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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.io.ByteArrayInputStream;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.math.BigInteger;
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import java.net.HttpURLConnection;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Vector;
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import javax.activation.DataHandler;
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import javax.activation.DataSource;
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import javax.mail.internet.MimeBodyPart;
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import javax.mail.internet.MimeMultipart;
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import org.apache.commons.io.IOUtils;
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import org.dataone.client.D1Client;
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import org.dataone.client.MNode;
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import org.dataone.client.ObjectFormatCache;
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import org.dataone.client.auth.CertificateManager;
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import org.dataone.ore.ResourceMapFactory;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.types.v1.AccessPolicy;
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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.Checksum;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.ObjectFormat;
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import org.dataone.service.types.v1.Permission;
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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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import org.dataone.service.types.v1.SystemMetadata;
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import org.dataone.service.types.v1.util.ChecksumUtil;
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import org.dataone.service.util.Constants;
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import org.dspace.foresite.ResourceMap;
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import org.ecoinformatics.datamanager.DataManager;
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import org.ecoinformatics.datamanager.database.DatabaseConnectionPoolInterface;
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import org.ecoinformatics.datamanager.parser.DataPackage;
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import edu.ucsb.nceas.metacat.MetaCatServlet;
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import edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.restservice.InputStreamDataSource;
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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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private Session session = null;
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private String subjectDN = 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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// TODO: use specific certificate?
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this.session = null; //new Session();
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this.subjectDN = CertificateManager.getInstance().getSubjectDN(CertificateManager.getInstance().loadCertificate());
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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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//String sourceSessionid = loginSource();
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//do a query
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String params = "returndoctype=eml://ecoinformatics.org/eml-2.1.0&" +
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"returndoctype=eml://ecoinformatics.org/eml-2.0.1&" +
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"returndoctype=eml://ecoinformatics.org/eml-2.0.0&";
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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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printHeader("Searching source");
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System.out.println("searching '" + sourceUrl + "' for '" + query + "'");
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InputStream is = getResponse(sourceUrl, "/metacat", 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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printHeader("Parsing source results");
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System.out.println("creating MN with url: " + destinationUrl + "/");
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MNode mn = D1Client.getMN(destinationUrl + "/");
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printHeader("Processing " + docs.size() + " results.");
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for (int i=0; i<docs.size(); i++) {
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// for generating the ORE map
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Map<Identifier, List<Identifier>> idMap = new HashMap<Identifier, List<Identifier>>();
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List<Identifier> dataIds = new ArrayList<Identifier>();
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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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printHeader("Getting document " + doc.docid + " from source " + sourceUrl);
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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("doctext: " + doctext);
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is = stringToStream(doctext);
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//parse the document
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DatabaseConnectionPoolInterface connectionPool = MetacatDatabaseConnectionPoolFactory.getDatabaseConnectionPoolInterface();
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DataManager dataManager = DataManager.getInstance(connectionPool, connectionPool.getDBAdapterName());
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DataPackage dataPackage = dataManager.parseMetadata(is);
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if (dataPackage == null) {
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continue;
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}
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//go through the DistributionMetadata and download any described data
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is = stringToStream(doctext);
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doc.doctext = doctext;
