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5394
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berkley
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/**
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* '$RCSfile$'
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* Purpose: A Class that implements administrative methods
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* Copyright: 2010 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* Authors: Michael Daigle
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*
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* '$Author: berkley $'
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* '$Date: 2010-06-08 12:34:30 -0700 (Tue, 08 Jun 2010) $'
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* '$Revision: 5374 $'
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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.util;
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import java.security.MessageDigest;
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import java.util.*;
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import java.io.*;
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import java.net.*;
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import javax.activation.DataHandler;
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import javax.activation.DataSource;
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import javax.mail.MessagingException;
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import javax.mail.internet.MimeBodyPart;
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import javax.mail.internet.MimeMultipart;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import javax.xml.parsers.ParserConfigurationException;
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import org.apache.commons.io.IOUtils;
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import edu.ucsb.nceas.metacat.MetacatHandler;
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import edu.ucsb.nceas.metacat.MetacatResultSet;
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import edu.ucsb.nceas.metacat.MetacatResultSet.Document;
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import edu.ucsb.nceas.metacat.dataone.CrudService;
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import edu.ucsb.nceas.metacat.restservice.InputStreamDataSource;
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.types.AuthToken;
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import org.dataone.service.types.Checksum;
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import org.dataone.service.types.ChecksumAlgorithm;
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import org.dataone.service.types.NodeReference;
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import org.dataone.service.types.ObjectFormat;
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import org.dataone.service.types.Principal;
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import org.dataone.service.types.SystemMetadata;
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import org.dataone.service.types.Identifier;
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import org.dataone.client.D1Client;
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//import sun.tools.jstat.Identifier;
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import com.gc.iotools.stream.is.InputStreamFromOutputStream;
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/**
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* @author berkley
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* A class to populate a metacat instance based on documents returned from a query
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*/
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public class MetacatPopulator
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{
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private String sourceUrl = null;
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private String destinationUrl = null;
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private String query = null;
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private String username = null;
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private String password = null;
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/**
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* create a new MetacatPopulator with given source and destination urls.
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* These should be
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* of the form "http://<url>/<metacat_instance>"
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* If username and/or password is null, the query will be run as public
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* @param sourceUrl
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* @param destUrl
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* @param query
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* @param username
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* @param password
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*/
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public MetacatPopulator(String sourceUrl, String destUrl, String query, String username, String password)
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{
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this.sourceUrl = sourceUrl;
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this.query = query;
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this.username = username;
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this.password = password;
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this.destinationUrl = destUrl;
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}
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/**
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* populate from the source
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*/
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public void populate()
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throws Exception
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{
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5397
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berkley
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printHeader("Source login");
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5394
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berkley
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String sourceSessionid = loginSource();
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5397
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berkley
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5394
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berkley
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//do a query
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String params = "returndoctype=eml://ecoinformatics.org/eml-2.0.1&" +
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"returndoctype=eml://ecoinformatics.org/eml-2.0.0&" +
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"returndoctype=BIN&" +
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"returndoctype=http://dataone.org/service/types/SystemMetadata/0.1&";
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params += "action=query&";
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params += "qformat=xml&";
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params += "anyfield=" + query;
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berkley
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printHeader("Searching source");
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berkley
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System.out.println("searching '" + sourceUrl + "' for '" + query + "' with sessionid '" + sourceSessionid + "'");
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InputStream is = getResponse(sourceUrl, "/metacat",
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params, "POST");
