Metacat

/**

 *  '$RCSfile$'

 *    Purpose: A Class that represents an XML document

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

 *             National Center for Ecological Analysis and Synthesis

 *    Authors: Matt Jones

 *    Release: @release@

 *

 *   '$Author: bojilova $'

 *     '$Date: 2001-01-31 10:50:25 -0800 (Wed, 31 Jan 2001) $'

 * '$Revision: 691 $'

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat;

import java.sql.*;

import java.io.File;

import java.io.FileReader;

import java.io.IOException;

import java.io.PrintWriter;

import java.io.Reader;

import java.io.StringWriter;

import java.io.Writer;

import java.io.InputStreamReader;

import java.util.Iterator;

import java.util.Stack;

import java.util.TreeSet;

import java.util.Enumeration;

import org.xml.sax.AttributeList;

import org.xml.sax.ContentHandler;

import org.xml.sax.DTDHandler;

import org.xml.sax.EntityResolver;

import org.xml.sax.ErrorHandler;

import org.xml.sax.InputSource;

import org.xml.sax.XMLReader;

import org.xml.sax.SAXException;

import org.xml.sax.SAXParseException;

import org.xml.sax.helpers.XMLReaderFactory;

import java.net.URL;

/**

 * A class that represents an XML document. It can be created with a simple

 * document identifier from a database connection.  It also will write an

 * XML text document to a database connection using SAX.

 */

public class DocumentImpl {

  static final int ALL = 1;

  static final int WRITE = 2;

  static final int READ = 4;

  private Connection conn = null;

  private String docid = null;

  private String docname = null;

  private String doctype = null;

// DOCTITLE attr cleared from the db

//  private String doctitle = null;

  private String createdate = null;

  private String updatedate = null;

  private String system_id = null;

  private String userowner = null;

  private String userupdated = null;

  private int rev;

  private int serverlocation;

  private int publicaccess; 

  private long rootnodeid;

  private ElementNode rootNode = null;

  private TreeSet nodeRecordList = null;

  /**

   * Constructor, creates document from database connection, used 

   * for reading the document

   *

   * @param conn the database connection from which to read the document

   * @param docid the identifier of the document to be created

   */

  public DocumentImpl(Connection conn, String docid) throws McdbException 

  {

    try { 

      this.conn = conn;

      this.docid = docid;

      DocumentIdentifier id = new DocumentIdentifier(docid);

      // Look up the document information

      getDocumentInfo(docid);

      // Download all of the document nodes using a single SQL query

      // The sort order of the records is determined by the NodeComparator

      // class, and needs to represent a depth-first traversal for the

      // toXml() method to work properly

      nodeRecordList = getNodeRecordList(rootnodeid);

    } catch (McdbException ex) {

      throw ex;

    } catch (Throwable t) {

      throw new McdbException("Error reading document from " +

                              "DocumentImpl.DocumentImpl: " + docid);

    }

  }

  /** 

   * Construct a new document instance, writing the contents to the database.

   * This method is called from DBSAXHandler because we need to know the

   * root element name for documents without a DOCTYPE before creating it.

   *

   * @param conn the JDBC Connection to which all information is written

   * @param rootnodeid - sequence id of the root node in the document

   * @param docname - the name of DTD, i.e. the name immediately following 

   *        the DOCTYPE keyword ( should be the root element name ) or

   *        the root element name if no DOCTYPE declaration provided

   *        (Oracle's and IBM parsers are not aware if it is not the 

   *        root element name)

   * @param doctype - Public ID of the DTD, i.e. the name immediately 

   *                  following the PUBLIC keyword in DOCTYPE declaration or

   *                  the docname if no Public ID provided or

   *                  null if no DOCTYPE declaration provided

   * @param docid the docid to use for the INSERT OR UPDATE

   * @param action the action to be performed (INSERT OR UPDATE)

   * @param user the user that owns the document

   * @param pub flag for public "read" access on document

   * @param serverCode the serverid from xml_replication on which this document

   *        resides.

