/src/edu/ucsb/nceas/metacat/DocumentImpl.java - Annotate - Metacat - Ecoinformatics Redmine

metacat/src/edu/ucsb/nceas/metacat/DocumentImpl.java @ 1075

-            jones
+/**
  *  '$RCSfile$'
  *    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@
+ *
  *   '$Author$'
  *     '$Date$'
  * '$Revision$'
             jones
  * 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
-            jones
+ */
 package edu.ucsb.nceas.metacat;
 import java.sql.*;
-            jones
+import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
-            jones
+import java.io.PrintWriter;
-            jones
+import java.io.Reader;
 import java.io.StringWriter;
 import java.io.Writer;
-            berkley
+import java.io.InputStreamReader;
-            tao
+import java.io.*;
-            jones
+import java.text.SimpleDateFormat;
 import java.util.Date;
-            jones
+import java.util.Iterator;
-            jones
+import java.util.Stack;
-            jones
+import java.util.TreeSet;
-            berkley
+import java.util.Enumeration;
             jones
 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;
-            berkley
+import java.net.URL;
-            bojilova
+import edu.ucsb.nceas.dbadapter.AbstractDatabase;
             bojilova
-            jones
+/**
  * A class that represents an XML document. It can be created with a simple
-            jones
+ * document identifier from a database connection.  It also will write an
  * XML text document to a database connection using SAX.
-            jones
+ */
 public class DocumentImpl {
-            bojilova
+  static final int ALL = 1;
   static final int WRITE = 2;
   static final int READ = 4;
-            bojilova
+  private static final AbstractDatabase dbAdapter = MetaCatUtil.dbAdapter;
             bojilova
-            jones
+  private Connection conn = null;
   private String docid = null;
-            tao
+  private String updatedVersion=null;
-            jones
+  private String docname = null;
   private String doctype = null;
-            bojilova
+// DOCTITLE attr cleared from the db
 //  private String doctitle = null;
-            berkley
+  private String createdate = null;
   private String updatedate = null;
-            jones
+  private String system_id = null;
-            berkley
+  private String userowner = null;
   private String userupdated = null;
-            berkley
+  private int rev;
-            berkley
+  private int serverlocation;
-            tao
+  private String docHomeServer;
-            bojilova
+  private String publicaccess;
-            jones
+  private long rootnodeid;
   private ElementNode rootNode = null;
-            jones
+  private TreeSet nodeRecordList = null;
             bojilova
   /**
-            jones
+   * Constructor used to create a document and read the document information
    * from the database.  If readNodes is false, then the node data is not
    * read at this time, but is deferred until it is needed (such as when a
    * call to toXml() is made).
             bojilova
    * @param conn the database connection from which to read the document
-            jones
+   * @param docid the identifier of the document to be created
    * @param readNodes flag indicating whether the xmlnodes should be read
-            bojilova
+   */
-            bojilova
+  public DocumentImpl(Connection conn, String docid, boolean readNodes)
          throws McdbException
             bojilova
-            jones
+    try {
       this.conn = conn;
       this.docid = docid;
       // Look up the document information
       getDocumentInfo(docid);
             jones
-            jones
+      if (readNodes) {
-            jones
+        // 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);
             jones
             jones
-            jones
+    } catch (McdbException ex) {
       throw ex;
     } catch (Throwable t) {
       throw new McdbException("Error reading document from " +
                               "DocumentImpl.DocumentImpl: " + docid);
             jones
             bojilova
             jones
   /**
-            jones
+   * Constructor, creates document from database connection, used
    * for reading the document
             jones
    * @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
+  {
-            jones
+    this(conn, docid, true);
             jones
-            jones
+  /**
-            jones
+   * 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.
             jones
    * @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
-            bojilova
+   * @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.
             jones
    */
   public DocumentImpl(Connection conn, long rootnodeid, String docname,
-            berkley
+                      String doctype, String docid, String action, String user,
-            bojilova
+                      String pub, String catalogid, int serverCode)
-            berkley
+                      throws SQLException, Exception
+  {
     this.conn = conn;
     this.rootnodeid = rootnodeid;
     this.docname = docname;
     this.doctype = doctype;
     this.docid = docid;
-            bojilova
+    writeDocumentToDB(action, user, pub, catalogid, serverCode);
             berkley
-            tao
+  /**
    * 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.
+   *
    * In this constructor, the docid is without rev. There is a string rev to
    * specify the revision user want to upadate. The revion is only need to be
    * greater than current one. It is not need to be sequent number just after
    * current one. So it is only used in update action
    * @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 UPDATE, no version number
    * @param version, need to be 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 newRevision,
                       String action, String user,
                       String pub, String catalogId, int serverCode)
                       throws SQLException, Exception
+  {
     this.conn = conn;
     this.rootnodeid = rootNodeId;
     this.docname = docName;
     this.doctype = docType;
     this.docid = docId;
     this.updatedVersion = newRevision;
     writeDocumentToDB(action, user, pub, catalogId, serverCode);
+  }
-            jones
+  /**
-            tao
+   * This method will be call in handleUploadRequest in MetacatServlet class
    */
   public static void registerDocument(
                      String docname, String doctype, String accnum, String user)
                      throws SQLException, AccessionNumberException, Exception
+  {
     Connection dbConn = null;
     MetaCatUtil ut = new MetaCatUtil();
-            tao
+    try
+    {
       dbConn = ut.openDBConnection();
       // get server location for this doc
       int serverLocation=getServerLocationNumber(dbConn,accnum);
       dbConn.close();
       registerDocument(docname, doctype,accnum, user, serverLocation);
+    }
     catch (Exception e)
+    {
       throw e;
+    }
     finally
+    {
       try
+      {
         dbConn.close();
+      }
       catch (Exception ee)
       {}
+    }
             tao
+  }
   /**
-            jones
+   * Register a document that resides on the filesystem with the database.
    * (ie, just an entry in xml_documents, nothing in xml_nodes).
    * Creates a reference to a filesystem document (used for non-xml data files).
-            tao
+   * This class only be called in MetaCatServerlet.
-            jones
+   * @param conn the JDBC Connection to which all information is written
    * @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 accnum the accession number to use for the INSERT OR UPDATE, which
    *               includes a revision number for this revision of the document
    *               (e.g., knb.1.1)
    * @param user the user that owns the document
    * @param serverCode the serverid from xml_replication on which this document
    *        resides.
    */
   public static void registerDocument(
                      String docname, String doctype, String accnum,
                      String user, int serverCode)
                      throws SQLException, AccessionNumberException, Exception
+  {
     Connection dbconn = null;
     MetaCatUtil util = new MetaCatUtil();
-            tao
+    AccessionNumber ac;
-            jones
+    try {
       dbconn = util.openDBConnection();
-            tao
+      String docIdWithoutRev=MetaCatUtil.getDocIdFromString(accnum);
       int userSpecifyRev=MetaCatUtil.getVersionFromString(accnum);
       int revInDataBase=getLatestRevisionNumber(dbconn, docIdWithoutRev);
       //revIndataBase=-1, there is no record in xml_documents table
       //the data file is a new one, inert it into table
       //user specified rev should be great than 0
       if (revInDataBase==-1 && userSpecifyRev>0 )
+      {
         ac = new AccessionNumber(dbconn, accnum, "insert");
+      }
       //rev is greater the last revsion number and revInDataBase isn't -1
       // it is a updated data file
       else if (userSpecifyRev>revInDataBase && revInDataBase>0)
+      {
         //archive the old entry
         archiveDocRevision(dbconn, docIdWithoutRev, user);
         //delete the old entry in xml_documents
         deleteXMLDocuments(dbconn, docIdWithoutRev);
         ac = new AccessionNumber(dbconn, accnum, "update");
+      }
       //other situation
       else
+      {
         throw new Exception("Revision number couldn't be "
                     +userSpecifyRev);
+      }
-            jones
+      String docid = ac.getDocid();
       String rev = ac.getRev();
       SimpleDateFormat formatter = new SimpleDateFormat ("yy-MM-dd HH:mm:ss");
       Date localtime = new Date();
       String dateString = formatter.format(localtime);
-            tao
+      String sqlDateString = "to_date('" + dateString +
                                           "', 'YY-MM-DD HH24:MI:SS')";
             jones
       StringBuffer sql = new StringBuffer();
       sql.append("insert into xml_documents (docid, docname, doctype, ");
-            tao
+      sql.append("user_owner, user_updated, server_location, rev,date_created");
-            jones
+      sql.append(", date_updated, public_access) values ('");
       sql.append(docid).append("','");
       sql.append(docname).append("','");
       sql.append(doctype).append("','");
       sql.append(user).append("','");
       sql.append(user).append("','");
       sql.append(serverCode).append("','");
       sql.append(rev).append("',");
       sql.append(sqlDateString).append(",");
       sql.append(sqlDateString).append(",");
       sql.append("'0')");
       PreparedStatement pstmt = dbconn.prepareStatement(sql.toString());
       pstmt.execute();
       pstmt.close();
       dbconn.close();
             tao
     finally
+    {
       try
+      {
         dbconn.close();
+      }
       catch (SQLException sqlE)
+      {
         util.debugMessage("Error in DocumentImpl.registerDocument:" +
                                 sqlE.getMessage(), 30);
+      }
             jones
+  }
             tao
-            tao
+    /**
    * Register a document that resides on the filesystem with the database.
