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/**
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* '$RCSfile$'
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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: @tao@
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* Release: @release@
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*
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* '$Author: tao $'
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* '$Date: 2002-11-12 11:42:55 -0800 (Tue, 12 Nov 2002) $'
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* '$Revision: 1331 $'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat;
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import edu.ucsb.nceas.morpho.datapackage.PackageUtil;
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import edu.ucsb.nceas.morpho.datapackage.Triple;
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import edu.ucsb.nceas.morpho.datapackage.TripleCollection;
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import java.io.FileOutputStream;
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import java.io.PrintWriter;
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import java .io.StringReader;
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import java.sql.ResultSet;
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import java.sql.PreparedStatement;
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import java.sql.SQLException;
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import java.util.Vector;
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import org.apache.xerces.parsers.DOMParser;
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import org.apache.xpath.XPathAPI;
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import org.w3c.dom.Attr;
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import org.w3c.dom.NamedNodeMap;
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import org.w3c.dom.NodeList;
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import org.w3c.dom.Document;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import org.w3c.dom.DocumentType;
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import org.xml.sax.InputSource;
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/**
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* This class is used to clean up access table in knb. It will delete any access
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* control rules which are not in access xml doc (someone add them into table
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* directly). It will update data set doc according new triples in access table.
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*/
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public class CleanupAccessTable
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{
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private static final String TRIPLESTAG = "//triple";
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private static final String IDENTIFIER = "//identifier";
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private static final String RELATIONSHIP = "provides access control rules for";
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public static final String DELIMITER = "!";
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private static final String DOT = ".";
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private static final String LOGFILENAME = "log";
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private static final String ALLOW = "allow";
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private static final String ALLOWPATH ="//allow";
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private static final String DENY = "deny";
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private static final String DENYPATH = "//deny";
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/**
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* A method to add a new triple to a data set doc and update data set doc
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* in metacat db
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*
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* @param accessionNumber the accession number of the data set doc
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* @param newTripleVector the vector containing new triples need to be added
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* into the data set doc
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*/
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public static void addNewTripleIntoDataset(String accessionNumber,
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Vector newTripleVector)
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{
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String docidWithoutVersion = null;
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int rev = 0;
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// check parameter
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if (newTripleVector.size()==0 || accessionNumber == null ||
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accessionNumber.equals(""))
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{
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return;
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}
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DocumentImpl doc = null;
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try
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{
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docidWithoutVersion = MetaCatUtil.getDocIdFromString(accessionNumber);
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rev = MetaCatUtil.getVersionFromString(accessionNumber);
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doc = new DocumentImpl(accessionNumber);
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}
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catch (Exception e)
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{
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MetaCatUtil.debugMessage("error in create an document: "
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+ e.getMessage(), 30);
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return;
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}
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String xmlDoc = doc.toString();
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// create new triple collection
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TripleCollection newTripleForDataSet = new TripleCollection();
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for (int i = 0; i<newTripleVector.size(); i++)
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{
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//Add new tripe
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Triple triple = (Triple)newTripleVector.elementAt(i);
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MetaCatUtil.debugMessage("New triple: "+triple.toString(), 30);
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newTripleForDataSet.addTriple(triple);
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}
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xmlDoc = addTriplesToTriplesString(newTripleForDataSet, xmlDoc, TRIPLESTAG);
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// Update accessNumber
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Vector oldAccessNumberVector = new Vector();
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Vector newAccessNumberVector = new Vector();
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oldAccessNumberVector.addElement(accessionNumber);
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//increase rev number
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rev++;
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accessionNumber = docidWithoutVersion + "." + rev;
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newAccessNumberVector.addElement(accessionNumber);
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xmlDoc = incRevInTriples(xmlDoc, oldAccessNumberVector,
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newAccessNumberVector, TRIPLESTAG);
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// update database
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StringReader xml = new StringReader(xmlDoc);
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String pub = "no";
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StringReader dtd = null;
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String doAction = "UPDATE";
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boolean validate = true;
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DBConnection dbConn = null;
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int serialNumber = -1;
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try
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{
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dbConn=DBConnectionPool.
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getDBConnection("DBQuery.getDataPackageId");
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serialNumber=dbConn.getCheckOutSerialNumber();
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DocumentImpl.write(dbConn, xml, pub, dtd, doAction,
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accessionNumber, null, null, validate);
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MetaCatUtil.debugMessage("update data set file: "+ accessionNumber, 30);
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writeToLogFile("Update data set file: " + accessionNumber);
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writeToLogFile("New triples added are: "+ newTripleVector.toString());
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writeToLogFile("\n");
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}
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catch (Exception e)
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{
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MetaCatUtil.debugMessage("error in addNewTripleIntoDataset: "+
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e.getMessage(), 30);
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}
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finally
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{
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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}
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}
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/**
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* method to add a collection of triples to a triples string. this method
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* searches for any triples already in the string and appends the new
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* ones after the existing ones.
