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/**
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* '$RCSfile$'
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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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*
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* '$Author: jones $'
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* '$Date: 2010-02-03 17:58:12 -0900 (Wed, 03 Feb 2010) $'
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* '$Revision: 5211 $'
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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 java.io.BufferedInputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileReader;
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import java.io.IOException;
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import java.io.OutputStream;
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import java.io.OutputStreamWriter;
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import java.io.PrintWriter;
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import java.io.StringReader;
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import java.io.ByteArrayOutputStream;
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import java.io.Writer;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Timestamp;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.Enumeration;
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import java.util.HashMap;
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import java.util.Hashtable;
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import java.util.Iterator;
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import java.util.Map;
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import java.util.Timer;
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import java.util.Vector;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipOutputStream;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletOutputStream;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import javax.servlet.http.HttpSession;
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import javax.activation.MimetypesFileTypeMap;
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import org.apache.log4j.Logger;
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import org.ecoinformatics.eml.EMLParser;
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import au.com.bytecode.opencsv.CSVWriter;
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import com.oreilly.servlet.multipart.FilePart;
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import com.oreilly.servlet.multipart.MultipartParser;
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import com.oreilly.servlet.multipart.ParamPart;
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import com.oreilly.servlet.multipart.Part;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlInterface;
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import edu.ucsb.nceas.metacat.cart.CartManager;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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import edu.ucsb.nceas.metacat.dataquery.DataQuery;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler;
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import edu.ucsb.nceas.metacat.service.SessionService;
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import edu.ucsb.nceas.metacat.service.XMLSchemaService;
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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
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import edu.ucsb.nceas.metacat.shared.ServiceException;
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import edu.ucsb.nceas.metacat.spatial.SpatialHarvester;
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import edu.ucsb.nceas.metacat.spatial.SpatialQuery;
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import edu.ucsb.nceas.metacat.util.AuthUtil;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.metacat.util.MetacatUtil;
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import edu.ucsb.nceas.metacat.util.RequestUtil;
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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import edu.ucsb.nceas.utilities.FileUtil;
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import edu.ucsb.nceas.utilities.LSIDUtil;
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import edu.ucsb.nceas.utilities.ParseLSIDException;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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/**
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* General entry point for the Metacat server which is called from various
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* mechanisms such as the standard MetacatServlet class and the various web
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* service servlets such as RestServlet class. All application logic should be
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* encapsulated in this class, and the calling classes should only contain
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* parameter marshaling and demarshaling code, delegating all else to this
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* MetacatHandler instance.
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* @author Matthew Jones
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*/
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public class MetacatHandler {
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private static boolean _sitemapScheduled = false;
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// Constants -- these should be final in a servlet
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private static final String PROLOG = "<?xml version=\"1.0\"?>";
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private static final String SUCCESS = "<success>";
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private static final String SUCCESSCLOSE = "</success>";
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private static final String ERROR = "<error>";
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private static final String ERRORCLOSE = "</error>";
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private Timer timer;
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public MetacatHandler(Timer timer) {
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this.timer = timer;
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}
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protected void handleDataquery(
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Hashtable<String, String[]> params,
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HttpServletResponse response,
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String sessionId) throws PropertyNotFoundException, IOException {
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DataQuery dq = null;
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if (sessionId != null) {
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dq = new DataQuery(sessionId);
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}
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else {
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dq = new DataQuery();
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}
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String dataqueryXML = (params.get("dataquery"))[0];
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ResultSet rs = null;
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try {
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rs = dq.executeQuery(dataqueryXML);
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} catch (Exception e) {
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//probably need to do something here
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e.printStackTrace();
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return;
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}
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//process the result set
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String qformat = "csv";
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String[] temp = params.get("qformat");
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if (temp != null && temp.length > 0) {
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qformat = temp[0];
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}
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String fileName = "query-results." + qformat;
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//get the results as csv file
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if (qformat != null && qformat.equalsIgnoreCase("csv")) {
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response.setContentType("text/csv");
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//response.setContentType("application/csv");
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response.setHeader("Content-Disposition", "attachment; filename=" + fileName);
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Writer writer = new OutputStreamWriter(response.getOutputStream());
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CSVWriter csv = new CSVWriter(writer, CSVWriter.DEFAULT_SEPARATOR, CSVWriter.NO_QUOTE_CHARACTER);
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try {
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csv.writeAll(rs, true);
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csv.flush();
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response.flushBuffer();
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rs.close();
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} catch (SQLException e) {
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e.printStackTrace();
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}
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return;
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}
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}
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protected void handleEditCart(
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Hashtable<String, String[]> params,
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HttpServletResponse response,
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String sessionId) throws PropertyNotFoundException, IOException {
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CartManager cm = null;
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if (sessionId != null) {
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cm = new CartManager(sessionId);
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}
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else {
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cm = new CartManager();
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}
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String editOperation = (params.get("operation"))[0];
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String[] docids = params.get("docid");
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String[] field = params.get("field");
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String[] path = params.get("path");
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Map<String,String> fields = null;
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if (field != null && path != null) {
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fields = new HashMap<String,String>();
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fields.put(field[0], path[0]);
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}
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//TODO handle attribute map (metadata fields)
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cm.editCart(editOperation, docids, fields);
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}
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// ///////////////////////////// METACAT SPATIAL ///////////////////////////
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/**
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* handles all spatial queries -- these queries may include any of the
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* queries supported by the WFS / WMS standards
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*
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* handleSQuery(out, params, response, username, groupnames, sess_id);
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*/
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protected void handleSpatialQuery(PrintWriter out, Hashtable<String, String[]> params,
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HttpServletResponse response,
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String username, String[] groupnames,
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String sess_id) throws PropertyNotFoundException {
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Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
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229
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if ( !PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) {
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response.setContentType("text/html");
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out.println("<html> Metacat Spatial Option is turned off </html>");
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out.close();
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return ;
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}
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235
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236
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/*
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237
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* Perform spatial query against spatial cache
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*/
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float _xmax = Float.valueOf( (params.get("xmax"))[0] ).floatValue();
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float _ymax = Float.valueOf( (params.get("ymax"))[0] ).floatValue();
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float _xmin = Float.valueOf( (params.get("xmin"))[0] ).floatValue();
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float _ymin = Float.valueOf( (params.get("ymin"))[0] ).floatValue();
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SpatialQuery sq = new SpatialQuery();
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Vector<String> docids = sq.filterByBbox( _xmin, _ymin, _xmax, _ymax );
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// logMetacat.info(" --- Spatial Query completed. Passing on the SQuery
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// handler");
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247
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// logMetacat.warn("\n\n ******* after spatial query, we've got " +
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248
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// docids.size() + " docids \n\n");
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249
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250
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/*
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251
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* Create an array matching docids
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252
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*/
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253
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String [] docidArray = new String[docids.size()];
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254
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docids.toArray(docidArray);
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255
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256
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/*
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257
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* Create squery string
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258
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*/
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259
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String squery = DocumentIdQuery.createDocidQuery( docidArray );
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260
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// logMetacat.info("-----------\n" + squery + "\n------------------");
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261
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String[] queryArray = new String[1];
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262
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queryArray[0] = squery;
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263
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params.put("query", queryArray);
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264
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265
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/*
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266
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* Determine qformat
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267
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*/
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268
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String[] qformatArray = new String[1];
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269
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try {
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270
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String _skin = (params.get("skin"))[0];
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271
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qformatArray[0] = _skin;
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272
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} catch (java.lang.NullPointerException e) {
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273
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// should be "default" but keep this for backwards compatibility
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274
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// with knp site
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275
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logMetacat.warn("MetaCatServlet.handleSpatialQuery - No SKIN specified for metacat actions=spatial_query... defaulting to 'knp' skin !\n");
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276
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qformatArray[0] = "knp";
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277
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}
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278
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params.put("qformat", qformatArray);
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279
|
|
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280
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// change the action
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281
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String[] actionArray = new String[1];
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282
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actionArray[0] = "squery";
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283
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params.put("action", actionArray);
|
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284
|
|
|
285
|
/*
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|
286
|
* Pass the docids to the DBQuery contructor
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|
287
|
*/
|
|
288
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// This is a hack to get the empty result set to show...
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289
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// Otherwise dbquery sees no docidOverrides and does a full % percent
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290
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// query
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291
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if (docids.size() == 0)
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292
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docids.add("");
|
|
293
|
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294
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DBQuery queryobj = new DBQuery(docids);
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295
|
queryobj.findDocuments(response, out, params, username, groupnames, sess_id);
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296
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|
|
297
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}
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298
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|
|
299
|
// LOGIN & LOGOUT SECTION
|
|
300
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/**
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|
301
|
* Handle the login request. Create a new session object. Do user
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302
|
* authentication through the session.
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|
303
|
*/
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|
304
|
public void handleLoginAction(PrintWriter out, Hashtable<String, String[]> params,
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305
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HttpServletRequest request, HttpServletResponse response) {
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306
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Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
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|
307
|
AuthSession sess = null;
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308
|
|
|
309
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if(params.get("username") == null){
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|
310
|
response.setContentType("text/xml");
|
|
311
|
out.println("<?xml version=\"1.0\"?>");
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|
312
|
out.println("<error>");
|
|
313
|
out.println("Username not specified");
|
|
314
|
out.println("</error>");
|
|
315
|
return;
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|
316
|
}
|
|
317
|
|
|
318
|
// }
|
|
319
|
|
|
320
|
if(params.get("password") == null){
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321
|
response.setContentType("text/xml");
|
|
322
|
out.println("<?xml version=\"1.0\"?>");
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323
|
out.println("<error>");
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|
324
|
out.println("Password not specified");
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|
325
|
out.println("</error>");
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|
326
|
return;
|
|
327
|
}
|
|
328
|
|
|
329
|
String un = (params.get("username"))[0];
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|
330
|
logMetacat.info("MetaCatServlet.handleLoginAction - user " + un + " is trying to login");
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331
|
String pw = (params.get("password"))[0];
|
|
332
|
|
|
333
|
String qformat = "xml";
|
|
334
|
if (params.get("qformat") != null) {
|
|
335
|
qformat = (params.get("qformat"))[0];
|
|
336
|
}
|
|
337
|
|
|
338
|
try {
|
|
339
|
sess = new AuthSession();
|
|
340
|
} catch (Exception e) {
|
|
341
|
String errorMsg = "MetacatServlet.handleLoginAction - Problem in MetacatServlet.handleLoginAction() authenicating session: "
|
|
342
|
+ e.getMessage();
|
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343
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logMetacat.error(errorMsg);
|
|
344
|
out.println(errorMsg);
|
|
345
|
e.printStackTrace(System.out);
|
|
346
|
return;
|
|
347
|
}
|
|
348
|
boolean isValid = sess.authenticate(request, un, pw);
|
|
349
|
|
|
350
|
//if it is authernticate is true, store the session
|
|
351
|
if (isValid) {
|
|
352
|
HttpSession session = sess.getSessions();
|
|
353
|
String id = session.getId();
|
|
354
|
|
|
355
|
logMetacat.debug("MetaCatServlet.handleLoginAction - Store session id " + id
|
|
356
|
+ " which has username" + session.getAttribute("username")
|
|
357
|
+ " into hash in login method");
|
|
358
|
try {
|
|
359
|
System.out.println("registering session with id " + id);
|
|
360
|
System.out.println("username: " + (String) session.getAttribute("username"));
|
|
361
|
SessionService.getInstance().registerSession(id,
|
|
362
|
(String) session.getAttribute("username"),
|
|
363
|
(String[]) session.getAttribute("groupnames"),
|
|
364
|
(String) session.getAttribute("password"),
|
|
365
|
(String) session.getAttribute("name"));
|
|
366
|
|
|
367
|
|
|
368
|
} catch (ServiceException se) {
|
|
369
|
String errorMsg = "MetacatServlet.handleLoginAction - service problem registering session: "
|
|
370
|
+ se.getMessage();
|
|
371
|
logMetacat.error("MetaCatServlet.handleLoginAction - " + errorMsg);
|
|
372
|
out.println(errorMsg);
|
|
373
|
se.printStackTrace(System.out);
|
|
374
|
return;
|
|
375
|
}
|
|
376
|
}
|
|
377
|
|
|
378
|
// format and transform the output
|
|
379
|
if (qformat.equals("xml")) {
|
|
380
|
response.setContentType("text/xml");
|
|
381
|
out.println(sess.getMessage());
|
|
382
|
} else {
|
|
383
|
try {
|
|
384
|
DBTransform trans = new DBTransform();
|
|
385
|
response.setContentType("text/html");
|
|
386
|
trans.transformXMLDocument(sess.getMessage(),
|
|
387
|
"-//NCEAS//login//EN", "-//W3C//HTML//EN", qformat,
|
|
388
|
out, null, null);
|
|
389
|
} catch (Exception e) {
|
|
390
|
logMetacat.error("MetaCatServlet.handleLoginAction - General error"
|
|
391
|
+ e.getMessage());
|
|
392
|
e.printStackTrace(System.out);
|
|
393
|
}
|
|
394
|
}
|
|
395
|
}
|
|
396
|
|
|
397
|
/**
|
|
398
|
* Handle the logout request. Close the connection.
|
|
399
|
*/
|
|
400
|
public void handleLogoutAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
401
|
HttpServletRequest request, HttpServletResponse response) {
|
|
402
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
403
|
String qformat = "xml";
|
|
404
|
if(params.get("qformat") != null){
|
|
405
|
qformat = params.get("qformat")[0];
|
|
406
|
}
|
|
407
|
|
|
408
|
// close the connection
|
|
409
|
HttpSession sess = request.getSession(false);
|
|
410
|
logMetacat.info("MetaCatServlet.handleLogoutAction - After get session in logout request");
|
|
411
|
if (sess != null) {
|
|
412
|
logMetacat.info("MetaCatServlet.handleLogoutAction - The session id " + sess.getId()
|
|
413
|
+ " will be invalidate in logout action");
|
|
414
|
logMetacat.info("MetaCatServlet.handleLogoutAction - The session contains user "
|
|
415
|
+ sess.getAttribute("username")
|
|
416
|
+ " will be invalidate in logout action");
|
|
417
|
sess.invalidate();
|
|
418
|
SessionService.getInstance().unRegisterSession(sess.getId());
|
|
419
|
}
|
|
420
|
|
|
421
|
// produce output
|
|
422
|
StringBuffer output = new StringBuffer();
|
|
423
|
output.append("<?xml version=\"1.0\"?>");
|
|
424
|
output.append("<logout>");
|
|
425
|
output.append("User logged out");
|
|
426
|
output.append("</logout>");
|
|
427
|
|
|
428
|
//format and transform the output
|
|
429
|
if (qformat.equals("xml")) {
|
|
430
|
response.setContentType("text/xml");
|
|
431
|
out.println(output.toString());
|
|
432
|
} else {
|
|
433
|
try {
|
|
434
|
DBTransform trans = new DBTransform();
|
|
435
|
response.setContentType("text/html");
|
|
436
|
trans.transformXMLDocument(output.toString(),
|
|
437
|
"-//NCEAS//login//EN", "-//W3C//HTML//EN", qformat,
|
|
438
|
out, null, null);
|
|
439
|
} catch (Exception e) {
|
|
440
|
logMetacat.error(
|
|
441
|
"MetaCatServlet.handleLogoutAction - General error: "
|
|
442
|
+ e.getMessage());
|
|
443
|
e.printStackTrace(System.out);
|
|
444
|
}
|
|
445
|
}
|
|
446
|
}
|
|
447
|
|
|
448
|
// END OF LOGIN & LOGOUT SECTION
|
|
449
|
|
|
450
|
// SQUERY & QUERY SECTION
|
|
451
|
/**
|
|
452
|
* Retreive the squery xml, execute it and display it
|
|
453
|
*
|
|
454
|
* @param out the output stream to the client
|
|
455
|
* @param params the Hashtable of parameters that should be included in the
|
|
456
|
* squery.
|
|
457
|
* @param response the response object linked to the client
|
|
458
|
* @param conn the database connection
|
|
459
|
*/
|
|
460
|
protected void handleSQuery(PrintWriter out, Hashtable<String, String[]> params,
|
|
461
|
HttpServletResponse response, String user, String[] groups,
|
|
462
|
String sessionid) throws PropertyNotFoundException {
|
|
463
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
464
|
long squeryWarnLimit = Long.parseLong(PropertyService.getProperty("database.squeryTimeWarnLimit"));
|
|
465
|
|
|
466
|
long startTime = System.currentTimeMillis();
|
|
467
|
DBQuery queryobj = new DBQuery();
|
|
468
|
queryobj.findDocuments(response, out, params, user, groups, sessionid);
|
|
469
|
long outPutTime = System.currentTimeMillis();
|
|
470
|
long runTime = outPutTime - startTime;
|
|
471
|
|
|
472
|
if (runTime > squeryWarnLimit) {
|
|
473
|
logMetacat.warn("MetaCatServlet.handleSQuery - Long running squery. Total time: " + runTime +
|
|
474
|
" ms, squery: " + ((String[])params.get("query"))[0]);
|
|
475
|
}
|
|
476
|
logMetacat.debug("MetaCatServlet.handleSQuery - squery: " + ((String[])params.get("query"))[0] +
|
|
477
|
" ran in " + runTime + " ms");
|
|
478
|
}
|
|
479
|
|
|
480
|
/**
|
|
481
|
* Create the xml query, execute it and display the results.
|
|
482
|
*
|
|
483
|
* @param out the output stream to the client
|
|
484
|
* @param params the Hashtable of parameters that should be included in the
|
|
485
|
* squery.
