Metacat

package edu.ucsb.nceas.metacat;

import org.w3c.dom.*;

import org.xml.sax.*;

import org.xml.sax.Parser;

import oracle.xml.parser.v2.*;    //Oracle parser

//import org.apache.xerces.parsers.*;  //Apache/IBM/Xerces parser

/**

 * XMLValidate.java

 *         Purpose: A Class that validates XML documents

 *   			   This class is uses a specific parser

 * 				and calls the GenericXMLValidate class

 *                 to do the actual validation

 *       Copyright: 2000 Regents of the University of California and the

 *                  National Center for Ecological Analysis and Synthesis

 *                  April 28, 2000

 * 

 * @author Dan Higgins

 * @version Version 1.0

 */

public class XMLValidate

{

    String doc;

    SAXParser par;

    public boolean validating = false; 

    public XMLValidate( String docname){

        doc = docname;

            par = new SAXParser();           // works for both Xerces and Oracle

/*            try {   //Xerces

            par.setFeature("http://xml.org/sax/features/validation",true);  

            }

            catch (Exception e) 

                {System.out.println("Could not set Validation!!!");

                System.exit(0);}

                // Xerces end 

*/                

                par = new SAXParser();           // works for both Xerces and Oracle

                par.setValidationMode(true);     // Oracle

        GenericXMLValidate gxv = new GenericXMLValidate(par);

        if (gxv.validate(doc)) {

            System.out.println("XML is validated");

        }

        else {

            System.out.print(gxv.returnErrors());    

        }

    }

    public static void main(String[] args) {

        if (args.length!=1) {

            System.out.println("Usage: java XMLValidate <xmlfile or URL>");

            System.exit(0);

        }

        String doc = args[0];

        new XMLValidate(doc);

    }

}

/**

 *        Name: DBSAXWriter.java

 *     Purpose: A Class that reads in an XML text document and

 *              write its contents to a database connection using SAX

 *   Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *     Authors: Matt Jones

 *

 *     Version: '$Id$'

 */

package edu.ucsb.nceas.metacat;

import org.xml.sax.*;

import java.io.*;

import java.net.URL;

import java.net.MalformedURLException;

import java.sql.*;

import java.util.Stack;

// Extensions to the SAX Interfaces for Namespace support.

import oracle.xml.parser.v2.XMLDocumentHandler;

import oracle.xml.parser.v2.DefaultXMLDocumentHandler;

import oracle.xml.parser.v2.NSName;

import oracle.xml.parser.v2.SAXAttrList;

import oracle.xml.parser.v2.SAXParser;

/**

 * A Class that reads in an XML text document and

 * write its contents to a database connection using SAX

 */

public class DBSAXWriter {

  static  String 	defaultDB = "jdbc:oracle:thin:@penelope.nceas.ucsb.edu:1526:DEV8";

  private Connection	conn = null;

  /**

   * the main routine used to test the DBSAXWriter utility.

   *

   * Usage: java DBSAXWriter <filename> <user> <password> [dbstring]

   *

   * @param filename the filename to be loaded into the database

   * @param user the username to use for the database connection

   * @param password the password to use for the database connection

   * @param dbstring the connection info to use for the database connection

   */

  static public void main(String[] args) {

     if (args.length < 3)

     {

        System.err.println("Wrong number of arguments!!!");

        System.err.println("USAGE: java DBSAXWriter " +

                           "<filename> <user> <password> [dbstring]");

        return;

     } else {

        try {

          String filename = args[0];

          String user     = args[1];

          String password = args[2];

          String dbstring = null;

          if (args.length <= 3) {

            dbstring = defaultDB;

          } else {

            dbstring = args[3];

          }

          // Open a connection to the database

          Connection dbconn = MetaCatUtil.openDBConnection(

                "oracle.jdbc.driver.OracleDriver",

                dbstring, user, password);

          new DBSAXWriter(filename, dbconn);

          System.out.println("Document processing finished for: " + filename);

        } catch (Exception e) {

          System.err.println("EXCEPTION HANDLING REQUIRED");

          System.err.println(e.getMessage());

          e.printStackTrace(System.err);

        }

     }

  }

  /**

   * construct a new instance of the class to write an XML file to the database

   *

   * @param filename the filename to be loaded into the database

   * @param conn the database connection to which to write the XML file

   */

  public DBSAXWriter( Reader xml, Connection conn)

                  throws IOException, 

                         SQLException, 

                         ClassNotFoundException

  {

    this.conn = conn;

    try {

        SAXParser parser = initializeParser(conn);

        parser.parse(xml);

