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/**
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 *  '$RCSfile$'
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 *  Copyright: 2000-2011 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: leinfelder $'
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 *     '$Date: 2014-08-06 13:09:47 -0700 (Wed, 06 Aug 2014) $'
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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.dataone;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.Date;
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import java.util.Hashtable;
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import java.util.List;
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import java.util.Set;
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import java.util.Timer;
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import java.util.concurrent.locks.Lock;
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import javax.servlet.http.HttpServletRequest;
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import org.apache.commons.io.IOUtils;
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import org.apache.log4j.Logger;
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import org.dataone.client.v2.CNode;
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import org.dataone.client.v2.itk.D1Client;
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import org.dataone.client.v2.formats.ObjectFormatCache;
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import org.dataone.service.exceptions.BaseException;
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import org.dataone.service.exceptions.IdentifierNotUnique;
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import org.dataone.service.exceptions.InsufficientResources;
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import org.dataone.service.exceptions.InvalidRequest;
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.exceptions.UnsupportedType;
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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.DescribeResponse;
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import org.dataone.service.types.v1.Group;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v2.Log;
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import org.dataone.service.types.v2.Node;
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import org.dataone.service.types.v1.Event;
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.NodeType;
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import org.dataone.service.types.v2.ObjectFormat;
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import org.dataone.service.types.v1.Permission;
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import org.dataone.service.types.v1.Replica;
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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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import org.dataone.service.types.v2.SystemMetadata;
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import org.dataone.service.types.v1.util.AuthUtils;
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import org.dataone.service.types.v1.util.ChecksumUtil;
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import org.dataone.service.util.Constants;
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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import edu.ucsb.nceas.metacat.DocumentImpl;
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import edu.ucsb.nceas.metacat.EventLog;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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import edu.ucsb.nceas.metacat.MetacatHandler;
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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.dataone.hazelcast.HazelcastService;
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import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
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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.utilities.PropertyNotFoundException;
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public abstract class D1NodeService {
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  private static Logger logMetacat = Logger.getLogger(D1NodeService.class);
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  /** For logging the operations */
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  protected HttpServletRequest request;
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  /* reference to the metacat handler */
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  protected MetacatHandler handler;
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  /* parameters set in the incoming request */
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  private Hashtable<String, String[]> params;
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  /**
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   * limit paged results sets to a configured maximum
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   */
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  protected static int MAXIMUM_DB_RECORD_COUNT = 7000;
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112
  static {
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		try {
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			MAXIMUM_DB_RECORD_COUNT = Integer.valueOf(PropertyService.getProperty("database.webResultsetSize"));
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		} catch (Exception e) {
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			logMetacat.warn("Could not set MAXIMUM_DB_RECORD_COUNT", e);
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		}
118
	}
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120
  /**
121
   * out-of-band session object to be used when not passed in as a method parameter
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   */
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  protected Session session;
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  /**
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   * Constructor - used to set the metacatUrl from a subclass extending D1NodeService
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   * 
128
   * @param metacatUrl - the URL of the metacat service, including the ending /d1
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   */
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  public D1NodeService(HttpServletRequest request) {
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		this.request = request;
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	}
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  /**
135
   * retrieve the out-of-band session
136
   * @return
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   */
138
  	public Session getSession() {
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		return session;
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	}
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  	/**
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  	 * Set the out-of-band session
144
  	 * @param session
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  	 */
146
	public void setSession(Session session) {
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		this.session = session;
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	}
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  /**
151
   * This method provides a lighter weight mechanism than 
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   * getSystemMetadata() for a client to determine basic 
153
   * properties of the referenced object.
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   * 
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   * @param session - the Session object containing the credentials for the Subject
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   * @param pid - the identifier of the object to be described
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   * 
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   * @return describeResponse - A set of values providing a basic description 
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   *                            of the object.
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   * 
161
   * @throws InvalidToken
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   * @throws ServiceFailure
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   * @throws NotAuthorized
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   * @throws NotFound
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   * @throws NotImplemented
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   * @throws InvalidRequest
167
   */
168
  public DescribeResponse describe(Session session, Identifier pid) 
169
      throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
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    // get system metadata and construct the describe response
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      SystemMetadata sysmeta = getSystemMetadata(session, pid);
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      DescribeResponse describeResponse = 
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      	new DescribeResponse(sysmeta.getFormatId(), sysmeta.getSize(), 
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      			sysmeta.getDateSysMetadataModified(),
176
      			sysmeta.getChecksum(), sysmeta.getSerialVersion());
177

    
178
      return describeResponse;
179

    
180
  }
181
  
182
  /**
183
   * Deletes an object from the Member Node, where the object is either a 
184
   * data object or a science metadata object.
185
   * 
186
   * @param session - the Session object containing the credentials for the Subject
187
   * @param pid - The object identifier to be deleted
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   * 
189
   * @return pid - the identifier of the object used for the deletion
190
   * 
191
   * @throws InvalidToken
192
   * @throws ServiceFailure
193
   * @throws NotAuthorized
194
   * @throws NotFound
195
   * @throws NotImplemented
196
   * @throws InvalidRequest
197
   */
198
  public Identifier delete(Session session, Identifier pid) 
199
      throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
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      String localId = null;
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      if (session == null) {
203
      	throw new InvalidToken("1330", "No session has been provided");
204
      }
205
      // just for logging purposes
206
      String username = session.getSubject().getValue();
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      // do we have a valid pid?
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      if (pid == null || pid.getValue().trim().equals("")) {
210
          throw new ServiceFailure("1350", "The provided identifier was invalid.");
211
      }
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      // check for the existing identifier
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      try {
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          localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
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      } catch (McdbDocNotFoundException e) {
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          throw new NotFound("1340", "The object with the provided " + "identifier was not found.");
218
      }
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220
      try {
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          // delete the document, as admin
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          DocumentImpl.delete(localId, null, null, null, true);
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          EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), username, localId, Event.DELETE.xmlValue());
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          // archive it
226
          // DocumentImpl.delete() now sets this
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          // see https://redmine.dataone.org/issues/3406
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//          SystemMetadata sysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
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//          sysMeta.setArchived(true);
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//          sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
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//          HazelcastService.getInstance().getSystemMetadataMap().put(pid, sysMeta);
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233
      } catch (McdbDocNotFoundException e) {
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          throw new NotFound("1340", "The provided identifier was invalid.");
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236
      } catch (SQLException e) {
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          throw new ServiceFailure("1350", "There was a problem deleting the object." + "The error message was: " + e.getMessage());
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239
      } catch (InsufficientKarmaException e) {
240
          if ( logMetacat.isDebugEnabled() ) {
241
              e.printStackTrace();
242
          }
243
          throw new NotAuthorized("1320", "The provided identity does not have " + "permission to DELETE objects on the Member Node.");
244
      
245
      } catch (Exception e) { // for some reason DocumentImpl throws a general Exception
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          throw new ServiceFailure("1350", "There was a problem deleting the object." + "The error message was: " + e.getMessage());
247
      }
248

    
249
      return pid;
250
  }
251
  
252
  /**
253
   * Low level, "are you alive" operation. A valid ping response is 
254
   * indicated by a HTTP status of 200.
255
   * 
256
   * @return true if the service is alive
257
   * 
258
   * @throws NotImplemented
259
   * @throws ServiceFailure
260
   * @throws InsufficientResources
261
   */
262
  public Date ping() 
263
      throws NotImplemented, ServiceFailure, InsufficientResources {
264

