Metacat

import com.oreilly.servlet.multipart.FilePart;

import com.oreilly.servlet.multipart.MultipartParser;

import com.oreilly.servlet.multipart.ParamPart;

import com.oreilly.servlet.multipart.Part;

import java.io.IOException;

import java.io.FileInputStream;

import java.io.BufferedInputStream;

import java.util.ResourceBundle;

import java.util.Random;

import java.net.URL;

import java.net.MalformedURLException;

import java.sql.PreparedStatement;

import java.sql.ResultSet;

import java.sql.Connection;

import java.sql.SQLException;

import java.lang.reflect.*;

import java.net.*;

import java.util.zip.*;

import javax.servlet.ServletInputStream;

import javax.servlet.http.HttpUtils;

import javax.servlet.ServletOutputStream;

import org.ecoinformatics.eml.EMLParser;

import org.xml.sax.SAXException;

 *

 * <p>Valid parameters are:<br>

 * action=query -- query the values of all elements and attributes

 *                     and return a result set of nodes<br>

 * action=squery -- structured query (see pathquery.dtd)<br>

 * action= -- export a zip format for data packadge<br>

 * action=read -- read any metadata/data file from Metacat and from Internet<br>

 * action=insert -- insert an XML document into the database store<br>

 * action=update -- update an XML document that is in the database store<br>

 * action=delete --  delete an XML document from the database store<br>

 * action=validate -- vallidate the xml contained in valtext<br>

 * doctype -- document type list returned by the query (publicID)<br>

 * qformat=xml -- display resultset from query in XML<br>

 * qformat=html -- display resultset from query in HTML<br>

 * qformat=zip -- zip resultset from query<br>

 * docid=34 -- display the document with the document ID number 34<br>

 * doctext -- XML text of the document to load into the database<br>

 * acltext -- XML access text for a document to load into the database<br>

 * dtdtext -- XML DTD text for a new DTD to load into Metacat XML Catalog<br>

 * query -- actual query text (to go with 'action=query' or 'action=squery')<br>

 * valtext -- XML text to be validated<br>

 * action=getaccesscontrol -- retrieve acl info for Metacat document<br>

 * action=getdoctypes -- retrieve all doctypes (publicID)<br>

 * action=getdtdschema -- retrieve a DTD or Schema file<br>

 * action=getdataguide -- retrieve a Data Guide<br>

 * action=getprincipals -- retrieve a list of principals in XML<br>

 * datadoc -- data document name (id)<br>

 * The particular combination of parameters that are valid for each

 * particular action value is quite specific.  This documentation

 * will be reorganized to reflect this information.

public class MetaCatServlet extends HttpServlet {

  private ServletConfig config = null;

  private ServletContext context = null;

  private String resultStyleURL = null;

  private String xmlcatalogfile = null;

  private String saxparser = null;

  private String datafilepath = null;

  private File dataDirectory = null;

  private String servletpath = null;

  private String htmlpath = null;

  private PropertyResourceBundle options = null;

  private MetaCatUtil util = null;

  private DBConnectionPool connPool = null;

  private Hashtable sessionHash = new Hashtable();

  private static final String PROLOG = "<?xml version=\"1.0\"?>";

  private static final String SUCCESS = "<success>";

  private static final String SUCCESSCLOSE = "</success>";

  private static final String ERROR = "<error>";

  private static final String ERRORCLOSE = "</error>";

  public static final String SCHEMALOCATIONKEYWORD = ":schemaLocation";

  public static final String NONAMESPACELOCATION = ":noNamespaceSchemaLocation";

  public static final String EML2KEYWORD =":eml";

  public static final String XMLFORMAT = "xml";

  private static final String CONFIG_DIR  = "WEB-INF";

  private static final String CONFIG_NAME = "metacat.properties";

  /**

   * Initialize the servlet by creating appropriate database connections

   */

  public void init( ServletConfig config ) throws ServletException {

    try {

      super.init( config );

      this.config = config;

      this.context = config.getServletContext();

      System.out.println("MetaCatServlet Initialize");

      // Initialize the properties file for our options

      String dirPath = context.getRealPath(CONFIG_DIR);