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String response = streamToString(is);
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//System.out.println("response: " + response);
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Vector<Document> docs = parseResponse(response);
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5397
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berkley
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printHeader("Parsing source results");
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D1Client d1 = new D1Client(destinationUrl + "/");
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printHeader("logging in to the destination " + destinationUrl);
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AuthToken authtoken = d1.login(username, password);
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5394
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berkley
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for(int i=0; i<docs.size(); i++)
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{
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//for each document in the query
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Document doc = docs.get(i);
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String docid = doc.docid;
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//get the doc from source
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berkley
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printHeader("Getting document " + doc.docid + " from source " + sourceUrl);
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berkley
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params = "action=read&qformat=xml&docid=" + docid;
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is = getResponse(sourceUrl, "/metacat", params, "POST");
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String doctext = streamToString(is);
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//System.out.println("Done retrieving document: " + doctext);
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is = stringToStream(doctext);
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doc.doctext = doctext;
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5397
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berkley
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printHeader("creating document on destination " + destinationUrl);
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5394
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berkley
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SystemMetadata sysmeta = generateSystemMetadata(doc);
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berkley
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try
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{
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Identifier id = d1.create(authtoken, sysmeta.getIdentifier(),
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IOUtils.toInputStream(doc.doctext), sysmeta);
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System.out.println("Success inserting document " + id.getValue());
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}
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catch(Exception e)
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{
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System.out.println("Could not create document with id " +
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sysmeta.getIdentifier().getValue() + " : " + e.getMessage());
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}
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finally
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{
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printHeader("Done inserting document " + sysmeta.getIdentifier().getValue());
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}
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5394
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berkley
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}
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logout();
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}
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berkley
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private void printHeader(String s)
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{
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System.out.println("****** " + s + " *******");
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}
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5394
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berkley
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/**
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* produce an md5 checksum for item
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*/
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private String checksum(InputStream is)
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throws Exception
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{
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byte[] buffer = new byte[1024];
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MessageDigest complete = MessageDigest.getInstance("MD5");
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int numRead;
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do
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{
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numRead = is.read(buffer);
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if (numRead > 0)
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{
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complete.update(buffer, 0, numRead);
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}
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} while (numRead != -1);
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return getHex(complete.digest());
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}
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/**
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* convert a byte array to a hex string
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*/
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private static String getHex( byte [] raw )
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{
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final String HEXES = "0123456789ABCDEF";
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if ( raw == null ) {
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return null;
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}
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final StringBuilder hex = new StringBuilder( 2 * raw.length );
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for ( final byte b : raw ) {
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hex.append(HEXES.charAt((b & 0xF0) >> 4))
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.append(HEXES.charAt((b & 0x0F)));
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}
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return hex.toString();
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}
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/**
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* @param doc
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* @return
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*/
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private SystemMetadata generateSystemMetadata(Document doc)
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throws Exception
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{
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SystemMetadata sm = new SystemMetadata();
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//set the id
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Identifier id = new Identifier();
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id.setValue(doc.docid);
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sm.setIdentifier(id);
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//set the object format
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ObjectFormat format = ObjectFormat.convert(doc.doctype);