    
265
      // test if we can get a database connection
266
      int serialNumber = -1;
267
      DBConnection dbConn = null;
268
      try {
269
          dbConn = DBConnectionPool.getDBConnection("MNodeService.ping");
270
          serialNumber = dbConn.getCheckOutSerialNumber();
271
      } catch (SQLException e) {
272
      	ServiceFailure sf = new ServiceFailure("", e.getMessage());
273
      	sf.initCause(e);
274
          throw sf;
275
      } finally {
276
          // Return the database connection
277
          DBConnectionPool.returnDBConnection(dbConn, serialNumber);
278
      }
279

    
280
      return Calendar.getInstance().getTime();
281
  }
282
  
283
  /**
284
   * Adds a new object to the Node, where the object is either a data 
285
   * object or a science metadata object. This method is called by clients 
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   * to create new data objects on Member Nodes or internally for Coordinating
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   * Nodes
288
   * 
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   * @param session - the Session object containing the credentials for the Subject
290
   * @param pid - The object identifier to be created
291
   * @param object - the object bytes
292
   * @param sysmeta - the system metadata that describes the object  
293
   * 
294
   * @return pid - the object identifier created
295
   * 
296
   * @throws InvalidToken
297
   * @throws ServiceFailure
298
   * @throws NotAuthorized
299
   * @throws IdentifierNotUnique
300
   * @throws UnsupportedType
301
   * @throws InsufficientResources
302
   * @throws InvalidSystemMetadata
303
   * @throws NotImplemented
304
   * @throws InvalidRequest
305
   */
306
  public Identifier create(Session session, Identifier pid, InputStream object,
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    SystemMetadata sysmeta) 
308
    throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique, 
309
    UnsupportedType, InsufficientResources, InvalidSystemMetadata, 
310
    NotImplemented, InvalidRequest {
311

    
312
    Identifier resultPid = null;
313
    String localId = null;
314
    boolean allowed = false;
315
    
316
    // check for null session
317
    if (session == null) {
318
    	throw new InvalidToken("4894", "Session is required to WRITE to the Node.");
319
    }
320
    Subject subject = session.getSubject();
321

    
322
    Subject publicSubject = new Subject();
323
    publicSubject.setValue(Constants.SUBJECT_PUBLIC);
324
	// be sure the user is authenticated for create()
325
    if (subject == null || subject.getValue() == null || 
326
        subject.equals(publicSubject) ) {
327
      throw new NotAuthorized("1100", "The provided identity does not have " +
328
        "permission to WRITE to the Node.");
329
      
330
    }
331
    
332
    // verify the pid is valid format
333
    if (!isValidIdentifier(pid)) {
334
    	throw new InvalidRequest("1202", "The provided identifier is invalid.");
335
    }
336
    
337
    // verify that pid == SystemMetadata.getIdentifier()
338
    logMetacat.debug("Comparing pid|sysmeta_pid: " + 
339
      pid.getValue() + "|" + sysmeta.getIdentifier().getValue());
340
    if (!pid.getValue().equals(sysmeta.getIdentifier().getValue())) {
341
        throw new InvalidSystemMetadata("1180", 
342
            "The supplied system metadata is invalid. " +
343
            "The identifier " + pid.getValue() + " does not match identifier" +
344
            "in the system metadata identified by " +
345
            sysmeta.getIdentifier().getValue() + ".");
346
        
347
    }
348

    
349
    logMetacat.debug("Checking if identifier exists: " + pid.getValue());
350
    // Check that the identifier does not already exist
351
    if (IdentifierManager.getInstance().identifierExists(pid.getValue())) {
352
	    	throw new IdentifierNotUnique("1120", 
353
			          "The requested identifier " + pid.getValue() +
354
			          " is already used by another object and" +
355
			          "therefore can not be used for this object. Clients should choose" +
356
			          "a new identifier that is unique and retry the operation or " +
357
			          "use CN.reserveIdentifier() to reserve one.");
358
    	
359
    }
360
    
361
    // TODO: this probably needs to be refined more
362
    try {
363
      allowed = isAuthorized(session, pid, Permission.WRITE);
364
            
365
    } catch (NotFound e) {
366
      // The identifier doesn't exist, writing should be fine.
367
      allowed = true;
368
    }
369
    
370
    // verify checksum, only if we can reset the inputstream
371
    if (object.markSupported()) {
372
        logMetacat.debug("Checking checksum for: " + pid.getValue());
373
	    String checksumAlgorithm = sysmeta.getChecksum().getAlgorithm();
374
	    String checksumValue = sysmeta.getChecksum().getValue();
375
	    try {
376
			String computedChecksumValue = ChecksumUtil.checksum(object, checksumAlgorithm).getValue();
377
			// it's very important that we don't consume the stream
378
			object.reset();
379
			if (!computedChecksumValue.equals(checksumValue)) {
380
			    logMetacat.error("Checksum for " + pid.getValue() + " does not match system metadata, computed = " + computedChecksumValue );
381
				throw new InvalidSystemMetadata("4896", "Checksum given does not match that of the object");
382
			}
383
		} catch (Exception e) {
384
			String msg = "Error verifying checksum values";
385
	      	logMetacat.error(msg, e);
386
	        throw new ServiceFailure("1190", msg + ": " + e.getMessage());
387
		}
388
    } else {
389
    	logMetacat.warn("mark is not supported on the object's input stream - cannot verify checksum without consuming stream");
390
    }
391
    	
392
    // we have the go ahead
393
    if ( allowed ) {
394
      
395
        logMetacat.debug("Allowed to insert: " + pid.getValue());
396

    
397
      // Science metadata (XML) or science data object?
398
      // TODO: there are cases where certain object formats are science metadata
399
      // but are not XML (netCDF ...).  Handle this.
400
      if ( isScienceMetadata(sysmeta) ) {
401
        
402
        // CASE METADATA:
403
      	String objectAsXML = "";
404
        try {
405
	        objectAsXML = IOUtils.toString(object, "UTF-8");
406
	        localId = insertOrUpdateDocument(objectAsXML, pid, session, "insert");
407
	        //localId = im.getLocalId(pid.getValue());
408

    
409
        } catch (IOException e) {
410
        	String msg = "The Node is unable to create the object. " +
411
          "There was a problem converting the object to XML";
412
        	logMetacat.info(msg);
413
          throw new ServiceFailure("1190", msg + ": " + e.getMessage());
414

    
415
        }
416
                    
417
      } else {
418
	        
419
	      // DEFAULT CASE: DATA (needs to be checked and completed)
420
	      localId = insertDataObject(object, pid, session);
421
      }   
422
    
423
    }
424

    
425
    logMetacat.debug("Done inserting new object: " + pid.getValue());
426
    
427
    // save the sysmeta
428
    try {
429
    	// lock and unlock of the pid happens in the subclass
430
    	HazelcastService.getInstance().getSystemMetadataMap().put(sysmeta.getIdentifier(), sysmeta);
431
    	// submit for indexing
432
        MetacatSolrIndex.getInstance().submit(sysmeta.getIdentifier(), sysmeta, null, true);
433
        
434
    } catch (Exception e) {
435
    	logMetacat.error("Problem creating system metadata: " + pid.getValue(), e);
436
        throw new ServiceFailure("1190", e.getMessage());
437
	}
438
    
439
    // setting the resulting identifier failed
440
    if (localId == null ) {
441
      throw new ServiceFailure("1190", "The Node is unable to create the object. ");
442
    }
443