      File propertyFile = new File(dirPath,CONFIG_NAME);

      Options options = null;

      try {

          options = Options.initialize(propertyFile);

          MetaCatUtil.debugMessage("Options configured: " +

            options.getOption("configured"), 20);

      } catch (IOException ioe) {

        MetaCatUtil.debugMessage("Error in loading options: "

           +ioe.getMessage(), 20);

      }

      util = new MetaCatUtil();

      //initial DBConnection pool

      connPool = DBConnectionPool.getInstance();

      // Get the configuration file information

      resultStyleURL = util.getOption("resultStyleURL");

      xmlcatalogfile = util.getOption("xmlcatalogfile");

      saxparser = util.getOption("saxparser");

      datafilepath = util.getOption("datafilepath");

      dataDirectory = new File(datafilepath);

      servletpath = util.getOption("servletpath");

      htmlpath = util.getOption("htmlpath");

    } catch ( ServletException ex ) {

      throw ex;

    } catch (SQLException e) {

      MetaCatUtil.debugMessage("Error in MetacatServlet.init: "

                                          +e.getMessage(), 20);

    }

  }

  /**

   * Close all db connections from the pool

   */

  public void destroy() {

      // Close all db connection

      System.out.println("Destroying MetacatServlet");

      connPool.release();

  }

  /** Handle "GET" method requests from HTTP clients */

  public void doGet (HttpServletRequest request, HttpServletResponse response)

    throws ServletException, IOException {

    // Process the data and send back the response

    handleGetOrPost(request, response);

  }

  /** Handle "POST" method requests from HTTP clients */

  public void doPost( HttpServletRequest request, HttpServletResponse response)

    throws ServletException, IOException {

    // Process the data and send back the response

    handleGetOrPost(request, response);

  }

  /**

   * Control servlet response depending on the action parameter specified

   */

  private void handleGetOrPost(HttpServletRequest request,

                               HttpServletResponse response)

                               throws ServletException, IOException

  {

    if ( util == null ) {

        util = new MetaCatUtil();

    }

    /*MetaCatUtil.debugMessage("Connection pool size: "

                                     +connPool.getSizeOfDBConnectionPool(),10);

    MetaCatUtil.debugMessage("Free DBConnection number: "

                                  +connPool.getFreeDBConnectionNumber(), 10);*/

    //If all DBConnection in the pool are free and DBConnection pool

    //size is greater than initial value, shrink the connection pool

    //size to initial value

    DBConnectionPool.shrinkDBConnectionPoolSize();

    //Debug message to print out the method which have a busy DBConnection

    connPool.printMethodNameHavingBusyDBConnection();

    String ctype = request.getContentType();

    if (ctype != null && ctype.startsWith("multipart/form-data")) {

      handleMultipartForm(request, response);

    } else {

      String name = null;

      String[] value = null;

      String[] docid = new String[3];

      Hashtable params = new Hashtable();

      Enumeration paramlist = request.getParameterNames();

      while (paramlist.hasMoreElements()) {

        name = (String)paramlist.nextElement();

        value = request.getParameterValues(name);

        // Decode the docid and mouse click information

        if (name.endsWith(".y")) {

          docid[0] = name.substring(0,name.length()-2);

          params.put("docid", docid);

          name = "ypos";

        }

        if (name.endsWith(".x")) {

          name = "xpos";

        }

        params.put(name,value);

      }

      //handle param is emptpy

      if (params.isEmpty() || params == null)

      {

        return;

      }

      //if the user clicked on the input images, decode which image

      //was clicked then set the action.

