copier.hibernate2dto(Study.clreplaced, study, new Clreplaced<?>[] {}, createCollectionPropertyNames);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
11
View Complete Implementation : WorkflowResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
private Doreplacedent detachWorkflowList(List<Workflow> workflows) {
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<WorkflowList> jaxbTool = new JaxbObject<>();
WorkflowList eList = new WorkflowList();
eList.setList(new ArrayList());
for (Workflow workflow : workflows) {
Workflow dto = copier.hibernate2dto(Workflow.clreplaced, workflow);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
return line;
}
10
View Complete Implementation : ExperimentIDFilter.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
// String path = getRequest().getResourceRef().getPath();getAttribute();
Collection<Experiment> experiments = null;
Map<String, Object> requestAttributes = getRequestAttributes();
if (requestAttributes.containsKey("studyId")) {
Object val = requestAttributes.get("studyId");
if (val != null) {
StudyService ss = BeanFactory.getStudyServiceBean();
Study s = (Study) testIfNull(ss.findBySWAccession(parseClientInt(val.toString())));
experiments = (SortedSet<Experiment>) testIfNull(s.getExperiments());
}
} else {
StringBuilder sb = new StringBuilder();
for (String key : requestAttributes.keySet()) {
sb.append(key);
}
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "This resource cannot handle these data types: " + sb.toString());
}
if (experiments.isEmpty()) {
throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "There are no experiments for this resource");
}
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<ExperimentList> jaxbTool = new JaxbObject<>();
ExperimentList eList = new ExperimentList();
eList.setList(new ArrayList());
for (Experiment experiment : experiments) {
Experiment dto = copier.hibernate2dto(Experiment.clreplaced, experiment);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
10
View Complete Implementation : FileChildWorkflowRunsResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
protected WorkflowRunList2 handleWorkflowRunsViaChild(final Set<File> files, final Hibernate3DtoCopier copier) {
final WorkflowRunList2 results = new WorkflowRunList2();
for (File file : files) {
// 1) check if we have children in the processing tree that are relevant
for (Processing p : file.getProcessings()) {
for (Processing c : p.getChildren()) {
if (c.getWorkflowRun() == null) {
continue;
}
WorkflowRun dto = copier.hibernate2dto(WorkflowRun.clreplaced, c.getWorkflowRun());
results.add(dto);
}
}
}
if (results.getList().size() > 0) {
Log.debug("Found " + results.getList().size() + " workflow runs via Processing children");
} else {
Log.debug("Did not find any workflow runs via Processing children");
}
return results;
}
10
View Complete Implementation : ProcessIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
JaxbObject<Lane> jaxbTool = new JaxbObject<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
authenticate();
ProcessingService ss = BeanFactory.getProcessingServiceBean();
Processing processing = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<Processing>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(Processing.clreplaced, new String[] { "processingAttributes" });
Processing dto = copier.hibernate2dto(Processing.clreplaced, processing, new Clreplaced<?>[] {}, createCollectionPropertyNames);
if (fields.contains("workflowRun")) {
WorkflowRun wr = processing.getWorkflowRun();
if (wr != null) {
WorkflowRun copyWR = copier.hibernate2dto(WorkflowRun.clreplaced, wr);
dto.setWorkflowRun(copyWR);
} else {
Log.info("Could not be found : workflow run");
}
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : IusIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
IUSService ss = BeanFactory.getIUSServiceBean();
IUS ius = testIfNull(ss.findBySWAccession(getId()));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<IUS> jaxbTool = new JaxbObject<>();