    
444
    resultPid = pid;
445
    
446
    logMetacat.debug("create() complete for object: " + pid.getValue());
447

    
448
    return resultPid;
449
  }
450

    
451
  /**
452
   * Return the log records associated with a given event between the start and 
453
   * end dates listed given a particular Subject listed in the Session
454
   * 
455
   * @param session - the Session object containing the credentials for the Subject
456
   * @param fromDate - the start date of the desired log records
457
   * @param toDate - the end date of the desired log records
458
   * @param event - restrict log records of a specific event type
459
   * @param start - zero based offset from the first record in the 
460
   *                set of matching log records. Used to assist with 
461
   *                paging the response.
462
   * @param count - maximum number of log records to return in the response. 
463
   *                Used to assist with paging the response.
464
   * 
465
   * @return the desired log records
466
   * 
467
   * @throws InvalidToken
468
   * @throws ServiceFailure
469
   * @throws NotAuthorized
470
   * @throws InvalidRequest
471
   * @throws NotImplemented
472
   */
473
  public Log getLogRecords(Session session, Date fromDate, Date toDate, 
474
      String event, String pidFilter, Integer start, Integer count) throws InvalidToken, ServiceFailure,
475
      NotAuthorized, InvalidRequest, NotImplemented {
476

    
477
	  // only admin access to this method
478
	  // see https://redmine.dataone.org/issues/2855
479
	  if (!isAdminAuthorized(session)) {
480
		  throw new NotAuthorized("1460", "Only the CN or admin is allowed to harvest logs from this node");
481
	  }
482
	  
483
    IdentifierManager im = IdentifierManager.getInstance();
484
    EventLog el = EventLog.getInstance();
485
    if ( fromDate == null ) {
486
      logMetacat.debug("setting fromdate from null");
487
      fromDate = new Date(1);
488
    }
489
    if ( toDate == null ) {
490
      logMetacat.debug("setting todate from null");
491
      toDate = new Date();
492
    }
493

    
494
    if ( start == null ) {
495
    	start = 0;	
496
    }
497
    
498
    if ( count == null ) {
499
    	count = 1000;
500
    }
501
    
502
    // safeguard against large requests
503
    if (count > MAXIMUM_DB_RECORD_COUNT) {
504
    	count = MAXIMUM_DB_RECORD_COUNT;
505
    }
506

    
507
    String[] filterDocid = null;
508
    if (pidFilter != null) {
509
		try {
510
	      String localId = im.getLocalId(pidFilter);
511
	      filterDocid = new String[] {localId};
512
	    } catch (Exception ex) { 
513
	    	String msg = "Could not find localId for given pidFilter '" + pidFilter + "'";
514
	        logMetacat.warn(msg, ex);
515
	        //throw new InvalidRequest("1480", msg);
516
	    }
517
    }
518
    
519
    logMetacat.debug("fromDate: " + fromDate);
520
    logMetacat.debug("toDate: " + toDate);
521

    
522
    Log log = el.getD1Report(null, null, filterDocid, event,
523
        new java.sql.Timestamp(fromDate.getTime()),
524
        new java.sql.Timestamp(toDate.getTime()), false, start, count);
525
    
526
    logMetacat.info("getLogRecords");
527
    return log;
528
  }
529
    
530
  /**
531
   * Return the object identified by the given object identifier
532
   * 
533
   * @param session - the Session object containing the credentials for the Subject
534
   * @param pid - the object identifier for the given object
535
   * 
536
   * TODO: The D1 Authorization API doesn't provide information on which 
537
   * authentication system the Subject belongs to, and so it's not possible to
538
   * discern which Person or Group is a valid KNB LDAP DN.  Fix this.
539
   * 
540
   * @return inputStream - the input stream of the given object
541
   * 
542
   * @throws InvalidToken
543
   * @throws ServiceFailure
544
   * @throws NotAuthorized
545
   * @throws InvalidRequest
546
   * @throws NotImplemented
547
   */
548
  public InputStream get(Session session, Identifier pid) 
549
    throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 
550
    NotImplemented {
551
    
552
    InputStream inputStream = null; // bytes to be returned
553
    handler = new MetacatHandler(new Timer());
554
    boolean allowed = false;
555
    String localId; // the metacat docid for the pid
556
    
557
    // get the local docid from Metacat
558
    try {
559
      localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
560
    
561
    } catch (McdbDocNotFoundException e) {
562
      throw new NotFound("1020", "The object specified by " + 
563
                         pid.getValue() +
564
                         " does not exist at this node.");
565
    }
566
    
567
    // check for authorization
568
    try {
569
		allowed = isAuthorized(session, pid, Permission.READ);
570
	} catch (InvalidRequest e) {
571
		throw new ServiceFailure("1030", e.getDescription());
572
	}
573
    
574
    // if the person is authorized, perform the read
575
    if (allowed) {
576
      try {
577
        inputStream = handler.read(localId);
578
      } catch (Exception e) {
579
        throw new NotFound("1020", "The object specified by " + 
580
            pid.getValue() +
581
            "could not be returned due to error: " +
582
            e.getMessage());
583
      }
584
    }
585

    
586
    // if we fail to set the input stream
587
    if ( inputStream == null ) {
588
      throw new NotFound("1020", "The object specified by " + 
589
                         pid.getValue() +
590
                         "does not exist at this node.");
591
    }
592
    
593
	// log the read event
594
    String principal = Constants.SUBJECT_PUBLIC;
595
    if (session != null && session.getSubject() != null) {
596
    	principal = session.getSubject().getValue();
597
    }
598
    EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), principal, localId, "read");
599
    
600
    return inputStream;
601
  }
602

    
603
  /**
604
   * Return the system metadata for a given object
605
   * 
606
   * @param session - the Session object containing the credentials for the Subject
607
   * @param pid - the object identifier for the given object
608
   * 
609
   * @return inputStream - the input stream of the given system metadata object
610
   * 
611
   * @throws InvalidToken
612
   * @throws ServiceFailure
613
   * @throws NotAuthorized
614
   * @throws NotFound
615
   * @throws InvalidRequest
616
   * @throws NotImplemented
617
   */
618
    public SystemMetadata getSystemMetadata(Session session, Identifier pid)
619
        throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
620
        NotImplemented {
621

    
622
        boolean isAuthorized = false;
623
        SystemMetadata systemMetadata = null;
624
        List<Replica> replicaList = null;
625
        NodeReference replicaNodeRef = null;
626
        List<Node> nodeListBySubject = null;
627
        Subject subject = null;
628
        
629
        if (session != null ) {
630
            subject = session.getSubject();
631
        }
632
        
633
        // check normal authorization
634
        BaseException originalAuthorizationException = null;
635
        if (!isAuthorized) {
636
            try {
637
                isAuthorized = isAuthorized(session, pid, Permission.READ);
638

    
639
            } catch (InvalidRequest e) {
640
                throw new ServiceFailure("1090", e.getDescription());
641
            } catch (NotAuthorized nae) {
642
            	// catch this for later
643
            	originalAuthorizationException = nae;
644
			}
645
        }
646
        
647
        // get the system metadata first because we need the replica list for auth
648
        systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
649
        
650
        // check the replica information to expand access to MNs that might need it
651
        if (!isAuthorized) {
652
        	
653
	        try {
654
	        	
655
	            // if MNs are listed as replicas, allow access
656
	            if ( systemMetadata != null ) {
657
	                replicaList = systemMetadata.getReplicaList();
658
	                // only check if there are in fact replicas listed
659
	                if ( replicaList != null ) {
660
	                    
