net.sf.beanlib.hibernate3.Hibernate3DtoCopier.hibernate2dto() - java examples

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 7

19 View Complete Implementation : WorkflowRunIdFilesResource.java
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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * {@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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * {@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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
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
/**
 * <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
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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
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
/**
 * <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
/**
 * <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
/**
 * {@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
/**
 * <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
/**
 * <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
/**
 * <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
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
/**
 * <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
/**
 * <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
/**
 * {@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
/**
 * <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
/**
 * <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
/**
 * <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
/**
 * <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
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
/**
 * 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
/**
 * <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));
    }
}