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1
/**
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 *  '$RCSfile$'
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 *    Purpose: A Class that represents an XML document
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 *  Copyright: 2000 Regents of the University of California and the
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 *             National Center for Ecological Analysis and Synthesis
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 *    Authors: Matt Jones
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 *    Release: @release@
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 *
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 *   '$Author: tao $'
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 *     '$Date: 2002-05-08 16:04:58 -0700 (Wed, 08 May 2002) $'
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 * '$Revision: 1063 $'
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 *
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 * This program is free software; you can redistribute it and/or modify
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 * it under the terms of the GNU General Public License as published by
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 * the Free Software Foundation; either version 2 of the License, or
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 * (at your option) any later version.
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 *
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 * This program is distributed in the hope that it will be useful,
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 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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 * GNU General Public License for more details.
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 *
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 * You should have received a copy of the GNU General Public License
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 * along with this program; if not, write to the Free Software
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 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
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 */
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package edu.ucsb.nceas.metacat;
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import java.sql.*;
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import java.io.File;
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import java.io.FileReader;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.io.Reader;
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import java.io.StringWriter;
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import java.io.Writer;
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import java.io.InputStreamReader;
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import java.io.*;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.Iterator;
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import java.util.Stack;
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import java.util.TreeSet;
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import java.util.Enumeration;
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import org.xml.sax.AttributeList;
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import org.xml.sax.ContentHandler;
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import org.xml.sax.DTDHandler;
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import org.xml.sax.EntityResolver;
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import org.xml.sax.ErrorHandler;
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import org.xml.sax.InputSource;
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import org.xml.sax.XMLReader;
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import org.xml.sax.SAXException;
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import org.xml.sax.SAXParseException;
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import org.xml.sax.helpers.XMLReaderFactory;
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import java.net.URL;
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import edu.ucsb.nceas.dbadapter.AbstractDatabase;
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/**
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 * A class that represents an XML document. It can be created with a simple
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 * document identifier from a database connection.  It also will write an
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 * XML text document to a database connection using SAX.
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 */
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public class DocumentImpl {
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  static final int ALL = 1;
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  static final int WRITE = 2;
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  static final int READ = 4;
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  private static final AbstractDatabase dbAdapter = MetaCatUtil.dbAdapter;
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  private Connection conn = null;
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  private String docid = null;
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  private String updatedVersion=null;
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  private String docname = null;
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  private String doctype = null;
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// DOCTITLE attr cleared from the db
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//  private String doctitle = null;
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  private String createdate = null;
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  private String updatedate = null;
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  private String system_id = null;
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  private String userowner = null;
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  private String userupdated = null;
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  private int rev;
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  private int serverlocation;
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  private String docHomeServer;
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  private String publicaccess; 
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  private long rootnodeid;
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  private ElementNode rootNode = null;
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  private TreeSet nodeRecordList = null;
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  /**
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   * Constructor used to create a document and read the document information
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   * from the database.  If readNodes is false, then the node data is not 
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   * read at this time, but is deferred until it is needed (such as when a 
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   * call to toXml() is made).  
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   *
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   * @param conn the database connection from which to read the document
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   * @param docid the identifier of the document to be created
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   * @param readNodes flag indicating whether the xmlnodes should be read
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   */
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  public DocumentImpl(Connection conn, String docid, boolean readNodes) 
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         throws McdbException 
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  {
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    try {
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      this.conn = conn;
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      this.docid = docid;
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      // Look up the document information
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      getDocumentInfo(docid);
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      if (readNodes) {
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        // Download all of the document nodes using a single SQL query
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        // The sort order of the records is determined by the NodeComparator
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        // class, and needs to represent a depth-first traversal for the
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        // toXml() method to work properly
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        nodeRecordList = getNodeRecordList(rootnodeid);
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      }
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    } catch (McdbException ex) {
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      throw ex;
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    } catch (Throwable t) {
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      throw new McdbException("Error reading document from " +
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                              "DocumentImpl.DocumentImpl: " + docid);
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    }
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  }
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  /**
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   * Constructor, creates document from database connection, used 
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   * for reading the document
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   *
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   * @param conn the database connection from which to read the document
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   * @param docid the identifier of the document to be created
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   */
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  public DocumentImpl(Connection conn, String docid) throws McdbException 
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  {
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    this(conn, docid, true);
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  }
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  /** 
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   * Construct a new document instance, writing the contents to the database.
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   * This method is called from DBSAXHandler because we need to know the
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   * root element name for documents without a DOCTYPE before creating it.
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   *
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   * @param conn the JDBC Connection to which all information is written
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   * @param rootnodeid - sequence id of the root node in the document
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   * @param docname - the name of DTD, i.e. the name immediately following 
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   *        the DOCTYPE keyword ( should be the root element name ) or
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   *        the root element name if no DOCTYPE declaration provided
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   *        (Oracle's and IBM parsers are not aware if it is not the 
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   *        root element name)
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   * @param doctype - Public ID of the DTD, i.e. the name immediately 
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   *                  following the PUBLIC keyword in DOCTYPE declaration or
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   *                  the docname if no Public ID provided or
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   *                  null if no DOCTYPE declaration provided
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   * @param docid the docid to use for the INSERT OR UPDATE
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   * @param action the action to be performed (INSERT OR UPDATE)
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   * @param user the user that owns the document
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   * @param pub flag for public "read" access on document
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   * @param serverCode the serverid from xml_replication on which this document
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   *        resides.
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   *
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   */
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  public DocumentImpl(Connection conn, long rootnodeid, String docname, 
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                      String doctype, String docid, String action, String user,
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                      String pub, String catalogid, int serverCode)
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                      throws SQLException, Exception
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  {
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    this.conn = conn;
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    this.rootnodeid = rootnodeid;
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    this.docname = docname;
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    this.doctype = doctype;
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    this.docid = docid;
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    writeDocumentToDB(action, user, pub, catalogid, serverCode);
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  }
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  /** 
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   * Construct a new document instance, writing the contents to the database.
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   * This method is called from DBSAXHandler because we need to know the
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   * root element name for documents without a DOCTYPE before creating it.
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   *
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   * In this constructor, the docid is without rev. There is a string rev to 
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   * specify the revision user want to upadate. The revion is only need to be
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   * greater than current one. It is not need to be sequent number just after
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   * current one. So it is only used in update action
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   * @param conn the JDBC Connection to which all information is written
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   * @param rootnodeid - sequence id of the root node in the document
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   * @param docname - the name of DTD, i.e. the name immediately following 
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   *        the DOCTYPE keyword ( should be the root element name ) or
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   *        the root element name if no DOCTYPE declaration provided
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   *        (Oracle's and IBM parsers are not aware if it is not the 
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   *        root element name)
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   * @param doctype - Public ID of the DTD, i.e. the name immediately 
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   *                  following the PUBLIC keyword in DOCTYPE declaration or
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   *                  the docname if no Public ID provided or
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   *                  null if no DOCTYPE declaration provided
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   * @param docid the docid to use for the UPDATE, no version number
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   * @param version, need to be update
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   * @param action the action to be performed (INSERT OR UPDATE)
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   * @param user the user that owns the document
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   * @param pub flag for public "read" access on document
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   * @param serverCode the serverid from xml_replication on which this document
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   *        resides.
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   *
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   */
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  public DocumentImpl(Connection conn, long rootNodeId, String docName, 
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                      String docType, String docId, String newRevision, 
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                      String action, String user,
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                      String pub, String catalogId, int serverCode)
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                      throws SQLException, Exception
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  {
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    this.conn = conn;
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    this.rootnodeid = rootNodeId;
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    this.docname = docName;
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    this.doctype = docType;
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    this.docid = docId;
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    this.updatedVersion = newRevision;
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    writeDocumentToDB(action, user, pub, catalogId, serverCode);
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  }
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  /**
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   * This method will be call in handleUploadRequest in MetacatServlet class
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   */
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  public static void registerDocument(
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                     String docname, String doctype, String accnum, String user)
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                     throws SQLException, AccessionNumberException, Exception
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  {
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    Connection dbConn = null;
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    MetaCatUtil ut = new MetaCatUtil();
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    try
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    {
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      dbConn = ut.openDBConnection();
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      // get server location for this doc
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      int serverLocation=getServerLocationNumber(dbConn,accnum);
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      dbConn.close();
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      registerDocument(docname, doctype,accnum, user, serverLocation);
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    }
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    catch (Exception e)
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    {
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      throw e;
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    }
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    finally
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    {
247
      try
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      {
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        dbConn.close();
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      }
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      catch (Exception ee)
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      {}
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    }
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  }
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  /**
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   * Register a document that resides on the filesystem with the database.
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   * (ie, just an entry in xml_documents, nothing in xml_nodes).
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   * Creates a reference to a filesystem document (used for non-xml data files).
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   * This class only be called in MetaCatServerlet.
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   * @param conn the JDBC Connection to which all information is written
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   * @param docname - the name of DTD, i.e. the name immediately following 
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   *        the DOCTYPE keyword ( should be the root element name ) or
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   *        the root element name if no DOCTYPE declaration provided
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   *        (Oracle's and IBM parsers are not aware if it is not the 
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   *        root element name)
267
   * @param doctype - Public ID of the DTD, i.e. the name immediately 
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   *                  following the PUBLIC keyword in DOCTYPE declaration or
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   *                  the docname if no Public ID provided or
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   *                  null if no DOCTYPE declaration provided
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   * @param accnum the accession number to use for the INSERT OR UPDATE, which 
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   *               includes a revision number for this revision of the document 
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   *               (e.g., knb.1.1)
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   * @param user the user that owns the document
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   * @param serverCode the serverid from xml_replication on which this document
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   *        resides.
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   */
278
  public static void registerDocument(
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                     String docname, String doctype, String accnum, 
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                     String user, int serverCode)
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                     throws SQLException, AccessionNumberException, Exception
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  {
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    Connection dbconn = null;
284
    MetaCatUtil util = new MetaCatUtil();
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    AccessionNumber ac;
286
    try {
287
      dbconn = util.openDBConnection();
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      String docIdWithoutRev=MetaCatUtil.getDocIdFromString(accnum);
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      int userSpecifyRev=MetaCatUtil.getVersionFromString(accnum);
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      int revInDataBase=getLatestRevisionNumber(dbconn, docIdWithoutRev);
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      //revIndataBase=-1, there is no record in xml_documents table
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      //the data file is a new one, inert it into table
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      //user specified rev should be great than 0
294
      if (revInDataBase==-1 && userSpecifyRev>0 )
295
      {
296
        ac = new AccessionNumber(dbconn, accnum, "insert");
297
      }
298
      //rev is greater the last revsion number and revInDataBase isn't -1
299
      // it is a updated data file
300
      else if (userSpecifyRev>revInDataBase && revInDataBase>0)
301
      {
302
        