CollectionPropertyName<IUS>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(IUS.clreplaced, new String[] { "iusAttributes" });
IUS dto = copier.hibernate2dto(IUS.clreplaced, ius, new Clreplaced<?>[] {}, createCollectionPropertyNames);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : SampleResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject jaxbTool;
for (String key : queryValues.keySet()) {
Log.debug("key: " + key + " -> " + queryValues.get(key));
}
SampleService ss = BeanFactory.getSampleServiceBean();
if (queryValues.get("replacedle") != null) {
jaxbTool = new JaxbObject<>();
Sample sample = (Sample) testIfNull(ss.findByreplacedle(queryValues.get("replacedle")));
Sample dto = copier.hibernate2dto(Sample.clreplaced, sample);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
} else if (queryValues.get("name") != null) {
jaxbTool = new JaxbObject<>();
Sample sample = (Sample) testIfNull(ss.findByName(queryValues.get("name")));
Sample dto = copier.hibernate2dto(Sample.clreplaced, sample);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
} else if (queryValues.get("matches") != null) {
jaxbTool = new JaxbObject<>();
String name = queryValues.get("matches");
List<Sample> samples = (List<Sample>) testIfNull(ss.matchName(name));
SampleList eList = new SampleList();
eList.setList(new ArrayList());
for (Sample sample : samples) {
Sample dto = copier.hibernate2dto(Sample.clreplaced, sample);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
} else {
jaxbTool = new JaxbObject<>();
List<Sample> samples = (List<Sample>) testIfNull(ss.list());
SampleList eList = new SampleList();
eList.setList(new ArrayList());
for (Sample sample : samples) {
Sample dto = copier.hibernate2dto(Sample.clreplaced, sample);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
}
9
View Complete Implementation : WorkflowIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
WorkflowService ss = BeanFactory.getWorkflowServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Workflow> jaxbTool = new JaxbObject<>();
Workflow workflow = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<Workflow>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(Workflow.clreplaced, new String[] { "workflowAttributes" });
Workflow dto = copier.hibernate2dto(Workflow.clreplaced, workflow, new Clreplaced<?>[] {}, createCollectionPropertyNames);
if (fields.contains("params")) {
SortedSet<WorkflowParam> wps = workflow.getWorkflowParams();
if (wps != null) {
SortedSet<WorkflowParam> copiedParams = new TreeSet<>();
for (WorkflowParam param : workflow.getWorkflowParams()) {
copiedParams.add(copier.hibernate2dto(WorkflowParam.clreplaced, param));
}
dto.setWorkflowParams(copiedParams);
} else {
Log.info("Could not be found: workflow params");
}
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : WorkflowParamResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
WorkflowParamService ss = BeanFactory.getWorkflowParamServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Doreplacedent line;
if (queryValues.get("id") != null) {
JaxbObject<WorkflowParam> jaxbTool = new JaxbObject<>();
WorkflowParam wp = ((WorkflowParam) testIfNull(ss.findByID(parseClientInt(queryValues.get("id")))));
WorkflowParam dto = copier.hibernate2dto(WorkflowParam.clreplaced, wp);
Workflow w = wp.getWorkflow();
Workflow detachedW = copier.hibernate2dto(Workflow.clreplaced, w);
dto.setWorkflow(detachedW);
line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
} else {
JaxbObject<WorkflowParam> jaxbTool = new JaxbObject<>();
List<WorkflowParam> wps = (List<WorkflowParam>) testIfNull(ss.list());
WorkflowParamList list = new WorkflowParamList();
for (WorkflowParam wp : wps) {
list.add(copier.hibernate2dto(WorkflowParam.clreplaced, wp));
}
line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
}
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : WorkflowParamValueResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* postJaxb.
* </p>
*
* @param enreplacedy
* a {@link org.restlet.representation.Representation} object.
