Metacat

    for (int i=0; i < query.length(); i++) { 

      // go throught the remainder of the query one character at a time.

      if (query.charAt(i) == '=') { 

        // if the current char is a # then the preceding should be a name

        if (!poundflag && ampflag) {

          params[arrcount][0] = temp.trim();

          temp = "";

        } else { 

          //if there are two #s or &s in a row throw an exception.

          throw new MalformedURLException("metacatURL: Two parameter names " +                                            "not allowed in sequence");

        }

        poundflag = true;

        ampflag = false;

      } else if (query.charAt(i) == '&' || i == query.length()-1) { 

        //the text preceding the & should be the param value.

        if (i == query.length() - 1) { 

          //if at the end of the string grab the last value and append it.

          if (query.charAt(i) != '=') { 

            temp += query.charAt(i);

        }

        if (!ampflag && poundflag) {

          params[arrcount][1] = temp.trim();

          parameters.put(params[arrcount][0], params[arrcount][1]);

          temp = "";

          arrcount++; //increment the array to the next row.

          //if there are two =s or &s in a row through an exception

          throw new MalformedURLException("metacatURL: Two parameter values " +

                                          "not allowed in sequence");

        poundflag = false;

        ampflag = true;

      } else { 

        //get the next character in the string

        temp += query.charAt(i);

import java.io.Reader;

import java.io.BufferedReader;

import java.io.File;

import java.io.FileOutputStream;

import java.io.InputStreamReader;

import java.io.DataInputStream;

 * action=read -- display an XML document in XML or HTML<br>

 * action=getdatadoc -- retrieve a stored datadocument<br>

        //out.println("docid => " + docid[0]);

      //pwout.println(name + " => " + value[0]);

    //MBJELIMINATE String action = decodeMouseAction(params);

    //if(action.equals("error"))

    //{

      //util.debugMessage("Line 218: Action is: " + action);

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

    //}

        try

        {

        }

        catch(IllegalStateException ise)

        {

    if(action.equals("query"))

    {

    } 

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

    {

      if(params.containsKey("query"))

      {

      }

      else

      {

    }

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

      //PrintWriter out = response.getWriter();

      try {

        handleReadAction(/*out,*/ params, response, username);

      } catch (ClassNotFoundException e) {

        System.out.println("Error in MetacatServlet.handlGetOrPost: " + 

                            e.getMessage());

      } catch (SQLException se) {

        System.out.println("Error in MetaCatServlet.handleGetOrPost: " + 

                            se.getMessage());

      }

    } 

/*

    else if (action.equals("getrelateddocument")) {

      try {

        handleGetRelatedDocumentAction(out, params, response);

      } catch (ClassNotFoundException e) {

        out.println(e.getMessage());

      } catch (SQLException se) {

        out.println(se.getMessage());

      }

    }

*/

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

      PrintWriter out = response.getWriter();

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

      PrintWriter out = response.getWriter();

      try{

        handleViewAbstractAction(out, params, response);

      }

      catch(Exception e)

      {

        out.println("error viewing abstract from " + 

                    "MetacatServlet.handleGetorPost: " + e.getMessage());

      }

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

      response.setContentType("application/zip");

      ServletOutputStream out = response.getOutputStream();

      handleGetDataDocumentAction(out, params, response);  

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

      PrintWriter out = response.getWriter();

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

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

      PrintWriter out = response.getWriter();

      handleGetDoctypesAction(out, params, response);  

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

      PrintWriter out = response.getWriter();

      handleGetPrincipalsAction(out, username, password);  

    //out.close();

  /**

   * decodes the mouse click information coming from the client.

   * This function may be overwritten to provide specific functionality

   * for different applications.

   * @param params the parameters from the CGI

   * @return action the action to be performed or "error" if an error was

   * generated

   */

  protected String decodeMouseAction(Hashtable params)

  {

    // Determine what type of request the user made

    // if the action parameter is set, use it as a default

    // but if the ypos param is set, calculate the action needed

    String action=null;

    long ypos = 0;

    try {

      ypos = (new Long(((String[])params.get("ypos"))[0]).longValue());

      //out.println("<P>YPOS IS " + ypos);

      if (ypos <= 13) {

        action = "read";

      } else if (ypos > 13 && ypos <= 27) {

        action = "validate";

      } else if (ypos > 27) {

        action = "transform";

      }

      return action;

    } catch (Exception npe) {

      //

      // MBJ -- NOTE that this should be handled more gracefully with

      //        the new exception infrastructure -- this "error" return

      //        value is inappropriate

      //out.println("<P>Caught exception looking for Y value.");

      return "error";

    }  

  }

  /**

   * sends the port number that the data socket is running on.  This is a 

   * parameter set in the metacat.properties file.