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* @param triples the collection of triples to add
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* @param dataPackageString the xml document of data set
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* @param triplesTag the trip tag in xml docment
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*/
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private static String addTriplesToTriplesString(TripleCollection triples,
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String dataPackageString,
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String triplesTag)
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{
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//String triplesTag = morpho.getConfiguration().get("triplesTag", 0);
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Document doc = null;
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DOMParser parser = new DOMParser();
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InputSource in;
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StringReader sr;
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try
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{ //parse the wizard created file with existing triples
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sr = new StringReader(dataPackageString);
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in = new InputSource(sr);
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}
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catch(Exception fnf)
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{
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fnf.printStackTrace();
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return null;
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}
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try
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{
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parser.parse(in);
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sr.close();
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}
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catch(Exception e1)
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{
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System.err.println(e1.toString());
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}
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doc = parser.getDocument();
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//get the DOM rep of the document with existing triples
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NodeList tripleNodeList = triples.getNodeList();
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NodeList docTriplesNodeList = null;
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try
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{
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//find where the triples go in the file
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docTriplesNodeList = XPathAPI.selectNodeList(doc, triplesTag);
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}
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catch(Exception se)
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{
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System.err.println(se.toString());
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}
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Node docNode = doc.getDocumentElement();
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for(int j=0; j<tripleNodeList.getLength(); j++)
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{ //add the triples to the appropriate position in the file
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Node n = doc.importNode(tripleNodeList.item(j), true);
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int end = docTriplesNodeList.getLength() - 1;
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Node triplesNode = docTriplesNodeList.item(end);
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Node parent = triplesNode.getParentNode();
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if(triplesNode.getNextSibling() == null)
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{
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parent.appendChild(n);
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}
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else
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{
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parent.insertBefore(n, triplesNode.getNextSibling());
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}
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}
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String docString = PackageUtil.printDoctype(doc);
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docString += PackageUtil.print(doc.getDocumentElement());
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return docString;
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}
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private static String incRevInTriples(String xml, Vector oldid,
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Vector newid, String triplePath)
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{
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MetaCatUtil.debugMessage("oldid: " + oldid.toString() +
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" newid: " + newid.toString(), 30);
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Document doc = null;
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DOMParser parser = new DOMParser();
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InputSource in;
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StringReader sr;
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try
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{ //parse the wizard created file with existing triples
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sr = new StringReader(xml);
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in = new InputSource(sr);
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}
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catch(Exception fnf)
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{
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fnf.printStackTrace();
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return null;
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}
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try
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{
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parser.parse(in);
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sr.close();
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}
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catch(Exception e1)
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{
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System.err.println(e1.toString());
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}
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doc = parser.getDocument();
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NodeList tripleList = null;
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try
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{
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//find where the triples go in the file
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tripleList = XPathAPI.selectNodeList(doc, triplePath);
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}
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catch(Exception se)
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{
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System.err.println("incRevInTriples() : parse threw: " +
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se.toString());
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}
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for(int i=0; i<tripleList.getLength(); i++)
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{
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Node triple = tripleList.item(i);
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NodeList children = triple.getChildNodes();
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String sub = null;
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String rel = null;
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String obj = null;
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if(children.getLength() > 2)
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{
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for(int j=0; j<children.getLength(); j++)
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{
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Node childNode = children.item(j);
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String nodename = childNode.getNodeName().trim().toUpperCase();
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if(nodename.equals("SUBJECT") || nodename.equals("OBJECT"))
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{
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String nodeval;
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try
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{
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nodeval = childNode.getFirstChild().getNodeValue().trim();
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}
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catch(NullPointerException npe)
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{
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continue;
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}
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if(oldid.contains(nodeval.trim()))
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{
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String newidS = "";
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for(int k=0; k<newid.size(); k++)
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{
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newidS = (String)newid.elementAt(k);
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if(nodeval.trim().equals(oldid.elementAt(k)))
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{
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break;
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}
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}
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MetaCatUtil.debugMessage("replacing: " + nodeval +
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" with " + newidS, 30);
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childNode.getFirstChild().setNodeValue(newidS);
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}
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}
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}
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}
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}
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323
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//increase the identifier
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NodeList identiferList = null;
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try
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{
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//find where the triples go in the file
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identiferList = XPathAPI.selectNodeList(doc, IDENTIFIER);
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}
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catch(Exception se)
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{
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System.err.println("incRevInTriples() : parse threw: " +
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se.toString());
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}
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for(int i=0; i<identiferList.getLength(); i++)
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{
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Node identifierNode = identiferList.item(i);
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String nodeName = identifierNode.getNodeName().trim().toUpperCase();
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if (nodeName.equals("IDENTIFIER"))
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{
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String nodeValue = null;
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try
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{
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nodeValue = identifierNode.getFirstChild().getNodeValue().trim();
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}
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catch(NullPointerException npe)
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{
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continue;
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}
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if(oldid.contains(nodeValue.trim()))
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{
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String newidS = "";
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for(int k=0; k<newid.size(); k++)
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{
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newidS = (String)newid.elementAt(k);
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if(nodeValue.trim().equals(oldid.elementAt(k)))
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{
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break;
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}
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}
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MetaCatUtil.debugMessage("replacing: " + nodeValue +
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" with " + newidS, 30);
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identifierNode.getFirstChild().setNodeValue(newidS);
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}
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368
|
|
369
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|
370
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}
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371
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}
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372
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|
373
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return PackageUtil.printDoctype(doc) +
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PackageUtil.print(doc.getDocumentElement());
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}
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376
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|
377
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|
378
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/*
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379
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*Give a docid to find a package accesssionNumber for it.
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380
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*/
|
381
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private static String getDataPackageAccessionNumber(String docId)
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{
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383
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String accessNumber = null;
|
384
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String packageIdWithoutVersion = null;
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385
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String rev = null;
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PreparedStatement pStmt = null;
|
387
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ResultSet rs=null;
|
388
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String query="SELECT docId from xml_relation where subject = ?";
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389
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DBConnection dbConn = null;
|
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int serialNumber = -1;
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391
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try
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392
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{
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393
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dbConn=DBConnectionPool.