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printHeader("creating document on destination " + destinationUrl);
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SystemMetadata sysmeta = generateSystemMetadata(doc);
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// iterate through the data objects
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if (dataPackage.getEntityList() != null) {
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for (int j=0; j < dataPackage.getEntityList().length; j++) {
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String dataDocUrl = dataPackage.getEntityList()[j].getURL();
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String dataDocMimeType = dataPackage.getEntityList()[j].getDataFormat();
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if (dataDocMimeType == null) {
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dataDocMimeType =
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ObjectFormatCache.getInstance().getFormat("application/octet-stream").getFmtid().getValue();
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}
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String dataDocLocalId = "";
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if (dataDocUrl.trim().startsWith("ecogrid://knb/")) { //we only handle ecogrid urls right now
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dataDocLocalId = dataDocUrl.substring(dataDocUrl.indexOf("ecogrid://knb/") +
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"ecogrid://knb/".length(), dataDocUrl.length());
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//get the file
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params = "action=read&qformat=xml&docid=" + dataDocLocalId;
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InputStream dataDocIs = getResponse(sourceUrl, "/metacat", params, "POST");
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String dataDocText = streamToString(dataDocIs);
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//set the id
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Identifier did = new Identifier();
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did.setValue(dataDocLocalId);
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// add the data identifier for ORE map
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dataIds.add(did);
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//create sysmeta for the data doc
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SystemMetadata dataDocSysMeta = generateSystemMetadata(doc);
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//overwrite the bogus values from the last call
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dataDocSysMeta.setIdentifier(did);
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ObjectFormat format = null;
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try {
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format = ObjectFormatCache.getInstance().getFormat(dataDocMimeType);
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dataDocSysMeta.setFmtid(format.getFmtid());
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} catch (NotFound e) {
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System.out.println(e.getMessage());
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}
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dataDocIs = stringToStream(dataDocText);
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Checksum checksum = ChecksumUtil.checksum(dataDocIs, "MD5");
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dataDocSysMeta.setChecksum(checksum);
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String sizeStr =
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Long.toString(dataDocText.getBytes(MetaCatServlet.DEFAULT_ENCODING).length);
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dataDocSysMeta.setSize(new BigInteger(sizeStr));
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boolean error = false;
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//create the data doc on d1
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try {
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mn.create(session, dataDocSysMeta.getIdentifier(), IOUtils.toInputStream(dataDocText), dataDocSysMeta);
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}
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catch(Exception e) {
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error = true;
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System.out.println("ERROR: Could not create data document with id " +
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dataDocSysMeta.getIdentifier().getValue() + " : " + e.getMessage());
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}
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finally {
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if (error) {
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printHeader("Insertion of document " + dataDocSysMeta.getIdentifier().getValue() +
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"FAILED.");
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}
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else {
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printHeader("Done inserting document " + dataDocSysMeta.getIdentifier().getValue() +
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" which is described by " + sysmeta.getIdentifier().getValue());
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}
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}
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}
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else {
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System.out.println("WARNING: Could not process describes url " +
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dataDocUrl + " for document " + doc.docid +
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". Only ecogrid://knb/ urls are currently supported.");
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}
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}
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}
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try {
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Identifier id =
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mn.create(session, sysmeta.getIdentifier(), IOUtils.toInputStream(doc.doctext), sysmeta);
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System.out.println("Success inserting document " + id.getValue());
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// no need for an ORE map if there's no data
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if (!dataIds.isEmpty()) {