661
	                    if ( subject != null ) {
662
	                        // get the list of nodes with a matching node subject
663
	                        try {
664
	                            nodeListBySubject = listNodesBySubject(session.getSubject());
665
	
666
	                        } catch (BaseException e) {
667
	                            // Unexpected error contacting the CN via D1Client
668
	                            String msg = "Caught an unexpected error while trying "
669
	                                    + "to potentially authorize system metadata access "
670
	                                    + "based on the session subject. The error was "
671
	                                    + e.getMessage();
672
	                            logMetacat.error(msg);
673
	                            if (logMetacat.isDebugEnabled()) {
674
	                                e.printStackTrace();
675
	
676
	                            }
677
	                            // isAuthorized is still false 
678
	                        }
679
	
680
	                    }
681
	                    if (nodeListBySubject != null) {
682
	                        // compare node ids to replica node ids
683
	                        outer: for (Replica replica : replicaList) {
684
	                            replicaNodeRef = replica.getReplicaMemberNode();
685
	
686
	                            for (Node node : nodeListBySubject) {
687
	                                if (node.getIdentifier().equals(replicaNodeRef)) {
688
	                                    // node id via session subject matches a replica node
689
	                                    isAuthorized = true;
690
	                                    break outer;
691
	                                }
692
	                            }
693
	                        }
694
	                    }
695
	                }
696
	            }
697
	            
698
	            // if we still aren't authorized, then we are done
699
	            if (!isAuthorized) {
700
	                throw new NotAuthorized("1400", Permission.READ
701
	                        + " not allowed on " + pid.getValue());
702
	            }
703

    
704
	        } catch (RuntimeException e) {
705
	        	e.printStackTrace();
706
	            // convert hazelcast RuntimeException to ServiceFailure
707
	            throw new ServiceFailure("1090", "Unexpected error getting system metadata for: " + 
708
	                pid.getValue());	
709
	        }
710
	        
711
        }
712
        
713
        // It wasn't in the map
714
        if ( systemMetadata == null ) {
715
            throw new NotFound("1420", "No record found for: " + pid.getValue());
716
        }
717
        
718
        return systemMetadata;
719
    }
720
     
721
    
722
    /**
723
     * Test if the specified session represents the authoritative member node for the
724
     * given object specified by the identifier. According the the DataONE documentation, 
725
     * the authoritative member node has all the rights of the *rightsHolder*.
726
     * @param session - the Session object containing the credentials for the Subject
727
     * @param pid - the Identifier of the data object
728
     * @return true if the session represents the authoritative mn.
729
     * @throws ServiceFailure 
730
     * @throws NotImplemented 
731
     */
732
    public boolean isAuthoritativeMNodeAdmin(Session session, Identifier pid) {
733
        boolean allowed = false;
734
        //check the parameters
735
        if(session == null) {
736
            logMetacat.debug("D1NodeService.isAuthoritativeMNodeAdmin - the session object is null and return false.");
737
            return allowed;
738
        } else if (pid == null || pid.getValue() == null || pid.getValue().trim().equals("")) {
739
            logMetacat.debug("D1NodeService.isAuthoritativeMNodeAdmin - the Identifier object is null (not being specified) and return false.");
740
            return allowed;
741
        }
742
        
743
        //Get the subject from the session
744
        Subject subject = session.getSubject();
745
        if(subject != null) {
746
            //Get the authoritative member node info from the system metadata
747
            SystemMetadata sysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
748
            if(sysMeta != null) {
749
                NodeReference authoritativeMNode = sysMeta.getAuthoritativeMemberNode();
750
                if(authoritativeMNode != null) {
751
                        CNode cn = null;
752
                        try {
753
                            cn = D1Client.getCN();
754
                        } catch (BaseException e) {
755
                            logMetacat.error("D1NodeService.isAuthoritativeMNodeAdmin - couldn't connect to the CN since "+
756
                                            e.getDescription()+ ". The false value will be returned for the AuthoritativeMNodeAdmin.");
757
                            return allowed;
758
                        }
759
                        
760
                        if(cn != null) {
761
                            List<Node> nodes = null;
762
                            try {
763
                                nodes = cn.listNodes().getNodeList();
764
                            } catch (NotImplemented e) {
765
                                logMetacat.error("D1NodeService.isAuthoritativeMNodeAdmin - couldn't get the member nodes list from the CN since "+e.getDescription()+ 
766
                                                ". The false value will be returned for the AuthoritativeMNodeAdmin.");
767
                                return allowed;
768
                            } catch (ServiceFailure ee) {
769
                                logMetacat.error("D1NodeService.isAuthoritativeMNodeAdmin - couldn't get the member nodes list from the CN since "+ee.getDescription()+ 
770
                                                ". The false value will be returned for the AuthoritativeMNodeAdmin.");
771
                                return allowed;
772
                            }
773
                            if(nodes != null) {
774
                                for(Node node : nodes) {
775
                                    //find the authoritative node and get its subjects
776
                                    if (node.getType() == NodeType.MN && node.getIdentifier() != null && node.getIdentifier().equals(authoritativeMNode)) {
777
                                        List<Subject> nodeSubjects = node.getSubjectList();
778
                                        if(nodeSubjects != null) {
779
                                            // check if the session subject is in the node subject list
780
                                            for (Subject nodeSubject : nodeSubjects) {
781
                                                logMetacat.debug("D1NodeService.isAuthoritativeMNodeAdmin(), comparing subjects: " +
782
                                                    nodeSubject.getValue() + " and " + subject.getValue());
783
                                                if ( nodeSubject != null && nodeSubject.equals(subject) ) {
784
                                                    allowed = true; // subject of session == target node subject
785
                                                    break;
786
                                                }
787
                                            }              
788
                                        }
789
                                      
790
                                    }
791
                                }
792
                            }
793
                        }
794
                }
795
            }
796
        }
797
        return allowed;
798
    }
799
    
800
    
801
  /**
802
   * Test if the user identified by the provided token has administrative authorization 
803
   * 
804
   * @param session - the Session object containing the credentials for the Subject
805
   * 
806
   * @return true if the user is admin
807
   * 
808
   * @throws ServiceFailure
809
   * @throws InvalidToken
810
   * @throws NotFound
811
   * @throws NotAuthorized
812
   * @throws NotImplemented
813
   */
814
  public boolean isAdminAuthorized(Session session) 
815
      throws ServiceFailure, InvalidToken, NotAuthorized,
816
      NotImplemented {
817

    
818
      boolean allowed = false;
819
      
820
      // must have a session in order to check admin 
821
      if (session == null) {
822
         logMetacat.debug("In isAdminAuthorized(), session is null ");
823
         return false;
824
      }
825
      
826
      logMetacat.debug("In isAdminAuthorized(), checking CN or MN authorization for " +
827
           session.getSubject().getValue());
828
      
829
      // check if this is the node calling itself (MN)
830
      allowed = isNodeAdmin(session);
831
      
832
      // check the CN list
833
      if (!allowed) {
834
	      List<Node> nodes = null;
835

    
836
    	  try {
837
		      // are we allowed to do this? only CNs are allowed
838
		      CNode cn = D1Client.getCN();
839
		      nodes = cn.listNodes().getNodeList();
840
    	  }
841
	      catch (Throwable e) {
842
	    	  logMetacat.warn(e.getMessage());
843
	    	  return false;  
844
	      }
845
		      