      } catch (SAXParseException e) {

        System.err.println(e.getMessage());

      } catch (SAXException e) {

        System.err.println(e.getMessage());

      } catch (Exception e) {

        System.err.println(e.toString());

      }

  }

  public DBSAXWriter( String filename, Connection conn)

                  throws IOException, 

                         SQLException, 

                         ClassNotFoundException

  {

     this.conn = conn;

     FileReader xmlfile = new FileReader(new File(filename).toString());

     try {

       SAXParser parser = initializeParser(conn);

       parser.parse(xmlfile);

     } catch (SAXParseException e) {

       System.err.println(e.getMessage());

     } catch (SAXException e) {

       System.err.println(e.getMessage());

     } catch (Exception e) {

       System.err.println(e.toString());

     }

  }

  private SAXParser initializeParser(Connection conn) {

    SAXParser parser = null;

    //

    // Set up the SAX document handlers for parsing

    //

    try {

      // Use the XMLDocumentHandler interface for namespace support

      // instead of org.xml.sax.DocumentHandler

      XMLDocumentHandler xmlDocHandler = new DBSAXHandler(conn);

      EntityResolver xmlEntityResolver = new DBEntityResolver(conn);

      DTDHandler xmlDTDHandler         = new DBDTDHandler(conn);

      // For all the other interface use the default provided by

      // Handler base

      HandlerBase defHandler = new HandlerBase();

      // Get an instance of the parser

      parser = new SAXParser();

      // Set Handlers in the parser

      // Set the DocumentHandler to XMLDocumentHandler

      parser.setDocumentHandler(xmlDocHandler);

      parser.setEntityResolver(xmlEntityResolver);

      parser.setDTDHandler(xmlDTDHandler);

      // Set the other Handler to the defHandler

      parser.setErrorHandler(defHandler);

    } catch (Exception e) {

       System.err.println(e.toString());

    }

    return parser;

  }

  /** Utility method to convert a file handle into a URL */

  static public URL fileToURL(File file) 

  {

     String path = file.getAbsolutePath();

     String fSep = System.getProperty("file.separator");

     if (fSep != null && fSep.length() == 1)

       path = path.replace(fSep.charAt(0), '/');

     if (path.length() > 0 && path.charAt(0) != '/')

       path = '/' + path;

     try {

       return new URL("file", null, path);

     }

     catch (java.net.MalformedURLException e) {

       /* According to the spec this could only happen if the file

	  protocol were not recognized. */

       throw new Error("unexpected MalformedURLException");

     }

  }

}

/**

 *        Name: DBTransform.java

 *     Purpose: A Class that transforms an XML text document

 *              into a another type using XSL

 *   Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *     Authors: Matt Jones

 *

 *     Version: '$Id$'

 */

package edu.ucsb.nceas.metacat;

import java.io.*;

import java.net.URL;

import java.net.MalformedURLException;

import java.sql.*;

import java.util.Stack;

import oracle.xml.parser.v2.XSLStylesheet;

import oracle.xml.parser.v2.XSLException;

import oracle.xml.parser.v2.XSLProcessor;

import oracle.xml.parser.v2.XMLDocument;

import oracle.xml.parser.v2.DOMParser;

/** 

 * A Class that transforms XML documents utitlizing XSL style sheets

 */

public class DBTransform {

  static  String 	defaultDB = "jdbc:oracle:thin:@localhost:1521:test";

  private Connection	conn = null;

  /**

   * construct a DBTransform instance.

   *

   * Generally, one calls transformXMLDocument() after constructing the instance

   *

   * @param conn the database connection from which to lookup the public ids

   */

  public DBTransform( Connection conn ) 

                  throws IOException, 

                         SQLException, 

                         ClassNotFoundException

  {

    this.conn = conn;

  }

  /**

   * Transform an XML document using the stylesheet reference from the db

   *

   * @param doc the document to be transformed

   * @param sourcetype the document type of the source

   * @param targettype the target document type

   */

  public void transformXMLDocument(String doc, String sourcetype, 

                String targettype, PrintWriter pw) {

    // Look up the stylesheet for this type combination

    String xsl_system_id = getSystemId("XSL", sourcetype, targettype);

    if (xsl_system_id != null) {

      // Create a stylesheet from the system id that was found

      try {

        XSLStylesheet style = new XSLStylesheet(new URL(xsl_system_id), null);

        DOMParser dp = new DOMParser();

        dp.setValidationMode(false);

        dp.parse((Reader)(new StringReader(doc)));

        new XSLProcessor().processXSL(style, dp.getDocument(), pw);

