public JSONObject plateElementsDataTable(HttpSession session, JSONObject json) {
    if (json.has("plateId")) {
      try {
        JSONObject j = new JSONObject();
        JSONArray jsonArray = new JSONArray();
        long plateId = json.getLong("plateId");

        Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
            requestManager.getPlateById(plateId);
        if (plate != null) {
          for (Plateable p : plate.getElements()) {
            if (p instanceof Library) {
              Library l = (Library) p;
              String strategyName = "No barcode";

              StringBuilder seqbuilder = new StringBuilder();
              if (!l.getTagBarcodes().isEmpty()) {
                int count = 1;
                Collection<TagBarcode> barcodes = l.getTagBarcodes().values();
                for (TagBarcode tb : barcodes) {
                  strategyName = tb.getStrategyName();
                  seqbuilder.append(tb.getSequence());
                  if (l.getTagBarcodes().values().size() > 1
                      && count < l.getTagBarcodes().values().size()) {
                    seqbuilder.append("-");
                  }
                  count++;
                }
              } else {
                log.info("No tag barcodes!");
              }

              jsonArray.add(
                  "['"
                      + l.getName()
                      + "','"
                      + l.getAlias()
                      + "','"
                      + strategyName
                      + "','"
                      + seqbuilder.toString()
                      + "','"
                      + "<a href=\"/miso/library/"
                      + l.getId()
                      + "\"><span class=\"ui-icon ui-icon-pencil\"></span></a>"
                      + "']");
            }
          }
        }
        j.put("elementsArray", jsonArray);
        return j;
      } catch (IOException e) {
        log.debug("Failed", e);
        return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
      }
    } else {
      return JSONUtils.SimpleJSONError("No plates to show");
    }
  }
 @RequestMapping(value = "projects", method = RequestMethod.GET)
 public @ResponseBody String jsonRest() throws IOException {
   StringBuilder sb = new StringBuilder();
   Collection<Project> lp = requestManager.listAllProjects();
   int pi = 0;
   for (Project p : lp) {
     pi++;
     sb.append(jsonRestProjectList(p.getProjectId()));
     if (pi < lp.size()) {
       sb.append(",");
     }
   }
   return "[" + sb.toString() + "]";
 }
  public JSONObject getTagBarcodesForMaterialType(HttpSession session, JSONObject json) {
    Map<String, Object> responseMap = new HashMap<String, Object>();
    if (json.has("materialType") && !"".equals(json.getString("materialType"))) {
      String materialType = json.getString("materialType");
      StringBuilder srb = new StringBuilder();
      srb.append("<select name='tagBarcode' id='tagBarcodes'>");
      srb.append("<option value='0' selected='selected'>No barcode</option>");
      //      for (TagBarcode tb :
      // requestManager.listPlateBarcodesByMaterialType(PlateMaterialType.get(materialType))) {
      //        srb.append("<option value='" + tb.getTagBarcodeId() + "'>" + tb.getName() + " ("+
      // tb.getSequence()+")</option>");
      //      }
      srb.append("</select>");

      responseMap.put("plateBarcodes", srb.toString());
    } else {
      return JSONUtils.SimpleJSONError("Unrecognised MaterialType");
    }
    return JSONUtils.JSONObjectResponse(responseMap);
  }
  public String jsonRestProjectList(Long projectId) throws IOException {
    StringBuilder sb = new StringBuilder();

    Project p = requestManager.getProjectById(projectId);
    sb.append("'id':'" + projectId + "'");
    sb.append(",");
    sb.append("'name':'" + p.getName() + "'");
    sb.append(",");
    sb.append("'alias':'" + p.getAlias() + "'");