*/
@Post("xml")
public void postJaxb(Representation enreplacedy) {
authenticate();
try {
JaxbObject<WorkflowParamValue> jo = new JaxbObject<>();
String text = enreplacedy.getText();
WorkflowParamValue p;
try {
p = (WorkflowParamValue) XmlTools.unMarshal(jo, new WorkflowParamValue(), text);
} catch (SAXException ex) {
throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
}
// persist p
WorkflowParamValueService wpvs = BeanFactory.getWorkflowParamValueServiceBean();
Integer id = wpvs.insert(registration, p);
WorkflowParamValue wpv = (WorkflowParamValue) testIfNull(wpvs.findByID(id));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
WorkflowParamValue detachWPV = copier.hibernate2dto(WorkflowParamValue.clreplaced, wpv);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachWPV);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
getResponse().setLocationRef(getRequest().getRootRef() + "/workflowparamvalues?id=" + detachWPV.getWorkflowParamValueId());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e);
} catch (IOException e) {
e.printStackTrace();
getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST, e);
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e);
}
}
9
View Complete Implementation : WorkflowRunResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
private void respondWithList(List<WorkflowRun> runs, Hibernate3DtoCopier copier) {
WorkflowRunList2 eList = new WorkflowRunList2();
ArrayList<WorkflowRun> list = new ArrayList<>();
JaxbObject<WorkflowRunList2> jaxbTool = new JaxbObject<>();
for (WorkflowRun run : runs) {
WorkflowRun dto = copier.hibernate2dto(WorkflowRun.clreplaced, run);
list.add(dto);
}
eList.setList(list);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : LaneIDFilter.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
// String path = getRequest().getResourceRef().getPath();getAttribute();
Collection<Lane> lanes = null;
Map<String, Object> requestAttributes = getRequestAttributes();
if (requestAttributes.containsKey("sequencerRunId")) {
Object val = requestAttributes.get("sequencerRunId");
if (val != null) {
SequencerRunService ss = BeanFactory.getSequencerRunServiceBean();
SequencerRun s = (SequencerRun) testIfNull(ss.findBySWAccession(parseClientInt(val.toString())));
lanes = (SortedSet<Lane>) testIfNull(s.getLanes());
}
} else if (requestAttributes.containsKey("iusId")) {
Object val = requestAttributes.get("iusId");
if (val != null) {
IUSService ss = BeanFactory.getIUSServiceBean();
IUS s = (IUS) testIfNull(ss.findBySWAccession(parseClientInt(val.toString())));
Lane lane = (Lane) testIfNull(s.getLane());
lanes = new ArrayList<>();
lanes.add(lane);
}
} else {
StringBuilder sb = new StringBuilder();
for (String key : requestAttributes.keySet()) {
sb.append(key);
}
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "This resource cannot handle these data types: " + sb.toString());
}
if (lanes.isEmpty()) {
throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "There are no lanes for this resource");
}
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<LaneList> jaxbTool = new JaxbObject<>();
LaneList eList = new LaneList();
eList.setList(new ArrayList());
for (Lane lane : lanes) {
Lane dto = copier.hibernate2dto(Lane.clreplaced, lane);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : SampleIDFilter.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
// String path = getRequest().getResourceRef().getPath();getAttribute();
Collection<Sample> samples = null;
Map<String, Object> requestAttributes = getRequestAttributes();
if (requestAttributes.containsKey("experimentId")) {
Object val = requestAttributes.get("experimentId");
if (val != null) {
ExperimentService es = BeanFactory.getExperimentServiceBean();
Experiment s = (Experiment) testIfNull(es.findBySWAccession(parseClientInt(val.toString())));
samples = (SortedSet<Sample>) testIfNull(s.getSamples());
}
} else if (requestAttributes.containsKey("parentId")) {
Object val = requestAttributes.get("parentId");
if (val != null) {
SampleService es = BeanFactory.getSampleServiceBean();
Sample s = (Sample) testIfNull(es.findBySWAccession(parseClientInt(val.toString())));
samples = (Set<Sample>) testIfNull(s.getChildren());
}
} else if (requestAttributes.containsKey("childId")) {
Object val = requestAttributes.get("childId");
if (val != null) {
SampleService es = BeanFactory.getSampleServiceBean();
Sample s = (Sample) testIfNull(es.findBySWAccession(parseClientInt(val.toString())));
samples = (Set<Sample>) testIfNull(s.getParents());
}
} else {
StringBuilder sb = new StringBuilder();
for (String key : requestAttributes.keySet()) {
sb.append(key);
}
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "This resource cannot handle these data types: " + sb.toString());
}
if (samples.isEmpty()) {
throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "There are no samples for this resource");
}
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<SampleList> jaxbTool = new JaxbObject<>();
SampleList eList = new SampleList();
eList.setList(new ArrayList());
for (Sample sample : samples) {
Sample dto = copier.hibernate2dto(Sample.clreplaced, sample);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : ProcessIdProcessResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* {@inheritDoc}
*/
@Override
public void handle(Request request, Response response) {
authenticate(request.getChallengeResponse().getIdentifier());
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
String id = request.getAttributes().get("processId").toString();
ProcessingService s = BeanFactory.getProcessingServiceBean();
Processing p = (Processing) testIfNull(s.findBySWAccession(parseClientInt(id)));
JaxbObject<ProcessingList> jaxbTool = new JaxbObject<>();
Set<Processing> parents = p.getParents();
ProcessingList list = new ProcessingList();
if (parents != null) {
for (Processing parent : parents) {
list.add(copier.hibernate2dto(Processing.clreplaced, parent));
}
} else {
Log.info("Could not find parents");
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
response.setEnreplacedy(XmlTools.getRepresentation(line));
}
9
View Complete Implementation : WorkflowRunIDProcessingsResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* collectProcessingList.