846
	      if ( nodes == null ) {
847
	    	  return false;
848
	          //throw new ServiceFailure("4852", "Couldn't get node list.");
849
	      }
850
	      
851
	      // find the node in the node list
852
	      for ( Node node : nodes ) {
853
	          
854
	          NodeReference nodeReference = node.getIdentifier();
855
	          logMetacat.debug("In isAdminAuthorized(), Node reference is: " + nodeReference.getValue());
856
	          
857
	          Subject subject = session.getSubject();
858
	          
859
	          if (node.getType() == NodeType.CN) {
860
	              List<Subject> nodeSubjects = node.getSubjectList();
861
	              
862
	              // check if the session subject is in the node subject list
863
	              for (Subject nodeSubject : nodeSubjects) {
864
	                  logMetacat.debug("In isAdminAuthorized(), comparing subjects: " +
865
	                      nodeSubject.getValue() + " and " + subject.getValue());
866
	                  if ( nodeSubject.equals(subject) ) {
867
	                      allowed = true; // subject of session == target node subject
868
	                      break;
869
	                      
870
	                  }
871
	              }              
872
	          }
873
	      }
874
      }
875
      
876
      return allowed;
877
  }
878
  
879
  /**
880
   * Test if the user identified by the provided token has administrative authorization 
881
   * on this node because they are calling themselves
882
   * 
883
   * @param session - the Session object containing the credentials for the Subject
884
   * 
885
   * @return true if the user is this node
886
   * @throws ServiceFailure 
887
   * @throws NotImplemented 
888
   */
889
  public boolean isNodeAdmin(Session session) throws NotImplemented, ServiceFailure {
890

    
891
      boolean allowed = false;
892
      
893
      // must have a session in order to check admin 
894
      if (session == null) {
895
         logMetacat.debug("In isNodeAdmin(), session is null ");
896
         return false;
897
      }
898
      
899
      logMetacat.debug("In isNodeAdmin(), MN authorization for " +
900
           session.getSubject().getValue());
901
      
902
      Node node = MNodeService.getInstance(request).getCapabilities();
903
      NodeReference nodeReference = node.getIdentifier();
904
      logMetacat.debug("In isNodeAdmin(), Node reference is: " + nodeReference.getValue());
905
      
906
      Subject subject = session.getSubject();
907
      
908
      if (node.getType() == NodeType.MN) {
909
          List<Subject> nodeSubjects = node.getSubjectList();
910
          
911
          // check if the session subject is in the node subject list
912
          for (Subject nodeSubject : nodeSubjects) {
913
              logMetacat.debug("In isNodeAdmin(), comparing subjects: " +
914
                  nodeSubject.getValue() + " and " + subject.getValue());
915
              if ( nodeSubject.equals(subject) ) {
916
                  allowed = true; // subject of session == this node's subect
917
                  break;
918
              }
919
          }              
920
      }
921
      
922
      return allowed;
923
  }
924
  
925
  /**
926
   * Test if the user identified by the provided token has authorization 
927
   * for the operation on the specified object.
928
   * 
929
   * @param session - the Session object containing the credentials for the Subject
930
   * @param pid - The identifer of the resource for which access is being checked
931
   * @param operation - The type of operation which is being requested for the given pid
932
   *
933
   * @return true if the operation is allowed
934
   * 
935
   * @throws ServiceFailure
936
   * @throws InvalidToken
937
   * @throws NotFound
938
   * @throws NotAuthorized
939
   * @throws NotImplemented
940
   * @throws InvalidRequest
941
   */
942
  public boolean isAuthorized(Session session, Identifier pid, Permission permission)
943
    throws ServiceFailure, InvalidToken, NotFound, NotAuthorized,
944
    NotImplemented, InvalidRequest {
945

    
946
    boolean allowed = false;
947
    
948
    if (permission == null) {
949
    	throw new InvalidRequest("1761", "Permission was not provided or is invalid");
950
    }
951
    
952
    // permissions are hierarchical
953
    List<Permission> expandedPermissions = null;
954
    
955
    // always allow CN access
956
    if ( isAdminAuthorized(session) ) {
957
        allowed = true;
958
        return allowed;
959
        
960
    }
961
    
962
    // the authoritative member node of the pid always has the access as well.
963
    if (isAuthoritativeMNodeAdmin(session, pid)) {
964
        allowed = true;
965
        return allowed;
966
    }
967
    
968
    // get the subject[s] from the session
969
	//defer to the shared util for recursively compiling the subjects	
970
	Set<Subject> subjects = AuthUtils.authorizedClientSubjects(session);
971
    
972
	// track the identities we have checked against
973
	StringBuffer includedSubjects = new StringBuffer();
974
    	
975
    // get the system metadata
976
    String pidStr = pid.getValue();
977
    SystemMetadata systemMetadata = null;
978
    try {
979
        systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
980

    
981
    } catch (Exception e) {
982
        // convert Hazelcast RuntimeException to NotFound
983
        logMetacat.error("An error occurred while getting system metadata for identifier " +
984
            pid.getValue() + ". The error message was: " + e.getMessage());
985
        throw new NotFound("1800", "No record found for " + pidStr);
986
        
987
    } 
988
    
989
    // throw not found if it was not found
990
    if (systemMetadata == null) {
991
    	throw new NotFound("1800", "No system metadata could be found for given PID: " + pidStr);
992
    }
993
	    
994
    // do we own it?
995
    for (Subject s: subjects) {
996
      logMetacat.debug("Comparing \t" + 
997
                       systemMetadata.getRightsHolder().getValue() +
998
                       " \tagainst \t" + s.getValue());
999
      	includedSubjects.append(s.getValue() + "; ");
1000
    	allowed = systemMetadata.getRightsHolder().equals(s);
1001
    	if (allowed) {
1002
    		return allowed;
1003
    	}
1004
    }    
1005
    
1006
    // otherwise check the access rules
1007
    try {
1008
	    List<AccessRule> allows = systemMetadata.getAccessPolicy().getAllowList();
1009
	    search: // label break
1010
	    for (AccessRule accessRule: allows) {
1011
	      for (Subject s: subjects) {
1012
	        logMetacat.debug("Checking allow access rule for subject: " + s.getValue());
1013
	        if (accessRule.getSubjectList().contains(s)) {
1014
	        	logMetacat.debug("Access rule contains subject: " + s.getValue());
1015
	        	for (Permission p: accessRule.getPermissionList()) {
1016
		        	logMetacat.debug("Checking permission: " + p.xmlValue());
1017
	        		expandedPermissions = expandPermissions(p);
1018
	        		allowed = expandedPermissions.contains(permission);
1019
	        		if (allowed) {
1020
			        	logMetacat.info("Permission granted: " + p.xmlValue() + " to " + s.getValue());
1021
	        			break search; //label break
1022
	        		}
1023
	        	}
1024
        		
1025
	        }
1026
	      }
1027
	    }
1028
    } catch (Exception e) {
1029
    	// catch all for errors - safe side should be to deny the access
1030
    	logMetacat.error("Problem checking authorization - defaulting to deny", e);
1031
		allowed = false;
1032
	  
1033
    }
1034
    
1035
    // throw or return?
1036
    if (!allowed) {
1037
      throw new NotAuthorized("1820", permission + " not allowed on " + pidStr + " for subject[s]: " + includedSubjects.toString() );
1038
    }
1039
    