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// generate the ORE map for this datapackage
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Identifier resourceMapId = new Identifier();
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resourceMapId.setValue("resourceMap_" + sysmeta.getIdentifier().getValue());
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idMap.put(sysmeta.getIdentifier(), dataIds);
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ResourceMap rm = ResourceMapFactory.getInstance().createResourceMap(resourceMapId, idMap);
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String resourceMapXML = ResourceMapFactory.getInstance().serializeResourceMap(rm);
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Document rmDoc = new Document(resourceMapId.getValue(), "http://www.openarchives.org/ore/terms", "", "");
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rmDoc.doctext = resourceMapXML;
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SystemMetadata resourceMapSysMeta = generateSystemMetadata(rmDoc);
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mn.create(session, resourceMapId, IOUtils.toInputStream(resourceMapXML), resourceMapSysMeta);
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// clean up the permissions (FORCE public read)
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for (Identifier dataId: dataIds) {
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mn.setAccessPolicy(session, dataId, sysmeta.getAccessPolicy());
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System.out.println("Set public access policy for: " + dataId.getValue());
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}
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}
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}
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catch(Exception e) {
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e.printStackTrace();
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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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printHeader("Done processing document " + sysmeta.getIdentifier().getValue());
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}
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}
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//logout();
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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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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.trim());
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sm.setIdentifier(id);
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//set the object format
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ObjectFormat format = ObjectFormatCache.getInstance().getFormat(doc.doctype);
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if (format == null) {
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if (doc.doctype.trim().equals("BIN")) {
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format = ObjectFormatCache.getInstance().getFormat("application/octet-stream");
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}
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else {
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format = ObjectFormatCache.getInstance().getFormat("text/plain");
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}
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}
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sm.setFmtid(format.getFmtid());
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//create the checksum
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ByteArrayInputStream bais = new ByteArrayInputStream(doc.doctext.getBytes(MetaCatServlet.DEFAULT_ENCODING));
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Checksum checksum = ChecksumUtil.checksum(bais, "MD5");
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sm.setChecksum(checksum);
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//set the size
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String sizeStr = Long.toString(doc.doctext.getBytes(MetaCatServlet.DEFAULT_ENCODING).length);
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sm.setSize(new BigInteger(sizeStr));
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//submitter, rights holder
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Subject p = new Subject();
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p.setValue(subjectDN);
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sm.setSubmitter(p);
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sm.setRightsHolder(p);
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try {
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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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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(PropertyService.getProperty("dataone.memberNodeId"));
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sm.setOriginMemberNode(nr);
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sm.setAuthoritativeMemberNode(nr);
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// create access policy
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AccessPolicy accessPolicy = new AccessPolicy();
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AccessRule accessRule = new AccessRule();
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accessRule.addPermission(Permission.READ);
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Subject subject = new Subject();
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subject.setValue(Constants.SUBJECT_PUBLIC);
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accessRule.addSubject(subject);
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accessPolicy.addAllow(accessRule);
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sm.setAccessPolicy(accessPolicy);
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return sm;
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}
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private void printHeader(String s) {
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System.out.println("****** " + s + " *******");
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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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387
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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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400
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if(sessionid != null)