   *

   */

  public DocumentImpl(Connection conn, long rootnodeid, String docname, 

                      String doctype, String docid, String action, String user,

                      String pub, int serverCode)

                      throws SQLException, Exception

  {

    this.conn = conn;

    this.rootnodeid = rootnodeid;

    this.docname = docname;

    this.doctype = doctype;

    this.docid = docid;

    writeDocumentToDB(action, user, pub, serverCode);

  }

// NOT USED ANY MORE

//  public DocumentImpl(Connection conn, long rootnodeid, String docname, 

//                      String doctype, String docid, String action, String user)

//                      throws SQLException, Exception

//  {

//    this.conn = conn;

//    this.rootnodeid = rootnodeid;

//    this.docname = docname;

//    this.doctype = doctype;

//    this.docid = docid;

//    writeDocumentToDB(action, user);

//  }

  /**

   * get the document name

   */

  public String getDocname() {

    return docname;

  }

  /**

   * get the document type (which is the PublicID)

   */

  public String getDoctype() {

    return doctype;

  }

  /**

   * get the system identifier

   */

  public String getSystemID() {

    return system_id;

  }

  /**

   * get the root node identifier

   */

  public long getRootNodeID() {

    return rootnodeid;

  }

  /**

   * get the creation date

   */

  public String getCreateDate() {

    return createdate;

  }

  /**

   * get the update date

   */

  public String getUpdateDate() {

    return updatedate;

  }

  /** 

   * Get the document identifier (docid)

   */

  public String getDocID() {

    return docid;

  }

// DOCTITLE attr cleared from the db

//  /**

//   *get the document title

//   */

//  public String getDocTitle() {

//    return doctitle;

//  }

  public String getUserowner() {

    return userowner;

  }

  public String getUserupdated() {

    return userupdated;

  }

  public int getServerlocation() {

    return serverlocation;

  }

  public int getPublicaccess() {

    return publicaccess;

  }

  public int getRev() {

    return rev;

  }

  /**

   * Print a string representation of the XML document

   */

  public String toString()

  {

    StringWriter docwriter = new StringWriter();

    this.toXml(docwriter);

    String document = docwriter.toString();

    return document;

  }

  /**

   * Get a text representation of the XML document as a string

   * This older algorithm uses a recursive tree of Objects to represent the

   * nodes of the tree.  Each object is passed the data for the document 

   * and searches all of the document data to find its children nodes and

   * recursively build.  Thus, because each node reads the whole document,

   * this algorithm is extremely slow for larger documents, and the time

   * to completion is O(N^N) wrt the number of nodes.  See toXml() for a

   * better algorithm.

   */

  public String readUsingSlowAlgorithm()

  {

    StringBuffer doc = new StringBuffer();

    // Create the elements from the downloaded data in the TreeSet

    rootNode = new ElementNode(nodeRecordList, rootnodeid);

    // Append the resulting document to the StringBuffer and return it

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

    if (docname != null) {

      if ((doctype != null) && (system_id != null)) {

        doc.append("<!DOCTYPE " + docname + " PUBLIC \"" + doctype + 

                   "\" \"" + system_id + "\">\n");

      } else {

        doc.append("<!DOCTYPE " + docname + ">\n");

      }

    }

    doc.append(rootNode.toString());

    return (doc.toString());

  }

  /**

   * Print a text representation of the XML document to a Writer

   *

   * @param pw the Writer to which we print the document

   */

  public void toXml(Writer pw)

  {

    PrintWriter out = null;

    if (pw instanceof PrintWriter) {

      out = (PrintWriter)pw;

    } else {

      out = new PrintWriter(pw);

    }

    MetaCatUtil util = new MetaCatUtil();

    Stack openElements = new Stack();

    boolean atRootElement = true;

    boolean previousNodeWasElement = false;

    // Step through all of the node records we were given

    Iterator it = nodeRecordList.iterator();

    while (it.hasNext()) {

      NodeRecord currentNode = (NodeRecord)it.next();