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if(format == null)
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{
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if(doc.doctype.trim().equals("BIN"))
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{
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format = ObjectFormat.APPLICATIONOCTETSTREAM;
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}
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else
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{
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format = ObjectFormat.convert("text/plain");
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}
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}
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sm.setObjectFormat(format);
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//create the checksum
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ByteArrayInputStream bais = new ByteArrayInputStream(doc.doctext.getBytes());
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String checksumS = checksum(bais);
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ChecksumAlgorithm ca = ChecksumAlgorithm.convert("MD5");
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Checksum checksum = new Checksum();
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checksum.setValue(checksumS);
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checksum.setAlgorithm(ca);
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sm.setChecksum(checksum);
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//set the size
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sm.setSize(doc.doctext.getBytes().length);
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//submitter
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Principal p = new Principal();
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p.setValue("");
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sm.setSubmitter(p);
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sm.setRightsHolder(p);
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try
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{
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Date dateCreated = parseMetacatDate(doc.createDate);
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sm.setDateUploaded(dateCreated);
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Date dateUpdated = parseMetacatDate(doc.updateDate);
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sm.setDateSysMetadataModified(dateUpdated);
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}
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catch(Exception e)
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{
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System.out.println("couldn't parse a date: " + e.getMessage());
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Date dateCreated = new Date();
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sm.setDateUploaded(dateCreated);
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Date dateUpdated = new Date();
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sm.setDateSysMetadataModified(dateUpdated);
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}
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NodeReference nr = new NodeReference();
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nr.setValue(sourceUrl);
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sm.setOriginMemberNode(nr);
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sm.setAuthoritativeMemberNode(nr);
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return sm;
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}
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/**
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* parse the metacat date which looks like 2010-06-08 (YYYY-MM-DD) into
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* a proper date object
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* @param date
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* @return
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*/
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private Date parseMetacatDate(String date)
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{
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String year = date.substring(0, 4);
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String month = date.substring(5, 7);
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String day = date.substring(8, 10);
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Calendar c = Calendar.getInstance();
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c.set(new Integer(year).intValue(),
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new Integer(month).intValue(),
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new Integer(day).intValue());
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return c.getTime();
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}
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/**
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* send a request to the resource
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*/
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private InputStream sendRequest(String contextRootUrl, String resource,
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String sessionid, String method, String urlParamaters,
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String contentType, InputStream dataStream)
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throws Exception
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{
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HttpURLConnection connection = null ;
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String restURL = contextRootUrl + resource;
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if (urlParamaters != null) {
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if (restURL.indexOf("?") == -1)
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restURL += "?";
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restURL += urlParamaters;
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if(restURL.indexOf(" ") != -1)
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{
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restURL = restURL.replaceAll("\\s", "%20");
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}
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}
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if(sessionid != null)
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{
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if(restURL.indexOf("?") == -1)
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{
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restURL += "?sessionid=" + sessionid;
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}
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else
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{
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restURL += "&sessionid=" + sessionid;
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}
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}
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URL u = null;
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InputStream content = null;
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System.out.println("url: " + restURL);
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System.out.println("method: " + method);
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u = new URL(restURL);
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connection = (HttpURLConnection) u.openConnection();
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if (contentType!=null) {
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connection.setRequestProperty("Content-Type",contentType);
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}
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connection.setDoOutput(true);
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connection.setDoInput(true);