    * (ie, just an entry in xml_documents, nothing in xml_nodes).
    * Creates a reference to a filesystem document (used for non-xml data files)
    * This method will be called for register data file in xml_documents in
    * Replication.
    * This method is revised from registerDocument.
+   *
    * @param conn the JDBC Connection to which all information is written
    * @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 accnum the accession number to use for the INSERT OR UPDATE, which
    *               includes a revision number for this revision of the document
    *               (e.g., knb.1.1)
    * @param user the user that owns the document
    * @param serverCode the serverid from xml_replication on which this document
    *        resides.
    */
   public static void registerDocumentInReplication(
                      String docname, String doctype, String accnum,
                      String user, int serverCode)
                      throws SQLException, AccessionNumberException, Exception
+  {
     Connection dbconn = null;
     MetaCatUtil util = new MetaCatUtil();
     AccessionNumber ac;
     try {
       dbconn = util.openDBConnection();
       String docIdWithoutRev=MetaCatUtil.getDocIdFromString(accnum);
       int userSpecifyRev=MetaCatUtil.getVersionFromString(accnum);
       int revInDataBase=getLatestRevisionNumber(dbconn, docIdWithoutRev);
       //revIndataBase=-1, there is no record in xml_documents table
       //the data file is a new one, inert it into table
       //user specified rev should be great than 0
       if (revInDataBase==-1 && userSpecifyRev>0 )
+      {
             tao
-            tao
+        ac = new AccessionNumber(dbconn, accnum, "insert");
+      }
       //rev is greater the last revsion number and revInDataBase isn't -1
       // it is a updated data file
       else if (userSpecifyRev>revInDataBase && revInDataBase>0)
+      {
         //archive the old entry
         archiveDocRevision(dbconn, docIdWithoutRev, user);
         //delete the old entry in xml_documents
         deleteXMLDocuments(dbconn, docIdWithoutRev);
         ac = new AccessionNumber(dbconn, accnum, "update");
+      }
       //other situation
       else
+      {
         throw new Exception("Revision number couldn't be "
                     +userSpecifyRev);
+      }
       String docid = ac.getDocid();
       String rev = ac.getRev();
       SimpleDateFormat formatter = new SimpleDateFormat ("yy-MM-dd HH:mm:ss");
       Date localtime = new Date();
       String dateString = formatter.format(localtime);
       String sqlDateString = "to_date('" + dateString +
                                           "', 'YY-MM-DD HH24:MI:SS')";
       StringBuffer sql = new StringBuffer();
       sql.append("insert into xml_documents (docid, docname, doctype, ");
       sql.append("user_owner, user_updated, server_location, rev,date_created");
       sql.append(", date_updated, public_access) values ('");
       sql.append(docid).append("','");
       sql.append(docname).append("','");
       sql.append(doctype).append("','");
       sql.append(user).append("','");
       sql.append(user).append("','");
       sql.append(serverCode).append("','");
       sql.append(rev).append("',");
       sql.append(sqlDateString).append(",");
       sql.append(sqlDateString).append(",");
       sql.append("'0')");
       PreparedStatement pstmt = dbconn.prepareStatement(sql.toString());
       pstmt.execute();
       pstmt.close();
       dbconn.close();
             tao
     finally
+    {
       try
+      {
         dbconn.close();
+      }
       catch (SQLException sqlE)
+      {
         util.debugMessage("Error in DocumentImpl.registerDocument:" +
                                 sqlE.getMessage());
+      }
             tao
+  }
-            tao
+ /**
-            tao
+   * This method will register a data file entry in xml_documents and save a
-            tao
+   * data file input Stream into file system.. It is only used in force
    * replication
             tao
    * @param  input, the input stream which contain the file content.
    * @param  , the input stream which contain the file content
    * @param docname - the name of DTD, for data file, it is a docid number.
    * @param doctype - "BIN" for data file
    * @param accnum the accession number to use for the INSERT OR UPDATE, which
    *               includes a revision number for this revision of the document
    *               (e.g., knb.1.1)
    * @param user the user that owns the document
    * @param serverCode the serverid from xml_replication on which this document
    *        resides.
    */
  public static void writeDataFile(InputStream input, String filePath,
-            tao
+                                  String docname, String doctype, String accnum,
                                   String user, String docHomeServer)
-            tao
+                     throws SQLException, AccessionNumberException, Exception
+ {
-            tao
+   int serverCode=-2;
-            tao
+    if (filePath==null||filePath.equals(""))
+    {
       throw new
             Exception("Please specify the directory where file will be store");
+    }
     if (accnum==null||accnum.equals(""))
+    {
       throw new Exception("Please specify the stored file name");
+    }
             tao
     //get server code for the home server
     serverCode=getServerCode(docHomeServer);
     //if the server is not in the xml replication table, insert it.
     if (serverCode==-1)
+    {
       insertServerIntoReplicationTable(docHomeServer);
       //get server code again
       serverCode=getServerCode(docHomeServer);
+    }
-            tao
+    //make sure user have file lock grant(local metacat means have it too)
-            tao
+    //if (getDataFileLockGrant(accnum))
     //{
-            tao
+      //register data file into xml_documents table
-            tao
+      registerDocumentInReplication(docname, doctype, accnum, user, serverCode);
-            tao
+      //write inputstream into file system.
       File dataDirectory = new File(filePath);
       File newFile = new File(dataDirectory, accnum);
       // create a buffered byte output stream
       // that uses a default-sized output buffer
       FileOutputStream fos = new FileOutputStream(newFile);
       BufferedOutputStream outPut = new BufferedOutputStream(fos);
       BufferedInputStream bis = null;
       bis = new BufferedInputStream(input);
       byte[] buf = new byte[4 * 1024]; // 4K buffer
       int b = bis.read(buf);
       while (b != -1)
+      {
         outPut.write(buf, 0, b);
         b = bis.read(buf);
+      }
       bis.close();
 	    outPut.close();
 	    fos.close();
             tao
-            tao
+    //}//if
             tao
             jones
             tao
   public static boolean getDataFileLockGrant(String accnum)
                                                   throws Exception
+  {
     Connection dbConn = null;
     MetaCatUtil ut= new MetaCatUtil();
-            tao
+    try
+    {
       dbConn = ut.openDBConnection();
       int serverLocation=getServerLocationNumber(dbConn,accnum);
       dbConn.close();
       return getDataFileLockGrant(accnum,serverLocation);
+    }
     catch (Exception e)
+    {
       try
+      {
         dbConn.close();
+      }
       catch (Exception ee)
       {}
       throw e;
+    }
             tao
-            jones
+  /**
-            tao
+   * The method will check if metacat can get data file lock grant
    * If server code is 1, it get.
