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

Examples of uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryImpl


              String type = j.getString("libraryType");
              String selectionType = j.getString("selectionType");
              String strategyType = j.getString("strategyType");
              String locationBarcode = j.getString("locationBarcode");

              Library library = new LibraryImpl();
              library.setSample(sample);

              String libAlias = libraryNamingScheme.generateNameFor("alias", library);

              library.setAlias(libAlias);
              library.setSecurityProfile(sp);
              library.setDescription(descr);
              library.setPlatformName(platform);
              library.setCreationDate(new Date());
              library.setLocationBarcode(locationBarcode);
              library.setQcPassed(false);
              library.setLibraryType(requestManager.getLibraryTypeByDescription(type));
              library.setLibrarySelectionType(requestManager.getLibrarySelectionTypeByName(selectionType));
              library.setLibraryStrategyType(requestManager.getLibraryStrategyTypeByName(strategyType));

              boolean paired = false;
              if (!"".equals(j.getString("paired"))) {
                paired = j.getBoolean("paired");
              }
              library.setPaired(paired);

              if (j.has("tagBarcodes") && !"".equals(j.getString("tagBarcodes")) && !j.getString("tagBarcodes").contains("Select")) {
                String[] codes = j.getString("tagBarcodes").split(Pattern.quote("|"));
                HashMap<Integer, TagBarcode> barcodes = new HashMap<Integer, TagBarcode>();
                int count = 1;
                for (String code : codes) {
                  try {
                    long cl = Long.parseLong(code);
                    barcodes.put(count, requestManager.getTagBarcodeById(cl));
                  }
                  catch (NumberFormatException e) {
                    e.printStackTrace();
                    return JSONUtils.SimpleJSONError("Cannot save Library. It looks like there are tag barcodes for the library of "+sample.getAlias()+", but they cannot be processed");
                  }
                  finally {
                     count++;
                  }
                }
                library.setTagBarcodes(barcodes);
              }

              saveSet.add(library);
            }
            else {
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