303
        //archive the old entry 
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        archiveDocRevision(dbconn, docIdWithoutRev, user);
305
        //delete the old entry in xml_documents
306
        deleteXMLDocuments(dbconn, docIdWithoutRev);
307
        ac = new AccessionNumber(dbconn, accnum, "update");
308
      }
309
      //other situation
310
      else
311
      {
312
        
313
        throw new Exception("Revision number couldn't be "
314
                    +userSpecifyRev);
315
      }
316
      String docid = ac.getDocid();
317
      String rev = ac.getRev();
318
      SimpleDateFormat formatter = new SimpleDateFormat ("yy-MM-dd HH:mm:ss");
319
      Date localtime = new Date();
320
      String dateString = formatter.format(localtime);
321
  
322
      String sqlDateString = "to_date('" + dateString + 
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                                          "', 'YY-MM-DD HH24:MI:SS')";
324
  
325
      StringBuffer sql = new StringBuffer();
326
      sql.append("insert into xml_documents (docid, docname, doctype, ");
327
      sql.append("user_owner, user_updated, server_location, rev,date_created");
328
      sql.append(", date_updated, public_access) values ('");
329
      sql.append(docid).append("','");
330
      sql.append(docname).append("','");
331
      sql.append(doctype).append("','");
332
      sql.append(user).append("','");
333
      sql.append(user).append("','");
334
      sql.append(serverCode).append("','");
335
      sql.append(rev).append("',");
336
      sql.append(sqlDateString).append(",");
337
      sql.append(sqlDateString).append(",");
338
      sql.append("'0')");
339
      PreparedStatement pstmt = dbconn.prepareStatement(sql.toString());
340
      pstmt.execute();
341
      pstmt.close();
342
      dbconn.close();
343
    } 
344
    finally 
345
    {
346
      try
347
      {
348
        dbconn.close();
349
      }
350
      catch (SQLException sqlE)
351
      {
352
        util.debugMessage("Error in DocumentImpl.registerDocument:" +
353
                                sqlE.getMessage(), 30);
354
      }
355
    }    
356
  }
357
  
358
    /**
359
   * Register a document that resides on the filesystem with the database.
360
   * (ie, just an entry in xml_documents, nothing in xml_nodes).
361
   * Creates a reference to a filesystem document (used for non-xml data files)
362
   * This method will be called for register data file in xml_documents in 
363
   * Replication.
364
   * This method is revised from registerDocument.
365
   *
366
   * @param conn the JDBC Connection to which all information is written
367
   * @param docname - the name of DTD, i.e. the name immediately following 
368
   *        the DOCTYPE keyword ( should be the root element name ) or
369
   *        the root element name if no DOCTYPE declaration provided
370
   *        (Oracle's and IBM parsers are not aware if it is not the 
371
   *        root element name)
372
   * @param doctype - Public ID of the DTD, i.e. the name immediately 
373
   *                  following the PUBLIC keyword in DOCTYPE declaration or
374
   *                  the docname if no Public ID provided or
375
   *                  null if no DOCTYPE declaration provided
376
   * @param accnum the accession number to use for the INSERT OR UPDATE, which 
377
   *               includes a revision number for this revision of the document 
378
   *               (e.g., knb.1.1)
379
   * @param user the user that owns the document
380
   * @param serverCode the serverid from xml_replication on which this document
381
   *        resides.
382
   */
383
  public static void registerDocumentInReplication(
384
                     String docname, String doctype, String accnum, 
385
                     String user, int serverCode)
386
                     throws SQLException, AccessionNumberException, Exception
387
  {
388
    Connection dbconn = null;
389
    MetaCatUtil util = new MetaCatUtil();
390
    AccessionNumber ac;
391
    try {
392
      dbconn = util.openDBConnection();
393
      String docIdWithoutRev=MetaCatUtil.getDocIdFromString(accnum);
394
      int userSpecifyRev=MetaCatUtil.getVersionFromString(accnum);
395
      int revInDataBase=getLatestRevisionNumber(dbconn, docIdWithoutRev);
396
      //revIndataBase=-1, there is no record in xml_documents table
397
      //the data file is a new one, inert it into table
398
      //user specified rev should be great than 0
399
      if (revInDataBase==-1 && userSpecifyRev>0 )
400
      {
401
       
402
        ac = new AccessionNumber(dbconn, accnum, "insert");
403
      }
404
      //rev is greater the last revsion number and revInDataBase isn't -1
405
      // it is a updated data file
406
      else if (userSpecifyRev>revInDataBase && revInDataBase>0)
407
      {
408
        
409
        //archive the old entry 
410
        archiveDocRevision(dbconn, docIdWithoutRev, user);
411
        //delete the old entry in xml_documents
412
        deleteXMLDocuments(dbconn, docIdWithoutRev);
413
        ac = new AccessionNumber(dbconn, accnum, "update");
414
      }
415
      //other situation
416
      else
417
      {
418
        
419
        throw new Exception("Revision number couldn't be "
420
                    +userSpecifyRev);
421
      }
422
      String docid = ac.getDocid();
423
      String rev = ac.getRev();
424
      SimpleDateFormat formatter = new SimpleDateFormat ("yy-MM-dd HH:mm:ss");
425
      Date localtime = new Date();
426
      String dateString = formatter.format(localtime);
427
  
428
      String sqlDateString = "to_date('" + dateString + 
429
                                          "', 'YY-MM-DD HH24:MI:SS')";
430
  
431
      StringBuffer sql = new StringBuffer();
432
      sql.append("insert into xml_documents (docid, docname, doctype, ");
433
      sql.append("user_owner, user_updated, server_location, rev,date_created");
434
      sql.append(", date_updated, public_access) values ('");
435
      sql.append(docid).append("','");
436
      sql.append(docname).append("','");
437
      sql.append(doctype).append("','");
438
      sql.append(user).append("','");
439
      sql.append(user).append("','");
440
      sql.append(serverCode).append("','");
441
      sql.append(rev).append("',");
442
      sql.append(sqlDateString).append(",");
443
      sql.append(sqlDateString).append(",");
444
      sql.append("'0')");
445
      PreparedStatement pstmt = dbconn.prepareStatement(sql.toString());
446
      pstmt.execute();
447
      pstmt.close();
448
      dbconn.close();
449
    } 
450
    finally 
451
    {
452
      try
453
      {
454
        dbconn.close();
455
      }
456
      catch (SQLException sqlE)
457
      {
458
        util.debugMessage("Error in DocumentImpl.registerDocument:" +
459
                                sqlE.getMessage());
460
      }
461
    }    
462
  }
463
  
464
 /**
465
   * This method will register a data file entry in xml_documents and save a
466
   * data file input Stream into file system.. It is only used in force 
467
   * replication
468
   *
469
   * @param  input, the input stream which contain the file content.
470
   * @param  , the input stream which contain the file content
471
   * @param docname - the name of DTD, for data file, it is a docid number.
472
   * @param doctype - "BIN" for data file
473
   * @param accnum the accession number to use for the INSERT OR UPDATE, which 
474
   *               includes a revision number for this revision of the document 
475
   *               (e.g., knb.1.1)
476
   * @param user the user that owns the document
477
   * @param serverCode the serverid from xml_replication on which this document
478
   *        resides.
479
   */
480
 public static void writeDataFile(InputStream input, String filePath, 
481
                                  String docname, String doctype, String accnum, 
482
                                  String user, String docHomeServer)
483
                     throws SQLException, AccessionNumberException, Exception
484
 {
485
   int serverCode=-2;
486
    if (filePath==null||filePath.equals(""))
487
    {
488
      throw new 
489
            Exception("Please specify the directory where file will be store");
490
    }
491
    if (accnum==null||accnum.equals(""))
492
    {
493
      throw new Exception("Please specify the stored file name");
494
    }
495
    
496
    //get server code for the home server
497
    serverCode=getServerCode(docHomeServer);
498
    //if the server is not in the xml replication table, insert it.
499
    if (serverCode==-1)
500
    {
501
      insertServerIntoReplicationTable(docHomeServer);
502
      //get server code again
503
      serverCode=getServerCode(docHomeServer);
504
    }
505
    
506
    //make sure user have file lock grant(local metacat means have it too)
507
    if (getDataFileLockGrant(accnum))
508
    {
509
      //register data file into xml_documents table
510
      registerDocumentInReplication(docname, doctype, accnum, user, serverCode);
511
      //write inputstream into file system.
512
      File dataDirectory = new File(filePath);
513
      File newFile = new File(dataDirectory, accnum); 
514
       
515
      // create a buffered byte output stream
516
      // that uses a default-sized output buffer
517
      FileOutputStream fos = new FileOutputStream(newFile);
518
      BufferedOutputStream outPut = new BufferedOutputStream(fos);
519

    
520
      BufferedInputStream bis = null;
521
      bis = new BufferedInputStream(input);
522
      byte[] buf = new byte[4 * 1024]; // 4K buffer
523
      int b = bis.read(buf);
524
       
525
      while (b != -1) 
526
      {
527
        outPut.write(buf, 0, b);
528
        b = bis.read(buf);
529
      }
530
      bis.close();
531
	    outPut.close();
532
	    fos.close();
533
    
534
    }//if
535
 }
536
  
537

    
538
  
539
  public static boolean getDataFileLockGrant(String accnum) 
540
                                                  throws Exception
541
  { 
542
    Connection dbConn = null;
543
    MetaCatUtil ut= new MetaCatUtil();
544
    try
545
    {
546
      dbConn = ut.openDBConnection();
547
      int serverLocation=getServerLocationNumber(dbConn,accnum);
548
      dbConn.close();
549
      return getDataFileLockGrant(accnum,serverLocation);
550
    }
551
    catch (Exception e)
552
    {
553
      try
554
      {
555
        dbConn.close();
556
      }
557
      catch (Exception ee)
558
      {}
559
      throw e;
560
    }
561
  }
562
    
