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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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38 |
561
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berkley
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import java.io.InputStreamReader;
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1029
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tao
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import java.io.*;
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798
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jones
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import java.text.SimpleDateFormat;
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42 |
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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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48 |
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import org.xml.sax.AttributeList;
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49 |
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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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956
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tao
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private String updatedVersion=null;
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393
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jones
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private String docname = null;
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79 |
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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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1059
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tao
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private String docHomeServer;
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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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95 |
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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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104 |
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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125 |
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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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129 |
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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133 |
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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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138 |
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public DocumentImpl(Connection conn, String docid) throws McdbException
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139 |
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{
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140 |
801
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jones
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this(conn, docid, true);
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141 |
393
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jones
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}
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142 |
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143 |
396
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jones
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/**
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144 |
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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145 |
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* This method is called from DBSAXHandler because we need to know the
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146 |
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* root element name for documents without a DOCTYPE before creating it.
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147 |
396
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jones
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*
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148 |
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* @param conn the JDBC Connection to which all information is written
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149 |
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* @param rootnodeid - sequence id of the root node in the document
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150 |
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* @param docname - the name of DTD, i.e. the name immediately following
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151 |
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* the DOCTYPE keyword ( should be the root element name ) or
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152 |
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* the root element name if no DOCTYPE declaration provided
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153 |
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* (Oracle's and IBM parsers are not aware if it is not the
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154 |
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* root element name)
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155 |
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* @param doctype - Public ID of the DTD, i.e. the name immediately
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156 |
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* following the PUBLIC keyword in DOCTYPE declaration or
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157 |
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* the docname if no Public ID provided or
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158 |
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* null if no DOCTYPE declaration provided
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159 |
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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160 |
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* @param action the action to be performed (INSERT OR UPDATE)
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161 |
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* @param user the user that owns the document
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162 |
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* @param pub flag for public "read" access on document
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163 |
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* @param serverCode the serverid from xml_replication on which this document
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164 |
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* resides.
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165 |
396
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jones
|
*
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166 |
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*/
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167 |
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public DocumentImpl(Connection conn, long rootnodeid, String docname,
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168 |
549
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berkley
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String doctype, String docid, String action, String user,
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169 |
697
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bojilova
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String pub, String catalogid, int serverCode)
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170 |
549
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berkley
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throws SQLException, Exception
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171 |
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{
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172 |
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this.conn = conn;
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173 |
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this.rootnodeid = rootnodeid;
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174 |
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this.docname = docname;
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175 |
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this.doctype = doctype;
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176 |
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this.docid = docid;
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177 |
697
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bojilova
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writeDocumentToDB(action, user, pub, catalogid, serverCode);
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178 |
549
|
berkley
|
}
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179 |
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|
180 |
956
|
tao
|
/**
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181 |
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* Construct a new document instance, writing the contents to the database.
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182 |
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* This method is called from DBSAXHandler because we need to know the
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183 |
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* root element name for documents without a DOCTYPE before creating it.
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184 |
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*
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185 |
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* In this constructor, the docid is without rev. There is a string rev to
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186 |
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* specify the revision user want to upadate. The revion is only need to be
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187 |
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* greater than current one. It is not need to be sequent number just after
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188 |
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* current one. So it is only used in update action
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189 |
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* @param conn the JDBC Connection to which all information is written
|
190 |
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* @param rootnodeid - sequence id of the root node in the document
|
191 |
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* @param docname - the name of DTD, i.e. the name immediately following
|
192 |
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* the DOCTYPE keyword ( should be the root element name ) or
|
193 |
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* the root element name if no DOCTYPE declaration provided
|
194 |
|
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* (Oracle's and IBM parsers are not aware if it is not the
|
195 |
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* root element name)
|
196 |
|
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* @param doctype - Public ID of the DTD, i.e. the name immediately
|
197 |
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* following the PUBLIC keyword in DOCTYPE declaration or
|
198 |
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* the docname if no Public ID provided or
|
199 |
|
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* null if no DOCTYPE declaration provided
|
200 |
|
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* @param docid the docid to use for the UPDATE, no version number
|
201 |
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* @param version, need to be update
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202 |
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* @param action the action to be performed (INSERT OR UPDATE)
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203 |
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* @param user the user that owns the document
|
204 |
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* @param pub flag for public "read" access on document
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205 |
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* @param serverCode the serverid from xml_replication on which this document
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206 |
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* resides.
|
207 |
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*
|
208 |
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*/
|
209 |
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public DocumentImpl(Connection conn, long rootNodeId, String docName,
|
210 |
|
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String docType, String docId, String newRevision,
|
211 |
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String action, String user,
|
212 |
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String pub, String catalogId, int serverCode)
|
213 |
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throws SQLException, Exception
|
214 |
|
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{
|
215 |
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this.conn = conn;
|
216 |
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this.rootnodeid = rootNodeId;
|
217 |
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this.docname = docName;
|
218 |
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this.doctype = docType;
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219 |
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this.docid = docId;
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220 |
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this.updatedVersion = newRevision;
|
221 |
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writeDocumentToDB(action, user, pub, catalogId, serverCode);
|
222 |
|
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}
|
223 |
|
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|
224 |
798
|
jones
|
/**
|
225 |
1026
|
tao
|
* This method will be call in handleUploadRequest in MetacatServlet class
|
226 |
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*/
|
227 |
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public static void registerDocument(
|
228 |
|
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String docname, String doctype, String accnum, String user)
|
229 |
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throws SQLException, AccessionNumberException, Exception
|
230 |
|
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{
|
231 |
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|
Connection dbConn = null;
|
232 |
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MetaCatUtil ut = new MetaCatUtil();
|
233 |
1063
|
tao
|
try
|
234 |
|
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{
|
235 |
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dbConn = ut.openDBConnection();
|
236 |
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// get server location for this doc
|
237 |
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int serverLocation=getServerLocationNumber(dbConn,accnum);
|
238 |
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dbConn.close();
|
239 |
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registerDocument(docname, doctype,accnum, user, serverLocation);
|
240 |
|
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}
|
241 |
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catch (Exception e)
|
242 |
|
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{
|
243 |
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throw e;
|
244 |
|
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}
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245 |
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finally
|
246 |
|
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{
|
247 |
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try
|
248 |
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{
|
249 |
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dbConn.close();
|
250 |
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}
|
251 |
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catch (Exception ee)
|
252 |
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{}
|
253 |
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}
|
254 |
1026
|
tao
|
|
255 |
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}
|
256 |
|
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/**
|
257 |
798
|
jones
|
* Register a document that resides on the filesystem with the database.
|
258 |
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* (ie, just an entry in xml_documents, nothing in xml_nodes).
|
259 |
|
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* Creates a reference to a filesystem document (used for non-xml data files).
|
260 |
1055
|
tao
|
* This class only be called in MetaCatServerlet.
|
261 |
798
|
jones
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* @param conn the JDBC Connection to which all information is written
|
262 |
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* @param docname - the name of DTD, i.e. the name immediately following
|
263 |
|
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* the DOCTYPE keyword ( should be the root element name ) or
|
264 |
|
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* the root element name if no DOCTYPE declaration provided
|
265 |
|
|
* (Oracle's and IBM parsers are not aware if it is not the
|
266 |
|
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* root element name)
|
267 |
|
|
* @param doctype - Public ID of the DTD, i.e. the name immediately
|
268 |
|
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* following the PUBLIC keyword in DOCTYPE declaration or
|
269 |
|
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* the docname if no Public ID provided or
|
270 |
|
|
* null if no DOCTYPE declaration provided
|
271 |
|
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* @param accnum the accession number to use for the INSERT OR UPDATE, which
|
272 |
|
|
* includes a revision number for this revision of the document
|
273 |
|
|
* (e.g., knb.1.1)
|
274 |
|
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* @param user the user that owns the document
|
275 |
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* @param serverCode the serverid from xml_replication on which this document
|
276 |
|
|
* resides.
