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393
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jones
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/**
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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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* '$Author$'
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* '$Date$'
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* '$Revision$'
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669
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jones
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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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393
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jones
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*/
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package edu.ucsb.nceas.metacat;
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import java.sql.*;
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429
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jones
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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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393
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jones
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import java.io.PrintWriter;
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429
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jones
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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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561
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berkley
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import java.io.InputStreamReader;
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393
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jones
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798
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jones
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import java.text.SimpleDateFormat;
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import java.util.Date;
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429
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jones
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import java.util.Iterator;
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407
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jones
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import java.util.Stack;
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429
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jones
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import java.util.TreeSet;
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577
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berkley
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import java.util.Enumeration;
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407
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jones
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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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561
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berkley
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import java.net.URL;
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777
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bojilova
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import edu.ucsb.nceas.dbadapter.AbstractDatabase;
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747
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bojilova
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393
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jones
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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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407
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jones
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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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393
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jones
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*/
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public class DocumentImpl {
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425
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bojilova
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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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777
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bojilova
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private static final AbstractDatabase dbAdapter = MetaCatUtil.dbAdapter;
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425
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bojilova
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393
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jones
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private Connection conn = null;
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private String docid = null;
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private String docname = null;
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private String doctype = null;
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691
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bojilova
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// DOCTITLE attr cleared from the db
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// private String doctitle = null;
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465
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berkley
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private String createdate = null;
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private String updatedate = null;
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393
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jones
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private String system_id = null;
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561
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berkley
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private String userowner = null;
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private String userupdated = null;
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575
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berkley
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private int rev;
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561
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berkley
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private int serverlocation;
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697
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bojilova
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private String publicaccess;
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393
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jones
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private long rootnodeid;
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private ElementNode rootNode = null;
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429
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jones
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private TreeSet nodeRecordList = null;
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790
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bojilova
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/**
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800
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jones
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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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790
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bojilova
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*
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* @param conn the database connection from which to read the document
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800
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jones
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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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790
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bojilova
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*/
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802
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bojilova
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public DocumentImpl(Connection conn, String docid, boolean readNodes)
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throws McdbException
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790
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bojilova
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{
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801
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jones
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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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800
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jones
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801
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jones
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if (readNodes) {
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800
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jones
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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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801
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jones
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}
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800
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jones
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801
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jones
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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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800
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jones
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}
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790
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bojilova
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}
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393
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jones
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/**
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396
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jones
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* Constructor, creates document from database connection, used
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* for reading the document
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393
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jones
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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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801
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jones
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this(conn, docid, true);
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393
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jones
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}
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396
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jones
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/**
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415
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jones
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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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396
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jones
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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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153 |
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* @param doctype - Public ID of the DTD, i.e. the name immediately
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154 |
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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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157 |
680
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bojilova
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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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396
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jones
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*
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*/
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public DocumentImpl(Connection conn, long rootnodeid, String docname,
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166 |
549
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berkley
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String doctype, String docid, String action, String user,
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167 |
697
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bojilova
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String pub, String catalogid, int serverCode)
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168 |
549
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berkley
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throws SQLException, Exception
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{
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170 |
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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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697
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bojilova
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writeDocumentToDB(action, user, pub, catalogid, serverCode);
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176 |
549
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berkley
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}
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177 |
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178 |
798
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jones
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/**
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179 |
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* Register a document that resides on the filesystem with the database.
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180 |
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* (ie, just an entry in xml_documents, nothing in xml_nodes).
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181 |
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* Creates a reference to a filesystem document (used for non-xml data files).
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182 |
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*
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183 |
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* @param conn the JDBC Connection to which all information is written
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184 |
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* @param docname - the name of DTD, i.e. the name immediately following
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185 |
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* the DOCTYPE keyword ( should be the root element name ) or
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186 |
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* the root element name if no DOCTYPE declaration provided
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187 |
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* (Oracle's and IBM parsers are not aware if it is not the
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188 |
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* root element name)
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189 |
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* @param doctype - Public ID of the DTD, i.e. the name immediately
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190 |
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* following the PUBLIC keyword in DOCTYPE declaration or
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191 |
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* the docname if no Public ID provided or
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192 |
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* null if no DOCTYPE declaration provided
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193 |
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* @param accnum the accession number to use for the INSERT OR UPDATE, which
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194 |
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* includes a revision number for this revision of the document
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195 |
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* (e.g., knb.1.1)
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196 |
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* @param user the user that owns the document
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197 |
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* @param serverCode the serverid from xml_replication on which this document
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198 |
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* resides.
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199 |
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*/
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200 |
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public static void registerDocument(
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201 |
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String docname, String doctype, String accnum,
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202 |
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String user, int serverCode)
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203 |
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throws SQLException, AccessionNumberException, Exception
|
204 |
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{
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205 |
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Connection dbconn = null;
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206 |
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MetaCatUtil util = new MetaCatUtil();
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207 |
407
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jones
|
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208 |
798
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jones
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try {
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209 |
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dbconn = util.openDBConnection();
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210 |
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211 |
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AccessionNumber ac = new AccessionNumber(dbconn, accnum, "insert");
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212 |
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String docid = ac.getDocid();
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213 |
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String rev = ac.getRev();
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214 |
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215 |
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SimpleDateFormat formatter = new SimpleDateFormat ("yy-MM-dd HH:mm:ss");
|
216 |
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Date localtime = new Date();
|
217 |
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String dateString = formatter.format(localtime);
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218 |
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|
219 |
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String sqlDateString = "to_date('" + dateString + "', 'YY-MM-DD HH24:MI:SS')";
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220 |
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221 |
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StringBuffer sql = new StringBuffer();
|
222 |
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sql.append("insert into xml_documents (docid, docname, doctype, ");
|
223 |
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sql.append("user_owner, user_updated, server_location, rev, date_created");
|
224 |
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sql.append(", date_updated, public_access) values ('");
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225 |
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sql.append(docid).append("','");
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226 |
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sql.append(docname).append("','");
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227 |
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sql.append(doctype).append("','");
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228 |
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sql.append(user).append("','");
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229 |
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sql.append(user).append("','");
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230 |
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sql.append(serverCode).append("','");
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231 |
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sql.append(rev).append("',");
|
232 |
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sql.append(sqlDateString).append(",");
|
233 |
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sql.append(sqlDateString).append(",");
|
234 |
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sql.append("'0')");
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235 |
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//System.out.println("sql: " + sql.toString());
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236 |
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237 |
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PreparedStatement pstmt = dbconn.prepareStatement(sql.toString());
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238 |
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pstmt.execute();
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239 |
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pstmt.close();
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240 |
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dbconn.close();
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241 |
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} finally {
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242 |
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util.returnConnection(dbconn);
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243 |
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}
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244 |
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}
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245 |
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246 |
393
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jones
|
/**
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247 |
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* get the document name
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248 |
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*/
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249 |
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public String getDocname() {
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250 |
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return docname;
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251 |
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}
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252 |
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253 |
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/**
|
254 |
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* get the document type (which is the PublicID)
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255 |
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*/
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256 |
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public String getDoctype() {
|
257 |
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return doctype;
|
258 |
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}
|
259 |
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|
260 |
|
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/**
|
261 |
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* get the system identifier
|
262 |
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*/
|
263 |
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public String getSystemID() {
|
264 |
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return system_id;
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265 |
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}
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266 |
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267 |
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/**
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268 |
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* get the root node identifier
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269 |
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*/
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270 |
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public long getRootNodeID() {
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271 |
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return rootnodeid;
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272 |
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}
|
273 |
465
|
berkley
|
|
274 |
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/**
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275 |
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* get the creation date
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276 |
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*/
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277 |
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public String getCreateDate() {
|
278 |
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return createdate;
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279 |
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}
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280 |
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|
281 |
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/**
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282 |
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* get the update date
|
283 |
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*/
|
284 |
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public String getUpdateDate() {
|
285 |
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return updatedate;
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286 |
|
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}
|
287 |
393
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jones
|
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288 |
396
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jones
|
/**
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289 |
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* Get the document identifier (docid)
|
290 |
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*/
|
291 |
|
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public String getDocID() {
|
292 |
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return docid;
|
293 |
|
|
}
|
294 |
465
|
berkley
|
|
295 |
691
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bojilova
|
// DOCTITLE attr cleared from the db
|
296 |
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// /**
|
297 |
|
|
// *get the document title
|
298 |
|
|
// */
|
299 |
|
|
// public String getDocTitle() {
|
300 |
|
|
// return doctitle;
|
301 |
|
|
// }
|
302 |
561
|
berkley
|
|
303 |
|
|
public String getUserowner() {
|
304 |
|
|
return userowner;
|
305 |
|
|
}
|
306 |
|
|
|
307 |
|
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public String getUserupdated() {
|
308 |
|
|
return userupdated;
|
309 |
|
|
}
|
310 |
|
|
|
311 |
|
|
public int getServerlocation() {
|
312 |
|
|
return serverlocation;
|
313 |
|
|
}
|
314 |
|
|
|
315 |
697
|
bojilova
|
public String getPublicaccess() {
|
316 |
561
|
berkley
|
return publicaccess;
|
317 |
|
|
}
|
318 |
575
|
berkley
|
|
319 |
|
|
public int getRev() {
|
320 |
|
|
return rev;
|
321 |
|
|
}
|
322 |
396
|
jones
|
|
323 |
393
|
jones
|
/**
|
324 |
429
|
jones
|
* Print a string representation of the XML document
|
325 |
393
|
jones
|
*/
|
326 |
|
|
public String toString()
|
327 |
|
|
{
|
328 |
429
|
jones
|
StringWriter docwriter = new StringWriter();
|
329 |
800
|
jones
|
try {
|
330 |
|
|
this.toXml(docwriter);
|
331 |
|
|
} catch (McdbException mcdbe) {
|
332 |
|
|
return null;
|
333 |
|
|
}
|
334 |
429
|
jones
|
String document = docwriter.toString();
|
335 |
|
|
return document;
|
336 |
|
|
}
|
337 |
|
|
|
338 |
|
|
/**
|
339 |
|
|
* Get a text representation of the XML document as a string
|
340 |
|
|
* This older algorithm uses a recursive tree of Objects to represent the
|
341 |
|
|
* nodes of the tree. Each object is passed the data for the document
|
342 |
|
|
* and searches all of the document data to find its children nodes and
|
343 |
|
|
* recursively build. Thus, because each node reads the whole document,
|
344 |
|
|
* this algorithm is extremely slow for larger documents, and the time
|
345 |
|
|
* to completion is O(N^N) wrt the number of nodes. See toXml() for a
|
346 |
|
|
* better algorithm.
