Examples of org.molgenis.framework.db.Database

org.molgenis.framework.db.Database
Interface to manage and search persistent data Entity objects. It wraps basic functionality such as find, count, add, update and delete. It also has batch functions to add data in vast amount, especially added to support large scale data storage such as needed in life sciences. Furthermore, it has transaction capabilities, i.e., to add, update, and remove many entities as if it was one operation (ensuring all actions are complete succesfully or if it fails halfway, it gets undone).

  {
    // System.out.println("FrontControllerAuthenticator LOGIN called");
    try
    {


      Database db = request.getDatabase();


      if (db.getLogin().isAuthenticated())
      {
        return LoginStatus.ALREADY_LOGGED_IN;
      }


      // try to login
      boolean loggedIn = db.getLogin().login(db, username, password);


      // System.out.println("FrontControllerAuthenticator loggedIn: " +
      // loggedIn);


      if (loggedIn)
      {
        // TODO: Missing redirect???
        // Login login = new
        // org.molgenis.auth.DatabaseLogin(request.getDatabase(),
        // "ClusterDemo");


        // store login in session
        request.getRequest().getSession().setAttribute("login", db.getLogin());
        return LoginStatus.SUCCESSFULLY_LOGGED_IN;
      }
      else
      {
        return LoginStatus.AUTHENTICATION_FAILURE;

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  {
    // System.out.println("FrontControllerAuthenticator LOGOUT called");
    try
    {


      Database db = request.getDatabase();


      if (!db.getLogin().isAuthenticated())
      {
        return LogoutStatus.ALREADY_LOGGED_OUT;
      }


      // logout from database

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  {
    Tuple tuple0 = mock(Tuple.class);
    when(tuple0.getColNames()).thenReturn(Arrays.asList("Name", "Continent")).getMock();
    when(tuple0.getString("Name")).thenReturn("Netherlands");


    Database db = mock(Database.class);
    String query = "SELECT Name, Continent FROM Country";
    QueryRule queryRule = new QueryRule("Code", Operator.EQUALS, "NLD");
    when(db.sql(query, queryRule)).thenReturn(Arrays.asList(tuple0));
    when(db.sql("SELECT COUNT(*) FROM Country", queryRule)).thenReturn(Arrays.asList(tuple0));


    TupleTable jdbcTable = new JdbcTable(db, query, Arrays.asList(queryRule));
    try
    {
      // check columns

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    res.getResponse().setBufferSize(10000);
    res.getResponse().setContentType("text/html; charset=UTF-8");


    PrintWriter out = res.getResponse().getWriter();
    Database db = req.getDatabase();


    try
    {


      AuthStatus authStatus = MolgenisServiceAuthenticationHelper.handleAuthentication(req, out);


      if (!authStatus.isShowApi())
      {
        out.println("<html><body>");
        out.println(authStatus.getPrintMe());
        out.println("</body></html>");
      }
      else
      {
        // if no type selected: show data type choice
        if (req.getString(INPUT_DATATYPE) == null)
        {
          out.println("<html><body>");
          authStatus.getPrintMe();
          if (req.getDatabase().getLogin().isAuthenticated())
          {
            out.println(MolgenisServiceAuthenticationHelper.displayLogoutForm());
          }
          showDataTypeChoice(out, req);
          out.println("</body></html>");
        }
        // if no data provided, show csv input form
        else if (req.get(INPUT_DATA) == null && req.get(INPUT_FILE) == null)
        {
          out.println("<html><body>");
          authStatus.getPrintMe();
          if (req.getDatabase().getLogin().isAuthenticated())
          {
            out.println(MolgenisServiceAuthenticationHelper.displayLogoutForm());
          }
          showCsvInputForm(out, req);
          out.println("</body></html>");
        }
        // process request
        else
        {
          processRequest(req, out);
        }
      }
    }
    catch (Exception e)
    {
      out.println(e.getMessage());
      e.printStackTrace();
      logger.error(e.getMessage());
    }
    finally
    {
      out.flush();
      out.close();
      db.close();
    }


    logger.info("servlet took: " + (System.currentTimeMillis() - start_time) + " ms");
    logger.info("------------");

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    entityClass = req.getDatabase().getClassForName(simpleEntityName);


    String action = req.getString(INPUT_ACTION);


    // create a database
    Database db = req.getDatabase();