|
277 |
|
|
*/
|
278 |
|
|
public static void registerDocument(
|
279 |
|
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String docname, String doctype, String accnum,
|
280 |
|
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String user, int serverCode)
|
281 |
|
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throws SQLException, AccessionNumberException, Exception
|
282 |
|
|
{
|
283 |
|
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Connection dbconn = null;
|
284 |
|
|
MetaCatUtil util = new MetaCatUtil();
|
285 |
965
|
tao
|
AccessionNumber ac;
|
286 |
798
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jones
|
try {
|
287 |
|
|
dbconn = util.openDBConnection();
|
288 |
965
|
tao
|
String docIdWithoutRev=MetaCatUtil.getDocIdFromString(accnum);
|
289 |
|
|
int userSpecifyRev=MetaCatUtil.getVersionFromString(accnum);
|
290 |
|
|
int revInDataBase=getLatestRevisionNumber(dbconn, docIdWithoutRev);
|
291 |
|
|
//revIndataBase=-1, there is no record in xml_documents table
|
292 |
|
|
//the data file is a new one, inert it into table
|
293 |
|
|
//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
|
304 |
|
|
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 |
798
|
jones
|
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 |
946
|
tao
|
String sqlDateString = "to_date('" + dateString +
|
323 |
|
|
"', 'YY-MM-DD HH24:MI:SS')";
|
324 |
798
|
jones
|
|
325 |
|
|
StringBuffer sql = new StringBuffer();
|
326 |
|
|
sql.append("insert into xml_documents (docid, docname, doctype, ");
|
327 |
946
|
tao
|
sql.append("user_owner, user_updated, server_location, rev,date_created");
|
328 |
798
|
jones
|
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 |
1063
|
tao
|
}
|
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 |
798
|
jones
|
}
|
356 |
|
|
}
|
357 |
1029
|
tao
|
|
358 |
1055
|
tao
|
/**
|
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 |
1063
|
tao
|
|
402 |
1055
|
tao
|
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 |
1063
|
tao
|
}
|
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 |
1055
|
tao
|
}
|
462 |
|
|
}
|
463 |
|
|
|
464 |
1021
|
tao
|
/**
|
465 |
1029
|
tao
|
* This method will register a data file entry in xml_documents and save a
|
466 |
1055
|
tao
|
* data file input Stream into file system.. It is only used in force
|
467 |
|
|
* replication
|
468 |
1029
|
tao
|
*
|
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 |
1063
|
tao
|
String docname, String doctype, String accnum,
|
482 |
|
|
String user, String docHomeServer)
|
483 |
1029
|
tao
|
throws SQLException, AccessionNumberException, Exception
|
484 |
|
|
{
|
485 |
1063
|
tao
|
int serverCode=-2;
|
486 |
1029
|
tao
|
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 |
1063
|
tao
|
|
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 |
1029
|
tao
|
//make sure user have file lock grant(local metacat means have it too)
|
507 |
1069
|
tao
|
//if (getDataFileLockGrant(accnum))
|
508 |
|
|
//{
|
509 |
1029
|
tao
|
//register data file into xml_documents table
|
510 |
1055
|
tao
|
registerDocumentInReplication(docname, doctype, accnum, user, serverCode);
|
511 |
1029
|
tao
|
//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 |
1063
|
tao
|
|
534 |
1069
|
tao
|
//}//if
|
535 |
1029
|
tao
|
}
|
536 |
|
|
|
537 |
798
|
jones
|
|
538 |
1026
|
tao
|
|
539 |
|
|
public static boolean getDataFileLockGrant(String accnum)
|
540 |
|
|
throws Exception
|
541 |
|
|
{
|
542 |
|
|
Connection dbConn = null;
|
543 |
|
|
MetaCatUtil ut= new MetaCatUtil();
|
544 |
1063
|
tao
|
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 |
1026
|
tao
|
}
|
562 |
|
|
|
563 |
393
|
jones
|
/**
|
564 |
1026
|
tao
|
* 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 |
393
|
jones
|
* 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 |
465
|
berkley
|
|
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 |
393
|
jones
|
|
683 |
396
|
jones
|
/**
|
684 |
|
|
* Get the document identifier (docid)
|
685 |
|
|
*/
|
686 |
|
|
public String getDocID() {
|
687 |
|
|
return docid;
|
688 |
|
|
}
|
689 |
465
|
berkley
|
|
690 |
691
|
bojilova
|
// DOCTITLE attr cleared from the db
|
691 |
|
|
// /**
|
692 |
|
|
// *get the document title
|
693 |
|
|
// */
|
694 |
|
|
// public String getDocTitle() {
|
695 |
|
|
// return doctitle;
|
696 |
|
|
// }
|
697 |
561
|
berkley
|
|
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 |
1059
|
tao
|
public String getDocHomeServer() {
|
711 |
|
|
return docHomeServer;
|
712 |
1055
|
tao
|
}
|
713 |
1059
|
tao
|
|
714 |
1055
|
tao
|
|
715 |
1059
|
tao
|
|
716 |
697
|
bojilova
|
public String getPublicaccess() {
|
717 |
561
|
berkley
|
return publicaccess;
|
718 |
|
|
}
|
719 |
575
|
berkley
|
|
720 |
|
|
public int getRev() {
|
721 |
|
|
return rev;
|
722 |
|
|
}
|
723 |
956
|
tao
|
|
724 |
|
|
/**
|
725 |
429
|
jones
|
* Print a string representation of the XML document
|
726 |
393
|
jones
|
*/
|
727 |
|
|
public String toString()
|
728 |
|
|
{
|
729 |
429
|
jones
|
StringWriter docwriter = new StringWriter();
|
730 |
800
|
jones
|
try {
|
731 |
|
|
this.toXml(docwriter);
|
732 |
|
|
} catch (McdbException mcdbe) {
|
733 |
|
|
return null;
|
734 |
|
|
}
|
735 |
429
|
jones
|
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 |
800
|
jones
|
public String readUsingSlowAlgorithm() throws McdbException
|
750 |
429
|
jones
|
{
|
751 |
393
|
jones
|
StringBuffer doc = new StringBuffer();
|
752 |
|
|
|
753 |
800
|
jones
|
// 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 |
429
|
jones
|
// Create the elements from the downloaded data in the TreeSet
|
759 |
|
|
rootNode = new ElementNode(nodeRecordList, rootnodeid);
|
760 |
|
|
|
761 |
393
|
jones
|
// 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 |
429
|
jones
|
* 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 |
800
|
jones
|
public void toXml(Writer pw) throws McdbException
|
783 |
429
|
jones
|
{
|
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 |
800
|
jones
|
// 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 |
429
|
jones
|
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 |
451
|
bojilova
|
if (previousNodeWasElement) {
|
832 |
|
|
out.print(">");
|
833 |
|
|
previousNodeWasElement = false;
|
834 |
|
|
}
|
835 |
826
|
bojilova
|
if ( currentElement.nodeprefix != null ) {
|
836 |
|
|
out.print("</" + currentElement.nodeprefix + ":" +
|
837 |
|
|
currentElement.nodename + ">" );
|
838 |
|
|
} else {
|
839 |
|
|
out.print("</" + currentElement.nodename + ">" );
|
840 |
|
|
}
|
841 |
429
|
jones
|
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 |
826
|
bojilova
|
if ( currentNode.nodeprefix != null ) {
|
872 |
|
|
out.print("<" + currentNode.nodeprefix + ":" + currentNode.nodename);
|
873 |
|
|
} else {
|
874 |
|
|
out.print("<" + currentNode.nodename);
|
875 |
|
|
}
|
876 |
429
|
jones
|
|
877 |
|
|
// Handle the ATTRIBUTE nodes
|
878 |
|
|
} else if (currentNode.nodetype.equals("ATTRIBUTE")) {
|
879 |
826
|
bojilova
|
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 |
821
|
bojilova
|
|
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 |
429
|
jones
|
} 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 |
686
|
berkley
|
while(!openElements.empty())
|
927 |
|
|
{
|
928 |
|
|
NodeRecord currentElement = (NodeRecord)openElements.pop();
|
929 |
|
|
util.debugMessage("\n POPPED: " + currentElement.nodename);
|
930 |
826
|
bojilova
|
if ( currentElement.nodeprefix != null ) {
|
931 |
|
|
out.print("</" + currentElement.nodeprefix + ":" +
|
932 |
|
|
currentElement.nodename + ">" );
|
933 |
|
|
} else {
|
934 |
|
|
out.print("</" + currentElement.nodename + ">" );
|
935 |
|
|
}
|
936 |
686
|
berkley
|
}
|
937 |
429
|
jones
|
out.flush();
|
938 |
|
|
}
|
939 |
622
|
berkley
|
|
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 |
667
|
berkley
|
pstmt.close();
|
960 |
622
|
berkley
|
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 |
429
|
jones
|
|
980 |
800
|
jones
|
private void getDocumentInfo(String docid) throws McdbException,
|
981 |
622
|
berkley
|
AccessionNumberException
|
982 |
|
|
{
|
983 |
|
|
getDocumentInfo(new DocumentIdentifier(docid));
|
984 |
|
|
}
|
985 |
|
|
|
986 |
429
|
jones
|
/**
|
987 |
393
|
jones
|
* Look up the document type information from the database
|
988 |
|
|
*
|
989 |
|
|
* @param docid the id of the document to look up
|
990 |
|
|
*/
|
991 |
622
|
berkley
|
private void getDocumentInfo(DocumentIdentifier docid) throws McdbException
|
992 |
393
|
jones
|
{
|
993 |
|
|
PreparedStatement pstmt;
|
994 |
622
|
berkley
|
String table = "xml_documents";
|
995 |
1059
|
tao
|
|
996 |
622
|
berkley
|
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 |
675
|
berkley
|
System.out.println("error in DocumentImpl.getDocumentInfo: " +
|
1006 |
|
|
e.getMessage());
|
1007 |
622
|
berkley
|
}
|
1008 |
|
|
|
1009 |
|
|
//deal with the key words here.