    return "{" + sb.toString() + "}";
  }
 @Override
 public Set<File> generateFilePath(SequencerPoolPartition partition, Dilution l)
     throws SubmissionException {
   Pool<? extends Poolable> pool = partition.getPool();
   if (pool != null) {
     if (pool.getExperiments() != null) {
       Collection<Experiment> experiments = pool.getExperiments();
       Experiment experiment = experiments.iterator().next();
       StringBuilder filePath = new StringBuilder();
       if (!"".equals(basePath)) {
         filePath.append(
             partition.getSequencerPartitionContainer().getRun().getFilePath()
                 + "/Data/Intensities/BaseCalls/PAP/Project_"
                 + experiment.getStudy().getProject().getAlias()
                 + "/Sample_"
                 + l.getLibrary().getName()
                 + "/"
                 + l.getLibrary().getName());
       } else {
         filePath.append(
             basePath
                 + "/"
                 + experiment.getStudy().getProject().getAlias()
                 + "/Sample_"
                 + l.getLibrary().getName()
                 + "/"
                 + l.getLibrary().getName());
       }
       if (l.getLibrary().getTagBarcodes() != null && !l.getLibrary().getTagBarcodes().isEmpty()) {
         filePath.append("_");
         for (TagBarcode tb : l.getLibrary().getTagBarcodes().values()) {
           filePath.append(tb.getSequence());
         }
       }
       filePath.append("_L00" + partition.getPartitionNumber() + "*.fastq.gz");
       Set<File> files = new HashSet<File>();
       files.add(new File(filePath.toString()));
       return files;
     } else {
       throw new SubmissionException("partition.getPool=null!");
     }
   } else {
     throw new SubmissionException("Collection of experiments is empty");
   }
 }
  @Override
  public Set<File> generateFilePaths(SequencerPoolPartition partition) throws SubmissionException {
    log.debug("Generating filepaths for partition " + partition.getId());
    Set<File> filePaths = new HashSet<File>();

    Pool pool = partition.getPool();
    if (pool == null) {
      throw new SubmissionException("partition.getPool=null!");
    } else {
      Collection<Experiment> experiments = pool.getExperiments();
      if (experiments.isEmpty()) {
        throw new SubmissionException("Collection or experiments is empty");
      } else {
        Collection<LibraryDilution> libraryDilutions = pool.getDilutions();
        if (libraryDilutions.isEmpty()) {
          throw new SubmissionException("Collection or libraryDilutions is empty");
        } else {
          for (Experiment e : experiments) {
            StringBuilder filePath = new StringBuilder();

            filePath.append(partition.getSequencerPartitionContainer().getRun().getFilePath());
            filePath.append("/Data/Intensities/BaseCalls/PAP/Project_");
            filePath.append(e.getStudy().getProject().getAlias());
            filePath.append("/Sample_");

            for (LibraryDilution l : libraryDilutions) {
              // filePath.append(l.getLibrary().getName()+"/");
              /*
                      +l.getLibrary().getName()+"_"+l.getLibrary().getTagBarcode().getSequence());
              filePath.append("L00"+lane.getPartitionNumber())
              */
              String folder = filePath.toString() + l.getLibrary().getName() + "/*.fastq.gz";
              // System.out.println(folder);
              File file = new File(folder);
              filePaths.add(file);
            }
          }
        }
      }
    }
    return (filePaths);
  }
  @RequestMapping(value = "project/{projectId}", method = RequestMethod.GET)
  public @ResponseBody String jsonRestProject(@PathVariable Long projectId, ModelMap model)
      throws IOException {
    StringBuilder sb = new StringBuilder();

    Project p = requestManager.getProjectById(projectId);
    sb.append("'id':'" + projectId + "'");
    sb.append(",");
    sb.append("'name':'" + p.getName() + "'");
    sb.append(",");
    sb.append("'alias':'" + p.getAlias() + "'");
    sb.append(",");
    sb.append("'progress':'" + p.getProgress().name() + "'");
    sb.append(",");
    sb.append("'description':'" + p.getDescription() + "'");
    sb.append(",");

    sb.append("'overviews':[");
    if (p.getOverviews().size() > 0) {
      int oi = 0;
      for (ProjectOverview overview : p.getOverviews()) {
        oi++;
        sb.append("{");
        sb.append("'allSampleQcPassed':" + overview.getAllSampleQcPassed());
        sb.append(",");
        sb.append("'libraryPreparationComplete':" + overview.getLibraryPreparationComplete());
        sb.append(",");
        sb.append("'allLibrariesQcPassed':" + overview.getAllLibrariesQcPassed());
        sb.append(",");
        sb.append("'allPoolsConstructed':" + overview.getAllPoolsConstructed());
        sb.append(",");
        sb.append("'allRunsCompleted':" + overview.getAllRunsCompleted());
        sb.append(",");
        sb.append("'primaryAnalysisCompleted':" + overview.getPrimaryAnalysisCompleted());
        sb.append("}");
        if (oi < p.getOverviews().size()) {
          sb.append(",");
        }
      }
    }
    sb.append("]");
    sb.append(",");

