net.sf.beanlib.hibernate3.Hibernate3DtoCopier - java examples

Here are the examples of the java api net.sf.beanlib.hibernate3.Hibernate3DtoCopier taken from open source projects. By voting up you can indicate which examples are most useful and appropriate.

69 Examples 7

18 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));
}

18 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));
}

17 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));
}

17 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));
}

17 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));
}

17 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));
}

17 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;
}

17 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));
}

17 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));
}

17 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));
}

16 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));
}

16 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));
}

16 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));
}

16 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;
}

16 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;
}

16 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 : 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;
}

16 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;
}

16 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;
}

16 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));
}

15 View Complete Implementation : ProcessResource.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<Processing> jo = new JaxbObject<>();
        String text = enreplacedy.getText();
        Processing p;
        try {
            p = (Processing) XmlTools.unMarshal(jo, new Processing(), text);
        } catch (SAXException ex) {
            throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
        }
        if (p.getOwner() != null) {
            p.setOwner(BeanFactory.getRegistrationServiceBean().findByEmailAddress(p.getOwner().getEmailAddress()));
        } else {
            p.setOwner(registration);
        }
        // persist p
        ProcessingService ps = BeanFactory.getProcessingServiceBean();
        Integer id = ps.insert(registration, p);
        Processing newProcessing = testIfNull(ps.findBySWAccession(id));
        Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
        Processing detachedP = copier.hibernate2dto(Processing.clreplaced, newProcessing);
        Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedP);
        getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
        getResponse().setLocationRef(getRequest().getRootRef() + "/processes/" + detachedP.getSwAccession());
        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);
    }
}

15 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));
    }
}

15 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));
}

15 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));
}

15 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));
}

14 View Complete Implementation : StudyResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
/**
 * <p>
 * postJaxb.
 * </p>
 *
 * @param enreplacedy
 *            a {@link org.restlet.representation.Representation} object.
 * @throws org.restlet.resource.ResourceException
 *             if any.
 */
@Post("xml")
public void postJaxb(Representation enreplacedy) throws ResourceException {
    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();
        Integer swAccession = service.insert(registration, p);
        Study study = (Study) testIfNull(service.findBySWAccession(swAccession));
        Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
        Study detachedStudy = copier.hibernate2dto(Study.clreplaced, study);
        Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedStudy);
        getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
        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);
    }
}

14 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);
    }
}

14 View Complete Implementation : FileChildWorkflowRunsResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
/**
 * <p>
 * getXml.
 * </p>
 *
 * @throws java.sql.SQLException
 */
@Get
public void getXml() throws SQLException {
    authenticate();
    final Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
    JaxbObject jaxbTool;
    Log.debug("Dealing with FileChildWorkflowRunsResource");
    if (queryValues.keySet().contains(DIRECT_SEARCH) && queryValues.get(DIRECT_SEARCH).equalsIgnoreCase("true")) {
        handleDirectGetXML();
        return;
    }
    FileService fs = BeanFactory.getFileServiceBean();
    Set<File> files = new HashSet<>();
    SEARCH_TYPE searchType = SEARCH_TYPE.CHILDREN_VIA_PROCESSING_RELATIONSHIP;
    Log.debug("File service started");
    for (String key : queryValues.keySet()) {
        Log.debug("key: " + key + " -> " + queryValues.get(key));
        if (key.equals("files")) {
            String value = queryValues.get(key);
            String[] filesSWIDs = value.split(",");
            for (String swid : filesSWIDs) {
                File findByID = (File) testIfNull(fs.findBySWAccession(Integer.valueOf(swid)));
                files.add(findByID);
            }
        }
        if (key.equals("search")) {
            String value = queryValues.get(key);
            try {
                searchType = SEARCH_TYPE.valueOf(value);
            } catch (IllegalArgumentException e) {
                throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "Object cannot be found");
            }
        }
    }
    Log.debug("Working with " + files.size() + " files and doing a search of type: " + searchType.toString());
    // these variables will be used to return information
    jaxbTool = new JaxbObject<>();
    WorkflowRunList2 eList = new WorkflowRunList2();
    eList.setList(new ArrayList());
    Log.debug("JaxbObjects started");
    replacedert eList.getList().isEmpty();
    // the logic here is, we consider first workflow_run children found via the children of the processing
    // if that is empty, then we consider workflow_run found via the IUS (ius_workflow_run table)
    // if that is empty, then we consider workflow_run found via the lane (lane_workflow_run table)
    if (searchType == SEARCH_TYPE.CHILDREN_VIA_PROCESSING_RELATIONSHIP) {
        eList = handleWorkflowRunsViaChild(files, copier);
    } else if (searchType == SEARCH_TYPE.CHILDREN_VIA_IUS_WORKFLOW_RUN) {
        eList = handleWorkflowRunsViaIUS(files, copier);
    } else if (searchType == SEARCH_TYPE.CHILDREN_VIA_LANE_WORKFLOW_RUN) {
        eList = handleWorkflowRunsViaLane(files, copier);
    }
    final Doreplacedent line = XmlTools.marshalToDoreplacedent(jaxbTool, eList);
    getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
    getResponse().setStatus(Status.SUCCESS_CREATED);
}