|
|
486
|
* @param response the response object linked to the client
|
|
487
|
*/
|
|
488
|
protected void handleQuery(PrintWriter out, Hashtable<String, String[]> params,
|
|
489
|
HttpServletResponse response, String user, String[] groups,
|
|
490
|
String sessionid) throws PropertyNotFoundException {
|
|
491
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
492
|
long queryWarnLimit = Long.parseLong(PropertyService.getProperty("database.queryTimeWarnLimit"));
|
|
493
|
|
|
494
|
//create the query and run it
|
|
495
|
String xmlquery = DBQuery.createSQuery(params);
|
|
496
|
String[] queryArray = new String[1];
|
|
497
|
queryArray[0] = xmlquery;
|
|
498
|
params.put("query", queryArray);
|
|
499
|
long startTime = System.currentTimeMillis();
|
|
500
|
DBQuery queryobj = new DBQuery();
|
|
501
|
queryobj.findDocuments(response, out, params, user, groups, sessionid);
|
|
502
|
long outPutTime = System.currentTimeMillis();
|
|
503
|
long runTime = outPutTime -startTime;
|
|
504
|
|
|
505
|
if (runTime > queryWarnLimit) {
|
|
506
|
logMetacat.warn("MetaCatServlet.handleQuery - Long running squery. Total time: " + runTime +
|
|
507
|
" ms, squery: " + ((String[])params.get("query"))[0]);
|
|
508
|
}
|
|
509
|
logMetacat.debug("MetaCatServlet.handleQuery - query: " + ((String[])params.get("query"))[0] +
|
|
510
|
" ran in " + runTime + " ms");
|
|
511
|
}
|
|
512
|
|
|
513
|
// END OF SQUERY & QUERY SECTION
|
|
514
|
|
|
515
|
//Export section
|
|
516
|
/**
|
|
517
|
* Handle the "export" request of data package from Metacat in zip format
|
|
518
|
*
|
|
519
|
* @param params the Hashtable of HTTP request parameters
|
|
520
|
* @param response the HTTP response object linked to the client
|
|
521
|
* @param user the username sent the request
|
|
522
|
* @param groups the user's groupnames
|
|
523
|
*/
|
|
524
|
protected void handleExportAction(Hashtable<String, String[]> params,
|
|
525
|
HttpServletResponse response,
|
|
526
|
String user, String[] groups, String passWord) {
|
|
527
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
528
|
// Output stream
|
|
529
|
ServletOutputStream out = null;
|
|
530
|
// Zip output stream
|
|
531
|
ZipOutputStream zOut = null;
|
|
532
|
DBQuery queryObj = null;
|
|
533
|
|
|
534
|
String[] docs = new String[10];
|
|
535
|
String docId = "";
|
|
536
|
|
|
537
|
try {
|
|
538
|
// read the params
|
|
539
|
if (params.containsKey("docid")) {
|
|
540
|
docs = params.get("docid");
|
|
541
|
}
|
|
542
|
// Create a DBuery to handle export
|
|
543
|
queryObj = new DBQuery();
|
|
544
|
// Get the docid
|
|
545
|
docId = docs[0];
|
|
546
|
// Make sure the client specify docid
|
|
547
|
if (docId == null || docId.equals("")) {
|
|
548
|
response.setContentType("text/xml"); //MIME type
|
|
549
|
// Get a printwriter
|
|
550
|
PrintWriter pw = response.getWriter();
|
|
551
|
// Send back message
|
|
552
|
pw.println("<?xml version=\"1.0\"?>");
|
|
553
|
pw.println("<error>");
|
|
554
|
pw.println("You didn't specify requested docid");
|
|
555
|
pw.println("</error>");
|
|
556
|
// Close printwriter
|
|
557
|
pw.close();
|
|
558
|
return;
|
|
559
|
}
|
|
560
|
// Get output stream
|
|
561
|
out = response.getOutputStream();
|
|
562
|
response.setContentType("application/zip"); //MIME type
|
|
563
|
response.setHeader("Content-Disposition",
|
|
564
|
"attachment; filename="
|
|
565
|
+ docId + ".zip"); // Set the name of the zip file
|
|
566
|
|
|
567
|
zOut = new ZipOutputStream(out);
|
|
568
|
zOut = queryObj
|
|
569
|
.getZippedPackage(docId, out, user, groups, passWord);
|
|
570
|
zOut.finish(); //terminate the zip file
|
|
571
|
zOut.close(); //close the zip stream
|
|
572
|
|
|
573
|
} catch (Exception e) {
|
|
574
|
try {
|
|
575
|
response.setContentType("text/xml"); //MIME type
|
|
576
|
// Send error message back
|
|
577
|
if (out != null) {
|
|
578
|
PrintWriter pw = new PrintWriter(out);
|
|
579
|
pw.println("<?xml version=\"1.0\"?>");
|
|
580
|
pw.println("<error>");
|
|
581
|
pw.println(e.getMessage());
|
|
582
|
pw.println("</error>");
|
|
583
|
// Close printwriter
|
|
584
|
pw.close();
|
|
585
|
// Close output stream
|
|
586
|
out.close();
|
|
587
|
}
|
|
588
|
// Close zip output stream
|
|
589
|
if (zOut != null) {
|
|
590
|
zOut.close();
|
|
591
|
}
|
|
592
|
} catch (IOException ioe) {
|
|
593
|
logMetacat.error("MetaCatServlet.handleExportAction - Problem with the servlet output: "
|
|
594
|
+ ioe.getMessage());
|
|
595
|
e.printStackTrace(System.out);
|
|
596
|
}
|
|
597
|
|
|
598
|
logMetacat.error("MetaCatServlet.handleExportAction - General error: "
|
|
599
|
+ e.getMessage());
|
|
600
|
e.printStackTrace(System.out);
|
|
601
|
|
|
602
|
}
|
|
603
|
|
|
604
|
}
|
|
605
|
|
|
606
|
/**
|
|
607
|
* In eml2 document, the xml can have inline data and data was stripped off
|
|
608
|
* and store in file system. This action can be used to read inline data
|
|
609
|
* only
|
|
610
|
*
|
|
611
|
* @param params the Hashtable of HTTP request parameters
|
|
612
|
* @param response the HTTP response object linked to the client
|
|
613
|
* @param user the username sent the request
|
|
614
|
* @param groups the user's groupnames
|
|
615
|
*/
|
|
616
|
protected void handleReadInlineDataAction(Hashtable<String, String[]> params,
|
|
617
|
HttpServletRequest request, HttpServletResponse response,
|
|
618
|
String user, String passWord, String[] groups) {
|
|
619
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
620
|
String[] docs = new String[10];
|
|
621
|
String inlineDataId = null;
|
|
622
|
String docId = "";
|
|
623
|
ServletOutputStream out = null;
|
|
624
|
|
|
625
|
try {
|
|
626
|
// read the params
|
|
627
|
if (params.containsKey("inlinedataid")) {
|
|
628
|
docs = params.get("inlinedataid");
|
|
629
|
}
|
|
630
|
// Get the docid
|
|
631
|
inlineDataId = docs[0];
|
|
632
|
// Make sure the client specify docid
|
|
633
|
if (inlineDataId == null || inlineDataId.equals("")) {
|
|
634
|
throw new Exception("You didn't specify requested inlinedataid"); }
|
|
635
|
|
|
636
|
// check for permission
|
|
637
|
docId =
|
|
638
|
DocumentUtil.getDocIdWithoutRevFromInlineDataID(inlineDataId);
|
|
639
|
PermissionController controller = new PermissionController(docId);
|
|
640
|
// check top level read permission
|
|
641
|
if (!controller.hasPermission(user, groups,
|
|
642
|
AccessControlInterface.READSTRING)) {
|
|
643
|
throw new Exception("User " + user
|
|
644
|
+ " doesn't have permission " + " to read document "
|
|
645
|
+ docId);
|
|
646
|
} else {
|
|
647
|
//check data access level
|
|
648
|
try {
|
|
649
|
Hashtable<String,String> unReadableInlineDataList =
|
|
650
|
PermissionController.getUnReadableInlineDataIdList(docId,
|
|
651
|
user, groups, false);
|
|
652
|
String inlineDataIdWithoutRev = DocumentUtil.getInlineDataIdWithoutRev(inlineDataId);
|
|
653
|
if (unReadableInlineDataList.containsValue(inlineDataIdWithoutRev)) {
|
|
654
|
throw new Exception("User " + user
|
|
655
|
+ " doesn't have permission " + " to read inlinedata "
|
|
656
|
+ inlineDataId);
|
|
657
|
|
|
658
|
}//if
|
|
659
|
}//try
|
|
660
|
catch (Exception e) {
|
|
661
|
throw e;
|
|
662
|
}//catch
|
|
663
|
}//else
|
|
664
|
|
|
665
|
// Get output stream
|
|
666
|
out = response.getOutputStream();
|
|
667
|
// read the inline data from the file
|
|
668
|
String inlinePath = PropertyService.getProperty("application.inlinedatafilepath");
|
|
669
|
File lineData = new File(inlinePath, inlineDataId);
|
|
670
|
FileInputStream input = new FileInputStream(lineData);
|
|
671
|
byte[] buffer = new byte[4 * 1024];
|
|
672
|
int bytes = input.read(buffer);
|
|
673
|
while (bytes != -1) {
|
|
674
|
out.write(buffer, 0, bytes);
|
|
675
|
bytes = input.read(buffer);
|
|
676
|
}
|
|
677
|
out.close();
|
|
678
|
|
|
679
|
EventLog.getInstance().log(request.getRemoteAddr(), user,
|
|
680
|
inlineDataId, "readinlinedata");
|
|
681
|
} catch (Exception e) {
|
|
682
|
try {
|
|
683
|
PrintWriter pw = null;
|
|
684
|
// Send error message back
|
|
685
|
if (out != null) {
|
|
686
|
pw = new PrintWriter(out);
|
|
687
|
} else {
|
|
688
|
pw = response.getWriter();
|
|
689
|
}
|
|
690
|
pw.println("<?xml version=\"1.0\"?>");
|
|
691
|
pw.println("<error>");
|
|
692
|
pw.println(e.getMessage());
|
|
693
|
pw.println("</error>");
|
|
694
|
// Close printwriter
|
|
695
|
pw.close();
|
|
696
|
// Close output stream if out is not null
|
|
697
|
if (out != null) {
|
|
698
|
out.close();
|
|
699
|
}
|
|
700
|
} catch (IOException ioe) {
|
|
701
|
logMetacat.error("MetaCatServlet.handleReadInlineDataAction - Problem with the servlet output: "
|
|
702
|
+ ioe.getMessage());
|
|
703
|
e.printStackTrace(System.out);
|
|
704
|
}
|
|
705
|
logMetacat.error("MetaCatServlet.handleReadInlineDataAction - General error: "
|
|
706
|
+ e.getMessage());
|
|
707
|
e.printStackTrace(System.out);
|
|
708
|
}
|
|
709
|
}
|
|
710
|
|
|
711
|
/**
|
|
712
|
* Handle the "read" request of metadata/data files from Metacat or any
|
|
713
|
* files from Internet; transformed metadata XML document into HTML
|
|
714
|
* presentation if requested; zip files when more than one were requested.
|
|
715
|
*
|
|
716
|
* @param params the Hashtable of HTTP request parameters
|
|
717
|
* @param request the HTTP request object linked to the client
|
|
718
|
* @param response the HTTP response object linked to the client
|
|
719
|
* @param user the username sent the request
|
|
720
|
* @param groups the user's groupnames
|
|
721
|
*/
|
|
722
|
public void handleReadAction(Hashtable<String, String[]> params, HttpServletRequest request,
|
|
723
|
HttpServletResponse response, String user, String passWord,
|
|
724
|
String[] groups) {
|
|
725
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
726
|
ServletOutputStream out = null;
|
|
727
|
ZipOutputStream zout = null;
|
|
728
|
PrintWriter pw = null;
|
|
729
|
boolean zip = false;
|
|
730
|
boolean withInlineData = true;
|
|
731
|
|
|
732
|
try {
|
|
733
|
String[] docs = new String[0];
|
|
734
|
String docid = "";
|
|
735
|
String qformat = "";
|
|
736
|
|
|
737
|
// read the params
|
|
738
|
if (params.containsKey("docid")) {
|
|
739
|
docs = params.get("docid");
|
|
740
|
}
|
|
741
|
if (params.containsKey("qformat")) {
|
|
742
|
qformat = params.get("qformat")[0];
|
|
743
|
}
|
|
744
|
// the param for only metadata (eml)
|
|
745
|
// we don't support read a eml document without inline data now.
|
|
746
|
/*if (params.containsKey("inlinedata")) {
|
|
747
|
|
|
748
|
String inlineData = ((String[]) params.get("inlinedata"))[0];
|
|
749
|
if (inlineData.equalsIgnoreCase("false")) {
|
|
750
|
withInlineData = false;
|
|
751
|
}
|
|
752
|
}*/
|
|
753
|
if ((docs.length > 1) || qformat.equals("zip")) {
|
|
754
|
zip = true;
|
|
755
|
out = response.getOutputStream();
|
|
756
|
response.setContentType("application/zip"); //MIME type
|
|
757
|
zout = new ZipOutputStream(out);
|
|
758
|
}
|
|
759
|
// go through the list of docs to read
|
|
760
|
for (int i = 0; i < docs.length; i++) {
|
|
761
|
String providedFileName = null;
|
|
762
|
if (params.containsKey(docs[i])) {
|
|
763
|
providedFileName = params.get(docs[i])[0];
|
|
764
|
}
|
|
765
|
try {
|
|
766
|
|
|
767
|
URL murl = new URL(docs[i]);
|
|
768
|
Hashtable<String,String> murlQueryStr = MetacatUtil.parseQuery(
|
|
769
|
murl.getQuery());
|
|
770
|
// case docid="http://.../?docid=aaa"
|
|
771
|
// or docid="metacat://.../?docid=bbb"
|
|
772
|
if (murlQueryStr.containsKey("docid")) {
|
|
773
|
// get only docid, eliminate the rest
|
|
774
|
docid = murlQueryStr.get("docid");
|
|
775
|
if (zip) {
|
|
776
|
addDocToZip(request, docid, providedFileName, zout, user, groups);
|
|
777
|
} else {
|
|
778
|
readFromMetacat(request.getRemoteAddr(), response, response.getOutputStream(), docid, qformat,
|
|
779
|
user, groups, withInlineData, params);
|
|
780
|
}
|
|
781
|
|
|
782
|
// case docid="http://.../filename"
|
|
783
|
} else {
|
|
784
|
docid = docs[i];
|
|
785
|
if (zip) {
|
|
786
|
addDocToZip(request, docid, providedFileName, zout, user, groups);
|
|
787
|
} else {
|
|
788
|
readFromURLConnection(response, docid);
|
|
789
|
}
|
|
790
|
}
|
|
791
|
|
|
792
|
} catch (MalformedURLException mue) {
|
|
793
|
docid = docs[i];
|
|
794
|
if (zip) {
|
|
795
|
addDocToZip(request, docid, providedFileName, zout, user, groups);
|
|
796
|
} else {
|
|
797
|
if (out == null) {
|
|
798
|
out = response.getOutputStream();
|
|
799
|
}
|
|
800
|
readFromMetacat(request.getRemoteAddr(), response, out, docid, qformat,
|
|
801
|
user, groups, withInlineData, params);
|
|
802
|
}
|
|
803
|
}
|
|
804
|
}
|
|
805
|
|
|
806
|
if (zip) {
|
|
807
|
zout.finish(); //terminate the zip file
|
|
808
|