563
  /**
564
   * The method will check if metacat can get data file lock grant
565
   * If server code is 1, it get.
566
   * If server code is not 1 but call replication getlock successfully,
567
   * it get
568
   * else, it didn't get
569
   * @param accnum, the ID of the document 
570
   * @param action, the action to the document
571
   * @param serverCode, the server location code
572
   */
573
  public static boolean getDataFileLockGrant(String accnum, int serverCode)
574
                                          throws Exception 
575
  {
576
    boolean flag=true;
577
    MetaCatUtil util = new MetaCatUtil();
578
    String docid = util.getDocIdFromString(accnum);
579
    int rev = util.getVersionFromString(accnum);
580
    
581
    if (serverCode == 1)
582
    {
583
      flag=true;
584
      return flag;
585
    }
586
    
587
    //if((serverCode != 1 && action.equals("UPDATE")) )
588
    if (serverCode != 1)
589
    { //if this document being written is not a resident of this server then
590
      //we need to try to get a lock from it's resident server.  If the
591
      //resident server will not give a lock then we send the user a message
592
      //saying that he/she needs to download a new copy of the file and
593
      //merge the differences manually.
594
      
595
      String server = MetacatReplication.getServer(serverCode);
596
      MetacatReplication.replLog("attempting to lock " + accnum);
597
      URL u = new URL("https://" + server + "?server="
598
           +util.getLocalReplicationServerName()+"&action=getlock&updaterev=" 
599
           +rev + "&docid=" + docid);
600
      //System.out.println("sending message: " + u.toString());
601
      String serverResStr = MetacatReplication.getURLContent(u);
602
      String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);
603
      if(openingtag.equals("<lockgranted>"))
604
      {
605
        //the lock was granted go ahead with the insert
606
        //System.out.println("In lockgranted");
607
        MetacatReplication.replLog("lock granted for " + accnum + " from " +
608
                                      server);
609
        flag=true;  
610
        return flag;
611
      }//if
612

    
613
      else if(openingtag.equals("<filelocked>"))
614
      {//the file is currently locked by another user
615
       //notify our user to wait a few minutes, check out a new copy and try
616
       //again.
617
        //System.out.println("file locked");
618
        MetacatReplication.replLog("lock denied for " + accnum + " on " +
619
                                   server + " reason: file already locked");
620
        throw new Exception("The file specified is already locked by another " +
621
                            "user.  Please wait 30 seconds, checkout the " +
622
                            "newer document, merge your changes and try " +
623
                            "again.");
624
      }
625
      else if(openingtag.equals("<outdatedfile>"))
626
      {//our file is outdated.  notify our user to check out a new copy of the
627
       //file and merge his version with the new version.
628
        //System.out.println("outdated file");
629
        MetacatReplication.replLog("lock denied for " + accnum + " on " +
630
                                    server + " reason: local file outdated");
631
        throw new Exception("The file you are trying to update is an outdated" +
632
                            " version.  Please checkout the newest document, " +
633
                            "merge your changes and try again.");
634
      }//else if
635
    }//if
636
    
637
   return flag;
638
   
639
  }//getDataFileLockGrant
640
  
641
  /**
642
   * get the document name
643
   */
644
  public String getDocname() {
645
    return docname;
646
  }
647

    
648
  /**
649
   * get the document type (which is the PublicID)
650
   */
651
  public String getDoctype() {
652
    return doctype;
653
  }
654

    
655
  /**
656
   * get the system identifier
657
   */
658
  public String getSystemID() {
659
    return system_id;
660
  }
661

    
662
  /**
663
   * get the root node identifier
664
   */
665
  public long getRootNodeID() {
666
    return rootnodeid;
667
  }
668
  
669
  /**
670
   * get the creation date
671
   */
672
  public String getCreateDate() {
673
    return createdate;
674
  }
675
  
676
  /**
677
   * get the update date
678
   */
679
  public String getUpdateDate() {
680
    return updatedate;
681
  }
682

    
683
  /** 
684
   * Get the document identifier (docid)
685
   */
686
  public String getDocID() {
687
    return docid;
688
  }
689
  
690
// DOCTITLE attr cleared from the db
691
//  /**
692
//   *get the document title
693
//   */
694
//  public String getDocTitle() {
695
//    return doctitle;
696
//  }
697
  
698
  public String getUserowner() {
699
    return userowner;
700
  }
701
  
702
  public String getUserupdated() {
703
    return userupdated;
704
  }
705
  
706
  public int getServerlocation() {
707
    return serverlocation;
708
  }
709
  
710
  public String getDocHomeServer() {
711
    return docHomeServer;
712
  }
713
  
714
 
715
 
716
  public String getPublicaccess() {
717
    return publicaccess;
718
  }
719
  
720
  public int getRev() {
721
    return rev;
722
  }
723
  
724
   /**
725
   * Print a string representation of the XML document
726
   */
727
  public String toString()
728
  {
729
    StringWriter docwriter = new StringWriter();
730
    try {
731
      this.toXml(docwriter);
732
    } catch (McdbException mcdbe) {
733
      return null;
734
    }
735
    String document = docwriter.toString();
736
    return document;
737
  }
738

    
739
  /**
740
   * Get a text representation of the XML document as a string
741
   * This older algorithm uses a recursive tree of Objects to represent the
742
   * nodes of the tree.  Each object is passed the data for the document 
743
   * and searches all of the document data to find its children nodes and
744
   * recursively build.  Thus, because each node reads the whole document,
745
   * this algorithm is extremely slow for larger documents, and the time
746
   * to completion is O(N^N) wrt the number of nodes.  See toXml() for a
747
   * better algorithm.
748
   */
749
  public String readUsingSlowAlgorithm() throws McdbException
750
  {
751
    StringBuffer doc = new StringBuffer();
752

    
753
    // First, check that we have the needed node data, and get it if not
754
    if (nodeRecordList == null) {
755
      nodeRecordList = getNodeRecordList(rootnodeid);
756
    }
757

    
758
    // Create the elements from the downloaded data in the TreeSet
759
    rootNode = new ElementNode(nodeRecordList, rootnodeid);
760

    
761
    // Append the resulting document to the StringBuffer and return it
762
    doc.append("<?xml version=\"1.0\"?>\n");
763
      
764
    if (docname != null) {
765
      if ((doctype != null) && (system_id != null)) {
766
        doc.append("<!DOCTYPE " + docname + " PUBLIC \"" + doctype + 
767
                   "\" \"" + system_id + "\">\n");
768
      } else {
769
        doc.append("<!DOCTYPE " + docname + ">\n");
770
      }
771
    }
772
    doc.append(rootNode.toString());
773
  
774
    return (doc.toString());
775
  }
776

    
777
  /**
778
   * Print a text representation of the XML document to a Writer
779
   *
780
   * @param pw the Writer to which we print the document
781
   */
782
  public void toXml(Writer pw) throws McdbException
783
  {
784
    PrintWriter out = null;
785
    if (pw instanceof PrintWriter) {
786
      out = (PrintWriter)pw;
787
    } else {
788
      out = new PrintWriter(pw);
789
    }
790

    
791
    MetaCatUtil util = new MetaCatUtil();
792
    
793
    // First, check that we have the needed node data, and get it if not
794
    if (nodeRecordList == null) {
795
      nodeRecordList = getNodeRecordList(rootnodeid);
796
    }
797

    
798
    Stack openElements = new Stack();
799
    boolean atRootElement = true;
800
    boolean previousNodeWasElement = false;
801

    
802
    // Step through all of the node records we were given
803
    Iterator it = nodeRecordList.iterator();
804
    while (it.hasNext()) {
805
      NodeRecord currentNode = (NodeRecord)it.next();
806
      //util.debugMessage("[Got Node ID: " + currentNode.nodeid +
807
                          //" (" + currentNode.parentnodeid +
808
                          //", " + currentNode.nodeindex + 
809
                          //", " + currentNode.nodetype + 
810
                          //", " + currentNode.nodename + 
811
                          //", " + currentNode.nodedata + ")]");
812
      // Print the end tag for the previous node if needed
813
      //
814
      // This is determined by inspecting the parent nodeid for the
815
      // currentNode.  If it is the same as the nodeid of the last element
816
      // that was pushed onto the stack, then we are still in that previous
817
      // parent element, and we do nothing.  However, if it differs, then we
818
      // have returned to a level above the previous parent, so we go into
819
      // a loop and pop off nodes and print out their end tags until we get
820
      // the node on the stack to match the currentNode parentnodeid
821
      //
822
      // So, this of course means that we rely on the list of elements
823
      // having been sorted in a depth first traversal of the nodes, which
824
      // is handled by the NodeComparator class used by the TreeSet
825
      if (!atRootElement) {
826
        NodeRecord currentElement = (NodeRecord)openElements.peek();
827
        if ( currentNode.parentnodeid != currentElement.nodeid ) {
828
          while ( currentNode.parentnodeid != currentElement.nodeid ) {
829
            currentElement = (NodeRecord)openElements.pop();
830
            util.debugMessage("\n POPPED: " + currentElement.nodename);
831
            if (previousNodeWasElement) {
832
              out.print(">");
833
              previousNodeWasElement = false;
834
            }  
835
            if ( currentElement.nodeprefix != null ) {
836
              out.print("</" + currentElement.nodeprefix + ":" + 
837
                        currentElement.nodename + ">" );
838
            } else {
839
              out.print("</" + currentElement.nodename + ">" );
840
            }
841
            currentElement = (NodeRecord)openElements.peek();
842
          }
843
        }
844
      }
845

    
846
      // Handle the DOCUMENT node
847
      if (currentNode.nodetype.equals("DOCUMENT")) {
848
        out.println("<?xml version=\"1.0\"?>");
849
      
850
        if (docname != null) {
851
          if ((doctype != null) && (system_id != null)) {
852
            out.println("<!DOCTYPE " + docname + " PUBLIC \"" + doctype + 
853
                       "\" \"" + system_id + "\">");
854
          } else {
855
            out.println("<!DOCTYPE " + docname + ">");
856
          }
857
        }
858