|
347 |
|
|
*/
|
348 |
800
|
jones
|
public String readUsingSlowAlgorithm() throws McdbException
|
349 |
429
|
jones
|
{
|
350 |
393
|
jones
|
StringBuffer doc = new StringBuffer();
|
351 |
|
|
|
352 |
800
|
jones
|
// First, check that we have the needed node data, and get it if not
|
353 |
|
|
if (nodeRecordList == null) {
|
354 |
|
|
nodeRecordList = getNodeRecordList(rootnodeid);
|
355 |
|
|
}
|
356 |
|
|
|
357 |
429
|
jones
|
// Create the elements from the downloaded data in the TreeSet
|
358 |
|
|
rootNode = new ElementNode(nodeRecordList, rootnodeid);
|
359 |
|
|
|
360 |
393
|
jones
|
// Append the resulting document to the StringBuffer and return it
|
361 |
|
|
doc.append("<?xml version=\"1.0\"?>\n");
|
362 |
|
|
|
363 |
|
|
if (docname != null) {
|
364 |
|
|
if ((doctype != null) && (system_id != null)) {
|
365 |
|
|
doc.append("<!DOCTYPE " + docname + " PUBLIC \"" + doctype +
|
366 |
|
|
"\" \"" + system_id + "\">\n");
|
367 |
|
|
} else {
|
368 |
|
|
doc.append("<!DOCTYPE " + docname + ">\n");
|
369 |
|
|
}
|
370 |
|
|
}
|
371 |
|
|
doc.append(rootNode.toString());
|
372 |
|
|
|
373 |
|
|
return (doc.toString());
|
374 |
|
|
}
|
375 |
|
|
|
376 |
|
|
/**
|
377 |
429
|
jones
|
* Print a text representation of the XML document to a Writer
|
378 |
|
|
*
|
379 |
|
|
* @param pw the Writer to which we print the document
|
380 |
|
|
*/
|
381 |
800
|
jones
|
public void toXml(Writer pw) throws McdbException
|
382 |
429
|
jones
|
{
|
383 |
|
|
PrintWriter out = null;
|
384 |
|
|
if (pw instanceof PrintWriter) {
|
385 |
|
|
out = (PrintWriter)pw;
|
386 |
|
|
} else {
|
387 |
|
|
out = new PrintWriter(pw);
|
388 |
|
|
}
|
389 |
|
|
|
390 |
|
|
MetaCatUtil util = new MetaCatUtil();
|
391 |
|
|
|
392 |
800
|
jones
|
// First, check that we have the needed node data, and get it if not
|
393 |
|
|
if (nodeRecordList == null) {
|
394 |
|
|
nodeRecordList = getNodeRecordList(rootnodeid);
|
395 |
|
|
}
|
396 |
|
|
|
397 |
429
|
jones
|
Stack openElements = new Stack();
|
398 |
|
|
boolean atRootElement = true;
|
399 |
|
|
boolean previousNodeWasElement = false;
|
400 |
|
|
|
401 |
|
|
// Step through all of the node records we were given
|
402 |
|
|
Iterator it = nodeRecordList.iterator();
|
403 |
|
|
while (it.hasNext()) {
|
404 |
|
|
NodeRecord currentNode = (NodeRecord)it.next();
|
405 |
|
|
//util.debugMessage("[Got Node ID: " + currentNode.nodeid +
|
406 |
|
|
//" (" + currentNode.parentnodeid +
|
407 |
|
|
//", " + currentNode.nodeindex +
|
408 |
|
|
//", " + currentNode.nodetype +
|
409 |
|
|
//", " + currentNode.nodename +
|
410 |
|
|
//", " + currentNode.nodedata + ")]");
|
411 |
|
|
// Print the end tag for the previous node if needed
|
412 |
|
|
//
|
413 |
|
|
// This is determined by inspecting the parent nodeid for the
|
414 |
|
|
// currentNode. If it is the same as the nodeid of the last element
|
415 |
|
|
// that was pushed onto the stack, then we are still in that previous
|
416 |
|
|
// parent element, and we do nothing. However, if it differs, then we
|
417 |
|
|
// have returned to a level above the previous parent, so we go into
|
418 |
|
|
// a loop and pop off nodes and print out their end tags until we get
|
419 |
|
|
// the node on the stack to match the currentNode parentnodeid
|
420 |
|
|
//
|
421 |
|
|
// So, this of course means that we rely on the list of elements
|
422 |
|
|
// having been sorted in a depth first traversal of the nodes, which
|
423 |
|
|
// is handled by the NodeComparator class used by the TreeSet
|
424 |
|
|
if (!atRootElement) {
|
425 |
|
|
NodeRecord currentElement = (NodeRecord)openElements.peek();
|
426 |
|
|
if ( currentNode.parentnodeid != currentElement.nodeid ) {
|
427 |
|
|
while ( currentNode.parentnodeid != currentElement.nodeid ) {
|
428 |
|
|
currentElement = (NodeRecord)openElements.pop();
|
429 |
|
|
util.debugMessage("\n POPPED: " + currentElement.nodename);
|
430 |
451
|
bojilova
|
if (previousNodeWasElement) {
|
431 |
|
|
out.print(">");
|
432 |
|
|
previousNodeWasElement = false;
|
433 |
|
|
}
|
434 |
826
|
bojilova
|
if ( currentElement.nodeprefix != null ) {
|
435 |
|
|
out.print("</" + currentElement.nodeprefix + ":" +
|
436 |
|
|
currentElement.nodename + ">" );
|
437 |
|
|
} else {
|
438 |
|
|
out.print("</" + currentElement.nodename + ">" );
|
439 |
|
|
}
|
440 |
429
|
jones
|
currentElement = (NodeRecord)openElements.peek();
|
441 |
|
|
}
|
442 |
|
|
}
|
443 |
|
|
}
|
444 |
|
|
|
445 |
|
|
// Handle the DOCUMENT node
|
446 |
|
|
if (currentNode.nodetype.equals("DOCUMENT")) {
|
447 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
448 |
|
|
|
449 |
|
|
if (docname != null) {
|
450 |
|
|
if ((doctype != null) && (system_id != null)) {
|
451 |
|
|
out.println("<!DOCTYPE " + docname + " PUBLIC \"" + doctype +
|
452 |
|
|
"\" \"" + system_id + "\">");
|
453 |
|
|
} else {
|
454 |
|
|
out.println("<!DOCTYPE " + docname + ">");
|
455 |
|
|
}
|
456 |
|
|
}
|
457 |
|
|
|
458 |
|
|
// Handle the ELEMENT nodes
|
459 |
|
|
} else if (currentNode.nodetype.equals("ELEMENT")) {
|
460 |
|
|
if (atRootElement) {
|
461 |
|
|
atRootElement = false;
|
462 |
|
|
} else {
|
463 |
|
|
if (previousNodeWasElement) {
|
464 |
|
|
out.print(">");
|
465 |
|
|
}
|
466 |
|
|
}
|
467 |
|
|
openElements.push(currentNode);
|
468 |
|
|
util.debugMessage("\n PUSHED: " + currentNode.nodename);
|
469 |
|
|
previousNodeWasElement = true;
|
470 |
826
|
bojilova
|
if ( currentNode.nodeprefix != null ) {
|
471 |
|
|
out.print("<" + currentNode.nodeprefix + ":" + currentNode.nodename);
|
472 |
|
|
} else {
|
473 |
|
|
out.print("<" + currentNode.nodename);
|
474 |
|
|
}
|
475 |
429
|
jones
|
|
476 |
|
|
// Handle the ATTRIBUTE nodes
|
477 |
|
|
} else if (currentNode.nodetype.equals("ATTRIBUTE")) {
|
478 |
826
|
bojilova
|
if ( currentNode.nodeprefix != null ) {
|
479 |
|
|
out.print(" " + currentNode.nodeprefix + ":" + currentNode.nodename +
|
480 |
|
|
"=\"" + currentNode.nodedata + "\"");
|
481 |
|
|
} else {
|
482 |
|
|
out.print(" " + currentNode.nodename + "=\"" +
|
483 |
|
|
currentNode.nodedata + "\"");
|
484 |
|
|
}
|
485 |
821
|
bojilova
|
|
486 |
|
|
// Handle the NAMESPACE nodes
|
487 |
|
|
} else if (currentNode.nodetype.equals("NAMESPACE")) {
|
488 |
|
|
out.print(" xmlns:" + currentNode.nodename + "=\""
|
489 |
|
|
+ currentNode.nodedata + "\"");
|
490 |
|
|
|
491 |
|
|
// Handle the TEXT nodes
|
492 |
429
|
jones
|
} else if (currentNode.nodetype.equals("TEXT")) {
|
493 |
|
|
if (previousNodeWasElement) {
|
494 |
|
|
out.print(">");
|
495 |
|
|
}
|
496 |
|
|
out.print(currentNode.nodedata);
|
497 |
|
|
previousNodeWasElement = false;
|
498 |
|
|
|
499 |
|
|
// Handle the COMMENT nodes
|
500 |
|
|
} else if (currentNode.nodetype.equals("COMMENT")) {
|
501 |
|
|
if (previousNodeWasElement) {
|
502 |
|
|
out.print(">");
|
503 |
|
|
}
|
504 |
|
|
out.print("<!--" + currentNode.nodedata + "-->");
|
505 |
|
|
previousNodeWasElement = false;
|
506 |
|
|
|
507 |
|
|
// Handle the PI nodes
|
508 |
|
|
} else if (currentNode.nodetype.equals("PI")) {
|
509 |
|
|
if (previousNodeWasElement) {
|
510 |
|
|
out.print(">");
|
511 |
|
|
}
|
512 |
|
|
out.print("<?" + currentNode.nodename + " " +
|
513 |
|
|
currentNode.nodedata + "?>");
|
514 |
|
|
previousNodeWasElement = false;
|
515 |
|
|
|
516 |
|
|
// Handle any other node type (do nothing)
|
517 |
|
|
} else {
|
518 |
|
|
// Any other types of nodes are not handled.