    * If server code is not 1 but call replication getlock successfully,
    * it get
    * else, it didn't get
    * @param accnum, the ID of the document
    * @param action, the action to the document
    * @param serverCode, the server location code
    */
   public static boolean getDataFileLockGrant(String accnum, int serverCode)
                                           throws Exception
+  {
     boolean flag=true;
     MetaCatUtil util = new MetaCatUtil();
     String docid = util.getDocIdFromString(accnum);
     int rev = util.getVersionFromString(accnum);
     if (serverCode == 1)
+    {
       flag=true;
       return flag;
+    }
     //if((serverCode != 1 && action.equals("UPDATE")) )
     if (serverCode != 1)
     { //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.
       String server = MetacatReplication.getServer(serverCode);
       MetacatReplication.replLog("attempting to lock " + accnum);
       URL u = new URL("https://" + server + "?server="
            +util.getLocalReplicationServerName()+"&action=getlock&updaterev="
            +rev + "&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
         //System.out.println("In lockgranted");
         MetacatReplication.replLog("lock granted for " + accnum + " from " +
                                       server);
         flag=true;
         return flag;
       }//if
       else if(openingtag.equals("<filelocked>"))
       {//the file is currently locked by another user
        //notify our user to wait a few minutes, check out a new copy and try
        //again.
         //System.out.println("file locked");
         MetacatReplication.replLog("lock denied for " + accnum + " on " +
                                    server + " reason: file already locked");
         throw new Exception("The file specified is already locked by another " +
                             "user.  Please wait 30 seconds, checkout the " +
                             "newer document, merge your changes and try " +
                             "again.");
+      }
       else if(openingtag.equals("<outdatedfile>"))
       {//our file is outdated.  notify our user to check out a new copy of the
        //file and merge his version with the new version.
         //System.out.println("outdated file");
         MetacatReplication.replLog("lock denied for " + accnum + " on " +
                                     server + " reason: local file outdated");
         throw new Exception("The file you are trying to update is an outdated" +
                             " version.  Please checkout the newest document, " +
                             "merge your changes and try again.");
       }//else if
     }//if
    return flag;
   }//getDataFileLockGrant
   /**
-            jones
+   * 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;
+  }
             berkley
   /**
    * get the creation date
    */
   public String getCreateDate() {
     return createdate;
+  }
   /**
    * get the update date
    */
   public String getUpdateDate() {
     return updatedate;
+  }
             jones
-            jones
+  /**
    * Get the document identifier (docid)
    */
   public String getDocID() {
     return docid;
+  }
             berkley
-            bojilova
+// DOCTITLE attr cleared from the db
 //  /**
 //   *get the document title
 //   */
 //  public String getDocTitle() {
 //    return doctitle;
 //  }
             berkley
   public String getUserowner() {
     return userowner;
+  }
   public String getUserupdated() {
     return userupdated;
+  }
   public int getServerlocation() {
     return serverlocation;
+  }
-            tao
+  public String getDocHomeServer() {
     return docHomeServer;
             tao
             tao
             tao
             tao
-            bojilova
+  public String getPublicaccess() {
-            berkley
+    return publicaccess;
+  }
             berkley
   public int getRev() {
     return rev;
+  }
             tao
    /**
-            jones
+   * Print a string representation of the XML document
-            jones
+   */
   public String toString()
+  {
-            jones
+    StringWriter docwriter = new StringWriter();
-            jones
+    try {
       this.toXml(docwriter);
     } catch (McdbException mcdbe) {
       return null;
+    }
-            jones
+    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.
    */
-            jones
+  public String readUsingSlowAlgorithm() throws McdbException
             jones
-            jones
+    StringBuffer doc = new StringBuffer();
-            jones
+    // First, check that we have the needed node data, and get it if not
     if (nodeRecordList == null) {
       nodeRecordList = getNodeRecordList(rootnodeid);
+    }
-            jones
+    // Create the elements from the downloaded data in the TreeSet
     rootNode = new ElementNode(nodeRecordList, rootnodeid);
-            jones
+    // 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());
+  }
   /**
-            jones
+   * Print a text representation of the XML document to a Writer
+   *
    * @param pw the Writer to which we print the document
    */
-            jones
+  public void toXml(Writer pw) throws McdbException
             jones
     PrintWriter out = null;
     if (pw instanceof PrintWriter) {
       out = (PrintWriter)pw;
     } else {
       out = new PrintWriter(pw);
+    }
     MetaCatUtil util = new MetaCatUtil();
-            jones
+    // First, check that we have the needed node data, and get it if not
     if (nodeRecordList == null) {
       nodeRecordList = getNodeRecordList(rootnodeid);
+    }
-            jones
+    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);
-            bojilova
+            if (previousNodeWasElement) {
               out.print(">");
               previousNodeWasElement = false;
+            }
-            bojilova
+            if ( currentElement.nodeprefix != null ) {
               out.print("</" + currentElement.nodeprefix + ":" +
                         currentElement.nodename + ">" );
             } else {
               out.print("</" + currentElement.nodename + ">" );
+            }
-            jones
+            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;
-            bojilova
+        if ( currentNode.nodeprefix != null ) {
           out.print("<" + currentNode.nodeprefix + ":" + currentNode.nodename);
         } else {
           out.print("<" + currentNode.nodename);
+        }
             jones
       // Handle the ATTRIBUTE nodes
       } else if (currentNode.nodetype.equals("ATTRIBUTE")) {
-            bojilova
+        if ( currentNode.nodeprefix != null ) {
           out.print(" " + currentNode.nodeprefix + ":" + currentNode.nodename +
                     "=\"" + currentNode.nodedata + "\"");
         } else {
           out.print(" " + currentNode.nodename + "=\"" +
                     currentNode.nodedata + "\"");
+        }
             bojilova
       // Handle the NAMESPACE nodes
       } else if (currentNode.nodetype.equals("NAMESPACE")) {
         out.print(" xmlns:" + currentNode.nodename + "=\""
                  + currentNode.nodedata + "\"");
       // Handle the TEXT nodes
-            jones
+      } 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
-            berkley
+    while(!openElements.empty())
+    {
       NodeRecord currentElement = (NodeRecord)openElements.pop();
       util.debugMessage("\n POPPED: " + currentElement.nodename);
-            bojilova
+      if ( currentElement.nodeprefix != null ) {
         out.print("</" + currentElement.nodeprefix + ":" +
                   currentElement.nodename + ">" );
       } else {
         out.print("</" + currentElement.nodename + ">" );
+      }
             berkley
-            jones
+    out.flush();
+  }
             berkley
   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);
-            berkley
+      pstmt.close();
-            berkley
+      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");
+  }
             jones
-            jones
+  private void getDocumentInfo(String docid) throws McdbException,
-            berkley
+                                                    AccessionNumberException
+  {
     getDocumentInfo(new DocumentIdentifier(docid));
+  }
-            jones
+  /**
-            jones
+   * Look up the document type information from the database
+   *
    * @param docid the id of the document to look up
    */
-            berkley
+  private void getDocumentInfo(DocumentIdentifier docid) throws McdbException
             jones
     PreparedStatement pstmt;
-            berkley
+    String table = "xml_documents";
             tao
-            berkley
+    try
+    {
       if(isRevisionOnly(docid))
       { //pull the document from xml_revisions instead of from xml_documents;
         table = "xml_revisions";
+      }
+    }
     catch(Exception e)
+    {
-            berkley
+      System.out.println("error in DocumentImpl.getDocumentInfo: " +
                           e.getMessage());
             berkley
     //deal with the key words here.