    
859
      // Handle the ELEMENT nodes
860
      } else if (currentNode.nodetype.equals("ELEMENT")) {
861
        if (atRootElement) {
862
          atRootElement = false;
863
        } else {
864
          if (previousNodeWasElement) {
865
            out.print(">");
866
          }
867
        }
868
        openElements.push(currentNode);
869
        util.debugMessage("\n PUSHED: " + currentNode.nodename);
870
        previousNodeWasElement = true;
871
        if ( currentNode.nodeprefix != null ) {
872
          out.print("<" + currentNode.nodeprefix + ":" + currentNode.nodename);
873
        } else {
874
          out.print("<" + currentNode.nodename);
875
        }
876

    
877
      // Handle the ATTRIBUTE nodes
878
      } else if (currentNode.nodetype.equals("ATTRIBUTE")) {
879
        if ( currentNode.nodeprefix != null ) {
880
          out.print(" " + currentNode.nodeprefix + ":" + currentNode.nodename +
881
                    "=\"" + currentNode.nodedata + "\"");
882
        } else {
883
          out.print(" " + currentNode.nodename + "=\"" +
884
                    currentNode.nodedata + "\"");
885
        }
886

    
887
      // Handle the NAMESPACE nodes
888
      } else if (currentNode.nodetype.equals("NAMESPACE")) {
889
        out.print(" xmlns:" + currentNode.nodename + "=\""
890
                 + currentNode.nodedata + "\"");
891

    
892
      // Handle the TEXT nodes
893
      } else if (currentNode.nodetype.equals("TEXT")) {
894
        if (previousNodeWasElement) {
895
          out.print(">");
896
        }
897
        out.print(currentNode.nodedata);
898
        previousNodeWasElement = false;
899

    
900
      // Handle the COMMENT nodes
901
      } else if (currentNode.nodetype.equals("COMMENT")) {
902
        if (previousNodeWasElement) {
903
          out.print(">");
904
        }
905
        out.print("<!--" + currentNode.nodedata + "-->");
906
        previousNodeWasElement = false;
907

    
908
      // Handle the PI nodes
909
      } else if (currentNode.nodetype.equals("PI")) {
910
        if (previousNodeWasElement) {
911
          out.print(">");
912
        }
913
        out.print("<?" + currentNode.nodename + " " +
914
                        currentNode.nodedata + "?>");
915
        previousNodeWasElement = false;
916

    
917
      // Handle any other node type (do nothing)
918
      } else {
919
        // Any other types of nodes are not handled.
920
        // Probably should throw an exception here to indicate this
921
      }
922
      out.flush();
923
    }
924

    
925
    // Print the final end tag for the root element
926
    while(!openElements.empty())
927
    {
928
      NodeRecord currentElement = (NodeRecord)openElements.pop();
929
      util.debugMessage("\n POPPED: " + currentElement.nodename);
930
      if ( currentElement.nodeprefix != null ) {
931
        out.print("</" + currentElement.nodeprefix + ":" + 
932
                  currentElement.nodename + ">" );
933
      } else {
934
        out.print("</" + currentElement.nodename + ">" );
935
      }
936
    }
937
    out.flush();
938
  }
939
  
940
  private boolean isRevisionOnly(DocumentIdentifier docid) throws Exception
941
  {
942
    //System.out.println("inRevisionOnly");
943
    PreparedStatement pstmt;
944
    String rev = docid.getRev();
945
    String newid = docid.getIdentifier();
946
    pstmt = conn.prepareStatement("select rev from xml_documents " +
947
                                  "where docid like '" + newid + "'");
948
    pstmt.execute();
949
    ResultSet rs = pstmt.getResultSet();
950
    boolean tablehasrows = rs.next();
951
    if(rev.equals("newest") || rev.equals("all"))
952
    {
953
      return false;
954
    }
955
    
956
    if(tablehasrows)
957
    {
958
      int r = rs.getInt(1);
959
      pstmt.close();
960
      if(new Integer(rev).intValue() == r)
961
      { //the current revision in in xml_documents
962
        //System.out.println("returning false");
963
        return false;
964
      }
965
      else if(new Integer(rev).intValue() < r)
966
      { //the current revision is in xml_revisions.
967
        //System.out.println("returning true");
968
        return true;
969
      }
970
      else if(new Integer(rev).intValue() > r)
971
      { //error, rev cannot be greater than r
972
        throw new Exception("requested revision cannot be greater than " +
973
                            "the latest revision number.");
974
      }
975
    }
976
    throw new Exception("the requested docid '" + docid.toString() + 
977
                        "' does not exist");
978
  }
979

    
980
  private void getDocumentInfo(String docid) throws McdbException, 
981
                                                    AccessionNumberException
982
  {
983
    getDocumentInfo(new DocumentIdentifier(docid));
984
  }
985
  
986
  /**
987
   * Look up the document type information from the database
988
   *
989
   * @param docid the id of the document to look up
990
   */
991
  private void getDocumentInfo(DocumentIdentifier docid) throws McdbException 
992
  {
993
    PreparedStatement pstmt;
994
    String table = "xml_documents";
995
        
996
    try
997
    {
998
      if(isRevisionOnly(docid))
999
      { //pull the document from xml_revisions instead of from xml_documents;
1000
        table = "xml_revisions";
1001
      }
1002
    }
1003
    catch(Exception e)
1004
    {
1005
      System.out.println("error in DocumentImpl.getDocumentInfo: " + 
1006
                          e.getMessage());
1007
    }
1008
    
1009
    //deal with the key words here.
1010
    
1011
    if(docid.getRev().equals("all"))
1012
    {
1013
      
1014
    }
1015
    
1016
    try {
1017
      StringBuffer sql = new StringBuffer();
1018
// DOCTITLE attr cleared from the db
1019
//      sql.append("SELECT docname, doctype, rootnodeid, doctitle, ");
1020
      sql.append("SELECT docname, doctype, rootnodeid, ");
1021
      sql.append("date_created, date_updated, user_owner, user_updated, ");
1022
      sql.append("server_location, public_access, rev");
1023
      sql.append(" FROM ").append(table);
1024
      sql.append(" WHERE docid LIKE '").append(docid.getIdentifier());
1025
      sql.append("' and rev like '").append(docid.getRev()).append("'");
1026
      //System.out.println(sql.toString());
1027
      pstmt =
1028
        conn.prepareStatement(sql.toString());
1029
      // Bind the values to the query
1030
      //pstmt.setString(1, docid.getIdentifier());
1031
      //pstmt.setString(2, docid.getRev());
1032

    
1033
      pstmt.execute();
1034
      ResultSet rs = pstmt.getResultSet();
1035
      boolean tableHasRows = rs.next();
1036
      if (tableHasRows) {
1037
        this.docname        = rs.getString(1);
1038
        this.doctype        = rs.getString(2);
1039
        this.rootnodeid     = rs.getLong(3);
1040
// DOCTITLE attr cleared from the db
1041
//        this.doctitle       = rs.getString(4);
1042
        this.createdate     = rs.getString(4);
1043
        this.updatedate     = rs.getString(5);
1044
        this.userowner      = rs.getString(6);
1045
        this.userupdated    = rs.getString(7);
1046
        this.serverlocation = rs.getInt(8);
1047
        this.publicaccess   = rs.getString(9);
1048
        this.rev            = rs.getInt(10);
1049
      } 
1050
      pstmt.close();
1051
      
1052
      //get doc  home server name
1053
      
1054
      pstmt = conn.prepareStatement("select server " +
1055
                        "from xml_replication where serverid = ?");
1056
                        
1057
      
1058
      pstmt.setInt(1, serverlocation);
1059
      pstmt.execute();
1060
      rs = pstmt.getResultSet();
1061
      tableHasRows = rs.next();
1062
      if (tableHasRows)
1063
      {
1064
        
1065
          String server = rs.getString(1);
1066
          //get homeserver name
1067
          if(!server.equals("localhost"))
1068
          {
1069
            this.docHomeServer=server;
1070
          }
1071
          else
1072
          {
1073
            this.docHomeServer=MetaCatUtil.getLocalReplicationServerName();
1074
          }
1075
          MetaCatUtil.debugMessage("server: "+docHomeServer, 50);
1076
        
1077
      }
1078
      pstmt.close();
1079
      if (this.doctype != null) {
1080
        pstmt =
1081
          conn.prepareStatement("SELECT system_id " +
1082
                                  "FROM xml_catalog " +
1083
                                 "WHERE public_id = ?");
1084
        // Bind the values to the query
1085
        pstmt.setString(1, doctype);
1086
  
1087
        pstmt.execute();
1088
        rs = pstmt.getResultSet();
1089
        tableHasRows = rs.next();
1090
        if (tableHasRows) {
1091
          this.system_id  = rs.getString(1);
1092
        } 
1093
        pstmt.close();
1094
      }
1095
    } catch (SQLException e) {
1096
      System.out.println("error in DocumentImpl.getDocumentInfo: " + 
1097
                          e.getMessage());
1098
      e.printStackTrace(System.out);
1099
      throw new McdbException("Error accessing database connection in " +
1100
                              "DocumentImpl.getDocumentInfo: ", e);
1101
    }
1102

    
1103
    if (this.docname == null) {
1104
      throw new McdbDocNotFoundException("Document not found: " + docid);
1105
    }
1106
  }
1107

    
1108
  /**
1109
   * Look up the node data from the database
1110
   *
1111
   * @param rootnodeid the id of the root node of the node tree to look up
1112
   */
1113
  private TreeSet getNodeRecordList(long rootnodeid) throws McdbException 
1114
  {
1115
    PreparedStatement pstmt;
1116
    TreeSet nodeRecordList = new TreeSet(new NodeComparator());
1117
    long nodeid = 0;
1118
    long parentnodeid = 0;
1119
    long nodeindex = 0;
1120
    String nodetype = null;
1121
    String nodename = null;
1122
    String nodeprefix = null;
1123
    String nodedata = null;
1124
    String quotechar = dbAdapter.getStringDelimiter();
1125