14 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;
}

14 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;
}

14 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));
    }
}

14 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));
}

14 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));
    }
}

13 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));
}

13 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));
}

13 View Complete Implementation : FileResource.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<File> jo = new JaxbObject<>();
        File p = null;
        try {
            String text = enreplacedy.getText();
            p = (File) XmlTools.unMarshal(jo, new File(), text);
        } catch (SAXException ex) {
            throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
        }
        if (p.getOwner() == null) {
            p.setOwner(registration);
        } else {
            Registration reg = BeanFactory.getRegistrationServiceBean().findByEmailAddress(p.getOwner().getEmailAddress());
            if (reg != null) {
                p.setOwner(reg);
            } else {
                Log.info("Could not be found: " + p.getOwner());
            }
        }
        // persist p
        FileService fileService = BeanFactory.getFileServiceBean();
        // attributes seem to screw this up, so remove them and add them afterwards
        // and yes, this is a total hack
        Set<FileAttribute> fileAttributes = Sets.newTreeSet();
        fileAttributes.addAll(p.getFileAttributes());
        p.getFileAttributes().clear();
        Integer swAccession = fileService.insert(registration, p);
        File file = testIfNull(fileService.findBySWAccession(swAccession));
        Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
        File detachedFile = copier.hibernate2dto(File.clreplaced, file);
        // this is incredibly sad
        if (fileAttributes.size() > 0) {
            File newFile = testIfNull(fileService.findBySWAccession(swAccession));
            DatabaseIDResource.mergeAttributes(newFile.getFileAttributes(), fileAttributes, file);
            fileService.update(registration, newFile);
        }
        Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedFile);
        getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
        getResponse().setLocationRef(getRequest().getRootRef() + "/files/" + detachedFile.getSwAccession());
        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);
// }
}

13 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));
}

13 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;
}

13 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));
}

13 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));
}

12 View Complete Implementation : WorkflowParamResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
/**
 * <p>
 * postJaxb.
 * </p>
 *
 * @param enreplacedy
 *            a {@link org.restlet.representation.Representation} object.
 */
@Post
public void postJaxb(Representation enreplacedy) {
    authenticate();
    try {
        JaxbObject<WorkflowParam> jo = new JaxbObject<>();
        String text = enreplacedy.getText();
        WorkflowParam p;
        try {
            p = (WorkflowParam) XmlTools.unMarshal(jo, new WorkflowParam(), text);
        } catch (SAXException ex) {
            throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
        }
        WorkflowService wos = BeanFactory.getWorkflowServiceBean();
        Workflow w = (Workflow) testIfNull(wos.findByID(p.getWorkflow().getWorkflowId()));
        w.givesPermission(registration);
        p.setWorkflow(w);
        // persist p
        WorkflowParamService ws = BeanFactory.getWorkflowParamServiceBean();
        Integer id = ws.insert(registration, p);
        WorkflowParam wp = (WorkflowParam) testIfNull(ws.findByID(id));
        Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
        WorkflowParam detachedWP = copier.hibernate2dto(WorkflowParam.clreplaced, wp);
        Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedWP);
        getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
        getResponse().setLocationRef(getRequest().getRootRef() + "/workflowparams?id=" + detachedWP.getWorkflowParamId());
        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);
    }
}