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getDBConnection("DBQuery.getDataPackageId");
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serialNumber=dbConn.getCheckOutSerialNumber();
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pStmt=dbConn.prepareStatement(query);
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//bind the value to query
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pStmt.setString(1, docId);
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//execute the query
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pStmt.execute();
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rs=pStmt.getResultSet();
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//process the result
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if (rs.next()) //There are some records for the id in docId fields
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404
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{
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packageIdWithoutVersion=rs.getString(1);//get data package id
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}
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407
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pStmt.close();
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rev = getRevNumber(packageIdWithoutVersion);
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409
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accessNumber = packageIdWithoutVersion+"."+rev;
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410
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MetaCatUtil.debugMessage("DataPackageId: "+accessNumber, 50);
|
411
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}//try
|
412
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catch (SQLException e)
|
413
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{
|
414
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MetaCatUtil.debugMessage("Error in isDataPackageId: "
|
415
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+e.getMessage(), 30);
|
416
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}
|
417
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finally
|
418
|
{
|
419
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try
|
420
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{
|
421
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pStmt.close();
|
422
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}//try
|
423
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catch (SQLException ee)
|
424
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{
|
425
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MetaCatUtil.debugMessage("Error in isDataPackageId: "
|
426
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+ ee.getMessage(), 30);
|
427
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}//catch
|
428
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finally
|
429
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{
|
430
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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431
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}//finally
|
432
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}//finally
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433
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return accessNumber;
|
434
|
}//isDataPackageId()
|
435
|
|
436
|
/**
|
437
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* Get a dev number from a given docid(without dev)
|
438
|
*/
|
439
|
public static String getRevNumber(String docId)
|
440
|
{
|
441
|
DBConnection dbConn = null;
|
442
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int serialNumber = -1;
|
443
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String query = "SELECT rev from xml_documents where docid = ?";
|
444
|
PreparedStatement pStmt = null;
|
445
|
ResultSet rs = null;
|
446
|
String rev = null;
|
447
|
try
|
448
|
{
|
449
|
dbConn=DBConnectionPool.
|
450
|
getDBConnection("DBQuery.getDataPackageId");
|
451
|
serialNumber=dbConn.getCheckOutSerialNumber();
|
452
|
pStmt=dbConn.prepareStatement(query);
|
453
|
//bind the value to query
|
454
|
pStmt.setString(1, docId);
|
455
|
//execute the query
|
456
|
pStmt.execute();
|
457
|
rs=pStmt.getResultSet();
|
458
|
//process the result
|
459
|
if (rs.next()) //There are some records for the id in docId fields
|
460
|
{
|
461
|
rev=rs.getString(1);//get data package id
|
462
|
}
|
463
|
pStmt.close();
|
464
|
}
|
465
|
catch (SQLException e)
|
466
|
{
|
467
|
MetaCatUtil.debugMessage("the error in getRevNumber: "+
|
468
|
e.getMessage(), 30);
|
469
|
}
|
470
|
finally
|
471
|
{
|
472
|
try
|
473
|
{
|
474
|
pStmt.close();
|
475
|
}
|
476
|
catch (SQLException ee)
|
477
|
{
|
478
|
MetaCatUtil.debugMessage("the error in getRevNumber2: "+
|
479
|
ee.getMessage(), 30);
|
480
|
}
|
481
|
finally
|
482
|
{
|
483
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
484
|
return rev;
|
485
|
}
|
486
|
}
|
487
|
|
488
|
}
|
489
|
/**
|
490
|
* Delete a access control rule which is not in access xml document
|
491
|
*/
|
492
|
public static void deleteAccessRule(String aclDocid, String accessRule)
|
493
|
{
|
494
|
String principal = null;
|
495
|
String allowType = null;
|
496
|
String permission = null;
|
497
|
String allowOrder = null;
|
498
|
String [] parseAccessRuleArray = null;
|
499
|
DBConnection dbConn = null;
|
500
|
int serialNumber = -1;
|
501
|
String query = "delete from xml_access where accessfileid = ? " +
|
502
|
"and principal_name = ? and perm_type = ? "+
|
503
|
"and permission = ? and perm_order = ?";
|
504
|
PreparedStatement pStmt = null;
|
505
|
String rev = null;
|
506
|
// parse the access rule
|
507
|
parseAccessRuleArray = parseAccessRule(accessRule);
|
508
|
if ( parseAccessRuleArray == null)
|
509
|
{
|
510
|
MetaCatUtil.debugMessage("couldn't parse docid: "+aclDocid, 30);
|
511
|
return;
|
512
|
}
|
513
|
else
|
514
|
{
|
515
|
principal = parseAccessRuleArray[0];
|
516
|
allowType = parseAccessRuleArray[1];
|
517
|
permission = parseAccessRuleArray[2];
|
518
|
allowOrder = parseAccessRuleArray[3];
|
519
|
|
520
|
}
|
521
|
|
522
|
try
|
523
|
{
|
524
|
dbConn=DBConnectionPool.