* </p>
*
* @param wrSWA
* a int.
* @return a {@link java.util.List} object.
* @throws java.sql.SQLException
* if any.
*/
public List<Processing> collectProcessingList(int wrSWA) throws SQLException {
WorkflowRunService wrs = BeanFactory.getWorkflowRunServiceBean();
WorkflowRun run = (WorkflowRun) testIfNull(wrs.findBySWAccession(wrSWA));
SortedSet<Processing> procs = new TreeSet<>(new Comparator<Processing>() {
@Override
public int compare(Processing t, Processing t1) {
return t.getCreateTimestamp().compareTo(t1.getCreateTimestamp());
}
});
if (run.getProcessings() != null)
procs.addAll(run.getProcessings());
if (run.getOffspringProcessings() != null)
procs.addAll(run.getOffspringProcessings());
List<Processing> procDto = new ArrayList<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
for (Processing p : procs) {
procDto.add(copier.hibernate2dto(Processing.clreplaced, p));
}
return procDto;
}
8
View Complete Implementation : ExperimentResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
ExperimentService ss = BeanFactory.getExperimentServiceBean();
logger.debug("registration: " + registration);
List<Experiment> experiments = (List<Experiment>) testIfNull(ss.list());
logger.debug("experiments: " + experiments.size() + " " + experiments);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<ExperimentList> jaxbTool = new JaxbObject<>();
ExperimentList eList = new ExperimentList();
eList.setList(new ArrayList());
for (Experiment experiment : experiments) {
Experiment dto = copier.hibernate2dto(Experiment.clreplaced, experiment);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
8
View Complete Implementation : SequencerRunIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
SequencerRunService ss = BeanFactory.getSequencerRunServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<SequencerRun> jaxbTool = new JaxbObject<>();
SequencerRun run = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<File>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(File.clreplaced, new String[] { "sequencerRunAttributes" });
SequencerRun dto = copier.hibernate2dto(SequencerRun.clreplaced, run, new Clreplaced<?>[] {}, createCollectionPropertyNames);
if (fields.contains("lanes")) {
SortedSet<Lane> laneList = new TreeSet<>();
SortedSet<Lane> lanes = run.getLanes();
if (lanes != null) {
for (Lane lane : lanes) {
laneList.add(copier.hibernate2dto(Lane.clreplaced, lane));
}
dto.setLanes(laneList);
} else {
Log.info("Could not be found: lanes");
}
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
7
View Complete Implementation : FileChildWorkflowRunsResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
protected WorkflowRunList2 handleWorkflowRunsViaLane(final Set<File> files, final Hibernate3DtoCopier copier) {
final WorkflowRunList2 result = new WorkflowRunList2();
Set<WorkflowRun> parentWorkflowRuns = new HashSet<>();
for (File file : files) {
// 3) check if we have children in the lane_workflow_runs that are relevant
for (Processing p : file.getProcessings()) {
WorkflowRun parentRun = p.getWorkflowRun();
if (parentRun == null) {
parentRun = p.getWorkflowRunByAncestorWorkflowRunId();
}
if (parentRun == null) {
continue;
}
parentWorkflowRuns.add(parentRun);
for (Lane lane : parentRun.getLanes()) {
for (WorkflowRun anyRun : lane.getWorkflowRuns()) {
if (isWorkflowRunAttached(parentWorkflowRuns, anyRun))
continue;
final WorkflowRun dto = copier.hibernate2dto(WorkflowRun.clreplaced, anyRun);
result.add(dto);
}
}
}
}
if (result.getList().size() > 0) {
Log.debug("Found " + result.getList().size() + " workflow runs via lane");
} else {
Log.debug("Did not find any workflow runs via lane");
}
return result;
}
7
View Complete Implementation : FileResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*
* @throws java.io.IOException
* if any.