      //util.debugMessage("[Got Node ID: " + currentNode.nodeid +

                          //" (" + currentNode.parentnodeid +

                          //", " + currentNode.nodeindex + 

                          //", " + currentNode.nodetype + 

                          //", " + currentNode.nodename + 

                          //", " + currentNode.nodedata + ")]");

      // Print the end tag for the previous node if needed

      //

      // This is determined by inspecting the parent nodeid for the

      // currentNode.  If it is the same as the nodeid of the last element

      // that was pushed onto the stack, then we are still in that previous

      // parent element, and we do nothing.  However, if it differs, then we

      // have returned to a level above the previous parent, so we go into

      // a loop and pop off nodes and print out their end tags until we get

      // the node on the stack to match the currentNode parentnodeid

      //

      // So, this of course means that we rely on the list of elements

      // having been sorted in a depth first traversal of the nodes, which

      // is handled by the NodeComparator class used by the TreeSet

      if (!atRootElement) {

        NodeRecord currentElement = (NodeRecord)openElements.peek();

        if ( currentNode.parentnodeid != currentElement.nodeid ) {

          while ( currentNode.parentnodeid != currentElement.nodeid ) {

            currentElement = (NodeRecord)openElements.pop();

            util.debugMessage("\n POPPED: " + currentElement.nodename);

            if (previousNodeWasElement) {

              out.print(">");

              previousNodeWasElement = false;

            }  

            out.print("</" + currentElement.nodename + ">" );

            currentElement = (NodeRecord)openElements.peek();

          }

        }

      }

      // Handle the DOCUMENT node

      if (currentNode.nodetype.equals("DOCUMENT")) {

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

        if (docname != null) {

          if ((doctype != null) && (system_id != null)) {

            out.println("<!DOCTYPE " + docname + " PUBLIC \"" + doctype + 

                       "\" \"" + system_id + "\">");

          } else {

            out.println("<!DOCTYPE " + docname + ">");

          }

        }

      // Handle the ELEMENT nodes

      } else if (currentNode.nodetype.equals("ELEMENT")) {

        if (atRootElement) {

          atRootElement = false;

        } else {

          if (previousNodeWasElement) {

            out.print(">");

          }

        }

        openElements.push(currentNode);

        util.debugMessage("\n PUSHED: " + currentNode.nodename);

        previousNodeWasElement = true;

        out.print("<" + currentNode.nodename);

      // Handle the ATTRIBUTE nodes

      } else if (currentNode.nodetype.equals("ATTRIBUTE")) {

        out.print(" " + currentNode.nodename + "=\""

                 + currentNode.nodedata + "\"");

      } else if (currentNode.nodetype.equals("TEXT")) {

        if (previousNodeWasElement) {

          out.print(">");

        }

        out.print(currentNode.nodedata);

        previousNodeWasElement = false;

      // Handle the COMMENT nodes

      } else if (currentNode.nodetype.equals("COMMENT")) {

        if (previousNodeWasElement) {

          out.print(">");

        }

        out.print("<!--" + currentNode.nodedata + "-->");

        previousNodeWasElement = false;

      // Handle the PI nodes

      } else if (currentNode.nodetype.equals("PI")) {

        if (previousNodeWasElement) {

          out.print(">");

        }

        out.print("<?" + currentNode.nodename + " " +

                        currentNode.nodedata + "?>");

        previousNodeWasElement = false;

      // Handle any other node type (do nothing)

      } else {

        // Any other types of nodes are not handled.