|
1010 |
|
|
|
1011 |
|
|
if(docid.getRev().equals("all"))
|
1012 |
|
|
{
|
1013 |
|
|
|
1014 |
|
|
}
|
1015 |
|
|
|
1016 |
393
|
jones
|
try {
|
1017 |
622
|
berkley
|
StringBuffer sql = new StringBuffer();
|
1018 |
691
|
bojilova
|
// DOCTITLE attr cleared from the db
|
1019 |
|
|
// sql.append("SELECT docname, doctype, rootnodeid, doctitle, ");
|
1020 |
|
|
sql.append("SELECT docname, doctype, rootnodeid, ");
|
1021 |
697
|
bojilova
|
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 |
622
|
berkley
|
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 |
393
|
jones
|
pstmt =
|
1028 |
622
|
berkley
|
conn.prepareStatement(sql.toString());
|
1029 |
393
|
jones
|
// Bind the values to the query
|
1030 |
622
|
berkley
|
//pstmt.setString(1, docid.getIdentifier());
|
1031 |
|
|
//pstmt.setString(2, docid.getRev());
|
1032 |
393
|
jones
|
|
1033 |
|
|
pstmt.execute();
|
1034 |
|
|
ResultSet rs = pstmt.getResultSet();
|
1035 |
|
|
boolean tableHasRows = rs.next();
|
1036 |
|
|
if (tableHasRows) {
|
1037 |
561
|
berkley
|
this.docname = rs.getString(1);
|
1038 |
|
|
this.doctype = rs.getString(2);
|
1039 |
|
|
this.rootnodeid = rs.getLong(3);
|
1040 |
691
|
bojilova
|
// DOCTITLE attr cleared from the db
|
1041 |
|
|
// this.doctitle = rs.getString(4);
|
1042 |
692
|
bojilova
|
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 |
697
|
bojilova
|
this.publicaccess = rs.getString(9);
|
1048 |
|
|
this.rev = rs.getInt(10);
|
1049 |
393
|
jones
|
}
|
1050 |
818
|
berkley
|
pstmt.close();
|
1051 |
1059
|
tao
|
|
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 |
393
|
jones
|
if (this.doctype != null) {
|
1080 |
|
|
pstmt =
|
1081 |
|
|
conn.prepareStatement("SELECT system_id " +
|
1082 |
|
|
"FROM xml_catalog " +
|
1083 |
769
|
bojilova
|
"WHERE public_id = ?");
|
1084 |
393
|
jones
|
// 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 |
818
|
berkley
|
pstmt.close();
|
1094 |
393
|
jones
|
}
|
1095 |
|
|
} catch (SQLException e) {
|
1096 |
675
|
berkley
|
System.out.println("error in DocumentImpl.getDocumentInfo: " +
|
1097 |
|
|
e.getMessage());
|
1098 |
622
|
berkley
|
e.printStackTrace(System.out);
|
1099 |
675
|
berkley
|
throw new McdbException("Error accessing database connection in " +
|
1100 |
|
|
"DocumentImpl.getDocumentInfo: ", e);
|
1101 |
393
|
jones
|
}
|
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 |
396
|
jones
|
* @param rootnodeid the id of the root node of the node tree to look up
|
1112 |
393
|
jones
|
*/
|
1113 |
396
|
jones
|
private TreeSet getNodeRecordList(long rootnodeid) throws McdbException
|
1114 |
393
|
jones
|
{
|
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 |
826
|
bojilova
|
String nodeprefix = null;
|
1123 |
393
|
jones
|
String nodedata = null;
|
1124 |
899
|
berkley
|
String quotechar = dbAdapter.getStringDelimiter();
|
1125 |
393
|
jones
|
|
1126 |
|
|
try {
|
1127 |
|
|
pstmt =
|
1128 |
|
|
conn.prepareStatement("SELECT nodeid,parentnodeid,nodeindex, " +
|
1129 |
899
|
berkley
|
"nodetype,nodename,nodeprefix,nodedata " +
|
1130 |
396
|
jones
|
"FROM xml_nodes WHERE rootnodeid = ?");
|
1131 |
393
|
jones
|
|
1132 |
|
|
// Bind the values to the query
|
1133 |
396
|
jones
|
pstmt.setLong(1, rootnodeid);
|
1134 |
393
|
jones
|
|
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 |
826
|
bojilova
|
nodeprefix = rs.getString(6);
|
1145 |
|
|
nodedata = rs.getString(7);
|
1146 |
899
|
berkley
|
nodedata = MetaCatUtil.normalize(nodedata);
|
1147 |
393
|
jones
|
// add the data to the node record list hashtable
|
1148 |
826
|
bojilova
|
NodeRecord currentRecord = new NodeRecord(nodeid,parentnodeid,nodeindex,
|
1149 |
946
|
tao
|
nodetype, nodename, nodeprefix, nodedata);
|
1150 |
393
|
jones
|
nodeRecordList.add(currentRecord);
|
1151 |
|
|
|
1152 |
|
|
// Advance to the next node
|
1153 |
|
|
tableHasRows = rs.next();
|
1154 |
|
|
}
|
1155 |
|
|
pstmt.close();
|
1156 |
|
|
|
1157 |
|
|
} catch (SQLException e) {
|
1158 |
826
|
bojilova
|
throw new McdbException("Error in DocumentImpl.getNodeRecordList " +
|
1159 |
|
|
e.getMessage());
|
1160 |
393
|
jones
|
}
|
1161 |
|
|
|
1162 |
|
|
if (nodeRecordList != null) {
|
1163 |
|
|
return nodeRecordList;
|
1164 |
|
|
} else {
|
1165 |
|
|
throw new McdbException("Error getting node data: " + docid);
|
1166 |
|
|
}
|
1167 |
|
|
}
|
1168 |
549
|
berkley
|
|
1169 |
697
|
bojilova
|
// 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 |
393
|
jones
|
|
1178 |
459
|
bojilova
|
/** creates SQL code and inserts new document into DB connection */
|
1179 |
680
|
bojilova
|
private void writeDocumentToDB(String action, String user, String pub,
|
1180 |
697
|
bojilova
|
String catalogid, int serverCode)
|
1181 |
459
|
bojilova
|
throws SQLException, Exception {
|
1182 |
754
|
bojilova
|
String sysdate = dbAdapter.getDateTimeFunction();
|
1183 |
747
|
bojilova
|
|
1184 |
459
|
bojilova
|
try {
|
1185 |
|
|
PreparedStatement pstmt = null;
|
1186 |
|
|
|
1187 |
|
|
if (action.equals("INSERT")) {
|
1188 |
|
|
//AccessionNumber ac = new AccessionNumber();
|
1189 |
|
|
//this.docid = ac.generate(docid, "INSERT");
|
1190 |
1069
|
tao
|
System.out.println("before pstmt");
|
1191 |
459
|
bojilova
|
pstmt = conn.prepareStatement(
|
1192 |
697
|
bojilova
|
"INSERT INTO xml_documents " +
|
1193 |
|
|
"(docid, rootnodeid, docname, doctype, " +
|
1194 |
|
|
"user_owner, user_updated, date_created, date_updated, " +
|
1195 |
|
|
"public_access, catalog_id, server_location) " +
|
1196 |
747
|
bojilova
|
"VALUES (?, ?, ?, ?, ?, ?, " + sysdate + ", " + sysdate +
|
1197 |
|
|
", ?, ?, ?)");
|
1198 |
549
|
berkley
|
//note that the server_location is set to 1.
|
1199 |
|
|
//this means that "localhost" in the xml_replication table must
|
1200 |
|
|
//always be the first entry!!!!!
|
1201 |
|
|
|
1202 |
459
|
bojilova
|
// Bind the values to the query
|
1203 |
|
|
pstmt.setString(1, this.docid);
|
1204 |
|
|
pstmt.setLong(2, rootnodeid);
|
1205 |
|
|
pstmt.setString(3, docname);
|
1206 |
|
|
pstmt.setString(4, doctype);
|
1207 |
|
|
pstmt.setString(5, user);
|
1208 |
|
|
pstmt.setString(6, user);
|
1209 |
1069
|
tao
|
//public access is usefulless, so set it to null
|
1210 |
|
|
pstmt.setString(7, null);
|
1211 |
|
|
/*if ( pub == null ) {
|
1212 |
680
|
bojilova
|
pstmt.setString(7, null);
|
1213 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
|
1214 |
680
|
bojilova
|
pstmt.setInt(7, 1);
|
1215 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
|
1216 |
680
|
bojilova
|
pstmt.setInt(7, 0);
|
1217 |
1069
|
tao
|
}*/
|
1218 |
697
|
bojilova
|
pstmt.setString(8, catalogid);
|
1219 |
|
|
pstmt.setInt(9, serverCode);
|
1220 |
459
|
bojilova
|
} else if (action.equals("UPDATE")) {
|
1221 |
|
|
|
1222 |
|
|
// Save the old document entry in a backup table
|
1223 |
|
|
DocumentImpl.archiveDocRevision( conn, docid, user );
|
1224 |
575
|
berkley
|
DocumentImpl thisdoc = new DocumentImpl(conn, docid);
|
1225 |
|
|
int thisrev = thisdoc.getRev();
|
1226 |
956
|
tao
|
|
1227 |
|
|
//if the updated vesion is not greater than current one,
|
1228 |
|
|
//throw it into a exception
|
1229 |
|
|
if (Integer.parseInt(updatedVersion)<=thisrev)
|
1230 |
|
|
{
|
1231 |
|
|
throw new Exception("Next revision number couldn't be less"
|
1232 |
|
|
+" than or equal "+ thisrev);
|
1233 |
|
|
}
|
1234 |
|
|
else
|
1235 |
|
|
{
|
1236 |
|
|
//set the user specified revision
|
1237 |
|
|
thisrev=Integer.parseInt(updatedVersion);
|
1238 |
|
|
}
|
1239 |
|
|
|
1240 |
459
|
bojilova
|
// Delete index for the old version of docid
|
1241 |
|
|
// The new index is inserting on the next calls to DBSAXNode
|
1242 |
|
|
pstmt = conn.prepareStatement(
|
1243 |
|
|
"DELETE FROM xml_index WHERE docid='" + this.docid + "'");
|
1244 |
|
|
pstmt.execute();
|
1245 |
818
|
berkley
|
pstmt.close();
|
1246 |
459
|
bojilova
|
|
1247 |
|
|
// Update the new document to reflect the new node tree
|
1248 |
|
|
pstmt = conn.prepareStatement(
|
1249 |
|
|
"UPDATE xml_documents " +
|
1250 |
|
|
"SET rootnodeid = ?, docname = ?, doctype = ?, " +
|
1251 |
747
|
bojilova
|
"user_updated = ?, date_updated = " + sysdate + ", " +
|
1252 |
697
|
bojilova
|
"server_location = ?, rev = ?, public_access = ?, catalog_id = ? " +
|
1253 |
769
|
bojilova
|
"WHERE docid = ?");
|
1254 |
459
|
bojilova
|
// Bind the values to the query
|
1255 |
|
|
pstmt.setLong(1, rootnodeid);
|
1256 |
|
|
pstmt.setString(2, docname);
|
1257 |
|
|
pstmt.setString(3, doctype);
|
1258 |
|
|
pstmt.setString(4, user);
|
1259 |
549
|
berkley
|
pstmt.setInt(5, serverCode);
|
1260 |
575
|
berkley
|
pstmt.setInt(6, thisrev);
|
1261 |
1069
|
tao
|
pstmt.setString(7, null);
|
1262 |
|
|
/*if ( pub == null ) {
|
1263 |
680
|
bojilova
|
pstmt.setString(7, null);
|
1264 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("YES") || pub.equals("1") ) {
|
1265 |
680
|
bojilova
|
pstmt .setInt(7, 1);
|
1266 |
697
|
bojilova
|
} else if ( pub.toUpperCase().equals("NO") || pub.equals("0") ) {
|
1267 |
680
|
bojilova
|
pstmt.setInt(7, 0);
|
1268 |
1069
|
tao
|
}*/
|
1269 |
697
|
bojilova
|
pstmt.setString(8, catalogid);
|
1270 |
|
|
pstmt.setString(9, this.docid);
|
1271 |
575
|
berkley
|
|
1272 |
459
|
bojilova
|
} else {
|
1273 |
|
|
System.err.println("Action not supported: " + action);
|
1274 |
|
|
}
|
1275 |
|
|
|
1276 |
|
|
// Do the insertion
|
1277 |
|
|
pstmt.execute();
|
1278 |
1069
|
tao
|
System.out.println("after excecute");
|
1279 |
459
|
bojilova
|
pstmt.close();
|
1280 |
|
|
|
1281 |
|
|
} catch (SQLException sqle) {
|
1282 |
|
|
throw sqle;
|
1283 |
|
|
} catch (Exception e) {
|
1284 |
|
|
throw e;
|
1285 |
|
|
}
|
1286 |
|
|
}
|
1287 |
|
|
|
1288 |
|
|
/**
|
1289 |
407
|
jones
|
* Write an XML file to the database, given a filename
|
1290 |
393
|
jones
|
*
|
1291 |
408
|
jones
|
* @param conn the JDBC connection to the database
|
1292 |
407
|
jones
|
* @param filename the filename to be loaded into the database
|
1293 |
680
|
bojilova
|
* @param pub flag for public "read" access on document
|
1294 |
|
|
* @param dtdfilename the dtd to be uploaded on server's file system
|
1295 |
407
|
jones
|
* @param action the action to be performed (INSERT OR UPDATE)
|
1296 |
|
|
* @param docid the docid to use for the INSERT OR UPDATE
|
1297 |
680
|
bojilova
|
* @param user the user that owns the document
|
1298 |
802
|
bojilova
|
* @param groups the groups to which user belongs
|
1299 |
393
|
jones
|
*/
|
1300 |
598
|
bojilova
|
public static String write(Connection conn,String filename,
|
1301 |
680
|
bojilova
|
String pub, String dtdfilename,
|
1302 |
598
|
bojilova
|
String action, String docid, String user,
|
1303 |
802
|
bojilova
|
String[] groups )
|
1304 |
457
|
bojilova
|
throws Exception {
|
1305 |
598
|
bojilova
|
|
1306 |
|
|
Reader dtd = null;
|
1307 |
|
|
if ( dtdfilename != null ) {
|
1308 |
|
|
dtd = new FileReader(new File(dtdfilename).toString());
|
1309 |
|
|
}
|
1310 |
555
|
bojilova
|
return write ( conn, new FileReader(new File(filename).toString()),
|
1311 |
802
|
bojilova
|
pub, dtd, action, docid, user, groups, false);
|
1312 |
407
|
jones
|
}
|
1313 |
598
|
bojilova
|
|
1314 |
680
|
bojilova
|
public static String write(Connection conn,Reader xml,String pub,Reader dtd,
|
1315 |
598
|
bojilova
|
String action, String docid, String user,
|
1316 |
802
|
bojilova
|
String[] groups, boolean validate)
|
1317 |
549
|
berkley
|
throws Exception {
|
1318 |
1012
|
tao
|
//this method will be called in handleUpdateOrInsert method
|
1319 |
|
|
//in MetacatServlet class
|
1320 |
|
|
// get server location for this doc
|
1321 |
|
|
int serverLocation=getServerLocationNumber(conn,docid);
|
1322 |
|
|
//System.out.println("server location: "+serverLocation);
|
1323 |
|
|
return write(conn,xml,pub,dtd,action,docid,user,groups,serverLocation,false,
|
1324 |
|
|
validate);
|
1325 |
598
|
bojilova
|
}
|
1326 |
|
|
|
1327 |
680
|
bojilova
|
public static String write(Connection conn, Reader xml, String pub,
|
1328 |
598
|
bojilova
|
String action, String docid, String user,
|
1329 |
802
|
bojilova
|
String[] groups )
|
1330 |
598
|
bojilova
|
throws Exception {
|
1331 |
571
|
berkley
|
if(action.equals("UPDATE"))
|
1332 |
|
|
{//if the document is being updated then use the servercode from the
|
1333 |
|
|
//originally inserted document.