      String action = ((String[])params.get("action"))[0];

      util.debugMessage("Line 230: Action is: " + action, 1);

      // This block handles session management for the servlet

      // by looking up the current session information for all actions

      // other than "login" and "logout"

      String username = null;

      String password = null;

      String[] groupnames = null;

      String sess_id = null;

      // handle login action

      if (action.equals("login")) {

        PrintWriter out = response.getWriter();

        handleLoginAction(out, params, request, response);

        out.close();

      // handle logout action

      } else if (action.equals("logout")) {

        PrintWriter out = response.getWriter();

        handleLogoutAction(out, params, request, response);

        out.close();

      // handle shrink DBConnection request

      } else if (action.equals("shrink")) {

        PrintWriter out = response.getWriter();

        boolean success = false;

        //If all DBConnection in the pool are free and DBConnection pool

        //size is greater than initial value, shrink the connection pool

        //size to initial value

        success = DBConnectionPool.shrinkConnectionPoolSize();

        if (success)

        {

          //if successfully shrink the pool size to initial value

          out.println("DBConnection Pool shrink successfully");

        }//if

        else

        {

          out.println("DBConnection pool couldn't shrink successfully");

       //close out put

        out.close();

      // aware of session expiration on every request

      }

      else

      {

        HttpSession sess = request.getSession(true);

        if (sess.isNew() && !params.containsKey("sessionid")) {

          // session expired or has not been stored b/w user requests

          MetaCatUtil.debugMessage("in session is new or no sessionid", 40);

          username = "public";

          sess.setAttribute("username", username);

        }

        else

        {

          MetaCatUtil.debugMessage("in session is not new or " +

                                    " has sessionid parameter", 40);

          try

          {

            if(params.containsKey("sessionid"))

            {

              sess_id = ((String[])params.get("sessionid"))[0];

              MetaCatUtil.debugMessage("in has sessionid " + sess_id, 40);

              if(sessionHash.containsKey(sess_id))

              {

                MetaCatUtil.debugMessage("find the id " + sess_id +

                                         " in hash table", 40);

                sess = (HttpSession)sessionHash.get(sess_id);

              }

            }

            else

            {

              // we already store the session in login, so we don't need here

              /*MetaCatUtil.debugMessage("in no sessionid parameter ", 40);

              sess_id = (String)sess.getId();

              MetaCatUtil.debugMessage("storing the session id "+ sess_id +

                  " which has username " + sess.getAttribute("username") +

                 " into session hash in handleGetOrPost method", 35);

              sessionHash.put(sess_id, sess);*/

            }

          }

          catch(IllegalStateException ise)

          {

            System.out.println("error in handleGetOrPost: this shouldn't " +

                               "happen: the session should be valid: " +

                               ise.getMessage());

          }

          username = (String)sess.getAttribute("username");

          MetaCatUtil.debugMessage("The user name from session is: "+

                                   username, 20);

          password = (String)sess.getAttribute("password");

          groupnames = (String[])sess.getAttribute("groupnames");

        }

        //make user user username should be public

        if (username == null || (username.trim().equals("")))

        {

          username = "public";

        }

        MetaCatUtil.debugMessage("The user is : "+ username, 5);

      }

       // Now that we know the session is valid, we can delegate the request

      // to a particular action handler

      if(action.equals("query")) {

        PrintWriter out = response.getWriter();

        handleQuery(out,params,response,username,groupnames,sess_id);

        out.close();

      } else if(action.equals("squery")) {

        PrintWriter out = response.getWriter();

        if(params.containsKey("query")) {

         handleSQuery(out, params,response,username,groupnames,sess_id);

         out.close();

        } else {

          out.println("Illegal action squery without \"query\" parameter");

          out.close();

        }

      } else if (action.equals("export")) {

        handleExportAction(params, response, username, groupnames, password);

      } else if (action.equals("read")) {

        handleReadAction(params, response, username,password, groupnames);

      } else if (action.equals("readinlinedata")) {

        handleReadInlineDataAction(params, response, username,

                                   password, groupnames);

      } else if (action.equals("insert") || action.equals("update")) {

        PrintWriter out = response.getWriter();

        if ( (username != null) &&  !username.equals("public") ) {

          handleInsertOrUpdateAction(out,params,username,groupnames);

        } else {

          out.println("Permission denied for user "+username +" " + action);

       }

        out.close();

      } else if (action.equals("delete")) {

        PrintWriter out = response.getWriter();

        if ( (username != null) &&  !username.equals("public") ) {

          handleDeleteAction(out, params, response, username, groupnames);

        } else {

          out.println("Permission denied for " + action);

        }

        out.close();

      } else if (action.equals("validate")) {

        PrintWriter out = response.getWriter();

        handleValidateAction(out, params);

        out.close();