|
519 |
|
|
// Probably should throw an exception here to indicate this
|
520 |
|
|
}
|
521 |
|
|
out.flush();
|
522 |
|
|
}
|
523 |
|
|
|
524 |
|
|
// Print the final end tag for the root element
|
525 |
686
|
berkley
|
while(!openElements.empty())
|
526 |
|
|
{
|
527 |
|
|
NodeRecord currentElement = (NodeRecord)openElements.pop();
|
528 |
|
|
util.debugMessage("\n POPPED: " + currentElement.nodename);
|
529 |
826
|
bojilova
|
if ( currentElement.nodeprefix != null ) {
|
530 |
|
|
out.print("</" + currentElement.nodeprefix + ":" +
|
531 |
|
|
currentElement.nodename + ">" );
|
532 |
|
|
} else {
|
533 |
|
|
out.print("</" + currentElement.nodename + ">" );
|
534 |
|
|
}
|
535 |
686
|
berkley
|
}
|
536 |
429
|
jones
|
out.flush();
|
537 |
|
|
}
|
538 |
622
|
berkley
|
|
539 |
|
|
private boolean isRevisionOnly(DocumentIdentifier docid) throws Exception
|
540 |
|
|
{
|
541 |
|
|
//System.out.println("inRevisionOnly");
|
542 |
|
|
PreparedStatement pstmt;
|
543 |
|
|
String rev = docid.getRev();
|
544 |
|
|
String newid = docid.getIdentifier();
|
545 |
|
|
pstmt = conn.prepareStatement("select rev from xml_documents " +
|
546 |
|
|
"where docid like '" + newid + "'");
|
547 |
|
|
pstmt.execute();
|
548 |
|
|
ResultSet rs = pstmt.getResultSet();
|
549 |
|
|
boolean tablehasrows = rs.next();
|
550 |
|
|
if(rev.equals("newest") || rev.equals("all"))
|
551 |
|
|
{
|
552 |
|
|
return false;
|
553 |
|
|
}
|
554 |
|
|
|
555 |
|
|
if(tablehasrows)
|
556 |
|
|
{
|
557 |
|
|
int r = rs.getInt(1);
|
558 |
667
|
berkley
|
pstmt.close();
|
559 |
622
|
berkley
|
if(new Integer(rev).intValue() == r)
|
560 |
|
|
{ //the current revision in in xml_documents
|
561 |
|
|
//System.out.println("returning false");
|
562 |
|
|
return false;
|
563 |
|
|
}
|
564 |
|
|
else if(new Integer(rev).intValue() < r)
|
565 |
|
|
{ //the current revision is in xml_revisions.
|
566 |
|
|
//System.out.println("returning true");
|
567 |
|
|
return true;
|
568 |
|
|
}
|
569 |
|
|
else if(new Integer(rev).intValue() > r)
|
570 |
|
|
{ //error, rev cannot be greater than r
|
571 |
|
|
throw new Exception("requested revision cannot be greater than " +
|
572 |
|
|
"the latest revision number.");
|
573 |
|
|
}
|
574 |
|
|
}
|
575 |
|
|
throw new Exception("the requested docid '" + docid.toString() +
|
576 |
|
|
"' does not exist");
|
577 |
|
|
}
|
578 |
429
|
jones
|
|
579 |
800
|
jones
|
private void getDocumentInfo(String docid) throws McdbException,
|
580 |
622
|
berkley
|
AccessionNumberException
|
581 |
|
|
{
|
582 |
|
|
getDocumentInfo(new DocumentIdentifier(docid));
|
583 |
|
|
}
|
584 |
|
|
|
585 |
429
|
jones
|
/**
|
586 |
393
|
jones
|
* Look up the document type information from the database
|
587 |
|
|
*
|
588 |
|
|
* @param docid the id of the document to look up
|
589 |
|
|
*/
|
590 |
622
|
berkley
|
private void getDocumentInfo(DocumentIdentifier docid) throws McdbException
|
591 |
393
|
jones
|
{
|
592 |
|
|
PreparedStatement pstmt;
|
593 |
622
|
berkley
|
String table = "xml_documents";
|
594 |
|
|
|
595 |
|
|
try
|
596 |
|
|
{
|
597 |
|
|
if(isRevisionOnly(docid))
|
598 |
|
|
{ //pull the document from xml_revisions instead of from xml_documents;
|
599 |
|
|
table = "xml_revisions";
|
600 |
|
|
}
|
601 |
|
|
}
|
602 |
|
|
catch(Exception e)
|
603 |
|
|
{
|
604 |
675
|
berkley
|
System.out.println("error in DocumentImpl.getDocumentInfo: " +
|
605 |
|
|
e.getMessage());
|
606 |
622
|
berkley
|
}
|
607 |
|
|
|
608 |
|
|
//deal with the key words here.