      } catch (Exception e) {

        pw.println(xsl_system_id + "Error transforming document:\n" + 

                   e.getMessage());

      }

    } else {

      // No stylesheet registered form this document type, so just return the 

      // XML stream we were passed

      pw.print(doc);

    }

  }

  /**

   * Lookup a stylesheet reference from the db catalog

   *

   * @param objecttype the type of the object we want to retrieve

   * @param sourcetype the document type of the source

   * @param targettype the document type of the target

   */

  public String getSystemId(String objecttype, String sourcetype, 

                String targettype) {

    // Look up the System ID of a particular object

    PreparedStatement pstmt;

    String the_system_id = null;

    try {

      pstmt =

        conn.prepareStatement("SELECT system_id " +

                "FROM xml_catalog " +

                "WHERE entity_type LIKE ? " +

                "AND source_doctype LIKE ? " +

                "AND target_doctype LIKE ? ");

      // Bind the values to the query

      pstmt.setString(1, objecttype);

      pstmt.setString(2, sourcetype);

      pstmt.setString(3, targettype);

      pstmt.execute();

      try {

        ResultSet rs = pstmt.getResultSet();

        try {

          boolean tableHasRows = rs.next();

          if (tableHasRows) {

            try {

              the_system_id = rs.getString(1);

            } catch (SQLException e) {

              System.out.println("Error with getString: " + e.getMessage());                }

          } else {

            the_system_id = null; 

          }

        } catch (SQLException e) {

          System.err.println("Error with next: " + e.getMessage());

          return ("Error with next: " + e.getMessage());

        }

      } catch (SQLException e) {

        System.err.println("Error with getrset: " + e.getMessage());

        return ("Error with getrset: " + e.getMessage());

      }

      pstmt.close();

    } catch (SQLException e) {

      System.err.println("Error getting id: " + e.getMessage());

      return ("Error getting id: " + e.getMessage());

    }

    return the_system_id;

  }

  /**

   * the main routine used to test the transform utility.

   *

   * Usage: java transform <user> <password> [dbstring]

   *

   * @param user the username to use for the database connection

   * @param password the password to use for the database connection

   * @param dbstring the connection info to use for the database connection

   */

  static public void main(String[] args) {

     if (args.length < 2)

     {

        System.err.println("Wrong number of arguments!!!");

        System.err.println("USAGE: java transform " +

                           "<user> <password> [dbstring]");

        return;

     } else {

        try {

          String user     = args[0];

          String password = args[1];

          String dbstring = null;

          if (args.length <= 2) {

            dbstring = defaultDB;

          } else {

            dbstring = args[2];

          }

          // Open a connection to the database

          Connection dbconn = MetaCatUtil.openDBConnection( 

                              "oracle.jdbc.driver.OracleDriver",

                              dbstring, user, password);

          // Create a test document

          StringBuffer testdoc = new StringBuffer();

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

          testdoc.append("<eml-dataset><metafile_id>NCEAS-0001</metafile_id>");

          testdoc.append("<dataset_id>DS001</dataset_id>");

          testdoc.append("<title>My test doc</title></eml-dataset>");

          // Transform the document to the new doctype

          DBTransform dbt = new DBTransform(dbconn);

          dbt.transformXMLDocument(testdoc.toString(), 

                                   "-//NCEAS//eml-dataset//EN", 

                                   "-//W3C//HTML//EN", 

                                   new PrintWriter(System.out));

        } catch (Exception e) {

          System.err.println("EXCEPTION HANDLING REQUIRED");

          System.err.println(e.getMessage());

          e.printStackTrace(System.err);

        }

     }

  }

  public void dbg(int position) {

    System.err.println("Debug flag: " + position);

  }

}

/**

 *        Name: MetaCatUtil.java

 *     Purpose: A Class that implements utility methods for a metadata catalog

 *   Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *     Authors: Matt Jones

 * 

 *     Version: '$Id$'

 */

package edu.ucsb.nceas.metacat;

import java.sql.Connection;

import java.sql.DriverManager;

import java.sql.SQLException;

/**

 * A suite of utility classes for the metadata catalog server

 */

public class MetaCatUtil {

  static  String 	user = "jones";

  static  String 	password = "your-pw-goes-here";

  static  String 	defaultDB = "jdbc:oracle:thin:@localhost:1521:test";

  /** 

   * Utility method to establish a JDBC database connection 

   *

   * @param dbDriver the string representing the database driver

   * @param connection the string representing the database connectin parameters

   * @param user name of the user to use for database connection

   * @param password password for the user to use for database connection

   */

  public static Connection openDBConnection(String dbDriver, String connection,

                String user, String password)

                throws SQLException, ClassNotFoundException {

     // Load the Oracle JDBC driver

     Class.forName (dbDriver);

     // Connect to the database

     Connection conn = DriverManager.getConnection( connection, user, password);

     return conn;

  }

}

/**

 *        Name: DBSimpleQuery.java

 *     Purpose: A Class that searches a relational DB for elements and 

 *              attributes that have free text matches to the query string.  