      } else if (action.equals("setaccess")) {

         PrintWriter out = response.getWriter();

         handleSetAccessAction(out, params, username);

        out.close();

      } else if (action.equals("getaccesscontrol")) {

        PrintWriter out = response.getWriter();

        handleGetAccessControlAction(out,params,response,username,groupnames);

        out.close();

      } else if (action.equals("getprincipals")) {

        PrintWriter out = response.getWriter();

        handleGetPrincipalsAction(out, username, password);

        out.close();

      } else if (action.equals("getdoctypes")) {

        PrintWriter out = response.getWriter();

        handleGetDoctypesAction(out, params, response);

        out.close();

      } else if (action.equals("getdtdschema")) {

        PrintWriter out = response.getWriter();

        handleGetDTDSchemaAction(out, params, response);

        out.close();

      } else if (action.equals("getlastdocid")) {

        PrintWriter out = response.getWriter();

        handleGetMaxDocidAction(out, params, response);

        out.close();

      } else if (action.equals("getrevisionanddoctype")) {

        PrintWriter out = response.getWriter();

        handleGetRevisionAndDocTypeAction(out, params);

        out.close();

      } else if (action.equals("getversion")) {

          response.setContentType("text/xml");

          PrintWriter out = response.getWriter();

          out.println(Version.getVersionAsXml());

          out.close();

      } else if (action.equals("login") || action.equals("logout")) {

      } else if (action.equals("protocoltest")) {

        String testURL = "metacat://dev.nceas.ucsb.edu/NCEAS.897766.9";

        try {

          testURL = ((String[])params.get("url"))[0];

        } catch (Throwable t) {

        }

        String phandler = System.getProperty("java.protocol.handler.pkgs");

        response.setContentType("text/html");

        PrintWriter out = response.getWriter();

        out.println("<body bgcolor=\"white\">");

        out.println("<p>Handler property: <code>" + phandler + "</code></p>");

        out.println("<p>Starting test for:<br>");

        out.println("    " + testURL + "</p>");

        try {

          URL u = new URL(testURL);

          out.println("<pre>");

          out.println("Protocol: " + u.getProtocol());

          out.println("    Host: " + u.getHost());

          out.println("    Port: " + u.getPort());

          out.println("    Path: " + u.getPath());

          out.println("     Ref: " + u.getRef());

          String pquery = u.getQuery();

          out.println("   Query: " + pquery);

          out.println("  Params: ");

          if (pquery != null) {

            Hashtable qparams = util.parseQuery(u.getQuery());

            for (Enumeration en = qparams.keys(); en.hasMoreElements(); ) {

              String pname = (String)en.nextElement();

              String pvalue = (String)qparams.get(pname);

              out.println("    " + pname + ": " + pvalue);

            }

          }

          out.println("</pre>");

          out.println("</body>");

          out.close();

        } catch (MalformedURLException mue) {

          System.out.println("bad url from MetacatServlet.handleGetOrPost");

          out.println(mue.getMessage());

          mue.printStackTrace(out);

          out.close();

        }

      } else {

        PrintWriter out = response.getWriter();

        out.println("<?xml version=\"1.0\"?>");

        out.println("<error>");

        out.println("Error: action not registered.  Please report this error.");

        out.println("</error>");

        out.close();

      }

      //util.closeConnections();

      // Close the stream to the client

      //out.close();

  }

  // LOGIN & LOGOUT SECTION

  /**

   * Handle the login request. Create a new session object.

   * Do user authentication through the session.

   */

  private void handleLoginAction(PrintWriter out, Hashtable params,

               HttpServletRequest request, HttpServletResponse response) {

    AuthSession sess = null;

    String un = ((String[])params.get("username"))[0];

    MetaCatUtil.debugMessage("user " + un + " try to login", 20);

    String pw = ((String[])params.get("password"))[0];

    String action = ((String[])params.get("action"))[0];

    String qformat = ((String[])params.get("qformat"))[0];

    try {

      sess = new AuthSession();

    } catch (Exception e) {

      System.out.println("error in MetacatServlet.handleLoginAction: " +

                          e.getMessage());

      out.println(e.getMessage());

      return;

    boolean isValid = sess.authenticate(request, un, pw);