|
609 |
|
|
|
610 |
|
|
if(docid.getRev().equals("all"))
|
611 |
|
|
{
|
612 |
|
|
|
613 |
|
|
}
|
614 |
|
|
|
615 |
393
|
jones
|
try {
|
616 |
622
|
berkley
|
StringBuffer sql = new StringBuffer();
|
617 |
691
|
bojilova
|
// DOCTITLE attr cleared from the db
|
618 |
|
|
// sql.append("SELECT docname, doctype, rootnodeid, doctitle, ");
|
619 |
|
|
sql.append("SELECT docname, doctype, rootnodeid, ");
|
620 |
697
|
bojilova
|
sql.append("date_created, date_updated, user_owner, user_updated, ");
|
621 |
|
|
sql.append("server_location, public_access, rev");
|
622 |
|
|
sql.append(" FROM ").append(table);
|
623 |
622
|
berkley
|
sql.append(" WHERE docid LIKE '").append(docid.getIdentifier());
|
624 |
|
|
sql.append("' and rev like '").append(docid.getRev()).append("'");
|
625 |
|
|
//System.out.println(sql.toString());
|
626 |
393
|
jones
|
pstmt =
|
627 |
622
|
berkley
|
conn.prepareStatement(sql.toString());
|
628 |
393
|
jones
|
// Bind the values to the query
|
629 |
622
|
berkley
|
//pstmt.setString(1, docid.getIdentifier());
|
630 |
|
|
//pstmt.setString(2, docid.getRev());
|
631 |
393
|
jones
|
|
632 |
|
|
pstmt.execute();
|
633 |
|
|
ResultSet rs = pstmt.getResultSet();
|
634 |
|
|
boolean tableHasRows = rs.next();
|
635 |
|
|
if (tableHasRows) {
|
636 |
561
|
berkley
|
this.docname = rs.getString(1);
|
637 |
|
|
this.doctype = rs.getString(2);
|
638 |
|
|
this.rootnodeid = rs.getLong(3);
|
639 |
691
|
bojilova
|
// DOCTITLE attr cleared from the db
|
640 |
|
|
// this.doctitle = rs.getString(4);
|
641 |
692
|
bojilova
|
this.createdate = rs.getString(4);
|
642 |
|
|
this.updatedate = rs.getString(5);
|
643 |
|
|
this.userowner = rs.getString(6);
|
644 |
|
|
this.userupdated = rs.getString(7);
|
645 |
|
|
this.serverlocation = rs.getInt(8);
|
646 |
697
|
bojilova
|
this.publicaccess = rs.getString(9);
|
647 |
|
|
this.rev = rs.getInt(10);
|
648 |
393
|
jones
|
}
|
649 |
818
|
berkley
|
pstmt.close();
|
650 |
393
|
jones
|
if (this.doctype != null) {
|
651 |
|
|
pstmt =
|
652 |
|
|
conn.prepareStatement("SELECT system_id " +
|
653 |
|
|
"FROM xml_catalog " +
|
654 |
769
|
bojilova
|
"WHERE public_id = ?");
|
655 |
393
|
jones
|
// Bind the values to the query
|
656 |
|
|
pstmt.setString(1, doctype);
|
657 |
|
|
|
658 |
|
|
pstmt.execute();
|
659 |
|
|
rs = pstmt.getResultSet();
|
660 |
|
|
tableHasRows = rs.next();
|
661 |
|
|
if (tableHasRows) {
|
662 |
|
|
this.system_id = rs.getString(1);
|
663 |
|
|
}
|
664 |
818
|
berkley
|
pstmt.close();
|
665 |
393
|
jones
|
}
|
666 |
|
|
} catch (SQLException e) {
|
667 |
675
|
berkley
|
System.out.println("error in DocumentImpl.getDocumentInfo: " +
|
668 |
|
|
e.getMessage());
|
669 |
622
|
berkley
|
e.printStackTrace(System.out);
|
670 |
675
|
berkley
|
throw new McdbException("Error accessing database connection in " +
|
671 |
|
|
"DocumentImpl.getDocumentInfo: ", e);
|
672 |
393
|
jones
|
}
|
673 |
|
|
|
674 |
|
|
if (this.docname == null) {
|
675 |
|
|
throw new McdbDocNotFoundException("Document not found: " + docid);
|
676 |
|
|
}
|
677 |
|
|
}
|
678 |
|
|
|
679 |
|
|
/**
|
680 |
|
|
* Look up the node data from the database
|
681 |
|
|
*
|
682 |
396
|
jones
|
* @param rootnodeid the id of the root node of the node tree to look up
|
683 |
393
|
jones
|
*/
|
684 |
396
|
jones
|
private TreeSet getNodeRecordList(long rootnodeid) throws McdbException
|
685 |
393
|
jones
|
{
|
686 |
|
|
PreparedStatement pstmt;
|
687 |
|
|
TreeSet nodeRecordList = new TreeSet(new NodeComparator());
|
688 |
|
|
long nodeid = 0;
|
689 |
|
|
long parentnodeid = 0;
|
690 |
|
|
long nodeindex = 0;
|
691 |
|
|
String nodetype = null;
|
692 |
|
|
String nodename = null;
|
693 |
826
|
bojilova
|
String nodeprefix = null;
|
694 |
393
|
jones
|
String nodedata = null;
|
695 |
|
|
|
696 |
|
|
try {
|
697 |
|
|
pstmt =
|
698 |
|
|
conn.prepareStatement("SELECT nodeid,parentnodeid,nodeindex, " +
|
699 |
826
|
bojilova
|
"nodetype,nodename,nodeprefix,"+
|
700 |
393
|
jones
|
"replace(" +
|
701 |
|
|
"replace(" +
|
702 |
|
|
"replace(nodedata,'&','&') " +
|
703 |
|
|
",'<','<') " +
|
704 |
|
|
",'>','>') " +
|
705 |
396
|
jones
|
"FROM xml_nodes WHERE rootnodeid = ?");
|
706 |
393
|
jones
|
|
707 |
|
|
// Bind the values to the query
|
708 |
396
|
jones
|
pstmt.setLong(1, rootnodeid);
|
709 |
393
|
jones
|
|
710 |
|
|
pstmt.execute();
|
711 |
|
|
ResultSet rs = pstmt.getResultSet();
|
712 |
|
|
boolean tableHasRows = rs.next();
|
713 |
|
|
while (tableHasRows) {
|
714 |
|
|
nodeid = rs.getLong(1);
|
715 |
|
|
parentnodeid = rs.getLong(2);
|
716 |
|
|
nodeindex = rs.getLong(3);
|
717 |
|
|
nodetype = rs.getString(4);
|
718 |
|
|
nodename = rs.getString(5);
|
719 |
826
|
bojilova
|
nodeprefix = rs.getString(6);
|
720 |
|
|
nodedata = rs.getString(7);
|
721 |
393
|
jones
|
|
722 |
|
|
// add the data to the node record list hashtable
|
723 |
826
|
bojilova
|
NodeRecord currentRecord = new NodeRecord(nodeid,parentnodeid,nodeindex,
|
724 |
|
|
nodetype, nodename, nodeprefix, nodedata);
|
725 |
393
|
jones
|
nodeRecordList.add(currentRecord);
|
726 |
|
|
|
727 |
|
|
// Advance to the next node
|
728 |
|
|
tableHasRows = rs.next();
|
729 |
|
|
}
|
730 |
|
|
pstmt.close();
|
731 |
|
|
|
732 |
|
|
} catch (SQLException e) {
|
733 |
826
|
bojilova
|
throw new McdbException("Error in DocumentImpl.getNodeRecordList " +
|
734 |
|
|
e.getMessage());
|
735 |
393
|
jones
|
}
|
736 |
|
|
|
737 |
|
|
if (nodeRecordList != null) {
|
738 |
|
|
return nodeRecordList;
|
739 |
|
|
} else {
|
740 |
|
|
throw new McdbException("Error getting node data: " + docid);
|
741 |
|
|
}
|
742 |
|
|
}
|
743 |
549
|
berkley
|
|
744 |
697
|
bojilova
|
// NOT USED ANY MORE
|
745 |
|
|
// /** creates SQL code and inserts new document into DB connection
|
746 |
|
|
// default serverCode of 1*/
|
747 |
|
|
// private void writeDocumentToDB(String action, String user)
|
748 |
|
|
// throws SQLException, Exception
|
749 |
|
|
// {
|
750 |
|
|
// writeDocumentToDB(action, user, null, 1);
|
751 |
|
|
// }
|
752 |
393
|
jones
|
|
753 |
459
|
bojilova
|
/** creates SQL code and inserts new document into DB connection */
|
754 |
680
|
bojilova
|
private void writeDocumentToDB(String action, String user, String pub,
|
755 |
697
|
bojilova
|
String catalogid, int serverCode)
|
756 |
459
|
bojilova
|
throws SQLException, Exception {
|
757 |
747
|
bojilova
|
|
758 |
754
|
bojilova
|
String sysdate = dbAdapter.getDateTimeFunction();
|
759 |
747
|
bojilova
|
|
760 |
459
|
bojilova
|
try {
|
761 |
|
|
PreparedStatement pstmt = null;
|
762 |
|
|
|
763 |
|
|
if (action.equals("INSERT")) {
|
764 |
|
|
//AccessionNumber ac = new AccessionNumber();
|
765 |
|
|
//this.docid = ac.generate(docid, "INSERT");
|
766 |
|
|
pstmt = conn.prepareStatement(
|
767 |
697
|
bojilova
|
"INSERT INTO xml_documents " +
|
768 |
|
|
"(docid, rootnodeid, docname, doctype, " +
|
769 |
|
|
"user_owner, user_updated, date_created, date_updated, " +
|
770 |
|
|
"public_access, catalog_id, server_location) " +
|
771 |
747
|
bojilova
|
"VALUES (?, ?, ?, ?, ?, ?, " + sysdate + ", " + sysdate +
|
772 |
|
|
", ?, ?, ?)");
|
773 |
549
|
berkley
|
//note that the server_location is set to 1.
|
774 |
|
|
//this means that "localhost" in the xml_replication table must
|
775 |
|
|
//always be the first entry!!!!!