zout.close(); //close the zip stream
|
|
809
|
}
|
|
810
|
|
|
811
|
} catch (McdbDocNotFoundException notFoundE) {
|
|
812
|
// To handle doc not found exception
|
|
813
|
// the docid which didn't be found
|
|
814
|
String notFoundDocId = notFoundE.getUnfoundDocId();
|
|
815
|
String notFoundRevision = notFoundE.getUnfoundRevision();
|
|
816
|
logMetacat.warn("MetaCatServlet.handleReadAction - Missed id: " + notFoundDocId);
|
|
817
|
logMetacat.warn("MetaCatServlet.handleReadAction - Missed rev: " + notFoundRevision);
|
|
818
|
try {
|
|
819
|
// read docid from remote server
|
|
820
|
readFromRemoteMetaCat(response, notFoundDocId,
|
|
821
|
notFoundRevision, user, passWord, out, zip, zout);
|
|
822
|
// Close zout outputstream
|
|
823
|
if (zout != null) {
|
|
824
|
zout.close();
|
|
825
|
}
|
|
826
|
// close output stream
|
|
827
|
if (out != null) {
|
|
828
|
out.close();
|
|
829
|
}
|
|
830
|
|
|
831
|
} catch (Exception exc) {
|
|
832
|
logMetacat.error("MetaCatServlet.handleReadAction - General error: "
|
|
833
|
+ exc.getMessage());
|
|
834
|
exc.printStackTrace(System.out);
|
|
835
|
try {
|
|
836
|
if (out != null) {
|
|
837
|
response.setContentType("text/xml");
|
|
838
|
// Send back error message by printWriter
|
|
839
|
pw = new PrintWriter(out);
|
|
840
|
pw.println("<?xml version=\"1.0\"?>");
|
|
841
|
pw.println("<error>");
|
|
842
|
pw.println(notFoundE.getMessage());
|
|
843
|
pw.println("</error>");
|
|
844
|
pw.close();
|
|
845
|
out.close();
|
|
846
|
|
|
847
|
} else {
|
|
848
|
response.setContentType("text/xml"); //MIME type
|
|
849
|
// Send back error message if out = null
|
|
850
|
if (pw == null) {
|
|
851
|
// If pw is null, open the respnose
|
|
852
|
pw = response.getWriter();
|
|
853
|
}
|
|
854
|
pw.println("<?xml version=\"1.0\"?>");
|
|
855
|
pw.println("<error>");
|
|
856
|
pw.println(notFoundE.getMessage());
|
|
857
|
pw.println("</error>");
|
|
858
|
pw.close();
|
|
859
|
}
|
|
860
|
// close zout
|
|
861
|
if (zout != null) {
|
|
862
|
zout.close();
|
|
863
|
}
|
|
864
|
} catch (IOException ie) {
|
|
865
|
logMetacat.error("MetaCatServlet.handleReadAction - Problem with the servlet output: "
|
|
866
|
+ ie.getMessage());
|
|
867
|
ie.printStackTrace(System.out);
|
|
868
|
}
|
|
869
|
}
|
|
870
|
} catch (Exception e) {
|
|
871
|
try {
|
|
872
|
|
|
873
|
if (out != null) {
|
|
874
|
response.setContentType("text/xml"); //MIME type
|
|
875
|
pw = new PrintWriter(out);
|
|
876
|
pw.println("<?xml version=\"1.0\"?>");
|
|
877
|
pw.println("<error>");
|
|
878
|
pw.println(e.getMessage());
|
|
879
|
pw.println("</error>");
|
|
880
|
pw.close();
|
|
881
|
out.close();
|
|
882
|
} else {
|
|
883
|
response.setContentType("text/xml"); //MIME type
|
|
884
|
// Send back error message if out = null
|
|
885
|
if (pw == null) {
|
|
886
|
pw = response.getWriter();
|
|
887
|
}
|
|
888
|
pw.println("<?xml version=\"1.0\"?>");
|
|
889
|
pw.println("<error>");
|
|
890
|
pw.println(e.getMessage());
|
|
891
|
pw.println("</error>");
|
|
892
|
pw.close();
|
|
893
|
|
|
894
|
}
|
|
895
|
// Close zip output stream
|
|
896
|
if (zout != null) {
|
|
897
|
zout.close();
|
|
898
|
}
|
|
899
|
|
|
900
|
} catch (Exception e2) {
|
|
901
|
logMetacat.error("MetaCatServlet.handleReadAction - Problem with the servlet output: "
|
|
902
|
+ e2.getMessage());
|
|
903
|
e2.printStackTrace(System.out);
|
|
904
|
|
|
905
|
}
|
|
906
|
|
|
907
|
logMetacat.error("MetaCatServlet.handleReadAction - General error: "
|
|
908
|
+ e.getMessage());
|
|
909
|
e.printStackTrace(System.out);
|
|
910
|
}
|
|
911
|
}
|
|
912
|
|
|
913
|
/**
|
|
914
|
*
|
|
915
|
* @return
|
|
916
|
*/
|
|
917
|
public MetacatResultSet query(String metacatUrl, Hashtable<String, String[]>params,
|
|
918
|
String username, String[] groups, String sessionid)
|
|
919
|
throws Exception
|
|
920
|
{
|
|
921
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
|
922
|
PrintWriter out = new PrintWriter(baos);
|
|
923
|
handleQuery(out, params, null, username, groups, sessionid);
|
|
924
|
out.flush();
|
|
925
|
baos.flush();
|
|
926
|
//baos.close();
|
|
927
|
//System.out.println("result from query: " + baos.toString());
|
|
928
|
MetacatResultSet rs = new MetacatResultSet(baos.toString());
|
|
929
|
return rs;
|
|
930
|
}
|
|
931
|
|
|
932
|
/**
|
|
933
|
* set the access permissions on the document specified
|
|
934
|
*/
|
|
935
|
public void setAccess(String metacatUrl, String username, String docid, String principal,
|
|
936
|
String permission, String permissionType, String permissionOrder)
|
|
937
|
throws Exception
|
|
938
|
{
|
|
939
|
Hashtable<String,String[]> params = new Hashtable<String,String[]>();
|
|
940
|
params.put("principal", new String[] {principal});
|
|
941
|
params.put("permission", new String[] {permission});
|
|
942
|
params.put("permType", new String[] {permissionType});
|
|
943
|
params.put("permOrder", new String[] {permissionOrder});
|
|
944
|
params.put("docid", new String[]{docid});
|
|
945
|
|
|
946
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
|
947
|
PrintWriter out = new PrintWriter(baos);
|
|
948
|
handleSetAccessAction(out, params, username, null, null);
|
|
949
|
String resp = baos.toString();
|
|
950
|
System.out.println("response from MetacatHandler.setAccess: " + resp);
|
|
951
|
}
|
|
952
|
|
|
953
|
/** read metadata or data from Metacat
|
|
954
|
* @throws PropertyNotFoundException
|
|
955
|
* @throws ParseLSIDException
|
|
956
|
* @throws InsufficientKarmaException
|
|
957
|
*/
|
|
958
|
public void readFromMetacat(String ipAddress,
|
|
959
|
HttpServletResponse response, OutputStream out, String docid, String qformat,
|
|
960
|
String user, String[] groups, boolean withInlineData,
|
|
961
|
Hashtable<String, String[]> params) throws ClassNotFoundException,
|
|
962
|
IOException, SQLException, McdbException, PropertyNotFoundException,
|
|
963
|
ParseLSIDException, InsufficientKarmaException {
|
|
964
|
|
|
965
|
Logger logMetacat = Logger.getLogger(MetacatHandler.class);
|
|
966
|
try {
|
|
967
|
|
|
968
|
if (docid.startsWith("urn:")) {
|
|
969
|
docid = LSIDUtil.getDocId(docid, true);
|
|
970
|
}
|
|
971
|
|
|
972
|
// here is hack for handle docid=john.10(in order to tell mike.jim.10.1
|
|
973
|
// mike.jim.10, we require to provide entire docid with rev). But
|
|
974
|
// some old client they only provide docid without rev, so we need
|
|
975
|
// to handle this suituation. First we will check how many
|
|
976
|
// seperator here, if only one, we will append the rev in xml_documents
|
|
977
|
// to the id.
|
|
978
|
docid = appendRev(docid);
|
|
979
|
|
|
980
|
DocumentImpl doc = new DocumentImpl(docid, false);
|
|
981
|
|
|
982
|
//check the permission for read
|
|
983
|
if (!DocumentImpl.hasReadPermission(user, groups, docid)) {
|
|
984
|
|
|
985
|
InsufficientKarmaException e = new InsufficientKarmaException("User " + user
|
|
986
|
+ " does not have permission"
|
|
987
|
+ " to read the document with the docid " + docid);
|
|
988
|
throw e;
|
|
989
|
}
|
|
990
|
|
|
991
|
if (doc.getRootNodeID() == 0) {
|
|
992
|
// this is data file, so find the path on disk for the file
|
|
993
|
String filepath = PropertyService.getProperty("application.datafilepath");
|
|
994
|
if (!filepath.endsWith("/")) {
|
|
995
|
filepath += "/";
|
|
996
|
}
|
|
997
|
String filename = filepath + docid;
|
|
998
|
FileInputStream fin = null;
|
|
999
|
fin = new FileInputStream(filename);
|
|
1000
|
|
|
1001
|
if (response != null) {
|
|
1002
|
// MIME type
|
|
1003
|
//String contentType = servletContext.getMimeType(filename);
|
|
1004
|
String contentType = (new MimetypesFileTypeMap()).getContentType(filename);
|
|
1005
|
if (contentType == null) {
|
|
1006
|
ContentTypeProvider provider = new ContentTypeProvider(
|
|
1007
|
docid);
|
|
1008
|
contentType = provider.getContentType();
|
|
1009
|
logMetacat.info("MetaCatServlet.readFromMetacat - Final contenttype is: "
|
|
1010
|
+ contentType);
|
|
1011
|
}
|
|
1012
|
response.setContentType(contentType);
|
|
1013
|
|
|
1014
|
// Set the output filename on the response
|
|
1015
|
String outputname = generateOutputName(docid, params, doc);
|
|
1016
|
response.setHeader("Content-Disposition",
|
|
1017
|
"attachment; filename=\"" + outputname + "\"");
|
|
1018
|
}
|
|
1019
|
|
|
1020
|
// Write the data to the output stream
|
|
1021
|
try {
|
|
1022
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1023
|
int b = fin.read(buf);
|
|
1024
|
while (b != -1) {
|
|
1025
|
out.write(buf, 0, b);
|
|
1026
|
b = fin.read(buf);
|
|
1027
|
}
|
|
1028
|
} finally {
|
|
1029
|
if (fin != null) fin.close();
|
|
1030
|
}
|
|
1031
|
|
|
1032
|
} else {
|
|
1033
|
// this is metadata doc
|
|
1034
|
if (qformat.equals("xml") || qformat.equals("")) {
|
|
1035
|
// if equals "", that means no qformat is specified. hence
|
|
1036
|
// by default the document should be returned in xml format
|
|
1037
|
// set content type first
|
|
1038
|
|
|
1039
|
if (response != null) {
|
|
1040
|
response.setContentType("text/xml"); //MIME type
|
|
1041
|
response.setHeader("Content-Disposition",
|
|
1042
|
"attachment; filename=" + docid + ".xml");
|
|
1043
|
}
|
|
1044
|
|
|
1045
|
// Try to get the metadata file from disk. If it isn't
|
|
1046
|
// found, create it from the db and write it to disk then.
|
|
1047
|
try {
|
|
1048
|
PrintWriter pw = new PrintWriter(out);
|
|
1049
|
doc.toXml(pw, user, groups, withInlineData);
|
|
1050
|
} catch (McdbException e) {
|
|
1051
|
// any exceptions in reading the xml from disc, and we go back to the
|
|
1052
|
// old way of creating the xml directly.
|
|
1053
|
logMetacat.error("MetaCatServlet.readFromMetacat - could not read from document file " + docid
|
|
1054
|
+ ": " + e.getMessage());
|
|
1055
|
e.printStackTrace(System.out);
|
|
1056
|
PrintWriter pw = new PrintWriter(out);
|
|
1057
|
doc.toXmlFromDb(pw, user, groups, withInlineData);
|
|
1058
|
}
|
|
1059
|
} else {
|
|
1060
|
// TODO MCD, this should read from disk as well?
|
|
1061
|
//*** This is a metadata doc, to be returned in a skin/custom format.
|
|
1062
|
//*** Add param to indicate if public has read access or not.
|
|
1063
|
logMetacat.debug("User: \n" + user);
|
|
1064
|
if (!user.equals("public")) {
|
|
1065
|
if (DocumentImpl.hasReadPermission("public", null, docid))
|
|
1066
|
params.put("publicRead", new String[] {"true"});
|
|
1067
|
else
|
|
1068
|
params.put("publicRead", new String[] {"false"});
|
|
1069
|
}
|
|
1070
|
|
|
1071
|
if (response != null) {
|
|
1072
|
response.setContentType("text/html"); //MIME type
|
|
1073
|
}
|
|
1074
|
|
|
1075
|
PrintWriter pw = new PrintWriter(out);
|
|
1076
|
|
|
1077
|
// Look up the document type
|
|
1078
|
String doctype = doc.getDoctype();
|
|
1079
|
// Transform the document to the new doctype
|
|
1080
|
DBTransform dbt = new DBTransform();
|
|
1081
|
dbt.transformXMLDocument(doc.toString(user, groups,
|
|
1082
|
withInlineData), doctype, "-//W3C//HTML//EN",
|
|
1083
|
qformat, pw, params, null);
|
|
1084
|
}
|
|
1085
|
|
|
1086
|
}
|
|
1087
|
EventLog.getInstance().log(ipAddress, user, docid, "read");
|
|
1088
|
} catch (PropertyNotFoundException except) {
|
|
1089
|
throw except;
|
|
1090
|
}
|
|
1091
|
}
|
|
1092
|
|
|
1093
|
/**
|
|
1094
|
* Create a filename to be used for naming a downloaded document
|
|
1095
|
* @param docid the identifier of the document to be named
|
|
1096
|
* @param params the parameters of the request
|
|
1097
|
* @param doc the DocumentImpl of the document to be named
|
|
1098
|
* @return String containing a name for the download
|
|
1099
|
*/
|
|
1100
|
private String generateOutputName(String docid,
|
|
1101
|
Hashtable<String, String[]> params, DocumentImpl doc) {
|
|
1102
|
String outputname = null;
|
|
1103
|
// check for the existence of a metadatadocid parameter,
|
|
1104
|
// if this is sent, then send a filename which contains both
|
|
1105
|
// the metadata docid and the data docid, so the link with
|
|
1106
|
// metadata is explicitly encoded in the filename.
|
|
1107
|
String metadatadocid = null;
|
|
1108
|
Vector<String> nameparts = new Vector<String>();
|
|
1109
|
|
|
1110
|
if(params.containsKey("metadatadocid")) {
|
|
1111
|
metadatadocid = params.get("metadatadocid")[0];
|
|
1112
|
}
|
|
1113
|
if (metadatadocid != null && !metadatadocid.equals("")) {
|
|
1114
|
nameparts.add(metadatadocid);
|
|
1115
|
}
|
|
1116
|
// we'll always have the docid, include it in the name
|
|
1117
|
String doctype = doc.getDoctype();
|
|
1118
|
// TODO: fix this to lookup the associated FGDC metadata document,
|
|
1119
|
// and grab the doctype tag for it. These should be set to something
|
|
1120
|
// consistent, not 'metadata' as it stands...