1040
    return allowed;
1041
    
1042
  }
1043
  
1044
  /*
1045
   * parse a logEntry and get the relevant field from it
1046
   * 
1047
   * @param fieldname
1048
   * @param entry
1049
   * @return
1050
   */
1051
  private String getLogEntryField(String fieldname, String entry) {
1052
    String begin = "<" + fieldname + ">";
1053
    String end = "</" + fieldname + ">";
1054
    // logMetacat.debug("looking for " + begin + " and " + end +
1055
    // " in entry " + entry);
1056
    String s = entry.substring(entry.indexOf(begin) + begin.length(), entry
1057
        .indexOf(end));
1058
    logMetacat.debug("entry " + fieldname + " : " + s);
1059
    return s;
1060
  }
1061

    
1062
  /** 
1063
   * Determine if a given object should be treated as an XML science metadata
1064
   * object. 
1065
   * 
1066
   * @param sysmeta - the SystemMetadata describing the object
1067
   * @return true if the object should be treated as science metadata
1068
   */
1069
  public static boolean isScienceMetadata(SystemMetadata sysmeta) {
1070
    
1071
    ObjectFormat objectFormat = null;
1072
    boolean isScienceMetadata = false;
1073
    
1074
    try {
1075
      objectFormat = ObjectFormatCache.getInstance().getFormat(sysmeta.getFormatId());
1076
      if ( objectFormat.getFormatType().equals("METADATA") ) {
1077
      	isScienceMetadata = true;
1078
      	
1079
      }
1080
      
1081
       
1082
    } catch (ServiceFailure e) {
1083
      logMetacat.debug("There was a problem determining if the object identified by" + 
1084
          sysmeta.getIdentifier().getValue() + 
1085
          " is science metadata: " + e.getMessage());
1086
    
1087
    } catch (NotFound e) {
1088
      logMetacat.debug("There was a problem determining if the object identified by" + 
1089
          sysmeta.getIdentifier().getValue() + 
1090
          " is science metadata: " + e.getMessage());
1091
    
1092
    }
1093
    
1094
    return isScienceMetadata;
1095

    
1096
  }
1097
  
1098
  /**
1099
   * Check fro whitespace in the given pid.
1100
   * null pids are also invalid by default
1101
   * @param pid
1102
   * @return
1103
   */
1104
  public static boolean isValidIdentifier(Identifier pid) {
1105
	  if (pid != null && pid.getValue() != null && pid.getValue().length() > 0) {
1106
		  return !pid.getValue().matches(".*\\s+.*");
1107
	  } 
1108
	  return false;
1109
  }
1110
  
1111
  
1112
  /**
1113
   * Insert or update an XML document into Metacat
1114
   * 
1115
   * @param xml - the XML document to insert or update
1116
   * @param pid - the identifier to be used for the resulting object
1117
   * 
1118
   * @return localId - the resulting docid of the document created or updated
1119
   * 
1120
   */
1121
  public String insertOrUpdateDocument(String xml, Identifier pid, 
1122
    Session session, String insertOrUpdate) 
1123
    throws ServiceFailure {
1124
    
1125
  	logMetacat.debug("Starting to insert xml document...");
1126
    IdentifierManager im = IdentifierManager.getInstance();
1127

    
1128
    // generate pid/localId pair for sysmeta
1129
    String localId = null;
1130
    
1131
    if(insertOrUpdate.equals("insert")) {
1132
      localId = im.generateLocalId(pid.getValue(), 1);
1133
      
1134
    } else {
1135
      //localid should already exist in the identifier table, so just find it
1136
      try {
1137
        logMetacat.debug("Updating pid " + pid.getValue());
1138
        logMetacat.debug("looking in identifier table for pid " + pid.getValue());
1139
        
1140
        localId = im.getLocalId(pid.getValue());
1141
        
1142
        logMetacat.debug("localId: " + localId);
1143
        //increment the revision
1144
        String docid = localId.substring(0, localId.lastIndexOf("."));
1145
        String revS = localId.substring(localId.lastIndexOf(".") + 1, localId.length());
1146
        int rev = new Integer(revS).intValue();
1147
        rev++;
1148
        docid = docid + "." + rev;
1149
        localId = docid;
1150
        logMetacat.debug("incremented localId: " + localId);
1151
      
1152
      } catch(McdbDocNotFoundException e) {
1153
        throw new ServiceFailure("1030", "D1NodeService.insertOrUpdateDocument(): " +
1154
            "pid " + pid.getValue() + 
1155
            " should have been in the identifier table, but it wasn't: " + 
1156
            e.getMessage());
1157
      
1158
      }
1159
      
1160
    }
1161

    
1162
    params = new Hashtable<String, String[]>();
1163
    String[] action = new String[1];
1164
    action[0] = insertOrUpdate;
1165
    params.put("action", action);
1166
    String[] docid = new String[1];
1167
    docid[0] = localId;
1168
    params.put("docid", docid);
1169
    String[] doctext = new String[1];
1170
    doctext[0] = xml;
1171
    params.put("doctext", doctext);
1172
    
1173
    String username = Constants.SUBJECT_PUBLIC;
1174
    String[] groupnames = null;
1175
    if (session != null ) {
1176
    	username = session.getSubject().getValue();
1177
    	if (session.getSubjectInfo() != null) {
1178
    		List<Group> groupList = session.getSubjectInfo().getGroupList();
1179
    		if (groupList != null) {
1180
    			groupnames = new String[groupList.size()];
1181
    			for (int i = 0; i < groupList.size(); i++ ) {
1182
    				groupnames[i] = groupList.get(i).getGroupName();
1183
    			}
1184
    		}
1185
    	}
1186
    }
1187
    
1188
    // do the insert or update action
1189
    handler = new MetacatHandler(new Timer());
1190
    String result = handler.handleInsertOrUpdateAction(request.getRemoteAddr(), request.getHeader("User-Agent"), null, 
1191
                        null, params, username, groupnames, false, false);
1192
    
1193
    if(result.indexOf("<error>") != -1) {
1194
    	String detailCode = "";
1195
    	if ( insertOrUpdate.equals("insert") ) {
1196
    		// make sure to remove the mapping so that subsequent attempts do not fail with IdentifierNotUnique
1197
    		im.removeMapping(pid.getValue(), localId);
1198
    		detailCode = "1190";
1199
    		
1200
    	} else if ( insertOrUpdate.equals("update") ) {
1201
    		detailCode = "1310";
1202
    		
1203
    	}
1204
        throw new ServiceFailure(detailCode, 
1205
          "Error inserting or updating document: " + result);
1206
    }
1207
    logMetacat.debug("Finsished inserting xml document with id " + localId);
1208
    
1209
    return localId;
1210
  }
1211
  
1212
  /**
1213
   * Insert a data document
1214
   * 
1215
   * @param object
1216
   * @param pid
1217
   * @param sessionData
1218
   * @throws ServiceFailure
1219
   * @returns localId of the data object inserted
1220
   */
1221
  public String insertDataObject(InputStream object, Identifier pid, 
1222
          Session session) throws ServiceFailure {
1223
      
1224
    String username = Constants.SUBJECT_PUBLIC;
1225
    String[] groupnames = null;
1226
    if (session != null ) {
1227
    	username = session.getSubject().getValue();
1228
    	if (session.getSubjectInfo() != null) {
1229
    		List<Group> groupList = session.getSubjectInfo().getGroupList();
1230
    		if (groupList != null) {
1231
    			groupnames = new String[groupList.size()];
1232
    			for (int i = 0; i < groupList.size(); i++ ) {
1233
    				groupnames[i] = groupList.get(i).getGroupName();
1234
    			}
1235
    		}
1236
    	}
1237
    }
1238
  