|
776 |
|
|
|
777 |
459
|
bojilova
|
// Bind the values to the query
|
778 |
|
|
pstmt.setString(1, this.docid);
|
779 |
|
|
pstmt.setLong(2, rootnodeid);
|
780 |
|
|
pstmt.setString(3, docname);
|
781 |
|
|
pstmt.setString(4, doctype);
|
782 |
|
|
pstmt.setString(5, user);
|
783 |
|
|
pstmt.setString(6, user);
|
784 |
680
|
bojilova
|
if ( pub == null ) {
|
785 |
|
|
pstmt.setString(7, null);
|
786 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
|
787 |
680
|
bojilova
|
pstmt.setInt(7, 1);
|
788 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
|
789 |
680
|
bojilova
|
pstmt.setInt(7, 0);
|
790 |
|
|
}
|
791 |
697
|
bojilova
|
pstmt.setString(8, catalogid);
|
792 |
|
|
pstmt.setInt(9, serverCode);
|
793 |
459
|
bojilova
|
} else if (action.equals("UPDATE")) {
|
794 |
|
|
|
795 |
|
|
// Save the old document entry in a backup table
|
796 |
|
|
DocumentImpl.archiveDocRevision( conn, docid, user );
|
797 |
575
|
berkley
|
DocumentImpl thisdoc = new DocumentImpl(conn, docid);
|
798 |
|
|
int thisrev = thisdoc.getRev();
|
799 |
|
|
thisrev++;
|
800 |
459
|
bojilova
|
// Delete index for the old version of docid
|
801 |
|
|
// The new index is inserting on the next calls to DBSAXNode
|
802 |
|
|
pstmt = conn.prepareStatement(
|
803 |
|
|
"DELETE FROM xml_index WHERE docid='" + this.docid + "'");
|
804 |
|
|
pstmt.execute();
|
805 |
818
|
berkley
|
pstmt.close();
|
806 |
459
|
bojilova
|
|
807 |
|
|
// Update the new document to reflect the new node tree
|
808 |
|
|
pstmt = conn.prepareStatement(
|
809 |
|
|
"UPDATE xml_documents " +
|
810 |
|
|
"SET rootnodeid = ?, docname = ?, doctype = ?, " +
|
811 |
747
|
bojilova
|
"user_updated = ?, date_updated = " + sysdate + ", " +
|
812 |
697
|
bojilova
|
"server_location = ?, rev = ?, public_access = ?, catalog_id = ? " +
|
813 |
769
|
bojilova
|
"WHERE docid = ?");
|
814 |
459
|
bojilova
|
// Bind the values to the query
|
815 |
|
|
pstmt.setLong(1, rootnodeid);
|
816 |
|
|
pstmt.setString(2, docname);
|
817 |
|
|
pstmt.setString(3, doctype);
|
818 |
|
|
pstmt.setString(4, user);
|
819 |
549
|
berkley
|
pstmt.setInt(5, serverCode);
|
820 |
575
|
berkley
|
pstmt.setInt(6, thisrev);
|
821 |
680
|
bojilova
|
if ( pub == null ) {
|
822 |
|
|
pstmt.setString(7, null);
|
823 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
|
824 |
680
|
bojilova
|
pstmt .setInt(7, 1);
|
825 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
|
826 |
680
|
bojilova
|
pstmt.setInt(7, 0);
|
827 |
|
|
}
|
828 |
697
|
bojilova
|
pstmt.setString(8, catalogid);
|
829 |
|
|
pstmt.setString(9, this.docid);
|
830 |
575
|
berkley
|
|
831 |
459
|
bojilova
|
} else {
|
832 |
|
|
System.err.println("Action not supported: " + action);
|
833 |
|
|
}
|
834 |
|
|
|
835 |
|
|
// Do the insertion
|
836 |
|
|
pstmt.execute();
|
837 |
|
|
pstmt.close();
|
838 |
|
|
|
839 |
|
|
} catch (SQLException sqle) {
|
840 |
|
|
throw sqle;
|
841 |
|
|
} catch (Exception e) {
|
842 |
|
|
throw e;
|
843 |
|
|
}
|
844 |
|
|
}
|
845 |
|
|
|
846 |
|
|
/**
|
847 |
407
|
jones
|
* Write an XML file to the database, given a filename
|
848 |
393
|
jones
|
*
|
849 |
408
|
jones
|
* @param conn the JDBC connection to the database
|
850 |
407
|
jones
|
* @param filename the filename to be loaded into the database
|
851 |
680
|
bojilova
|
* @param pub flag for public "read" access on document
|
852 |
|
|
* @param dtdfilename the dtd to be uploaded on server's file system
|
853 |
407
|
jones
|
* @param action the action to be performed (INSERT OR UPDATE)
|
854 |
|
|
* @param docid the docid to use for the INSERT OR UPDATE
|
855 |
680
|
bojilova
|
* @param user the user that owns the document
|
856 |
802
|
bojilova
|
* @param groups the groups to which user belongs
|
857 |
393
|
jones
|
*/
|
858 |
598
|
bojilova
|
public static String write(Connection conn,String filename,
|
859 |
680
|
bojilova
|
String pub, String dtdfilename,
|
860 |
598
|
bojilova
|
String action, String docid, String user,
|
861 |
802
|
bojilova
|
String[] groups )
|
862 |
457
|
bojilova
|
throws Exception {
|
863 |
598
|
bojilova
|
|
864 |
|
|
Reader dtd = null;
|
865 |
|
|
if ( dtdfilename != null ) {
|
866 |
|
|
dtd = new FileReader(new File(dtdfilename).toString());
|
867 |
|
|
}
|
868 |
555
|
bojilova
|
return write ( conn, new FileReader(new File(filename).toString()),
|
869 |
802
|
bojilova
|
pub, dtd, action, docid, user, groups, false);
|
870 |
407
|
jones
|
}
|
871 |
598
|
bojilova
|
|
872 |
680
|
bojilova
|
public static String write(Connection conn,Reader xml,String pub,Reader dtd,
|
873 |
598
|
bojilova
|
String action, String docid, String user,
|
874 |
802
|
bojilova
|
String[] groups, boolean validate)
|
875 |
549
|
berkley
|
throws Exception {
|
876 |
802
|
bojilova
|
return write(conn,xml,pub,dtd,action,docid,user,groups,1,false,validate);
|
877 |
598
|
bojilova
|
}
|
878 |
|
|
|
879 |
680
|
bojilova
|
public static String write(Connection conn, Reader xml, String pub,
|
880 |
598
|
bojilova
|
String action, String docid, String user,
|
881 |
802
|
bojilova
|
String[] groups )
|
882 |
598
|
bojilova
|
throws Exception {
|
883 |
571
|
berkley
|
if(action.equals("UPDATE"))
|
884 |
|
|
{//if the document is being updated then use the servercode from the
|
885 |
|
|
//originally inserted document.
|
886 |
|
|
DocumentImpl doc = new DocumentImpl(conn, docid);
|
887 |
|
|
int servercode = doc.getServerlocation();
|
888 |
802
|
bojilova
|
return write(conn, xml, pub, action, docid, user, groups, servercode);
|
889 |
571
|
berkley
|
}
|
890 |
|
|
else
|
891 |
|
|
{//if the file is being inserted then the servercode is always 1
|
892 |
802
|
bojilova
|
return write(conn, xml, pub, action, docid, user, groups, 1);
|
893 |
571
|
berkley
|
}
|
894 |
549
|
berkley
|
}
|
895 |
|
|
|
896 |
559
|
berkley
|
public static String write( Connection conn, Reader xml,
|
897 |
|
|
String action, String docid, String user,
|
898 |
802
|
bojilova
|
String[] groups, int serverCode )
|
899 |
598
|
bojilova
|
throws Exception
|
900 |
559
|
berkley
|
{
|
901 |
802
|
bojilova
|
return write(conn,xml,null,action,docid,user,groups,serverCode);
|
902 |
559
|
berkley
|
}
|
903 |
|
|
|
904 |
680
|
bojilova
|
public static String write( Connection conn, Reader xml, String pub,
|
905 |
577
|
berkley
|
String action, String docid, String user,
|
906 |
802
|
bojilova
|
String[] groups, int serverCode)
|
907 |
598
|
bojilova
|
throws Exception
|
908 |
577
|
berkley
|
{
|
909 |
802
|
bojilova
|
return write(conn,xml,pub,null,action,docid,user,groups,
|
910 |
695
|
bojilova
|
serverCode,false,false);
|
911 |
577
|
berkley
|
}
|
912 |
|
|
|
913 |
680
|
bojilova
|
public static String write( Connection conn, Reader xml, String pub,
|
914 |
600
|
bojilova
|
String action, String docid, String user,
|
915 |
802
|
bojilova
|
String[] groups, int serverCode, boolean override)
|
916 |
600
|
bojilova
|
throws Exception
|
917 |
|
|
{
|
918 |
802
|
bojilova
|
return write(conn,xml,pub,null,action,docid,user,groups,
|
919 |
695
|
bojilova
|
serverCode,override,false);
|
920 |
600
|
bojilova
|
}
|
921 |
|
|
|
922 |
407
|
jones
|
/**
|
923 |
|
|
* Write an XML file to the database, given a Reader
|
924 |
|
|
*
|
925 |
408
|
jones
|
* @param conn the JDBC connection to the database
|
926 |
407
|
jones
|
* @param xml the xml stream to be loaded into the database
|
927 |
680
|
bojilova
|
* @param pub flag for public "read" access on xml document
|
928 |
|
|
* @param dtd the dtd to be uploaded on server's file system
|
929 |
734
|
bojilova
|
* @param action the action to be performed (INSERT or UPDATE)
|
930 |
|
|
* @param accnum the docid + rev# to use on INSERT or UPDATE
|
931 |
580
|
berkley
|
* @param user the user that owns the document
|
932 |
802
|
bojilova
|
* @param groups the groups to which user belongs
|
933 |
580
|
berkley
|
* @param serverCode the serverid from xml_replication on which this document
|
934 |
|
|
* resides.