|
|
1121
|
//if (!doctype.equals("metadata")) {
|
|
1122
|
// nameparts.add(docid);
|
|
1123
|
//}
|
|
1124
|
nameparts.add(docid);
|
|
1125
|
// Set the name of the data file to the entity name plus docid,
|
|
1126
|
// or if that is unavailable, use the docid alone
|
|
1127
|
String docname = doc.getDocname();
|
|
1128
|
if (docname != null && !docname.equals("")) {
|
|
1129
|
nameparts.add(docname);
|
|
1130
|
}
|
|
1131
|
// combine the name elements with a dash, using a 'join' equivalent
|
|
1132
|
String delimiter = "-";
|
|
1133
|
Iterator<String> iter = nameparts.iterator();
|
|
1134
|
StringBuffer buffer = new StringBuffer(iter.next());
|
|
1135
|
while (iter.hasNext()) buffer.append(delimiter).append(iter.next());
|
|
1136
|
outputname = buffer.toString();
|
|
1137
|
return outputname;
|
|
1138
|
}
|
|
1139
|
|
|
1140
|
/**
|
|
1141
|
* read data from URLConnection
|
|
1142
|
*/
|
|
1143
|
private void readFromURLConnection(HttpServletResponse response,
|
|
1144
|
String docid) throws IOException, MalformedURLException {
|
|
1145
|
ServletOutputStream out = response.getOutputStream();
|
|
1146
|
//String contentType = servletContext.getMimeType(docid); //MIME type
|
|
1147
|
String contentType = (new MimetypesFileTypeMap()).getContentType(docid);
|
|
1148
|
if (contentType == null) {
|
|
1149
|
if (docid.endsWith(".xml")) {
|
|
1150
|
contentType = "text/xml";
|
|
1151
|
} else if (docid.endsWith(".css")) {
|
|
1152
|
contentType = "text/css";
|
|
1153
|
} else if (docid.endsWith(".dtd")) {
|
|
1154
|
contentType = "text/plain";
|
|
1155
|
} else if (docid.endsWith(".xsd")) {
|
|
1156
|
contentType = "text/xml";
|
|
1157
|
} else if (docid.endsWith("/")) {
|
|
1158
|
contentType = "text/html";
|
|
1159
|
} else {
|
|
1160
|
File f = new File(docid);
|
|
1161
|
if (f.isDirectory()) {
|
|
1162
|
contentType = "text/html";
|
|
1163
|
} else {
|
|
1164
|
contentType = "application/octet-stream";
|
|
1165
|
}
|
|
1166
|
}
|
|
1167
|
}
|
|
1168
|
response.setContentType(contentType);
|
|
1169
|
// if we decide to use "application/octet-stream" for all data returns
|
|
1170
|
// response.setContentType("application/octet-stream");
|
|
1171
|
|
|
1172
|
// this is http url
|
|
1173
|
URL url = new URL(docid);
|
|
1174
|
BufferedInputStream bis = null;
|
|
1175
|
try {
|
|
1176
|
bis = new BufferedInputStream(url.openStream());
|
|
1177
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1178
|
int b = bis.read(buf);
|
|
1179
|
while (b != -1) {
|
|
1180
|
out.write(buf, 0, b);
|
|
1181
|
b = bis.read(buf);
|
|
1182
|
}
|
|
1183
|
} finally {
|
|
1184
|
if (bis != null) bis.close();
|
|
1185
|
}
|
|
1186
|
|
|
1187
|
}
|
|
1188
|
|
|
1189
|
/**
|
|
1190
|
* read file/doc and write to ZipOutputStream
|
|
1191
|
*
|
|
1192
|
* @param docid
|
|
1193
|
* @param zout
|
|
1194
|
* @param user
|
|
1195
|
* @param groups
|
|
1196
|
* @throws ClassNotFoundException
|
|
1197
|
* @throws IOException
|
|
1198
|
* @throws SQLException
|
|
1199
|
* @throws McdbException
|
|
1200
|
* @throws Exception
|
|
1201
|
*/
|
|
1202
|
private void addDocToZip(HttpServletRequest request, String docid, String providedFileName,
|
|
1203
|
ZipOutputStream zout, String user, String[] groups) throws
|
|
1204
|
ClassNotFoundException, IOException, SQLException, McdbException,
|
|
1205
|
Exception {
|
|
1206
|
byte[] bytestring = null;
|
|
1207
|
ZipEntry zentry = null;
|
|
1208
|
|
|
1209
|
try {
|
|
1210
|
URL url = new URL(docid);
|
|
1211
|
|
|
1212
|
// this http url; read from URLConnection; add to zip
|
|
1213
|
//use provided file name if we have one
|
|
1214
|
if (providedFileName != null && providedFileName.length() > 1) {
|
|
1215
|
zentry = new ZipEntry(providedFileName);
|
|
1216
|
}
|
|
1217
|
else {
|
|
1218
|
zentry = new ZipEntry(docid);
|
|
1219
|
}
|
|
1220
|
zout.putNextEntry(zentry);
|
|
1221
|
BufferedInputStream bis = null;
|
|
1222
|
try {
|
|
1223
|
bis = new BufferedInputStream(url.openStream());
|
|
1224
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1225
|
int b = bis.read(buf);
|
|
1226
|
while (b != -1) {
|
|
1227
|
zout.write(buf, 0, b);
|
|
1228
|
b = bis.read(buf);
|
|
1229
|
}
|
|
1230
|
} finally {
|
|
1231
|
if (bis != null) bis.close();
|
|
1232
|
}
|
|
1233
|
zout.closeEntry();
|
|
1234
|
|
|
1235
|
} catch (MalformedURLException mue) {
|
|
1236
|
|
|
1237
|
// this is metacat doc (data file or metadata doc)
|
|
1238
|
try {
|
|
1239
|
DocumentImpl doc = new DocumentImpl(docid, false);
|
|
1240
|
|
|
1241
|
//check the permission for read
|
|
1242
|
if (!DocumentImpl.hasReadPermission(user, groups, docid)) {
|
|
1243
|
Exception e = new Exception("User " + user
|
|
1244
|
+ " does not have "
|
|
1245
|
+ "permission to read the document with the docid "
|
|
1246
|
+ docid);
|
|
1247
|
throw e;
|
|
1248
|
}
|
|
1249
|
|
|
1250
|
if (doc.getRootNodeID() == 0) {
|
|
1251
|
// this is data file; add file to zip
|
|
1252
|
String filepath = PropertyService.getProperty("application.datafilepath");
|
|
1253
|
if (!filepath.endsWith("/")) {
|
|
1254
|
filepath += "/";
|
|
1255
|
}
|
|
1256
|
String filename = filepath + docid;
|
|
1257
|
FileInputStream fin = null;
|
|
1258
|
fin = new FileInputStream(filename);
|
|
1259
|
try {
|
|
1260
|
//use provided file name if we have one
|
|
1261
|
if (providedFileName != null && providedFileName.length() > 1) {
|
|
1262
|
zentry = new ZipEntry(providedFileName);
|
|
1263
|
}
|
|
1264
|
else {
|
|
1265
|
zentry = new ZipEntry(docid);
|
|
1266
|
}
|
|
1267
|
zout.putNextEntry(zentry);
|
|
1268
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1269
|
int b = fin.read(buf);
|
|
1270
|
while (b != -1) {
|
|
1271
|
zout.write(buf, 0, b);
|
|
1272
|
b = fin.read(buf);
|
|
1273
|
}
|
|
1274
|
} finally {
|
|
1275
|
if (fin != null) fin.close();
|
|
1276
|
}
|
|
1277
|
zout.closeEntry();
|
|
1278
|
|
|
1279
|
} else {
|
|
1280
|
// this is metadata doc; add doc to zip
|
|
1281
|
bytestring = doc.toString().getBytes();
|
|
1282
|
//use provided file name if given
|
|
1283
|
if (providedFileName != null && providedFileName.length() > 1) {
|
|
1284
|
zentry = new ZipEntry(providedFileName);
|
|
1285
|
}
|
|
1286
|
else {
|
|
1287
|
zentry = new ZipEntry(docid + ".xml");
|
|
1288
|
}
|
|
1289
|
zentry.setSize(bytestring.length);
|
|
1290
|
zout.putNextEntry(zentry);
|
|
1291
|
zout.write(bytestring, 0, bytestring.length);
|
|
1292
|
zout.closeEntry();
|
|
1293
|
}
|
|
1294
|
EventLog.getInstance().log(request.getRemoteAddr(), user,
|
|
1295
|
docid, "read");
|
|
1296
|
} catch (Exception except) {
|
|
1297
|
throw except;
|
|
1298
|
}
|
|
1299
|
}
|
|
1300
|
}
|
|
1301
|
|
|
1302
|
/**
|
|
1303
|
* If metacat couldn't find a data file or document locally, it will read
|
|
1304
|
* this docid from its home server. This is for the replication feature
|
|
1305
|
*/
|
|
1306
|
private void readFromRemoteMetaCat(HttpServletResponse response,
|
|
1307
|
String docid, String rev, String user, String password,
|
|
1308
|
ServletOutputStream out, boolean zip, ZipOutputStream zout)
|
|
1309
|
throws Exception {
|
|
1310
|
// Create a object of RemoteDocument, "" is for zipEntryPath
|
|
1311
|
RemoteDocument remoteDoc = new RemoteDocument(docid, rev, user,
|
|
1312
|
password, "");
|
|
1313
|
String docType = remoteDoc.getDocType();
|
|
1314
|
// Only read data file
|
|
1315
|
if (docType.equals("BIN")) {
|
|
1316
|
// If it is zip format
|
|
1317
|
if (zip) {
|
|
1318
|
remoteDoc.readDocumentFromRemoteServerByZip(zout);
|
|
1319
|
} else {
|
|
1320
|
if (out == null) {
|
|
1321
|
out = response.getOutputStream();
|
|
1322
|
}
|
|
1323
|
response.setContentType("application/octet-stream");
|
|
1324
|
remoteDoc.readDocumentFromRemoteServer(out);
|
|
1325
|
}
|
|
1326
|
} else {
|
|
1327
|
throw new Exception("Docid: " + docid + "." + rev
|
|
1328
|
+ " couldn't find");
|
|
1329
|
}
|
|
1330
|
}
|
|
1331
|
|
|
1332
|
/**
|
|
1333
|
* Handle the database putdocument request and write an XML document to the
|
|
1334
|
* database connection
|
|
1335
|
*/
|
|
1336
|
public String handleInsertOrUpdateAction(String ipAddress,
|
|
1337
|
HttpServletResponse response, PrintWriter out, Hashtable<String, String[]> params,
|
|
1338
|
String user, String[] groups) {
|
|
1339
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
1340
|
DBConnection dbConn = null;
|
|
1341
|
int serialNumber = -1;
|
|
1342
|
String output = "";
|
|
1343
|
String qformat = null;
|
|
1344
|
if(params.containsKey("qformat"))
|
|
1345
|
{
|
|
1346
|
qformat = params.get("qformat")[0];
|
|
1347
|
}
|
|
1348
|
|
|
1349
|
if(params.get("docid") == null){
|
|
1350
|
String msg = "<?xml version=\"1.0\"?>" +
|
|
1351
|
"<error>" +
|
|
1352
|
"Docid not specified" +
|
|
1353
|
"</error>";
|
|
1354
|
if(out != null)
|
|
1355
|
{
|
|
1356
|
out.println(msg);
|
|
1357
|
logMetacat.error("MetaCatServlet.handleInsertOrUpdateAction - Docid not specified");
|
|
1358
|
}
|
|
1359
|
return msg;
|
|
1360
|
}
|
|
1361
|
|
|
1362
|
try {
|
|
1363
|
if (!AuthUtil.canInsertOrUpdate(user, groups)) {
|
|
1364
|
String msg = "<?xml version=\"1.0\"?>" +
|
|
1365
|
"<error>" +
|
|
1366
|
"User '" + user + "' not allowed to insert and update" +
|
|
1367
|
"</error>";
|
|
1368
|
if(out != null)
|
|
1369
|
{
|
|
1370
|
out.println(msg);
|
|
1371
|
}
|
|
1372
|
|
|
1373
|
logMetacat.error("MetaCatServlet.handleInsertOrUpdateAction - User '" + user + "' not allowed to insert and update");
|
|
1374
|
return msg;
|
|
1375
|
}
|
|
1376
|
} catch (MetacatUtilException ue) {
|
|
1377
|
logMetacat.error("MetaCatServlet.handleInsertOrUpdateAction - Could not determine if user could insert or update: "
|
|
1378
|
+ ue.getMessage());
|
|
1379
|
ue.printStackTrace(System.out);
|
|
1380
|
// TODO: This is a bug, as it allows one to bypass the access check -- need to throw an exception
|
|
1381
|
}
|
|
1382
|
|
|
1383
|
try {
|
|
1384
|
// Get the document indicated
|
|
1385
|
logMetacat.debug("MetaCatServlet.handleInsertOrUpdateAction - params: " + params.toString());
|
|
1386
|
|
|
1387
|
String[] doctext = params.get("doctext");
|
|
1388
|
String pub = null;
|
|
1389
|
if (params.containsKey("public")) {
|
|
1390
|
pub = params.get("public")[0];
|
|
1391
|
}
|
|
1392
|
|
|
1393
|
StringReader dtd = null;
|
|
1394
|
if (params.containsKey("dtdtext")) {
|
|
1395
|
String[] dtdtext = params.get("dtdtext");
|
|
1396
|
try {
|
|
1397
|
if (!dtdtext[0].equals("")) {
|
|
1398
|
dtd = new StringReader(dtdtext[0]);
|
|
1399
|
}
|
|
1400
|
} catch (NullPointerException npe) {
|
|
1401
|
}
|
|
1402
|
}
|
|
1403
|
|
|
1404
|
if(doctext == null){
|
|
1405
|
String msg = "<?xml version=\"1.0\"?>" +
|
|
1406
|
"<error>" +
|
|
1407
|
"Document text not submitted." +
|
|
1408
|
"</error>";
|
|
1409
|
if(out != null)
|
|
1410
|
{
|
|
1411
|
out.println(msg);
|
|
1412
|
}
|
|
1413
|
|
|
1414
|
// TODO: this should really throw an exception
|
|
1415
|
return msg;
|
|
1416
|
}
|
|
1417
|
|
|
1418
|
logMetacat.debug("MetaCatServlet.handleInsertOrUpdateAction - the xml document in metacat servlet (before parsing):\n" + doctext[0]);
|
|
1419
|
StringReader xmlReader = new StringReader(doctext[0]);
|
|
1420
|
boolean validate = false;
|
|
1421
|
DocumentImplWrapper documentWrapper = null;
|
|
1422
|
try {
|
|
1423
|
// look inside XML Document for <!DOCTYPE ... PUBLIC/SYSTEM ...
|
|
1424
|
// >
|
|
1425
|
// in order to decide whether to use validation parser
|
|
1426
|
validate = needDTDValidation(xmlReader);
|
|
1427
|
if (validate) {
|
|
1428
|
// set a dtd base validation parser
|
|
1429
|
String rule = DocumentImpl.DTD;
|
|
1430
|
documentWrapper = new DocumentImplWrapper(rule, validate);
|
|
1431
|
} else {
|
|
1432
|
|
|
1433
|
String namespace = XMLSchemaService.findDocumentNamespace(xmlReader);
|
|
1434
|
|
|
1435
|
if (namespace != null) {
|
|
1436
|
if (namespace.compareTo(DocumentImpl.EML2_0_0NAMESPACE) == 0
|
|
1437
|
|| namespace.compareTo(
|
|
1438
|
DocumentImpl.EML2_0_1NAMESPACE) == 0) {
|
|
1439
|
// set eml2 base validation parser
|
|
1440
|
String rule = DocumentImpl.EML200;
|
|
1441
|
// using emlparser to check id validation
|
|
1442
|
@SuppressWarnings("unused")
|
|
1443
|
EMLParser parser = new EMLParser(doctext[0]);
|
|
1444
|
documentWrapper = new DocumentImplWrapper(rule, true);
|
|
1445
|
} else if (namespace.compareTo(
|
|
1446
|
DocumentImpl.EML2_1_0NAMESPACE) == 0) {
|
|
1447
|
// set eml2 base validation parser
|
|
1448
|
String rule = DocumentImpl.EML210;
|
|
1449
|
// using emlparser to check id validation
|
|
1450
|
@SuppressWarnings("unused")
|
|
1451
|
EMLParser parser = new EMLParser(doctext[0]);
|
|
1452
|
documentWrapper = new DocumentImplWrapper(rule, true);
|
|
1453
|
} else {
|
|
1454
|
// set schema base validation parser
|
|
1455
|
String rule = DocumentImpl.SCHEMA;
|
|
1456
|
documentWrapper = new DocumentImplWrapper(rule, true);
|
|
1457
|
}
|
|
1458
|
} else {
|
|
1459
|
documentWrapper = new DocumentImplWrapper("", false);
|
|
1460
|
}
|
|
1461
|
}
|
|
1462
|
|
|
1463
|
String[] action = params.get("action");
|
|
1464
|
String[] docid = params.get("docid");
|
|
1465
|
String newdocid = null;
|
|
1466
|
|
|
1467
|
String doAction = null;
|
|
1468
|
if (action[0].equals("insert") || action[0].equals("insertmultipart")) {
|
|
1469
|
doAction = "INSERT";
|
|
1470
|
} else if (action[0].equals("update")) {
|
|
1471
|
doAction = "UPDATE";
|
|
1472
|
}
|
|
1473
|
|
|
1474
|
try {
|
|
1475
|
// get a connection from the pool
|
|
1476
|
dbConn = DBConnectionPool
|
|
1477
|
.getDBConnection("MetaCatServlet.handleInsertOrUpdateAction");
|
|
1478
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1479
|
|
|
1480
|
// write the document to the database and disk
|
|
1481
|
String accNumber = docid[0];
|
|
1482
|
logMetacat.debug("MetaCatServlet.handleInsertOrUpdateAction - " + doAction + " "
|
|
1483
|
+ accNumber + "...");
|
|
1484
|
if (accNumber == null || accNumber.equals("")) {
|
|
1485
|
logMetacat.warn("MetaCatServlet.handleInsertOrUpdateAction - writing with null acnumber");
|
|
1486
|
newdocid = documentWrapper.write(dbConn, doctext[0], pub, dtd,
|
|
1487
|
doAction, null, user, groups);
|
|
1488
|
EventLog.getInstance().log(ipAddress, user, "", action[0]);
|
|
1489
|
} else {
|
|
1490
|
newdocid = documentWrapper.write(dbConn, doctext[0], pub, dtd,
|
|
1491
|
doAction, accNumber, user, groups);
|
|
1492
|
|
|
1493
|
EventLog.getInstance().log(ipAddress, user, accNumber, action[0]);
|
|
1494
|
}
|
|
1495
|
} finally {
|
|
1496
|
// Return db connection
|
|
1497
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1498
|
}
|
|
1499
|
|
|
1500
|
// set content type and other response header fields first
|
|
1501
|
//response.setContentType("text/xml");
|
|
1502
|
output += "<?xml version=\"1.0\"?>";
|
|
1503
|
output += "<success>";
|
|
1504
|
output += "<docid>" + newdocid + "</docid>";
|
|
1505
|
output += "</success>";
|
|
1506
|
|
|
1507
|
} catch (NullPointerException npe) {
|
|
1508
|
//response.setContentType("text/xml");
|
|
1509
|
output += "<?xml version=\"1.0\"?>";
|
|
1510
|
output += "<error>";
|
|
1511
|
output += npe.getMessage();
|
|
1512
|
output += "</error>";
|
|
1513
|
logMetacat.warn("MetaCatServlet.handleInsertOrUpdateAction - Null pointer error when writing eml document to the database: " + npe.getMessage());
|
|
1514
|
npe.printStackTrace();
|
|
1515
|
}
|
|
1516
|
} catch (Exception e) {
|
|
1517
|
//response.setContentType("text/xml");
|
|
1518
|
output += "<?xml version=\"1.0\"?>";
|
|
1519
|
output += "<error>";
|
|
1520
|
output += e.getMessage();
|
|
1521
|
output += "</error>";
|
|
1522
|
logMetacat.warn("MetaCatServlet.handleInsertOrUpdateAction - General error when writing eml document to the database: " + e.getMessage());
|
|
1523
|
e.printStackTrace();
|
|
1524
|
}
|
|
1525
|
|
|
1526
|
if (qformat == null || qformat.equals("xml")) {
|
|
1527
|
if(response != null)
|
|
1528
|
{
|
|
1529
|
response.setContentType("text/xml");
|
|
1530
|
out.println(output);
|
|
1531
|
}
|
|
1532
|
return output;
|
|
1533
|
} else {
|
|
1534
|
try {
|
|
1535
|
DBTransform trans = new DBTransform();
|
|
1536
|
response.setContentType("text/html");
|
|
1537
|
trans.transformXMLDocument(output,
|
|
1538
|
"message", "-//W3C//HTML//EN", qformat,
|
|
1539
|
out, null, null);
|
|
1540
|
} catch (Exception e) {
|
|
1541
|
|
|
1542
|
logMetacat.error("MetaCatServlet.handleInsertOrUpdateAction - General error: "
|
|
1543
|
+ e.getMessage());
|
|
1544
|
e.printStackTrace(System.out);
|
|
1545
|
}
|
|
1546
|
}
|
|
1547
|
return null;
|
|
1548
|
}
|
|
1549
|
|
|
1550
|
/**
|
|
1551
|
* Parse XML Document to look for <!DOCTYPE ... PUBLIC/SYSTEM ... > in
|
|
1552
|
* order to decide whether to use validation parser
|