*/
@Get
public void getXml() throws IOException {
authenticate();
FileService ss = BeanFactory.getFileServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
if (queryValues.get("id") != null) {
JaxbObject<File> jaxbTool = new JaxbObject<>();
File p = testIfNull(ss.findByID(parseClientInt(queryValues.get("id"))));
File dto = copier.hibernate2dto(File.clreplaced, p);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
} else if (queryValues.get("path") != null) {
JaxbObject<File> jaxbTool = new JaxbObject<>();
File p = testIfNull(ss.findByPath(queryValues.get("path")));
File dto = copier.hibernate2dto(File.clreplaced, p);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
} else {
JaxbObject<FileList> jaxbTool = new JaxbObject<>();
List<File> files = testIfNull(ss.findByOwnerId(registration.getRegistrationId()));
FileList eList = new FileList();
eList.setList(new ArrayList());
for (File file : files) {
File dto = copier.hibernate2dto(File.clreplaced, file);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
}
7
View Complete Implementation : ProcessResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Doreplacedent line;
ProcessingService ss = BeanFactory.getProcessingServiceBean();
if (queryValues.get("id") != null) {
JaxbObject<Processing> jaxbTool = new JaxbObject<>();
Processing p = (Processing) testIfNull(ss.findByID(parseClientInt(queryValues.get("id"))));
Processing dto = copier.hibernate2dto(Processing.clreplaced, p);
if (fields.contains("files")) {
Set<File> files = p.getFiles();
Set<File> copiedFiles = new HashSet<>();
if (files != null) {
for (File file : files) {
copiedFiles.add(copier.hibernate2dto(File.clreplaced, file));
}
dto.setFiles(copiedFiles);
} else {
Log.info("Could not be found :files");
}
}
line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
} else {
JaxbObject<ProcessingList> jaxbTool = new JaxbObject<>();
ProcessingList list = new ProcessingList();
List<Processing> processings = (List<Processing>) testIfNull(ss.list());
for (Processing p : processings) {
list.add(copier.hibernate2dto(Processing.clreplaced, p));
}
line = XmlTools.marshalToDoreplacedent(jaxbTool, list);
}
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
7
View Complete Implementation : StudyIDResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* {@inheritDoc}
*
* @return
*/
@Override
@Put
public Representation put(Representation enreplacedy) {
Representation representation = null;
try {
JaxbObject<Study> jo = new JaxbObject<>();
String text = enreplacedy.getText();
Study p = null;
try {
p = (Study) XmlTools.unMarshal(jo, new Study(), text);
} catch (SAXException ex) {
throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
}
if (p.getOwner() == null) {
p.setOwner(registration);
}
// persist object
StudyService service = BeanFactory.getStudyServiceBean();
Study study = testIfNull(service.findByID(p.getStudyId()));
if (null != p.getStudyAttributes()) {
// SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
StudyIDResource.mergeAttributes(study.getStudyAttributes(), p.getStudyAttributes(), study);
}
String replacedle = p.getreplacedle();
String description = p.getDescription();
String alias = p.getAlias();
String accession = p.getAccession();
String status = p.getStatus();
String abstractStr = p.getAbstractStr();
String newType = p.getNewType();
String centerName = p.getCenterName();
String centerProjectName = p.getCenterProjectName();
Integer projectId = p.getProjectId();
Boolean isSelected = p.getIsSelected();
Boolean isHasFile = p.getIsHasFile();
String html = p.getHtml();
Integer existingTypeInt = p.getExistingTypeInt();
if (null != replacedle) {
study.setreplacedle(replacedle);
}
if (null != description) {
study.setDescription(description);
}
if (null != alias) {
study.setAlias(alias);
}
if (null != accession) {
study.setAccession(accession);
}
if (null != status) {