|
525
|
getDBConnection("DBQuery.getDataPackageId");
|
526
|
serialNumber=dbConn.getCheckOutSerialNumber();
|
527
|
pStmt=dbConn.prepareStatement(query);
|
528
|
//bind the value to query
|
529
|
pStmt.setString(1, aclDocid);
|
530
|
pStmt.setString(2, principal);
|
531
|
pStmt.setString(3, allowType);
|
532
|
pStmt.setInt(4, (new Integer(permission)).intValue());
|
533
|
pStmt.setString(5, allowOrder);
|
534
|
//execute the query
|
535
|
pStmt.execute();
|
536
|
pStmt.close();
|
537
|
MetaCatUtil.debugMessage("delete rules: "+accessRule+" for "
|
538
|
+aclDocid+" in table", 30);
|
539
|
writeToLogFile("Delete rules: "+accessRule+" for "
|
540
|
+aclDocid+" in xml_access table");
|
541
|
}
|
542
|
catch (SQLException e)
|
543
|
{
|
544
|
MetaCatUtil.debugMessage("the error in deleteAccessRule(): "+
|
545
|
e.getMessage(), 30);
|
546
|
}
|
547
|
finally
|
548
|
{
|
549
|
try
|
550
|
{
|
551
|
pStmt.close();
|
552
|
}
|
553
|
catch (SQLException ee)
|
554
|
{
|
555
|
MetaCatUtil.debugMessage("the error in getRevNumber2: "+
|
556
|
ee.getMessage(), 30);
|
557
|
}
|
558
|
finally
|
559
|
{
|
560
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
561
|
|
562
|
}
|
563
|
}
|
564
|
}
|
565
|
|
566
|
/*
|
567
|
* Add a access control rule which is not in access xml document
|
568
|
*/
|
569
|
public static void addAccessRules(String aclDocid, Vector accessRules)
|
570
|
throws Exception
|
571
|
{
|
572
|
String principal = null;
|
573
|
String allowType = null;
|
574
|
String permission = null;
|
575
|
String allowOrder = null;
|
576
|
String revOfAcl = null;
|
577
|
String accessionNumberOfAcl = null;
|
578
|
String newAccessionNumerOfAcl = null;
|
579
|
String datasetDocId = null;
|
580
|
String accessionNumberOfDataset = null;
|
581
|
String newAccessionNumberOfDataset = null;
|
582
|
int revOfDataset = 0;
|
583
|
Vector xmlRuleVector = new Vector();
|
584
|
Vector oldAccessionNumberVector = new Vector();
|
585
|
Vector newAccessionNumberVector = new Vector();
|
586
|
|
587
|
//checking parameter
|
588
|
if (aclDocid==null|| accessRules==null || accessRules.size() == 0)
|
589
|
{
|
590
|
return;
|
591
|
}
|
592
|
|
593
|
// get xmlString for acl document
|
594
|
String oldxmlStringofAcl = getXMLStringFromDocId(aclDocid);
|
595
|
|
596
|
|
597
|
for(int i = 0; i<accessRules.size(); i++)
|
598
|
{
|
599
|
String oneRule = (String)accessRules.elementAt(i);
|
600
|
// parse the access rule
|
601
|
String [] parseAccessRuleArray = parseAccessRule(oneRule);
|
602
|
if ( parseAccessRuleArray == null)
|
603
|
{
|
604
|
MetaCatUtil.debugMessage("couldn't parse docid: "+aclDocid, 30);
|
605
|
continue;
|
606
|
}
|
607
|
else
|
608
|
{
|
609
|
principal = parseAccessRuleArray[0];
|
610
|
allowType = parseAccessRuleArray[1];
|
611
|
permission = parseAccessRuleArray[2];
|
612
|
allowOrder = parseAccessRuleArray[3];
|
613
|
//only for the allowtype is allow or deny
|
614
|
if (allowType.equals(ALLOW) || allowType.equals(DENY))
|
615
|
{
|
616
|
try
|
617
|
{
|
618
|
String xmlRule = ruleToXML(allowType, principal, permission);
|
619
|
xmlRuleVector.addElement(xmlRule);
|
620
|
}
|
621
|
catch(Exception e)
|
622
|
{
|
623
|
MetaCatUtil.debugMessage("error in ruletoxml: "+e.getMessage(), 30);
|
624
|
continue;
|
625
|
}
|
626
|
}//if
|
627
|
|
628
|
}//else
|
629
|
}//for
|
630
|
// create new rules xml document
|
631
|
String patchRuleXmlAdded = createXMLStringForAllAddingRules(xmlRuleVector);
|
632
|
String newACLXmlString = updateACLXml(patchRuleXmlAdded, oldxmlStringofAcl);
|
633
|
MetaCatUtil.debugMessage("new acl xml: "+newACLXmlString, 30);
|
634
|
// update acl file and write back to db
|
635
|
revOfAcl = getRevNumber(aclDocid);
|
636
|
accessionNumberOfAcl = aclDocid+DOT+revOfAcl;
|
637
|
oldAccessionNumberVector.addElement(accessionNumberOfAcl);
|
638
|
MetaCatUtil.debugMessage("old accession number of acl: "+
|
639
|
accessionNumberOfAcl, 30);
|
640
|
revOfAcl = (new Integer((new Integer(revOfAcl)).intValue()+1)).toString();
|
641
|
newAccessionNumerOfAcl = aclDocid+DOT+revOfAcl;
|
642
|
newAccessionNumberVector.addElement(newAccessionNumerOfAcl);
|
643
|
MetaCatUtil.debugMessage("new accession number of acl: "+
|
644
|
newAccessionNumerOfAcl, 30);
|
645
|
StringReader xmlAcl = new StringReader(newACLXmlString);
|
646
|
String pub = "no";
|
647
|
StringReader dtd = null;
|
648
|
String doAction = "UPDATE";
|
649
|
boolean validate = true;
|
650
|
DBConnection dbConn = null;
|
651
|
int serialNumber = -1;
|
652
|
try
|
653
|
{
|
654
|
dbConn=DBConnectionPool.