|
1553
|
*/
|
|
1554
|
private static boolean needDTDValidation(StringReader xmlreader)
|
|
1555
|
throws IOException {
|
|
1556
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
1557
|
StringBuffer cbuff = new StringBuffer();
|
|
1558
|
java.util.Stack<String> st = new java.util.Stack<String>();
|
|
1559
|
boolean validate = false;
|
|
1560
|
boolean commented = false;
|
|
1561
|
int c;
|
|
1562
|
int inx;
|
|
1563
|
|
|
1564
|
// read from the stream until find the keywords
|
|
1565
|
while ((st.empty() || st.size() < 4) && ((c = xmlreader.read()) != -1)) {
|
|
1566
|
cbuff.append((char) c);
|
|
1567
|
|
|
1568
|
if ((inx = cbuff.toString().indexOf("<!--")) != -1) {
|
|
1569
|
commented = true;
|
|
1570
|
}
|
|
1571
|
|
|
1572
|
// "<!DOCTYPE" keyword is found; put it in the stack
|
|
1573
|
if ((inx = cbuff.toString().indexOf("<!DOCTYPE")) != -1) {
|
|
1574
|
cbuff = new StringBuffer();
|
|
1575
|
st.push("<!DOCTYPE");
|
|
1576
|
}
|
|
1577
|
// "PUBLIC" keyword is found; put it in the stack
|
|
1578
|
if ((inx = cbuff.toString().indexOf("PUBLIC")) != -1) {
|
|
1579
|
cbuff = new StringBuffer();
|
|
1580
|
st.push("PUBLIC");
|
|
1581
|
}
|
|
1582
|
// "SYSTEM" keyword is found; put it in the stack
|
|
1583
|
if ((inx = cbuff.toString().indexOf("SYSTEM")) != -1) {
|
|
1584
|
cbuff = new StringBuffer();
|
|
1585
|
st.push("SYSTEM");
|
|
1586
|
}
|
|
1587
|
// ">" character is found; put it in the stack
|
|
1588
|
// ">" is found twice: fisrt from <?xml ...?>
|
|
1589
|
// and second from <!DOCTYPE ... >
|
|
1590
|
if ((inx = cbuff.toString().indexOf(">")) != -1) {
|
|
1591
|
cbuff = new StringBuffer();
|
|
1592
|
st.push(">");
|
|
1593
|
}
|
|
1594
|
}
|
|
1595
|
|
|
1596
|
// close the stream
|
|
1597
|
xmlreader.reset();
|
|
1598
|
|
|
1599
|
// check the stack whether it contains the keywords:
|
|
1600
|
// "<!DOCTYPE", "PUBLIC" or "SYSTEM", and ">" in this order
|
|
1601
|
if (st.size() == 4) {
|
|
1602
|
if ((st.pop()).equals(">")
|
|
1603
|
&& ((st.peek()).equals("PUBLIC") | (st.pop()).equals("SYSTEM"))
|
|
1604
|
&& (st.pop()).equals("<!DOCTYPE")) {
|
|
1605
|
validate = true && !commented;
|
|
1606
|
}
|
|
1607
|
}
|
|
1608
|
|
|
1609
|
logMetacat.info("MetaCatServlet.needDTDValidation - Validation for dtd is " + validate);
|
|
1610
|
return validate;
|
|
1611
|
}
|
|
1612
|
|
|
1613
|
// END OF INSERT/UPDATE SECTION
|
|
1614
|
|
|
1615
|
/**
|
|
1616
|
* Handle the database delete request and delete an XML document from the
|
|
1617
|
* database connection
|
|
1618
|
*/
|
|
1619
|
public void handleDeleteAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
1620
|
HttpServletRequest request, HttpServletResponse response,
|
|
1621
|
String user, String[] groups) {
|
|
1622
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
1623
|
String[] docid = params.get("docid");
|
|
1624
|
|
|
1625
|
if(docid == null){
|
|
1626
|
response.setContentType("text/xml");
|
|
1627
|
out.println("<?xml version=\"1.0\"?>");
|
|
1628
|
out.println("<error>");
|
|
1629
|
out.println("Docid not specified.");
|
|
1630
|
out.println("</error>");
|
|
1631
|
logMetacat.error("MetaCatServlet.handleDeleteAction - Docid not specified for the document to be deleted.");
|
|
1632
|
} else {
|
|
1633
|
|
|
1634
|
// delete the document from the database
|
|
1635
|
try {
|
|
1636
|
|
|
1637
|
try {
|
|
1638
|
// null means notify server is null
|
|
1639
|
DocumentImpl.delete(docid[0], user, groups, null);
|
|
1640
|
EventLog.getInstance().log(request.getRemoteAddr(),
|
|
1641
|
user, docid[0], "delete");
|
|
1642
|
response.setContentType("text/xml");
|
|
1643
|
out.println("<?xml version=\"1.0\"?>");
|
|
1644
|
out.println("<success>");
|
|
1645
|
out.println("Document deleted.");
|
|
1646
|
out.println("</success>");
|
|
1647
|
logMetacat.info("MetaCatServlet.handleDeleteAction - Document deleted.");
|
|
1648
|
|
|
1649
|
// Delete from spatial cache if runningSpatialOption
|
|
1650
|
if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) {
|
|
1651
|
SpatialHarvester sh = new SpatialHarvester();
|
|
1652
|
sh.addToDeleteQue( DocumentUtil.getSmartDocId( docid[0] ) );
|
|
1653
|
sh.destroy();
|
|
1654
|
}
|
|
1655
|
|
|
1656
|
} catch (AccessionNumberException ane) {
|
|
1657
|
response.setContentType("text/xml");
|
|
1658
|
out.println("<?xml version=\"1.0\"?>");
|
|
1659
|
out.println("<error>");
|
|
1660
|
//out.println("Error deleting document!!!");
|
|
1661
|
out.println(ane.getMessage());
|
|
1662
|
out.println("</error>");
|
|
1663
|
logMetacat.error("MetaCatServlet.handleDeleteAction - Document could not be deleted: "
|
|
1664
|
+ ane.getMessage());
|
|
1665
|
ane.printStackTrace(System.out);
|
|
1666
|
}
|
|
1667
|
} catch (Exception e) {
|
|
1668
|
response.setContentType("text/xml");
|
|
1669
|
out.println("<?xml version=\"1.0\"?>");
|
|
1670
|
out.println("<error>");
|
|
1671
|
out.println(e.getMessage());
|
|
1672
|
out.println("</error>");
|
|
1673
|
logMetacat.error("MetaCatServlet.handleDeleteAction - Document could not be deleted: "
|
|
1674
|
+ e.getMessage());
|
|
1675
|
e.printStackTrace(System.out);
|
|
1676
|
}
|
|
1677
|
}
|
|
1678
|
}
|
|
1679
|
|
|
1680
|
/**
|
|
1681
|
* Handle the validation request and return the results to the requestor
|
|
1682
|
*/
|
|
1683
|
protected void handleValidateAction(PrintWriter out, Hashtable<String, String[]> params) {
|
|
1684
|
|
|
1685
|
// Get the document indicated
|
|
1686
|
String valtext = null;
|
|
1687
|
DBConnection dbConn = null;
|
|
1688
|
int serialNumber = -1;
|
|
1689
|
|
|
1690
|
try {
|
|
1691
|
valtext = params.get("valtext")[0];
|
|
1692
|
} catch (Exception nullpe) {
|
|
1693
|
|
|
1694
|
String docid = null;
|
|
1695
|
try {
|
|
1696
|
// Find the document id number
|
|
1697
|
docid = params.get("docid")[0];
|
|
1698
|
|
|
1699
|
// Get the document indicated from the db
|
|
1700
|
DocumentImpl xmldoc = new DocumentImpl(docid, false);
|
|
1701
|
valtext = xmldoc.toString();
|
|
1702
|
|
|
1703
|
} catch (NullPointerException npe) {
|
|
1704
|
|
|
1705
|
out.println("<error>Error getting document ID: " + docid
|
|
1706
|
+ "</error>");
|
|
1707
|
//if ( conn != null ) { util.returnConnection(conn); }
|
|
1708
|
return;
|
|
1709
|
} catch (Exception e) {
|
|
1710
|
|
|
1711
|
out.println(e.getMessage());
|
|
1712
|
}
|
|
1713
|
}
|
|
1714
|
|
|
1715
|
try {
|
|
1716
|
// get a connection from the pool
|
|
1717
|
dbConn = DBConnectionPool
|
|
1718
|
.getDBConnection("MetaCatServlet.handleValidateAction");
|
|
1719
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1720
|
DBValidate valobj = new DBValidate(dbConn);
|
|
1721
|
// boolean valid = valobj.validateString(valtext);
|
|
1722
|
|
|
1723
|
// set content type and other response header fields first
|
|
1724
|
|
|
1725
|
out.println(valobj.returnErrors());
|
|
1726
|
|
|
1727
|
} catch (NullPointerException npe2) {
|
|
1728
|
// set content type and other response header fields first
|
|
1729
|
|
|
1730
|
out.println("<error>Error validating document.</error>");
|
|
1731
|
} catch (Exception e) {
|
|
1732
|
|
|
1733
|
out.println(e.getMessage());
|
|
1734
|
} finally {
|
|
1735
|
// Return db connection
|
|
1736
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1737
|
}
|
|
1738
|
}
|
|
1739
|
|
|
1740
|
/**
|
|
1741
|
* Handle "getrevsionanddoctype" action Given a docid, return it's current
|
|
1742
|
* revision and doctype from data base The output is String look like
|
|
1743
|
* "rev;doctype"
|
|
1744
|
*/
|
|
1745
|
protected void handleGetRevisionAndDocTypeAction(PrintWriter out,
|
|
1746
|
Hashtable<String, String[]> params) {
|
|
1747
|
// To store doc parameter
|
|
1748
|
String[] docs = new String[10];
|
|
1749
|
// Store a single doc id
|
|
1750
|
String givenDocId = null;
|
|
1751
|
// Get docid from parameters
|
|
1752
|
if (params.containsKey("docid")) {
|
|
1753
|
docs = params.get("docid");
|
|
1754
|
}
|
|
1755
|
// Get first docid form string array
|
|
1756
|
givenDocId = docs[0];
|
|
1757
|
|
|
1758
|
try {
|
|
1759
|
// Make sure there is a docid
|
|
1760
|
if (givenDocId == null || givenDocId.equals("")) { throw new Exception(
|
|
1761
|
"User didn't specify docid!"); }//if
|
|
1762
|
|
|
1763
|
// Create a DBUtil object
|
|
1764
|
DBUtil dbutil = new DBUtil();
|
|
1765
|
// Get a rev and doctype
|
|
1766
|
String revAndDocType = dbutil
|
|
1767
|
.getCurrentRevisionAndDocTypeForGivenDocument(givenDocId);
|
|
1768
|
out.println(revAndDocType);
|
|
1769
|
|
|
1770
|
} catch (Exception e) {
|
|
1771
|
// Handle exception
|
|
1772
|
out.println("<?xml version=\"1.0\"?>");
|
|
1773
|
out.println("<error>");
|
|
1774
|
out.println(e.getMessage());
|
|
1775
|
out.println("</error>");
|
|
1776
|
}
|
|
1777
|
|
|
1778
|
}
|
|
1779
|
|
|
1780
|
/**
|
|
1781
|
* Handle "getaccesscontrol" action. Read Access Control List from db
|
|
1782
|
* connection in XML format
|
|
1783
|
*/
|
|
1784
|
protected void handleGetAccessControlAction(PrintWriter out,
|
|
1785
|
Hashtable<String,String[]> params, HttpServletResponse response, String username,
|
|
1786
|
String[] groupnames) {
|
|
1787
|
|
|
1788
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
1789
|
|
|
1790
|
String docid = params.get("docid")[0];
|
|
1791
|
if (docid.startsWith("urn:")) {
|
|
1792
|
try {
|
|
1793
|
String actualDocId = LSIDUtil.getDocId(docid, false);
|
|
1794
|
docid = actualDocId;
|
|
1795
|
} catch (ParseLSIDException ple) {
|
|
1796
|
logMetacat.error("MetaCatServlet.handleGetAccessControlAction - MetaCatServlet.handleGetAccessControlAction - " +
|
|
1797
|
"could not parse lsid: " + docid + " : " + ple.getMessage());
|
|
1798
|
ple.printStackTrace(System.out);
|
|
1799
|
}
|
|
1800
|
}
|
|
1801
|
|
|
1802
|
String qformat = "xml";
|
|
1803
|
if (params.get("qformat") != null) {
|
|
1804
|
qformat = (params.get("qformat"))[0];
|
|
1805
|
}
|
|
1806
|
|
|
1807
|
try {
|
|
1808
|
AccessControlForSingleFile acfsf = new AccessControlForSingleFile(docid);
|
|
1809
|
String acltext = acfsf.getACL(username, groupnames);
|
|
1810
|
if (qformat.equals("xml")) {
|
|
1811
|
response.setContentType("text/xml");
|
|
1812
|
out.println(acltext);
|
|
1813
|
} else {
|
|
1814
|
DBTransform trans = new DBTransform();
|
|
1815
|
response.setContentType("text/html");
|
|
1816
|
trans.transformXMLDocument(acltext,"-//NCEAS//getaccesscontrol//EN",
|
|
1817
|
"-//W3C//HTML//EN", qformat, out, params, null);
|
|
1818
|
}
|
|
1819
|
} catch (Exception e) {
|
|
1820
|
out.println("<?xml version=\"1.0\"?>");
|
|
1821
|
out.println("<error>");
|
|
1822
|
out.println(e.getMessage());
|
|
1823
|
out.println("</error>");
|
|
1824
|
}
|
|
1825
|
// finally {
|
|
1826
|
// // Retrun db connection to pool
|
|
1827
|
// DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1828
|
// }
|
|
1829
|
}
|
|
1830
|
|
|
1831
|
/**
|
|
1832
|
* Handle the "getprincipals" action. Read all principals from
|
|
1833
|
* authentication scheme in XML format
|
|
1834
|
*/
|
|
1835
|
protected void handleGetPrincipalsAction(PrintWriter out, String user,
|
|
1836
|
String password) {
|
|
1837
|
try {
|
|
1838
|
AuthSession auth = new AuthSession();
|
|
1839
|
String principals = auth.getPrincipals(user, password);
|
|
1840
|
out.println(principals);
|
|
1841
|
|
|
1842
|
} catch (Exception e) {
|
|
1843
|
out.println("<?xml version=\"1.0\"?>");
|
|
1844
|
out.println("<error>");
|
|
1845
|
out.println(e.getMessage());
|
|
1846
|
out.println("</error>");
|
|
1847
|
}
|
|
1848
|
}
|
|
1849
|
|
|
1850
|
/**
|
|
1851
|
* Handle "getdoctypes" action. Read all doctypes from db connection in XML
|
|
1852
|
* format
|
|
1853
|
*/
|
|
1854
|
protected void handleGetDoctypesAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
1855
|
HttpServletResponse response) {
|
|
1856
|
try {
|
|
1857
|
DBUtil dbutil = new DBUtil();
|
|
1858
|
String doctypes = dbutil.readDoctypes();
|
|
1859
|
out.println(doctypes);
|
|
1860
|
} catch (Exception e) {
|
|
1861
|
out.println("<?xml version=\"1.0\"?>");
|
|
1862
|
out.println("<error>");
|
|
1863
|
out.println(e.getMessage());
|
|
1864
|
out.println("</error>");
|
|
1865
|
}
|
|
1866
|
}
|
|
1867
|
|
|
1868
|
/**
|
|
1869
|
* Handle the "getdtdschema" action. Read DTD or Schema file for a given
|
|
1870
|
* doctype from Metacat catalog system
|
|
1871
|
*/
|
|
1872
|
protected void handleGetDTDSchemaAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
1873
|
HttpServletResponse response) {
|
|
1874
|
|
|
1875
|
String doctype = null;
|
|
1876
|
String[] doctypeArr = params.get("doctype");
|
|
1877
|
|
|
1878
|
// get only the first doctype specified in the list of doctypes
|
|
1879
|
// it could be done for all doctypes in that list
|
|
1880
|
if (doctypeArr != null) {
|
|
1881
|
doctype = params.get("doctype")[0];
|
|
1882
|
}
|
|
1883
|
|
|
1884
|
try {
|
|
1885
|
DBUtil dbutil = new DBUtil();
|
|
1886
|
String dtdschema = dbutil.readDTDSchema(doctype);
|
|
1887
|
out.println(dtdschema);
|
|
1888
|
|
|
1889
|
} catch (Exception e) {
|
|
1890
|
out.println("<?xml version=\"1.0\"?>");
|
|
1891
|
out.println("<error>");
|
|
1892
|
out.println(e.getMessage());
|
|
1893
|
out.println("</error>");
|
|
1894
|
}
|
|
1895
|
|
|
1896
|
}
|
|
1897
|
|
|
1898
|
/**
|
|
1899
|
* Check if the document is registered in either the xml_documents or xml_revisions table
|
|
1900
|
* @param out the writer to write the xml results to
|
|
1901
|
* @param params request parameters
|
|
1902
|
* @param response the http servlet response
|
|
1903
|
*/
|
|
1904
|
public void handleIdIsRegisteredAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
1905
|
HttpServletResponse response) {
|
|
1906
|
String id = null;
|
|
1907
|
boolean exists = false;
|
|
1908
|
if(params.get("docid") != null) {
|
|
1909
|
id = params.get("docid")[0];
|
|
1910
|
}
|
|
1911
|
|
|
1912
|
try {
|
|
1913
|
DBUtil dbutil = new DBUtil();
|
|
1914
|
exists = dbutil.idExists(id);
|
|
1915
|
} catch (Exception e) {
|
|
1916
|
out.println("<?xml version=\"1.0\"?>");
|
|
1917
|
out.println("<error>");
|
|
1918
|
out.println(e.getMessage());
|
|
1919
|
out.println("</error>");
|
|
1920
|
}
|
|
1921
|
|
|
1922
|
out.println("<?xml version=\"1.0\"?>");
|
|
1923
|
out.println("<isRegistered>");
|
|
1924
|
out.println("<docid>" + id + "</docid>");
|
|
1925
|
out.println("<exists>" + exists + "</exists>");
|
|
1926
|
out.println("</isRegistered>");
|
|
1927
|
}
|
|
1928
|
|
|
1929
|
/**
|
|
1930
|
* Handle the "getalldocids" action. return a list of all docids registered
|
|
1931
|
* in the system
|
|
1932
|
*/
|
|
1933
|
public void handleGetAllDocidsAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
1934
|
HttpServletResponse response) {
|
|
1935
|
String scope = null;
|
|
1936
|
if(params.get("scope") != null) {
|
|
1937
|
scope = params.get("scope")[0];
|
|
1938
|
}
|
|
1939
|
|
|
1940
|
try {
|
|
1941
|
DBUtil dbutil = new DBUtil();
|
|
1942
|
Vector<String> docids = dbutil.getAllDocids(scope);
|
|
1943
|
out.println("<?xml version=\"1.0\"?>");
|
|
1944
|
out.println("<idList>");
|
|
1945
|
out.println(" <scope>" + scope + "</scope>");
|
|
1946
|
for(int i=0; i<docids.size(); i++) {
|
|
1947
|
String docid = docids.elementAt(i);
|
|
1948
|
out.println(" <docid>" + docid + "</docid>");
|
|
1949
|
}
|
|
1950
|
out.println("</idList>");
|
|
1951
|
|
|
1952
|
} catch (Exception e) {
|
|
1953
|
out.println("<?xml version=\"1.0\"?>");
|
|
1954
|
out.println("<error>");
|
|
1955
|
out.println(e.getMessage());
|
|
1956
|
out.println("</error>");
|
|
1957
|
}
|
|
1958
|
}
|
|
1959
|
|
|
1960
|
/**
|
|
1961
|
* Handle the "getlastdocid" action. Get the latest docid with rev number
|
|
1962
|
* from db connection in XML format
|
|
1963
|
*/
|
|
1964
|
public void handleGetMaxDocidAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
1965
|
HttpServletResponse response) {
|
|
1966
|
|
|
1967
|
String scope = params.get("scope")[0];
|
|
1968
|
if (scope == null) {
|
|
1969
|
scope = params.get("username")[0];
|
|
1970
|
}
|
|
1971
|
|
|
1972
|
try {
|
|
1973
|
|
|
1974
|
DBUtil dbutil = new DBUtil();
|
|
1975
|
String lastDocid = dbutil.getMaxDocid(scope);
|
|
1976
|
out.println("<?xml version=\"1.0\"?>");
|
|
1977
|
out.println("<lastDocid>");
|
|
1978
|
out.println(" <scope>" + scope + "</scope>");
|
|
1979
|
out.println(" <docid>" + lastDocid + "</docid>");
|
|
1980
|
out.println("</lastDocid>");
|
|
1981
|
|
|
1982
|
} catch (Exception e) {
|
|
1983
|
out.println("<?xml version=\"1.0\"?>");
|
|
1984
|
out.println("<error>");
|
|
1985
|
out.println(e.getMessage());
|
|
1986
|
out.println("</error>");
|
|
1987
|
}
|
|
1988
|
}
|
|
1989
|
|
|
1990
|
/**
|
|
1991
|
* Print a report from the event log based on filter parameters passed in
|
|
1992
|
* from the web.