     if(docid.getRev().equals("all"))
+    {
+    }
-            jones
+    try {
-            berkley
+      StringBuffer sql = new StringBuffer();
-            bojilova
+// DOCTITLE attr cleared from the db
 //      sql.append("SELECT docname, doctype, rootnodeid, doctitle, ");
       sql.append("SELECT docname, doctype, rootnodeid, ");
-            bojilova
+      sql.append("date_created, date_updated, user_owner, user_updated, ");
       sql.append("server_location, public_access, rev");
       sql.append(" FROM ").append(table);
-            berkley
+      sql.append(" WHERE docid LIKE '").append(docid.getIdentifier());
       sql.append("' and rev like '").append(docid.getRev()).append("'");
       //System.out.println(sql.toString());
-            jones
+      pstmt =
-            berkley
+        conn.prepareStatement(sql.toString());
-            jones
+      // Bind the values to the query
-            berkley
+      //pstmt.setString(1, docid.getIdentifier());
       //pstmt.setString(2, docid.getRev());
             jones
       pstmt.execute();
       ResultSet rs = pstmt.getResultSet();
       boolean tableHasRows = rs.next();
       if (tableHasRows) {
-            berkley
+        this.docname        = rs.getString(1);
         this.doctype        = rs.getString(2);
         this.rootnodeid     = rs.getLong(3);
-            bojilova
+// DOCTITLE attr cleared from the db
 //        this.doctitle       = rs.getString(4);
-            bojilova
+        this.createdate     = rs.getString(4);
         this.updatedate     = rs.getString(5);
         this.userowner      = rs.getString(6);
         this.userupdated    = rs.getString(7);
         this.serverlocation = rs.getInt(8);
-            bojilova
+        this.publicaccess   = rs.getString(9);
         this.rev            = rs.getInt(10);
             jones
-            berkley
+      pstmt.close();
             tao
       //get doc  home server name
       pstmt = conn.prepareStatement("select server " +
                         "from xml_replication where serverid = ?");
       pstmt.setInt(1, serverlocation);
       pstmt.execute();
       rs = pstmt.getResultSet();
       tableHasRows = rs.next();
       if (tableHasRows)
+      {
           String server = rs.getString(1);
           //get homeserver name
           if(!server.equals("localhost"))
+          {
             this.docHomeServer=server;
+          }
           else
+          {
             this.docHomeServer=MetaCatUtil.getLocalReplicationServerName();
+          }
           MetaCatUtil.debugMessage("server: "+docHomeServer, 50);
+      }
       pstmt.close();
-            jones
+      if (this.doctype != null) {
         pstmt =
           conn.prepareStatement("SELECT system_id " +
                                   "FROM xml_catalog " +
-            bojilova
+                                 "WHERE public_id = ?");
-            jones
+        // 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);
+        }
-            berkley
+        pstmt.close();
             jones
     } catch (SQLException e) {
-            berkley
+      System.out.println("error in DocumentImpl.getDocumentInfo: " +
                           e.getMessage());
-            berkley
+      e.printStackTrace(System.out);
-            berkley
+      throw new McdbException("Error accessing database connection in " +
                               "DocumentImpl.getDocumentInfo: ", e);
             jones
     if (this.docname == null) {
       throw new McdbDocNotFoundException("Document not found: " + docid);
+    }
+  }
   /**
    * Look up the node data from the database
+   *
-            jones
+   * @param rootnodeid the id of the root node of the node tree to look up
-            jones
+   */
-            jones
+  private TreeSet getNodeRecordList(long rootnodeid) throws McdbException
             jones
     PreparedStatement pstmt;
     TreeSet nodeRecordList = new TreeSet(new NodeComparator());
     long nodeid = 0;
     long parentnodeid = 0;
     long nodeindex = 0;
     String nodetype = null;
     String nodename = null;
-            bojilova
+    String nodeprefix = null;
-            jones
+    String nodedata = null;
-            berkley
+    String quotechar = dbAdapter.getStringDelimiter();
             jones
     try {
       pstmt =
       conn.prepareStatement("SELECT nodeid,parentnodeid,nodeindex, " +
-            berkley
+           "nodetype,nodename,nodeprefix,nodedata " +
-            jones
+           "FROM xml_nodes WHERE rootnodeid = ?");
             jones
       // Bind the values to the query
-            jones
+      pstmt.setLong(1, rootnodeid);
             jones
       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);
-            bojilova
+        nodeprefix = rs.getString(6);
         nodedata = rs.getString(7);
-            berkley
+        nodedata = MetaCatUtil.normalize(nodedata);
-            jones
+        // add the data to the node record list hashtable
-            bojilova
+        NodeRecord currentRecord = new NodeRecord(nodeid,parentnodeid,nodeindex,
-            tao
+                                      nodetype, nodename, nodeprefix, nodedata);
-            jones
+        nodeRecordList.add(currentRecord);
         // Advance to the next node
         tableHasRows = rs.next();
+      }
       pstmt.close();
     } catch (SQLException e) {
-            bojilova
+      throw new McdbException("Error in DocumentImpl.getNodeRecordList " +
                               e.getMessage());
             jones
     if (nodeRecordList != null) {
       return nodeRecordList;
     } else {
       throw new McdbException("Error getting node data: " + docid);
+    }
+  }
             berkley
-            bojilova
+// NOT USED ANY MORE
 //  /** 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);
 //  }
             jones
-            bojilova
+ /** creates SQL code and inserts new document into DB connection */
-            bojilova
+  private void writeDocumentToDB(String action, String user, String pub,
-            bojilova
+                                 String catalogid, int serverCode)
-            bojilova
+               throws SQLException, Exception {
-            bojilova
+    String sysdate = dbAdapter.getDateTimeFunction();
             bojilova
-            bojilova
+    try {
       PreparedStatement pstmt = null;
       if (action.equals("INSERT")) {
         //AccessionNumber ac = new AccessionNumber();
         //this.docid = ac.generate(docid, "INSERT");
-            tao
+        System.out.println("before pstmt");
-            bojilova
+        pstmt = conn.prepareStatement(
-            bojilova
+                "INSERT INTO xml_documents " +
                 "(docid, rootnodeid, docname, doctype, " +
                 "user_owner, user_updated, date_created, date_updated, " +
-            tao
+                "public_access, catalog_id, server_location, rev) " +
-            bojilova
+                "VALUES (?, ?, ?, ?, ?, ?, " + sysdate + ", " + sysdate +
-            tao
+                ", ?, ?, ?, ?)");
-            berkley
+        //note that the server_location is set to 1.
         //this means that "localhost" in the xml_replication table must
         //always be the first entry!!!!!