|
655
|
getDBConnection("CleanupAccessTable.addAccessRules");
|
656
|
serialNumber=dbConn.getCheckOutSerialNumber();
|
657
|
DocumentImpl.write(dbConn, xmlAcl, pub, dtd, doAction,
|
658
|
newAccessionNumerOfAcl, null, null, validate);
|
659
|
|
660
|
writeToLogFile("updated acl file: " + newAccessionNumerOfAcl);
|
661
|
writeToLogFile("New rules added are: "+ patchRuleXmlAdded.toString());
|
662
|
}
|
663
|
finally
|
664
|
{
|
665
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
666
|
}
|
667
|
|
668
|
// we need to inrease accessnumber in dataset and write it back to db
|
669
|
accessionNumberOfDataset = getDataPackageAccessionNumber(aclDocid);
|
670
|
oldAccessionNumberVector.addElement(accessionNumberOfDataset);
|
671
|
DocumentImpl doc = new DocumentImpl(accessionNumberOfDataset);
|
672
|
String xmlOfDataset = doc.toString();
|
673
|
MetaCatUtil.debugMessage("old access of dataset: "+
|
674
|
accessionNumberOfDataset, 30);
|
675
|
datasetDocId = MetaCatUtil.getDocIdFromString(accessionNumberOfDataset);
|
676
|
revOfDataset = MetaCatUtil.getVersionFromString(accessionNumberOfDataset);
|
677
|
revOfDataset++;
|
678
|
newAccessionNumberOfDataset = datasetDocId+DOT+revOfDataset;
|
679
|
newAccessionNumberVector.addElement(newAccessionNumberOfDataset);
|
680
|
MetaCatUtil.debugMessage("new accessionNumber of dataset: "+
|
681
|
newAccessionNumberOfDataset, 30);
|
682
|
String newDatasetString = incRevInTriples(xmlOfDataset,
|
683
|
oldAccessionNumberVector,
|
684
|
newAccessionNumberVector,
|
685
|
TRIPLESTAG);
|
686
|
StringReader xmlDataset = new StringReader(newDatasetString);
|
687
|
MetaCatUtil.debugMessage("new dataset xml: "+newDatasetString, 30);
|
688
|
try
|
689
|
{
|
690
|
dbConn=DBConnectionPool.
|
691
|
getDBConnection("CleanupAccessTable.addAccessRules");
|
692
|
serialNumber=dbConn.getCheckOutSerialNumber();
|
693
|
DocumentImpl.write(dbConn, xmlDataset, pub, dtd, doAction,
|
694
|
newAccessionNumberOfDataset, null, null, validate);
|
695
|
|
696
|
writeToLogFile("Update data set file: " + newAccessionNumberOfDataset);
|
697
|
writeToLogFile("old accessionNumber: " +
|
698
|
oldAccessionNumberVector.toString() +
|
699
|
" were replaced by: " +
|
700
|
newAccessionNumberVector.toString());
|
701
|
writeToLogFile("\n");
|
702
|
}
|
703
|
finally
|
704
|
{
|
705
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
706
|
}
|
707
|
|
708
|
|
709
|
}
|
710
|
|
711
|
/*
|
712
|
* Method to add rule(xml format ) to the orginal acl xml
|
713
|
*/
|
714
|
private static String updateACLXml(String patchXML, String originalXML)
|
715
|
{
|
716
|
Document doc = getDOMDocumentFromString(originalXML);
|
717
|
Document docPatch = getDOMDocumentFromString(patchXML);
|
718
|
NodeList allowInPatch = getNodeList(docPatch, ALLOWPATH);
|
719
|
|
720
|
NodeList denyInPatch = getNodeList(docPatch, DENYPATH);
|
721
|
|
722
|
NodeList allowInOrigin= getNodeList(doc, ALLOWPATH);
|
723
|
|
724
|
NodeList denyInorigin = getNodeList(doc,DENYPATH);
|
725
|
|
726
|
|
727
|
|
728
|
//for allow rule
|
729
|
|
730
|
for(int j=0; j<allowInPatch.getLength(); j++)
|
731
|
{
|
732
|
int end = allowInOrigin.getLength() - 1;
|
733
|
Node allowNode = allowInOrigin.item(end);
|
734
|
Node parent = allowNode.getParentNode();
|
735
|
//add the triples to the appropriate position in the file
|
736
|
Node n = doc.importNode(allowInPatch.item(j), true);
|
737
|
if(allowNode.getNextSibling() == null)
|
738
|
{
|
739
|
parent.appendChild(n);
|
740
|
}
|
741
|
else
|
742
|
{
|
743
|
parent.insertBefore(n, allowNode.getNextSibling());
|
744
|
}
|
745
|
}
|
746
|
|
747
|
// for deny rule
|
748
|
for (int i=0; i<denyInPatch.getLength(); i++)
|
749
|
{
|
750
|
int endOfDeny = denyInorigin.getLength()-1;
|
751
|
if (endOfDeny != -1)
|
752
|
{
|
753
|
// already has deny rule in access document
|
754
|
Node denyNode = denyInorigin.item(endOfDeny);
|
755
|
Node parentOfDeny = denyNode.getParentNode();
|
756
|
Node n = doc.importNode(denyInPatch.item(i), true);
|
757
|
if (denyNode.getNextSibling() == null)
|
758
|
{
|
759
|
parentOfDeny.appendChild(n);
|
760
|
}
|
761
|
else
|
762
|
{
|
763
|
parentOfDeny.insertBefore(n, denyNode.getNextSibling());
|
764
|
}
|
765
|
}
|
766
|
else
|
767
|
{
|
768
|
// no deny rule in access file, just append the deny rule to allow rule
|
769
|
int end = allowInOrigin.getLength() - 1;
|
770
|
Node allowNode = allowInOrigin.item(end);
|
771
|
Node parent = allowNode.getParentNode();
|
772
|
//add the triples to the appropriate position in the file
|
773
|
Node n = doc.importNode(denyInPatch.item(i), true);
|
774
|
parent.appendChild(n);
|
775
|
|
776
|
}
|
777
|
}
|
778
|
String docString = PackageUtil.printDoctype(doc);
|
779
|
docString += PackageUtil.print(doc.getDocumentElement());
|
780
|
return docString;
|
781
|
}
|
782
|
|
783
|
/*
|
784
|
* Transfer a rule to String
|
785
|
*/
|
786
|
private static String ruleToXML(String allowType, String principal,
|
787
|
String permission) throws Exception
|
788
|
{
|
789
|
Vector permissionVector = transferPermission(permission);
|
790
|
StringBuffer sb = new StringBuffer();
|
791
|
sb.append("<");
|
792
|
sb.append(allowType);
|
793
|
sb.append(">");
|
794
|
sb.append("<principal>").append(principal).append("</principal>");
|
795
|
// add permission
|
796
|
for ( int i = 0; i < permissionVector.size(); i++)
|
797
|
{
|
798
|
String permissionString = (String)permissionVector.elementAt(i);
|
799
|
sb.append("<permission>").append(permissionString).