1239
    // generate pid/localId pair for object
1240
    logMetacat.debug("Generating a pid/localId mapping");
1241
    IdentifierManager im = IdentifierManager.getInstance();
1242
    String localId = im.generateLocalId(pid.getValue(), 1);
1243
  
1244
    // Save the data file to disk using "localId" as the name
1245
    String datafilepath = null;
1246
	try {
1247
		datafilepath = PropertyService.getProperty("application.datafilepath");
1248
	} catch (PropertyNotFoundException e) {
1249
		ServiceFailure sf = new ServiceFailure("1190", "Lookup data file path" + e.getMessage());
1250
		sf.initCause(e);
1251
		throw sf;
1252
	}
1253
    boolean locked = false;
1254
	try {
1255
		locked = DocumentImpl.getDataFileLockGrant(localId);
1256
	} catch (Exception e) {
1257
		ServiceFailure sf = new ServiceFailure("1190", "Could not lock file for writing:" + e.getMessage());
1258
		sf.initCause(e);
1259
		throw sf;
1260
	}
1261

    
1262
    logMetacat.debug("Case DATA: starting to write to disk.");
1263
	if (locked) {
1264

    
1265
          File dataDirectory = new File(datafilepath);
1266
          dataDirectory.mkdirs();
1267
  
1268
          File newFile = writeStreamToFile(dataDirectory, localId, object);
1269
  
1270
          // TODO: Check that the file size matches SystemMetadata
1271
          // long size = newFile.length();
1272
          // if (size == 0) {
1273
          //     throw new IOException("Uploaded file is 0 bytes!");
1274
          // }
1275
  
1276
          // Register the file in the database (which generates an exception
1277
          // if the localId is not acceptable or other untoward things happen
1278
          try {
1279
            logMetacat.debug("Registering document...");
1280
            DocumentImpl.registerDocument(localId, "BIN", localId,
1281
                    username, groupnames);
1282
            logMetacat.debug("Registration step completed.");
1283
            
1284
          } catch (SQLException e) {
1285
            //newFile.delete();
1286
            logMetacat.debug("SQLE: " + e.getMessage());
1287
            e.printStackTrace(System.out);
1288
            throw new ServiceFailure("1190", "Registration failed: " + 
1289
            		e.getMessage());
1290
            
1291
          } catch (AccessionNumberException e) {
1292
            //newFile.delete();
1293
            logMetacat.debug("ANE: " + e.getMessage());
1294
            e.printStackTrace(System.out);
1295
            throw new ServiceFailure("1190", "Registration failed: " + 
1296
            	e.getMessage());
1297
            
1298
          } catch (Exception e) {
1299
            //newFile.delete();
1300
            logMetacat.debug("Exception: " + e.getMessage());
1301
            e.printStackTrace(System.out);
1302
            throw new ServiceFailure("1190", "Registration failed: " + 
1303
            	e.getMessage());
1304
          }
1305
  
1306
          logMetacat.debug("Logging the creation event.");
1307
          EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), username, localId, "create");
1308
  
1309
          // Schedule replication for this data file, the "insert" action is important here!
1310
          logMetacat.debug("Scheduling replication.");
1311
          ForceReplicationHandler frh = new ForceReplicationHandler(localId, "insert", false, null);
1312
      }
1313
      
1314
      return localId;
1315
    
1316
  }
1317

    
1318
  /**
1319
   * Insert a systemMetadata document and return its localId
1320
   */
1321
  public void insertSystemMetadata(SystemMetadata sysmeta) 
1322
      throws ServiceFailure {
1323
      
1324
  	  logMetacat.debug("Starting to insert SystemMetadata...");
1325
      sysmeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
1326
      logMetacat.debug("Inserting new system metadata with modified date " + 
1327
          sysmeta.getDateSysMetadataModified());
1328
      
1329
      //insert the system metadata
1330
      try {
1331
        // note: the calling subclass handles the map hazelcast lock/unlock
1332
      	HazelcastService.getInstance().getSystemMetadataMap().put(sysmeta.getIdentifier(), sysmeta);
1333
      	// submit for indexing
1334
        MetacatSolrIndex.getInstance().submit(sysmeta.getIdentifier(), sysmeta, null, true);
1335
      } catch (Exception e) {
1336
          throw new ServiceFailure("1190", e.getMessage());
1337
          
1338
	    }  
1339
  }
1340

    
1341
  /**
1342
   * Update a systemMetadata document
1343
   * 
1344
   * @param sysMeta - the system metadata object in the system to update
1345
   */
1346
    protected void updateSystemMetadata(SystemMetadata sysMeta)
1347
        throws ServiceFailure {
1348

    
1349
        logMetacat.debug("D1NodeService.updateSystemMetadata() called.");
1350
        sysMeta.setDateSysMetadataModified(new Date());
1351
        try {
1352
            HazelcastService.getInstance().getSystemMetadataMap().lock(sysMeta.getIdentifier());
1353
            HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);
1354
            // submit for indexing
1355
            MetacatSolrIndex.getInstance().submit(sysMeta.getIdentifier(), sysMeta, null, true);
1356
        } catch (Exception e) {
1357
            throw new ServiceFailure("4862", e.getMessage());
1358

    
1359
        } finally {
1360
            HazelcastService.getInstance().getSystemMetadataMap().unlock(sysMeta.getIdentifier());
1361

    
1362
        }
1363

    
1364
    }
1365
    
1366
	public boolean updateSystemMetadata(Session session, Identifier pid,
1367
			SystemMetadata sysmeta) throws NotImplemented, NotAuthorized,
1368
			ServiceFailure, InvalidRequest, InvalidSystemMetadata, InvalidToken {
1369
		
1370
		// The lock to be used for this identifier
1371
      Lock lock = null;
1372

    
1373
      // TODO: control who can call this?
1374
      if (session == null) {
1375
          //TODO: many of the thrown exceptions do not use the correct error codes
1376
          //check these against the docs and correct them
1377
          throw new NotAuthorized("4861", "No Session - could not authorize for registration." +
1378
                  "  If you are not logged in, please do so and retry the request.");
1379
      }
1380
      
1381
      // verify that guid == SystemMetadata.getIdentifier()
1382
      logMetacat.debug("Comparing guid|sysmeta_guid: " + pid.getValue() + 
1383
          "|" + sysmeta.getIdentifier().getValue());
1384
      
1385
      if (!pid.getValue().equals(sysmeta.getIdentifier().getValue())) {
1386
          throw new InvalidRequest("4863", 
1387
              "The identifier in method call (" + pid.getValue() + 
1388
              ") does not match identifier in system metadata (" +
1389
              sysmeta.getIdentifier().getValue() + ").");
1390
      }
1391

    
1392
      // do the actual update
1393
      this.updateSystemMetadata(sysmeta);
1394
      
1395
      try {
1396
    	  String localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
1397
    	  EventLog.getInstance().log(request.getRemoteAddr(), 
1398
    	          request.getHeader("User-Agent"), session.getSubject().getValue(), 
1399
    	          localId, "updateSystemMetadata");
1400
      } catch (McdbDocNotFoundException e) {
1401
    	  // do nothing, no localId to log with
1402
    	  logMetacat.warn("Could not log 'updateSystemMetadata' event because no localId was found for pid: " + pid.getValue());
1403
      }
1404
      