    sb.append("'samples':[");
    Collection<Sample> samples = requestManager.listAllSamplesByProjectId(projectId);
    if (samples.size() > 0) {
      int si = 0;
      for (Sample sample : samples) {
        si++;
        String sampleQubit = "not available";
        if (requestManager.listAllSampleQCsBySampleId(sample.getId()).size() > 0) {
          ArrayList<SampleQC> sampleQcList =
              new ArrayList(requestManager.listAllSampleQCsBySampleId(sample.getId()));
          SampleQC lastQc = sampleQcList.get(sampleQcList.size() - 1);
          sampleQubit = (lastQc.getResults() != null ? lastQc.getResults().toString() : "");
        }
        sb.append("{");
        sb.append("'alias':'" + sample.getAlias() + "'");
        sb.append(",");
        sb.append(
            "'qcPassed':'"
                + (sample.getQcPassed() != null ? sample.getQcPassed().toString() : "")
                + "'");
        sb.append(",");

        sb.append(
            "'receivedDate':'"
                + (sample.getReceivedDate() != null
                    ? LimsUtils.getDateAsString(sample.getReceivedDate())
                    : "not available")
                + "'");
        sb.append(",");
        sb.append(
            "'sampleType':'"
                + (sample.getSampleType() != null ? sample.getSampleType() : "")
                + "'");
        sb.append(",");
        sb.append("'sampleQubit':'" + sampleQubit + "'");
        sb.append("}");

        if (si < samples.size()) {
          sb.append(",");
        }
      }
    }
    sb.append("]");
    sb.append(",");

    sb.append("'runs':[");
    Collection<Run> runs = requestManager.listAllRunsByProjectId(projectId);
    if (runs.size() > 0) {
      int ri = 0;
      for (Run run : runs) {
        ri++;
        if (!run.getStatus().getHealth().getKey().equals("Failed")) {
          ArrayList<String> runSamples = new ArrayList();
          Collection<SequencerPartitionContainer<SequencerPoolPartition>> spcs =
              requestManager.listSequencerPartitionContainersByRunId(run.getId());
          if (spcs.size() > 0) {
            for (SequencerPartitionContainer<SequencerPoolPartition> spc : spcs) {

              if (spc.getPartitions().size() > 0) {
                for (SequencerPoolPartition spp : spc.getPartitions()) {
                  if (spp.getPool() != null) {
                    if (spp.getPool().getDilutions().size() > 0) {
                      for (Dilution dilution : spp.getPool().getDilutions()) {
                        Sample sample = dilution.getLibrary().getSample();
                        if (sample.getProject().equals(p)) {
                          runSamples.add(sample.getAlias());
                        }
                      }
                    }
                  }
                }
              }
            }
          }

          sb.append("{");
          sb.append("'name':'" + run.getName() + "'");
          sb.append(",");
          sb.append(
              "'status':'"
                  + (run.getStatus() != null && run.getStatus().getHealth() != null
                      ? run.getStatus().getHealth().getKey()
                      : "")
                  + "'");
          sb.append(",");
          sb.append(
              "'startDate':'"
                  + (run.getStatus() != null && run.getStatus().getStartDate() != null
                      ? run.getStatus().getStartDate().toString()
                      : "")
                  + "'");
          sb.append(",");
          sb.append(
              "'completionDate':'"
                  + (run.getStatus() != null && run.getStatus().getCompletionDate() != null
                      ? run.getStatus().getCompletionDate().toString()
                      : "")
                  + "'");
          sb.append(",");
          sb.append(
              "'platformType':'"
                  + (run.getPlatformType() != null ? run.getPlatformType().getKey() : "")
                  + "'");
          sb.append(",");
          sb.append("'samples':[");
          if (runSamples.size() > 0) {
            int rsi = 0;
            for (String alias : runSamples) {
              rsi++;
              sb.append("{'sampleAlias':'" + alias + "'}");
              if (rsi < runSamples.size()) {
                sb.append(",");
              }
            }
          }
          sb.append("]");
          sb.append("}");
          if (ri < runs.size()) {
            sb.append(",");
          }
        }
      }
    }
    sb.append("]");

    return "{" + sb.toString() + "}";
  }
  private Map<String, Run> processRunJSON(
      HealthType ht, JSONArray runs, RequestManager requestManager) {
    Map<String, Run> updatedRuns = new HashMap<String, Run>();
    List<Run> runsToSave = new ArrayList<Run>();
    // 2011-01-25 15:37:27.093
    DateFormat logDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
    DateFormat simpleLogDateFormat = new SimpleDateFormat("yyyyMMdd");
    Pattern simpleDateRegex = Pattern.compile("[0-9]{8}");