        // Probably should throw an exception here to indicate this

      }

      out.flush();

    }

    // Print the final end tag for the root element

    while(!openElements.empty())

    {

      NodeRecord currentElement = (NodeRecord)openElements.pop();

      util.debugMessage("\n POPPED: " + currentElement.nodename);

      out.print("</" + currentElement.nodename + ">" );

    }

    out.flush();

  }

  private boolean isRevisionOnly(DocumentIdentifier docid) throws Exception

  {

    //System.out.println("inRevisionOnly");

    PreparedStatement pstmt;

    String rev = docid.getRev();

    String newid = docid.getIdentifier();

    pstmt = conn.prepareStatement("select rev from xml_documents " +

                                  "where docid like '" + newid + "'");

    pstmt.execute();

    ResultSet rs = pstmt.getResultSet();

    boolean tablehasrows = rs.next();

    if(rev.equals("newest") || rev.equals("all"))

    {

      return false;

    }

    if(tablehasrows)

    {

      int r = rs.getInt(1);

      pstmt.close();

      if(new Integer(rev).intValue() == r)

      { //the current revision in in xml_documents

        //System.out.println("returning false");

        return false;

      }

      else if(new Integer(rev).intValue() < r)

      { //the current revision is in xml_revisions.

        //System.out.println("returning true");

        return true;

      }

      else if(new Integer(rev).intValue() > r)

      { //error, rev cannot be greater than r

        throw new Exception("requested revision cannot be greater than " +

                            "the latest revision number.");

      }

    }

    throw new Exception("the requested docid '" + docid.toString() + 

                        "' does not exist");

  }

  private void getDocumentInfo(String docid) throws McdbException, 

                                                    AccessionNumberException

  {

    getDocumentInfo(new DocumentIdentifier(docid));

  }

  /**

   * Look up the document type information from the database

   *

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

   */

  private void getDocumentInfo(DocumentIdentifier docid) throws McdbException 

  {

    PreparedStatement pstmt;

    String table = "xml_documents";

    try

    {

      if(isRevisionOnly(docid))

      { //pull the document from xml_revisions instead of from xml_documents;

        table = "xml_revisions";

      }

    }

    catch(Exception e)

    {

      System.out.println("error in DocumentImpl.getDocumentInfo: " + 

                          e.getMessage());

    }

    //deal with the key words here.

    if(docid.getRev().equals("all"))

    {

    }

    try {

      StringBuffer sql = new StringBuffer();

// DOCTITLE attr cleared from the db

//      sql.append("SELECT docname, doctype, rootnodeid, doctitle, ");

      sql.append("SELECT docname, doctype, rootnodeid, ");

      sql.append("date_created, date_updated, ");

      sql.append("user_owner, user_updated, server_location, ");

      sql.append("rev FROM ").append(table);

      sql.append(" WHERE docid LIKE '").append(docid.getIdentifier());

      sql.append("' and rev like '").append(docid.getRev()).append("'");

      //System.out.println(sql.toString());

      pstmt =

        conn.prepareStatement(sql.toString());

      // Bind the values to the query

      //pstmt.setString(1, docid.getIdentifier());

      //pstmt.setString(2, docid.getRev());

      pstmt.execute();

      ResultSet rs = pstmt.getResultSet();

      boolean tableHasRows = rs.next();

      if (tableHasRows) {

        this.docname        = rs.getString(1);

        this.doctype        = rs.getString(2);

        this.rootnodeid     = rs.getLong(3);

// DOCTITLE attr cleared from the db

//        this.doctitle       = rs.getString(4);

        this.createdate     = rs.getString(5);

        this.updatedate     = rs.getString(6);

        this.userowner      = rs.getString(7);

        this.userupdated    = rs.getString(8);

        this.serverlocation = rs.getInt(9);

        //this.publicaccess   = rs.getInt(10);

        this.rev            = rs.getInt(10);

      } 

      if (this.doctype != null) {

        pstmt =

          conn.prepareStatement("SELECT system_id " +

                                  "FROM xml_catalog " +

                                 "WHERE public_id LIKE ?");

        // Bind the values to the query

        pstmt.setString(1, doctype);

        pstmt.execute();

        rs = pstmt.getResultSet();

        tableHasRows = rs.next();

        if (tableHasRows) {

          this.system_id  = rs.getString(1);

        } 

        //pstmt.close();

      }

    } catch (SQLException e) {

      System.out.println("error in DocumentImpl.getDocumentInfo: " + 

                          e.getMessage());

      e.printStackTrace(System.out);

      throw new McdbException("Error accessing database connection in " +

                              "DocumentImpl.getDocumentInfo: ", e);