12 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);
    }
}

11 View Complete Implementation : ExperimentResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
/**
 * <p>
 * postJaxb.
 * </p>
 *
 * @param enreplacedy
 *            a {@link org.restlet.representation.Representation} object.
 * @throws org.restlet.resource.ResourceException
 *             if any.
 */
@Post("xml")
public void postJaxb(Representation enreplacedy) throws ResourceException {
    authenticate();
    try {
        JaxbObject<Experiment> jo = new JaxbObject<>();
        String text = enreplacedy.getText();
        Experiment o = null;
        try {
            o = (Experiment) XmlTools.unMarshal(jo, new Experiment(), text);
        } catch (SAXException ex) {
            throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
        }
        // SEQWARE-1548
        o = testIfNull(o);
        if (o.getOwner() == null) {
            o.setOwner(registration);
        } else {
            Registration reg = BeanFactory.getRegistrationServiceBean().findByEmailAddress(testIfNull(o.getOwner().getEmailAddress()));
            if (reg != null) {
                o.setOwner(reg);
            } else {
                logger.info("Could not be found: " + o.getOwner());
            }
        }
        if (o.getStudy() != null) {
            StudyService ss = BeanFactory.getStudyServiceBean();
            Study newStudy = (Study) testIfNull(ss.findBySWAccession(o.getStudy().getSwAccession()));
            o.setStudy(newStudy);
        }
        // persist object
        ExperimentService service = BeanFactory.getExperimentServiceBean();
        Integer swAccession = service.insert(registration, o);
        Experiment experiment = (Experiment) testIfNull(service.findBySWAccession(swAccession));
        Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
        Experiment detachedExperiment = copier.hibernate2dto(Experiment.clreplaced, experiment);
        Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedExperiment);
        getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
        getResponse().setLocationRef(getRequest().getRootRef() + "/experiments/" + detachedExperiment.getSwAccession());
        getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
        getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (IOException e) {
        e.printStackTrace();
        getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage());
    } catch (Exception e) {
        e.printStackTrace();
        getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}

11 View Complete Implementation : IusResource.java
Copyright GNU General Public License v3.0
Author : SeqWare
/**
 * <p>
 * postJaxb.
 * </p>
 *
 * @param enreplacedy
 *            a {@link org.restlet.representation.Representation} object.
 * @throws org.restlet.resource.ResourceException
 *             if any.
 */
@Post("xml")
public void postJaxb(Representation enreplacedy) throws ResourceException {
    authenticate();
    try {
        JaxbObject<IUS> jo = new JaxbObject<>();
        String text = enreplacedy.getText();
        IUS o = null;
        try {
            o = (IUS) XmlTools.unMarshal(jo, new IUS(), text);
        } catch (SAXException ex) {
            throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
        }
        if (o.getOwner() == null) {
            o.setOwner(registration);
        } else {
            Registration reg = BeanFactory.getRegistrationServiceBean().findByEmailAddress(o.getOwner().getEmailAddress());
            if (reg != null) {
                o.setOwner(reg);
            } else {
                logger.info("Could not be found: " + o.getOwner());
            }
        }
        // attempt to save foreign keys, I guess this is replacing an empty object with a fully populated one?
        if (o.getLane() != null) {
            LaneService ps = BeanFactory.getLaneServiceBean();
            Lane lane = (Lane) testIfNull(ps.findByID(o.getLane().getLaneId()));
            o.setLane(lane);
        }
        // attempt to save foreign keys, I guess this is replacing an empty object with a fully populated one?
        if (o.getSample() != null) {
            SampleService ps = BeanFactory.getSampleServiceBean();
            Sample sample = (Sample) testIfNull(ps.findByID(o.getSample().getSampleId()));
            o.setSample(sample);
        }
        // persist object
        IUSService service = BeanFactory.getIUSServiceBean();
        Integer swAccession = service.insert(registration, o);
        IUS obj = (IUS) testIfNull(service.findBySWAccession(swAccession));
        Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
        IUS detachedIUS = copier.hibernate2dto(IUS.clreplaced, obj);
        Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedIUS);
        getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
        getResponse().setLocationRef(getRequest().getRootRef() + "/ius/" + detachedIUS.getSwAccession());
        getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
        getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (IOException e) {
        e.printStackTrace();
        getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
    } catch (Exception e) {
        e.printStackTrace();
        getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}

11 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));
}

11 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));
}

11 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));
}

11 View Complete Implementation : WorkflowResource.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<Workflow> jo = new JaxbObject<>();
        String text = enreplacedy.getText();
        Workflow p;
        try {
            p = (Workflow) XmlTools.unMarshal(jo, new Workflow(), text);
        } catch (SAXException ex) {
            throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENreplacedY, ex);
        }
        if (p.getOwner() != null) {
            Registration r = BeanFactory.getRegistrationServiceBean().findByEmailAddress(p.getOwner().getEmailAddress());
            if (r != null) {
                p.setOwner(r);
            } else {
                Log.info("Could not be found: owner" + p.getOwner());
            }
        } else {
            p.setOwner(registration);
        }
        // persist p
        WorkflowService ws = BeanFactory.getWorkflowServiceBean();
        Integer id = ws.insert(registration, p);
        Workflow w = (Workflow) testIfNull(ws.findBySWAccession(id));
        Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
        Workflow detachedW = copier.hibernate2dto(Workflow.clreplaced, w);
        Doreplacedent line = XmlTools.marshalToDoreplacedent(jo, detachedW);
        getResponse().setEnreplacedy(XmlTools.getRepresentation(line));
        getResponse().setLocationRef(getRequest().getRootRef() + "/workflows/" + detachedW.getSwAccession());
        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);
    }
}

10 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));
}

10 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));
}