Package uk.ac.bbsrc.tgac.miso.core.data.impl.ls454

Examples of uk.ac.bbsrc.tgac.miso.core.data.impl.ls454.LS454Pool

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    return new IlluminaPool(user);
  }

  @Override
  public LS454Pool getLS454Pool() {
    return new LS454Pool();
  }
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  public LS454Pool getLS454Pool() {
    return new LS454Pool();
  }

  public LS454Pool getLS454Pool(User user) {
    return new LS454Pool(user);
  }
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  @RequestMapping(value = "/new/dilution/{dilutionId}", method = RequestMethod.GET)
  public ModelAndView setupFormWithDilution(@PathVariable Long dilutionId,
                                ModelMap model) throws IOException {
    try {
      User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
      LS454Pool pool = dataObjectFactory.getLS454Pool(user);
      model.put("title", "New 454 Pool");

      if (!pool.userCanRead(user)) {
        throw new SecurityException("Permission denied.");
      }

      if (dilutionId != null) {
          emPCRDilution ed = requestManager.getEmPcrDilutionById(dilutionId);
        if (ed != null) {
          pool.addPoolableElement(ed);
        }
      }

      model.put("formObj", pool);
      model.put("pool", pool);
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  }


  @RequestMapping(value = "/import", method = RequestMethod.POST)
  public String importEmPCRDilutionsToPool(HttpServletRequest request, ModelMap model) throws IOException {
    LS454Pool p = (LS454Pool)model.get("pool");
    String[] dils = request.getParameterValues("importdilslist");
    for (String s : dils) {
      emPCRDilution ld = requestManager.getEmPcrDilutionByBarcode(s);
      if (ld != null) {
        try {
          p.addPoolableElement(ld);
        }
        catch (MalformedDilutionException e) {
          log.debug("Cannot add emPCR dilution "+s+" to pool " + p.getName());
          e.printStackTrace();
        }
      }
    }

    requestManager.savePool(p);
    return "redirect:/miso/pool/ls454/" + p.getId();
  }
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          try {
            if (attemptRunPopulation) {
              if (r == null) {
                log.debug("\\_ Saving new run and status: " + is.getRunName());
                r = new LS454Run();
                r.setAlias(run.getString("runName"));
                r.setDescription(m.group(3));
                //TODO check this properly
                r.setPairedEnd(false);
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  }

  public JSONObject changeLS454Container(HttpSession session, JSONObject json) {
    StringBuilder b = new StringBuilder();
    int numContainers = json.getInt("numContainers");
    LS454Run run = (LS454Run) session.getAttribute("run_" + json.getString("run_cId"));
    run.getSequencerPartitionContainers().clear();

    for (int i = 0; i < numContainers; i++) {
      b.append("<h2>Container " + (i + 1) + "</h2>");
      b.append("<table class='in'>");
      b.append("<tr><td>ID:</td><td><button onclick='Run.container.lookupContainer(this, " + i + ");' type='button' class='right-button ui-state-default ui-corner-all'>Lookup</button><div style='overflow:hidden'><input type='text' id='sequencerPartitionContainers[" + i + "].identificationBarcode' name='sequencerPartitionContainers[" + i + "].identificationBarcode'/></div></td></tr>");
      b.append("<tr><td>Location:</td><td><input type='text' id='sequencerPartitionContainers[" + i + "].locationBarcode' name='sequencerPartitionContainers[" + i + "].locationBarcode'/></td></tr>");
      b.append("<tr><td>Paired:</td><td><input type='checkbox' id='sequencerPartitionContainers[" + i + "].paired' name='sequencerPartitionContainers[" + i + "].paired'/></td></tr>");
      b.append("</table>");
      b.append("<div id='partitionErrorDiv'> </div>");
      b.append("<div id='partitionDiv'>");
      b.append("<input id='chamber1' name='container" + i + "Select' onchange='Run.ui.changeLS454Chamber(this, " + i + ");' type='radio' value='1'/>1 ");
      b.append("<input id='chamber2' name='container" + i + "Select' onchange='Run.ui.changeLS454Chamber(this, " + i + ");' type='radio' value='2'/>2 ");
      b.append("<input id='chamber4' name='container" + i + "Select' onchange='Run.ui.changeLS454Chamber(this, " + i + ");' type='radio' value='4'/>4 ");
      b.append("<input id='chamber8' name='container" + i + "Select' onchange='Run.ui.changeLS454Chamber(this, " + i + ");' type='radio' value='8'/>8 ");
      b.append("<input id='chamber16' name='container" + i + "Select' onchange='Run.ui.changeLS454Chamber(this, " + i + ");' type='radio' value='16'/>16<br/>");
      b.append("<div id='containerdiv" + i + "'> </div>");
      b.append("</div>");

      SequencerPartitionContainer<SequencerPoolPartition> f = dataObjectFactory.getSequencerPartitionContainer();
      run.addSequencerPartitionContainer(f);
    }
    return JSONUtils.SimpleJSONResponse(b.toString());
  }
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    StringBuilder b = new StringBuilder();
    b.append("<table class='in'>");
    b.append("<th>Chamber No.</th>");
    b.append("<th>Pool</th>");

    LS454Run run = (LS454Run) session.getAttribute("run_" + json.getString("run_cId"));
    SequencerPartitionContainer<SequencerPoolPartition> f = run.getSequencerPartitionContainers().get(container);
    f.setPartitionLimit(numChambers);
    f.initEmptyPartitions();

    for (int i = 0; i < numChambers; i++) {
      b.append("<tr><td>" + (i + 1) + "</td>");
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      throw new SecurityException();
    }
  }

  public Run getLs454Run() {
    return new LS454Run();
  }
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  public Run getLs454Run() {
    return new LS454Run();
  }

  public Run getLs454Run(User user) {
    return new LS454Run(user);
  }
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    return new LS454Run(user);
  }

  public Run getLs454Run(Experiment experiment, User user) {
    if (experiment.userCanWrite(user)) {
      return new LS454Run(user);
    }
    else {
      throw new SecurityException();
    }
  }
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Related Classes of uk.ac.bbsrc.tgac.miso.core.data.impl.ls454.LS454Pool

  • com.eaglegenomics.simlims.core.SecurityProfile
  • uk.ac.bbsrc.tgac.miso.core.data.impl.StatusImpl
  • uk.ac.bbsrc.tgac.miso.core.factory.TgacDataObjectFactory
  • uk.ac.bbsrc.tgac.miso.notification.consumer.service.mechanism.LS454NotificationMessageConsumerMechanism
  • uk.ac.bbsrc.tgac.miso.spring.ajax.RunControllerHelperService
  • uk.ac.bbsrc.tgac.miso.webapp.controller.EditLS454PoolController
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