    //if it is authernticate is true, store the session

    if (isValid)

      HttpSession session = sess.getSessions();

      String id = session.getId();

      MetaCatUtil.debugMessage("Store session id " + id +

               "which has username" + session.getAttribute("username")+

               " into hash in login method", 35);

      sessionHash.put(id, session);

    }

    // format and transform the output

    if (qformat.equals("xml")) {

      response.setContentType("text/xml");

      out.println(sess.getMessage());

    } else {

      try {

        DBTransform trans = new DBTransform();

        response.setContentType("text/html");

        trans.transformXMLDocument(sess.getMessage(), "-//NCEAS//login//EN",

                                   "-//W3C//HTML//EN", qformat, out, null);

      } catch(Exception e) {

        MetaCatUtil.debugMessage("Error in MetaCatServlet.handleLoginAction: "

                                +e.getMessage(), 30);

      }

    // any output is returned

    }

  }

  /**

   * Handle the logout request. Close the connection.

   */

  private void handleLogoutAction(PrintWriter out, Hashtable params,

               HttpServletRequest request, HttpServletResponse response) {

    String qformat = ((String[])params.get("qformat"))[0];

    // close the connection

    HttpSession sess = request.getSession(false);

    MetaCatUtil.debugMessage("After get session in logout request", 40);

    if (sess != null)

    {

     MetaCatUtil.debugMessage("The session id " + sess.getId() +

                              " will be invalidate in logout action", 30);

     MetaCatUtil.debugMessage("The session contains user " +

                               sess.getAttribute("username") +

                               " will be invalidate in logout action", 30);

      sess.invalidate();

    }

    // produce output

    StringBuffer output = new StringBuffer();

    output.append("<?xml version=\"1.0\"?>");

    output.append("<logout>");

    output.append("User logged out");

    output.append("</logout>");

    //format and transform the output

    if (qformat.equals("xml")) {

      response.setContentType("text/xml");

      out.println(output.toString());

    } else {

      try {

        DBTransform trans = new DBTransform();

        response.setContentType("text/html");

        trans.transformXMLDocument(output.toString(), "-//NCEAS//login//EN",

                                   "-//W3C//HTML//EN", qformat, out, null);

      } catch(Exception e) {

        MetaCatUtil.debugMessage("Error in MetaCatServlet.handleLogoutAction"

                                  +e.getMessage(), 30);

      }

    }

  }

  // END OF LOGIN & LOGOUT SECTION

  // SQUERY & QUERY SECTION

  /**

   * Retreive the squery xml, execute it and display it

   *

   * @param out the output stream to the client

   * @param params the Hashtable of parameters that should be included

   * in the squery.

   * @param response the response object linked to the client

   * @param conn the database connection

   */

  protected void handleSQuery(PrintWriter out, Hashtable params,

                 HttpServletResponse response, String user, String[] groups,

                 String sessionid)

  {

    double startTime = System.currentTimeMillis()/1000;

    DBQuery queryobj = new DBQuery(saxparser);

    queryobj.findDocuments(response, out, params, user, groups, sessionid);

    double outPutTime = System.currentTimeMillis()/1000;

    MetaCatUtil.debugMessage("total search time: "+(outPutTime-startTime), 30);

  }

   /**

    * Create the xml query, execute it and display the results.

    *

    * @param out the output stream to the client

    * @param params the Hashtable of parameters that should be included

    * in the squery.

    * @param response the response object linked to the client

    */

  protected void handleQuery(PrintWriter out, Hashtable params,

                 HttpServletResponse response, String user, String[] groups,

                 String sessionid)

  {

    //create the query and run it

    String xmlquery = DBQuery.createSQuery(params);

    String []queryArray = new String[1];

    queryArray[0] = xmlquery;

    params.put("query", queryArray);

    double startTime = System.currentTimeMillis()/1000;

    DBQuery queryobj = new DBQuery(saxparser);

    queryobj.findDocuments(response, out, params, user, groups, sessionid);

    double outPutTime = System.currentTimeMillis()/1000;