|
800
|
append("</permission>");
|
801
|
}
|
802
|
sb.append("</");
|
803
|
sb.append(allowType);
|
804
|
sb.append(">");
|
805
|
return sb.toString();
|
806
|
}
|
807
|
|
808
|
/*
|
809
|
* Method tansfer permission form number(4) to string (read)
|
810
|
*/
|
811
|
private static Vector transferPermission(String permission) throws Exception
|
812
|
{
|
813
|
Vector result = new Vector();
|
814
|
String read = "read";
|
815
|
String write = "write";
|
816
|
String all = "all";
|
817
|
int permissionInInt = (new Integer(permission)).intValue();
|
818
|
switch (permissionInInt)
|
819
|
{
|
820
|
case 2:
|
821
|
result.addElement(write);
|
822
|
break;
|
823
|
case 4:
|
824
|
result.addElement(read);
|
825
|
break;
|
826
|
case 6:
|
827
|
result.addElement(write);
|
828
|
result.addElement(read);
|
829
|
break;
|
830
|
case 7:
|
831
|
result.addElement(all);
|
832
|
break;
|
833
|
}//switch
|
834
|
return result;
|
835
|
}
|
836
|
|
837
|
|
838
|
/*
|
839
|
* A method create a complete xml string for given a vector
|
840
|
*/
|
841
|
private static String createXMLStringForAllAddingRules(Vector rules)
|
842
|
{
|
843
|
String root = "rule";
|
844
|
StringBuffer sb = new StringBuffer();
|
845
|
sb.append("<?xml version=\"1.0\"?>");
|
846
|
sb.append("<" + root + ">");
|
847
|
|
848
|
for(int i=0; i<rules.size(); i++)
|
849
|
{
|
850
|
sb.append((String)rules.elementAt(i));
|
851
|
}
|
852
|
sb.append("</" + root + ">");
|
853
|
MetaCatUtil.debugMessage("new xml for adding rules: "+sb.toString(), 30);
|
854
|
return sb.toString();
|
855
|
|
856
|
}
|
857
|
|
858
|
/*
|
859
|
* A method to get nodelist for given xmlString and path
|
860
|
*/
|
861
|
private static NodeList getNodeList(Document doc, String path)
|
862
|
{
|
863
|
NodeList list = null;
|
864
|
try
|
865
|
{
|
866
|
//find where the triples go in the file
|
867
|
list = XPathAPI.selectNodeList(doc, path);
|
868
|
}
|
869
|
catch(Exception se)
|
870
|
{
|
871
|
System.err.println(se.toString());
|
872
|
}
|
873
|
return list;
|
874
|
}
|
875
|
|
876
|
/*
|
877
|
* Method to get xml string for given docid
|
878
|
*/
|
879
|
private static String getXMLStringFromDocId(String docId)
|
880
|
{
|
881
|
DocumentImpl doc = null;
|
882
|
String docidWithoutVersion = null;
|
883
|
String rev = null;
|
884
|
String accessionNumber = null;
|
885
|
String xmlDoc = null;
|
886
|
if (docId == null || docId.equals(""))
|
887
|
{
|
888
|
return null;
|
889
|
}
|
890
|
|
891
|
try
|
892
|
{
|
893
|
docidWithoutVersion = MetaCatUtil.getDocIdFromString(docId);
|
894
|
rev = getRevNumber(docidWithoutVersion);
|
895
|
accessionNumber = docidWithoutVersion+DOT+rev;
|
896
|
doc = new DocumentImpl(accessionNumber);
|
897
|
}
|
898
|
catch (Exception e)
|
899
|
{
|
900
|
MetaCatUtil.debugMessage("error in create an document: "
|
901
|
+ e.getMessage(), 30);
|
902
|
return null;
|
903
|
}
|
904
|
xmlDoc = doc.toString();
|
905
|
return xmlDoc;
|
906
|
}
|
907
|
|
908
|
|
909
|
|
910
|
/*
|
911
|
* method to get a dom docoument by given a xml string
|
912
|
*/
|
913
|
private static Document getDOMDocumentFromString(String xml)
|
914
|
{
|
915
|
Document doc = null;
|
916
|
DOMParser parser = new DOMParser();
|
917
|
InputSource in = null;
|
918
|
StringReader sr = null;
|
919
|
String xmlString = null;
|
920
|
//checking parameter
|
921
|
if (xml==null || xml.equals(""))
|
922
|
{
|
923
|
return null;
|
924
|
}
|
925
|
|
926
|
try
|
927
|
{ //parse the wizard created file with existing triples
|
928
|
sr = new StringReader(xml);
|
929
|
in = new InputSource(sr);
|
930
|
}
|
931
|
catch(Exception fnf)
|
932
|
{
|
933
|
fnf.printStackTrace();
|
934
|
return null;
|
935
|
}
|
936
|
try
|
937
|
{
|
938
|
parser.parse(in);
|
939
|
sr.close();
|
940
|
}
|
941
|
catch(Exception e1)
|
942
|
{
|
943
|
System.err.println(e1.toString());
|
944
|
return null;
|
945
|
}
|
946
|
doc = parser.getDocument();
|
947
|
return doc;
|
948
|
}
|
949
|
|
950
|
/*
|
951
|
* parse the string and get a array cotains principle name(index 0),
|
952
|
* allow type (index1), permission (index2), and allow order(index, 4)
|
953
|
*/
|
954
|
private static String[] parseAccessRule(String accessRule)
|
955
|
{
|
956
|
String principal = null;
|
957
|
String allowType = null;
|
958
|
String permission = null;
|
959
|
String allowOrder = null;
|
960
|
String [] result = new String[4];
|
961
|
int count = 0;
|
962
|
int index = 0;
|
963
|
char delimiter = DELIMITER.charAt(0);
|
964
|
|
965
|
if (accessRule== null)
|
966
|
{
|
967
|
return result;
|
968
|
}
|
969
|
for (int i=0; i<accessRule.length(); i++)
|
970
|
{
|
971
|
|
972
|
char charInString = accessRule.charAt(i);
|
973
|
// find a symbol !