 *              It returns a result set consisting of the root nodeid for 

 *              each document that satisfies the query

 *   Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *     Authors: Matt Jones

 *

 *     Version: '$Id$'

 */

package edu.ucsb.nceas.metacat;

import java.io.*;

import java.net.URL;

import java.net.MalformedURLException;

import java.sql.*;

import java.util.Stack;

import java.util.Hashtable;

import java.util.Enumeration;

/** 

 * A Class that searches a relational DB for elements and attributes that

 * have free text matches to the query string.  It returns a result set 

 * consisting of the root nodeid for each document that satisfies the query

 */

public class DBSimpleQuery {

  static  String 	defaultDB = "jdbc:oracle:thin:@localhost:1521:test";

  private Connection	conn = null;

  /**

   * the main routine used to test the DBSimpleQuery utility.

   *

   * Usage: java DBSimpleQuery <query> <user> <password> [dbstring]

   *

   * @param query the text to search for in the element and attribute content

   * @param user the username to use for the database connection

   * @param password the password to use for the database connection

   * @param dbstring the connection info to use for the database connection

   */

  static public void main(String[] args) {

     if (args.length < 3)

     {

        System.err.println("Wrong number of arguments!!!");

        System.err.println("USAGE: java DBSimpleQuery " +

                           "<query> <user> <password> [dbstring]");

        return;

     } else {

        try {

          String query    = args[0];

          String user     = args[1];

          String password = args[2];

          String dbstring = null;

          if (args.length <= 3) {

            dbstring = defaultDB;

          } else {

            dbstring = args[3];

          }

          // Open a connection to the database

          Connection dbconn = MetaCatUtil.openDBConnection( 

                              "oracle.jdbc.driver.OracleDriver",

                              dbstring, user, password);

          // Execute the simple query

          DBSimpleQuery rd = new DBSimpleQuery(dbconn);

          Hashtable nodelist = rd.findDocuments(query);

          // Print the reulting root nodes

          StringBuffer result = new StringBuffer();

          long docid = 0;

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

          result.append("<resultset>\n");

          Enumeration doclist = nodelist.keys(); 

          while (doclist.hasMoreElements()) {

            docid = ((Long)doclist.nextElement()).longValue();

            result.append("  <docid>").append(docid).append("</docid>\n");

          }

          result.append("</resultset>");

          System.out.println(result);

        } catch (Exception e) {

          System.err.println("EXCEPTION HANDLING REQUIRED");

          System.err.println(e.getMessage());

          e.printStackTrace(System.err);

        }

     }

  }

  /**

   * construct an instance of the DBSimpleQuery class 

   *

   * <p>Generally, one would call the findDocuments() routine after creating 

   * an instance to specify the search query</p>

   *

   * @param conn the JDBC connection that we use for the query

   */

  public DBSimpleQuery( Connection conn ) 

                  throws IOException, 

                         SQLException, 

                         ClassNotFoundException

  {

    this.conn = conn;

  }

  /** 

   * routine to search the elements and attributes looking to match query

   *

   * @param query the text to search for

   */

  public Hashtable findDocuments(String query) {

      Hashtable	nodeListResult = new Hashtable();

      Hashtable	rootListResult = new Hashtable();

      Hashtable	 docListResult = new Hashtable();

      PreparedStatement pstmt;

      long nodeid;

      try {

        pstmt =

          conn.prepareStatement("SELECT nodeid " +

                  "FROM xml_nodes WHERE nodedata LIKE ?");

        // Bind the values to the query

        pstmt.setString(1, query);

        pstmt.execute();

        try {

          ResultSet rs = pstmt.getResultSet();

          try {

            boolean tableHasRows = rs.next();

            while (tableHasRows) {

              try {

                nodeid = rs.getLong(1);

                nodeListResult.put(new Long(nodeid),new Long(nodeid));

              } catch (SQLException e) {

                System.out.println("Error with getInt: " + e.getMessage());

              }

              // Advance to the next record in the cursor

              tableHasRows = rs.next();

            }

          } catch (SQLException e) {

            System.out.println("Error with next: " + e.getMessage());

          }

        } catch (SQLException e) {

          System.out.println("Error with getrset: " + e.getMessage());