    MetaCatUtil.debugMessage("total search time: "+(outPutTime-startTime), 30);

    //handleSQuery(out, params, response,user, groups, sessionid);

  }

  // END OF SQUERY & QUERY SECTION

 //Exoport section

 /**

   * Handle the "export" request of data package from Metacat in zip format

   * @param params the Hashtable of HTTP request parameters

   * @param response the HTTP response object linked to the client

   * @param user the username sent the request

   * @param groups the user's groupnames

   */

  private void handleExportAction(Hashtable params,

    HttpServletResponse response, String user, String[] groups, String passWord)

  {

    // Output stream

    ServletOutputStream out = null;

    // Zip output stream

    ZipOutputStream zOut = null;

    DocumentImpl docImpls=null;

    DBQuery queryObj=null;

    String[] docs = new String[10];

    String docId = "";

    try

      // read the params

      if (params.containsKey("docid"))

      {

        docs = (String[])params.get("docid");

      }//if

      // Create a DBuery to handle export

      queryObj = new DBQuery(saxparser);

      // Get the docid

      docId=docs[0];

      // Make sure the client specify docid

      if (docId == null || docId.equals(""))

      {

        response.setContentType("text/xml"); //MIME type

        // Get a printwriter

        PrintWriter pw = response.getWriter();

        // Send back message

        pw.println("<?xml version=\"1.0\"?>");

        pw.println("<error>");

        pw.println("You didn't specify requested docid");

        pw.println("</error>");

        // Close printwriter

        pw.close();

        return;

      }//if

      // Get output stream

      out = response.getOutputStream();

      response.setContentType("application/zip"); //MIME type

      zOut = new ZipOutputStream(out);

      zOut =queryObj.getZippedPackage(docId, out, user, groups, passWord);

      zOut.finish(); //terminate the zip file

      zOut.close();  //close the zip stream

    }//try

    catch (Exception e)

    {

      try

      {

        response.setContentType("text/xml"); //MIME type

        // Send error message back

        if (out != null)

        {

            PrintWriter pw = new PrintWriter(out);

            pw.println("<?xml version=\"1.0\"?>");

            pw.println("<error>");

            pw.println(e.getMessage());

            pw.println("</error>");

            // Close printwriter

            pw.close();

            // Close output stream

            out.close();

        }//if

        // Close zip output stream

        if ( zOut != null )

        {

          zOut.close();

        }//if

      }//try

      catch (IOException ioe)

      {

        MetaCatUtil.debugMessage("Problem with the servlet output " +

                           "in MetacatServlet.handleExportAction: " +

                           ioe.getMessage(), 30);

      }//catch

      MetaCatUtil.debugMessage("Error in MetacatServlet.handleExportAction: " +

                         e.getMessage(), 30);

      e.printStackTrace(System.out);

    }//catch

  }//handleExportAction

   //read inline data section

 /**

   * In eml2 document, the xml can have inline data and data was stripped off

   * and store in file system. This action can be used to read inline data only

   * @param params the Hashtable of HTTP request parameters

   * @param response the HTTP response object linked to the client

   * @param user the username sent the request

   * @param groups the user's groupnames

   */

  private void handleReadInlineDataAction(Hashtable params,

                                          HttpServletResponse response,

                                          String user, String passWord,

                                          String[] groups)

  {

    String[] docs = new String[10];

    String inlineDataId = null;

    String docId = "";

    ServletOutputStream out = null;

    try

      // read the params

      if (params.containsKey("inlinedataid"))

      {

        docs = (String[])params.get("inlinedataid");

      }//if

      // Get the docid

      inlineDataId=docs[0];

      // Make sure the client specify docid

      if (inlineDataId == null || inlineDataId.equals(""))

      {

        throw new Exception("You didn't specify requested inlinedataid");

      }//if

      // check for permission

      docId = MetaCatUtil.getDocIdWithoutRevFromInlineDataID(inlineDataId);

      PermissionController controller = new PermissionController(docId);

      // check top level read permission

      if (!controller.hasPermission(user, groups,

                                    AccessControlInterface.READSTRING))

      {

          throw new Exception("User "+ user + " doesn't have permission "+

                              " to read document " + docId);