|
974
|
if (charInString == delimiter)
|
975
|
{
|
976
|
count ++;
|
977
|
}
|
978
|
else
|
979
|
{
|
980
|
continue;
|
981
|
}
|
982
|
|
983
|
switch (count)
|
984
|
{
|
985
|
case 1:
|
986
|
{
|
987
|
// get principal
|
988
|
principal = accessRule.substring(0, i);
|
989
|
// remeber the index
|
990
|
index = i;
|
991
|
break;
|
992
|
}
|
993
|
case 2:
|
994
|
{
|
995
|
allowType = accessRule.substring(index+1, i);
|
996
|
index = i;
|
997
|
break;
|
998
|
}
|
999
|
case 3:
|
1000
|
{
|
1001
|
permission = accessRule.substring(index+1, i);
|
1002
|
index = i;
|
1003
|
allowOrder = accessRule.substring(index+1, accessRule.length());
|
1004
|
break;
|
1005
|
}
|
1006
|
}//switch
|
1007
|
}//for
|
1008
|
|
1009
|
// if the string exactly has 3 !, add it to array
|
1010
|
if ( count == 3)
|
1011
|
{
|
1012
|
result[0] = principal;
|
1013
|
result[1] = allowType;
|
1014
|
result[2] = permission;
|
1015
|
result[3] = allowOrder;
|
1016
|
}//if
|
1017
|
return result;
|
1018
|
}
|
1019
|
|
1020
|
/**
|
1021
|
* A method get acl docid list from xml_access table
|
1022
|
*/
|
1023
|
public static Vector readAccessDocIdFromDB()
|
1024
|
{
|
1025
|
Vector docidList = new Vector();
|
1026
|
String docid = null;
|
1027
|
DBConnection conn = null;
|
1028
|
int serialNumber = -1;
|
1029
|
PreparedStatement pstmt = null;
|
1030
|
try
|
1031
|
{
|
1032
|
//get connection from DBConnectionPool
|
1033
|
conn = DBConnectionPool.
|
1034
|
getDBConnection("CleanupAccessTable.readAccessDocIdFromDB");
|
1035
|
serialNumber=conn.getCheckOutSerialNumber();
|
1036
|
|
1037
|
// delete all acl records for resources related to @aclid if any
|
1038
|
pstmt = conn.prepareStatement("SELECT accessfileid FROM xml_access");
|
1039
|
pstmt.execute();
|
1040
|
ResultSet rs = pstmt.getResultSet();
|
1041
|
boolean hasRows = rs.next();
|
1042
|
int i = 0;
|
1043
|
while (hasRows)
|
1044
|
{
|
1045
|
docid = rs.getString(1);
|
1046
|
// if hashtable doesn't has the rule add to hashtable
|
1047
|
if (docid !=null && !docidList.contains(docid))
|
1048
|
{
|
1049
|
docidList.addElement(docid);
|
1050
|
|
1051
|
}
|
1052
|
hasRows = rs.next();
|
1053
|
// reset value
|
1054
|
docid = null;
|
1055
|
|
1056
|
}//while
|
1057
|
|
1058
|
}
|
1059
|
catch (SQLException e)
|
1060
|
{
|
1061
|
MetaCatUtil.debugMessage("error in readAccessDocIdFromDB: "+
|
1062
|
e.getMessage(), 30);
|
1063
|
}
|
1064
|
finally
|
1065
|
{
|
1066
|
try
|
1067
|
{
|
1068
|
pstmt.close();
|
1069
|
}
|
1070
|
catch (SQLException ee)
|
1071
|
{
|
1072
|
MetaCatUtil.debugMessage("error in readAccessDocIdFromDB: "+
|
1073
|
ee.getMessage(), 30);
|
1074
|
}
|
1075
|
finally
|
1076
|
{
|
1077
|
//retrun DBConnection
|
1078
|
DBConnectionPool.returnDBConnection(conn,serialNumber);
|
1079
|
return docidList;
|
1080
|
}
|
1081
|
}
|
1082
|
|
1083
|
}
|
1084
|
|
1085
|
/**
|
1086
|
* Method to delete rules which is not in xml access file
|
1087
|
*/
|
1088
|
public static void addAccessRulesToDocument(String aclDocId,
|
1089
|
Vector rulesFromDB,
|
1090
|
Vector rulesFromDocument)
|
1091
|
{
|
1092
|
|
1093
|
try
|
1094
|
{
|
1095
|
Vector rulesAdded = new Vector();
|
1096
|
//check for every rules
|
1097
|
for (int j=0; j< rulesFromDB.size(); j++)
|
1098
|
{
|
1099
|
String oneRule = (String)rulesFromDB.elementAt(j);
|
1100
|
// if onerules get from db not in xml_access, delete it
|
1101
|
if (!rulesFromDocument.contains(oneRule))
|
1102
|
{
|
1103
|
MetaCatUtil.debugMessage("one rule: "+oneRule, 30);
|
1104
|
rulesAdded.addElement(oneRule);
|
1105
|
}//if
|
1106
|
oneRule = null;
|
1107
|
}//for
|
1108
|
addAccessRules(aclDocId, rulesAdded);
|
1109
|
}
|
1110
|
catch (Exception e)
|
1111
|
{
|
1112
|
MetaCatUtil.debugMessage("error delete addAccessRulesToDocument(): "+