   */

  private void handleGetDataPortAction(PrintWriter out, Hashtable params, 

                                       HttpServletResponse response, 

                                       String username, String groupname,

                                       String sess_id)

  {

    int port;

    String filedir = null;

    try

    {

      filedir = util.getOption("datafilepath");

      Random r = new Random();

      port = r.nextInt(65000);  //pick a random port between 0-65000

      //System.out.println("random port is: " + port);

      while(!DataFileServer.portIsAvailable(port))

      {

        port = r.nextInt(65000);

        //System.out.println("next port used: " + port);

      }

      DataFileServer dfs = new DataFileServer(port, username, sess_id);

      dfs.start();

      //System.out.println("filedir: " + filedir);

      //System.out.println("port: " + port);

      response.setContentType("text/xml");

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

      out.println("<port>");

      out.print(port);

      out.print("</port>");

    }

	  catch (Exception e) 

    {

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

                          e.getMessage());

    }

  }

/* WITHOUT XSLT transformation

    // redirects response to html page

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

      // user authentication successful

      if (isValid) {

        response.sendRedirect(

                 response.encodeRedirectUrl(htmlpath + "/metacat.html"));

      // unsuccessful user authentication 

      } else {

        response.sendRedirect(htmlpath + "/login.html");

      }

    // any output is returned  

    } else {

      response.setContentType("text/xml");

      out.println(sess.getMessage()); 

    }

*/        

/* WITHOUT XSLT transformation

    // redirects response to html page

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

        response.sendRedirect(htmlpath + "/index.html"); 

      } catch(Exception e) {

        util.returnConnection(conn); 

      } 

    // any output is returned  

    } else {

      response.setContentType("text/xml");

      out.println(output.toString()); 

    }

*/

  /**

   * Handle the request to view the abstract of a document.

   * The abstractpath CGI parameter gives the xml path to the abstract

   * node.  

  private void handleViewAbstractAction(PrintWriter out, Hashtable params,

               HttpServletResponse response) throws IOException, SQLException

    String abstractpath = null;

    String docid = null;

    Connection conn = null;

    response.setContentType("text/html");

    try

    {

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

      if(params.containsKey("abstractpath"))

      {

        //the CGI parameter abstractpath holds the path to the abstract

        //that should be displayed.

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

      else

      {

        out.println("error: no abstractpath parameter"); 

      conn = util.getConnection();

      Object[] abstracts = DBQuery.getNodeContent(abstractpath, docid, conn);

      out.println("<html><head><title>Abstract</title></head>");

      out.println("<body bgcolor=\"white\"><h1>Abstract</h1>");

      for(int i=0; i<abstracts.length; i++)

      {

        out.println("<p>" + (String)abstracts[i] + "</p>");

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

    }

    catch (IOException ioe)

    {

       util.debugMessage("error in MetacatServlet.handlegetabstract: " + 

                          ioe.getMessage());

       System.out.println("IO error in MetacatServlet.handlegetabstract: " + 

                          ioe.getMessage());

    }

    catch(SQLException sqle)

    {

      util.debugMessage("sql error in MetacatServLet.handlegetabstract: " + 

                         sqle.getMessage());

      System.out.println("sql error in MetacatServLet.handlegetabstract: " + 

                         sqle.getMessage());

    }

    catch(Exception e)

    {

      util.debugMessage("error in handlegetabstract: " + e.getMessage());

      System.out.println("error in MetacatServlEt.handlegetabstract: " + 

    util.returnConnection(conn);

  /** 

   * Handle the database getrelateddocument request and return a XML document, 

   * possibly transformed from XML into HTML

   */

  private void handleGetRelatedDocumentAction(PrintWriter out, Hashtable params,

               HttpServletResponse response, URL murl) 

               throws ClassNotFoundException, IOException, SQLException 

    String docid = null;

    //if(params.containsKey("url"))