|
1334 |
|
|
DocumentImpl doc = new DocumentImpl(conn, docid);
|
1335 |
|
|
int servercode = doc.getServerlocation();
|
1336 |
802
|
bojilova
|
return write(conn, xml, pub, action, docid, user, groups, servercode);
|
1337 |
571
|
berkley
|
}
|
1338 |
|
|
else
|
1339 |
|
|
{//if the file is being inserted then the servercode is always 1
|
1340 |
802
|
bojilova
|
return write(conn, xml, pub, action, docid, user, groups, 1);
|
1341 |
571
|
berkley
|
}
|
1342 |
549
|
berkley
|
}
|
1343 |
|
|
|
1344 |
559
|
berkley
|
public static String write( Connection conn, Reader xml,
|
1345 |
|
|
String action, String docid, String user,
|
1346 |
802
|
bojilova
|
String[] groups, int serverCode )
|
1347 |
598
|
bojilova
|
throws Exception
|
1348 |
559
|
berkley
|
{
|
1349 |
802
|
bojilova
|
return write(conn,xml,null,action,docid,user,groups,serverCode);
|
1350 |
559
|
berkley
|
}
|
1351 |
|
|
|
1352 |
680
|
bojilova
|
public static String write( Connection conn, Reader xml, String pub,
|
1353 |
577
|
berkley
|
String action, String docid, String user,
|
1354 |
802
|
bojilova
|
String[] groups, int serverCode)
|
1355 |
598
|
bojilova
|
throws Exception
|
1356 |
577
|
berkley
|
{
|
1357 |
802
|
bojilova
|
return write(conn,xml,pub,null,action,docid,user,groups,
|
1358 |
695
|
bojilova
|
serverCode,false,false);
|
1359 |
577
|
berkley
|
}
|
1360 |
|
|
|
1361 |
680
|
bojilova
|
public static String write( Connection conn, Reader xml, String pub,
|
1362 |
600
|
bojilova
|
String action, String docid, String user,
|
1363 |
802
|
bojilova
|
String[] groups, int serverCode, boolean override)
|
1364 |
600
|
bojilova
|
throws Exception
|
1365 |
|
|
{
|
1366 |
802
|
bojilova
|
return write(conn,xml,pub,null,action,docid,user,groups,
|
1367 |
695
|
bojilova
|
serverCode,override,false);
|
1368 |
600
|
bojilova
|
}
|
1369 |
|
|
|
1370 |
407
|
jones
|
/**
|
1371 |
|
|
* Write an XML file to the database, given a Reader
|
1372 |
|
|
*
|
1373 |
408
|
jones
|
* @param conn the JDBC connection to the database
|
1374 |
407
|
jones
|
* @param xml the xml stream to be loaded into the database
|
1375 |
680
|
bojilova
|
* @param pub flag for public "read" access on xml document
|
1376 |
|
|
* @param dtd the dtd to be uploaded on server's file system
|
1377 |
734
|
bojilova
|
* @param action the action to be performed (INSERT or UPDATE)
|
1378 |
|
|
* @param accnum the docid + rev# to use on INSERT or UPDATE
|
1379 |
580
|
berkley
|
* @param user the user that owns the document
|
1380 |
802
|
bojilova
|
* @param groups the groups to which user belongs
|
1381 |
580
|
berkley
|
* @param serverCode the serverid from xml_replication on which this document
|
1382 |
|
|
* resides.
|
1383 |
|
|
* @param override flag to stop insert replication checking.
|
1384 |
|
|
* if override = true then a document not belonging to the local server
|
1385 |
|
|
* will not be checked upon update for a file lock.
|
1386 |
|
|
* if override = false then a document not from this server, upon
|
1387 |
|
|
* update will be locked and version checked.
|
1388 |
407
|
jones
|
*/
|
1389 |
559
|
berkley
|
|
1390 |
680
|
bojilova
|
public static String write( Connection conn,Reader xml,String pub,Reader dtd,
|
1391 |
734
|
bojilova
|
String action, String accnum, String user,
|
1392 |
802
|
bojilova
|
String[] groups, int serverCode, boolean override,
|
1393 |
695
|
bojilova
|
boolean validate)
|
1394 |
598
|
bojilova
|
throws Exception
|
1395 |
573
|
berkley
|
{
|
1396 |
779
|
bojilova
|
// NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
|
1397 |
1012
|
tao
|
MetaCatUtil util = new MetaCatUtil();
|
1398 |
779
|
bojilova
|
AccessionNumber ac = new AccessionNumber(conn, accnum, action);
|
1399 |
|
|
String docid = ac.getDocid();
|
1400 |
|
|
String rev = ac.getRev();
|
1401 |
590
|
berkley
|
MetaCatUtil.debugMessage("action: " + action + " servercode: " +
|
1402 |
1055
|
tao
|
serverCode + " override: " + override, 10);
|
1403 |
580
|
berkley
|
|
1404 |
577
|
berkley
|
if((serverCode != 1 && action.equals("UPDATE")) && !override)
|
1405 |
559
|
berkley
|
{ //if this document being written is not a resident of this server then
|
1406 |
|
|
//we need to try to get a lock from it's resident server. If the
|
1407 |
|
|
//resident server will not give a lock then we send the user a message
|
1408 |
|
|
//saying that he/she needs to download a new copy of the file and
|
1409 |
|
|
//merge the differences manually.
|
1410 |
567
|
berkley
|
int istreamInt;
|
1411 |
561
|
berkley
|
char istreamChar;
|
1412 |
779
|
bojilova
|
DocumentIdentifier id = new DocumentIdentifier(accnum);
|
1413 |
|
|
String updaterev = id.getRev();
|
1414 |
561
|
berkley
|
String server = MetacatReplication.getServer(serverCode);
|
1415 |
734
|
bojilova
|
MetacatReplication.replLog("attempting to lock " + accnum);
|
1416 |
1012
|
tao
|
URL u = new URL("https://" + server + "?server="
|
1417 |
|
|
+util.getLocalReplicationServerName()+"&action=getlock&updaterev="
|
1418 |
|
|
+updaterev + "&docid=" + docid);
|
1419 |
|
|
//System.out.println("sending message: " + u.toString());
|
1420 |
569
|
berkley
|
String serverResStr = MetacatReplication.getURLContent(u);
|
1421 |
946
|
tao
|
String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);
|
1422 |
561
|
berkley
|
if(openingtag.equals("<lockgranted>"))
|
1423 |
|
|
{//the lock was granted go ahead with the insert
|
1424 |
571
|
berkley
|
try
|
1425 |
|
|
{
|
1426 |
1012
|
tao
|
//System.out.println("In lockgranted");
|
1427 |
734
|
bojilova
|
MetacatReplication.replLog("lock granted for " + accnum + " from " +
|
1428 |
584
|
berkley
|
server);
|
1429 |
956
|
tao
|
XMLReader parser = initializeParser(conn, action, docid, updaterev,
|
1430 |
|
|
validate, user, groups, pub, serverCode, dtd);
|
1431 |
571
|
berkley
|
conn.setAutoCommit(false);
|
1432 |
695
|
bojilova
|
parser.parse(new InputSource(xml));
|
1433 |
571
|
berkley
|
conn.commit();
|
1434 |
|
|
conn.setAutoCommit(true);
|
1435 |
|
|
}
|
1436 |
|
|
catch (Exception e)
|
1437 |
|
|
{
|
1438 |
|
|
conn.rollback();
|
1439 |
|
|
conn.setAutoCommit(true);
|
1440 |
|
|
throw e;
|
1441 |
|
|
}
|
1442 |
|
|
|
1443 |
590
|
berkley
|
|
1444 |
1039
|
tao
|
|
1445 |
|
|
//If Metacat is super hub, tell all servers in its server list to get
|
1446 |
|
|
//the new document, ture mean it is xml document
|
1447 |
|
|
if ((util.getOption("hub")).equals("super"))
|
1448 |
|
|
{
|
1449 |
|
|
ForceReplicationHandler frh = new ForceReplicationHandler(accnum,
|
1450 |
|
|
true, ReplicationHandler.buildServerList(conn));
|
1451 |
|
|
}
|
1452 |
|
|
else
|
1453 |
|
|
{
|
1454 |
|
|
//after inserting the document locally, tell the document's homeserver
|
1455 |
|
|
//to come get a copy from here.
