Example #1
0
  /** getXml. */
  @Get
  public void getXml() {
    authenticate();
    WorkflowService ss = BeanFactory.getWorkflowServiceBean();
    Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
    JaxbObject<Workflow> jaxbTool = new JaxbObject<Workflow>();
    Workflow workflow = (Workflow) testIfNull(ss.findBySWAccession(Integer.parseInt(getId())));
    Workflow dto = copier.hibernate2dto(Workflow.class, workflow);

    if (fields.contains("params")) {
      SortedSet<WorkflowParam> wps = workflow.getWorkflowParams();
      if (wps != null) {
        SortedSet<WorkflowParam> copiedParams = new TreeSet<WorkflowParam>();
        for (WorkflowParam param : workflow.getWorkflowParams()) {
          copiedParams.add(copier.hibernate2dto(WorkflowParam.class, param));
        }
        dto.setWorkflowParams(copiedParams);
      } else {
        Log.info("Could not be found: workflow params");
      }
    }
    if (fields.contains("attributes")) {
      Set<WorkflowAttribute> was = workflow.getWorkflowAttributes();
      if (was != null && !was.isEmpty()) {
        Set<WorkflowAttribute> newwas = new TreeSet<WorkflowAttribute>();
        for (WorkflowAttribute wa : was) {
          newwas.add(copier.hibernate2dto(WorkflowAttribute.class, wa));
        }
        dto.setWorkflowAttributes(newwas);
      }
    }

    Document line = XmlTools.marshalToDocument(jaxbTool, dto);
    getResponse().setEntity(XmlTools.getRepresentation(line));
  }
  /** getXml. */
  @Get
  public void getXml() {
    JaxbObject<Lane> jaxbTool = new JaxbObject<>();
    Hibernate3DtoCopier copier = new Hibernate3DtoCopier();

    Lane dto;
    authenticate();

    LaneService ss = BeanFactory.getLaneServiceBean();
    Lane lane = testIfNull(ss.findBySWAccession(getId()));
    CollectionPropertyName<Lane>[] createCollectionPropertyNames =
        CollectionPropertyName.createCollectionPropertyNames(
            Lane.class, new String[] {"laneAttributes"});
    dto =
        copier.hibernate2dto(
            Lane.class,
            lane,
            new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
            createCollectionPropertyNames);

    if (fields.contains("sequencerRun")) {
      SequencerRun sr = lane.getSequencerRun();
      if (sr != null) {
        SequencerRun copySR = copier.hibernate2dto(SequencerRun.class, sr);
        dto.setSequencerRun(copySR);
      } else {
        Log.info("Could not be found sequencer run");
      }
    }

    Document line = XmlTools.marshalToDocument(jaxbTool, dto);
    getResponse().setEntity(XmlTools.getRepresentation(line));
  }
  /** getXml. */
  @Get
  public void getXml() {
    authenticate();

    JaxbObject<Lane> jaxbTool = new JaxbObject<>();
    Hibernate3DtoCopier copier = new Hibernate3DtoCopier();

    SampleService ss = BeanFactory.getSampleServiceBean();
    Sample sample = testIfNull(ss.findBySWAccession(getId()));
    CollectionPropertyName<Sample>[] createCollectionPropertyNames =
        CollectionPropertyName.createCollectionPropertyNames(
            Sample.class, new String[] {"sampleAttributes"});
    Sample dto =
        copier.hibernate2dto(
            Sample.class, sample, new Class<?>[] {}, createCollectionPropertyNames);

    if (fields.contains("lanes")) {
      SortedSet<Lane> lanes = sample.getLanes();
      if (lanes != null) {
        SortedSet<Lane> copiedLanes = new TreeSet<>();
        for (Lane lane : lanes) {
          copiedLanes.add(copier.hibernate2dto(Lane.class, lane));
        }
        dto.setLanes(copiedLanes);
      } else {
        Log.info("Could not be found: lanes");
      }
    }
    if (fields.contains("ius")) {
      SortedSet<IUS> ius = sample.getIUS();
      if (ius != null) {
        SortedSet<IUS> copiedIUS = new TreeSet<>();
        for (IUS i : ius) {
          copiedIUS.add(copier.hibernate2dto(IUS.class, i));
        }
        dto.setIUS(copiedIUS);
      }
      {
        Log.info("Could not be found : ius");
      }
    }