    StringBuilder sb = new StringBuilder();

    for (JSONObject run : (Iterable<JSONObject>) runs) {
      String runName = run.getString("runName");
      sb.append("Processing " + runName + "\n");
      log.debug("Processing " + runName);

      if (run.has("status")) {
        String xml = run.getString("status");
        Status is = new SolidStatus(xml);
        is.setHealth(ht);
        is.setRunName(runName);

        Run r = null;
        Matcher m = p.matcher(runName);
        if (m.matches()) {
          try {
            r = requestManager.getRunByAlias(runName);
          } catch (IOException ioe) {
            log.warn(
                "Cannot find run by this alias. This usually means the run hasn't been previously imported. If attemptRunPopulation is false, processing will not take place for this run!");
          }
        }

        try {
          if (attemptRunPopulation) {
            if (r == null) {
              log.debug("Saving new run and status: " + is.getRunName());
              r = new SolidRun(xml);
              r.getStatus().setHealth(ht);
              if (run.has("fullPath")) {
                r.setFilePath(run.getString("fullPath"));
              }

              SequencerReference sr = null;
              if (run.has("sequencerName")) {
                sr = requestManager.getSequencerReferenceByName(run.getString("sequencerName"));
                r.getStatus().setInstrumentName(run.getString("sequencerName"));
                r.setSequencerReference(sr);
              }
              if (r.getSequencerReference() == null) {
                sr = requestManager.getSequencerReferenceByName(m.group(1));
                r.getStatus().setInstrumentName(m.group(1));
                r.setSequencerReference(sr);
              }
              if (r.getSequencerReference() == null) {
                sr = requestManager.getSequencerReferenceByName(r.getStatus().getInstrumentName());
                r.setSequencerReference(sr);
              }

              if (r.getSequencerReference() != null) {
                if (run.has("startDate")) {
                  try {
                    log.debug("Updating start date:" + run.getString("startDate"));

                    Matcher m2 = simpleDateRegex.matcher(run.getString("startDate"));
                    if (m2.matches()) {
                      r.getStatus()
                          .setStartDate(simpleLogDateFormat.parse(run.getString("startDate")));
                    } else {
                      r.getStatus().setStartDate(logDateFormat.parse(run.getString("startDate")));
                    }
                  } catch (ParseException e) {
                    log.error(e.getMessage());
                    e.printStackTrace();
                  }
                }

                if (run.has("completionDate")) {
                  try {
                    if (run.get("completionDate") != null
                        && !run.getString("completionDate").equals("null")) {
                      log.debug("Updating completion date:" + run.getString("completionDate"));
                      r.getStatus()
                          .setCompletionDate(logDateFormat.parse(run.getString("completionDate")));
                    } else {
                      r.getStatus().setCompletionDate(null);
                    }
                  } catch (ParseException e) {
                    log.error(e.getMessage());
                    e.printStackTrace();
                  }
                }
              }
            } else {
              log.debug("Updating existing run and status: " + is.getRunName());

              r.setAlias(runName);
              r.setPlatformType(PlatformType.SOLID);

              if (r.getSequencerReference() == null) {
                SequencerReference sr = null;
                if (run.has("sequencerName")) {
                  sr = requestManager.getSequencerReferenceByName(run.getString("sequencerName"));
                  r.getStatus().setInstrumentName(run.getString("sequencerName"));
                  r.setSequencerReference(sr);
                }
                if (r.getSequencerReference() == null) {
                  sr = requestManager.getSequencerReferenceByName(m.group(1));
                  r.getStatus().setInstrumentName(m.group(1));
                  r.setSequencerReference(sr);
                }
                if (r.getSequencerReference() == null) {
                  sr =
                      requestManager.getSequencerReferenceByName(r.getStatus().getInstrumentName());
                  r.setSequencerReference(sr);
                }
              }
              if (r.getSequencerReference() != null) {
                if (run.has("startDate")) {
                  try {
                    log.debug("Updating start date:" + run.getString("startDate"));

                    Matcher m2 = simpleDateRegex.matcher(run.getString("startDate"));
                    if (m2.matches()) {
                      r.getStatus()
                          .setStartDate(simpleLogDateFormat.parse(run.getString("startDate")));
                    } else {
                      r.getStatus().setStartDate(logDateFormat.parse(run.getString("startDate")));
                    }
                  } catch (ParseException e) {
                    log.error(e.getMessage());
                    e.printStackTrace();
                  }
                }

                if (run.has("completionDate")) {
                  try {
                    if (run.get("completionDate") != null
                        && !run.getString("completionDate").equals("null")) {
                      log.debug("Updating completion date:" + run.getString("completionDate"));
                      r.getStatus()
                          .setCompletionDate(logDateFormat.parse(run.getString("completionDate")));
                    } else {
                      r.getStatus().setCompletionDate(null);
                    }
                  } catch (ParseException e) {
                    log.error(e.getMessage());
                    e.printStackTrace();
                  }
                }