|
1456 |
|
|
|
1457 |
|
|
ForceReplicationHandler frh = new ForceReplicationHandler(accnum,
|
1458 |
|
|
true, ReplicationHandler.getHomeServer(docid));
|
1459 |
|
|
}
|
1460 |
779
|
bojilova
|
return (accnum);
|
1461 |
561
|
berkley
|
}
|
1462 |
734
|
bojilova
|
|
1463 |
561
|
berkley
|
else if(openingtag.equals("<filelocked>"))
|
1464 |
|
|
{//the file is currently locked by another user
|
1465 |
|
|
//notify our user to wait a few minutes, check out a new copy and try
|
1466 |
|
|
//again.
|
1467 |
584
|
berkley
|
//System.out.println("file locked");
|
1468 |
734
|
bojilova
|
MetacatReplication.replLog("lock denied for " + accnum + " on " +
|
1469 |
584
|
berkley
|
server + " reason: file already locked");
|
1470 |
571
|
berkley
|
throw new Exception("The file specified is already locked by another " +
|
1471 |
|
|
"user. Please wait 30 seconds, checkout the " +
|
1472 |
|
|
"newer document, merge your changes and try " +
|
1473 |
|
|
"again.");
|
1474 |
561
|
berkley
|
}
|
1475 |
|
|
else if(openingtag.equals("<outdatedfile>"))
|
1476 |
|
|
{//our file is outdated. notify our user to check out a new copy of the
|
1477 |
|
|
//file and merge his version with the new version.
|
1478 |
584
|
berkley
|
//System.out.println("outdated file");
|
1479 |
734
|
bojilova
|
MetacatReplication.replLog("lock denied for " + accnum + " on " +
|
1480 |
584
|
berkley
|
server + " reason: local file outdated");
|
1481 |
571
|
berkley
|
throw new Exception("The file you are trying to update is an outdated" +
|
1482 |
|
|
" version. Please checkout the newest document, " +
|
1483 |
|
|
"merge your changes and try again.");
|
1484 |
561
|
berkley
|
}
|
1485 |
559
|
berkley
|
}
|
1486 |
571
|
berkley
|
|
1487 |
425
|
bojilova
|
if ( action.equals("UPDATE") ) {
|
1488 |
441
|
bojilova
|
// check for 'write' permission for 'user' to update this document
|
1489 |
628
|
berkley
|
|
1490 |
802
|
bojilova
|
if ( !hasPermission(conn, user, groups, docid) ) {
|
1491 |
441
|
bojilova
|
throw new Exception("User " + user +
|
1492 |
734
|
bojilova
|
" does not have permission to update XML Document #" + accnum);
|
1493 |
425
|
bojilova
|
}
|
1494 |
|
|
}
|
1495 |
|
|
|
1496 |
571
|
berkley
|
try
|
1497 |
638
|
bojilova
|
{
|
1498 |
956
|
tao
|
|
1499 |
|
|
XMLReader parser = initializeParser(conn, action, docid, rev, validate,
|
1500 |
802
|
bojilova
|
user, groups, pub, serverCode, dtd);
|
1501 |
555
|
bojilova
|
conn.setAutoCommit(false);
|
1502 |
|
|
parser.parse(new InputSource(xml));
|
1503 |
|
|
conn.commit();
|
1504 |
|
|
conn.setAutoCommit(true);
|
1505 |
571
|
berkley
|
}
|
1506 |
|
|
catch (Exception e)
|
1507 |
|
|
{
|
1508 |
555
|
bojilova
|
conn.rollback();
|
1509 |
|
|
conn.setAutoCommit(true);
|
1510 |
|
|
throw e;
|
1511 |
|
|
}
|
1512 |
577
|
berkley
|
|
1513 |
|
|
//force replicate out the new document to each server in our server list.
|
1514 |
|
|
if(serverCode == 1)
|
1515 |
1012
|
tao
|
{
|
1516 |
|
|
|
1517 |
|
|
//start the thread to replicate this new document out to the other servers
|
1518 |
1021
|
tao
|
//true mean it is xml document
|
1519 |
|
|
ForceReplicationHandler frh = new ForceReplicationHandler
|
1520 |
1039
|
tao
|
(accnum, action, true,ReplicationHandler.buildServerList(conn));
|
1521 |
956
|
tao
|
|
1522 |
577
|
berkley
|
}
|
1523 |
457
|
bojilova
|
|
1524 |
779
|
bojilova
|
return(accnum);
|
1525 |
393
|
jones
|
}
|
1526 |
396
|
jones
|
|
1527 |
407
|
jones
|
/**
|
1528 |
1055
|
tao
|
* Write an XML file to the database during replication
|
1529 |
|
|
*
|
1530 |
|
|
* @param conn the JDBC connection to the database
|
1531 |
|
|
* @param xml the xml stream to be loaded into the database
|
1532 |
|
|
* @param pub flag for public "read" access on xml document
|
1533 |
|
|
* @param dtd the dtd to be uploaded on server's file system
|
1534 |
|
|
* @param action the action to be performed (INSERT or UPDATE)
|
1535 |
|
|
* @param accnum the docid + rev# to use on INSERT or UPDATE
|
1536 |
|
|
* @param user the user that owns the document
|
1537 |
|
|
* @param groups the groups to which user belongs
|
1538 |
|
|
* @param homeServer the name of server which the document origanlly create
|
1539 |
|
|
* @param validate, if the xml document is valid or not
|
1540 |
|
|
*/
|
1541 |
|
|
|
1542 |
|
|
public static String writeReplication( Connection conn,Reader xml,String pub,
|
1543 |
|
|
Reader dtd, String action, String accnum, String user,
|
1544 |
|
|
String[] groups,String homeServer, boolean validate)
|
1545 |
|
|
throws Exception
|
1546 |
|
|
{
|
1547 |
|
|
// NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
|
1548 |
|
|
MetaCatUtil util = new MetaCatUtil();
|
1549 |
1069
|
tao
|
//AccessionNumber ac = new AccessionNumber(conn, accnum, action);
|
1550 |
|
|
//String docid = ac.getDocid();
|
1551 |
|
|
// String rev = ac.getRev();
|
1552 |
|
|
String docid=util.getDocIdFromString(accnum);
|
1553 |
|
|
String rev=(new Integer(util.getVersionFromString(accnum))).toString();
|
1554 |
|
|
|
1555 |
|
|
//check if xml_documents table has the document or not
|
1556 |
|
|
//if not, set action to insert
|
1557 |
|
|
if (getLatestRevisionNumber(conn,docid)==-1)
|
1558 |
|
|
{
|
1559 |
|
|
action="INSERT";
|
1560 |
|
|
}
|
1561 |
|
|
|
1562 |
1055
|
tao
|
int serverCode=-2;
|
1563 |
|
|
//get server code for the home server
|
1564 |
|
|
serverCode=getServerCode(homeServer);
|
1565 |
|
|
//if the server is not in the xml replication table, insert it.
|
1566 |
|
|
if (serverCode==-1)
|
1567 |
|
|
{
|
1568 |
|
|
insertServerIntoReplicationTable(homeServer);
|
1569 |
|
|
//get server code again
|
1570 |
|
|
serverCode=getServerCode(homeServer);
|
1571 |
|
|
}
|
1572 |
|
|
|
1573 |
|
|
MetaCatUtil.debugMessage("action: " + action + " servercode: " +
|
1574 |
|
|
serverCode, 10);
|
1575 |
|
|
|
1576 |
1069
|
tao
|
/*if((serverCode != 1 && action.equals("UPDATE")) )
|
1577 |
|
|
{
|
1578 |
1055
|
tao
|
int istreamInt;
|
1579 |
|
|
char istreamChar;
|
1580 |
|
|
DocumentIdentifier id = new DocumentIdentifier(accnum);
|
1581 |
|
|
String updaterev = id.getRev();
|
1582 |
|
|
String server = MetacatReplication.getServer(serverCode);
|
1583 |
|
|
MetacatReplication.replLog("attempting to lock " + accnum);
|
1584 |
|
|
URL u = new URL("https://" + server + "?server="
|
1585 |
|
|
+util.getLocalReplicationServerName()+"&action=getlock&updaterev="
|
1586 |
|
|
+updaterev + "&docid=" + docid);
|
1587 |
1069
|
tao
|
|
1588 |
1055
|
tao
|
String serverResStr = MetacatReplication.getURLContent(u);
|
1589 |
|
|
String openingtag =serverResStr.substring(0, serverResStr.indexOf(">")+1);
|
1590 |
|
|
if(openingtag.equals("<lockgranted>"))
|
1591 |
1069
|
tao
|
{
|
1592 |
1055
|
tao
|
try
|
1593 |
|
|
{
|
1594 |
1069
|
tao
|
|
1595 |
1055
|
tao
|
MetacatReplication.replLog("lock granted for " + accnum + " from " +
|
1596 |
|
|
server);
|
1597 |
|
|
XMLReader parser = initializeParser(conn, action, docid, updaterev,
|
1598 |
|
|
validate, user, groups, pub, serverCode, dtd);
|
1599 |
|
|
conn.setAutoCommit(false);
|
1600 |
|
|
parser.parse(new InputSource(xml));
|
1601 |
|
|
conn.commit();
|
1602 |
|
|
conn.setAutoCommit(true);
|
1603 |
|
|
}
|
1604 |
|
|
catch (Exception e)
|
1605 |
|
|
{
|
1606 |
|
|
conn.rollback();
|
1607 |
|
|
conn.setAutoCommit(true);
|
1608 |
|
|
throw e;
|
1609 |
|
|
}
|
1610 |
|
|
return (accnum);
|
1611 |
|
|
}
|
1612 |
|
|
|
1613 |
|
|
else if(openingtag.equals("<filelocked>"))
|
1614 |
1069
|
tao
|
{
|
1615 |
1055
|
tao
|
MetacatReplication.replLog("lock denied for " + accnum + " on " +
|
1616 |
|
|
server + " reason: file already locked");
|
1617 |
|
|
throw new Exception("The file specified is already locked by another " +
|
1618 |
|
|
"user. Please wait 30 seconds, checkout the " +
|
1619 |
|
|
"newer document, merge your changes and try " +
|
1620 |
|
|
"again.");
|
1621 |
|
|
}
|
1622 |
|
|
else if(openingtag.equals("<outdatedfile>"))
|
1623 |
1069
|
tao
|
{
|
1624 |
1055
|
tao
|
MetacatReplication.replLog("lock denied for " + accnum + " on " +