    Document line = XmlTools.marshalToDocument(jaxbTool, dto);
    getResponse().setEntity(XmlTools.getRepresentation(line));
  }
Example #4
0
  /** getXml. */
  @Get
  public void getXml() {
    ExperimentService ss = BeanFactory.getExperimentServiceBean();
    Experiment experiment =
        (Experiment) testIfNull(ss.findBySWAccession(Integer.parseInt(getId())));
    Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
    JaxbObject<Experiment> jaxbTool = new JaxbObject<Experiment>();

    Experiment dto = copier.hibernate2dto(Experiment.class, experiment);
    if (fields.contains("attributes")) {
      Set<ExperimentAttribute> eas = experiment.getExperimentAttributes();
      if (eas != null && !eas.isEmpty()) {
        Set<ExperimentAttribute> newEas = new TreeSet<ExperimentAttribute>();
        for (ExperimentAttribute ea : eas) {
          newEas.add(copier.hibernate2dto(ExperimentAttribute.class, ea));
        }
        dto.setExperimentAttributes(newEas);
      }
    }
    Document line = XmlTools.marshalToDocument(jaxbTool, dto);

    getResponse().setEntity(XmlTools.getRepresentation(line));
  }
  /**
   * {@inheritDoc}
   *
   * @return
   */
  @Override
  @Put
  public Representation put(Representation entity) {
    authenticate();
    Representation representation = null;
    Lane newLane = null;
    JaxbObject<Lane> jo = new JaxbObject<>();
    try {

      String text = entity.getText();
      newLane = (Lane) XmlTools.unMarshal(jo, new Lane(), text);
    } catch (SAXException | IOException ex) {
      ex.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
    }
    try {
      LaneService fs = BeanFactory.getLaneServiceBean();
      Lane lane = testIfNull(fs.findByID(newLane.getLaneId()));
      lane.givesPermission(registration);
      // simple types
      String name = newLane.getName();
      String desc = newLane.getDescription();
      Integer laneIndex = newLane.getLaneIndex();
      String cycleDescriptor = newLane.getCycleDescriptor();
      Boolean skip = newLane.getSkip();
      String tags = newLane.getTags();
      String regions = newLane.getRegions();
      // foreign keys
      Sample sample = newLane.getSample();
      Registration owner = newLane.getOwner();

      Set<LaneAttribute> newAttributes = newLane.getLaneAttributes();

      if (name != null) {
        lane.setName(name);
      }
      if (desc != null) {
        lane.setDescription(desc);
      }
      if (laneIndex != null) {
        lane.setLaneIndex(laneIndex);
      }
      if (cycleDescriptor != null) {
        lane.setCycleDescriptor(cycleDescriptor);
      }
      if (skip != null) {
        lane.setSkip(skip);
      }
      if (tags != null) {
        lane.setTags(tags);
      }
      if (regions != null) {
        lane.setRegions(regions);
      }

      if (sample != null) {
        SampleService ss = BeanFactory.getSampleServiceBean();
        Sample newSample = ss.findByID(sample.getSampleId());
        if (newSample != null && newSample.givesPermission(registration)) {
          lane.setSample(newSample);
        } else if (newSample == null) {
          Log.info("Could not be found " + sample);
        }
      }

      if (owner != null) {
        RegistrationService rs = BeanFactory.getRegistrationServiceBean();
        Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
        if (newReg != null) {
          lane.setOwner(newReg);
        } else {
          Log.info("Could not be found " + owner);
        }
      } else if (lane.getOwner() == null) {
        lane.setOwner(registration);
      }
      if (newAttributes != null) {
        // SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
        LaneIDResource.mergeAttributes(lane.getLaneAttributes(), newAttributes, lane);
      }

      fs.update(registration, lane);

      Hibernate3DtoCopier copier = new Hibernate3DtoCopier();