    //{//the identifier for the related document is contained in the URL param

      try

      {

        DocumentImpl xmldoc=null;

        //MetacatURL murl = new MetacatURL(((String[])params.get("url"))[0]);

        if(murl.getProtocol().equals("metacat"))

        {//get the document from the database if it is the right type of url

          //Hashtable murlParams = murl.getHashParams();

          Hashtable murlParams = util.parseQuery(murl.getQuery());

          if(murlParams.containsKey("docid"))

          {//the docid should be first

            docid = (String)murlParams.get("docid"); //get the docid value

            conn = util.getConnection();

            xmldoc = new DocumentImpl(conn, docid);

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

            if (qformat.equals("xml")) 

            { 

              // set content type and other response header fields first

              response.setContentType("text/xml");

              xmldoc.toXml(out);

              //out.println(xmldoc);

            } 

            else if (qformat.equals("html")) 

            {

              response.setContentType("text/html");

              // Look up the document type

              String sourcetype = xmldoc.getDoctype();

              // Transform the document to the new doctype

              DBTransform dbt = new DBTransform(conn);

              dbt.transformXMLDocument(xmldoc.toString(), sourcetype, 

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

            }

            util.returnConnection(conn);

          else

          {

            //throw new Exception("handleGetDocument: bad URL");

            System.err.println("handleGetDocument: bad URL");

          }

        else if(murl.getProtocol().equals("http"))

        {//get the document from the internet

          //Hashtable murlParams = murl.getHashParams();

          Hashtable murlParams = util.parseQuery(murl.getQuery());

          if(murlParams.containsKey("httpurl"))

          {//httpurl is the param name for an http url.

            URL urlconn = new URL((String)murlParams.get("httpurl"));  

            //create a new url obj.

            //DataInputStream htmldoc = new DataInputStream(urlconn.openStream());

            BufferedReader htmldoc = new BufferedReader(

                                   new InputStreamReader(urlconn.openStream()));

            //bind a data stream.

            try

            { //display the document

              String line=null;

              while((line = htmldoc.readLine()) != null)

              {

                out.println(line); 

              }

            }

            catch(Exception e)

            {

              System.out.println("error viewing html document from " +

                            "MetacatServlet.handleGetRelatedDocumentAction: " +

                            e.getMessage()); 

            }

      catch (McdbException e) {

        response.setContentType("text/xml");

        e.toXml(out);

      } catch   (Throwable t) {

        response.setContentType("text/html");

        out.println(t.getMessage());

      } finally {

        util.returnConnection(conn);

      }

    //} // end if

  }   

  /** 

   * Handle the database read request and return an XML document, 

   * possibly transformed from XML into HTML

   */

  private void handleReadAction(/*PrintWriter out,*/ Hashtable params, 

               HttpServletResponse response, String username) 

               throws ClassNotFoundException, IOException, SQLException 

     PrintWriter out;

      //MetacatURL murl = new MetacatURL(((String[])params.get("docid"))[0]);

      if(params.containsKey(new String("qformat")) && 

         ((String[])params.get("qformat"))[0].equals("bin"))

      {

        handleGetData(params, response, username);

      else

      {

        out = response.getWriter();

        URL murl = new URL(((String[])params.get("docid"))[0]);

        handleGetRelatedDocumentAction(out, params, response, murl);

      }

    } catch (MalformedURLException mue) {

      out = response.getWriter();

      handleGetDocumentAction(out, params, response);

  /**

   * Handle the read of a data file.

   */

  private void handleGetData(Hashtable params, 

                             HttpServletResponse response, String username)

    String docid = null;

    try

    {

      URL murl = new URL(((String[])params.get("docid"))[0]);

      Hashtable murlParams = util.parseQuery(murl.getQuery());

      if(murlParams.containsKey("docid"))

      {

        docid = (String)murlParams.get("docid");

    }

    catch(MalformedURLException mue)

    {

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

    }

    File f = null;

    FileInputStream fin = null;

    Connection conn;

    try

    {

      StringBuffer sql = new StringBuffer();

      sql.append("select docname from xml_documents where docid like '");

      sql.append(docid).append("'");

      conn = util.openDBConnection();

      AccessControlList aclobj = new AccessControlList(conn);

      boolean hasPermission = aclobj.hasPermission("READ",username,docid);

      if(!hasPermission)