study.setStatus(status);
}
if (null != abstractStr) {
study.setAbstractStr(abstractStr);
}
if (null != newType) {
study.setNewType(newType);
}
if (null != centerName) {
study.setCenterName(centerName);
}
if (null != centerProjectName) {
study.setCenterProjectName(centerProjectName);
}
if (null != projectId) {
study.setProjectId(projectId);
}
if (null != isSelected) {
study.setIsSelected(isSelected);
}
if (null != isHasFile) {
study.setIsHasFile(isHasFile);
}
if (null != html) {
study.setHtml(html);
}
if (null != existingTypeInt) {
study.setExistingTypeInt(existingTypeInt);
}
service.update(study);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Study detachedStudy = copier.hibernate2dto(Study.clreplaced, study);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedStudy);
representation = XmlTools.getRepresentation(line);
getResponse().setEnreplacedy(representation);
getResponse().setLocationRef(getRequest().getRootRef() + "/studies/" + detachedStudy.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;
}
7
View Complete Implementation : StudyResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXML.
* </p>
*/
@Get
public void getXML() {
authenticate();
StudyService ss = BeanFactory.getStudyServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
List<Study> studies;
if (queryValues.get("replacedle") != null) {
studies = (List<Study>) testIfNull(ss.findByreplacedle(queryValues.get("replacedle")));
} else {
studies = (List<Study>) testIfNull(ss.list());
}
JaxbObject jaxbTool = new JaxbObject<>();
StudyList eList = new StudyList();
eList.setList(new ArrayList());
for (Study study : studies) {
CollectionPropertyName<Study>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(Study.clreplaced, new String[] { "existingType" });
Study dto = copier.hibernate2dto(Study.clreplaced, study, new Clreplaced[] { StudyType.clreplaced }, createCollectionPropertyNames);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
7
View Complete Implementation : WorkflowRunResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* postJaxb.
* </p>
*
* @param enreplacedy
* a {@link org.restlet.representation.Representation} object.
*/
@Post("xml")
public void postJaxb(Representation enreplacedy) {
authenticate();
WorkflowRun p = null;
JaxbObject<WorkflowRun> jo = new JaxbObject<>();
try {
String text = enreplacedy.getText();
p = (WorkflowRun) XmlTools.unMarshal(jo, new WorkflowRun(), text);
} catch (IOException e) {
e.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e);
} catch (SAXException ex) {
throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
}
try {
if (p.getOwner() != null) {
Registration reg = BeanFactory.getRegistrationServiceBean().findByEmailAddress(p.getOwner().getEmailAddress());
if (reg != null) {
p.setOwner(reg);
} else {
Log.info("Could not be found: owner " + p.getOwner());
}
} else {
p.setOwner(registration);
}
WorkflowRun wr = insertWorkflowRun(p);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
WorkflowRun detachedWR = copier.hibernate2dto(WorkflowRun.clreplaced, wr);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedWR);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
getResponse().setLocationRef(getRequest().getRootRef() + "/workflowruns/" + detachedWR.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e);
}
}
7
View Complete Implementation : WorkflowRunResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
WorkflowRunService ss = BeanFactory.getWorkflowRunServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
if (queryValues.get("id") != null) {
JaxbObject<WorkflowRun> jaxbTool = new JaxbObject<>();
WorkflowRun wr = (WorkflowRun) testIfNull(ss.findByID(parseClientInt(queryValues.get("id"))));
WorkflowRun dto = copier.hibernate2dto(WorkflowRun.clreplaced, wr);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
} else if (queryValues.get("email") != null) {