      Lane detachedLane =
          copier.hibernate2dto(
              Lane.class,
              lane,
              new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
              new CollectionPropertyName<?>[] {});

      Document line = XmlTools.marshalToDocument(jo, detachedLane);
      representation = XmlTools.getRepresentation(line);
      getResponse().setEntity(representation);
      getResponse()
          .setLocationRef(getRequest().getRootRef() + "/lanes/" + detachedLane.getSwAccession());
      getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
      getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (Exception e) {
      e.printStackTrace();
      getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }

    return representation;
  }
Example #6
0
  /** {@inheritDoc} */
  @Override
  @Put
  public Representation put(Representation entity) {
    authenticate();
    Representation representation = null;
    Experiment newObj = null;
    JaxbObject<Experiment> jo = new JaxbObject<Experiment>();
    try {
      String text = entity.getText();
      newObj = (Experiment) XmlTools.unMarshal(jo, new Experiment(), text);
    } catch (SAXException ex) {
      ex.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
    } catch (IOException e) {
      e.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e);
    }
    try {
      ExperimentService service = BeanFactory.getExperimentServiceBean();
      Experiment exp = (Experiment) testIfNull(service.findByID(newObj.getExperimentId()));
      exp.givesPermission(registration);

      // simple types
      String title = newObj.getTitle();
      String name = newObj.getName();
      String desc = newObj.getDescription();
      String alias = newObj.getAlias();
      String accession = newObj.getAccession();
      String status = newObj.getStatus();
      String centerName = newObj.getCenterName();
      String sequencerSpace = newObj.getSequenceSpace();
      String baseCaller = newObj.getBaseCaller();
      String qualityScorer = newObj.getQualityScorer();
      Integer qualityNumberLevels = newObj.getQualityNumberOfLevels();
      Integer qualityMultiplier = newObj.getQualityMultiplier();
      Long expectedNumberSpots = newObj.getExpectedNumberSpots();
      Long expectedNumberReads = newObj.getExpectedNumberReads();

      // foreign keys
      Study study = newObj.getStudy();
      Registration owner = newObj.getOwner();

      // sets
      Set<ExperimentAttribute> expAttributes = newObj.getExperimentAttributes();

      if (title != null) {
        exp.setTitle(title);
      }
      if (name != null) {
        exp.setName(name);
      }
      if (desc != null) {
        exp.setDescription(desc);
      }
      if (alias != null) {
        exp.setAlias(alias);
      }
      if (accession != null) {
        exp.setAccession(accession);
      }
      if (status != null) {
        exp.setStatus(status);
      }
      if (centerName != null) {
        exp.setCenterName(centerName);
      }
      if (sequencerSpace != null) {
        exp.setSequenceSpace(sequencerSpace);
      }
      if (baseCaller != null) {
        exp.setBaseCaller(baseCaller);
      }
      if (qualityScorer != null) {
        exp.setQualityScorer(qualityScorer);
      }
      if (qualityNumberLevels != null) {
        exp.setQualityNumberOfLevels(qualityNumberLevels);
      }
      if (qualityMultiplier != null) {
        exp.setQualityMultiplier(qualityMultiplier);
      }
      if (expectedNumberSpots != null) {
        exp.setExpectedNumberSpots(expectedNumberSpots);
      }
      if (expectedNumberReads != null) {
        exp.setExpectedNumberReads(expectedNumberReads);
      }

      if (study != null) {
        StudyService ss = BeanFactory.getStudyServiceBean();
        Study newStudy = ss.findByID(study.getStudyId());
        if (newStudy != null && newStudy.givesPermission(registration)) {
          exp.setStudy(newStudy);
        } else if (newStudy == null) {
          Log.info("Could not be found " + study);
        }
      }

      if (owner != null) {
        RegistrationService rs = BeanFactory.getRegistrationServiceBean();
        Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
        if (newReg != null) {
          exp.setOwner(newReg);
        } else {
          Log.info("Could not be found " + owner);
        }
      } else if (exp.getOwner() == null) {
        exp.setOwner(registration);
      }

      if (null != expAttributes) {
        exp.getExperimentAttributes().clear();
        for (ExperimentAttribute ea : expAttributes) {
          ea.setExperiment(exp);
          exp.getExperimentAttributes().add(ea);
        }
      }

      service.update(registration, exp);

      Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
      Experiment detachedLane = copier.hibernate2dto(Experiment.class, exp);

      Document line = XmlTools.marshalToDocument(jo, detachedLane);
      representation = XmlTools.getRepresentation(line);
      getResponse().setEntity(representation);
      getResponse()
          .setLocationRef(
              getRequest().getRootRef() + "/experiments/" + detachedLane.getSwAccession());
      getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
      getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (Exception e) {
      e.printStackTrace();
      getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }

    return representation;
  }
Example #7
0
  /** {@inheritDoc} */
  @Override
  public Representation put(Representation entity) {
    authenticate();
    Representation representation = null;
    Workflow newWorkflow = null;
    JaxbObject<Workflow> jo = new JaxbObject<Workflow>();
    try {
      String text = entity.getText();
      newWorkflow = (Workflow) XmlTools.unMarshal(jo, new Workflow(), text);
    } catch (SAXException ex) {
      ex.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex.getMessage());
    } catch (IOException e) {
      e.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage());
    }
    try {
      WorkflowService fs = BeanFactory.getWorkflowServiceBean();
      Workflow workflow = (Workflow) testIfNull(fs.findByID(newWorkflow.getWorkflowId()));
      workflow.givesPermission(registration);
      // simple types
      String name = newWorkflow.getName();
      String desc = newWorkflow.getDescription();
      String baseIniFile = newWorkflow.getBaseIniFile();
      String command = newWorkflow.getCommand();
      String cwd = newWorkflow.getCwd();
      String host = newWorkflow.getHost();
      String inputAlgorithm = newWorkflow.getInputAlgorithm();
      String permanentBundleLocation = newWorkflow.getPermanentBundleLocation();
      String seqwareVersion = newWorkflow.getSeqwareVersion();
      String template = newWorkflow.getTemplate();
      String username = newWorkflow.getUsername();
      String version = newWorkflow.getVersion();
      // foreign keys
      Registration owner = newWorkflow.getOwner();

      workflow.setName(name);
      workflow.setDescription(desc);
      workflow.setBaseIniFile(baseIniFile);
      workflow.setCommand(command);
      workflow.setCwd(cwd);
      workflow.setHost(host);
      workflow.setInputAlgorithm(inputAlgorithm);
      workflow.setPermanentBundleLocation(permanentBundleLocation);
      workflow.setSeqwareVersion(seqwareVersion);
      workflow.setTemplate(template);
      workflow.setUsername(username);
      workflow.setVersion(version);
      workflow.setUpdateTimestamp(new Date());
      workflow.setWorkflowClass(newWorkflow.getWorkflowClass());
      workflow.setWorkflowType(newWorkflow.getWorkflowType());
      workflow.setWorkflowEngine(newWorkflow.getWorkflowEngine());

      if (owner != null) {
        RegistrationService rs = BeanFactory.getRegistrationServiceBean();
        Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
        if (newReg != null) {
          workflow.setOwner(newReg);
        } else {
          Log.info("Could not be found: " + owner);
        }
      } else if (workflow.getOwner() == null) {
        workflow.setOwner(registration);
      }

      if (newWorkflow.getWorkflowAttributes() != null) {
        workflow.getWorkflowAttributes().clear();
        for (WorkflowAttribute wfa : newWorkflow.getWorkflowAttributes()) {
          wfa.setWorkflow(workflow);
          workflow.getWorkflowAttributes().add(wfa);
        }
      }
      fs.update(registration, workflow);
      Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
      Workflow detachedWorkflow = copier.hibernate2dto(Workflow.class, workflow);