      {

        response.setContentType("text/html");

        PrintWriter out = response.getWriter();

        out.println("Error: you do not have permission to view this document");

        return;

      }

      response.setContentType("application/octet-stream");

      ServletOutputStream sosout = response.getOutputStream(); 

      PreparedStatement pstmt = conn.prepareStatement(sql.toString());

      pstmt.execute();

      ResultSet rs = pstmt.getResultSet();

      boolean tablehasrows = rs.next();

      while(tablehasrows)

      {

        //get the file stream from the file then send it to the output stream

        String filepath = util.getOption("datafilepath");

        if(!filepath.endsWith("/"))

        {

          filepath += "/";

        f = new File(filepath + rs.getString(1)); 

        fin = new FileInputStream(f);

        int b = fin.read();

        while(b != -1)

        {

          sosout.write(b);

          b = fin.read();

        }

        tablehasrows = rs.next();

      fin.close();

      pstmt.close();

      conn.close();

    catch(Exception e)

    {

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

                          e.getMessage());

      e.printStackTrace(System.out);

    }

  /** 

   * Handle the database read request and return an XML document, 

   * possibly transformed from XML into HTML

   */

  private void handleGetDocumentAction(PrintWriter out, Hashtable params, 

               HttpServletResponse response) 

               throws ClassNotFoundException, IOException, SQLException {

    String docidstr = null;

    String docid = null;

    String doc = null;

      // Find the document id number

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

      docid = docidstr;

      DocumentImpl xmldoc = new DocumentImpl(conn, docid);

      // Get the document indicated from the db

      //doc = docreader.readXMLDocument(docid);

      // Return the document in XML or HTML format

      String qformat=null;

      if(params.containsKey("qformat"))

      {

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

      }

      else

      {

        qformat = "html";        

      }

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

        // set content type and other response header fields first

        response.setContentType("text/xml");

        xmldoc.toXml(out);

        //out.println(xmldoc);

      } else if (qformat.equals("html")) {

        response.setContentType("text/html");

        // Look up the document type

        String sourcetype = xmldoc.getDoctype();

        // Transform the document to the new doctype

        DBTransform dbt = new DBTransform(conn);

        dbt.transformXMLDocument(xmldoc.toString(), sourcetype, 

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

      }

    } catch (McdbException e) {

      response.setContentType("text/xml");

      e.toXml(out);

    } catch (Throwable t) {

      response.setContentType("text/html");

      out.println(t.getMessage());

    }    

  /** 

   * Handle the document request and return the results to the requestor

   * If a docid is passed in through the params then that document

   * will be retrieved form the DB and put in the zip file.

   * In addition if 1 or more relations parameters are passed, those file

   * will be zipped as well.  Currently this is only implemented for 

   * metacat:// and http:// files.  Support should be added for srb:// files

   * as well.

  private void handleGetDataDocumentAction(ServletOutputStream out, 

               Hashtable params, 

               HttpServletResponse response) {

  //find the related files, get them from their source and zip them into 

  //a zip file.

  try

    Connection conn = util.getConnection();

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

    ZipOutputStream zout = new ZipOutputStream(out);

    byte[] bytestring = null;

    ZipEntry zentry = null;

    DocumentImpl xmldoc = null;

    String[] reldocs = null;

    if(params.containsKey("relation"))

    { //get the relations from the parameters.

      reldocs = ((String[])params.get("relation"));

    }

    else

    { //let the for loop know that there are no relations to zip

      reldocs = new String[0];

    }

    //write the base file to the zip file.

    xmldoc = new DocumentImpl(conn, currentDocid);

    bytestring = (xmldoc.toString()).getBytes();

    zentry = new ZipEntry(currentDocid + ".xml");

    //create a new zip entry and write the file to the stream

    zentry.setSize(bytestring.length);

    zout.putNextEntry(zentry);

    zout.write(bytestring, 0, bytestring.length);

    zout.closeEntry(); //get ready for the next entry. 