        }

        pstmt.close();

      } catch (SQLException e) {

        System.out.println("Error getting id: " + e.getMessage());

      }

      Enumeration nodelist = nodeListResult.keys(); 

      while (nodelist.hasMoreElements()) {

        nodeid = ((Long)nodelist.nextElement()).longValue();

        try {

          pstmt =

            conn.prepareStatement("SELECT nodeid " +

                    "FROM xml_nodes START WITH nodeid = ? " +

                    "CONNECT BY nodeid = PRIOR parentnodeid");

          // Bind the values to the query

          pstmt.setLong(1, nodeid);

          pstmt.execute();

          try {

            ResultSet rs = pstmt.getResultSet();

            try {

              boolean tableHasRows = rs.next();

              while (tableHasRows) {

                try {

                  nodeid = rs.getLong(1);

                } catch (SQLException e) {

                  System.out.println("Error with getInt: " + e.getMessage());

                }

                // Advance to the next record in the cursor

                tableHasRows = rs.next();

              }

            } catch (SQLException e) {

              System.out.println("Error with next: " + e.getMessage());

            }

          } catch (SQLException e) {

            System.out.println("Error with getrset: " + e.getMessage());

          }

          pstmt.close();

        } catch (SQLException e) {

          System.out.println("Error getting id: " + e.getMessage());

        }

        // Record that the last record should be the root

        rootListResult.put(new Long(nodeid),new Long(nodeid));

      } 

      // Now look up the document id

      long docid = 0;

      String docname = null;

      String doctype = null;

      String doctitle = null;

      StringBuffer document = null; 

      Enumeration rootlist = rootListResult.keys();

      while (rootlist.hasMoreElements()) {

        nodeid = ((Long)rootlist.nextElement()).longValue();

        try {

          pstmt =

            conn.prepareStatement("SELECT docid,docname,doctype,doctitle " +

                    "FROM xml_documents " +

                    "WHERE rootnodeid = ?");

          // Bind the values to the query

          pstmt.setLong(1, nodeid);

          pstmt.execute();

          try {

            ResultSet rs = pstmt.getResultSet();

            try {

              boolean tableHasRows = rs.next();

              while (tableHasRows) {

                try {

                  docid = rs.getLong(1);

                  docname = rs.getString(2);

                  doctype = rs.getString(3);

                  doctitle = rs.getString(4);

                  document = new StringBuffer();

                  document.append("<docid>").append(docid).append("</docid>");

                  if (docname != null) {

                    document.append("<docname>" + docname + "</docname>");

                  }

                  if (doctype != null) {

                    document.append("<doctype>" + doctype + "</doctype>");

                  }

                  if (doctitle != null) {

                    document.append("<doctitle>" + doctitle + "</doctitle>");

                  }

                } catch (SQLException e) {

                  System.out.println("Error with getLong: " + e.getMessage());

                }

                // Advance to the next record in the cursor

                tableHasRows = rs.next();

              }

            } catch (SQLException e) {

              System.out.println("Error with next: " + e.getMessage());

            }

          } catch (SQLException e) {

            System.out.println("Error with getrset: " + e.getMessage());

          }

          pstmt.close();

        } catch (SQLException e) {

          System.out.println("Error getting id: " + e.getMessage());

        }

        // Store the document id and the root node id

        docListResult.put(new Long(docid),(String)document.toString());

      }

      return docListResult;

  }

}

/**

 *        Name: MetaCatServlet.java

 *     Purpose: A Class that implements a metadata catalog as a java Servlet

 *   Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *     Authors: Matt Jones, Dan Higgins

 * 

 *     Version: '$Id$'

 */

package edu.ucsb.nceas.metacat;

import java.io.PrintWriter;

import java.io.IOException;

import java.io.Reader;

import java.io.StringReader;

import java.io.BufferedReader;

import java.util.Enumeration;

import java.util.Hashtable;

import java.util.ResourceBundle;

import java.util.PropertyResourceBundle;

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 javax.servlet.ServletConfig;

import javax.servlet.ServletContext;

import javax.servlet.ServletException;

import javax.servlet.ServletInputStream;

import javax.servlet.http.HttpServlet;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import javax.servlet.http.HttpUtils;

import oracle.xml.parser.v2.XSLStylesheet;

import oracle.xml.parser.v2.XSLException;

import oracle.xml.parser.v2.XMLDocumentFragment;

import oracle.xml.parser.v2.XSLProcessor;

import oracle.xml.parser.v2.*;    //Oracle parser - DFH

import java.io.File;  //DFH

import java.io.FileInputStream; //DFH

/**

 * A metadata catalog server implemented as a Java Servlet

   *

   * <p>Valid parameters are:<br>

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

   *                     and return a result set of nodes<br>

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

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

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

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

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

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

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

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

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

   * valtext -- XML text to be validated

   * action=getdatadoc -- retreive a stored datadocument  //DFH

   * datadoc -- data document name (id)                   //DFH

 */

public class MetaCatServlet extends HttpServlet {

  private ServletConfig		config = null;

  private ServletContext	context = null;