    
1126
    try {
1127
      pstmt =
1128
      conn.prepareStatement("SELECT nodeid,parentnodeid,nodeindex, " +
1129
           "nodetype,nodename,nodeprefix,nodedata " +               
1130
           "FROM xml_nodes WHERE rootnodeid = ?");
1131

    
1132
      // Bind the values to the query
1133
      pstmt.setLong(1, rootnodeid);
1134

    
1135
      pstmt.execute();
1136
      ResultSet rs = pstmt.getResultSet();
1137
      boolean tableHasRows = rs.next();
1138
      while (tableHasRows) {
1139
        nodeid = rs.getLong(1);
1140
        parentnodeid = rs.getLong(2);
1141
        nodeindex = rs.getLong(3);
1142
        nodetype = rs.getString(4);
1143
        nodename = rs.getString(5);
1144
        nodeprefix = rs.getString(6);
1145
        nodedata = rs.getString(7);
1146
        nodedata = MetaCatUtil.normalize(nodedata);
1147
        // add the data to the node record list hashtable
1148
        NodeRecord currentRecord = new NodeRecord(nodeid,parentnodeid,nodeindex,
1149
                                      nodetype, nodename, nodeprefix, nodedata);
1150
        nodeRecordList.add(currentRecord);
1151

    
1152
        // Advance to the next node
1153
        tableHasRows = rs.next();
1154
      } 
1155
      pstmt.close();
1156

    
1157
    } catch (SQLException e) {
1158
      throw new McdbException("Error in DocumentImpl.getNodeRecordList " +
1159
                              e.getMessage());
1160
    }
1161

    
1162
    if (nodeRecordList != null) {
1163
      return nodeRecordList;
1164
    } else {
1165
      throw new McdbException("Error getting node data: " + docid);
1166
    }
1167
  }
1168
  
1169
// NOT USED ANY MORE
1170
//  /** creates SQL code and inserts new document into DB connection 
1171
//   default serverCode of 1*/
1172
//  private void writeDocumentToDB(String action, String user)
1173
//               throws SQLException, Exception
1174
//  {
1175
//    writeDocumentToDB(action, user, null, 1);
1176
//  }
1177

    
1178
 /** creates SQL code and inserts new document into DB connection */
1179
  private void writeDocumentToDB(String action, String user, String pub, 
1180
                                 String catalogid, int serverCode) 
1181
               throws SQLException, Exception {
1182
    String sysdate = dbAdapter.getDateTimeFunction();
1183

    
1184
    try {
1185
      PreparedStatement pstmt = null;
1186

    
1187
      if (action.equals("INSERT")) {
1188
        //AccessionNumber ac = new AccessionNumber();
1189
        //this.docid = ac.generate(docid, "INSERT");
1190
        pstmt = conn.prepareStatement(
1191
                "INSERT INTO xml_documents " +
1192
                "(docid, rootnodeid, docname, doctype, " + 
1193
                "user_owner, user_updated, date_created, date_updated, " + 
1194
                "public_access, catalog_id, server_location) " +
1195
                "VALUES (?, ?, ?, ?, ?, ?, " + sysdate + ", " + sysdate + 
1196
                ", ?, ?, ?)");
1197
        //note that the server_location is set to 1. 
1198
        //this means that "localhost" in the xml_replication table must
1199
        //always be the first entry!!!!!
1200
        
1201
        // Bind the values to the query
1202
        pstmt.setString(1, this.docid);
1203
        pstmt.setLong(2, rootnodeid);
1204
        pstmt.setString(3, docname);
1205
        pstmt.setString(4, doctype);
1206
        pstmt.setString(5, user);
1207
        pstmt.setString(6, user);
1208
        if ( pub == null ) {
1209
          pstmt.setString(7, null);
1210
        } else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
1211
          pstmt.setInt(7, 1);
1212
        } else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
1213
          pstmt.setInt(7, 0);
1214
        }
1215
        pstmt.setString(8, catalogid);
1216
        pstmt.setInt(9, serverCode);
1217
      } else if (action.equals("UPDATE")) {
1218

    
1219
        // Save the old document entry in a backup table
1220
        DocumentImpl.archiveDocRevision( conn, docid, user );
1221
        DocumentImpl thisdoc = new DocumentImpl(conn, docid);
1222
        int thisrev = thisdoc.getRev();
1223
        
1224
        //if the updated vesion is not greater than current one,
1225
        //throw it into a exception
1226
        if (Integer.parseInt(updatedVersion)<=thisrev)
1227
        {
1228
          throw new Exception("Next revision number couldn't be less"
1229
                               +" than or equal "+ thisrev);
1230
        }
1231
        else
1232
        {
1233
          //set the user specified revision 
1234
          thisrev=Integer.parseInt(updatedVersion);
1235
        }
1236
        
1237
        // Delete index for the old version of docid
1238
        // The new index is inserting on the next calls to DBSAXNode
1239
        pstmt = conn.prepareStatement(
1240
                "DELETE FROM xml_index WHERE docid='" + this.docid + "'");
1241
        pstmt.execute();
1242
        pstmt.close();
1243

    
1244
        // Update the new document to reflect the new node tree
1245
        pstmt = conn.prepareStatement(
1246
            "UPDATE xml_documents " +
1247
            "SET rootnodeid = ?, docname = ?, doctype = ?, " +
1248
            "user_updated = ?, date_updated = " + sysdate + ", " +
1249
            "server_location = ?, rev = ?, public_access = ?, catalog_id = ? " +
1250
            "WHERE docid = ?");
1251
        // Bind the values to the query
1252
        pstmt.setLong(1, rootnodeid);
1253
        pstmt.setString(2, docname);
1254
        pstmt.setString(3, doctype);
1255
        pstmt.setString(4, user);
1256
        pstmt.setInt(5, serverCode);
1257
        pstmt.setInt(6, thisrev);
1258
        if ( pub == null ) {
1259
          pstmt.setString(7, null);
1260
        } else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
1261
          pstmt .setInt(7, 1);
1262
        } else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
1263
          pstmt.setInt(7, 0);
1264
        }
1265
        pstmt.setString(8, catalogid);
1266
        pstmt.setString(9, this.docid);
1267

    
1268
      } else {
1269
        System.err.println("Action not supported: " + action);
1270
      }
1271

    
1272
      // Do the insertion
1273
      pstmt.execute();
1274
      pstmt.close();
1275

    
1276
    } catch (SQLException sqle) {
1277
      throw sqle;
1278
    } catch (Exception e) {
1279
      throw e;
1280
    }
1281
  }
1282

    
1283
  /**
1284
   * Write an XML file to the database, given a filename
1285
   *
1286
   * @param conn the JDBC connection to the database
1287
   * @param filename the filename to be loaded into the database
1288
   * @param pub flag for public "read" access on document
1289
   * @param dtdfilename the dtd to be uploaded on server's file system
1290
   * @param action the action to be performed (INSERT OR UPDATE)
1291
   * @param docid the docid to use for the INSERT OR UPDATE
1292
   * @param user the user that owns the document
1293
   * @param groups the groups to which user belongs
1294
   */
1295
  public static String write(Connection conn,String filename,
1296
                             String pub, String dtdfilename,
1297
                             String action, String docid, String user,
1298
                             String[] groups )
1299
                throws Exception {
1300
                  
1301
    Reader dtd = null;
1302
    if ( dtdfilename != null ) {
1303
      dtd = new FileReader(new File(dtdfilename).toString());
1304
    }
1305
    return write ( conn, new FileReader(new File(filename).toString()),
1306
                   pub, dtd, action, docid, user, groups, false);
1307
  }
1308

    
1309
  public static String write(Connection conn,Reader xml,String pub,Reader dtd,
1310
                             String action, String docid, String user,
1311
                             String[] groups, boolean validate)
1312
                throws Exception {
1313
    //this method will be called in handleUpdateOrInsert method 
1314
    //in MetacatServlet class
1315
    // get server location for this doc
1316
    int serverLocation=getServerLocationNumber(conn,docid);
1317
    //System.out.println("server location: "+serverLocation);
1318
    return write(conn,xml,pub,dtd,action,docid,user,groups,serverLocation,false,
1319
                 validate);
1320
  }
1321

    
1322
  public static String write(Connection conn, Reader xml, String pub,
1323
                             String action, String docid, String user,
1324
                             String[] groups )
1325
                throws Exception {
1326
    if(action.equals("UPDATE"))
1327
    {//if the document is being updated then use the servercode from the 
1328
     //originally inserted document.
1329
      DocumentImpl doc = new DocumentImpl(conn, docid);
1330
      int servercode = doc.getServerlocation();
1331
      return write(conn, xml, pub, action, docid, user, groups, servercode);
1332
    }
1333
    else
1334
    {//if the file is being inserted then the servercode is always 1
1335
      return write(conn, xml, pub, action, docid, user, groups, 1);
1336
    }
1337
  }
1338
  
1339
  public static String write( Connection conn, Reader xml,
1340
                              String action, String docid, String user,
1341
                              String[] groups, int serverCode )
1342
                throws Exception
1343
  {
1344
    return write(conn,xml,null,action,docid,user,groups,serverCode);
1345
  }
1346
  
1347
  public static String write( Connection conn, Reader xml, String pub,
1348
                              String action, String docid, String user,
1349
                              String[] groups, int serverCode) 
1350
                throws Exception
1351
  {
1352
    return write(conn,xml,pub,null,action,docid,user,groups,
1353
                 serverCode,false,false);
1354
  }
1355
  
1356
  public static String write( Connection conn, Reader xml, String pub,
1357
                              String action, String docid, String user,
1358
                              String[] groups, int serverCode, boolean override)
1359
                throws Exception
1360
  {
1361
    return write(conn,xml,pub,null,action,docid,user,groups,
1362
                 serverCode,override,false);
1363
  }
1364
  
1365
  /**
1366
   * Write an XML file to the database, given a Reader
1367
   *
1368
   * @param conn the JDBC connection to the database
1369
   * @param xml the xml stream to be loaded into the database
1370
   * @param pub flag for public "read" access on xml document
1371
   * @param dtd the dtd to be uploaded on server's file system
1372
   * @param action the action to be performed (INSERT or UPDATE)
1373
   * @param accnum the docid + rev# to use on INSERT or UPDATE
1374
   * @param user the user that owns the document
1375
   * @param groups the groups to which user belongs
1376
   * @param serverCode the serverid from xml_replication on which this document
1377
   *        resides.
1378
   * @param override flag to stop insert replication checking.
1379
   *        if override = true then a document not belonging to the local server
1380
   *        will not be checked upon update for a file lock.
1381
   *        if override = false then a document not from this server, upon 
1382
   *        update will be locked and version checked.
1383
   */
1384