-            bojilova
+        // 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);
-            tao
+        //public access is usefulless, so set it to null
         pstmt.setString(7, null);
         /*if ( pub == null ) {
-            bojilova
+          pstmt.setString(7, null);
-            bojilova
+        } else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
-            bojilova
+          pstmt.setInt(7, 1);
-            bojilova
+        } else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
-            bojilova
+          pstmt.setInt(7, 0);
-            tao
+        }*/
-            bojilova
+        pstmt.setString(8, catalogid);
         pstmt.setInt(9, serverCode);
-            tao
+        pstmt.setInt(10, Integer.parseInt(updatedVersion));
-            bojilova
+      } else if (action.equals("UPDATE")) {
-            tao
+        // Save the old document publicaccessentry in a backup table
-            bojilova
+        DocumentImpl.archiveDocRevision( conn, docid, user );
-            berkley
+        DocumentImpl thisdoc = new DocumentImpl(conn, docid);
         int thisrev = thisdoc.getRev();
             tao
         //if the updated vesion is not greater than current one,
         //throw it into a exception
         if (Integer.parseInt(updatedVersion)<=thisrev)
+        {
           throw new Exception("Next revision number couldn't be less"
                                +" than or equal "+ thisrev);
+        }
         else
+        {
           //set the user specified revision
           thisrev=Integer.parseInt(updatedVersion);
+        }
-            bojilova
+        // 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();
-            berkley
+        pstmt.close();
             bojilova
         // Update the new document to reflect the new node tree
         pstmt = conn.prepareStatement(
             "UPDATE xml_documents " +
             "SET rootnodeid = ?, docname = ?, doctype = ?, " +
-            bojilova
+            "user_updated = ?, date_updated = " + sysdate + ", " +
-            bojilova
+            "server_location = ?, rev = ?, public_access = ?, catalog_id = ? " +
-            bojilova
+            "WHERE docid = ?");
-            bojilova
+        // Bind the values to the query
         pstmt.setLong(1, rootnodeid);
         pstmt.setString(2, docname);
         pstmt.setString(3, doctype);
         pstmt.setString(4, user);
-            berkley
+        pstmt.setInt(5, serverCode);
-            berkley
+        pstmt.setInt(6, thisrev);
-            tao
+        pstmt.setString(7, null);
         /*if ( pub == null ) {
-            bojilova
+          pstmt.setString(7, null);
-            bojilova
+        } else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
-            bojilova
+          pstmt .setInt(7, 1);
-            bojilova
+        } else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
-            bojilova
+          pstmt.setInt(7, 0);
-            tao
+        }*/
-            bojilova
+        pstmt.setString(8, catalogid);
         pstmt.setString(9, this.docid);
             berkley
-            bojilova
+      } else {
         System.err.println("Action not supported: " + action);
+      }
       // Do the insertion
       pstmt.execute();
-            tao
+      System.out.println("after excecute");
-            bojilova
+      pstmt.close();
     } catch (SQLException sqle) {
       throw sqle;
     } catch (Exception e) {
       throw e;
+    }
+  }
   /**
-            jones
+   * Write an XML file to the database, given a filename
             jones
-            jones
+   * @param conn the JDBC connection to the database
-            jones
+   * @param filename the filename to be loaded into the database
-            bojilova
+   * @param pub flag for public "read" access on document
    * @param dtdfilename the dtd to be uploaded on server's file system
-            jones
+   * @param action the action to be performed (INSERT OR UPDATE)
    * @param docid the docid to use for the INSERT OR UPDATE
-            bojilova
+   * @param user the user that owns the document
-            bojilova
+   * @param groups the groups to which user belongs
-            jones
+   */
-            bojilova
+  public static String write(Connection conn,String filename,
-            bojilova
+                             String pub, String dtdfilename,
-            bojilova
+                             String action, String docid, String user,
-            bojilova
+                             String[] groups )
-            bojilova
+                throws Exception {
             bojilova
     Reader dtd = null;
     if ( dtdfilename != null ) {
       dtd = new FileReader(new File(dtdfilename).toString());
+    }
-            bojilova
+    return write ( conn, new FileReader(new File(filename).toString()),
-            bojilova
+                   pub, dtd, action, docid, user, groups, false);
             jones
             bojilova
-            bojilova
+  public static String write(Connection conn,Reader xml,String pub,Reader dtd,
-            bojilova
+                             String action, String docid, String user,
-            bojilova
+                             String[] groups, boolean validate)
-            berkley
+                throws Exception {
-            tao
+    //this method will be called in handleUpdateOrInsert method
     //in MetacatServlet class
     // get server location for this doc
     int serverLocation=getServerLocationNumber(conn,docid);
     //System.out.println("server location: "+serverLocation);
     return write(conn,xml,pub,dtd,action,docid,user,groups,serverLocation,false,
                  validate);
             bojilova
-            bojilova
+  public static String write(Connection conn, Reader xml, String pub,
-            bojilova
+                             String action, String docid, String user,
-            bojilova
+                             String[] groups )
-            bojilova
+                throws Exception {
-            berkley
+    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();
-            bojilova
+      return write(conn, xml, pub, action, docid, user, groups, servercode);
             berkley
     else
     {//if the file is being inserted then the servercode is always 1
-            bojilova
+      return write(conn, xml, pub, action, docid, user, groups, 1);
             berkley
             berkley
-            berkley
+  public static String write( Connection conn, Reader xml,
                               String action, String docid, String user,
-            bojilova
+                              String[] groups, int serverCode )
-            bojilova
+                throws Exception
             berkley
-            bojilova
+    return write(conn,xml,null,action,docid,user,groups,serverCode);
             berkley
-            bojilova
+  public static String write( Connection conn, Reader xml, String pub,
-            berkley
+                              String action, String docid, String user,
-            bojilova
+                              String[] groups, int serverCode)
-            bojilova
+                throws Exception
             berkley
-            bojilova
+    return write(conn,xml,pub,null,action,docid,user,groups,
-            bojilova
+                 serverCode,false,false);
             berkley
-            bojilova
+  public static String write( Connection conn, Reader xml, String pub,
-            bojilova
+                              String action, String docid, String user,
-            bojilova
+                              String[] groups, int serverCode, boolean override)
-            bojilova
+                throws Exception
+  {
-            bojilova
+    return write(conn,xml,pub,null,action,docid,user,groups,
-            bojilova
+                 serverCode,override,false);
             bojilova
-            jones
+  /**
    * Write an XML file to the database, given a Reader
+   *
-            jones
+   * @param conn the JDBC connection to the database
-            jones
+   * @param xml the xml stream to be loaded into the database
-            bojilova
+   * @param pub flag for public "read" access on xml document
    * @param dtd the dtd to be uploaded on server's file system
-            bojilova
+   * @param action the action to be performed (INSERT or UPDATE)
    * @param accnum the docid + rev# to use on INSERT or UPDATE
-            berkley
+   * @param user the user that owns the document
-            bojilova
+   * @param groups the groups to which user belongs
-            berkley
+   * @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.
-            jones
+   */
             berkley
-            bojilova
+  public static String write( Connection conn,Reader xml,String pub,Reader dtd,
-            bojilova
+                              String action, String accnum, String user,
-            bojilova
+                              String[] groups, int serverCode, boolean override,
-            bojilova
+                              boolean validate)
-            bojilova
+                throws Exception
             berkley
-            bojilova
+    // NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
-            tao
+    MetaCatUtil util = new MetaCatUtil();
-            bojilova
+    AccessionNumber ac = new AccessionNumber(conn, accnum, action);
     String docid = ac.getDocid();
     String rev = ac.getRev();
-            berkley
+    MetaCatUtil.debugMessage("action: " + action + " servercode: " +
-            tao
+                             serverCode + " override: " + override, 10);
             berkley
-            berkley
+    if((serverCode != 1 && action.equals("UPDATE")) && !override)
-            berkley
+    { //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.
-            berkley
+      int istreamInt;
-            berkley
+      char istreamChar;
-            bojilova
+      DocumentIdentifier id = new DocumentIdentifier(accnum);
       String updaterev = id.getRev();
-            berkley
+      String server = MetacatReplication.getServer(serverCode);
-            bojilova
+      MetacatReplication.replLog("attempting to lock " + accnum);
-            tao
+      URL u = new URL("https://" + server + "?server="
            +util.getLocalReplicationServerName()+"&action=getlock&updaterev="
            +updaterev + "&docid=" + docid);
       //System.out.println("sending message: " + u.toString());
-            berkley
+      String serverResStr = MetacatReplication.getURLContent(u);
-            tao
+      String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);
-            berkley
+      if(openingtag.equals("<lockgranted>"))
       {//the lock was granted go ahead with the insert
-            berkley
+        try
+        {
-            tao
+          //System.out.println("In lockgranted");
-            bojilova
+          MetacatReplication.replLog("lock granted for " + accnum + " from " +
-            berkley
+                                      server);
-            tao
+          XMLReader parser = initializeParser(conn, action, docid, updaterev,
                                   validate, user, groups, pub, serverCode, dtd);
-            berkley
+          conn.setAutoCommit(false);
-            bojilova
+          parser.parse(new InputSource(xml));
-            berkley
+          conn.commit();
           conn.setAutoCommit(true);
+        }
         catch (Exception e)
+        {
           conn.rollback();
           conn.setAutoCommit(true);
           throw e;
+        }
             berkley
             tao
         //If Metacat is super hub, tell all servers in its server list to get
         //the new document, ture mean it is xml document
         if ((util.getOption("hub")).equals("super"))
+        {
           ForceReplicationHandler frh = new ForceReplicationHandler(accnum,
                 true, ReplicationHandler.buildServerList(conn));
+        }
         else
+        {
           //after inserting the document locally, tell the document's homeserver
           //to come get a copy from here.