|
1113
|
e.getMessage(), 30);
|
1114
|
}
|
1115
|
}
|
1116
|
|
1117
|
/**
|
1118
|
* Method to updata data set files
|
1119
|
*/
|
1120
|
public static void updateDataSetFilesForNewTriples(String aclDocId,
|
1121
|
Vector docidFromAccessDB,
|
1122
|
Vector docidFromRelationDB)
|
1123
|
{
|
1124
|
String aclAccessionNumber = null;
|
1125
|
String revForAcl = null;
|
1126
|
String packagAccessionNumber = null;
|
1127
|
//checking for every acl id
|
1128
|
|
1129
|
try
|
1130
|
{
|
1131
|
//Get package and acl access number
|
1132
|
packagAccessionNumber = getDataPackageAccessionNumber(aclDocId);
|
1133
|
revForAcl = getRevNumber(aclDocId);
|
1134
|
aclAccessionNumber = aclDocId+DOT+revForAcl;
|
1135
|
//check for every docid in relation ship
|
1136
|
Vector newTripleVector = new Vector();
|
1137
|
for (int j=0; j<docidFromAccessDB.size(); j++)
|
1138
|
{
|
1139
|
String objectId = (String)docidFromAccessDB.elementAt(j);
|
1140
|
String objectAccessionNumber = null;
|
1141
|
String revForObject = null;
|
1142
|
// new triple
|
1143
|
if (!docidFromRelationDB.contains(objectId))
|
1144
|
{
|
1145
|
revForObject = getRevNumber(objectId);
|
1146
|
objectAccessionNumber = objectId+DOT+revForObject;
|
1147
|
Triple newTriple = new Triple(aclAccessionNumber, RELATIONSHIP,
|
1148
|
objectAccessionNumber);
|
1149
|
newTripleVector.add(newTriple);
|
1150
|
MetaCatUtil.debugMessage("find a new triple"+
|
1151
|
newTriple.toString(), 30);
|
1152
|
|
1153
|
}//if
|
1154
|
}//for
|
1155
|
// add new trip into data set
|
1156
|
addNewTripleIntoDataset(packagAccessionNumber, newTripleVector);
|
1157
|
|
1158
|
}
|
1159
|
catch (Exception e)
|
1160
|
{
|
1161
|
MetaCatUtil.debugMessage("error in updataDatasetFiles(): "+
|
1162
|
e.getMessage(), 30);
|
1163
|
}
|
1164
|
|
1165
|
|
1166
|
}
|
1167
|
|
1168
|
/*
|
1169
|
* Method to write information into log file
|
1170
|
*/
|
1171
|
private static void writeToLogFile(String message)
|
1172
|
{
|
1173
|
try
|
1174
|
{
|
1175
|
FileOutputStream fos = new FileOutputStream(LOGFILENAME, true);
|
1176
|
PrintWriter pw = new PrintWriter(fos);
|
1177
|
pw.println(message);
|
1178
|
pw.flush();
|
1179
|
}
|
1180
|
catch(Exception e)
|
1181
|
{
|
1182
|
MetaCatUtil.debugMessage("error writing to log: " + e.getMessage(), 30);
|
1183
|
|
1184
|
}
|
1185
|
}
|
1186
|
|
1187
|
public static void main(String[] agus)
|
1188
|
{
|
1189
|
|
1190
|
try
|
1191
|
{
|
1192
|
DBConnectionPool pool = DBConnectionPool.getInstance();
|
1193
|
Vector aclVector = readAccessDocIdFromDB();
|
1194
|
for (int i = 0; i < aclVector.size(); i++)
|
1195
|
{
|
1196
|
try
|
1197
|
{
|
1198
|
String aclDocId = (String)aclVector.elementAt(i);
|
1199
|
AccessRulesFromDocument xmlDocument = new
|
1200
|
AccessRulesFromDocument(aclDocId);
|
1201
|
AccessRulesFromDB db = new AccessRulesFromDB(aclDocId);
|
1202
|
Vector ruleFromDocument = xmlDocument.getAccessRuleVector();
|
1203
|
Vector ruleFromDB = db.getAccessRuleVector();
|
1204
|
Vector docIdFromRelation = xmlDocument.getACLObjects();
|
1205
|
Vector docIdFromAccess = db.getDocidAccessRuleApplied();
|
1206
|
// update rules in acl and triple in dataset file
|
1207
|
addAccessRulesToDocument(aclDocId, ruleFromDB, ruleFromDocument);
|
1208
|
//update triplse in dataset file
|
1209
|
updateDataSetFilesForNewTriples(aclDocId, docIdFromAccess,
|
1210
|
docIdFromRelation);
|
1211
|
}
|
1212
|
catch (Exception e)
|
1213
|
{
|
1214
|
MetaCatUtil.debugMessage("exception in main is: " +
|
1215
|
e.getMessage(), 30);
|
1216
|
}
|
1217
|
|
1218
|
}
|
1219
|
}
|
1220
|
catch(Exception ee)
|
1221
|
{
|
1222
|
MetaCatUtil.debugMessage("exception is: "+ee.getMessage(), 30);
|
1223
|
}
|
1224
|
}
|
1225
|
|
1226
|
}//cleanupAccessTable
|