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connection.setRequestMethod(method);
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if (!method.equals("GET")) {
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if (dataStream != null) {
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OutputStream out = connection.getOutputStream();
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IOUtils.copy(dataStream, out);
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}
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}
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return connection.getInputStream();
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}
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/**
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352 |
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* create a mime multipart message from object and sysmeta
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353 |
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*/
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354 |
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private MimeMultipart createMimeMultipart(InputStream object)
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355 |
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throws Exception
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356 |
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{
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final MimeMultipart mmp = new MimeMultipart();
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358 |
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MimeBodyPart objectPart = new MimeBodyPart();
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359 |
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objectPart.addHeaderLine("Content-Transfer-Encoding: base64");
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objectPart.setFileName("doctext");
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DataSource ds = new InputStreamDataSource("doctext", object);
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DataHandler dh = new DataHandler(ds);
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363 |
|
|
objectPart.setDataHandler(dh);
|
364 |
|
|
mmp.addBodyPart(objectPart);
|
365 |
|
|
return mmp;
|
366 |
|
|
}
|
367 |
|
|
|
368 |
|
|
/**
|
369 |
|
|
* parse a metacat query response and return a vector of docids
|
370 |
|
|
* @param response
|
371 |
|
|
* @return
|
372 |
|
|
*/
|
373 |
|
|
private Vector<Document> parseResponse(String response)
|
374 |
|
|
{
|
375 |
|
|
Vector<Document> v = new Vector<Document>();
|
376 |
|
|
int dstart = response.indexOf("<document>");
|
377 |
|
|
int dend = response.indexOf("</document>", dstart);
|
378 |
|
|
while(dstart != -1)
|
379 |
|
|
{
|
380 |
|
|
String doc = response.substring(dstart + "<document>".length(), dend);
|
381 |
|
|
//System.out.println("adding " + docid);
|
382 |
|
|
Document d = new Document(getFieldFromDoc(doc, "docid"),
|
383 |
|
|
getFieldFromDoc(doc, "doctype"),
|
384 |
|
|
getFieldFromDoc(doc, "createdate"),
|
385 |
|
|
getFieldFromDoc(doc, "updatedate"));
|
386 |
|
|
v.add(d);
|
387 |
|
|
dstart = response.indexOf("<document>", dend);
|
388 |
|
|
dend = response.indexOf("</document>", dstart);
|
389 |
|
|
}
|
390 |
|
|
|
391 |
|
|
return v;
|
392 |
|
|
}
|
393 |
|
|
|
394 |
|
|
private String getFieldFromDoc(String doc, String fieldname)
|
395 |
|
|
{
|
396 |
|
|
String field = "<" + fieldname + ">";
|
397 |
|
|
String fieldend = "</" + fieldname + ">";
|
398 |
|
|
int start = doc.indexOf(field);
|
399 |
|
|
int end = doc.indexOf(fieldend);
|
400 |
|
|
String s = doc.substring(start + field.length(), end);
|
401 |
|
|
System.out.println("field: " + fieldname + " : " + s);
|
402 |
|
|
return s;
|
403 |
|
|
}
|
404 |
|
|
|
405 |
|
|
/**
|
406 |
|
|
* login the source
|
407 |
|
|
* @return
|
408 |
|
|
* @throws Exception
|
409 |
|
|
*/
|
410 |
|
|
private String loginSource()
|
411 |
|
|
throws Exception
|
412 |
|
|
{
|
413 |
|
|
return login(sourceUrl);
|
414 |
|
|
}
|
415 |
|
|
|
416 |
|
|
/**
|
417 |
|
|
* login the destination
|
418 |
|
|
* @return
|
419 |
|
|
* @throws Exception
|
420 |
|
|
*/
|
421 |
|
|
private String loginDest()
|
422 |
|
|
throws Exception
|
423 |
|
|
{
|
424 |
|
|
return login(destinationUrl);
|
425 |
|
|
}
|
426 |
|
|
|
427 |
|
|
/**
|
428 |
|
|
* returns a sessionid
|
429 |
|
|
* @return
|
430 |
|
|
*/
|
431 |
|
|
private String login(String sourceUrl)
|
432 |
|
|
throws Exception
|
433 |
|
|
{
|
434 |
|
|
InputStream is = getResponse(sourceUrl, "/metacat",
|
435 |
|
|
"action=login&username=" + username + "&password=" + password + "&qformat=xml",
|
436 |
|
|
"POST");
|
437 |
|
|
String response = streamToString(is);
|
438 |
|
|
//System.out.println("response: " + response);
|
439 |
5397
|
berkley
|
if(response.indexOf("sessionId") == -1)
|
440 |
|
|
{
|
441 |
|
|
throw new Exception("Error logging into " + sourceUrl);
|
442 |
|
|
}
|
443 |
|
|
|
444 |
5394
|
berkley
|
String sessionid = response.substring(
|
445 |
|
|
response.indexOf("<sessionId>") + "<sessionId>".length(),
|
446 |
|
|
response.indexOf("</sessionId>"));
|
447 |
|
|
System.out.println("sessionid: " + sessionid);
|
448 |
|
|
return sessionid;
|
449 |
|
|
}
|
450 |
|
|
|
451 |
|
|
/**
|
452 |
|
|
* logout both the source and destination
|
453 |
|
|
* @throws Exception
|
454 |
|
|
*/
|
455 |
|
|
private void logout()
|
456 |
|
|
throws Exception
|
457 |
|
|
{
|
458 |
|
|
getResponse(sourceUrl, "/metacat", "action=logout&username=" + username, "POST");
|
459 |
|
|
getResponse(destinationUrl, "/metacat", "action=logout&username=" + username, "POST");
|
460 |
|
|
}
|
461 |
|
|
|
462 |
|
|
/**
|
463 |
|
|
* get an http response
|
464 |
|
|
* @param contextRootUrl
|
465 |
|
|
* @param resource
|
466 |
|
|
* @param urlParameters
|
467 |
|
|
* @param method
|
468 |
|
|
* @return
|
469 |
|
|
* @throws Exception
|
470 |
|
|
*/
|
471 |
|
|
private InputStream getResponse(String contextRootUrl, String resource,
|
472 |
|
|
String urlParameters, String method)
|
473 |
|
|
throws Exception
|
474 |
|
|
{
|
475 |
|
|
HttpURLConnection connection = null ;
|
476 |
|
|
|
477 |
|
|
String restURL = contextRootUrl+resource;
|
478 |
|
|
|
479 |
|
|
if (urlParameters != null) {
|
480 |
|
|
if (restURL.indexOf("?") == -1)
|
481 |
|
|
restURL += "?";
|
482 |
|
|
restURL += urlParameters;
|
483 |
|
|
if(restURL.indexOf(" ") != -1)
|
484 |
|
|
{
|
485 |
|
|
restURL = restURL.replaceAll("\\s", "%20");
|
486 |
|
|
}
|
487 |
|
|
}
|
488 |
|
|
|
489 |
|
|
URL u = null;
|
490 |
|
|
InputStream content = null;
|
491 |
|
|
System.out.println("url: " + restURL);
|
492 |
|
|
System.out.println("method: " + method);
|
493 |
|
|
u = new URL(restURL);
|
494 |
|
|
connection = (HttpURLConnection) u.openConnection();
|
495 |
|
|
connection.setDoOutput(true);
|
496 |
|
|
connection.setDoInput(true);
|
497 |
|
|
connection.setRequestMethod(method);
|
498 |
|
|
content = connection.getInputStream();
|
499 |
|
|
return content;
|
500 |
|
|
}
|
501 |
|
|
|
502 |
|
|
private String streamToString(InputStream is)
|
503 |
|
|
throws Exception
|
504 |
|
|
{
|
505 |
|
|
byte b[] = new byte[1024];
|
506 |
|
|
int numread = is.read(b, 0, 1024);
|
507 |
|
|
String response = new String();
|
508 |
|
|
while(numread != -1)
|
509 |
|
|
{
|
510 |
|
|
response += new String(b, 0, numread);
|
511 |
|
|
numread = is.read(b, 0, 1024);
|
512 |
|
|
}
|
513 |
|
|
return response;
|
514 |
|
|
}
|
515 |
|
|
|
516 |
|
|
private InputStream stringToStream(String s)
|
517 |
|
|
throws Exception
|
518 |
|
|
{
|
519 |
|
|
ByteArrayInputStream bais = new ByteArrayInputStream(s.getBytes());
|
520 |
|
|
return bais;
|
521 |
|
|
}
|
522 |
|
|
|
523 |
|
|
private class Document
|
524 |
|
|
{
|
525 |
|
|
public String docid;
|
526 |
|
|
public String doctype;
|
527 |
|
|
public String createDate;
|
528 |
|
|
public String updateDate;
|
529 |
|
|
public String doctext;
|
530 |
|
|
|
531 |
|
|
public Document(String docid, String doctype, String createDate, String updateDate)
|
532 |
|
|
{
|
533 |
|
|
this.docid = docid;
|
534 |
|
|
this.doctype = doctype;
|
535 |
|
|
this.createDate = createDate;
|
536 |
|
|
this.updateDate = updateDate;
|
537 |
|
|
}
|
538 |
|
|
}
|
539 |
|
|
}
|