           ForceReplicationHandler frh = new ForceReplicationHandler(accnum,
                 true, ReplicationHandler.getHomeServer(docid));
+        }
-            bojilova
+        return (accnum);
             berkley
             bojilova
-            berkley
+      else if(openingtag.equals("<filelocked>"))
       {//the file is currently locked by another user
        //notify our user to wait a few minutes, check out a new copy and try
        //again.
-            berkley
+        //System.out.println("file locked");
-            bojilova
+        MetacatReplication.replLog("lock denied for " + accnum + " on " +
-            berkley
+                                   server + " reason: file already locked");
-            berkley
+        throw new Exception("The file specified is already locked by another " +
                             "user.  Please wait 30 seconds, checkout the " +
                             "newer document, merge your changes and try " +
                             "again.");
             berkley
       else if(openingtag.equals("<outdatedfile>"))
       {//our file is outdated.  notify our user to check out a new copy of the
        //file and merge his version with the new version.
-            berkley
+        //System.out.println("outdated file");
-            bojilova
+        MetacatReplication.replLog("lock denied for " + accnum + " on " +
-            berkley
+                                    server + " reason: local file outdated");
-            berkley
+        throw new Exception("The file you are trying to update is an outdated" +
                             " version.  Please checkout the newest document, " +
                             "merge your changes and try again.");
             berkley
             berkley
             berkley
-            bojilova
+    if ( action.equals("UPDATE") ) {
-            bojilova
+      // check for 'write' permission for 'user' to update this document
             berkley
-            bojilova
+      if ( !hasPermission(conn, user, groups, docid) ) {
-            bojilova
+        throw new Exception("User " + user +
-            bojilova
+              " does not have permission to update XML Document #" + accnum);
             bojilova
+    }
-            berkley
+    try
             bojilova
             tao
       XMLReader parser = initializeParser(conn, action, docid, rev, validate,
-            bojilova
+                                          user, groups, pub, serverCode, dtd);
-            bojilova
+      conn.setAutoCommit(false);
       parser.parse(new InputSource(xml));
       conn.commit();
       conn.setAutoCommit(true);
             berkley
     catch (Exception e)
+    {
-            bojilova
+      conn.rollback();
       conn.setAutoCommit(true);
       throw e;
+    }
             berkley
     //force replicate out the new document to each server in our server list.
     if(serverCode == 1)
             tao
       //start the thread to replicate this new document out to the other servers
-            tao
+      //true mean it is xml document
       ForceReplicationHandler frh = new ForceReplicationHandler
-            tao
+                (accnum, action, true,ReplicationHandler.buildServerList(conn));
             tao
             berkley
             bojilova
-            bojilova
+    return(accnum);
             jones
             jones
-            jones
+  /**
-            tao
+   * Write an XML file to the database during replication
+   *
    * @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 accnum the docid + rev# to use on INSERT or UPDATE
    * @param user the user that owns the document
    * @param groups the groups to which user belongs
    * @param homeServer the name of server which the document origanlly create
    * @param validate, if the xml document is valid or not
    */
   public static String writeReplication( Connection conn,Reader xml,String pub,
                 Reader dtd, String action, String accnum, String user,
                             String[] groups,String homeServer, boolean validate)
                 throws Exception
+  {
     // NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
     MetaCatUtil util = new MetaCatUtil();
-            tao
+    //AccessionNumber ac = new AccessionNumber(conn, accnum, action);
     //String docid = ac.getDocid();
     // String rev = ac.getRev();
     String docid=util.getDocIdFromString(accnum);
     String rev=(new Integer(util.getVersionFromString(accnum))).toString();
     //check if xml_documents table has the document or not
     //if not, set action to insert
     if (getLatestRevisionNumber(conn,docid)==-1)
+    {
       action="INSERT";
+    }
-            tao
+    int serverCode=-2;
     //get server code for the home server
     serverCode=getServerCode(homeServer);
     //if the server is not in the xml replication table, insert it.
     if (serverCode==-1)
+    {
       insertServerIntoReplicationTable(homeServer);
       //get server code again
       serverCode=getServerCode(homeServer);
+    }
     MetaCatUtil.debugMessage("action: " + action + " servercode: " +
                              serverCode, 10);
-            tao
+    /*if((serverCode != 1 && action.equals("UPDATE")) )
+    {
-            tao
+      int istreamInt;
       char istreamChar;
       DocumentIdentifier id = new DocumentIdentifier(accnum);
       String updaterev = id.getRev();
       String server = MetacatReplication.getServer(serverCode);
       MetacatReplication.replLog("attempting to lock " + accnum);
       URL u = new URL("https://" + server + "?server="
            +util.getLocalReplicationServerName()+"&action=getlock&updaterev="
            +updaterev + "&docid=" + docid);
             tao
-            tao
+      String serverResStr = MetacatReplication.getURLContent(u);
       String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);
       if(openingtag.equals("<lockgranted>"))
             tao
-            tao
+        try
+        {
             tao
-            tao
+          MetacatReplication.replLog("lock granted for " + accnum + " from " +
                                       server);
           XMLReader parser = initializeParser(conn, action, docid, updaterev,
                                   validate, user, groups, 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;
+        }
         return (accnum);
+      }
       else if(openingtag.equals("<filelocked>"))
             tao
-            tao
+        MetacatReplication.replLog("lock denied for " + accnum + " on " +
                                    server + " reason: file already locked");
         throw new Exception("The file specified is already locked by another " +
                             "user.  Please wait 30 seconds, checkout the " +
                             "newer document, merge your changes and try " +
                             "again.");
+      }
       else if(openingtag.equals("<outdatedfile>"))
             tao
-            tao
+        MetacatReplication.replLog("lock denied for " + accnum + " on " +
                                     server + " reason: local file outdated");
         throw new Exception("The file you are trying to update is an outdated" +
                             " version.  Please checkout the newest document, " +
                             "merge your changes and try again.");
+      }
-            tao
+    }*/
             tao
-            tao
+    /*if ( action.equals("UPDATE") ) {
-            tao
+      if ( !hasPermission(conn, user, groups, docid) ) {
         throw new Exception("User " + user +
               " does not have permission to update XML Document #" + accnum);
+      }
-            tao
+    }*/
             tao
     try
+    {
       XMLReader parser = initializeParser(conn, action, docid, rev, validate,
                                           user, groups, 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;
+    }
     return(accnum);
+  }
   /**
-            jones
+   * Delete an XML file from the database (actually, just make it a revision
    * in the xml_revisions table)
+   *
    * @param docid the ID of the document to be deleted from the database
    */
-            bojilova
+  public static void delete( Connection conn, String accnum,
-            bojilova
+                                 String user, String[] groups )
-            bojilova
+                throws Exception
+  {
-            bojilova
+    // OLD
     //DocumentIdentifier id = new DocumentIdentifier(accnum);
     //String docid = id.getIdentifier();
     //String rev = id.getRev();
             berkley
-            bojilova
+    // OLD
-            bojilova
+    // Determine if the docid,rev are OK for DELETE
-            bojilova
+    //AccessionNumber ac = new AccessionNumber(conn);
     //docid = ac.generate(docid, rev, "DELETE");
             jones
-            bojilova
+    // NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
     AccessionNumber ac = new AccessionNumber(conn, accnum, "DELETE");
     String docid = ac.getDocid();
     String rev = ac.getRev();
-            bojilova
+    // check for 'write' permission for 'user' to delete this document
-            bojilova
+    if ( !hasPermission(conn, user, groups, docid) ) {
-            bojilova
+      throw new Exception("User " + user +
-            bojilova
+              " does not have permission to delete XML Document #" + accnum);
             bojilova
-            jones
+    conn.setAutoCommit(false);
     // Copy the record to the xml_revisions table
-            bojilova
+    DocumentImpl.archiveDocRevision( conn, docid, user );
             jones
-            jones
+    // Now delete it from the xml_documents table
             berkley
-            jones
+    Statement stmt = conn.createStatement();
-            bojilova
+    stmt.execute("DELETE FROM xml_index WHERE docid = '" + docid + "'");
-            bojilova
+    //stmt.execute("DELETE FROM xml_access WHERE docid = '" + docid + "'");
-            bojilova
+    stmt.execute("DELETE FROM xml_access WHERE accessfileid = '" + docid + "'");
     stmt.execute("DELETE FROM xml_relation WHERE docid = '" + docid + "'");
-            bojilova
+    stmt.execute("DELETE FROM xml_documents WHERE docid = '" + docid + "'");
-            jones
+    stmt.close();
     conn.commit();
-            bojilova
+    conn.setAutoCommit(true);
-            berkley
+    //IF this is a package document:
     //delete all of the relations that this document created.