      }//if

      // if the document has subtree control, we need to check subtree control

      else if(controller.hasSubTreeAccessControl())

      {

        // get node id for inlinedata

        long nodeId=getInlineDataNodeId(inlineDataId, docId);

        if (!controller.hasPermissionForSubTreeNode(user, groups,

                                     AccessControlInterface.READSTRING, nodeId))

        {

           throw new Exception("User "+ user + " doesn't have permission "+

                              " to read inlinedata " + inlineDataId);

        }//if

      }//else

      // Get output stream

      out = response.getOutputStream();

      // read the inline data from the file

      String inlinePath = MetaCatUtil.getOption("inlinedatafilepath");

      File lineData = new File(inlinePath, inlineDataId);

      FileInputStream input = new FileInputStream(lineData);

      byte [] buffer = new byte[4*1024];

      int bytes = input.read(buffer);

      while (bytes != -1)

      {

        out.write(buffer, 0, bytes);

        bytes = input.read(buffer);

      }

      out.close();

    }//try

    catch (Exception e)

    {

      try

      {

        PrintWriter pw = null;

        // Send error message back

        if (out != null)

        {

            pw = new PrintWriter(out);

        }//if

        else

        {

          pw = response.getWriter();

         pw.println("<?xml version=\"1.0\"?>");

         pw.println("<error>");

         pw.println(e.getMessage());

         pw.println("</error>");

         // Close printwriter

         pw.close();

         // Close output stream if out is not null

         if (out != null)

         {

           out.close();

         }

     }//try

     catch (IOException ioe)

     {

        MetaCatUtil.debugMessage("Problem with the servlet output " +

                           "in MetacatServlet.handleExportAction: " +

                           ioe.getMessage(), 30);

     }//catch

      MetaCatUtil.debugMessage("Error in MetacatServlet.handleReadInlineDataAction: "

                                + e.getMessage(), 30);

    }//catch

  }//handleReadInlineDataAction

  /*

   * Get the nodeid from xml_nodes for the inlinedataid

   */

  private long getInlineDataNodeId(String inLineDataId, String docId)

                                   throws SQLException

  {

    long nodeId = 0;

    String INLINE = "inline";

    boolean hasRow;

    PreparedStatement pStmt = null;

    DBConnection conn = null;

    int serialNumber = -1;

    String sql ="SELECT nodeid FROM xml_nodes WHERE docid=? AND nodedata=? " +

                "AND nodetype='TEXT' AND parentnodeid IN " +

                "(SELECT nodeid FROM xml_nodes WHERE docid=? AND " +

                "nodetype='ELEMENT' AND nodename='" + INLINE + "')";

    try

      //check out DBConnection

      conn=DBConnectionPool.getDBConnection("AccessControlList.isAllowFirst");

      serialNumber=conn.getCheckOutSerialNumber();

      pStmt = conn.prepareStatement(sql);

      //bind value

      pStmt.setString(1, docId);//docid

      pStmt.setString(2, inLineDataId);//inlinedataid

      pStmt.setString(3, docId);

      // excute query

      pStmt.execute();

      ResultSet rs = pStmt.getResultSet();

      hasRow=rs.next();

      // get result

      if (hasRow)

      {

        nodeId = rs.getLong(1);

      }//if

    }//try

    catch (SQLException e)

    {

      throw e;

    finally

    {

      try

      {

        pStmt.close();

      }

      finally

      {

        DBConnectionPool.returnDBConnection(conn, serialNumber);

      }

    }

    MetaCatUtil.debugMessage("The nodeid for inlinedataid " + inLineDataId +

                             " is: "+nodeId, 35);

    return nodeId;

  }

  // READ SECTION

  /**

   * Handle the "read" request of metadata/data files from Metacat

   * or any files from Internet;

   * transformed metadata XML document into HTML presentation if requested;

   * zip files when more than one were requested.

   *

   * @param params the Hashtable of HTTP request parameters

   * @param response the HTTP response object linked to the client

   * @param user the username sent the request

   * @param groups the user's groupnames

   */

  private void handleReadAction(Hashtable params, HttpServletResponse response,

                                String user, String passWord, String[] groups)

  {