|
|
1993
|
*
|
|
1994
|
* @param params the parameters from the web request
|
|
1995
|
* @param request the http request object for getting request details
|
|
1996
|
* @param response the http response object for writing output
|
|
1997
|
*/
|
|
1998
|
protected void handleGetLogAction(Hashtable<String, String[]> params, HttpServletRequest request,
|
|
1999
|
HttpServletResponse response, String username, String[] groups) {
|
|
2000
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2001
|
try {
|
|
2002
|
response.setContentType("text/xml");
|
|
2003
|
PrintWriter out = response.getWriter();
|
|
2004
|
|
|
2005
|
// Check that the user is authenticated as an administrator account
|
|
2006
|
if (!AuthUtil.isAdministrator(username, groups)) {
|
|
2007
|
out.print("<error>");
|
|
2008
|
out.print("The user \"" + username +
|
|
2009
|
"\" is not authorized for this action.");
|
|
2010
|
out.print("</error>");
|
|
2011
|
return;
|
|
2012
|
}
|
|
2013
|
|
|
2014
|
// Get all of the parameters in the correct formats
|
|
2015
|
String[] ipAddress = params.get("ipaddress");
|
|
2016
|
String[] principal = params.get("principal");
|
|
2017
|
String[] docid = params.get("docid");
|
|
2018
|
String[] event = params.get("event");
|
|
2019
|
String[] startArray = params.get("start");
|
|
2020
|
String[] endArray = params.get("end");
|
|
2021
|
String start = null;
|
|
2022
|
String end = null;
|
|
2023
|
if (startArray != null) {
|
|
2024
|
start = startArray[0];
|
|
2025
|
}
|
|
2026
|
if (endArray != null) {
|
|
2027
|
end = endArray[0];
|
|
2028
|
}
|
|
2029
|
Timestamp startDate = null;
|
|
2030
|
Timestamp endDate = null;
|
|
2031
|
SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
|
|
2032
|
try {
|
|
2033
|
if (start != null) {
|
|
2034
|
startDate = new Timestamp((format.parse(start)).getTime());
|
|
2035
|
}
|
|
2036
|
if (end != null) {
|
|
2037
|
endDate = new Timestamp((format.parse(end)).getTime());
|
|
2038
|
}
|
|
2039
|
} catch (ParseException e) {
|
|
2040
|
logMetacat.error("MetaCatServlet.handleGetLogAction - Failed to created Timestamp from input.");
|
|
2041
|
e.printStackTrace(System.out);
|
|
2042
|
}
|
|
2043
|
|
|
2044
|
// Request the report by passing the filter parameters
|
|
2045
|
out.println(EventLog.getInstance().getReport(ipAddress, principal,
|
|
2046
|
docid, event, startDate, endDate));
|
|
2047
|
out.close();
|
|
2048
|
} catch (IOException e) {
|
|
2049
|
logMetacat.error("MetaCatServlet.handleGetLogAction - Could not open http response for writing: "
|
|
2050
|
+ e.getMessage());
|
|
2051
|
e.printStackTrace(System.out);
|
|
2052
|
} catch (MetacatUtilException ue) {
|
|
2053
|
logMetacat.error("MetaCatServlet.handleGetLogAction - Could not determine if user is administrator: "
|
|
2054
|
+ ue.getMessage());
|
|
2055
|
ue.printStackTrace(System.out);
|
|
2056
|
}
|
|
2057
|
}
|
|
2058
|
|
|
2059
|
/**
|
|
2060
|
* Rebuild the index for one or more documents. If the docid parameter is
|
|
2061
|
* provided, rebuild for just that one document or list of documents. If
|
|
2062
|
* not, then rebuild the index for all documents in the xml_documents table.
|
|
2063
|
*
|
|
2064
|
* @param params
|
|
2065
|
* the parameters from the web request
|
|
2066
|
* @param request
|
|
2067
|
* the http request object for getting request details
|
|
2068
|
* @param response
|
|
2069
|
* the http response object for writing output
|
|
2070
|
* @param username
|
|
2071
|
* the username of the authenticated user
|
|
2072
|
*/
|
|
2073
|
protected void handleBuildIndexAction(Hashtable<String, String[]> params,
|
|
2074
|
HttpServletRequest request, HttpServletResponse response,
|
|
2075
|
String username, String[] groups) {
|
|
2076
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2077
|
|
|
2078
|
// Get all of the parameters in the correct formats
|
|
2079
|
String[] docid = params.get("docid");
|
|
2080
|
|
|
2081
|
// Rebuild the indices for appropriate documents
|
|
2082
|
try {
|
|
2083
|
response.setContentType("text/xml");
|
|
2084
|
PrintWriter out = response.getWriter();
|
|
2085
|
|
|
2086
|
// Check that the user is authenticated as an administrator account
|
|
2087
|
if (!AuthUtil.isAdministrator(username, groups)) {
|
|
2088
|
out.print("<error>");
|
|
2089
|
out.print("The user \"" + username +
|
|
2090
|
"\" is not authorized for this action.");
|
|
2091
|
out.print("</error>");
|
|
2092
|
return;
|
|
2093
|
}
|
|
2094
|
|
|
2095
|
// Process the documents
|
|
2096
|
out.println("<success>");
|
|
2097
|
if (docid == null || docid.length == 0) {
|
|
2098
|
// Process all of the documents
|
|
2099
|
try {
|
|
2100
|
Vector<String> documents = getDocumentList();
|
|
2101
|
Iterator<String> it = documents.iterator();
|
|
2102
|
while (it.hasNext()) {
|
|
2103
|
String id = it.next();
|
|
2104
|
buildDocumentIndex(id, out);
|
|
2105
|
}
|
|
2106
|
} catch (SQLException se) {
|
|
2107
|
out.print("<error>");
|
|
2108
|
out.print(se.getMessage());
|
|
2109
|
out.println("</error>");
|
|
2110
|
}
|
|
2111
|
} else {
|
|
2112
|
// Only process the requested documents
|
|
2113
|
for (int i = 0; i < docid.length; i++) {
|
|
2114
|
buildDocumentIndex(docid[i], out);
|
|
2115
|
}
|
|
2116
|
}
|
|
2117
|
out.println("</success>");
|
|
2118
|
out.close();
|
|
2119
|
} catch (IOException e) {
|
|
2120
|
logMetacat.error("MetaCatServlet.handleBuildIndexAction - Could not open http response for writing: "
|
|
2121
|
+ e.getMessage());
|
|
2122
|
e.printStackTrace(System.out);
|
|
2123
|
} catch (MetacatUtilException ue) {
|
|
2124
|
logMetacat.error("MetaCatServlet.handleBuildIndexAction - Could not determine if user is administrator: "
|
|
2125
|
+ ue.getMessage());
|
|
2126
|
ue.printStackTrace(System.out);
|
|
2127
|
}
|
|
2128
|
}
|
|
2129
|
|
|
2130
|
/**
|
|
2131
|
* Build the index for one document by reading the document and
|
|
2132
|
* calling its buildIndex() method.
|
|
2133
|
*
|
|
2134
|
* @param docid the document (with revision) to rebuild
|
|
2135
|
* @param out the PrintWriter to which output is printed
|
|
2136
|
*/
|
|
2137
|
private void buildDocumentIndex(String docid, PrintWriter out) {
|
|
2138
|
try {
|
|
2139
|
DocumentImpl doc = new DocumentImpl(docid, false);
|
|
2140
|
doc.buildIndex();
|
|
2141
|
out.print("<docid>" + docid);
|
|
2142
|
out.println("</docid>");
|
|
2143
|
} catch (McdbException me) {
|
|
2144
|
out.print("<error>");
|
|
2145
|
out.print(me.getMessage());
|
|
2146
|
out.println("</error>");
|
|
2147
|
}
|
|
2148
|
}
|
|
2149
|
|
|
2150
|
/**
|
|
2151
|
* Handle documents passed to metacat that are encoded using the
|
|
2152
|
* "multipart/form-data" mime type. This is typically used for uploading
|
|
2153
|
* data files which may be binary and large.
|
|
2154
|
*/
|
|
2155
|
protected void handleMultipartForm(HttpServletRequest request,
|
|
2156
|
HttpServletResponse response) {
|
|
2157
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2158
|
PrintWriter out = null;
|
|
2159
|
String action = null;
|
|
2160
|
|
|
2161
|
// Parse the multipart form, and save the parameters in a Hashtable and
|
|
2162
|
// save the FileParts in a hashtable
|
|
2163
|
|
|
2164
|
Hashtable<String,String[]> params = new Hashtable<String,String[]>();
|
|
2165
|
Hashtable<String,String> fileList = new Hashtable<String,String>();
|
|
2166
|
int sizeLimit = 1000;
|
|
2167
|
try {
|
|
2168
|
sizeLimit =
|
|
2169
|
(new Integer(PropertyService.getProperty("replication.datafilesizelimit"))).intValue();
|
|
2170
|
} catch (PropertyNotFoundException pnfe) {
|
|
2171
|
logMetacat.error("MetaCatServlet.handleMultipartForm - Could not determine data file size limit. Using 1000. "
|
|
2172
|
+ pnfe.getMessage());
|
|
2173
|
pnfe.printStackTrace(System.out);
|
|
2174
|
}
|
|
2175
|
logMetacat.debug("MetaCatServlet.handleMultipartForm - The size limit of uploaded data files is: " + sizeLimit);
|
|
2176
|
|
|
2177
|
try {
|
|
2178
|
MultipartParser mp = new MultipartParser(request,
|
|
2179
|
sizeLimit * 1024 * 1024);
|
|
2180
|
Part part;
|
|
2181
|
|
|
2182
|
while ((part = mp.readNextPart()) != null) {
|
|
2183
|
String name = part.getName();
|
|
2184
|
|
|
2185
|
if (part.isParam()) {
|
|
2186
|
// it's a parameter part
|
|
2187
|
ParamPart paramPart = (ParamPart) part;
|
|
2188
|
String[] values = new String[1];
|
|
2189
|
values[0] = paramPart.getStringValue();
|
|
2190
|
params.put(name, values);
|
|
2191
|
if (name.equals("action")) {
|
|
2192
|
action = values[0];
|
|
2193
|
}
|
|
2194
|
} else if (part.isFile()) {
|
|
2195
|
// it's a file part
|
|
2196
|
FilePart filePart = (FilePart) part;
|
|
2197
|
String fileName = filePart.getFileName();
|
|
2198
|
String fileTempLocation;
|
|
2199
|
|
|
2200
|
// the filePart will be clobbered on the next loop, save to disk
|
|
2201
|
fileTempLocation = MetacatUtil.writeTempUploadFile(filePart, fileName);
|
|
2202
|
fileList.put(name, fileTempLocation);
|
|
2203
|
fileList.put("filename", fileName);
|
|
2204
|
fileList.put("name", fileTempLocation);
|
|
2205
|
} else {
|
|
2206
|
logMetacat.info("MetaCatServlet.handleMultipartForm - Upload name '" + name + "' was empty.");
|
|
2207
|
}
|
|
2208
|
}
|
|
2209
|
} catch (IOException ioe) {
|
|
2210
|
try {
|
|
2211
|
out = response.getWriter();
|
|
2212
|
} catch (IOException ioe2) {
|
|
2213
|
logMetacat.fatal("MetaCatServlet.handleMultipartForm - Fatal Error: couldn't get response output stream.");
|
|
2214
|
}
|
|
2215
|
out.println("<?xml version=\"1.0\"?>");
|
|
2216
|
out.println("<error>");
|
|
2217
|
out.println("Error: problem reading multipart data: " + ioe.getMessage());
|
|
2218
|
out.println("</error>");
|
|
2219
|
out.close();
|
|
2220
|
return;
|
|
2221
|
}
|
|
2222
|
|
|
2223
|
// Get the session information
|
|
2224
|
String username = null;
|
|
2225
|
String password = null;
|
|
2226
|
String[] groupnames = null;
|
|
2227
|
String sess_id = null;
|
|
2228
|
|
|
2229
|
// be aware of session expiration on every request
|
|
2230
|
HttpSession sess = request.getSession(true);
|
|
2231
|
if (sess.isNew()) {
|
|
2232
|
// session expired or has not been stored b/w user requests
|
|
2233
|
username = "public";
|
|
2234
|
sess.setAttribute("username", username);
|
|
2235
|
} else {
|
|
2236
|
username = (String) sess.getAttribute("username");
|
|
2237
|
password = (String) sess.getAttribute("password");
|
|
2238
|
groupnames = (String[]) sess.getAttribute("groupnames");
|
|
2239
|
try {
|
|
2240
|
sess_id = (String) sess.getId();
|
|
2241
|
} catch (IllegalStateException ise) {
|
|
2242
|
System.out
|
|
2243
|
.println("error in handleMultipartForm: this shouldn't "
|
|
2244
|
+ "happen: the session should be valid: "
|
|
2245
|
+ ise.getMessage());
|
|
2246
|
}
|
|
2247
|
}
|
|
2248
|
|
|
2249
|
// Get the out stream
|
|
2250
|
try {
|
|
2251
|
out = response.getWriter();
|
|
2252
|
} catch (IOException ioe2) {
|
|
2253
|
logMetacat.error("MetaCatServlet.handleMultipartForm - Fatal Error: couldn't get response "
|
|
2254
|
+ "output stream.");
|
|
2255
|
ioe2.printStackTrace(System.out);
|
|
2256
|
}
|
|
2257
|
|
|
2258
|
if (action.equals("upload")) {
|
|
2259
|
if (username != null && !username.equals("public")) {
|
|
2260
|
handleUploadAction(request, out, params, fileList, username,
|
|
2261
|
groupnames, response);
|
|
2262
|
} else {
|
|
2263
|
out.println("<?xml version=\"1.0\"?>");
|
|
2264
|
out.println("<error>");
|
|
2265
|
out.println("Permission denied for " + action);
|
|
2266
|
out.println("</error>");
|
|
2267
|
}
|
|
2268
|
} else if(action.equals("insertmultipart")) {
|
|
2269
|
if (username != null && !username.equals("public")) {
|
|
2270
|
logMetacat.debug("MetaCatServlet.handleMultipartForm - handling multipart insert");
|
|
2271
|
handleInsertMultipartAction(request, response,
|
|
2272
|
out, params, fileList, username, groupnames);
|
|
2273
|
} else {
|
|
2274
|
out.println("<?xml version=\"1.0\"?>");
|
|
2275
|
out.println("<error>");
|
|
2276
|
out.println("Permission denied for " + action);
|
|
2277
|
out.println("</error>");
|
|
2278
|
}
|
|
2279
|
} else {
|
|
2280
|
/*
|
|
2281
|
* try { out = response.getWriter(); } catch (IOException ioe2) {
|
|
2282
|
* System.err.println("Fatal Error: couldn't get response output
|
|
2283
|
* stream.");
|
|
2284
|
*/
|
|
2285
|
out.println("<?xml version=\"1.0\"?>");
|
|
2286
|
out.println("<error>");
|
|
2287
|
out.println("Error: action not registered. Please report this error.");
|
|
2288
|
out.println("</error>");
|
|
2289
|
}
|
|
2290
|
out.close();
|
|
2291
|
}
|
|
2292
|
|
|
2293
|
/**
|
|
2294
|
* Handle the upload action by saving the attached file to disk and
|
|
2295
|
* registering it in the Metacat db
|
|
2296
|
*/
|
|
2297
|
private void handleInsertMultipartAction(HttpServletRequest request,
|
|
2298
|
HttpServletResponse response,
|
|
2299
|
PrintWriter out, Hashtable<String,String[]> params, Hashtable<String,String> fileList,
|
|
2300
|
String username, String[] groupnames)
|
|
2301
|
{
|
|
2302
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2303
|
String action = null;
|
|
2304
|
String docid = null;
|
|
2305
|
String qformat = null;
|
|
2306
|
String output = "";
|
|
2307
|
|
|
2308
|
/*
|
|
2309
|
* response.setContentType("text/xml"); try { out =
|
|
2310
|
* response.getWriter(); } catch (IOException ioe2) {
|
|
2311
|
* System.err.println("Fatal Error: couldn't get response output
|
|
2312
|
* stream.");
|
|
2313
|
*/
|
|
2314
|
|
|
2315
|
if (params.containsKey("docid"))
|
|
2316
|
{
|
|
2317
|
docid = params.get("docid")[0];
|
|
2318
|
}
|
|
2319
|
|
|
2320
|
if(params.containsKey("qformat"))
|
|
2321
|
{
|
|
2322
|
qformat = params.get("qformat")[0];
|
|
2323
|
}
|
|
2324
|
|
|
2325
|
// Make sure we have a docid and datafile
|
|
2326
|
if (docid != null && fileList.containsKey("datafile"))
|
|
2327
|
{
|
|
2328
|
logMetacat.info("MetaCatServlet.handleInsertMultipartAction - Uploading data docid: " + docid);
|
|
2329
|
// Get a reference to the file part of the form
|
|
2330
|
//FilePart filePart = (FilePart) fileList.get("datafile");
|
|
2331
|
String fileName = fileList.get("filename");
|
|
2332
|
logMetacat.debug("MetaCatServlet.handleInsertMultipartAction - Uploading filename: " + fileName);
|
|
2333
|
// Check if the right file existed in the uploaded data
|
|
2334
|
if (fileName != null)
|
|
2335
|
{
|
|
2336
|
|
|
2337
|
try
|
|
2338
|
{
|
|
2339
|
//logMetacat.info("Upload datafile " + docid
|
|
2340
|
// +"...", 10);
|
|
2341
|
//If document get lock data file grant
|
|
2342
|
if (DocumentImpl.getDataFileLockGrant(docid))
|
|
2343
|
{
|
|
2344
|
// Save the data file to disk using "docid" as the name
|
|
2345
|
String datafilepath = PropertyService.getProperty("application.datafilepath");
|
|
2346
|
File dataDirectory = new File(datafilepath);
|
|
2347
|
dataDirectory.mkdirs();
|
|
2348
|
File newFile = null;
|
|
2349
|
// File tempFile = null;
|
|
2350
|
String tempFileName = fileList.get("name");
|
|
2351
|
String newFileName = dataDirectory + File.separator + docid;
|
|
2352
|
long size = 0;
|
|
2353
|
boolean fileExists = false;
|
|
2354
|
|
|
2355
|
try
|
|
2356
|
{
|
|
2357
|
newFile = new File(newFileName);
|
|
2358
|
fileExists = newFile.exists();
|
|
2359
|
logMetacat.info("MetaCatServlet.handleInsertMultipartAction - new file status is: " + fileExists);