  Connection 		conn = null;

  DBSimpleQuery		queryobj = null;

  DBReader		docreader = null;

  DBTransform		dbt = null;

  String 	user = null;

  String 	password = null;

  String 	defaultDB = null;

  String 	resultStyleURL = null;

  String 	xmlcatalogfile = null;

  String    defaultdatapath = null;  // path to directory where data files that can be downloaded will be stored

  String    executescript  = null;  // script to get data file and put it in defaultdocpath dir

  PropertyResourceBundle options = null;

  /**

   * 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("Servlet Initialize");

      // Get the configuration file information

      options = (PropertyResourceBundle)PropertyResourceBundle.getBundle("edu.ucsb.nceas.metacat.metacat");

      user = (String)options.handleGetObject("user");

      password = (String)options.handleGetObject("password");

      defaultDB = (String)options.handleGetObject("defaultDB");

      resultStyleURL = (String)options.handleGetObject("resultStyleURL");

      xmlcatalogfile = (String)options.handleGetObject("xmlcatalogfile");

      defaultdatapath = (String)options.handleGetObject("defaultdatapath");

      executescript = (String)options.handleGetObject("executescript");

      try {

        // Open a connection to the database

        conn = MetaCatUtil.openDBConnection(

                "oracle.jdbc.driver.OracleDriver",

                defaultDB, user, password);

        queryobj = new DBSimpleQuery(conn);

        docreader = new DBReader(conn);

        dbt = new DBTransform(conn);

      } catch (Exception e) {

        System.err.println("Error opening database connection");

      }

    } catch ( ServletException ex ) {

      throw ex;

    }

  }

  /** 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 (conn == null) {

      System.err.println("Connection to database lost.  Reopening...");

      try {

        // Open a connection to the database

        conn = MetaCatUtil.openDBConnection(

                "oracle.jdbc.driver.OracleDriver",

                defaultDB, user, password);

        queryobj = new DBSimpleQuery(conn);

        docreader = new DBReader(conn);

        dbt = new DBTransform(conn);

      } catch (Exception e) {

        System.err.println("Error opening database connection");

      }

    }

    // Get a handle to the output stream back to the client

    PrintWriter out = response.getWriter();

    //response.setContentType("text/html");

    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);

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

        params.put("docid", docid);

        name = "ypos";

      }

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

        name = "xpos";

      }

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

      params.put(name,value);

    }

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

    long ypos = 0;

    try {

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

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

      if (ypos <= 13) {

        action = "getdocument";

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

        action = "validate";

      } else if (ypos > 27) {

        action = "transform";

      } else {

        action = "";

      }

    } catch (Exception npe) {

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

    }

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

      handleQueryAction(out, params, response);

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

      try {

        handleGetDocumentAction(out, params, response);

      } catch (ClassNotFoundException e) {

        out.println(e.getMessage());

      } catch (SQLException se) {

        out.println(se.getMessage());

      }

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

      handlePutDocumentAction(out, params, response);

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

      handleValidateAction(out, params, response);  

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

      handleGetDataDocumentAction(out, params, response);  

    } else {

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

    }

    // Close the stream to the client

    out.close();

  }

  /** 

   * Handle the database query request and return a result set, possibly

   * transformed from XML into HTML

   */

  private void handleQueryAction(PrintWriter out, Hashtable params, 

               HttpServletResponse response) {

      // Run the query

      Hashtable nodelist = null;

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

      if (queryobj != null) {

        nodelist = queryobj.findDocuments(query);

      } else {

        out.println("Query Object Init failed.");

	/*

        out.println(user);

        out.println(defaultDB);

        out.println(xmlcatalogfile);

        */

        return;

      }

      // Create a buffer to hold the xml result

      StringBuffer resultset = new StringBuffer();

      // Print the resulting root nodes

      Long nodeid;

      String document = null;

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

      //resultset.append("<!DOCTYPE resultset PUBLIC " +

      //               "\"-//NCEAS//resultset//EN\" \"resultset.dtd\">\n");

      resultset.append("<resultset>\n");

      resultset.append("  <query>" + query + "</query>");