    //zip up the related documents

    for(int i=0; i<reldocs.length; i++)

      //MetacatURL murl = new MetacatURL(((String)reldocs[i]));

      URL murl = new URL(((String)reldocs[i]));

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

      if(murl.getProtocol().equals("metacat"))

        //get the document from the database

        //xmldoc = new DocumentImpl(conn, (String)murl.getHashParam("docid"));

        xmldoc = new DocumentImpl(conn, (String)qparams.get("docid"));

        bytestring = (xmldoc.toString()).getBytes();

        zentry = new ZipEntry(qparams.get("docid") + ".xml");

        //create a new zip entry and write the file to the stream

        zentry.setSize(bytestring.length);

        zout.putNextEntry(zentry);

        zout.write(bytestring, 0, bytestring.length);

        zout.closeEntry(); //get ready for the next entry.

      else if(murl.getProtocol().equals("http"))

      {

        //Hashtable murlParams = murl.getHashParams();

        if(qparams.containsKey("httpurl"))

        {//httpurl is the param name for an http url.

          URL urlconn = new URL((String)qparams.get("httpurl"));  

          //create a new url obj.

          BufferedReader htmldoc = new BufferedReader(

                                   new InputStreamReader(urlconn.openStream()));

          //get the data from the web server

          try

          { //zip the document

            String line=null;

            zentry = new ZipEntry((String)qparams.get("filename"));

            //get just the filename from the URL.

            zout.putNextEntry(zentry);

            //make a new entry in the zip file stream

            while((line = htmldoc.readLine()) != null)

            {

              bytestring = (line.toString()).getBytes();

              zout.write(bytestring, 0, bytestring.length);

              //write out the file line by line

            }

            zout.closeEntry(); //close the entry in the file

          }

          catch(Exception e)

          {

            System.out.println("error downloading html document "+ 

                               "in metacatServlet.handleGetDataDocumentAction"); 

          }

        }

      }

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

    zout.close();   //close the stream.

    util.returnConnection(conn); //return the connection to the pool

  catch(Exception e)

  {

    System.out.println("Error creating zip file from " +

                       "MetacatServlet.handleGetDataDocumentAction: " + 

                        e.getMessage()); 

    e.printStackTrace(System.out);

  }

   /*

   //////////old code using a shell script/////////////////////////////////

      boolean error_flag = false;

      String error_message = "";

      // Get the document indicated

      String[] datadoc = (String[])params.get("datadoc");

      // defaultdatapath = "C:\\Temp\\";    // for testing only!!!

      // executescript = "test.bat";        // for testing only!!!

      // set content type and other response header fields first

      response.setContentType("application/octet-stream");

      if (defaultdatapath!=null) {

        if(!defaultdatapath.endsWith(System.getProperty("file.separator"))) {

          defaultdatapath=defaultdatapath+System.getProperty("file.separator");

        }

        System.out.println("Path= "+defaultdatapath+datadoc[0]);

        if (executescript!=null) {

          String command = null;

          File scriptfile = new File(executescript);

          if (scriptfile.exists()) {

            command=executescript+" "+datadoc[0]; // script includes path

        } else {     // look in defaultdatapath

            // on Win98 one MUST include the .bat extender

            command = defaultdatapath+executescript+" "+datadoc[0];  

        }

      System.out.println(command);

      try {

      Process proc = Runtime.getRuntime().exec(command);

      proc.waitFor();

      }

      catch (Exception eee) {

        System.out.println("Error running process!");

        error_flag = true;

        error_message = "Error running process!";}

      } // end executescript not null if

      File datafile = new File(defaultdatapath+datadoc[0]);

      try {

      FileInputStream fw = new FileInputStream(datafile);

      int x;

      while ((x = fw.read())!=-1) {

        out.write(x); }

        fw.close();

      } catch (Exception e) {

        System.out.println("Error in returning file\n"+e.getMessage());

        error_flag=true;

        error_message = error_message+"\nError in returning file\n"+

                        e.getMessage();

      }

    } // end defaultdatapath not null if

    */

  }

  /** 

   * Handle the "getprincipals" action.

   * Read all principals from authentication scheme in XML format

   */

  private void handleGetPrincipalsAction(PrintWriter out, String user,

                                         String password) {

    Connection conn = null;

    try {

        // get connection from the pool

        AuthSession auth = new AuthSession();

        String principals = auth.getPrincipals(user, password);

        out.println(principals);

    } catch (Exception e) {

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

      out.println("<error>");

      out.println(e.getMessage());

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

    } finally {

      util.returnConnection(conn);

    }  

  }