|
1625 |
|
|
server + " reason: local file outdated");
|
1626 |
|
|
throw new Exception("The file you are trying to update is an outdated" +
|
1627 |
|
|
" version. Please checkout the newest document, " +
|
1628 |
|
|
"merge your changes and try again.");
|
1629 |
|
|
}
|
1630 |
1069
|
tao
|
}*/
|
1631 |
1055
|
tao
|
|
1632 |
1069
|
tao
|
/*if ( action.equals("UPDATE") ) {
|
1633 |
|
|
|
1634 |
1055
|
tao
|
if ( !hasPermission(conn, user, groups, docid) ) {
|
1635 |
|
|
throw new Exception("User " + user +
|
1636 |
|
|
" does not have permission to update XML Document #" + accnum);
|
1637 |
|
|
}
|
1638 |
1069
|
tao
|
}*/
|
1639 |
1055
|
tao
|
|
1640 |
|
|
try
|
1641 |
|
|
{
|
1642 |
|
|
|
1643 |
|
|
XMLReader parser = initializeParser(conn, action, docid, rev, validate,
|
1644 |
|
|
user, groups, pub, serverCode, dtd);
|
1645 |
|
|
conn.setAutoCommit(false);
|
1646 |
|
|
parser.parse(new InputSource(xml));
|
1647 |
|
|
conn.commit();
|
1648 |
|
|
conn.setAutoCommit(true);
|
1649 |
|
|
}
|
1650 |
|
|
catch (Exception e)
|
1651 |
|
|
{
|
1652 |
|
|
conn.rollback();
|
1653 |
|
|
conn.setAutoCommit(true);
|
1654 |
|
|
throw e;
|
1655 |
|
|
}
|
1656 |
|
|
|
1657 |
|
|
return(accnum);
|
1658 |
|
|
}
|
1659 |
|
|
|
1660 |
|
|
|
1661 |
|
|
/**
|
1662 |
407
|
jones
|
* Delete an XML file from the database (actually, just make it a revision
|
1663 |
|
|
* in the xml_revisions table)
|
1664 |
|
|
*
|
1665 |
|
|
* @param docid the ID of the document to be deleted from the database
|
1666 |
|
|
*/
|
1667 |
734
|
bojilova
|
public static void delete( Connection conn, String accnum,
|
1668 |
802
|
bojilova
|
String user, String[] groups )
|
1669 |
734
|
bojilova
|
throws Exception
|
1670 |
|
|
{
|
1671 |
779
|
bojilova
|
// OLD
|
1672 |
|
|
//DocumentIdentifier id = new DocumentIdentifier(accnum);
|
1673 |
|
|
//String docid = id.getIdentifier();
|
1674 |
|
|
//String rev = id.getRev();
|
1675 |
628
|
berkley
|
|
1676 |
779
|
bojilova
|
// OLD
|
1677 |
734
|
bojilova
|
// Determine if the docid,rev are OK for DELETE
|
1678 |
779
|
bojilova
|
//AccessionNumber ac = new AccessionNumber(conn);
|
1679 |
|
|
//docid = ac.generate(docid, rev, "DELETE");
|
1680 |
396
|
jones
|
|
1681 |
779
|
bojilova
|
// NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
|
1682 |
|
|
AccessionNumber ac = new AccessionNumber(conn, accnum, "DELETE");
|
1683 |
|
|
String docid = ac.getDocid();
|
1684 |
|
|
String rev = ac.getRev();
|
1685 |
|
|
|
1686 |
|
|
|
1687 |
441
|
bojilova
|
// check for 'write' permission for 'user' to delete this document
|
1688 |
802
|
bojilova
|
if ( !hasPermission(conn, user, groups, docid) ) {
|
1689 |
441
|
bojilova
|
throw new Exception("User " + user +
|
1690 |
734
|
bojilova
|
" does not have permission to delete XML Document #" + accnum);
|
1691 |
425
|
bojilova
|
}
|
1692 |
|
|
|
1693 |
407
|
jones
|
conn.setAutoCommit(false);
|
1694 |
|
|
// Copy the record to the xml_revisions table
|
1695 |
425
|
bojilova
|
DocumentImpl.archiveDocRevision( conn, docid, user );
|
1696 |
396
|
jones
|
|
1697 |
407
|
jones
|
// Now delete it from the xml_documents table
|
1698 |
628
|
berkley
|
|
1699 |
407
|
jones
|
Statement stmt = conn.createStatement();
|
1700 |
425
|
bojilova
|
stmt.execute("DELETE FROM xml_index WHERE docid = '" + docid + "'");
|
1701 |
688
|
bojilova
|
//stmt.execute("DELETE FROM xml_access WHERE docid = '" + docid + "'");
|
1702 |
645
|
bojilova
|
stmt.execute("DELETE FROM xml_access WHERE accessfileid = '" + docid + "'");
|
1703 |
|
|
stmt.execute("DELETE FROM xml_relation WHERE docid = '" + docid + "'");
|
1704 |
785
|
bojilova
|
stmt.execute("DELETE FROM xml_documents WHERE docid = '" + docid + "'");
|
1705 |
407
|
jones
|
stmt.close();
|
1706 |
|
|
conn.commit();
|
1707 |
457
|
bojilova
|
conn.setAutoCommit(true);
|
1708 |
634
|
berkley
|
//IF this is a package document:
|
1709 |
|
|
//delete all of the relations that this document created.
|
1710 |
|
|
//if the deleted document is a package document its relations should
|
1711 |
|
|
//no longer be active if it has been deleted from the system.
|
1712 |
645
|
bojilova
|
|
1713 |
407
|
jones
|
}
|
1714 |
638
|
bojilova
|
|
1715 |
570
|
bojilova
|
/**
|
1716 |
802
|
bojilova
|
* Check for "WRITE" permission on @docid for @user and/or @groups
|
1717 |
570
|
bojilova
|
* from DB connection
|
1718 |
|
|
*/
|
1719 |
802
|
bojilova
|
private static boolean hasPermission ( Connection conn, String user,
|
1720 |
|
|
String[] groups, String docid )
|
1721 |
958
|
tao
|
throws SQLException, Exception
|
1722 |
570
|
bojilova
|
{
|
1723 |
802
|
bojilova
|
// Check for WRITE permission on @docid for @user and/or @groups
|
1724 |
570
|
bojilova
|
AccessControlList aclobj = new AccessControlList(conn);
|
1725 |
802
|
bojilova
|
return aclobj.hasPermission("WRITE", user, groups, docid);
|
1726 |
425
|
bojilova
|
}
|
1727 |
|
|
|
1728 |
946
|
tao
|
/**
|
1729 |
|
|
* Check for "READ" permission base on docid, user and group
|
1730 |
|
|
*@docid, the document
|
1731 |
|
|
*@user, user name
|
1732 |
|
|
*@group, user's group
|
1733 |
|
|
*
|
1734 |
|
|
*/
|
1735 |
|
|
public boolean hasReadPermission ( Connection conn, String user,
|
1736 |
|
|
String[] groups, String docId )
|
1737 |
958
|
tao
|
throws SQLException, Exception
|
1738 |
946
|
tao
|
{
|
1739 |
|
|
// Check for READ permission on @docid for @user and/or @groups
|
1740 |
|
|
AccessControlList aclObj = new AccessControlList(conn);
|
1741 |
|
|
return aclObj.hasPermission("READ", user, groups, docId);
|
1742 |
|
|
}
|
1743 |
|
|
|
1744 |
396
|
jones
|
/**
|
1745 |
407
|
jones
|
* Set up the parser handlers for writing the document to the database
|
1746 |
|
|
*/
|
1747 |
598
|
bojilova
|
private static XMLReader initializeParser(Connection conn, String action,
|
1748 |
956
|
tao
|
String docid, String rev, boolean validate,
|
1749 |
802
|
bojilova
|
String user, String[] groups, String pub,
|
1750 |
695
|
bojilova
|
int serverCode, Reader dtd)
|
1751 |
598
|
bojilova
|
throws Exception
|
1752 |
|
|
{
|
1753 |
407
|
jones
|
XMLReader parser = null;
|
1754 |
|
|
//
|
1755 |
|
|
// Set up the SAX document handlers for parsing
|
1756 |
|
|
//
|
1757 |
|
|
try {
|
1758 |
956
|
tao
|
//create a DBSAXHandler object which has the revision specification
|
1759 |
|
|
ContentHandler chandler = new DBSAXHandler(conn, action, docid, rev,
|
1760 |
802
|
bojilova
|
user, groups, pub, serverCode);
|
1761 |
645
|
bojilova
|
EntityResolver eresolver= new DBEntityResolver(conn,
|
1762 |
|
|
(DBSAXHandler)chandler, dtd);
|
1763 |
598
|
bojilova
|
DTDHandler dtdhandler = new DBDTDHandler(conn);
|
1764 |
407
|
jones
|
|
1765 |
|
|
// Get an instance of the parser
|
1766 |
802
|
bojilova
|
String parserName = MetaCatUtil.getOption("saxparser");
|
1767 |
407
|
jones
|
parser = XMLReaderFactory.createXMLReader(parserName);
|
1768 |
|
|
|
1769 |
660
|
bojilova
|
// Turn on validation
|
1770 |
695
|
bojilova
|
parser.setFeature("http://xml.org/sax/features/validation", validate);
|
1771 |
660
|
bojilova
|
// Turn off Including all external parameter entities
|
1772 |
|
|
// (the external DTD subset also)
|
1773 |
|
|
// Doesn't work well, probably the feature name is not correct
|
1774 |
|
|
// parser.setFeature(
|
1775 |
|
|
// "http://xml.org/sax/features/external-parameter-entities", false);
|
1776 |
407
|
jones
|
|
1777 |
|
|
// Set Handlers in the parser
|
1778 |
|
|
parser.setProperty("http://xml.org/sax/properties/declaration-handler",
|
1779 |
|
|
chandler);
|
1780 |
|
|
parser.setProperty("http://xml.org/sax/properties/lexical-handler",
|
1781 |
|
|
chandler);
|
1782 |
|
|
parser.setContentHandler((ContentHandler)chandler);
|
1783 |
598
|
bojilova
|
parser.setEntityResolver((EntityResolver)eresolver);
|
1784 |
407
|
jones
|
parser.setDTDHandler((DTDHandler)dtdhandler);
|
1785 |
|
|
parser.setErrorHandler((ErrorHandler)chandler);
|
1786 |
|
|
|
1787 |
|
|
} catch (Exception e) {
|
1788 |
457
|
bojilova
|
throw e;
|
1789 |
407
|
jones
|
}
|
1790 |
|
|
|
1791 |