|
|
2360
|
if(fileExists)
|
|
2361
|
{
|
|
2362
|
newFile.delete();
|
|
2363
|
newFile.createNewFile();
|
|
2364
|
fileExists = false;
|
|
2365
|
}
|
|
2366
|
|
|
2367
|
if ( fileExists == false )
|
|
2368
|
{
|
|
2369
|
// copy file to desired output location
|
|
2370
|
try
|
|
2371
|
{
|
|
2372
|
MetacatUtil.copyFile(tempFileName, newFileName);
|
|
2373
|
}
|
|
2374
|
catch (IOException ioe)
|
|
2375
|
{
|
|
2376
|
logMetacat.error("MetaCatServlet.handleInsertMultipartAction - IO Exception copying file: " +
|
|
2377
|
ioe.getMessage());
|
|
2378
|
ioe.printStackTrace(System.out);
|
|
2379
|
}
|
|
2380
|
size = newFile.length();
|
|
2381
|
if (size == 0)
|
|
2382
|
{
|
|
2383
|
throw new IOException("MetaCatServlet.handleInsertMultipartAction - Uploaded file is 0 bytes!");
|
|
2384
|
}
|
|
2385
|
}
|
|
2386
|
logMetacat.info("MetaCatServlet.handleInsertMultipartAction - Uploading the following to Metacat:" +
|
|
2387
|
fileName + ", " + docid + ", " +
|
|
2388
|
username + ", " + groupnames);
|
|
2389
|
FileReader fr = new FileReader(newFile);
|
|
2390
|
|
|
2391
|
char[] c = new char[1024];
|
|
2392
|
int numread = fr.read(c, 0, 1024);
|
|
2393
|
StringBuffer sb = new StringBuffer();
|
|
2394
|
while(numread != -1)
|
|
2395
|
{
|
|
2396
|
sb.append(c, 0, numread);
|
|
2397
|
numread = fr.read(c, 0, 1024);
|
|
2398
|
}
|
|
2399
|
|
|
2400
|
Enumeration<String> keys = params.keys();
|
|
2401
|
while(keys.hasMoreElements())
|
|
2402
|
{ //convert the params to arrays
|
|
2403
|
String key = keys.nextElement();
|
|
2404
|
String[] paramValue = params.get(key);
|
|
2405
|
String[] s = new String[1];
|
|
2406
|
s[0] = paramValue[0];
|
|
2407
|
params.put(key, s);
|
|
2408
|
}
|
|
2409
|
//add the doctext to the params
|
|
2410
|
String doctext = sb.toString();
|
|
2411
|
String[] doctextArr = new String[1];
|
|
2412
|
doctextArr[0] = doctext;
|
|
2413
|
params.put("doctext", doctextArr);
|
|
2414
|
//call the insert routine
|
|
2415
|
handleInsertOrUpdateAction(request.getRemoteAddr(), response, out,
|
|
2416
|
params, username, groupnames);
|
|
2417
|
}
|
|
2418
|
catch(Exception e)
|
|
2419
|
{
|
|
2420
|
throw e;
|
|
2421
|
}
|
|
2422
|
}
|
|
2423
|
}
|
|
2424
|
catch(Exception e)
|
|
2425
|
{
|
|
2426
|
logMetacat.error("MetaCatServlet.handleInsertMultipartAction - error uploading text file via multipart: " + e.getMessage());
|
|
2427
|
e.printStackTrace(System.out);;
|
|
2428
|
}
|
|
2429
|
}
|
|
2430
|
}
|
|
2431
|
}
|
|
2432
|
|
|
2433
|
/**
|
|
2434
|
* Handle the upload action by saving the attached file to disk and
|
|
2435
|
* registering it in the Metacat db
|
|
2436
|
*/
|
|
2437
|
private void handleUploadAction(HttpServletRequest request,
|
|
2438
|
PrintWriter out, Hashtable<String, String[]> params, Hashtable<String,String> fileList,
|
|
2439
|
String username, String[] groupnames, HttpServletResponse response) {
|
|
2440
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2441
|
//PrintWriter out = null;
|
|
2442
|
//Connection conn = null;
|
|
2443
|
// String action = null;
|
|
2444
|
String docid = null;
|
|
2445
|
String qformat = null;
|
|
2446
|
String output = "";
|
|
2447
|
|
|
2448
|
/*
|
|
2449
|
* response.setContentType("text/xml"); try { out =
|
|
2450
|
* response.getWriter(); } catch (IOException ioe2) {
|
|
2451
|
* System.err.println("Fatal Error: couldn't get response output
|
|
2452
|
* stream.");
|
|
2453
|
*/
|
|
2454
|
|
|
2455
|
if (params.containsKey("docid")) {
|
|
2456
|
docid = params.get("docid")[0];
|
|
2457
|
}
|
|
2458
|
|
|
2459
|
if(params.containsKey("qformat")) {
|
|
2460
|
qformat = params.get("qformat")[0];
|
|
2461
|
}
|
|
2462
|
|
|
2463
|
// Make sure we have a docid and datafile
|
|
2464
|
if (docid != null && fileList.containsKey("datafile")) {
|
|
2465
|
logMetacat.info("MetaCatServlet.handleUploadAction - Uploading data docid: " + docid);
|
|
2466
|
// Get a reference to the file part of the form
|
|
2467
|
//FilePart filePart = (FilePart) fileList.get("datafile");
|
|
2468
|
String fileName = fileList.get("filename");
|
|
2469
|
logMetacat.info("MetaCatServlet.handleUploadAction - Uploading filename: " + fileName);
|
|
2470
|
// Check if the right file existed in the uploaded data
|
|
2471
|
if (fileName != null) {
|
|
2472
|
|
|
2473
|
try {
|
|
2474
|
//logMetacat.info("Upload datafile " + docid
|
|
2475
|
// +"...", 10);
|
|
2476
|
//If document get lock data file grant
|
|
2477
|
if (DocumentImpl.getDataFileLockGrant(docid)) {
|
|
2478
|
// Save the data file to disk using "docid" as the name
|
|
2479
|
String datafilepath = PropertyService.getProperty("application.datafilepath");
|
|
2480
|
File dataDirectory = new File(datafilepath);
|
|
2481
|
dataDirectory.mkdirs();
|
|
2482
|
File newFile = null;
|
|
2483
|
// File tempFile = null;
|
|
2484
|
String tempFileName = fileList.get("name");
|
|
2485
|
String newFileName = dataDirectory + File.separator + docid;
|
|
2486
|
long size = 0;
|
|
2487
|
boolean fileExists = false;
|
|
2488
|
|
|
2489
|
try {
|
|
2490
|
newFile = new File(newFileName);
|
|
2491
|
fileExists = newFile.exists();
|
|
2492
|
logMetacat.info("MetaCatServlet.handleUploadAction - new file status is: " + fileExists);
|
|
2493
|
if ( fileExists == false ) {
|
|
2494
|
// copy file to desired output location
|
|
2495
|
try {
|
|
2496
|
MetacatUtil.copyFile(tempFileName, newFileName);
|
|
2497
|
} catch (IOException ioe) {
|
|
2498
|
logMetacat.error("IO Exception copying file: " +
|
|
2499
|
ioe.getMessage());
|
|
2500
|
ioe.printStackTrace(System.out);
|
|
2501
|
}
|
|
2502
|
size = newFile.length();
|
|
2503
|
if (size == 0) {
|
|
2504
|
throw new IOException("Uploaded file is 0 bytes!");
|
|
2505
|
}
|
|
2506
|
} // Latent bug here if the file already exists, then the
|
|
2507
|
// conditional fails but the document is still registered.
|
|
2508
|
// maybe this never happens because we already requested a lock?
|
|
2509
|
logMetacat.info("MetaCatServlet.handleUploadAction - Uploading the following to Metacat:" +
|
|
2510
|
fileName + ", " + docid + ", " +
|
|
2511
|
username + ", " + groupnames);
|
|
2512
|
//register the file in the database (which generates
|
|
2513
|
// an exception
|
|
2514
|
//if the docid is not acceptable or other untoward
|
|
2515
|
// things happen
|
|
2516
|
DocumentImpl.registerDocument(fileName, "BIN", docid,
|
|
2517
|
username, groupnames);
|
|
2518
|
} catch (Exception ee) {
|
|
2519
|
// If the file did not exist before this method was
|
|
2520
|
// called and an exception is generated while
|
|
2521
|
// creating or registering it, then we want to delete
|
|
2522
|
// the file from disk because the operation failed.
|
|
2523
|
// However, if the file already existed before the
|
|
2524
|
// method was called, then the exception probably
|
|
2525
|
// occurs when registering the document, and so we
|
|
2526
|
// want to leave the old file in place.
|
|
2527
|
if ( fileExists == false ) {
|
|
2528
|
newFile.delete();
|
|
2529
|
}
|
|
2530
|
|
|
2531
|
logMetacat.info("MetaCatServlet.handleUploadAction - in Exception: fileExists is " + fileExists);
|
|
2532
|
logMetacat.error("MetaCatServlet.handleUploadAction - Upload Error: " + ee.getMessage());
|
|
2533
|
throw ee;
|
|
2534
|
}
|
|
2535
|
|
|
2536
|
EventLog.getInstance().log(request.getRemoteAddr(),
|
|
2537
|
username, docid, "upload");
|
|
2538
|
// Force replication this data file
|
|
2539
|
// To data file, "insert" and update is same
|
|
2540
|
// The fourth parameter is null. Because it is
|
|
2541
|
// notification server
|
|
2542
|
// and this method is in MetaCatServerlet. It is
|
|
2543
|
// original command,
|
|
2544
|
// not get force replication info from another metacat
|
|
2545
|
ForceReplicationHandler frh = new ForceReplicationHandler(
|
|
2546
|
docid, "insert", false, null);
|
|
2547
|
logMetacat.debug("MetaCatServlet.handleUploadAction - ForceReplicationHandler created: " + frh.toString());
|
|
2548
|
|
|
2549
|
// set content type and other response header fields
|
|
2550
|
// first
|
|
2551
|
output += "<?xml version=\"1.0\"?>";
|
|
2552
|
output += "<success>";
|
|
2553
|
output += "<docid>" + docid + "</docid>";
|
|
2554
|
output += "<size>" + size + "</size>";
|
|
2555
|
output += "</success>";
|
|
2556
|
}
|
|
2557
|
|
|
2558
|
} catch (Exception e) {
|
|
2559
|
|
|
2560
|
output += "<?xml version=\"1.0\"?>";
|
|
2561
|
output += "<error>";
|
|
2562
|
output += e.getMessage();
|
|
2563
|
output += "</error>";
|
|
2564
|
}
|
|
2565
|
} else {
|
|
2566
|
// the field did not contain a file
|
|
2567
|
output += "<?xml version=\"1.0\"?>";
|
|
2568
|
output += "<error>";
|
|
2569
|
output += "The uploaded data did not contain a valid file.";
|
|
2570
|
output += "</error>";
|
|
2571
|
}
|
|
2572
|
} else {
|
|
2573
|
// Error bcse docid missing or file missing
|
|
2574
|
output += "<?xml version=\"1.0\"?>";
|
|
2575
|
output += "<error>";
|
|
2576
|
output += "The uploaded data did not contain a valid docid "
|
|
2577
|
+ "or valid file.";
|
|
2578
|
output += "</error>";
|
|
2579
|
}
|
|
2580
|
|
|
2581
|
if (qformat == null || qformat.equals("xml")) {
|
|
2582
|
response.setContentType("text/xml");
|
|
2583
|
out.println(output);
|
|
2584
|
} else {
|
|
2585
|
try {
|
|
2586
|
DBTransform trans = new DBTransform();
|
|
2587
|
response.setContentType("text/html");
|
|
2588
|
trans.transformXMLDocument(output,
|
|
2589
|
"message", "-//W3C//HTML//EN", qformat,
|
|
2590
|
out, null, null);
|
|
2591
|
} catch (Exception e) {
|
|
2592
|
|
|
2593
|
logMetacat.error("MetaCatServlet.handleUploadAction - General error: "
|
|
2594
|
+ e.getMessage());
|
|
2595
|
e.printStackTrace(System.out);
|
|
2596
|
}
|
|
2597
|
}
|
|
2598
|
}
|
|
2599
|
|
|
2600
|
/*
|
|
2601
|
* A method to handle set access action
|
|
2602
|
*/
|
|
2603
|
protected void handleSetAccessAction(PrintWriter out, Hashtable<String, String[]> params,
|
|
2604
|
String username, HttpServletRequest request, HttpServletResponse response) {
|
|
2605
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2606
|
String permission = null;
|
|
2607
|
String permType = null;
|
|
2608
|
String permOrder = null;
|
|
2609
|
Vector<String> errorList = new Vector<String>();
|
|
2610
|
String error = null;
|
|
2611
|
Vector<String> successList = new Vector<String>();
|
|
2612
|
String success = null;
|
|
2613
|
boolean isEmlPkgMember = false;
|
|
2614
|
|
|
2615
|
String[] docList = params.get("docid");
|
|
2616
|
String[] principalList = params.get("principal");
|
|
2617
|
String[] permissionList = params.get("permission");
|
|
2618
|
String[] permTypeList = params.get("permType");
|
|
2619
|
String[] permOrderList = params.get("permOrder");
|
|
2620
|
String[] qformatList = params.get("qformat");
|
|
2621
|
String[] accessBlock = params.get("accessBlock");
|
|
2622
|
if(accessBlock != null) {
|
|
2623
|
if (docList == null) {
|
|
2624
|
errorList.addElement("MetaCatServlet.handleSetAccessAction - Doc id missing. Please check your parameter list, it should look like: "
|
|
2625
|
+ "?action=setaccess&docid=<doc_id>&accessBlock=<access_section>");
|
|
2626
|
outputResponse(successList, errorList, out);
|
|
2627
|
return;
|
|
2628
|
}
|
|
2629
|
try {
|
|
2630
|
AccessControlForSingleFile accessControl =
|
|
2631
|
new AccessControlForSingleFile(docList[0]);
|
|
2632
|
accessControl.insertPermissions(accessBlock[0]);
|
|
2633
|
successList.addElement("MetaCatServlet.handleSetAccessAction - successfully replaced access block for doc id: " + docList[0]);
|
|
2634
|
} catch(AccessControlException ace) {
|
|
2635
|
errorList.addElement("MetaCatServlet.handleSetAccessAction - access control error when setting " +
|
|
2636
|
"access block: " + ace.getMessage());
|
|
2637
|
}
|
|
2638
|
outputResponse(successList, errorList, out);
|
|
2639
|
return;
|
|
2640
|
}
|
|
2641
|
|
|
2642
|
// Make sure the parameter is not null
|
|
2643
|
if (docList == null || principalList == null || permTypeList == null
|
|
2644
|
|| permissionList == null) {
|
|
2645
|
error = "MetaCatServlet.handleSetAccessAction - Please check your parameter list, it should look like: "
|
|
2646
|
+ "?action=setaccess&docid=pipeline.1.1&principal=public"
|
|
2647
|
+ "&permission=read&permType=allow&permOrder=allowFirst";
|
|
2648
|
errorList.addElement(error);
|
|
2649
|
outputResponse(successList, errorList, out);
|
|
2650
|
return;
|
|
2651
|
}
|
|
2652
|
|
|
2653
|
// Only select first element for permission, type and order
|
|
2654
|
permission = permissionList[0];
|
|
2655
|
permType = permTypeList[0];
|
|
2656
|
if (permOrderList != null) {
|
|
2657
|
permOrder = permOrderList[0];
|
|
2658
|
}
|
|
2659
|
|
|
2660
|
// Get package doctype set
|
|
2661
|
Vector<String> packageSet = null;
|
|
2662
|
try {
|
|
2663
|
packageSet =
|
|
2664
|
MetacatUtil.getOptionList(PropertyService.getProperty("xml.packagedoctypeset"));
|
|
2665
|
} catch (PropertyNotFoundException pnfe) {
|
|
2666
|
logMetacat.error("MetaCatServlet.handleSetAccessAction - Could not find package doctype set. Setting to null: "
|
|
2667
|
+ pnfe.getMessage());
|
|
2668
|
}
|
|
2669
|
//debug
|
|
2670
|
if (packageSet != null) {
|
|
2671
|
for (int i = 0; i < packageSet.size(); i++) {
|
|
2672
|
logMetacat.debug("MetaCatServlet.handleSetAccessAction - doctype in package set: "
|
|
2673
|
+ packageSet.elementAt(i));
|
|
2674
|
}
|
|
2675
|
}
|
|
2676
|
|
|
2677
|
// handle every accessionNumber
|
|
2678
|
for (int i = 0; i < docList.length; i++) {
|
|
2679
|
String docid = docList[i];
|
|
2680
|
if (docid.startsWith("urn:")) {
|
|
2681
|
try {
|
|
2682
|
String actualDocId = LSIDUtil.getDocId(docid, false);
|
|
2683
|
docid = actualDocId;
|
|
2684
|
} catch (ParseLSIDException ple) {
|
|
2685
|
logMetacat.error("MetaCatServlet.handleSetAccessAction - " +
|
|
2686
|
"could not parse lsid: " + docid + " : " + ple.getMessage());
|
|
2687
|
ple.printStackTrace(System.out);
|
|
2688
|
}
|
|
2689
|
}
|
|
2690
|
String accessionNumber = docid;
|
|
2691
|
String owner = null;
|
|
2692
|
String publicId = null;
|
|
2693
|
// Get document owner and public id
|
|
2694
|
try {
|
|
2695
|
owner = getFieldValueForDoc(accessionNumber, "user_owner");
|
|
2696
|
publicId = getFieldValueForDoc(accessionNumber, "doctype");
|
|
2697
|
} catch (Exception e) {
|
|
2698
|
logMetacat.error("MetaCatServlet.handleSetAccessAction - Error in handleSetAccessAction: "
|
|
2699
|
+ e.getMessage());
|
|
2700
|
e.printStackTrace(System.out);
|
|
2701
|
error = "Error in set access control for document - " + accessionNumber + e.getMessage();
|
|
2702
|
errorList.addElement(error);
|
|
2703
|
continue;
|
|
2704
|
}
|
|
2705
|
//check if user is the owner. Only owner can do owner
|
|
2706
|
if (username == null || owner == null || !username.equals(owner)) {
|
|
2707
|
error = "User - " + username + " does not have permission to set "
|
|
2708
|
+ "access control for docid - " + accessionNumber;
|
|
2709
|
errorList.addElement(error);
|
|
2710
|
System.out.println("user " + username + " does not have permission to set " +
|
|
2711
|
"access control for docid " + accessionNumber);
|
|
2712
|
continue;
|
|
2713
|
}
|
|
2714
|
|
|
2715
|
//*** Find out if the document is a Member of an EML package.