      Document line = XmlTools.marshalToDocument(jo, detachedWorkflow);
      representation = XmlTools.getRepresentation(line);
      getResponse().setEntity(representation);
      getResponse()
          .setLocationRef(
              getRequest().getRootRef() + "/workflows/" + detachedWorkflow.getSwAccession());
      getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
      getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (Exception e) {
      e.printStackTrace();
      getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }

    return representation;
  }
  /**
   * {@inheritDoc}
   *
   * @return
   */
  @Override
  @Put
  public Representation put(Representation entity) {
    authenticate();
    Representation representation = null;
    try {
      JaxbObject<Sample> jo = new JaxbObject<>();
      String text = entity.getText();
      Sample o = null;
      try {
        o = (Sample) XmlTools.unMarshal(jo, new Sample(), text);
      } catch (SAXException ex) {
        throw new ResourceException(Status.CLIENT_ERROR_UNPROCESSABLE_ENTITY, ex);
      }

      SampleService service = BeanFactory.getSampleServiceBean();
      Sample sample = testIfNull(service.findByID(o.getSampleId()));
      sample.givesPermission(registration);

      String anonymizedName = o.getAnonymizedName();
      String individualName = o.getIndividualName();
      Integer swAccession = o.getSwAccession();
      String name = o.getName();
      String title = o.getTitle();
      String alias = o.getAlias();
      String description = o.getDescription();
      String type = o.getType();
      String tags = o.getTags();
      String adapters = o.getAdapters();
      String regions = o.getRegions();
      Integer expectedNumRuns = o.getExpectedNumRuns();
      Integer expectedNumSpots = o.getExpectedNumSpots();
      Integer expectedNumReads = o.getExpectedNumReads();
      Boolean skip = o.getSkip();
      Boolean isSelected = o.getIsSelected();
      Boolean isHasFile = o.getIsHasFile();
      Integer countFile = o.getCountFile();

      if (null != anonymizedName) sample.setAnonymizedName(anonymizedName);
      if (null != individualName) sample.setIndividualName(individualName);
      if (null != swAccession) sample.setSwAccession(swAccession);
      if (null != name) sample.setName(name);
      if (null != title) sample.setTitle(title);
      if (null != alias) sample.setAlias(alias);
      if (null != description) sample.setDescription(description);
      if (null != type) sample.setType(type);
      if (null != tags) sample.setTags(tags);
      if (null != adapters) sample.setAdapters(adapters);
      if (null != regions) sample.setRegions(regions);
      if (null != expectedNumRuns) sample.setExpectedNumRuns(expectedNumRuns);
      if (null != expectedNumSpots) sample.setExpectedNumSpots(expectedNumSpots);
      if (null != expectedNumReads) sample.setExpectedNumReads(expectedNumReads);
      if (null != skip) sample.setSkip(skip);
      if (null != isSelected) sample.setIsSelected(isSelected);
      if (null != isHasFile) sample.setIsHasFile(isHasFile);
      if (null != countFile) sample.setCountFile(countFile);

      if (null != o.getSampleAttributes()) {
        // SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
        SampleIDResource.mergeAttributes(
            sample.getSampleAttributes(), o.getSampleAttributes(), sample);
      }
      if (null != o.getParents()) {
        SampleService ss = BeanFactory.getSampleServiceBean();
        Set<Sample> parents = new HashSet<>(sample.getParents());
        for (Sample s : o.getParents()) {
          parents.add(ss.findByID(s.getSampleId()));
        }
        sample.setParents(parents);
      }
      if (null != o.getChildren()) {
        SampleService ss = BeanFactory.getSampleServiceBean();
        Set<Sample> children = new HashSet<>(sample.getChildren());
        for (Sample s : o.getChildren()) {
          children.add(ss.findByID(s.getSampleId()));
        }
        sample.setChildren(children);
      }
      service.update(sample);

      // persist object
      Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
      Sample detachedSample = copier.hibernate2dto(Sample.class, sample);

      Document line = XmlTools.marshalToDocument(jo, detachedSample);
      getResponse().setEntity(XmlTools.getRepresentation(line));
      getResponse()
          .setLocationRef(
              getRequest().getRootRef() + "/samples/" + detachedSample.getSwAccession());
      getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
      getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e);
    } catch (Exception e) {
      e.printStackTrace();
      getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e);
    }

    return representation;
  }