|
|
return parser;
|
1792 |
|
|
}
|
1793 |
|
|
|
1794 |
459
|
bojilova
|
/** Save a document entry in the xml_revisions table */
|
1795 |
|
|
private static void archiveDocRevision(Connection conn, String docid,
|
1796 |
552
|
berkley
|
String user)
|
1797 |
1063
|
tao
|
{
|
1798 |
754
|
bojilova
|
String sysdate = dbAdapter.getDateTimeFunction();
|
1799 |
459
|
bojilova
|
// create a record in xml_revisions table
|
1800 |
|
|
// for that document as selected from xml_documents
|
1801 |
1063
|
tao
|
|
1802 |
|
|
try
|
1803 |
|
|
{
|
1804 |
|
|
PreparedStatement pstmt = conn.prepareStatement(
|
1805 |
459
|
bojilova
|
"INSERT INTO xml_revisions " +
|
1806 |
771
|
bojilova
|
"(docid, rootnodeid, docname, doctype, " +
|
1807 |
697
|
bojilova
|
"user_owner, user_updated, date_created, date_updated, " +
|
1808 |
|
|
"server_location, rev, public_access, catalog_id) " +
|
1809 |
771
|
bojilova
|
"SELECT ?, rootnodeid, docname, doctype, " +
|
1810 |
747
|
bojilova
|
"user_owner, ?, " + sysdate + ", " + sysdate + ", "+
|
1811 |
|
|
"server_location, rev, public_access, catalog_id " +
|
1812 |
459
|
bojilova
|
"FROM xml_documents " +
|
1813 |
|
|
"WHERE docid = ?");
|
1814 |
1063
|
tao
|
// Bind the values to the query and execute it
|
1815 |
|
|
pstmt.setString(1, docid);
|
1816 |
|
|
pstmt.setString(2, user);
|
1817 |
|
|
pstmt.setString(3, docid);
|
1818 |
|
|
pstmt.execute();
|
1819 |
|
|
pstmt.close();
|
1820 |
|
|
}
|
1821 |
|
|
catch (SQLException e)
|
1822 |
|
|
{
|
1823 |
|
|
}
|
1824 |
|
|
|
1825 |
459
|
bojilova
|
|
1826 |
|
|
}
|
1827 |
965
|
tao
|
|
1828 |
|
|
/**
|
1829 |
|
|
* delete a entry in xml_table for given docid
|
1830 |
|
|
* @param docId, the id of the document need to be delete
|
1831 |
|
|
*/
|
1832 |
|
|
private static void deleteXMLDocuments(Connection conn, String docId)
|
1833 |
|
|
throws SQLException
|
1834 |
|
|
{
|
1835 |
|
|
//delete a record
|
1836 |
|
|
PreparedStatement pStmt =
|
1837 |
|
|
conn.prepareStatement("DELETE FROM xml_documents WHERE docid = '"
|
1838 |
|
|
+ docId + "'");
|
1839 |
|
|
pStmt.execute();
|
1840 |
|
|
pStmt.close();
|
1841 |
459
|
bojilova
|
|
1842 |
965
|
tao
|
}//deleteXMLDocuments
|
1843 |
|
|
|
1844 |
407
|
jones
|
/**
|
1845 |
965
|
tao
|
* Get last revision number from database for a docid
|
1846 |
|
|
* If couldn't find an entry, -1 will return
|
1847 |
|
|
* The return value is integer because we want compare it to there new one
|
1848 |
|
|
* @param docid <sitecode>.<uniqueid> part of Accession Number
|
1849 |
|
|
*/
|
1850 |
|
|
private static int getLatestRevisionNumber(Connection conn, String docId)
|
1851 |
|
|
throws SQLException
|
1852 |
|
|
{
|
1853 |
|
|
int rev = 1;
|
1854 |
|
|
PreparedStatement pStmt;
|
1855 |
|
|
|
1856 |
|
|
pStmt = conn.prepareStatement
|
1857 |
|
|
("SELECT rev FROM xml_documents WHERE docid='" + docId + "'");
|
1858 |
|
|
pStmt.execute();
|
1859 |
|
|
|
1860 |
|
|
ResultSet rs = pStmt.getResultSet();
|
1861 |
|
|
boolean hasRow = rs.next();
|
1862 |
|
|
if (hasRow)
|
1863 |
|
|
{
|
1864 |
|
|
rev = rs.getInt(1);
|
1865 |
|
|
pStmt.close();
|
1866 |
|
|
}
|
1867 |
|
|
else
|
1868 |
|
|
{
|
1869 |
|
|
rev=-1;
|
1870 |
|
|
pStmt.close();
|
1871 |
|
|
}
|
1872 |
|
|
|
1873 |
|
|
return rev;
|
1874 |
|
|
}//getLatestRevisionNumber
|
1875 |
|
|
|
1876 |
|
|
/**
|
1877 |
1012
|
tao
|
* Get server location form database for a accNum
|
1878 |
|
|
*
|
1879 |
|
|
* @param accum <sitecode>.<uniqueid>.<rev>
|
1880 |
|
|
*/
|
1881 |
|
|
private static int getServerLocationNumber(Connection conn, String accNum)
|
1882 |
|
|
throws SQLException
|
1883 |
|
|
{
|
1884 |
|
|
//get rid of revNum part
|
1885 |
|
|
String docId=MetaCatUtil.getDocIdFromString(accNum);
|
1886 |
|
|
PreparedStatement pStmt;
|
1887 |
|
|
int serverLocation;
|
1888 |
|
|
|
1889 |
|
|
pStmt = conn.prepareStatement
|
1890 |
|
|
("SELECT server_location FROM xml_documents WHERE docid='" + docId + "'");
|
1891 |
|
|
pStmt.execute();
|
1892 |
|
|
|
1893 |
|
|
ResultSet rs = pStmt.getResultSet();
|
1894 |
|
|
boolean hasRow = rs.next();
|
1895 |
|
|
//if there is entry in xml_documents, get the serverlocation
|
1896 |
|
|
if (hasRow)
|
1897 |
|
|
{
|
1898 |
|
|
serverLocation = rs.getInt(1);
|
1899 |
|
|
pStmt.close();
|
1900 |
|
|
}
|
1901 |
|
|
else
|
1902 |
|
|
{
|
1903 |
|
|
// if htere is no entry in xml_documents, we consider it is new document
|
1904 |
|
|
// the server location is local host and value is 1
|
1905 |
|
|
serverLocation=1;
|
1906 |
|
|
pStmt.close();
|
1907 |
|
|
}
|
1908 |
|
|
|
1909 |
|
|
return serverLocation;
|
1910 |
|
|
}
|
1911 |
1055
|
tao
|
|
1912 |
1012
|
tao
|
/**
|
1913 |
1055
|
tao
|
* Given a server name, return its servercode in xml_replication table.
|
1914 |
|
|
* If no server is found, -1 will return
|
1915 |
|
|
* @param serverName,
|
1916 |
|
|
*/
|
1917 |
|
|
private static int getServerCode(String serverName)
|
1918 |
|
|
{
|
1919 |
|
|
PreparedStatement pStmt=null;
|
1920 |
|
|
int serverLocation=-2;
|
1921 |
|
|
Connection dbConn = null;
|
1922 |
|
|
MetaCatUtil util = new MetaCatUtil();
|
1923 |
|
|
|
1924 |
|
|
|
1925 |
|
|
//we should consider about local host too
|
1926 |
|
|
if (serverName.equals(util.getLocalReplicationServerName()))
|
1927 |
|
|
{
|
1928 |
|
|
serverLocation=1;
|
1929 |
|
|
return serverLocation;
|
1930 |
|
|
}
|
1931 |
|
|
|
1932 |
|
|
|
1933 |
|
|
try
|
1934 |
|
|
{
|
1935 |
|
|
//check xml_replication table
|
1936 |
1063
|
tao
|
dbConn=util.openDBConnection();
|
1937 |
1055
|
tao
|
pStmt = dbConn.prepareStatement
|
1938 |
|
|
("SELECT serverid FROM xml_replication WHERE server='" + serverName +"'");
|
1939 |
|
|
pStmt.execute();
|
1940 |
|
|
|
1941 |
|
|
ResultSet rs = pStmt.getResultSet();
|
1942 |
|
|
boolean hasRow = rs.next();
|
1943 |
|
|
//if there is entry in xml_replication, get the serverid
|
1944 |
|
|
if (hasRow)
|
1945 |
|
|
{
|
1946 |
|
|
serverLocation = rs.getInt(1);
|
1947 |
|
|
pStmt.close();
|
1948 |
|
|
}
|
1949 |
|
|
else
|
1950 |
|
|
{
|
1951 |
|
|
// if htere is no entry in xml_replication, -1 will return
|
1952 |
|
|
serverLocation=-1;
|
1953 |
|
|
pStmt.close();
|
1954 |
|
|
}
|
1955 |
|
|
}
|
1956 |
|
|
catch (Exception e)
|
1957 |
|
|
{
|
1958 |
|
|
util.debugMessage("Error in DocumentImpl.getServerCode(): "
|
1959 |
|
|
+e.getMessage(), 30);
|
1960 |
|
|
}
|
1961 |
|
|
finally
|
1962 |
|
|
{
|
1963 |
|
|
try
|
1964 |
|
|
{
|
1965 |
1063
|
tao
|
dbConn.close();
|
1966 |
1055
|
tao
|
}
|
1967 |
|
|
catch (Exception ee)
|
1968 |
|
|
{}
|
1969 |
|
|
}
|
1970 |
|
|
|
1971 |
|
|
|
1972 |
|
|
return serverLocation;
|
1973 |
|
|
}
|
1974 |
|
|
|
1975 |
|
|
/**
|
1976 |
|
|
* Insert a server into xml_replcation table
|
1977 |
|
|
* @param server, the name of server
|
1978 |
|
|
*/
|
1979 |
|
|
private static void insertServerIntoReplicationTable(String server)
|
1980 |
|
|
{
|
1981 |
|
|
PreparedStatement pStmt=null;
|
1982 |
|
|
Connection dbConn = null;
|
1983 |
|
|
int replicate = 1;
|
1984 |
|
|
MetaCatUtil util = new MetaCatUtil();
|
1985 |
|
|
try
|
1986 |
|
|
{
|
1987 |
1063
|
tao
|
dbConn=util.openDBConnection();
|
1988 |
1055
|
tao
|
pStmt = dbConn.prepareStatement("INSERT INTO xml_replication " +
|
1989 |
|
|
"(server, last_checked, replicate) " +
|
1990 |
|
|
"VALUES ('" + server + "', to_date(" +
|
1991 |
|
|
"'01/01/00', 'MM/DD/YY'), '" +
|
1992 |
|
|
replicate + "')");
|
1993 |
|
|
pStmt.execute();
|
1994 |
|
|
pStmt.close();
|
1995 |
|
|
dbConn.commit();
|
1996 |
|
|
}
|
1997 |
|
|
catch (Exception e)
|
1998 |
|
|
{
|
1999 |
|
|
util.debugMessage("Error in DocumentImpl.getServerCode(): "
|
2000 |
|
|
+e.getMessage(), 30);
|
2001 |
|
|
}
|
2002 |
|
|
finally
|
2003 |
|
|
{
|
2004 |
|
|
try
|
2005 |
|
|
{
|
2006 |
|
|
pStmt.close();
|
2007 |
1063
|
tao
|
dbConn.close();
|
2008 |
1055
|
tao
|
}
|
2009 |
|
|
catch (Exception ee)
|
2010 |
|
|
{}
|
2011 |
|
|
}
|
2012 |
|
|
|
2013 |
|
|
}
|
2014 |
|
|
|
2015 |
|
|
|
2016 |
|
|
/**
|
2017 |
407
|
jones
|
* the main routine used to test the DBWriter utility.