|
935 |
|
|
* @param override flag to stop insert replication checking.
|
936 |
|
|
* if override = true then a document not belonging to the local server
|
937 |
|
|
* will not be checked upon update for a file lock.
|
938 |
|
|
* if override = false then a document not from this server, upon
|
939 |
|
|
* update will be locked and version checked.
|
940 |
407
|
jones
|
*/
|
941 |
559
|
berkley
|
|
942 |
680
|
bojilova
|
public static String write( Connection conn,Reader xml,String pub,Reader dtd,
|
943 |
734
|
bojilova
|
String action, String accnum, String user,
|
944 |
802
|
bojilova
|
String[] groups, int serverCode, boolean override,
|
945 |
695
|
bojilova
|
boolean validate)
|
946 |
598
|
bojilova
|
throws Exception
|
947 |
573
|
berkley
|
{
|
948 |
779
|
bojilova
|
// NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
|
949 |
|
|
AccessionNumber ac = new AccessionNumber(conn, accnum, action);
|
950 |
|
|
String docid = ac.getDocid();
|
951 |
|
|
String rev = ac.getRev();
|
952 |
|
|
|
953 |
590
|
berkley
|
MetaCatUtil.debugMessage("action: " + action + " servercode: " +
|
954 |
|
|
serverCode + " override: " + override);
|
955 |
580
|
berkley
|
|
956 |
577
|
berkley
|
if((serverCode != 1 && action.equals("UPDATE")) && !override)
|
957 |
559
|
berkley
|
{ //if this document being written is not a resident of this server then
|
958 |
|
|
//we need to try to get a lock from it's resident server. If the
|
959 |
|
|
//resident server will not give a lock then we send the user a message
|
960 |
|
|
//saying that he/she needs to download a new copy of the file and
|
961 |
|
|
//merge the differences manually.
|
962 |
567
|
berkley
|
int istreamInt;
|
963 |
561
|
berkley
|
char istreamChar;
|
964 |
779
|
bojilova
|
DocumentIdentifier id = new DocumentIdentifier(accnum);
|
965 |
|
|
String updaterev = id.getRev();
|
966 |
561
|
berkley
|
String server = MetacatReplication.getServer(serverCode);
|
967 |
734
|
bojilova
|
MetacatReplication.replLog("attempting to lock " + accnum);
|
968 |
837
|
bojilova
|
URL u = new URL("https://" + server + "?action=getlock&updaterev=" +
|
969 |
779
|
bojilova
|
updaterev + "&docid=" + docid);
|
970 |
574
|
berkley
|
System.out.println("sending message: " + u.toString());
|
971 |
569
|
berkley
|
String serverResStr = MetacatReplication.getURLContent(u);
|
972 |
567
|
berkley
|
String openingtag = serverResStr.substring(0, serverResStr.indexOf(">")+1);
|
973 |
571
|
berkley
|
|
974 |
561
|
berkley
|
if(openingtag.equals("<lockgranted>"))
|
975 |
|
|
{//the lock was granted go ahead with the insert
|
976 |
571
|
berkley
|
try
|
977 |
|
|
{
|
978 |
734
|
bojilova
|
MetacatReplication.replLog("lock granted for " + accnum + " from " +
|
979 |
584
|
berkley
|
server);
|
980 |
734
|
bojilova
|
XMLReader parser = initializeParser(conn, action, docid, validate,
|
981 |
802
|
bojilova
|
user, groups, pub, serverCode, dtd);
|
982 |
571
|
berkley
|
conn.setAutoCommit(false);
|
983 |
695
|
bojilova
|
parser.parse(new InputSource(xml));
|
984 |
571
|
berkley
|
conn.commit();
|
985 |
|
|
conn.setAutoCommit(true);
|
986 |
|
|
}
|
987 |
|
|
catch (Exception e)
|
988 |
|
|
{
|
989 |
|
|
conn.rollback();
|
990 |
|
|
conn.setAutoCommit(true);
|
991 |
|
|
throw e;
|
992 |
|
|
}
|
993 |
|
|
|
994 |
|
|
//after inserting the document locally, tell the document's home server
|
995 |
|
|
//to come get a copy from here.
|
996 |
835
|
bojilova
|
ForceReplicationHandler frh = new ForceReplicationHandler(accnum);
|
997 |
590
|
berkley
|
|
998 |
779
|
bojilova
|
return (accnum);
|
999 |
561
|
berkley
|
}
|
1000 |
734
|
bojilova
|
|
1001 |
561
|
berkley
|
else if(openingtag.equals("<filelocked>"))
|
1002 |
|
|
{//the file is currently locked by another user
|
1003 |
|
|
//notify our user to wait a few minutes, check out a new copy and try
|
1004 |
|
|
//again.
|
1005 |
584
|
berkley
|
//System.out.println("file locked");
|
1006 |
734
|
bojilova
|
MetacatReplication.replLog("lock denied for " + accnum + " on " +
|
1007 |
584
|
berkley
|
server + " reason: file already locked");
|
1008 |
571
|
berkley
|
throw new Exception("The file specified is already locked by another " +
|
1009 |
|
|
"user. Please wait 30 seconds, checkout the " +
|
1010 |
|
|
"newer document, merge your changes and try " +
|
1011 |
|
|
"again.");
|
1012 |
561
|
berkley
|
}
|
1013 |
|
|
else if(openingtag.equals("<outdatedfile>"))
|
1014 |
|
|
{//our file is outdated. notify our user to check out a new copy of the
|
1015 |
|
|
//file and merge his version with the new version.
|
1016 |
584
|
berkley
|
//System.out.println("outdated file");
|
1017 |
734
|
bojilova
|
MetacatReplication.replLog("lock denied for " + accnum + " on " +
|
1018 |
584
|
berkley
|
server + " reason: local file outdated");
|
1019 |
571
|
berkley
|
throw new Exception("The file you are trying to update is an outdated" +
|
1020 |
|
|
" version. Please checkout the newest document, " +
|
1021 |
|
|
"merge your changes and try again.");
|
1022 |
561
|
berkley
|
}
|
1023 |
559
|
berkley
|
}
|
1024 |
571
|
berkley
|
|
1025 |
425
|
bojilova
|
if ( action.equals("UPDATE") ) {
|
1026 |
441
|
bojilova
|
// check for 'write' permission for 'user' to update this document
|
1027 |
628
|
berkley
|
|
1028 |
802
|
bojilova
|
if ( !hasPermission(conn, user, groups, docid) ) {
|
1029 |
441
|
bojilova
|
throw new Exception("User " + user +
|
1030 |
734
|
bojilova
|
" does not have permission to update XML Document #" + accnum);
|
1031 |
425
|
bojilova
|
}
|
1032 |
|
|
}
|
1033 |
|
|
|
1034 |
571
|
berkley
|
try
|
1035 |
638
|
bojilova
|
{
|
1036 |
734
|
bojilova
|
XMLReader parser = initializeParser(conn, action, docid, validate,
|
1037 |
802
|
bojilova
|
user, groups, pub, serverCode, dtd);
|
1038 |
555
|
bojilova
|
conn.setAutoCommit(false);
|
1039 |
|
|
parser.parse(new InputSource(xml));
|
1040 |
|
|
conn.commit();
|
1041 |
|
|
conn.setAutoCommit(true);
|
1042 |
571
|
berkley
|
}
|
1043 |
|
|
catch (Exception e)
|
1044 |
|
|
{
|
1045 |
555
|
bojilova
|
conn.rollback();
|
1046 |
|
|
conn.setAutoCommit(true);
|
1047 |
|
|
throw e;
|
1048 |
|
|
}
|
1049 |
577
|
berkley
|
|
1050 |
|
|
//force replicate out the new document to each server in our server list.