|
|
2716
|
//*** (for efficiency, only check if it isn't already true
|
|
2717
|
//*** for the case of multiple files).
|
|
2718
|
if (isEmlPkgMember == false)
|
|
2719
|
isEmlPkgMember = (DBUtil.findDataSetDocIdForGivenDocument(accessionNumber) != null);
|
|
2720
|
|
|
2721
|
// If docid publicid is BIN data file or other beta4, 6 package document
|
|
2722
|
// we could not do set access control. Because we don't want inconsistent
|
|
2723
|
// to its access docuemnt
|
|
2724
|
if (publicId != null && packageSet != null
|
|
2725
|
&& packageSet.contains(publicId) && isEmlPkgMember) {
|
|
2726
|
error = "Could not set access control to document " + accessionNumber
|
|
2727
|
+ "because it is in a pakcage and it has a access file for it";
|
|
2728
|
errorList.addElement(error);
|
|
2729
|
System.out.println("this is a beta4 or 6 document so we can't set the access element.");
|
|
2730
|
continue;
|
|
2731
|
}
|
|
2732
|
// for every principle
|
|
2733
|
for (int j = 0; j < principalList.length; j++) {
|
|
2734
|
String principal = principalList[j];
|
|
2735
|
try {
|
|
2736
|
//insert permission
|
|
2737
|
AccessControlForSingleFile accessControl =
|
|
2738
|
new AccessControlForSingleFile(accessionNumber);
|
|
2739
|
accessControl.insertPermissions(principal, Long.valueOf(permission), permType, permOrder);
|
|
2740
|
} catch (Exception ee) {
|
|
2741
|
logMetacat.error("MetaCatServlet.handleSetAccessAction - Error inserting permission: "
|
|
2742
|
+ ee.getMessage());
|
|
2743
|
ee.printStackTrace(System.out);
|
|
2744
|
error = "Failed to set access control for document "
|
|
2745
|
+ accessionNumber + " because " + ee.getMessage();
|
|
2746
|
errorList.addElement(error);
|
|
2747
|
continue;
|
|
2748
|
}
|
|
2749
|
}
|
|
2750
|
//force replication when this action is called
|
|
2751
|
boolean isXml = true;
|
|
2752
|
if (publicId.equalsIgnoreCase("BIN")) {
|
|
2753
|
isXml = false;
|
|
2754
|
}
|
|
2755
|
ForceReplicationHandler frh =
|
|
2756
|
new ForceReplicationHandler(accessionNumber, isXml, null);
|
|
2757
|
logMetacat.debug("MetaCatServlet.handleSetAccessAction - ForceReplicationHandler created: " + frh.toString());
|
|
2758
|
|
|
2759
|
}
|
|
2760
|
successList.addElement("MetaCatServlet.handleSetAccessAction - successfully added individual access for doc id: " + docList[0]);
|
|
2761
|
|
|
2762
|
if (params.get("forwardto") != null) {
|
|
2763
|
try {
|
|
2764
|
RequestUtil.forwardRequest(request, response, params);
|
|
2765
|
} catch (MetacatUtilException mue) {
|
|
2766
|
logMetacat.error("metaCatServlet.handleSetAccessAction - could not forward " +
|
|
2767
|
"request. Sending output to response writer");
|
|
2768
|
mue.printStackTrace(System.out);
|
|
2769
|
outputResponse(successList, errorList, out);
|
|
2770
|
}
|
|
2771
|
} else {
|
|
2772
|
outputResponse(successList, errorList, out);
|
|
2773
|
}
|
|
2774
|
}
|
|
2775
|
|
|
2776
|
/*
|
|
2777
|
* A method try to determin a docid's public id, if couldn't find null will
|
|
2778
|
* be returned.
|
|
2779
|
*/
|
|
2780
|
private String getFieldValueForDoc(String accessionNumber, String fieldName)
|
|
2781
|
throws Exception {
|
|
2782
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2783
|
if (accessionNumber == null || accessionNumber.equals("")
|
|
2784
|
|| fieldName == null || fieldName.equals("")) { throw new Exception(
|
|
2785
|
"Docid or field name was not specified"); }
|
|
2786
|
|
|
2787
|
PreparedStatement pstmt = null;
|
|
2788
|
ResultSet rs = null;
|
|
2789
|
String fieldValue = null;
|
|
2790
|
String docId = null;
|
|
2791
|
DBConnection conn = null;
|
|
2792
|
int serialNumber = -1;
|
|
2793
|
|
|
2794
|
// get rid of revision if access number has
|
|
2795
|
docId = DocumentUtil.getDocIdFromString(accessionNumber);
|
|
2796
|
try {
|
|
2797
|
//check out DBConnection
|
|
2798
|
conn = DBConnectionPool
|
|
2799
|
.getDBConnection("MetaCatServlet.getPublicIdForDoc");
|
|
2800
|
serialNumber = conn.getCheckOutSerialNumber();
|
|
2801
|
pstmt = conn.prepareStatement("SELECT " + fieldName
|
|
2802
|
+ " FROM xml_documents " + "WHERE docid = ? ");
|
|
2803
|
|
|
2804
|
pstmt.setString(1, docId);
|
|
2805
|
pstmt.execute();
|
|
2806
|
rs = pstmt.getResultSet();
|
|
2807
|
boolean hasRow = rs.next();
|
|
2808
|
// int perm = 0;
|
|
2809
|
if (hasRow) {
|
|
2810
|
fieldValue = rs.getString(1);
|
|
2811
|
} else {
|
|
2812
|
throw new Exception("Could not find document: "
|
|
2813
|
+ accessionNumber);
|
|
2814
|
}
|
|
2815
|
} catch (Exception e) {
|
|
2816
|
logMetacat.error("MetaCatServlet.getFieldValueForDoc - General error: "
|
|
2817
|
+ e.getMessage());
|
|
2818
|
throw e;
|
|
2819
|
} finally {
|
|
2820
|
try {
|
|
2821
|
rs.close();
|
|
2822
|
pstmt.close();
|
|
2823
|
|
|
2824
|
} finally {
|
|
2825
|
DBConnectionPool.returnDBConnection(conn, serialNumber);
|
|
2826
|
}
|
|
2827
|
}
|
|
2828
|
return fieldValue;
|
|
2829
|
}
|
|
2830
|
|
|
2831
|
/*
|
|
2832
|
* Get the list of documents from the database and return the list in an
|
|
2833
|
* Vector of identifiers.
|
|
2834
|
*
|
|
2835
|
* @ returns the array of identifiers
|
|
2836
|
*/
|
|
2837
|
private Vector<String> getDocumentList() throws SQLException {
|
|
2838
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2839
|
Vector<String> docList = new Vector<String>();
|
|
2840
|
PreparedStatement pstmt = null;
|
|
2841
|
ResultSet rs = null;
|
|
2842
|
DBConnection conn = null;
|
|
2843
|
int serialNumber = -1;
|
|
2844
|
|
|
2845
|
try {
|
|
2846
|
//check out DBConnection
|
|
2847
|
conn = DBConnectionPool
|
|
2848
|
.getDBConnection("MetaCatServlet.getDocumentList");
|
|
2849
|
serialNumber = conn.getCheckOutSerialNumber();
|
|
2850
|
pstmt = conn.prepareStatement("SELECT docid, rev"
|
|
2851
|
+ " FROM xml_documents ");
|
|
2852
|
pstmt.execute();
|
|
2853
|
rs = pstmt.getResultSet();
|
|
2854
|
while (rs.next()) {
|
|
2855
|
String docid = rs.getString(1);
|
|
2856
|
String rev = rs.getString(2);
|
|
2857
|
docList.add(docid + "." + rev);
|
|
2858
|
}
|
|
2859
|
} catch (SQLException e) {
|
|
2860
|
logMetacat.error("MetaCatServlet.getDocumentList - General exception: "
|
|
2861
|
+ e.getMessage());
|
|
2862
|
throw e;
|
|
2863
|
} finally {
|
|
2864
|
try {
|
|
2865
|
rs.close();
|
|
2866
|
pstmt.close();
|
|
2867
|
|
|
2868
|
} catch (SQLException se) {
|
|
2869
|
logMetacat.error("MetaCatServlet.getDocumentList - General exception: "
|
|
2870
|
+ se.getMessage());
|
|
2871
|
throw se;
|
|
2872
|
} finally {
|
|
2873
|
DBConnectionPool.returnDBConnection(conn, serialNumber);
|
|
2874
|
}
|
|
2875
|
}
|
|
2876
|
return docList;
|
|
2877
|
}
|
|
2878
|
|
|
2879
|
/*
|
|
2880
|
* A method to output setAccess action result
|
|
2881
|
*/
|
|
2882
|
private void outputResponse(Vector<String> successList, Vector<String> errorList,
|
|
2883
|
PrintWriter out) {
|
|
2884
|
boolean error = false;
|
|
2885
|
boolean success = false;
|
|
2886
|
// Output prolog
|
|
2887
|
out.println(PROLOG);
|
|
2888
|
// output success message
|
|
2889
|
if (successList != null) {
|
|
2890
|
for (int i = 0; i < successList.size(); i++) {
|
|
2891
|
out.println(SUCCESS);
|
|
2892
|
out.println(successList.elementAt(i));
|
|
2893
|
out.println(SUCCESSCLOSE);
|
|
2894
|
success = true;
|
|
2895
|
}
|
|
2896
|
}
|
|
2897
|
// output error message
|
|
2898
|
if (errorList != null) {
|
|
2899
|
for (int i = 0; i < errorList.size(); i++) {
|
|
2900
|
out.println(ERROR);
|
|
2901
|
out.println(errorList.elementAt(i));
|
|
2902
|
out.println(ERRORCLOSE);
|
|
2903
|
error = true;
|
|
2904
|
}
|
|
2905
|
}
|
|
2906
|
|
|
2907
|
// if no error and no success info, send a error that nothing happened
|
|
2908
|
if (!error && !success) {
|
|
2909
|
out.println(ERROR);
|
|
2910
|
out.println("Nothing happend for setaccess action");
|
|
2911
|
out.println(ERRORCLOSE);
|
|
2912
|
}
|
|
2913
|
}
|
|
2914
|
|
|
2915
|
/*
|
|
2916
|
* If the given docid only have one seperter, we need
|
|
2917
|
* append rev for it. The rev come from xml_documents
|
|
2918
|
*/
|
|
2919
|
private static String appendRev(String docid) throws PropertyNotFoundException, SQLException, McdbDocNotFoundException {
|
|
2920
|
// Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2921
|
String newAccNum = null;
|
|
2922
|
String separator = PropertyService.getProperty("document.accNumSeparator");
|
|
2923
|
int firstIndex = docid.indexOf(separator);
|
|
2924
|
int lastIndex = docid.lastIndexOf(separator);
|
|
2925
|
if (firstIndex == lastIndex) {
|
|
2926
|
|
|
2927
|
//only one seperater
|
|
2928
|
int rev = DBUtil.getLatestRevisionInDocumentTable(docid);
|
|
2929
|
if (rev == -1) {
|
|
2930
|
throw new McdbDocNotFoundException("the requested docid '"
|
|
2931
|
+ docid+ "' does not exist");
|
|
2932
|
} else {
|
|
2933
|
newAccNum = docid+ separator+ rev;
|
|
2934
|
}
|
|
2935
|
} else {
|
|
2936
|
// in other suituation we don't change the docid
|
|
2937
|
newAccNum = docid;
|
|
2938
|
}
|
|
2939
|
//logMetacat.debug("The docid will be read is "+newAccNum);
|
|
2940
|
return newAccNum;
|
|
2941
|
}
|
|
2942
|
|
|
2943
|
/**
|
|
2944
|
* Schedule the sitemap generator to run periodically and update all
|
|
2945
|
* of the sitemap files for search indexing engines.
|
|
2946
|
*
|
|
2947
|
* @param request a servlet request, from which we determine the context
|
|
2948
|
*/
|
|
2949
|
protected void scheduleSitemapGeneration(HttpServletRequest request) {
|
|
2950
|
Logger logMetacat = Logger.getLogger(MetaCatServlet.class);
|
|
2951
|
if (!_sitemapScheduled) {
|
|
2952
|
String directoryName = null;
|
|
2953
|
String skin = null;
|
|
2954
|
long sitemapInterval = 0;
|
|
2955
|
|
|
2956
|
try {
|
|
2957
|
directoryName = SystemUtil.getContextDir() + FileUtil.getFS() + "sitemaps";
|
|
2958
|
skin = PropertyService.getProperty("application.default-style");
|
|
2959
|
sitemapInterval =
|
|
2960
|
Integer.parseInt(PropertyService.getProperty("sitemap.interval"));
|
|
2961
|
} catch (PropertyNotFoundException pnfe) {
|
|
2962
|
logMetacat.error("MetaCatServlet.scheduleSitemapGeneration - Could not run site map generation because property "
|
|
2963
|
+ "could not be found: " + pnfe.getMessage());
|
|
2964
|
}
|
|
2965
|
|
|
2966
|
File directory = new File(directoryName);
|
|
2967
|
directory.mkdirs();
|
|
2968
|
String urlRoot = request.getRequestURL().toString();
|
|
2969
|
Sitemap smap = new Sitemap(directory, urlRoot, skin);
|
|
2970
|
long firstDelay = 60*1000; // 60 seconds delay
|
|
2971
|
timer.schedule(smap, firstDelay, sitemapInterval);
|
|
2972
|
_sitemapScheduled = true;
|
|
2973
|
}
|
|
2974
|
}
|
|
2975
|
|
|
2976
|
/**
|
|
2977
|
* @param sitemapScheduled toggle the _sitemapScheduled flag
|
|
2978
|
*/
|
|
2979
|
public void set_sitemapScheduled(boolean sitemapScheduled) {
|
|
2980
|
_sitemapScheduled = sitemapScheduled;
|
|
2981
|
}
|
|
2982
|
|
|
2983
|
}
|