|
2018 |
|
|
* <p>
|
2019 |
|
|
* Usage: java DocumentImpl <-f filename -a action -d docid>
|
2020 |
|
|
*
|
2021 |
|
|
* @param filename the filename to be loaded into the database
|
2022 |
|
|
* @param action the action to perform (READ, INSERT, UPDATE, DELETE)
|
2023 |
|
|
* @param docid the id of the document to process
|
2024 |
|
|
*/
|
2025 |
|
|
static public void main(String[] args) {
|
2026 |
|
|
|
2027 |
|
|
try {
|
2028 |
555
|
bojilova
|
String filename = null;
|
2029 |
598
|
bojilova
|
String dtdfilename = null;
|
2030 |
555
|
bojilova
|
String action = null;
|
2031 |
|
|
String docid = null;
|
2032 |
429
|
jones
|
boolean showRuntime = false;
|
2033 |
|
|
boolean useOldReadAlgorithm = false;
|
2034 |
407
|
jones
|
|
2035 |
408
|
jones
|
// Parse the command line arguments
|
2036 |
407
|
jones
|
for ( int i=0 ; i < args.length; ++i ) {
|
2037 |
|
|
if ( args[i].equals( "-f" ) ) {
|
2038 |
|
|
filename = args[++i];
|
2039 |
598
|
bojilova
|
} else if ( args[i].equals( "-r" ) ) {
|
2040 |
|
|
dtdfilename = args[++i];
|
2041 |
407
|
jones
|
} else if ( args[i].equals( "-a" ) ) {
|
2042 |
|
|
action = args[++i];
|
2043 |
|
|
} else if ( args[i].equals( "-d" ) ) {
|
2044 |
|
|
docid = args[++i];
|
2045 |
429
|
jones
|
} else if ( args[i].equals( "-t" ) ) {
|
2046 |
|
|
showRuntime = true;
|
2047 |
|
|
} else if ( args[i].equals( "-old" ) ) {
|
2048 |
|
|
useOldReadAlgorithm = true;
|
2049 |
407
|
jones
|
} else {
|
2050 |
|
|
System.err.println
|
2051 |
|
|
( " args[" +i+ "] '" +args[i]+ "' ignored." );
|
2052 |
|
|
}
|
2053 |
|
|
}
|
2054 |
|
|
|
2055 |
408
|
jones
|
// Check if the required arguments are provided
|
2056 |
407
|
jones
|
boolean argsAreValid = false;
|
2057 |
|
|
if (action != null) {
|
2058 |
|
|
if (action.equals("INSERT")) {
|
2059 |
|
|
if (filename != null) {
|
2060 |
|
|
argsAreValid = true;
|
2061 |
|
|
}
|
2062 |
|
|
} else if (action.equals("UPDATE")) {
|
2063 |
|
|
if ((filename != null) && (docid != null)) {
|
2064 |
|
|
argsAreValid = true;
|
2065 |
|
|
}
|
2066 |
|
|
} else if (action.equals("DELETE")) {
|
2067 |
|
|
if (docid != null) {
|
2068 |
|
|
argsAreValid = true;
|
2069 |
|
|
}
|
2070 |
|
|
} else if (action.equals("READ")) {
|
2071 |
|
|
if (docid != null) {
|
2072 |
|
|
argsAreValid = true;
|
2073 |
|
|
}
|
2074 |
|
|
}
|
2075 |
|
|
}
|
2076 |
|
|
|
2077 |
408
|
jones
|
// Print usage message if the arguments are not valid
|
2078 |
407
|
jones
|
if (!argsAreValid) {
|
2079 |
|
|
System.err.println("Wrong number of arguments!!!");
|
2080 |
|
|
System.err.println(
|
2081 |
598
|
bojilova
|
"USAGE: java DocumentImpl [-t] <-a INSERT> [-d docid] <-f filename> "+
|
2082 |
680
|
bojilova
|
"[-r dtdfilename]");
|
2083 |
407
|
jones
|
System.err.println(
|
2084 |
598
|
bojilova
|
" OR: java DocumentImpl [-t] <-a UPDATE -d docid -f filename> " +
|
2085 |
680
|
bojilova
|
"[-r dtdfilename]");
|
2086 |
407
|
jones
|
System.err.println(
|
2087 |
429
|
jones
|
" OR: java DocumentImpl [-t] <-a DELETE -d docid>");
|
2088 |
407
|
jones
|
System.err.println(
|
2089 |
429
|
jones
|
" OR: java DocumentImpl [-t] [-old] <-a READ -d docid>");
|
2090 |
407
|
jones
|
return;
|
2091 |
|
|
}
|
2092 |
429
|
jones
|
|
2093 |
|
|
// Time the request if asked for
|
2094 |
|
|
double startTime = System.currentTimeMillis();
|
2095 |
|
|
|
2096 |
407
|
jones
|
// Open a connection to the database
|
2097 |
|
|
MetaCatUtil util = new MetaCatUtil();
|
2098 |
|
|
Connection dbconn = util.openDBConnection();
|
2099 |
|
|
|
2100 |
463
|
berkley
|
double connTime = System.currentTimeMillis();
|
2101 |
408
|
jones
|
// Execute the action requested (READ, INSERT, UPDATE, DELETE)
|
2102 |
407
|
jones
|
if (action.equals("READ")) {
|
2103 |
|
|
DocumentImpl xmldoc = new DocumentImpl( dbconn, docid );
|
2104 |
429
|
jones
|
if (useOldReadAlgorithm) {
|
2105 |
|
|
System.out.println(xmldoc.readUsingSlowAlgorithm());
|
2106 |
|
|
} else {
|
2107 |
|
|
xmldoc.toXml(new PrintWriter(System.out));
|
2108 |
|
|
}
|
2109 |
408
|
jones
|
} else if (action.equals("DELETE")) {
|
2110 |
425
|
bojilova
|
DocumentImpl.delete(dbconn, docid, null, null);
|
2111 |
408
|
jones
|
System.out.println("Document deleted: " + docid);
|
2112 |
407
|
jones
|
} else {
|
2113 |
680
|
bojilova
|
String newdocid = DocumentImpl.write(dbconn, filename, null,
|
2114 |
598
|
bojilova
|
dtdfilename, action, docid,
|
2115 |
|
|
null, null);
|
2116 |
408
|
jones
|
if ((docid != null) && (!docid.equals(newdocid))) {
|
2117 |
|
|
if (action.equals("INSERT")) {
|
2118 |
|
|
System.out.println("New document ID generated!!! ");
|
2119 |
|
|
} else if (action.equals("UPDATE")) {
|
2120 |
|
|
System.out.println("ERROR: Couldn't update document!!! ");
|
2121 |
407
|
jones
|
}
|
2122 |
408
|
jones
|
} else if ((docid == null) && (action.equals("UPDATE"))) {
|
2123 |
|
|
System.out.println("ERROR: Couldn't update document!!! ");
|
2124 |
407
|
jones
|
}
|
2125 |
408
|
jones
|
System.out.println("Document processing finished for: " + filename
|
2126 |
|
|
+ " (" + newdocid + ")");
|
2127 |
407
|
jones
|
}
|
2128 |
|
|
|
2129 |
429
|
jones
|
double stopTime = System.currentTimeMillis();
|
2130 |
463
|
berkley
|
double dbOpenTime = (connTime - startTime)/1000;
|
2131 |
|
|
double insertTime = (stopTime - connTime)/1000;
|
2132 |
429
|
jones
|
double executionTime = (stopTime - startTime)/1000;
|
2133 |
|
|
if (showRuntime) {
|
2134 |
463
|
berkley
|
System.out.println("\n\nTotal Execution time was: " +
|
2135 |
|
|
executionTime + " seconds.");
|
2136 |
|
|
System.out.println("Time to open DB connection was: " + dbOpenTime +
|
2137 |
|
|
" seconds.");
|
2138 |
|
|
System.out.println("Time to insert document was: " + insertTime +
|
2139 |
|
|
" seconds.");
|
2140 |
429
|
jones
|
}
|
2141 |
463
|
berkley
|
dbconn.close();
|
2142 |
407
|
jones
|
} catch (McdbException me) {
|
2143 |
|
|
me.toXml(new PrintWriter(System.err));
|
2144 |
|
|
} catch (AccessionNumberException ane) {
|
2145 |
|
|
System.out.println(ane.getMessage());
|
2146 |
|
|
} catch (Exception e) {
|
2147 |
|
|
System.err.println("EXCEPTION HANDLING REQUIRED");
|
2148 |
|
|
System.err.println(e.getMessage());
|
2149 |
|
|
e.printStackTrace(System.err);
|
2150 |
|
|
}
|
2151 |
|
|
}
|
2152 |
393
|
jones
|
}
|