// SEQWARE-1134
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
RegistrationDTO regDTO = (RegistrationDTO) testIfNull(rs.findByEmailAddress(queryValues.get("email")));
Integer registrationId = regDTO.getRegistrationId();
List<WorkflowRun> runs = ss.findByOwnerID(registrationId);
respondWithList(runs, copier);
} else {
List<WorkflowRun> runs;
StringBuilder constraintBuilder = new StringBuilder();
for (String property : WorkflowRun.USABLE_CONSTRAINTS) {
if (queryValues.get(property) != null) {
if (constraintBuilder.length() != 0) {
constraintBuilder.append(" and ");
}
constraintBuilder.append("wr.").append(property).append("='").append(queryValues.get(property)).append("'");
}
}
if (constraintBuilder.length() != 0) {
Log.debug("WorkflowRunResource constraint: " + constraintBuilder.toString());
runs = ss.findByCriteria(constraintBuilder.toString());
} else {
runs = (List<WorkflowRun>) testIfNull(ss.list());
}
respondWithList(runs, copier);
}
}
6
View Complete Implementation : IUSIDFilter.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
// String path = getRequest().getResourceRef().getPath();getAttribute();
Collection<IUS> iuss = null;
Map<String, Object> requestAttributes = getRequestAttributes();
if (requestAttributes.containsKey("laneId")) {
Object val = requestAttributes.get("laneId");
if (val != null) {
LaneService ss = BeanFactory.getLaneServiceBean();
Lane s = (Lane) testIfNull(ss.findBySWAccession(parseClientInt(val.toString())));
iuss = (SortedSet<IUS>) testIfNull(s.getIUS());
}
} else if (requestAttributes.containsKey("sampleId")) {
Object val = requestAttributes.get("sampleId");
if (val != null) {
SampleService ss = BeanFactory.getSampleServiceBean();
Sample s = (Sample) testIfNull(ss.findBySWAccession(parseClientInt(val.toString())));
iuss = (SortedSet<IUS>) testIfNull(s.getIUS());
}
} else {
StringBuilder sb = new StringBuilder();
for (String key : requestAttributes.keySet()) {
sb.append(key);
}
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "This resource cannot handle these data types: " + sb.toString());
}
if (iuss.isEmpty()) {
throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "There are no IUSes for this resource");
}
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<IUSList> jaxbTool = new JaxbObject<>();
IUSList eList = new IUSList();
eList.setList(new ArrayList());
for (IUS ius : iuss) {
IUS dto = copier.hibernate2dto(IUS.clreplaced, ius);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
6
View Complete Implementation : FileChildWorkflowRunsResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
protected WorkflowRunList2 handleWorkflowRunsViaIUS(Set<File> files, final Hibernate3DtoCopier copier) {
WorkflowRunList2 result = new WorkflowRunList2();
Set<WorkflowRun> parentWorkflowRuns = new HashSet<>();
for (File file : files) {
// 2) check if we have children in the ius_workflow_runs that are relevant
for (Processing p : file.getProcessings()) {
WorkflowRun parentRun = p.getWorkflowRun();
if (parentRun == null) {
parentRun = p.getWorkflowRunByAncestorWorkflowRunId();
}
if (parentRun == null) {
continue;
}
parentWorkflowRuns.add(parentRun);
for (IUS ius : parentRun.getIus()) {
for (WorkflowRun anyRun : ius.getWorkflowRuns()) {
isWorkflowRunAttached(parentWorkflowRuns, anyRun);
WorkflowRun dto = copier.hibernate2dto(WorkflowRun.clreplaced, anyRun);
result.add(dto);
}
}
}
}
if (result.getList().size() > 0) {
Log.debug("Found " + result.getList().size() + " workflow runs via ius");
} else {
Log.debug("Did not find any workflow runs via ius");
}
return result;
}
6
View Complete Implementation : FileChildWorkflowRunsResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* Use SQL to directly retrieve relevant workflows runs (defined as any workflow runs that include one or more files in the set we were
* given)
*
* @param files