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{
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403
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if(restURL.indexOf("?") == -1)
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404
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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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412
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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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419
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if (contentType!=null) {
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420
|
connection.setRequestProperty("Content-Type",contentType);
|
421
|
}
|
422
|
|
423
|
connection.setDoOutput(true);
|
424
|
connection.setDoInput(true);
|
425
|
connection.setRequestMethod(method);
|
426
|
|
427
|
if (!method.equals("GET")) {
|
428
|
if (dataStream != null) {
|
429
|
OutputStream out = connection.getOutputStream();
|
430
|
IOUtils.copy(dataStream, out);
|
431
|
}
|
432
|
}
|
433
|
|
434
|
return connection.getInputStream();
|
435
|
}
|
436
|
|
437
|
/**
|
438
|
* create a mime multipart message from object and sysmeta
|
439
|
*/
|
440
|
private MimeMultipart createMimeMultipart(InputStream object)
|
441
|
throws Exception
|
442
|
{
|
443
|
final MimeMultipart mmp = new MimeMultipart();
|
444
|
MimeBodyPart objectPart = new MimeBodyPart();
|
445
|
objectPart.addHeaderLine("Content-Transfer-Encoding: base64");
|
446
|
objectPart.setFileName("doctext");
|
447
|
DataSource ds = new InputStreamDataSource("doctext", object);
|
448
|
DataHandler dh = new DataHandler(ds);
|
449
|
objectPart.setDataHandler(dh);
|
450
|
mmp.addBodyPart(objectPart);
|
451
|
return mmp;
|
452
|
}
|
453
|
|
454
|
/**
|
455
|
* parse a metacat query response and return a vector of docids
|
456
|
* @param response
|
457
|
* @return
|
458
|
*/
|
459
|
private Vector<Document> parseResponse(String response)
|
460
|
{
|
461
|
Vector<Document> v = new Vector<Document>();
|
462
|
int dstart = response.indexOf("<document>");
|
463
|
int dend = response.indexOf("</document>", dstart);
|
464
|
while(dstart != -1)
|
465
|
{
|
466
|
String doc = response.substring(dstart + "<document>".length(), dend);
|
467
|
//System.out.println("adding " + docid);
|
468
|
Document d = new Document(getFieldFromDoc(doc, "docid"),
|
469
|
getFieldFromDoc(doc, "doctype"),
|
470
|
getFieldFromDoc(doc, "createdate"),
|
471
|
getFieldFromDoc(doc, "updatedate"));
|
472
|
v.add(d);
|
473
|
dstart = response.indexOf("<document>", dend);
|
474
|
dend = response.indexOf("</document>", dstart);
|
475
|
}
|
476
|
|
477
|
return v;
|
478
|
}
|
479
|
|
480
|
private String getFieldFromDoc(String doc, String fieldname)
|
481
|
{
|
482
|
String field = "<" + fieldname + ">";
|
483
|
String fieldend = "</" + fieldname + ">";
|
484
|
int start = doc.indexOf(field);
|
485
|
int end = doc.indexOf(fieldend);
|
486
|
String s = doc.substring(start + field.length(), end);
|
487
|
//System.out.println("field: " + fieldname + " : " + s);
|
488
|
return s;
|
489
|
}
|
490
|
|
491
|
/**
|
492
|
* login the source
|
493
|
* @return
|
494
|
* @throws Exception
|
495
|
*/
|
496
|
private String loginSource()
|
497
|
throws Exception
|
498
|
{
|
499
|
return login(sourceUrl);
|
500
|
}
|
501
|
|
502
|
|
503
|
/**
|
504
|
* returns a sessionid
|
505
|
* @return
|
506
|
*/
|
507
|
private String login(String sourceUrl)
|
508
|
throws Exception
|
509
|
{
|
510
|
InputStream is = getResponse(sourceUrl, "/metacat",
|
511
|
"action=login&username=" + username + "&password=" + password + "&qformat=xml", "POST");
|
512
|
String response = streamToString(is);
|
513
|
//System.out.println("response: " + response);
|
514
|
if(response.indexOf("sessionId") == -1)
|
515
|
{
|
516
|
throw new Exception("Error logging into " + sourceUrl);
|
517
|
}
|
518
|
|
519
|
String sessionid = response.substring(
|
520
|
response.indexOf("<sessionId>") + "<sessionId>".length(),
|
521
|
response.indexOf("</sessionId>"));
|
522
|
System.out.println("sessionid: " + sessionid);
|
523
|
return sessionid;
|
524
|
}
|
525
|
|
526
|
/**
|
527
|
* logout both the source and destination
|
528
|
* @throws Exception
|
529
|
*/
|
530
|
private void logout()
|
531
|
throws Exception
|
532
|
{
|
533
|
getResponse(sourceUrl, "/metacat", "action=logout&username=" + username, "POST");
|
534
|
}
|
535
|
|
536
|
/**
|
537
|
* get an http response
|
538
|
* @param contextRootUrl
|
539
|
* @param resource
|
540
|
* @param urlParameters
|
541
|
* @param method
|
542
|
* @return
|
543
|
* @throws Exception
|
544
|
*/
|
545
|
private InputStream getResponse(String contextRootUrl, String resource,
|
546
|
String urlParameters, String method)
|
547
|
throws Exception
|
548
|
{
|
549
|
HttpURLConnection connection = null ;
|
550
|
|
551
|
String restURL = contextRootUrl+resource;
|
552
|
|
553
|
if (urlParameters != null) {
|
554
|
if (restURL.indexOf("?") == -1)
|
555
|
restURL += "?";
|
556
|
restURL += urlParameters;
|
557
|
if(restURL.indexOf(" ") != -1)
|
558
|
{
|
559
|
restURL = restURL.replaceAll("\\s", "%20");
|
560
|
}
|
561
|
}
|
562
|
|
563
|
URL u = null;
|
564
|
InputStream content = null;
|
565
|
System.out.println("url: " + restURL);
|
566
|
System.out.println("method: " + method);
|
567
|
u = new URL(restURL);
|
568
|
connection = (HttpURLConnection) u.openConnection();
|
569
|
connection.setDoOutput(true);
|
570
|
connection.setDoInput(true);
|
571
|
connection.setRequestMethod(method);
|
572
|
content = connection.getInputStream();
|
573
|
return content;
|
574
|
}
|
575
|
|
576
|
private String streamToString(InputStream is)
|
577
|
throws Exception
|
578
|
{
|
579
|
byte b[] = new byte[1024];
|
580
|
int numread = is.read(b, 0, 1024);
|
581
|
String response = new String();
|
582
|
while(numread != -1)
|
583
|
{
|
584
|
response += new String(b, 0, numread);
|
585
|
numread = is.read(b, 0, 1024);
|
586
|
}
|
587
|
return response;
|
588
|
}
|
589
|
|
590
|
private InputStream stringToStream(String s)
|
591
|
throws Exception
|
592
|
{
|
593
|
ByteArrayInputStream bais = new ByteArrayInputStream(s.getBytes(MetaCatServlet.DEFAULT_ENCODING));
|
594
|
return bais;
|
595
|
}
|
596
|
|
597
|
private class Document
|
598
|
{
|
599
|
public String docid;
|
600
|
public String doctype;
|
601
|
public String createDate;
|
602
|
public String updateDate;
|
603
|
public String doctext;
|
604
|
|
605
|
public Document(String docid, String doctype, String createDate, String updateDate)
|
606
|
{
|
607
|
this.docid = docid.trim();
|
608
|
this.doctype = doctype.trim();
|
609
|
this.createDate = createDate.trim();
|
610
|
this.updateDate = updateDate.trim();
|
611
|
}
|
612
|
}
|
613
|
}
|