|
1051 |
|
|
if(serverCode == 1)
|
1052 |
582
|
berkley
|
{ //start the thread to replicate this new document out to the other servers
|
1053 |
835
|
bojilova
|
ForceReplicationHandler frh = new ForceReplicationHandler(accnum, action);
|
1054 |
577
|
berkley
|
}
|
1055 |
457
|
bojilova
|
|
1056 |
779
|
bojilova
|
return(accnum);
|
1057 |
393
|
jones
|
}
|
1058 |
396
|
jones
|
|
1059 |
407
|
jones
|
/**
|
1060 |
|
|
* Delete an XML file from the database (actually, just make it a revision
|
1061 |
|
|
* in the xml_revisions table)
|
1062 |
|
|
*
|
1063 |
|
|
* @param docid the ID of the document to be deleted from the database
|
1064 |
|
|
*/
|
1065 |
734
|
bojilova
|
public static void delete( Connection conn, String accnum,
|
1066 |
802
|
bojilova
|
String user, String[] groups )
|
1067 |
734
|
bojilova
|
throws Exception
|
1068 |
|
|
{
|
1069 |
779
|
bojilova
|
// OLD
|
1070 |
|
|
//DocumentIdentifier id = new DocumentIdentifier(accnum);
|
1071 |
|
|
//String docid = id.getIdentifier();
|
1072 |
|
|
//String rev = id.getRev();
|
1073 |
628
|
berkley
|
|
1074 |
779
|
bojilova
|
// OLD
|
1075 |
734
|
bojilova
|
// Determine if the docid,rev are OK for DELETE
|
1076 |
779
|
bojilova
|
//AccessionNumber ac = new AccessionNumber(conn);
|
1077 |
|
|
//docid = ac.generate(docid, rev, "DELETE");
|
1078 |
396
|
jones
|
|
1079 |
779
|
bojilova
|
// NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
|
1080 |
|
|
AccessionNumber ac = new AccessionNumber(conn, accnum, "DELETE");
|
1081 |
|
|
String docid = ac.getDocid();
|
1082 |
|
|
String rev = ac.getRev();
|
1083 |
|
|
|
1084 |
|
|
|
1085 |
441
|
bojilova
|
// check for 'write' permission for 'user' to delete this document
|
1086 |
802
|
bojilova
|
if ( !hasPermission(conn, user, groups, docid) ) {
|
1087 |
441
|
bojilova
|
throw new Exception("User " + user +
|
1088 |
734
|
bojilova
|
" does not have permission to delete XML Document #" + accnum);
|
1089 |
425
|
bojilova
|
}
|
1090 |
|
|
|
1091 |
407
|
jones
|
conn.setAutoCommit(false);
|
1092 |
|
|
// Copy the record to the xml_revisions table
|
1093 |
425
|
bojilova
|
DocumentImpl.archiveDocRevision( conn, docid, user );
|
1094 |
396
|
jones
|
|
1095 |
407
|
jones
|
// Now delete it from the xml_documents table
|
1096 |
628
|
berkley
|
|
1097 |
407
|
jones
|
Statement stmt = conn.createStatement();
|
1098 |
425
|
bojilova
|
stmt.execute("DELETE FROM xml_index WHERE docid = '" + docid + "'");
|
1099 |
688
|
bojilova
|
//stmt.execute("DELETE FROM xml_access WHERE docid = '" + docid + "'");
|
1100 |
645
|
bojilova
|
stmt.execute("DELETE FROM xml_access WHERE accessfileid = '" + docid + "'");
|
1101 |
|
|
stmt.execute("DELETE FROM xml_relation WHERE docid = '" + docid + "'");
|
1102 |
785
|
bojilova
|
stmt.execute("DELETE FROM xml_documents WHERE docid = '" + docid + "'");
|
1103 |
407
|
jones
|
stmt.close();
|
1104 |
|
|
conn.commit();
|
1105 |
457
|
bojilova
|
conn.setAutoCommit(true);
|
1106 |
634
|
berkley
|
//IF this is a package document:
|
1107 |
|
|
//delete all of the relations that this document created.
|
1108 |
|
|
//if the deleted document is a package document its relations should
|
1109 |
|
|
//no longer be active if it has been deleted from the system.
|
1110 |
645
|
bojilova
|
|
1111 |
407
|
jones
|
}
|
1112 |
638
|
bojilova
|
|
1113 |
570
|
bojilova
|
/**
|
1114 |
802
|
bojilova
|
* Check for "WRITE" permission on @docid for @user and/or @groups
|
1115 |
570
|
bojilova
|
* from DB connection
|
1116 |
|
|
*/
|
1117 |
802
|
bojilova
|
private static boolean hasPermission ( Connection conn, String user,
|
1118 |
|
|
String[] groups, String docid )
|
1119 |
|
|
throws SQLException
|
1120 |
570
|
bojilova
|
{
|
1121 |
802
|
bojilova
|
// Check for WRITE permission on @docid for @user and/or @groups
|
1122 |
570
|
bojilova
|
AccessControlList aclobj = new AccessControlList(conn);
|
1123 |
802
|
bojilova
|
return aclobj.hasPermission("WRITE", user, groups, docid);
|
1124 |
425
|
bojilova
|
}
|
1125 |
|
|
|
1126 |
396
|
jones
|
/**
|
1127 |
407
|
jones
|
* Set up the parser handlers for writing the document to the database
|
1128 |
|
|
*/
|
1129 |
598
|
bojilova
|
private static XMLReader initializeParser(Connection conn, String action,
|
1130 |
695
|
bojilova
|
String docid, boolean validate,
|
1131 |
802
|
bojilova
|
String user, String[] groups, String pub,
|
1132 |
695
|
bojilova
|
int serverCode, Reader dtd)
|
1133 |
598
|
bojilova
|
throws Exception
|
1134 |
|
|
{
|
1135 |
407
|
jones
|
XMLReader parser = null;
|
1136 |
|
|
//
|
1137 |
|
|
// Set up the SAX document handlers for parsing
|
1138 |
|
|
//
|
1139 |
|
|
try {
|
1140 |
645
|
bojilova
|
ContentHandler chandler = new DBSAXHandler(conn, action, docid,
|
1141 |
802
|
bojilova
|
user, groups, pub, serverCode);
|
1142 |
645
|
bojilova
|
EntityResolver eresolver= new DBEntityResolver(conn,
|
1143 |
|
|
(DBSAXHandler)chandler, dtd);
|
1144 |
598
|
bojilova
|
DTDHandler dtdhandler = new DBDTDHandler(conn);
|
1145 |
407
|
jones
|
|
1146 |
|
|
// Get an instance of the parser
|
1147 |
802
|
bojilova
|
String parserName = MetaCatUtil.getOption("saxparser");
|
1148 |
407
|
jones
|
parser = XMLReaderFactory.createXMLReader(parserName);
|
1149 |
|
|
|
1150 |
660
|
bojilova
|
// Turn on validation
|
1151 |
695
|
bojilova
|
parser.setFeature("http://xml.org/sax/features/validation", validate);
|
1152 |
660
|
bojilova
|
// Turn off Including all external parameter entities
|
1153 |
|
|
// (the external DTD subset also)
|
1154 |
|
|
// Doesn't work well, probably the feature name is not correct
|
1155 |
|
|
// parser.setFeature(
|
1156 |
|
|
// "http://xml.org/sax/features/external-parameter-entities", false);
|
1157 |
407
|
jones
|
|
1158 |
|
|
// Set Handlers in the parser
|
1159 |
|
|
parser.setProperty("http://xml.org/sax/properties/declaration-handler",
|
1160 |
|
|
chandler);
|
1161 |
|
|
parser.setProperty("http://xml.org/sax/properties/lexical-handler",
|
1162 |
|
|
chandler);
|
1163 |
|
|
parser.setContentHandler((ContentHandler)chandler);
|
1164 |
598
|
bojilova
|
parser.setEntityResolver((EntityResolver)eresolver);
|
1165 |
407
|
jones
|
parser.setDTDHandler((DTDHandler)dtdhandler);
|
1166 |
|
|
parser.setErrorHandler((ErrorHandler)chandler);
|
1167 |
|
|
|
1168 |
|
|
} catch (Exception e) {
|
1169 |
457
|
bojilova
|
throw e;
|
1170 |
407
|
jones
|
}
|
1171 |
|
|
|
1172 |
|
|
return parser;
|
1173 |
|
|
}
|
1174 |
|
|
|
1175 |
459
|
bojilova
|
/** Save a document entry in the xml_revisions table */
|
1176 |
|
|
private static void archiveDocRevision(Connection conn, String docid,
|
1177 |
552
|
berkley
|
String user)
|
1178 |
|
|
throws SQLException {
|
1179 |
754
|
bojilova
|
String sysdate = dbAdapter.getDateTimeFunction();
|
1180 |
747
|
bojilova
|
|
1181 |
459
|
bojilova
|
// create a record in xml_revisions table
|
1182 |
|
|
// for that document as selected from xml_documents
|
1183 |
|
|
PreparedStatement pstmt = conn.prepareStatement(
|
1184 |
|
|
"INSERT INTO xml_revisions " +
|
1185 |
771
|
bojilova
|
"(docid, rootnodeid, docname, doctype, " +
|
1186 |
697
|
bojilova
|
"user_owner, user_updated, date_created, date_updated, " +
|
1187 |
|
|
"server_location, rev, public_access, catalog_id) " +
|
1188 |
771
|
bojilova
|
"SELECT ?, rootnodeid, docname, doctype, " +
|
1189 |
747
|
bojilova
|
"user_owner, ?, " + sysdate + ", " + sysdate + ", "+
|
1190 |
|
|
"server_location, rev, public_access, catalog_id " +
|
1191 |
459
|
bojilova
|
"FROM xml_documents " +
|
1192 |
|
|
"WHERE docid = ?");
|
1193 |
|
|
// Bind the values to the query and execute it
|
1194 |
|
|
pstmt.setString(1, docid);
|
1195 |
|
|
pstmt.setString(2, user);
|
1196 |
|
|
pstmt.setString(3, docid);
|
1197 |
|
|
pstmt.execute();
|
1198 |
|
|
pstmt.close();
|
1199 |
|
|
|
1200 |
|
|
}
|
1201 |
|
|
|
1202 |
407
|
jones
|
/**
|
1203 |
|
|
* the main routine used to test the DBWriter utility.