      Enumeration rootlist = nodelist.keys(); 

      while (rootlist.hasMoreElements()) {

        nodeid = (Long)rootlist.nextElement();

        document = (String)nodelist.get(nodeid);

        resultset.append("  <document>" + document + "</document>");

      }

      resultset.append("</resultset>");

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

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

        // set content type and other response header fields first

        response.setContentType("text/xml");

        out.println(resultset.toString());

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

        // set content type and other response header fields first

        response.setContentType("text/html");

        //out.println("Converting to HTML...");

        XMLDocumentFragment htmldoc = null;

        try {

          XSLStylesheet style = new XSLStylesheet(new URL(resultStyleURL), null);

          htmldoc = (new XSLProcessor()).processXSL(style, 

                     (Reader)(new StringReader(resultset.toString())),null);

          htmldoc.print(out);

        } catch (Exception e) {

          out.println("Error transforming document:\n" + e.getMessage());

        }

      }

  }

  /** 

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

   * possibly transformed from XML into HTML

   */

  private void handleGetDocumentAction(PrintWriter out, Hashtable params, 

               HttpServletResponse response) 

               throws ClassNotFoundException, IOException, SQLException {

    String docidstr = null;

    long docid = 0;

    String doc = null;

    try {

      // Find the document id number

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

      docid = (new Long(docidstr)).longValue();

      // Get the document indicated fromthe db

      doc = docreader.readXMLDocument(docid);

    } catch (NullPointerException npe) {

      response.setContentType("text/html");

      out.println("Error getting document ID: " + docidstr +" (" + docid + ")");

    }

      // Return the document in XML or HTML format

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

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

        // set content type and other response header fields first

        response.setContentType("text/xml");

        out.println(doc);

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

        // set content type and other response header fields first

        response.setContentType("text/html");

        // Look up the document type

        String sourcetype = docreader.getDoctypeInfo(docid).getDoctype();

        // Transform the document to the new doctype

        dbt.transformXMLDocument(doc, sourcetype, "-//W3C//HTML//EN", out);

      }

  }

  /** 

   * Handle the database putdocument request and write an XML document 

   * to the database connection

   */

  private void handlePutDocumentAction(PrintWriter out, Hashtable params, 

               HttpServletResponse response) {

      // Get the document indicated

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

      StringReader xml = new StringReader(doctext[0]);

      // write the document to the database

      try {

        DBSAXWriter dbw = new DBSAXWriter(xml, conn);

      } catch (SQLException e1) {

          out.println("Error 1 loading document:<p>\n" + e1.getMessage());

      }catch (IOException e2) {

          out.println("Error 2 loading document:<p>\n" + e2.getMessage());

      }catch (ClassNotFoundException e3) {

          out.println("Error 3 loading document:<p>\n" + e3.getMessage());

      }

      // set content type and other response header fields first

      response.setContentType("text/xml");

      out.println(doctext[0]);

  }

  /** 

   * Handle the validtion request and return the results 

   * to the requestor - DFH

   */

  private void handleValidateAction(PrintWriter out, Hashtable params, HttpServletResponse response) {

    // Get the document indicated

    String valtext = null;

    try {

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

    } catch (Exception nullpe) {

      String docidstr = null;

      long docid = 0;

      try {

        // Find the document id number

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

        docid = (new Long(docidstr)).longValue();

        // Get the document indicated fromthe db

        valtext = docreader.readXMLDocument(docid);

      } catch (NullPointerException npe) {

        response.setContentType("text/html");

        out.println("Error getting document ID: " + 

                     docidstr +" (" + docid + ")");

      }

    }

    SAXParser parser = new SAXParser();  // works for both Xerces and Oracle

    parser.setValidationMode(true);      // Oracle

    try {

      GenericXMLValidate gxv = new GenericXMLValidate(parser, xmlcatalogfile);

      boolean valid = gxv.validateString(valtext);

      // set content type and other response header fields first

      response.setContentType("text/html");

      out.println("<html>");

      out.println("<head><link rel=\"stylesheet\" type=\"text/css\" " +

                  "href=\"/xmltodb/rowcol.css\" /></head>");

      out.println("<body class=\"emlbody\">");

      if (valid) {

        out.println("The input XML is VALID!");

      } else {

        out.println("The input XML is NOT VALID<br />\n<pre>\n" 

                    + gxv.returnErrors() + "\n</pre>\n");

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

        //out.println(valtext);

      } 

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

    } catch (NullPointerException npe2) {

      // set content type and other response header fields first

      response.setContentType("text/html");