    
1385
  public static String write( Connection conn,Reader xml,String pub,Reader dtd,
1386
                              String action, String accnum, String user,
1387
                              String[] groups, int serverCode, boolean override,
1388
                              boolean validate)
1389
                throws Exception
1390
  {
1391
    // NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
1392
    MetaCatUtil util = new MetaCatUtil();
1393
    AccessionNumber ac = new AccessionNumber(conn, accnum, action);
1394
    String docid = ac.getDocid();
1395
    String rev = ac.getRev();
1396
    MetaCatUtil.debugMessage("action: " + action + " servercode: " + 
1397
                             serverCode + " override: " + override, 10);
1398
                        
1399
    if((serverCode != 1 && action.equals("UPDATE")) && !override)
1400
    { //if this document being written is not a resident of this server then
1401
      //we need to try to get a lock from it's resident server.  If the
1402
      //resident server will not give a lock then we send the user a message
1403
      //saying that he/she needs to download a new copy of the file and
1404
      //merge the differences manually.
1405
      int istreamInt; 
1406
      char istreamChar;
1407
      DocumentIdentifier id = new DocumentIdentifier(accnum);
1408
      String updaterev = id.getRev();
1409
      String server = MetacatReplication.getServer(serverCode);
1410
      MetacatReplication.replLog("attempting to lock " + accnum);
1411
      URL u = new URL("https://" + server + "?server="
1412
           +util.getLocalReplicationServerName()+"&action=getlock&updaterev=" 
1413
           +updaterev + "&docid=" + docid);
1414
      //System.out.println("sending message: " + u.toString());
1415
      String serverResStr = MetacatReplication.getURLContent(u);
1416
      String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);
1417
      if(openingtag.equals("<lockgranted>"))
1418
      {//the lock was granted go ahead with the insert
1419
        try 
1420
        {
1421
          //System.out.println("In lockgranted");
1422
          MetacatReplication.replLog("lock granted for " + accnum + " from " +
1423
                                      server);
1424
          XMLReader parser = initializeParser(conn, action, docid, updaterev,
1425
                                  validate, user, groups, pub, serverCode, dtd);
1426
          conn.setAutoCommit(false);
1427
          parser.parse(new InputSource(xml)); 
1428
          conn.commit();
1429
          conn.setAutoCommit(true);
1430
        } 
1431
        catch (Exception e) 
1432
        {
1433
          conn.rollback();
1434
          conn.setAutoCommit(true);
1435
          throw e;
1436
        }
1437
                
1438
        
1439
        
1440
        //If Metacat is super hub, tell all servers in its server list to get 
1441
        //the new document, ture mean it is xml document
1442
        if ((util.getOption("hub")).equals("super"))
1443
        {
1444
          ForceReplicationHandler frh = new ForceReplicationHandler(accnum, 
1445
                true, ReplicationHandler.buildServerList(conn));
1446
        }
1447
        else
1448
        {
1449
          //after inserting the document locally, tell the document's homeserver
1450
          //to come get a copy from here.
1451
         
1452
          ForceReplicationHandler frh = new ForceReplicationHandler(accnum, 
1453
                true, ReplicationHandler.getHomeServer(docid));
1454
        }
1455
        return (accnum);
1456
      }
1457

    
1458
      else if(openingtag.equals("<filelocked>"))
1459
      {//the file is currently locked by another user
1460
       //notify our user to wait a few minutes, check out a new copy and try
1461
       //again.
1462
        //System.out.println("file locked");
1463
        MetacatReplication.replLog("lock denied for " + accnum + " on " +
1464
                                   server + " reason: file already locked");
1465
        throw new Exception("The file specified is already locked by another " +
1466
                            "user.  Please wait 30 seconds, checkout the " +
1467
                            "newer document, merge your changes and try " +
1468
                            "again.");
1469
      }
1470
      else if(openingtag.equals("<outdatedfile>"))
1471
      {//our file is outdated.  notify our user to check out a new copy of the
1472
       //file and merge his version with the new version.
1473
        //System.out.println("outdated file");
1474
        MetacatReplication.replLog("lock denied for " + accnum + " on " +
1475
                                    server + " reason: local file outdated");
1476
        throw new Exception("The file you are trying to update is an outdated" +
1477
                            " version.  Please checkout the newest document, " +
1478
                            "merge your changes and try again.");
1479
      }
1480
    }
1481
    
1482
    if ( action.equals("UPDATE") ) {
1483
      // check for 'write' permission for 'user' to update this document
1484

    
1485
      if ( !hasPermission(conn, user, groups, docid) ) {
1486
        throw new Exception("User " + user + 
1487
              " does not have permission to update XML Document #" + accnum);
1488
      }          
1489
    }
1490

    
1491
    try 
1492
    { 
1493
      
1494
      XMLReader parser = initializeParser(conn, action, docid, rev, validate,
1495
                                          user, groups, pub, serverCode, dtd);
1496
      conn.setAutoCommit(false);
1497
      parser.parse(new InputSource(xml));
1498
      conn.commit();
1499
      conn.setAutoCommit(true);
1500
    } 
1501
    catch (Exception e) 
1502
    {
1503
      conn.rollback();
1504
      conn.setAutoCommit(true);
1505
      throw e;
1506
    }
1507
    
1508
    //force replicate out the new document to each server in our server list.
1509
    if(serverCode == 1)
1510
    { 
1511
      
1512
      //start the thread to replicate this new document out to the other servers
1513
      //true mean it is xml document
1514
      ForceReplicationHandler frh = new ForceReplicationHandler
1515
                (accnum, action, true,ReplicationHandler.buildServerList(conn));
1516
      
1517
    }
1518
      
1519
    return(accnum);
1520
  }
1521

    
1522
  /**
1523
   * Write an XML file to the database during replication
1524
   *
1525
   * @param conn the JDBC connection to the database
1526
   * @param xml the xml stream to be loaded into the database
1527
   * @param pub flag for public "read" access on xml document
1528
   * @param dtd the dtd to be uploaded on server's file system
1529
   * @param action the action to be performed (INSERT or UPDATE)
1530
   * @param accnum the docid + rev# to use on INSERT or UPDATE
1531
   * @param user the user that owns the document
1532
   * @param groups the groups to which user belongs
1533
   * @param homeServer the name of server which the document origanlly create
1534
   * @param validate, if the xml document is valid or not
1535
   */
1536

    
1537
  public static String writeReplication( Connection conn,Reader xml,String pub,
1538
                Reader dtd, String action, String accnum, String user,
1539
                            String[] groups,String homeServer, boolean validate)
1540
                throws Exception
1541
  {
1542
    // NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
1543
    MetaCatUtil util = new MetaCatUtil();
1544
    AccessionNumber ac = new AccessionNumber(conn, accnum, action);
1545
    String docid = ac.getDocid();
1546
    String rev = ac.getRev();
1547
    int serverCode=-2;
1548
    //get server code for the home server
1549
    serverCode=getServerCode(homeServer);
1550
    //if the server is not in the xml replication table, insert it.
1551
    if (serverCode==-1)
1552
    {
1553
      insertServerIntoReplicationTable(homeServer);
1554
      //get server code again
1555
      serverCode=getServerCode(homeServer);
1556
    }
1557
      
1558
    MetaCatUtil.debugMessage("action: " + action + " servercode: " + 
1559
                             serverCode, 10);
1560
                        
1561
    if((serverCode != 1 && action.equals("UPDATE")) )
1562
    { //if this document being written is not a resident of this server then
1563
      //we need to try to get a lock from it's resident server.  If the
1564
      //resident server will not give a lock then we send the user a message
1565
      //saying that he/she needs to download a new copy of the file and
1566
      //merge the differences manually.
1567
      int istreamInt; 
1568
      char istreamChar;
1569
      DocumentIdentifier id = new DocumentIdentifier(accnum);
1570
      String updaterev = id.getRev();
1571
      String server = MetacatReplication.getServer(serverCode);
1572
      MetacatReplication.replLog("attempting to lock " + accnum);
1573
      URL u = new URL("https://" + server + "?server="
1574
           +util.getLocalReplicationServerName()+"&action=getlock&updaterev=" 
1575
           +updaterev + "&docid=" + docid);
1576
      //System.out.println("sending message: " + u.toString());
1577
      String serverResStr = MetacatReplication.getURLContent(u);
1578
      String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);
1579
      if(openingtag.equals("<lockgranted>"))
1580
      {//the lock was granted go ahead with the insert
1581
        try 
1582
        {
1583
          //System.out.println("In lockgranted");
1584
          MetacatReplication.replLog("lock granted for " + accnum + " from " +
1585
                                      server);
1586
          XMLReader parser = initializeParser(conn, action, docid, updaterev,
1587
                                  validate, user, groups, pub, serverCode, dtd);
1588
          conn.setAutoCommit(false);
1589
          parser.parse(new InputSource(xml)); 
1590
          conn.commit();
1591
          conn.setAutoCommit(true);
1592
        } 
1593
        catch (Exception e) 
1594
        {
1595
          conn.rollback();
1596
          conn.setAutoCommit(true);
1597
          throw e;
1598
        }
1599
        return (accnum);
1600
      }
1601

    
1602
      else if(openingtag.equals("<filelocked>"))
1603
      {//the file is currently locked by another user
1604
       //notify our user to wait a few minutes, check out a new copy and try
1605
       //again.
1606
        //System.out.println("file locked");
1607
        MetacatReplication.replLog("lock denied for " + accnum + " on " +
1608
                                   server + " reason: file already locked");
1609
        throw new Exception("The file specified is already locked by another " +
1610
                            "user.  Please wait 30 seconds, checkout the " +
1611
                            "newer document, merge your changes and try " +
1612
                            "again.");
1613
      }
1614
      else if(openingtag.equals("<outdatedfile>"))
1615
      {//our file is outdated.  notify our user to check out a new copy of the
1616
       //file and merge his version with the new version.
1617
        //System.out.println("outdated file");
1618
        MetacatReplication.replLog("lock denied for " + accnum + " on " +
1619
                                    server + " reason: local file outdated");
1620
        throw new Exception("The file you are trying to update is an outdated" +
1621
                            " version.  Please checkout the newest document, " +
1622
                            "merge your changes and try again.");
1623
      }
1624
    }
1625
    