    }

    if (this.docname == null) {

      throw new McdbDocNotFoundException("Document not found: " + docid);

    }

  }

  /**

   * Look up the node data from the database

   *

   * @param rootnodeid the id of the root node of the node tree to look up

   */

  private TreeSet getNodeRecordList(long rootnodeid) throws McdbException 

  {

    PreparedStatement pstmt;

    TreeSet nodeRecordList = new TreeSet(new NodeComparator());

    long nodeid = 0;

    long parentnodeid = 0;

    long nodeindex = 0;

    String nodetype = null;

    String nodename = null;

    String nodedata = null;

    try {

      pstmt =

      conn.prepareStatement("SELECT nodeid,parentnodeid,nodeindex, " +

           "nodetype,nodename,"+               

           "replace(" +

           "replace(" +

           "replace(nodedata,'&','&') " +

           ",'<','&lt;') " +

           ",'>','>') " +

           "FROM xml_nodes WHERE rootnodeid = ?");

      // Bind the values to the query

      pstmt.setLong(1, rootnodeid);

      pstmt.execute();

      ResultSet rs = pstmt.getResultSet();

      boolean tableHasRows = rs.next();

      while (tableHasRows) {

        nodeid = rs.getLong(1);

        parentnodeid = rs.getLong(2);

        nodeindex = rs.getLong(3);

        nodetype = rs.getString(4);

        nodename = rs.getString(5);

        nodedata = rs.getString(6);

        // add the data to the node record list hashtable

        NodeRecord currentRecord = new NodeRecord(nodeid, parentnodeid, 

                                   nodeindex, nodetype, nodename, nodedata);

        nodeRecordList.add(currentRecord);

        // Advance to the next node

        tableHasRows = rs.next();

      } 

      pstmt.close();

    } catch (SQLException e) {

      throw new McdbException("Error accessing database connection from " +

                              "DocumentImpl.getNodeRecordList ", e);

    }

    if (nodeRecordList != null) {

      return nodeRecordList;

    } else {

      throw new McdbException("Error getting node data: " + docid);

    }

  }

  /** creates SQL code and inserts new document into DB connection 

   default serverCode of 1*/

  private void writeDocumentToDB(String action, String user)

               throws SQLException, Exception

  {

    writeDocumentToDB(action, user, null, 1);

  }

 /** creates SQL code and inserts new document into DB connection */

  private void writeDocumentToDB(String action, String user, String pub, 

                                 int serverCode) 

               throws SQLException, Exception {

    try {

      PreparedStatement pstmt = null;

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

        //AccessionNumber ac = new AccessionNumber();

        //this.docid = ac.generate(docid, "INSERT");

        pstmt = conn.prepareStatement(

            "INSERT INTO xml_documents " +

            "(docid, rootnodeid, docname, doctype, user_owner, user_updated, " +

            "date_created, date_updated, public_access, server_location) " +

            "VALUES (?, ?, ?, ?, ?, ?, sysdate, sysdate, ?, ?)");

        //note that the server_location is set to 1. 

        //this means that "localhost" in the xml_replication table must

        //always be the first entry!!!!!

        // Bind the values to the query

        pstmt.setString(1, this.docid);

        pstmt.setLong(2, rootnodeid);

        pstmt.setString(3, docname);

        pstmt.setString(4, doctype);

        pstmt.setString(5, user);

        pstmt.setString(6, user);

        if ( pub == null ) {

          pstmt.setString(7, null);

        } else if ( pub.toUpperCase().equals("YES") ) {

          pstmt.setInt(7, 1);

        } else if ( pub.toUpperCase().equals("NO") ) {

          pstmt.setInt(7, 0);

        }

        pstmt.setInt(8, serverCode);

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

        // Save the old document entry in a backup table

        DocumentImpl.archiveDocRevision( conn, docid, user );

        DocumentImpl thisdoc = new DocumentImpl(conn, docid);

        int thisrev = thisdoc.getRev();

        thisrev++;

