public JSONObject changePlateLocation(HttpSession session, JSONObject json) {
    Long plateId = json.getLong("plateId");
    String locationBarcode = json.getString("locationBarcode");

    try {
      String newLocation = LimsUtils.lookupLocation(locationBarcode);
      if (newLocation != null) {
        User user =
            securityManager.getUserByLoginName(
                SecurityContextHolder.getContext().getAuthentication().getName());
        // Plate<LinkedList<Plateable>, Plateable> plate = requestManager.<LinkedList<Plateable>,
        // Plateable> getPlateById(plateId);
        Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
            requestManager.getPlateById(plateId);
        plate.setLocationBarcode(locationBarcode);
        /*
        Note note = new Note();
        note.setInternalOnly(true);
        note.setText("Location changed to " + newLocation + " by " + user.getLoginName() + " on " + new Date());
        note.setOwner(user);
        note.setCreationDate(new Date());
        plate.getNotes().add(note);
        requestManager.saveSampleNote(sample, note);
        */
        requestManager.savePlate(plate);
      } else {
        return JSONUtils.SimpleJSONError("New location barcode not recognised");
      }
    } catch (IOException e) {
      e.printStackTrace();
      return JSONUtils.SimpleJSONError(e.getMessage());
    }

    return JSONUtils.SimpleJSONResponse("Plate saved successfully");
  }
  public JSONObject printPlateBarcodes(HttpSession session, JSONObject json) {
    try {
      User user =
          securityManager.getUserByLoginName(
              SecurityContextHolder.getContext().getAuthentication().getName());

      String serviceName = null;
      if (json.has("serviceName")) {
        serviceName = json.getString("serviceName");
      }

      MisoPrintService<File, PrintContext<File>> mps = null;
      if (serviceName == null) {
        Collection<MisoPrintService> services =
            printManager.listPrintServicesByBarcodeableClass(Plate.class);
        if (services.size() == 1) {
          mps = services.iterator().next();
        } else {
          return JSONUtils.SimpleJSONError(
              "No serviceName specified, but more than one available service able to print this barcode type.");
        }
      } else {
        mps = printManager.getPrintService(serviceName);
      }

      Queue<File> thingsToPrint = new LinkedList<File>();
      JSONArray ss = JSONArray.fromObject(json.getString("plates"));
      for (JSONObject s : (Iterable<JSONObject>) ss) {
        try {
          Long plateId = s.getLong("plateId");
          // Plate<LinkedList<Plateable>, Plateable>  plate = requestManager.<LinkedList<Plateable>,
          // Plateable> getPlateById(plateId);
          Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
              requestManager.getPlateById(plateId);
          // autosave the barcode if none has been previously generated
          if (plate.getIdentificationBarcode() == null
              || "".equals(plate.getIdentificationBarcode())) {
            requestManager.savePlate(plate);
          }
          File f = mps.getLabelFor(plate);
          if (f != null) thingsToPrint.add(f);
        } catch (IOException e) {
          e.printStackTrace();
          return JSONUtils.SimpleJSONError("Error printing barcodes: " + e.getMessage());
        }
      }
      PrintJob pj = printManager.print(thingsToPrint, mps.getName(), user);
      return JSONUtils.SimpleJSONResponse("Job " + pj.getJobId() + " : Barcodes printed.");
    } catch (MisoPrintException e) {
      e.printStackTrace();
      return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
    } catch (IOException e) {
      e.printStackTrace();
      return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
    }
  }
 public JSONObject downloadPlateInputForm(HttpSession session, JSONObject json) {
   if (json.has("documentFormat")) {
     String documentFormat = json.getString("documentFormat");
     try {
       File f =
           misoFileManager.getNewFile(
               Plate.class,
               "forms",
               "PlateInputForm-" + LimsUtils.getCurrentDateAsString() + "." + documentFormat);
       FormUtils.createPlateInputSpreadsheet(f);
       return JSONUtils.SimpleJSONResponse("" + f.getName().hashCode());
     } catch (Exception e) {
       e.printStackTrace();
       return JSONUtils.SimpleJSONError("Failed to get plate input form: " + e.getMessage());
     }
   } else {
     return JSONUtils.SimpleJSONError("Missing project ID or document format supplied.");
   }
 }
 public JSONObject deletePlate(HttpSession session, JSONObject json) {
   try {
     User user =
         securityManager.getUserByLoginName(
             SecurityContextHolder.getContext().getAuthentication().getName());
     if (user.isAdmin()) {
       if (json.has("plateId")) {
         Long plateId = json.getLong("plateId");
         requestManager.deletePlate(requestManager.getPlateById(plateId));
         return JSONUtils.SimpleJSONResponse("Plate deleted");
       } else {
         return JSONUtils.SimpleJSONError("No plate specified to delete.");
       }
     } else {
       return JSONUtils.SimpleJSONError("Only admins can delete objects.");
     }
   } catch (IOException e) {
     e.printStackTrace();
     return JSONUtils.SimpleJSONError("Error getting currently logged in user.");
   }
 }
Ejemplo n.º 5
0
  @Deprecated
  public JSONObject previewExperiment(HttpSession session, JSONObject json) {
    String experimentId = (String) json.get("experimentId");

    try {
      Experiment e = requestManager.getExperimentById(Long.parseLong(experimentId));
      Collection<Run> runs = requestManager.listRunsByExperimentId(e.getExperimentId());

      session.setAttribute("experiment", e);

      StringBuilder rb = new StringBuilder();
      for (Run r : runs) {
        rb.append("<li><a href='/miso/run/")
            .append(r.getRunId())
            .append("'>")
            .append(r.getName())
            .append("</a></li>");
      }

      StringBuilder sb = new StringBuilder();
      if (e.getPool() != null) {
        if (e.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
          for (Object dil : e.getPool().getDilutions()) {
            Sample s = ((LibraryDilution) dil).getLibrary().getSample();
            sb.append("<li><a href='/miso/sample/")
                .append(s.getSampleId())
                .append("'>")
                .append(s.getName())
                .append("</a></li>");
          }
        } else {
          for (Object dil : e.getPool().getDilutions()) {
            Sample s =
                ((emPCRDilution) dil).getEmPCR().getLibraryDilution().getLibrary().getSample();
            sb.append("<li><a href='/miso/sample/")
                .append(s.getSampleId())
                .append("'>")
                .append(s.getName())
                .append("</a></li>");
          }
        }
      }

      StringBuilder b = new StringBuilder();
      b.append(
          "<div onclick=\"Effect.toggle('preview"
              + experimentId
              + "','blind'); return false;\">"
              + "<img src=\"/styles/images/moreinfo.png\" class=\"previewimage\"/></div>");
      b.append("<br/><div id=\"preview" + experimentId + "\" class='exppreview'>");
      b.append("Title: <b>").append(e.getTitle()).append("</b><br/>");
      b.append("Description: <b>").append(e.getDescription()).append("</b><br/>");
      b.append("Samples: <ul class=\"bullets\">").append(sb.toString()).append("</ul>");
      b.append("Runs: <ul class=\"bullets\">").append(rb.toString()).append("</ul>");
      b.append("</div>");
      return JSONUtils.SimpleJSONResponse(b.toString());

    } catch (IOException e) {
      log.debug("Failed", e);
      return JSONUtils.SimpleJSONError("Failed");
    }
  }