1626
    if ( action.equals("UPDATE") ) {
1627
      // check for 'write' permission for 'user' to update this document
1628

    
1629
      if ( !hasPermission(conn, user, groups, docid) ) {
1630
        throw new Exception("User " + user + 
1631
              " does not have permission to update XML Document #" + accnum);
1632
      }          
1633
    }
1634

    
1635
    try 
1636
    { 
1637
      
1638
      XMLReader parser = initializeParser(conn, action, docid, rev, validate,
1639
                                          user, groups, pub, serverCode, dtd);
1640
      conn.setAutoCommit(false);
1641
      parser.parse(new InputSource(xml));
1642
      conn.commit();
1643
      conn.setAutoCommit(true);
1644
    } 
1645
    catch (Exception e) 
1646
    {
1647
      conn.rollback();
1648
      conn.setAutoCommit(true);
1649
      throw e;
1650
    }
1651

    
1652
    return(accnum);
1653
  }
1654

    
1655
  
1656
  /**
1657
   * Delete an XML file from the database (actually, just make it a revision
1658
   * in the xml_revisions table)
1659
   *
1660
   * @param docid the ID of the document to be deleted from the database
1661
   */
1662
  public static void delete( Connection conn, String accnum,
1663
                                 String user, String[] groups )
1664
                throws Exception 
1665
  {
1666
    // OLD
1667
    //DocumentIdentifier id = new DocumentIdentifier(accnum);
1668
    //String docid = id.getIdentifier();
1669
    //String rev = id.getRev();
1670
    
1671
    // OLD
1672
    // Determine if the docid,rev are OK for DELETE
1673
    //AccessionNumber ac = new AccessionNumber(conn);
1674
    //docid = ac.generate(docid, rev, "DELETE");
1675

    
1676
    // NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
1677
    AccessionNumber ac = new AccessionNumber(conn, accnum, "DELETE");
1678
    String docid = ac.getDocid();
1679
    String rev = ac.getRev();
1680
    
1681

    
1682
    // check for 'write' permission for 'user' to delete this document
1683
    if ( !hasPermission(conn, user, groups, docid) ) {
1684
      throw new Exception("User " + user + 
1685
              " does not have permission to delete XML Document #" + accnum);
1686
    }
1687

    
1688
    conn.setAutoCommit(false);
1689
    // Copy the record to the xml_revisions table
1690
    DocumentImpl.archiveDocRevision( conn, docid, user );
1691

    
1692
    // Now delete it from the xml_documents table
1693
    
1694
    Statement stmt = conn.createStatement();
1695
    stmt.execute("DELETE FROM xml_index WHERE docid = '" + docid + "'");
1696
    //stmt.execute("DELETE FROM xml_access WHERE docid = '" + docid + "'");
1697
    stmt.execute("DELETE FROM xml_access WHERE accessfileid = '" + docid + "'");
1698
    stmt.execute("DELETE FROM xml_relation WHERE docid = '" + docid + "'");
1699
    stmt.execute("DELETE FROM xml_documents WHERE docid = '" + docid + "'");
1700
    stmt.close();
1701
    conn.commit();
1702
    conn.setAutoCommit(true);
1703
    //IF this is a package document:
1704
    //delete all of the relations that this document created.
1705
    //if the deleted document is a package document its relations should 
1706
    //no longer be active if it has been deleted from the system.
1707
    
1708
  }
1709

    
1710
  /** 
1711
    * Check for "WRITE" permission on @docid for @user and/or @groups 
1712
    * from DB connection 
1713
    */
1714
  private static boolean hasPermission ( Connection conn, String user,
1715
                                  String[] groups, String docid ) 
1716
                  throws SQLException, Exception
1717
  {
1718
    // Check for WRITE permission on @docid for @user and/or @groups
1719
    AccessControlList aclobj = new AccessControlList(conn);
1720
    return aclobj.hasPermission("WRITE", user, groups, docid);
1721
  }
1722

    
1723
  /** 
1724
    * Check for "READ" permission base on docid, user and group
1725
    *@docid, the document
1726
    *@user, user name
1727
    *@group, user's group
1728
    * 
1729
    */
1730
  public boolean hasReadPermission ( Connection conn, String user,
1731
                                  String[] groups, String docId ) 
1732
                  throws SQLException, Exception
1733
  {
1734
    // Check for READ permission on @docid for @user and/or @groups
1735
    AccessControlList aclObj = new AccessControlList(conn);
1736
    return aclObj.hasPermission("READ", user, groups, docId);
1737
  }  
1738

    
1739
  /**
1740
   * Set up the parser handlers for writing the document to the database
1741
   */
1742
  private static XMLReader initializeParser(Connection conn, String action,
1743
                               String docid, String rev, boolean validate, 
1744
                                   String user, String[] groups, String pub, 
1745
                                   int serverCode, Reader dtd) 
1746
                           throws Exception 
1747
  {
1748
    XMLReader parser = null;
1749
    //
1750
    // Set up the SAX document handlers for parsing
1751
    //
1752
    try {
1753
      //create a DBSAXHandler object which has the revision specification
1754
      ContentHandler chandler = new DBSAXHandler(conn, action, docid, rev,
1755
                                                 user, groups, pub, serverCode);
1756
      EntityResolver eresolver= new DBEntityResolver(conn,
1757
                                                 (DBSAXHandler)chandler, dtd);
1758
      DTDHandler dtdhandler   = new DBDTDHandler(conn);
1759

    
1760
      // Get an instance of the parser
1761
      String parserName = MetaCatUtil.getOption("saxparser");
1762
      parser = XMLReaderFactory.createXMLReader(parserName);
1763

    
1764
      // Turn on validation
1765
      parser.setFeature("http://xml.org/sax/features/validation", validate);
1766
      // Turn off Including all external parameter entities
1767
      // (the external DTD subset also)
1768
      // Doesn't work well, probably the feature name is not correct
1769
      // parser.setFeature(
1770
      //  "http://xml.org/sax/features/external-parameter-entities", false);
1771
      
1772
      // Set Handlers in the parser
1773
      parser.setProperty("http://xml.org/sax/properties/declaration-handler",
1774
                         chandler);
1775
      parser.setProperty("http://xml.org/sax/properties/lexical-handler",
1776
                         chandler);
1777
      parser.setContentHandler((ContentHandler)chandler);
1778
      parser.setEntityResolver((EntityResolver)eresolver);
1779
      parser.setDTDHandler((DTDHandler)dtdhandler);
1780
      parser.setErrorHandler((ErrorHandler)chandler);
1781

    
1782
    } catch (Exception e) {
1783
      throw e;
1784
    }
1785

    
1786
    return parser;
1787
  }
1788

    
1789
  /** Save a document entry in the xml_revisions table */
1790
  private static void archiveDocRevision(Connection conn, String docid,
1791
                                         String user) 
1792
 {
1793
    String sysdate = dbAdapter.getDateTimeFunction();
1794
    // create a record in xml_revisions table 
1795
    // for that document as selected from xml_documents
1796
   
1797
   try
1798
   {
1799
     PreparedStatement pstmt = conn.prepareStatement(
1800
      "INSERT INTO xml_revisions " +
1801
        "(docid, rootnodeid, docname, doctype, " +
1802
        "user_owner, user_updated, date_created, date_updated, " +
1803
        "server_location, rev, public_access, catalog_id) " +
1804
      "SELECT ?, rootnodeid, docname, doctype, " + 
1805
        "user_owner, ?, " + sysdate + ", " + sysdate + ", "+
1806
        "server_location, rev, public_access, catalog_id " +
1807
      "FROM xml_documents " +
1808
      "WHERE docid = ?");
1809
      // Bind the values to the query and execute it
1810
      pstmt.setString(1, docid);
1811
      pstmt.setString(2, user);
1812
      pstmt.setString(3, docid);
1813
      pstmt.execute();
1814
      pstmt.close();
1815
   }
1816
   catch (SQLException e)
1817
   {
1818
   }
1819
   
1820

    
1821
  }
1822
  
1823
  /**
1824
    * delete a entry in xml_table for given docid
1825
    * @param docId, the id of the document need to be delete
1826
    */
1827
  private static void deleteXMLDocuments(Connection conn, String docId) 
1828
                                         throws SQLException 
1829
  {
1830
    //delete a record 
1831
    PreparedStatement pStmt = 
1832
             conn.prepareStatement("DELETE FROM xml_documents WHERE docid = '" 
1833
                                              + docId + "'");
1834
    pStmt.execute();
1835
    pStmt.close();
1836

    
1837
  }//deleteXMLDocuments
1838
  
1839
  /**
1840
    * Get last revision number from database for a docid
1841
    * If couldn't find an entry,  -1 will return
1842
    * The return value is integer because we want compare it to there new one
1843
    * @param docid <sitecode>.<uniqueid> part of Accession Number
1844
    */
1845
  private static int getLatestRevisionNumber(Connection conn, String docId)
1846
                                      throws SQLException
1847
  {
1848
    int rev = 1;
1849
    PreparedStatement pStmt;
1850
     
1851
    pStmt = conn.prepareStatement
1852
              ("SELECT rev FROM xml_documents WHERE docid='" + docId + "'");
1853
    pStmt.execute();
1854

    
1855
    ResultSet rs = pStmt.getResultSet();
1856
    boolean hasRow = rs.next();
1857
    if (hasRow)
1858
    {
1859
      rev = rs.getInt(1);
1860
      pStmt.close();
1861
    }
1862
    else
1863
    {
1864
      rev=-1;
1865
      pStmt.close();
1866
    }
1867
      