        // Delete index for the old version of docid

        // The new index is inserting on the next calls to DBSAXNode

        pstmt = conn.prepareStatement(

                "DELETE FROM xml_index WHERE docid='" + this.docid + "'");

        pstmt.execute();

        //pstmt.close();

        // Update the new document to reflect the new node tree

        pstmt = conn.prepareStatement(

            "UPDATE xml_documents " +

            "SET rootnodeid = ?, docname = ?, doctype = ?, " +

            "user_updated = ?, date_updated = sysdate, " +

            "server_location = ?, rev = ?, public_access = ? " +

            "WHERE docid LIKE ?");

        // Bind the values to the query

        pstmt.setLong(1, rootnodeid);

        pstmt.setString(2, docname);

        pstmt.setString(3, doctype);

        pstmt.setString(4, user);

        pstmt.setInt(5, serverCode);

        pstmt.setInt(6, thisrev);

        if ( pub == null ) {

          pstmt.setString(7, null);

        } else if ( pub.toUpperCase().equals("YES") ) {

          pstmt .setInt(7, 1);

        } else if ( pub.toUpperCase().equals("NO") ) {

          pstmt.setInt(7, 0);

        }

        pstmt.setString(8, this.docid);

      } else {

        System.err.println("Action not supported: " + action);

      }

      // Do the insertion

      pstmt.execute();

      pstmt.close();

    } catch (SQLException sqle) {

      throw sqle;

    } catch (Exception e) {

      throw e;

    }

  }

// DOCTITLE attr cleared from the db

//  /**

//   * Get the document title

//   */

//  public String getTitle() {

//    return doctitle;

//  }

// DOCTITLE attr cleared from the db

//  /**

//   * Set the document title

//   *

//   * @param title the new title for the document

//   */

//  public void setTitle( String title ) {

//    this.doctitle = title;

//    try {

//      PreparedStatement pstmt;

//      pstmt = conn.prepareStatement(

//            "UPDATE xml_documents " +

//            " SET doctitle = ? " +

//            "WHERE docid = ?");

//

//      // Bind the values to the query

//      pstmt.setString(1, doctitle);

//      pstmt.setString(2, docid);

//

//      // Do the insertion

//      pstmt.execute();

//      pstmt.close();

//    } catch (SQLException e) {

//      System.out.println("Error in DocumentImpl.setTitle: " + e.getMessage());

//    }

//  }

  /**

   * Write an XML file to the database, given a filename

   *

   * @param conn the JDBC connection to the database

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

   * @param pub flag for public "read" access on document

   * @param dtdfilename the dtd to be uploaded on server's file system

   * @param action the action to be performed (INSERT OR UPDATE)

   * @param docid the docid to use for the INSERT OR UPDATE

   * @param user the user that owns the document

   * @param group the group to which user belongs

   */

  public static String write(Connection conn,String filename,

                             String pub, String dtdfilename,

                             String action, String docid, String user,

                             String group )

                throws Exception {

    Reader dtd = null;

    if ( dtdfilename != null ) {

      dtd = new FileReader(new File(dtdfilename).toString());

    }

    return write ( conn, new FileReader(new File(filename).toString()),

                   pub, dtd, action, docid, user, group);

  }

  public static String write(Connection conn,Reader xml,String pub,Reader dtd,

                             String action, String docid, String user,

                             String group )

                throws Exception {

    return write ( conn, xml, pub, dtd, action, docid, user, group, 1, false);

  }

  public static String write(Connection conn, Reader xml, String pub,

                             String action, String docid, String user,

                             String group )

                throws Exception {

    if(action.equals("UPDATE"))

    {//if the document is being updated then use the servercode from the 

     //originally inserted document.