* @param interestingWorkflows
* @return
* @throws SQLException
*/
protected static WorkflowRunList2 directRetrieveWorkflowRuns(List<Integer> files, List<Integer> interestingWorkflows) throws SQLException {
final Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
final WorkflowRunList2 runs = new WorkflowRunList2();
runs.setList(new ArrayList());
if (files.size() > 0) {
ResultSet rs = null;
MetadataDB mdb = null;
try {
WorkflowRunService ss = BeanFactory.getWorkflowRunServiceBean();
StringBuilder query = new StringBuilder();
query.append("select distinct r.sw_accession from workflow_run r, workflow w, ");
query.append("workflow_run_input_files rf, file f WHERE r.workflow_run_id = rf.workflow_run_id " + "AND rf.file_id = f.file_id " + "AND w.workflow_id = r.workflow_id " + "AND (");
// handle file accessions
for (int i = 0; i < files.size() - 1; i++) {
Integer fInt = files.get(i);
query.append(" f.sw_accession = ").append(fInt).append(" OR");
}
Integer fInt = files.get(files.size() - 1);
query.append(" f.sw_accession = ").append(fInt).append(")");
// handle interesting workflow accessions
if (interestingWorkflows.size() > 0) {
query.append(" AND (");
for (int i = 0; i < interestingWorkflows.size() - 1; i++) {
Integer wInt = interestingWorkflows.get(i);
query.append(" w.sw_accession = ").append(wInt).append(" OR");
}
Integer wInt = interestingWorkflows.get(interestingWorkflows.size() - 1);
query.append(" w.sw_accession = ").append(wInt).append(")");
}
query.append(" ORDER BY sw_accession");
Log.info("Executing query: " + query);
mdb = DBAccess.get();
List<Integer> workflowSWIDs = mdb.executeQuery(query.toString(), new ResultSetHandler<List<Integer>>() {
@Override
public List<Integer> handle(ResultSet rs) throws SQLException {
List<Integer> ids = new ArrayList<>();
while (rs.next()) {
ids.add(rs.getInt("sw_accession"));
}
return ids;
}
});
for (int workflowSWID : workflowSWIDs) {
WorkflowRun workflowRun = (WorkflowRun) testIfNull(ss.findBySWAccession(workflowSWID));
CollectionPropertyName<WorkflowRun>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(WorkflowRun.clreplaced, new String[] { "inputFileAccessions" });
WorkflowRun dto = copier.hibernate2dto(WorkflowRun.clreplaced, workflowRun, ArrayUtils.EMPTY_CLreplaced_ARRAY, createCollectionPropertyNames);
runs.add(dto);
}
} finally {
if (mdb != null) {
DbUtils.closeQuietly(mdb.getDb(), mdb.getSql(), rs);
}
DBAccess.close();
}
}
return runs;
}
5
View Complete Implementation : SequencerRunResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
Copyright GNU General Public License v3.0
Author : SeqWare
/**
* <p>
* getXml.
* </p>
*/
@Get
public void getXml() {
authenticate();
SequencerRunService ss = BeanFactory.getSequencerRunServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
CollectionPropertyName<SequencerRun>[] createCollectionPropertyNames = CollectionPropertyName.createCollectionPropertyNames(SequencerRun.clreplaced, new String[] { "sequencerRunAttributes" });
if (queryValues.get("name") != null) {
String name = queryValues.get("name");
SequencerRun study = testIfNull(ss.findByName(name));
JaxbObject<SequencerRun> jaxbTool = new JaxbObject<>();
SequencerRun dto = copier.hibernate2dto(SequencerRun.clreplaced, study, new Clreplaced<?>[] {}, createCollectionPropertyNames);
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, dto);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
} else {
JaxbObject<SequencerRunList> jaxbTool = new JaxbObject<>();
List<SequencerRun> runs = testIfNull(ss.list());
SequencerRunList eList = new SequencerRunList();
eList.setList(new ArrayList());
for (SequencerRun sequencerRun : runs) {
SequencerRun dto = copier.hibernate2dto(SequencerRun.clreplaced, sequencerRun, new Clreplaced<?>[] {}, createCollectionPropertyNames);
eList.add(dto);
}
Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
}
}