    CsvReader csvReader;
    if (req.get(INPUT_DATA) != null)
    {
      csvReader = new CsvReader(new StringReader(req.getString(INPUT_DATA)));
    }
    else if (req.get(INPUT_FILE) != null)
    {
      csvReader = new CsvReader(req.getFile(INPUT_FILE));
    }
    else
      csvReader = null;


    try
    {
      int nRowsChanged = 0;
      if (action.equals("ADD"))
      {
        File temp = File.createTempFile("molgenis", "tab");
        CsvWriter csvWriter = new CsvWriter(temp);
        try
        {
          if (req.get(INPUT_SILENT) != null && req.getBoolean(INPUT_SILENT) == true)
          {
            csvWriter.close();
            csvWriter = null;
          }


          if (req.get(INPUT_DATA) != null)
          {
            logger.info("processing textarea upload...");
            nRowsChanged = db.add(entityClass, csvReader, csvWriter);
          }
          else if (req.get(INPUT_FILE) != null)
          {
            logger.info("processing file upload...");
            nRowsChanged = db.add(entityClass, csvReader, csvWriter);
          }
          else
          {
            logger.error("no input data or input file provided.");
            out.print("ERROR: no input data or input file provided.");
          }
          out.print("Uploaded " + formatter.format(nRowsChanged) + " rows of "
              + entityClass.getCanonicalName() + "\n");
        }
        finally
        {
          if (csvWriter != null) csvWriter.close();
        }
        BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(temp),
            Charset.forName("UTF-8")));
        try
        {
          String line = null;
          while ((line = reader.readLine()) != null)
          {
            out.println(line);
          }
        }
        finally
        {
          IOUtils.closeQuietly(reader);
        }
        boolean ok = temp.delete();
        if (!ok) logger.warn("failed to delete file: " + temp);
      }
      else if (action.equals("UPDATE"))
      {
        if (req.get(INPUT_DATA) != null)
        {
          nRowsChanged = db.update(entityClass, csvReader);
          out.print("Updated " + formatter.format(nRowsChanged) + " rows of "
              + entityClass.getCanonicalName() + "\n");
        }
        else if (req.get(INPUT_FILE) != null)
        {
          nRowsChanged = db.update(entityClass, csvReader);
          out.print("Updated " + formatter.format(nRowsChanged) + " rows of "
              + entityClass.getCanonicalName() + "\n");
        }
      }
      else if (action.equals("REMOVE"))
      {
        if (req.get(INPUT_DATA) != null)
        {
          nRowsChanged = db.remove(entityClass, csvReader);
          out.print("Removed " + formatter.format(nRowsChanged) + " rows of "
              + entityClass.getCanonicalName() + "\n");
        }
        else if (req.get(INPUT_FILE) != null)
        {
          nRowsChanged = db.remove(entityClass, csvReader);
          out.print("Removed " + formatter.format(nRowsChanged) + " rows of "
              + entityClass.getCanonicalName() + "\n");
        }
      }
      else

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   * @param response
   */
  public void handleRequest(MolgenisRequest request, MolgenisResponse response) throws DatabaseException, IOException
  {


    Database db = request.getDatabase();
    this.db = db;


    // logout
    final HttpSession session = request.getRequest().getSession();
    if (request.getRequest().getParameter("__action") != null
        && request.getRequest().getParameter("__action").equalsIgnoreCase("Logout"))
    {
      session.setAttribute("application", null);
    }


    // Get application from session
    ApplicationController appController = (ApplicationController) session.getAttribute("application");


    // Login credentials from FrontController
    Login userLogin = request.getDatabase().getLogin();


    // Create GUI if null
    if (appController == null)
    {
      // FIXME: never reached? isLoginRequired is FALSE in both
      // implementations?
      // also, what is request.getRequest().getParameter("logout") ?
      // and when session.isNew() ?
      if ((!userLogin.isAuthenticated() && userLogin.isLoginRequired())
          || (request.getRequest().getParameter("logout") != null && !session.isNew()))
      {
        response.getResponse().setHeader("WWW-Authenticate", "BASIC realm=\"MOLGENIS\"");
        response.getResponse().sendError(HttpServletResponse.SC_UNAUTHORIZED);
        session.invalidate();
        return;
      }
      appController = createUserInterface();
    }


    // Always pass login to GUI
    appController.setLogin(userLogin);