      DocumentImpl doc = new DocumentImpl(conn, docid);

      int servercode = doc.getServerlocation();

      return write(conn, xml, pub, action, docid, user, group, servercode);

    }

    else

    {//if the file is being inserted then the servercode is always 1

      return write(conn, xml, pub, action, docid, user, group, 1);

    }

  }

  public static String write( Connection conn, Reader xml,

                              String action, String docid, String user,

                              String group, int serverCode )

                throws Exception

  {

    return write(conn,xml,null,action,docid,user,group,serverCode);

  }

  public static String write( Connection conn, Reader xml, String pub,

                              String action, String docid, String user,

                              String group, int serverCode) 

                throws Exception

  {

    return write(conn,xml,pub,null,action,docid,user,group,serverCode,false);

  }

  public static String write( Connection conn, Reader xml, String pub,

                              String action, String docid, String user,

                              String group, int serverCode, boolean override)

                throws Exception

  {

    return write(conn,xml,pub,null,action,docid,user,group,serverCode,override);

  }

  /**

   * Write an XML file to the database, given a Reader

   *

   * @param conn the JDBC connection to the database

   * @param xml the xml stream to be loaded into the database

   * @param pub flag for public "read" access on xml document

   * @param dtd the dtd to be uploaded on server's file system

   * @param action the action to be performed (INSERT OR UPDATE)

   * @param docid the docid to use for the INSERT OR UPDATE

   * @param user the user that owns the document

   * @param group the group to which user belongs

   * @param serverCode the serverid from xml_replication on which this document

   *        resides.

   * @param override flag to stop insert replication checking.

   *        if override = true then a document not belonging to the local server

   *        will not be checked upon update for a file lock.

   *        if override = false then a document not from this server, upon 

   *        update will be locked and version checked.

   */

  public static String write( Connection conn,Reader xml,String pub,Reader dtd,

                              String action, String docid, String user,

                              String group, int serverCode, boolean override)

                throws Exception

  {

    //MOVED DOWN IN RelationHandler obj before write of relations

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

    //{

    //  RelationHandler.deleteRelations(docid);

    //}

    int updaterev;

    MetaCatUtil util = new MetaCatUtil();

        // Determine if the docid is OK for INSERT or UPDATE

    AccessionNumber ac = new AccessionNumber(conn);

    String newdocid = ac.generate(docid, action);

    MetaCatUtil.debugMessage("action: " + action + " servercode: " + 

                             serverCode + " override: " + override);

    if((serverCode != 1 && action.equals("UPDATE")) && !override)

    { //if this document being written is not a resident of this server then

      //we need to try to get a lock from it's resident server.  If the

      //resident server will not give a lock then we send the user a message

      //saying that he/she needs to download a new copy of the file and

      //merge the differences manually.

      int istreamInt; 

      char istreamChar;

      DocumentImpl newdoc = new DocumentImpl(conn, docid);

      updaterev = newdoc.getRev();

      String server = MetacatReplication.getServer(serverCode);

      MetacatReplication.replLog("attempting to lock " + docid);

      URL u = new URL("http://" + server + "?action=getlock&updaterev=" + 

                      updaterev + "&docid=" + docid);

      System.out.println("sending message: " + u.toString());

      String serverResStr = MetacatReplication.getURLContent(u);

      String openingtag = serverResStr.substring(0, serverResStr.indexOf(">")+1);

      if(openingtag.equals("<lockgranted>"))

      {//the lock was granted go ahead with the insert

        try 

        {

          MetacatReplication.replLog("lock granted for " + docid + " from " +

                                      server);

          XMLReader parser = initializeParser(conn, action, newdocid, 

                                              user, group, pub, serverCode, dtd);

          conn.setAutoCommit(false);

          parser.parse(new InputSource(xml));

          conn.commit();

          conn.setAutoCommit(true);

        } 

        catch (Exception e) 

        {

          conn.rollback();

          conn.setAutoCommit(true);

          throw e;

        }

        //after inserting the document locally, tell the document's home server

        //to come get a copy from here.

        ForceReplicationHandler frh = new ForceReplicationHandler(docid);

        if ( (docid != null) && !(newdocid.equals(docid)) ) 

        {

          return new String("New document ID generated:" + newdocid);