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

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

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    for (String s : codes) {
      if (LimsUtils.isBase64String(s)) {
        //Base64-encoded string, most likely a barcode image beeped in. decode and search
        s = new String(Base64.decodeBase64(s));
      }
      emPCRDilution ed = requestManager.getEmPcrDilutionByBarcode(s);
      if (ed != null) {
        sb.append("<span>");
        sb.append("<input type='checkbox' value='" + s + "' name='importdilslist' id='importdilslist_" + ed.getName() + "'/>");
        sb.append("<label for='importdilslist_" + ed.getName() + "'>" + ed.getName() + " (" + s + ")</label>");
        sb.append("</span>");
      }
    }
    sb.append("</div>");
    sb.append("<a onclick='Utils.ui.checkAll(\"importdilslist\"); return false;' href='javascript:void(0);'>All</a> " +
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        }
      }
      if (json.has("pcrId") && !json.get("pcrId").equals("")) {
        Long pcrId = Long.parseLong(json.getString("pcrId"));
        emPCR pcr = requestManager.getEmPcrById(pcrId);
        emPCRDilution newDilution = dataObjectFactory.getEmPCRDilution();
        newDilution.setSecurityProfile(pcr.getSecurityProfile());
        newDilution.setDilutionCreator(json.getString("pcrDilutionCreator"));
        newDilution.setCreationDate(new SimpleDateFormat("dd/MM/yyyy").parse(json.getString("pcrDilutionDate")));
        newDilution.setConcentration(Double.parseDouble(json.getString("results")));
        newDilution.setEmPCR(pcr);
        requestManager.saveEmPCRDilution(newDilution);

        StringBuilder sb = new StringBuilder();
        sb.append("<tr>");
        //sb.append("<th>ID</th><th>Done By</th><th>Date</th><th>Barcode</th><th>Results</th>");
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    }
  }

  public class LazyEmPCRDilutionMapper implements RowMapper<emPCRDilution> {
    public emPCRDilution mapRow(ResultSet rs, int rowNum) throws SQLException {
      emPCRDilution pcrDilution = dataObjectFactory.getEmPCRDilution();
      pcrDilution.setId(rs.getLong("dilutionId"));
      pcrDilution.setName(rs.getString("name"));
      pcrDilution.setConcentration(rs.getDouble("concentration"));
      pcrDilution.setIdentificationBarcode(rs.getString("identificationBarcode"));
      pcrDilution.setCreationDate(rs.getDate("creationDate"));
      pcrDilution.setDilutionCreator(rs.getString("dilutionUserName"));

      //pcrDilution.setLastUpdated(rs.getTimestamp("lastUpdated"));

      try {
        pcrDilution.setSecurityProfile(securityProfileDAO.get(rs.getLong("securityProfile_profileId")));
        pcrDilution.setEmPCR(emPcrDAO.lazyGet(rs.getLong("emPCR_pcrId")));
      }
      catch (IOException e) {
        log.error("Cannot map from database to emPCRDilution: ", e);
        e.printStackTrace();
      }
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    }
  }

  public class EmPCRDilutionMapper implements RowMapper<emPCRDilution> {
    public emPCRDilution mapRow(ResultSet rs, int rowNum) throws SQLException {
      emPCRDilution pcrDilution = dataObjectFactory.getEmPCRDilution();
      pcrDilution.setId(rs.getLong("dilutionId"));
      pcrDilution.setName(rs.getString("name"));
      pcrDilution.setConcentration(rs.getDouble("concentration"));
      pcrDilution.setIdentificationBarcode(rs.getString("identificationBarcode"));
      pcrDilution.setCreationDate(rs.getDate("creationDate"));
      pcrDilution.setDilutionCreator(rs.getString("dilutionUserName"));

      //pcrDilution.setLastUpdated(rs.getTimestamp("lastUpdated"));

      try {
        pcrDilution.setSecurityProfile(securityProfileDAO.get(rs.getLong("securityProfile_profileId")));
        pcrDilution.setEmPCR(emPcrDAO.get(rs.getLong("emPCR_pcrId")));
      }
      catch (IOException e1) {
        e1.printStackTrace();
      }
      return pcrDilution;
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                          }
                  )
  )
  public emPCRDilution getEmPCRDilutionById(long dilutionId) throws IOException {
    List eResults = template.query(EMPCR_DILUTION_SELECT_BY_DILUTION_ID, new Object[]{dilutionId}, new LazyEmPCRDilutionMapper());
    emPCRDilution e = eResults.size() > 0 ? (emPCRDilution) eResults.get(0) : null;
    return e;
  }
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    return e;
  }

  public emPCRDilution getEmPCRDilutionByBarcode(String barcode) throws IOException {
    List eResults = template.query(EMPCR_DILUTION_SELECT_BY_IDENTIFICATION_BARCODE, new Object[]{barcode}, new LazyEmPCRDilutionMapper());
    emPCRDilution e = eResults.size() > 0 ? (emPCRDilution) eResults.get(0) : null;
    return e;
  }
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      if (!pool.userCanRead(user)) {
        throw new SecurityException("Permission denied.");
      }

      if (dilutionId != null) {
          emPCRDilution ed = requestManager.getEmPcrDilutionById(dilutionId);
        if (ed != null) {
          pool.addPoolableElement(ed);
        }
      }
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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) {
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      if (!pool.userCanRead(user)) {
        throw new SecurityException("Permission denied.");
      }

      if (dilutionId != null) {
          emPCRDilution ed = requestManager.getEmPcrDilutionById(dilutionId);
        if (ed != null) {
          pool.addPoolableElement(ed);
        }
      }
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  @RequestMapping(value = "/import", method = RequestMethod.POST)
  public String importEmPCRDilutionsToPool(HttpServletRequest request, ModelMap model) throws IOException {
    SolidPool p = (SolidPool)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) {
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Related Classes of uk.ac.bbsrc.tgac.miso.core.data.impl.emPCRDilution

  • com.eaglegenomics.simlims.core.SecurityProfile
  • uk.ac.bbsrc.tgac.miso.spring.ajax.LibraryControllerHelperService
  • uk.ac.bbsrc.tgac.miso.spring.ajax.PoolControllerHelperService
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLDilutionDAO
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLDilutionDAO$EmPCRDilutionMapper
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLDilutionDAO$LazyEmPCRDilutionMapper
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLEmPCRDilutionDAO
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLEmPCRDilutionDAO$EmPCRDilutionMapper
  • uk.ac.bbsrc.tgac.miso.webapp.controller.EditLS454PoolController
  • uk.ac.bbsrc.tgac.miso.webapp.controller.EditSolidPoolController
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