    // handle request
    try
    {


      if (Show.SHOW_JQGRID.equals(request.getString(FormModel.INPUT_SHOW)))
      {
        ScreenController<? extends ScreenModel> controller = appController.get(request
            .getString(ScreenModel.INPUT_TARGET));
        controller.handleRequest(db, request, response.getResponse().getOutputStream());
      }
      // action == download an attached file
      // FIXME move to form controllers handlerequest...
      else if (FileInput.ACTION_DOWNLOAD.equals(request.getString(ScreenModel.INPUT_ACTION)))
      {
        // logger.info(requestTuple);


        File file = new File(db.getFilesource() + "/" + request.getString(FileInput.INPUT_CURRENT_DOWNLOAD));


        FileInputStream filestream = new FileInputStream(file);


        response.getResponse().setContentType("application/x-download");
        response.getResponse().setContentLength((int) file.length());

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      {
        iDisplayStart = req.getInt("iDisplayStart");
      }


      // create a query on entity
      Database db = req.getDatabase();
      Query<?> q = db.query(entityClass);


      // sorting
      // iSortCol_0 = sort column number
      // resolve using mDataProp_1='name'
      String sortField = req.getString("mDataProp_" + req.getString("iSortCol_0"));

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      Class<? extends Entity> entityClass = req.getDatabase().getClassForName(req.getString("entity"));


      /****** RETRIEVE DATA ******/


      // create a query on entity
      Database db = req.getDatabase();
      Query<?> q = db.query(entityClass);


      // search?
      if (!req.isNull("filter") && !"".equals(req.getString("filter")))
      {
        q.search(req.getString("filter").trim());

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    res.getResponse().setBufferSize(10000);
    res.getResponse().setContentType("text/html; charset=UTF-8");


    PrintWriter out = res.getResponse().getWriter();
    Database db = req.getDatabase();


    try
    {


      AuthStatus authStatus = MolgenisServiceAuthenticationHelper.handleAuthentication(req, out);


      if (!authStatus.isShowApi())
      {
        out.println("<html><body>");
        out.println(authStatus.getPrintMe());
        out.println("</body></html>");
      }
      else
      {


        String entityName = req.getRequest().getPathInfo().substring(req.getServicePath().length());


        if (entityName.startsWith("/"))
        {
          entityName = entityName.substring(1);
        }


        if (entityName.equals(""))
        {
          out.println("<html><body>");
          out.println(authStatus.getPrintMe());
          if (req.getDatabase().getLogin().isAuthenticated())
          {
            out.println(MolgenisServiceAuthenticationHelper.displayLogoutForm());
          }
          showAvailableDownloads(out, db, req);
          out.println("</body></html>");
        }
        else
        {
          // Check if this entity exists and is downloadable
          List<org.molgenis.model.elements.Entity> downloadableEntities = getDownloadableEntities(db);
          boolean found = false;
          for (int i = 0; i < downloadableEntities.size() && !found; i++)
          {
            String name = downloadableEntities.get(i).getName();
            if ((name != null) && name.equals(entityName))
            {
              found = true;
            }
          }


          if (!found)
          {
            res.getResponse().sendError(404);// NOT FOUND
            return;
          }


          if (req.getRequest().getQueryString() != null
              && req.getRequest().getQueryString().equals("__showQueryDialogue=true"))
          {
            out.println("<html><body>");
            out.println(authStatus.getPrintMe());
            if (req.getDatabase().getLogin().isAuthenticated())
            {
              out.println(MolgenisServiceAuthenticationHelper.displayLogoutForm());
            }
            showFilterableDownload(out, entityName, db);
            out.println("</body></html>");
          }
          else
          {
            executeQuery(out, req, db, entityName);
          }
        }
      }
    }
    catch (Exception e)
    {
      out.println(e.getMessage());
      e.printStackTrace();
      logger.error(e.getMessage());
    }
    finally
    {
      out.flush();
      out.close();
      db.close();
    }


    logger.info("servlet took: " + (System.currentTimeMillis() - start_time));
    logger.info("------------");

View Full Code Here

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Related Classes of org.molgenis.framework.db.Database

org.molgenis.framework.server.FrontControllerAuthenticator

org.molgenis.framework.server.services.MolgenisDataTableService

org.molgenis.framework.server.services.MolgenisDownloadService

org.molgenis.framework.server.services.MolgenisGuiService

org.molgenis.framework.server.services.MolgenisJqGridService

org.molgenis.framework.server.services.MolgenisUploadService

org.molgenis.framework.tupletable.impl.JdbcTableTest

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