     //if the deleted document is a package document its relations should
     //no longer be active if it has been deleted from the system.
             bojilova
             jones
             bojilova
-            bojilova
+  /**
-            bojilova
+    * Check for "WRITE" permission on @docid for @user and/or @groups
-            bojilova
+    * from DB connection
     */
-            bojilova
+  private static boolean hasPermission ( Connection conn, String user,
                                   String[] groups, String docid )
-            tao
+                  throws SQLException, Exception
             bojilova
-            bojilova
+    // Check for WRITE permission on @docid for @user and/or @groups
-            bojilova
+    AccessControlList aclobj = new AccessControlList(conn);
-            bojilova
+    return aclobj.hasPermission("WRITE", user, groups, docid);
             bojilova
-            tao
+  /**
     * Check for "READ" permission base on docid, user and group
     *@docid, the document
     *@user, user name
     *@group, user's group
+    *
     */
   public boolean hasReadPermission ( Connection conn, String user,
                                   String[] groups, String docId )
-            tao
+                  throws SQLException, Exception
             tao
     // Check for READ permission on @docid for @user and/or @groups
     AccessControlList aclObj = new AccessControlList(conn);
     return aclObj.hasPermission("READ", user, groups, docId);
+  }
-            jones
+  /**
-            jones
+   * Set up the parser handlers for writing the document to the database
    */
-            bojilova
+  private static XMLReader initializeParser(Connection conn, String action,
-            tao
+                               String docid, String rev, boolean validate,
-            bojilova
+                                   String user, String[] groups, String pub,
-            bojilova
+                                   int serverCode, Reader dtd)
-            bojilova
+                           throws Exception
+  {
-            jones
+    XMLReader parser = null;
     //
     // Set up the SAX document handlers for parsing
     //
     try {
-            tao
+      //create a DBSAXHandler object which has the revision specification
       ContentHandler chandler = new DBSAXHandler(conn, action, docid, rev,
-            bojilova
+                                                 user, groups, pub, serverCode);
-            bojilova
+      EntityResolver eresolver= new DBEntityResolver(conn,
                                                  (DBSAXHandler)chandler, dtd);
-            bojilova
+      DTDHandler dtdhandler   = new DBDTDHandler(conn);
             jones
       // Get an instance of the parser
-            bojilova
+      String parserName = MetaCatUtil.getOption("saxparser");
-            jones
+      parser = XMLReaderFactory.createXMLReader(parserName);
-            bojilova
+      // Turn on validation
-            bojilova
+      parser.setFeature("http://xml.org/sax/features/validation", validate);
-            bojilova
+      // Turn off Including all external parameter entities
       // (the external DTD subset also)
       // Doesn't work well, probably the feature name is not correct
       // parser.setFeature(
       //  "http://xml.org/sax/features/external-parameter-entities", false);
             jones
       // Set Handlers in the parser
       parser.setProperty("http://xml.org/sax/properties/declaration-handler",
                          chandler);
       parser.setProperty("http://xml.org/sax/properties/lexical-handler",
                          chandler);
       parser.setContentHandler((ContentHandler)chandler);
-            bojilova
+      parser.setEntityResolver((EntityResolver)eresolver);
-            jones
+      parser.setDTDHandler((DTDHandler)dtdhandler);
       parser.setErrorHandler((ErrorHandler)chandler);
     } catch (Exception e) {
-            bojilova
+      throw e;
             jones
     return parser;
+  }
-            bojilova
+  /** Save a document entry in the xml_revisions table */
   private static void archiveDocRevision(Connection conn, String docid,
-            berkley
+                                         String user)
             tao
-            bojilova
+    String sysdate = dbAdapter.getDateTimeFunction();
-            bojilova
+    // create a record in xml_revisions table
     // for that document as selected from xml_documents
             tao
    try
+   {
      PreparedStatement pstmt = conn.prepareStatement(
-            bojilova
+      "INSERT INTO xml_revisions " +
-            bojilova
+        "(docid, rootnodeid, docname, doctype, " +
-            bojilova
+        "user_owner, user_updated, date_created, date_updated, " +
         "server_location, rev, public_access, catalog_id) " +
-            bojilova
+      "SELECT ?, rootnodeid, docname, doctype, " +
-            bojilova
+        "user_owner, ?, " + sysdate + ", " + sysdate + ", "+
         "server_location, rev, public_access, catalog_id " +
-            bojilova
+      "FROM xml_documents " +
       "WHERE docid = ?");
-            tao
+      // Bind the values to the query and execute it
       pstmt.setString(1, docid);
       pstmt.setString(2, user);
       pstmt.setString(3, docid);
       pstmt.execute();
       pstmt.close();
+   }
    catch (SQLException e)
+   {
+   }
             bojilova
+  }
             tao
   /**
     * delete a entry in xml_table for given docid
     * @param docId, the id of the document need to be delete
     */
   private static void deleteXMLDocuments(Connection conn, String docId)
                                          throws SQLException
+  {
     //delete a record
     PreparedStatement pStmt =
              conn.prepareStatement("DELETE FROM xml_documents WHERE docid = '"
                                               + docId + "'");
     pStmt.execute();
     pStmt.close();
             bojilova
-            tao
+  }//deleteXMLDocuments
-            jones
+  /**
-            tao
+    * Get last revision number from database for a docid
     * If couldn't find an entry,  -1 will return
     * The return value is integer because we want compare it to there new one
     * @param docid <sitecode>.<uniqueid> part of Accession Number
     */
   private static int getLatestRevisionNumber(Connection conn, String docId)
                                       throws SQLException
+  {
     int rev = 1;
     PreparedStatement pStmt;
     pStmt = conn.prepareStatement
               ("SELECT rev FROM xml_documents WHERE docid='" + docId + "'");
     pStmt.execute();
     ResultSet rs = pStmt.getResultSet();
     boolean hasRow = rs.next();
     if (hasRow)
+    {
       rev = rs.getInt(1);
       pStmt.close();
+    }
     else
+    {
       rev=-1;
       pStmt.close();
+    }
     return rev;
   }//getLatestRevisionNumber
   /**
-            tao
+   * Get server location form database for a accNum
+   *
    * @param accum <sitecode>.<uniqueid>.<rev>
    */
   private static int getServerLocationNumber(Connection conn, String accNum)
                                             throws SQLException
+  {
     //get rid of revNum part
     String docId=MetaCatUtil.getDocIdFromString(accNum);
     PreparedStatement pStmt;
     int serverLocation;
     pStmt = conn.prepareStatement
       ("SELECT server_location FROM xml_documents WHERE docid='" + docId + "'");
     pStmt.execute();
     ResultSet rs = pStmt.getResultSet();
     boolean hasRow = rs.next();
     //if there is entry in xml_documents, get the serverlocation
     if (hasRow)
+    {
       serverLocation = rs.getInt(1);
       pStmt.close();
+    }
     else
+    {
       // if htere is no entry in xml_documents, we consider it is new document
       // the server location is local host and value is 1
       serverLocation=1;
       pStmt.close();
+    }
     return serverLocation;
+  }
             tao
-            tao
+  /**
-            tao
+   * Given a server name, return its servercode in xml_replication table.
