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");
    }
  }
Exemple #2
0
  @Test
  public void testLibraries() {
    try {
      // get row count of experiments in the dataset
      int expected = getDataSet().getTable("Library").getRowCount();

      // get number of experiments from the DAO
      int actual = getLibraryDAO().count();

      // test data contains 2 experiments, check size of returned list
      TestCase.assertEquals("Wrong number of Library", expected, actual);

      System.out.println("Expected number of Library: " + expected + ", actual: " + actual);

      for (Library d : random(getLibraryDAO(), actual, 5)) {
        TestCase.assertNotNull(d);
        TestCase.assertNotNull(d.getId());
      }
    } catch (Exception e) {
      e.printStackTrace();
      TestCase.fail();
    }
  }