|
1204 |
|
|
* <p>
|
1205 |
|
|
* Usage: java DocumentImpl <-f filename -a action -d docid>
|
1206 |
|
|
*
|
1207 |
|
|
* @param filename the filename to be loaded into the database
|
1208 |
|
|
* @param action the action to perform (READ, INSERT, UPDATE, DELETE)
|
1209 |
|
|
* @param docid the id of the document to process
|
1210 |
|
|
*/
|
1211 |
|
|
static public void main(String[] args) {
|
1212 |
|
|
|
1213 |
|
|
try {
|
1214 |
555
|
bojilova
|
String filename = null;
|
1215 |
598
|
bojilova
|
String dtdfilename = null;
|
1216 |
555
|
bojilova
|
String action = null;
|
1217 |
|
|
String docid = null;
|
1218 |
429
|
jones
|
boolean showRuntime = false;
|
1219 |
|
|
boolean useOldReadAlgorithm = false;
|
1220 |
407
|
jones
|
|
1221 |
408
|
jones
|
// Parse the command line arguments
|
1222 |
407
|
jones
|
for ( int i=0 ; i < args.length; ++i ) {
|
1223 |
|
|
if ( args[i].equals( "-f" ) ) {
|
1224 |
|
|
filename = args[++i];
|
1225 |
598
|
bojilova
|
} else if ( args[i].equals( "-r" ) ) {
|
1226 |
|
|
dtdfilename = args[++i];
|
1227 |
407
|
jones
|
} else if ( args[i].equals( "-a" ) ) {
|
1228 |
|
|
action = args[++i];
|
1229 |
|
|
} else if ( args[i].equals( "-d" ) ) {
|
1230 |
|
|
docid = args[++i];
|
1231 |
429
|
jones
|
} else if ( args[i].equals( "-t" ) ) {
|
1232 |
|
|
showRuntime = true;
|
1233 |
|
|
} else if ( args[i].equals( "-old" ) ) {
|
1234 |
|
|
useOldReadAlgorithm = true;
|
1235 |
407
|
jones
|
} else {
|
1236 |
|
|
System.err.println
|
1237 |
|
|
( " args[" +i+ "] '" +args[i]+ "' ignored." );
|
1238 |
|
|
}
|
1239 |
|
|
}
|
1240 |
|
|
|
1241 |
408
|
jones
|
// Check if the required arguments are provided
|
1242 |
407
|
jones
|
boolean argsAreValid = false;
|
1243 |
|
|
if (action != null) {
|
1244 |
|
|
if (action.equals("INSERT")) {
|
1245 |
|
|
if (filename != null) {
|
1246 |
|
|
argsAreValid = true;
|
1247 |
|
|
}
|
1248 |
|
|
} else if (action.equals("UPDATE")) {
|
1249 |
|
|
if ((filename != null) && (docid != null)) {
|
1250 |
|
|
argsAreValid = true;
|
1251 |
|
|
}
|
1252 |
|
|
} else if (action.equals("DELETE")) {
|
1253 |
|
|
if (docid != null) {
|
1254 |
|
|
argsAreValid = true;
|
1255 |
|
|
}
|
1256 |
|
|
} else if (action.equals("READ")) {
|
1257 |
|
|
if (docid != null) {
|
1258 |
|
|
argsAreValid = true;
|
1259 |
|
|
}
|
1260 |
|
|
}
|
1261 |
|
|
}
|
1262 |
|
|
|
1263 |
408
|
jones
|
// Print usage message if the arguments are not valid
|
1264 |
407
|
jones
|
if (!argsAreValid) {
|
1265 |
|
|
System.err.println("Wrong number of arguments!!!");
|
1266 |
|
|
System.err.println(
|
1267 |
598
|
bojilova
|
"USAGE: java DocumentImpl [-t] <-a INSERT> [-d docid] <-f filename> "+
|
1268 |
680
|
bojilova
|
"[-r dtdfilename]");
|
1269 |
407
|
jones
|
System.err.println(
|
1270 |
598
|
bojilova
|
" OR: java DocumentImpl [-t] <-a UPDATE -d docid -f filename> " +
|
1271 |
680
|
bojilova
|
"[-r dtdfilename]");
|
1272 |
407
|
jones
|
System.err.println(
|
1273 |
429
|
jones
|
" OR: java DocumentImpl [-t] <-a DELETE -d docid>");
|
1274 |
407
|
jones
|
System.err.println(
|
1275 |
429
|
jones
|
" OR: java DocumentImpl [-t] [-old] <-a READ -d docid>");
|
1276 |
407
|
jones
|
return;
|
1277 |
|
|
}
|
1278 |
429
|
jones
|
|
1279 |
|
|
// Time the request if asked for
|
1280 |
|
|
double startTime = System.currentTimeMillis();
|
1281 |
|
|
|
1282 |
407
|
jones
|
// Open a connection to the database
|
1283 |
|
|
MetaCatUtil util = new MetaCatUtil();
|
1284 |
|
|
Connection dbconn = util.openDBConnection();
|
1285 |
|
|
|
1286 |
463
|
berkley
|
double connTime = System.currentTimeMillis();
|
1287 |
408
|
jones
|
// Execute the action requested (READ, INSERT, UPDATE, DELETE)
|
1288 |
407
|
jones
|
if (action.equals("READ")) {
|
1289 |
|
|
DocumentImpl xmldoc = new DocumentImpl( dbconn, docid );
|
1290 |
429
|
jones
|
if (useOldReadAlgorithm) {
|
1291 |
|
|
System.out.println(xmldoc.readUsingSlowAlgorithm());
|
1292 |
|
|
} else {
|
1293 |
|
|
xmldoc.toXml(new PrintWriter(System.out));
|
1294 |
|
|
}
|
1295 |
408
|
jones
|
} else if (action.equals("DELETE")) {
|
1296 |
425
|
bojilova
|
DocumentImpl.delete(dbconn, docid, null, null);
|
1297 |
408
|
jones
|
System.out.println("Document deleted: " + docid);
|
1298 |
407
|
jones
|
} else {
|
1299 |
680
|
bojilova
|
String newdocid = DocumentImpl.write(dbconn, filename, null,
|
1300 |
598
|
bojilova
|
dtdfilename, action, docid,
|
1301 |
|
|
null, null);
|
1302 |
408
|
jones
|
if ((docid != null) && (!docid.equals(newdocid))) {
|
1303 |
|
|
if (action.equals("INSERT")) {
|
1304 |
|
|
System.out.println("New document ID generated!!! ");
|
1305 |
|
|
} else if (action.equals("UPDATE")) {
|
1306 |
|
|
System.out.println("ERROR: Couldn't update document!!! ");
|
1307 |
407
|
jones
|
}
|
1308 |
408
|
jones
|
} else if ((docid == null) && (action.equals("UPDATE"))) {
|
1309 |
|
|
System.out.println("ERROR: Couldn't update document!!! ");
|
1310 |
407
|
jones
|
}
|
1311 |
408
|
jones
|
System.out.println("Document processing finished for: " + filename
|
1312 |
|
|
+ " (" + newdocid + ")");
|
1313 |
407
|
jones
|
}
|
1314 |
|
|
|
1315 |
429
|
jones
|
double stopTime = System.currentTimeMillis();
|
1316 |
463
|
berkley
|
double dbOpenTime = (connTime - startTime)/1000;
|
1317 |
|
|
double insertTime = (stopTime - connTime)/1000;
|
1318 |
429
|
jones
|
double executionTime = (stopTime - startTime)/1000;
|
1319 |
|
|
if (showRuntime) {
|
1320 |
463
|
berkley
|
System.out.println("\n\nTotal Execution time was: " +
|
1321 |
|
|
executionTime + " seconds.");
|
1322 |
|
|
System.out.println("Time to open DB connection was: " + dbOpenTime +
|
1323 |
|
|
" seconds.");
|
1324 |
|
|
System.out.println("Time to insert document was: " + insertTime +
|
1325 |
|
|
" seconds.");
|
1326 |
429
|
jones
|
}
|
1327 |
463
|
berkley
|
dbconn.close();
|
1328 |
407
|
jones
|
} catch (McdbException me) {
|
1329 |
|
|
me.toXml(new PrintWriter(System.err));
|
1330 |
|
|
} catch (AccessionNumberException ane) {
|
1331 |
|
|
System.out.println(ane.getMessage());
|
1332 |
|
|
} catch (Exception e) {
|
1333 |
|
|
System.err.println("EXCEPTION HANDLING REQUIRED");
|
1334 |
|
|
System.err.println(e.getMessage());
|
1335 |
|
|
e.printStackTrace(System.err);
|
1336 |
|
|
}
|
1337 |
|
|
}
|
1338 |
393
|
jones
|
}
|