    * If no server is found, -1 will return
    * @param serverName,
    */
   private static int getServerCode(String serverName)
+  {
     PreparedStatement pStmt=null;
     int serverLocation=-2;
     Connection dbConn = null;
     MetaCatUtil util = new MetaCatUtil();
     //we should consider about local host too
     if (serverName.equals(util.getLocalReplicationServerName()))
+    {
       serverLocation=1;
       return serverLocation;
+    }
     try
+    {
       //check xml_replication table
-            tao
+      dbConn=util.openDBConnection();
-            tao
+      pStmt = dbConn.prepareStatement
       ("SELECT serverid FROM xml_replication WHERE server='" + serverName +"'");
       pStmt.execute();
       ResultSet rs = pStmt.getResultSet();
       boolean hasRow = rs.next();
       //if there is entry in xml_replication, get the serverid
       if (hasRow)
+      {
         serverLocation = rs.getInt(1);
         pStmt.close();
+      }
       else
+      {
         // if htere is no entry in xml_replication, -1 will return
         serverLocation=-1;
         pStmt.close();
+      }
+    }
     catch (Exception e)
+    {
       util.debugMessage("Error in DocumentImpl.getServerCode(): "
                                     +e.getMessage(), 30);
+    }
     finally
+    {
       try
+      {
-            tao
+        dbConn.close();
             tao
       catch (Exception ee)
       {}
+    }
     return serverLocation;
+  }
   /**
    * Insert a server into xml_replcation table
    * @param server, the name of server
    */
   private static void  insertServerIntoReplicationTable(String server)
+  {
     PreparedStatement pStmt=null;
     Connection dbConn = null;
     int replicate = 1;
     MetaCatUtil util = new MetaCatUtil();
     try
+    {
-            tao
+       dbConn=util.openDBConnection();
-            tao
+       pStmt = dbConn.prepareStatement("INSERT INTO xml_replication " +
                                       "(server, last_checked, replicate) " +
                                       "VALUES ('" + server + "', to_date(" +
                                       "'01/01/00', 'MM/DD/YY'), '" +
                                       replicate + "')");
         pStmt.execute();
         pStmt.close();
         dbConn.commit();
+    }
     catch (Exception e)
+    {
       util.debugMessage("Error in DocumentImpl.getServerCode(): "
                                     +e.getMessage(), 30);
+    }
     finally
+    {
       try
+      {
         pStmt.close();
-            tao
+        dbConn.close();
             tao
       catch (Exception ee)
       {}
+    }
+  }
   /**
-            jones
+   * the main routine used to test the DBWriter utility.
    * <p>
    * Usage: java DocumentImpl <-f filename -a action -d docid>
+   *
    * @param filename the filename to be loaded into the database
    * @param action the action to perform (READ, INSERT, UPDATE, DELETE)
    * @param docid the id of the document to process
    */
   static public void main(String[] args) {
     try {
-            bojilova
+      String filename    = null;
-            bojilova
+      String dtdfilename = null;
-            bojilova
+      String action      = null;
       String docid       = null;
-            jones
+      boolean showRuntime = false;
       boolean useOldReadAlgorithm = false;
             jones
-            jones
+      // Parse the command line arguments
-            jones
+      for ( int i=0 ; i < args.length; ++i ) {
         if ( args[i].equals( "-f" ) ) {
           filename =  args[++i];
-            bojilova
+        } else if ( args[i].equals( "-r" ) ) {
           dtdfilename =  args[++i];
-            jones
+        } else if ( args[i].equals( "-a" ) ) {
           action =  args[++i];
         } else if ( args[i].equals( "-d" ) ) {
           docid =  args[++i];
-            jones
+        } else if ( args[i].equals( "-t" ) ) {
           showRuntime = true;
         } else if ( args[i].equals( "-old" ) ) {
           useOldReadAlgorithm = true;
-            jones
+        } else {
           System.err.println
             ( "   args[" +i+ "] '" +args[i]+ "' ignored." );
+        }
+      }
-            jones
+      // Check if the required arguments are provided
-            jones
+      boolean argsAreValid = false;
       if (action != null) {
         if (action.equals("INSERT")) {
           if (filename != null) {
             argsAreValid = true;
+          }
         } else if (action.equals("UPDATE")) {
           if ((filename != null) && (docid != null)) {
             argsAreValid = true;
+          }
         } else if (action.equals("DELETE")) {
           if (docid != null) {
             argsAreValid = true;
+          }
         } else if (action.equals("READ")) {
           if (docid != null) {
             argsAreValid = true;
+          }
+        }
+      }
-            jones
+      // Print usage message if the arguments are not valid
-            jones
+      if (!argsAreValid) {
         System.err.println("Wrong number of arguments!!!");
         System.err.println(
-            bojilova
+          "USAGE: java DocumentImpl [-t] <-a INSERT> [-d docid] <-f filename> "+
-            bojilova
+          "[-r dtdfilename]");
-            jones
+        System.err.println(
-            bojilova
+          "   OR: java DocumentImpl [-t] <-a UPDATE -d docid -f filename> " +
-            bojilova
+          "[-r dtdfilename]");
-            jones
+        System.err.println(
-            jones
+          "   OR: java DocumentImpl [-t] <-a DELETE -d docid>");
-            jones
+        System.err.println(
-            jones
+          "   OR: java DocumentImpl [-t] [-old] <-a READ -d docid>");
-            jones
+        return;
+      }
             jones
       // Time the request if asked for
       double startTime = System.currentTimeMillis();
-            jones
+      // Open a connection to the database
       MetaCatUtil util = new MetaCatUtil();
       Connection dbconn = util.openDBConnection();
-            berkley
+      double connTime = System.currentTimeMillis();
-            jones
+      // Execute the action requested (READ, INSERT, UPDATE, DELETE)
-            jones
+      if (action.equals("READ")) {
           DocumentImpl xmldoc = new DocumentImpl( dbconn, docid );
-            jones
+          if (useOldReadAlgorithm) {
             System.out.println(xmldoc.readUsingSlowAlgorithm());
           } else {
             xmldoc.toXml(new PrintWriter(System.out));
+          }
-            jones
+      } else if (action.equals("DELETE")) {
-            bojilova
+        DocumentImpl.delete(dbconn, docid, null, null);
-            jones
+        System.out.println("Document deleted: " + docid);
-            jones
+      } else {
-            bojilova
+        String newdocid = DocumentImpl.write(dbconn, filename, null,
-            bojilova
+                                             dtdfilename, action, docid,
                                              null, null);
-            jones
+        if ((docid != null) && (!docid.equals(newdocid))) {
           if (action.equals("INSERT")) {
             System.out.println("New document ID generated!!! ");
           } else if (action.equals("UPDATE")) {
             System.out.println("ERROR: Couldn't update document!!! ");
             jones
-            jones
+        } else if ((docid == null) && (action.equals("UPDATE"))) {
           System.out.println("ERROR: Couldn't update document!!! ");
             jones
-            jones
+        System.out.println("Document processing finished for: " + filename
               + " (" + newdocid + ")");
             jones
-            jones
+      double stopTime = System.currentTimeMillis();
-            berkley
+      double dbOpenTime = (connTime - startTime)/1000;
       double insertTime = (stopTime - connTime)/1000;
-            jones
+      double executionTime = (stopTime - startTime)/1000;
       if (showRuntime) {
-            berkley
+        System.out.println("\n\nTotal Execution time was: " +
                            executionTime + " seconds.");
         System.out.println("Time to open DB connection was: " + dbOpenTime +
                            " seconds.");
         System.out.println("Time to insert document was: " + insertTime +
                            " seconds.");
             jones
-            berkley
+      dbconn.close();
-            jones
+    } catch (McdbException me) {
       me.toXml(new PrintWriter(System.err));
     } catch (AccessionNumberException ane) {
       System.out.println(ane.getMessage());
     } catch (Exception e) {
       System.err.println("EXCEPTION HANDLING REQUIRED");
       System.err.println(e.getMessage());
       e.printStackTrace(System.err);
+    }
+  }
             jones

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