1868
    return rev;
1869
  }//getLatestRevisionNumber
1870
  
1871
  /**
1872
   * Get server location form database for a accNum
1873
   * 
1874
   * @param accum <sitecode>.<uniqueid>.<rev>
1875
   */
1876
  private static int getServerLocationNumber(Connection conn, String accNum)
1877
                                            throws SQLException
1878
  {
1879
    //get rid of revNum part
1880
    String docId=MetaCatUtil.getDocIdFromString(accNum);
1881
    PreparedStatement pStmt;
1882
    int serverLocation;
1883
     
1884
    pStmt = conn.prepareStatement
1885
      ("SELECT server_location FROM xml_documents WHERE docid='" + docId + "'");
1886
    pStmt.execute();
1887

    
1888
    ResultSet rs = pStmt.getResultSet();
1889
    boolean hasRow = rs.next();
1890
    //if there is entry in xml_documents, get the serverlocation
1891
    if (hasRow)
1892
    {
1893
      serverLocation = rs.getInt(1);
1894
      pStmt.close();
1895
    }
1896
    else
1897
    {
1898
      // if htere is no entry in xml_documents, we consider it is new document
1899
      // the server location is local host and value is 1
1900
      serverLocation=1;
1901
      pStmt.close();
1902
    }
1903
      
1904
    return serverLocation;
1905
  }
1906
  
1907
  /**
1908
   * Given a server name, return its servercode in xml_replication table.
1909
   * If no server is found, -1 will return
1910
   * @param serverName, 
1911
   */
1912
  private static int getServerCode(String serverName) 
1913
  {
1914
    PreparedStatement pStmt=null;
1915
    int serverLocation=-2;
1916
    Connection dbConn = null;
1917
    MetaCatUtil util = new MetaCatUtil();
1918
    
1919
    
1920
    //we should consider about local host too
1921
    if (serverName.equals(util.getLocalReplicationServerName()))
1922
    { 
1923
      serverLocation=1;
1924
      return serverLocation;
1925
    }
1926
    
1927
   
1928
    try
1929
    {
1930
      //check xml_replication table
1931
      dbConn=util.openDBConnection();
1932
      pStmt = dbConn.prepareStatement
1933
      ("SELECT serverid FROM xml_replication WHERE server='" + serverName +"'");
1934
      pStmt.execute();
1935

    
1936
      ResultSet rs = pStmt.getResultSet();
1937
      boolean hasRow = rs.next();
1938
      //if there is entry in xml_replication, get the serverid
1939
      if (hasRow)
1940
      {
1941
        serverLocation = rs.getInt(1);
1942
        pStmt.close();
1943
      }
1944
      else
1945
      {
1946
        // if htere is no entry in xml_replication, -1 will return
1947
        serverLocation=-1;
1948
        pStmt.close();
1949
      }
1950
    }
1951
    catch (Exception e)
1952
    {
1953
      util.debugMessage("Error in DocumentImpl.getServerCode(): "
1954
                                    +e.getMessage(), 30);
1955
    }
1956
    finally
1957
    {
1958
      try
1959
      {
1960
        dbConn.close();
1961
      }
1962
      catch (Exception ee)
1963
      {}
1964
    }
1965
                 
1966
      
1967
    return serverLocation;
1968
  }
1969
  
1970
  /**
1971
   * Insert a server into xml_replcation table
1972
   * @param server, the name of server 
1973
   */
1974
  private static void  insertServerIntoReplicationTable(String server)
1975
  {
1976
    PreparedStatement pStmt=null;
1977
    Connection dbConn = null;
1978
    int replicate = 1;
1979
    MetaCatUtil util = new MetaCatUtil();
1980
    try
1981
    {
1982
       dbConn=util.openDBConnection();
1983
       pStmt = dbConn.prepareStatement("INSERT INTO xml_replication " +
1984
                                      "(server, last_checked, replicate) " +
1985
                                      "VALUES ('" + server + "', to_date(" +
1986
                                      "'01/01/00', 'MM/DD/YY'), '" +
1987
                                      replicate + "')");
1988
        pStmt.execute();
1989
        pStmt.close();
1990
        dbConn.commit();
1991
    }
1992
    catch (Exception e)
1993
    {
1994
      util.debugMessage("Error in DocumentImpl.getServerCode(): "
1995
                                    +e.getMessage(), 30);
1996
    }
1997
    finally
1998
    {
1999
      try
2000
      {
2001
        pStmt.close();
2002
        dbConn.close();
2003
      }
2004
      catch (Exception ee)
2005
      {}
2006
    }
2007

    
2008
  }
2009
  
2010
  
2011
  /**
2012
   * the main routine used to test the DBWriter utility.
2013
   * <p>
2014
   * Usage: java DocumentImpl <-f filename -a action -d docid>
2015
   *
2016
   * @param filename the filename to be loaded into the database
2017
   * @param action the action to perform (READ, INSERT, UPDATE, DELETE)
2018
   * @param docid the id of the document to process
2019
   */
2020
  static public void main(String[] args) {
2021
     
2022
    try {
2023
      String filename    = null;
2024
      String dtdfilename = null;
2025
      String action      = null;
2026
      String docid       = null;
2027
      boolean showRuntime = false;
2028
      boolean useOldReadAlgorithm = false;
2029

    
2030
      // Parse the command line arguments
2031
      for ( int i=0 ; i < args.length; ++i ) {
2032
        if ( args[i].equals( "-f" ) ) {
2033
          filename =  args[++i];
2034
        } else if ( args[i].equals( "-r" ) ) {
2035
          dtdfilename =  args[++i];
2036
        } else if ( args[i].equals( "-a" ) ) {
2037
          action =  args[++i];
2038
        } else if ( args[i].equals( "-d" ) ) {
2039
          docid =  args[++i];
2040
        } else if ( args[i].equals( "-t" ) ) {
2041
          showRuntime = true;
2042
        } else if ( args[i].equals( "-old" ) ) {
2043
          useOldReadAlgorithm = true;
2044
        } else {
2045
          System.err.println
2046
            ( "   args[" +i+ "] '" +args[i]+ "' ignored." );
2047
        }
2048
      }
2049
      
2050
      // Check if the required arguments are provided
2051
      boolean argsAreValid = false;
2052
      if (action != null) {
2053
        if (action.equals("INSERT")) {
2054
          if (filename != null) {
2055
            argsAreValid = true;
2056
          } 
2057
        } else if (action.equals("UPDATE")) {
2058
          if ((filename != null) && (docid != null)) {
2059
            argsAreValid = true;
2060
          } 
2061
        } else if (action.equals("DELETE")) {
2062
          if (docid != null) {
2063
            argsAreValid = true;
2064
          } 
2065
        } else if (action.equals("READ")) {
2066
          if (docid != null) {
2067
            argsAreValid = true;
2068
          } 
2069
        } 
2070
      } 
2071

    
2072
      // Print usage message if the arguments are not valid
2073
      if (!argsAreValid) {
2074
        System.err.println("Wrong number of arguments!!!");
2075
        System.err.println(
2076
          "USAGE: java DocumentImpl [-t] <-a INSERT> [-d docid] <-f filename> "+
2077
          "[-r dtdfilename]");
2078
        System.err.println(
2079
          "   OR: java DocumentImpl [-t] <-a UPDATE -d docid -f filename> " +
2080
          "[-r dtdfilename]");
2081
        System.err.println(
2082
          "   OR: java DocumentImpl [-t] <-a DELETE -d docid>");
2083
        System.err.println(
2084
          "   OR: java DocumentImpl [-t] [-old] <-a READ -d docid>");
2085
        return;
2086
      }
2087
      
2088
      // Time the request if asked for
2089
      double startTime = System.currentTimeMillis();
2090
      
2091
      // Open a connection to the database
2092
      MetaCatUtil util = new MetaCatUtil();
2093
      Connection dbconn = util.openDBConnection();
2094

    
2095
      double connTime = System.currentTimeMillis();
2096
      // Execute the action requested (READ, INSERT, UPDATE, DELETE)
2097
      if (action.equals("READ")) {
2098
          DocumentImpl xmldoc = new DocumentImpl( dbconn, docid );
2099
          if (useOldReadAlgorithm) {
2100
            System.out.println(xmldoc.readUsingSlowAlgorithm());
2101
          } else {
2102
            xmldoc.toXml(new PrintWriter(System.out));
2103
          }
2104
      } else if (action.equals("DELETE")) {
2105
        DocumentImpl.delete(dbconn, docid, null, null);
2106
        System.out.println("Document deleted: " + docid);
2107
      } else {
2108
        String newdocid = DocumentImpl.write(dbconn, filename, null,
2109
                                             dtdfilename, action, docid,
2110
                                             null, null);
2111
        if ((docid != null) && (!docid.equals(newdocid))) {
2112
          if (action.equals("INSERT")) {
2113
            System.out.println("New document ID generated!!! ");
2114
          } else if (action.equals("UPDATE")) {
2115
            System.out.println("ERROR: Couldn't update document!!! ");
2116
          }
2117
        } else if ((docid == null) && (action.equals("UPDATE"))) {
2118
          System.out.println("ERROR: Couldn't update document!!! ");
2119
        }
2120
        System.out.println("Document processing finished for: " + filename
2121
              + " (" + newdocid + ")");
2122
      }
2123

    
2124
      double stopTime = System.currentTimeMillis();
2125
      double dbOpenTime = (connTime - startTime)/1000;
2126
      double insertTime = (stopTime - connTime)/1000;
2127
      double executionTime = (stopTime - startTime)/1000;
2128
      if (showRuntime) {
2129
        System.out.println("\n\nTotal Execution time was: " + 
2130
                           executionTime + " seconds.");
2131
        System.out.println("Time to open DB connection was: " + dbOpenTime + 
2132
                           " seconds.");
2133
        System.out.println("Time to insert document was: " + insertTime +
2134
                           " seconds.");
2135
      }
2136
      dbconn.close();
2137
    } catch (McdbException me) {
2138
      me.toXml(new PrintWriter(System.err));
2139
    } catch (AccessionNumberException ane) {
2140
      System.out.println(ane.getMessage());
2141
    } catch (Exception e) {
2142
      System.err.println("EXCEPTION HANDLING REQUIRED");
2143
      System.err.println(e.getMessage());
2144
      e.printStackTrace(System.err);
2145
    }
2146
  }
2147
}
(24-24/41)