                // update path if changed
                if (run.has("fullPath")
                    && !"".equals(run.getString("fullPath"))
                    && r.getFilePath() != null
                    && !"".equals(r.getFilePath())) {
                  if (!run.getString("fullPath").equals(r.getFilePath())) {
                    log.debug(
                        "Updating run file path:"
                            + r.getFilePath()
                            + " -> "
                            + run.getString("fullPath"));
                    r.setFilePath(run.getString("fullPath"));
                  }
                }

                // update status if run isn't completed or failed
                if (!r.getStatus().getHealth().equals(HealthType.Completed)
                    && !r.getStatus().getHealth().equals(HealthType.Failed)) {
                  log.debug(
                      "Saving previously saved status: "
                          + is.getRunName()
                          + " ("
                          + r.getStatus().getHealth().getKey()
                          + " -> "
                          + is.getHealth().getKey()
                          + ")");
                  r.setStatus(is);
                }
              }
            }

            if (r.getSequencerReference() != null) {
              List<SequencerPartitionContainer<SequencerPoolPartition>> fs =
                  ((SolidRun) r).getSequencerPartitionContainers();
              if (fs.isEmpty()) {
                if (run.has("containerId") && !"".equals(run.getString("containerId"))) {
                  Collection<SequencerPartitionContainer<SequencerPoolPartition>> pfs =
                      requestManager.listSequencerPartitionContainersByBarcode(
                          run.getString("containerId"));
                  if (!pfs.isEmpty()) {
                    if (pfs.size() == 1) {
                      SequencerPartitionContainer lf =
                          new ArrayList<SequencerPartitionContainer<SequencerPoolPartition>>(pfs)
                              .get(0);
                      if (lf.getSecurityProfile() != null && r.getSecurityProfile() == null) {
                        r.setSecurityProfile(lf.getSecurityProfile());
                      }
                      if (lf.getPlatform() == null
                          && r.getSequencerReference().getPlatform() != null) {
                        lf.setPlatform(r.getSequencerReference().getPlatform());
                      }
                      //                      else {
                      //                        lf.setPlatformType(PlatformType.SOLID);
                      //                      }
                      ((RunImpl) r).addSequencerPartitionContainer(lf);
                    }
                  } else {
                    log.debug("No containers linked to run " + r.getId() + ": creating...");
                    SequencerPartitionContainer f = new SequencerPartitionContainerImpl();
                    f.setSecurityProfile(r.getSecurityProfile());
                    f.initEmptyPartitions();
                    f.setIdentificationBarcode(run.getString("containerNum"));
                    if (f.getPlatform() == null
                        && r.getSequencerReference().getPlatform() != null) {
                      f.setPlatform(r.getSequencerReference().getPlatform());
                    }
                    //                    else {
                    //                      f.setPlatformType(PlatformType.SOLID);
                    //                    }
                    // f.setPaired(r.getPairedEnd());
                    ((RunImpl) r).addSequencerPartitionContainer(f);
                  }
                }
              } else {
                SequencerPartitionContainer f = fs.iterator().next();
                log.debug("Got container " + f.getId());

                if (f.getSecurityProfile() == null) {
                  f.setSecurityProfile(r.getSecurityProfile());
                }

                if (f.getPlatform() == null && r.getSequencerReference().getPlatform() != null) {
                  f.setPlatform(r.getSequencerReference().getPlatform());
                }
                //                else {
                //                  f.setPlatformType(PlatformType.SOLID);
                //                }

                if (run.has("containerId") && !"".equals(run.getString("containerId"))) {
                  f.setIdentificationBarcode(run.getString("containerId"));
                }

                long flowId = requestManager.saveSequencerPartitionContainer(f);
                f.setId(flowId);
              }

              updatedRuns.put(r.getAlias(), r);
              runsToSave.add(r);
            }
          }
        } catch (IOException e) {
          log.error(e.getMessage());
          e.printStackTrace();
        }
      }
    }

    try {
      if (runsToSave.size() > 0) {
        int[] saved = requestManager.saveRuns(runsToSave);
        log.info("Batch saved " + saved.length + " / " + runs.size() + " runs");
      }
    } catch (IOException e) {
      log.error("Couldn't save run batch: " + e.getMessage());
      e.printStackTrace();
    }

    return updatedRuns;
  }