      //out.println(valtext); 

      out.println("Error validating document."); 

    }

  }

  /** 

   * Look up the document type from the database

   *

   * @param docid the id of the document to look up

   */

  private String OldgetDoctype(long docid) {

    PreparedStatement pstmt;

    String doctype = null;

    try {

      pstmt =

        conn.prepareStatement("SELECT doctype " + 

                                "FROM xml_documents " +

                               "WHERE docid = ?");

      // Bind the values to the query

      pstmt.setLong(1, new Long(docid).longValue());

      pstmt.execute();

      try {

        ResultSet rs = pstmt.getResultSet();

        try {

          boolean tableHasRows = rs.next();

          if (tableHasRows) {

            try {

              doctype  = rs.getString(1);

            } catch (SQLException e) {

              System.out.println("Error with getString: " + e.getMessage());

            }

          }

        } catch (SQLException e) {

          System.out.println("Error with next: " + e.getMessage());

        }

      } catch (SQLException e) {

        System.out.println("Error with getrset: " + e.getMessage());

      }

      pstmt.close();

    } catch (SQLException e) {

      System.out.println("Error getting id: " + e.getMessage());

    }

    return doctype;

  }

  /** 

   * Handle the document request and return the results 

   * to the requestor - DFH

   */

  private void handleGetDataDocumentAction(PrintWriter out, Hashtable params, HttpServletResponse response) {

      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]; }  // execute script includes path

        else {     // look in defaultdatapath

                command = defaultdatapath+executescript+" "+datadoc[0];  // on Win98 one MUST include the .bat extender

        }

      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

  }

}

/**

 *        Name: DBEntityResolver.java

 *     Purpose: A Class that implements org.xml.sax.EntityResolver interface

 *              for resolving external entities

 *   Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *     Authors: Jivka Bojilova

 *

 *     Version: '$Id$'

 */

package edu.ucsb.nceas.metacat;

import org.xml.sax.*;

import java.sql.*;

import java.net.URL;

import java.net.MalformedURLException;

import java.util.Stack;

import java.util.EmptyStackException;

/** 

 * A database aware Class implementing EntityResolver interface for the SAX parser to

 * call when processing the XML stream and intercepting any external entities

 * (including the external DTD subset and external parameter entities, if any) before including them.

 */

public class DBEntityResolver implements EntityResolver

{

   static String doctype = null;

   private Connection conn = null;

   private int pIdCounter = 0;

   private long currentElementNo;

   /** Construct an instance of the DBEntityResolver clas

    *

    * @param conn the JDBC connection to which information is written

    */

   public DBEntityResolver(Connection conn)

   {

      this.conn = conn;

   }

   /** The Parser call this method before opening any external entity 

     * except the top-level document entity (including the external DTD subset,

     * external entities referenced within the DTD, and external entities referenced 

     * within the document element)*/

   public InputSource resolveEntity (String publicId, String systemId)

            throws MalformedURLException

   {

     String dbSystemId;

     currentElementNo = DBSAXHandler.elementNo;

     if (publicId != null) {

        pIdCounter += 1;

        System.out.println("from DBEntityResolver: current element is " + DBSAXHandler.elementNo);

        System.out.println("from DBEntityResolver: " + pIdCounter + " " + publicId);

        // look at the db XML Catalog and get dbSystemId by this publicId

        if (currentElementNo == 0) {

            doctype = publicId;

            dbSystemId = getDTDSystemID (conn, publicId);

            if (dbSystemId == "")

                // register publicId in db and use the provided systemId

                if (systemId != "") {

                    new URL(systemId);

                    registerDTDSystemID (conn, doctype, publicId, systemId);

                    return null;

                }

            new URL(dbSystemId);

            return new InputSource(dbSystemId);

        } 

        /*else {

            // look at the db XML Catalog and get dbSystemId by this publicId for a given doctype

            dbSystemId = getEntitySystemID (conn, doctype, publicId);

            if (dbSystemId == "")

                // register publicId in db for a given doctype and use the provided systemId

                if (systemId != "") {

                    new URL(systemId);

                    registerEntityPublicID (conn, doctype, publicId, systemId);

                    return null;

                }

            new URL(dbSystemId);

            return new InputSource(dbSystemId);

        }*/  

     }

     // publicId is null => doctype is null => doctype = docname

     if ( systemId != null) {

        if (currentElementNo == 0) {

            doctype = DBSAXHandler.docname;

            dbSystemId = getDTDSystemID (conn, doctype);

            if (dbSystemId == "") {

                new URL(systemId);

                registerDTDSystemID (conn, doctype, doctype, systemId);

                return null;