1405
      return true;
1406
	}
1407
  
1408
  /**
1409
   * Given a Permission, returns a list of all permissions that it encompasses
1410
   * Permissions are hierarchical so that WRITE also allows READ.
1411
   * @param permission
1412
   * @return list of included Permissions for the given permission
1413
   */
1414
  protected List<Permission> expandPermissions(Permission permission) {
1415
	  	List<Permission> expandedPermissions = new ArrayList<Permission>();
1416
	    if (permission.equals(Permission.READ)) {
1417
	    	expandedPermissions.add(Permission.READ);
1418
	    }
1419
	    if (permission.equals(Permission.WRITE)) {
1420
	    	expandedPermissions.add(Permission.READ);
1421
	    	expandedPermissions.add(Permission.WRITE);
1422
	    }
1423
	    if (permission.equals(Permission.CHANGE_PERMISSION)) {
1424
	    	expandedPermissions.add(Permission.READ);
1425
	    	expandedPermissions.add(Permission.WRITE);
1426
	    	expandedPermissions.add(Permission.CHANGE_PERMISSION);
1427
	    }
1428
	    return expandedPermissions;
1429
  }
1430

    
1431
  /*
1432
   * Write a stream to a file
1433
   * 
1434
   * @param dir - the directory to write to
1435
   * @param fileName - the file name to write to
1436
   * @param data - the object bytes as an input stream
1437
   * 
1438
   * @return newFile - the new file created
1439
   * 
1440
   * @throws ServiceFailure
1441
   */
1442
  private File writeStreamToFile(File dir, String fileName, InputStream data) 
1443
    throws ServiceFailure {
1444
    
1445
    File newFile = new File(dir, fileName);
1446
    logMetacat.debug("Filename for write is: " + newFile.getAbsolutePath());
1447

    
1448
    try {
1449
        if (newFile.createNewFile()) {
1450
          // write data stream to desired file
1451
          OutputStream os = new FileOutputStream(newFile);
1452
          long length = IOUtils.copyLarge(data, os);
1453
          os.flush();
1454
          os.close();
1455
        } else {
1456
          logMetacat.debug("File creation failed, or file already exists.");
1457
          throw new ServiceFailure("1190", "File already exists: " + fileName);
1458
        }
1459
    } catch (FileNotFoundException e) {
1460
      logMetacat.debug("FNF: " + e.getMessage());
1461
      throw new ServiceFailure("1190", "File not found: " + fileName + " " 
1462
                + e.getMessage());
1463
    } catch (IOException e) {
1464
      logMetacat.debug("IOE: " + e.getMessage());
1465
      throw new ServiceFailure("1190", "File was not written: " + fileName 
1466
                + " " + e.getMessage());
1467
    }
1468

    
1469
    return newFile;
1470
  }
1471

    
1472
  /*
1473
   * Returns a list of nodes that have been registered with the DataONE infrastructure
1474
   * that match the given session subject
1475
   * @return nodes - List of nodes from the registry with a matching session subject
1476
   * 
1477
   * @throws ServiceFailure
1478
   * @throws NotImplemented
1479
   */
1480
  protected List<Node> listNodesBySubject(Subject subject) 
1481
      throws ServiceFailure, NotImplemented {
1482
      List<Node> nodeList = new ArrayList<Node>();
1483
      
1484
      CNode cn = D1Client.getCN();
1485
      List<Node> nodes = cn.listNodes().getNodeList();
1486
      
1487
      // find the node in the node list
1488
      for ( Node node : nodes ) {
1489
          
1490
          List<Subject> nodeSubjects = node.getSubjectList();
1491
          if (nodeSubjects != null) {    
1492
	          // check if the session subject is in the node subject list
1493
	          for (Subject nodeSubject : nodeSubjects) {
1494
	              if ( nodeSubject.equals(subject) ) { // subject of session == node subject
1495
	                  nodeList.add(node);  
1496
	              }                              
1497
	          }
1498
          }
1499
      }
1500
      
1501
      return nodeList;
1502
      
1503
  }
1504

    
1505
  /**
1506
   * Archives an object, where the object is either a 
1507
   * data object or a science metadata object.
1508
   * 
1509
   * @param session - the Session object containing the credentials for the Subject
1510
   * @param pid - The object identifier to be archived
1511
   * 
1512
   * @return pid - the identifier of the object used for the archiving
1513
   * 
1514
   * @throws InvalidToken
1515
   * @throws ServiceFailure
1516
   * @throws NotAuthorized
1517
   * @throws NotFound
1518
   * @throws NotImplemented
1519
   * @throws InvalidRequest
1520
   */
1521
  public Identifier archive(Session session, Identifier pid) 
1522
      throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
1523

    
1524
      String localId = null;
1525
      boolean allowed = false;
1526
      String username = Constants.SUBJECT_PUBLIC;
1527
      String[] groupnames = null;
1528
      if (session == null) {
1529
      	throw new InvalidToken("1330", "No session has been provided");
1530
      } else {
1531
          username = session.getSubject().getValue();
1532
          if (session.getSubjectInfo() != null) {
1533
              List<Group> groupList = session.getSubjectInfo().getGroupList();
1534
              if (groupList != null) {
1535
                  groupnames = new String[groupList.size()];
1536
                  for (int i = 0; i < groupList.size(); i++) {
1537
                      groupnames[i] = groupList.get(i).getGroupName();
1538
                  }
1539
              }
1540
          }
1541
      }
1542

    
1543
      // do we have a valid pid?
1544
      if (pid == null || pid.getValue().trim().equals("")) {
1545
          throw new ServiceFailure("1350", "The provided identifier was invalid.");
1546
      }
1547

    
1548
      // check for the existing identifier
1549
      try {
1550
          localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
1551
      } catch (McdbDocNotFoundException e) {
1552
          throw new NotFound("1340", "The object with the provided " + "identifier was not found.");
1553
      }
1554

    
1555
      // does the subject have archive (a D1 CHANGE_PERMISSION level) privileges on the pid?
1556
      try {
1557
			allowed = isAuthorized(session, pid, Permission.CHANGE_PERMISSION);
1558
		} catch (InvalidRequest e) {
1559
          throw new ServiceFailure("1350", e.getDescription());
1560
		}
1561
          
1562

    
1563
      if (allowed) {
1564
          try {
1565
              // archive the document
1566
              DocumentImpl.delete(localId, null, null, null, false);
1567
              EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), username, localId, Event.DELETE.xmlValue());
1568

    
1569
              // archive it
1570
              SystemMetadata sysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
1571
              sysMeta.setArchived(true);
1572
              sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
1573
              HazelcastService.getInstance().getSystemMetadataMap().put(pid, sysMeta);
1574
              // submit for indexing
1575
              // DocumentImpl call above should do this.
1576
              // see: https://projects.ecoinformatics.org/ecoinfo/issues/6030
1577
              //HazelcastService.getInstance().getIndexQueue().add(sysMeta);
1578
              
1579
          } catch (McdbDocNotFoundException e) {
1580
              throw new NotFound("1340", "The provided identifier was invalid.");
1581

    
1582
          } catch (SQLException e) {
1583
              throw new ServiceFailure("1350", "There was a problem archiving the object." + "The error message was: " + e.getMessage());
1584

    
1585
          } catch (InsufficientKarmaException e) {
1586
              throw new NotAuthorized("1320", "The provided identity does not have " + "permission to archive this object.");
1587

    
1588
          } catch (Exception e) { // for some reason DocumentImpl throws a general Exception
1589
              throw new ServiceFailure("1350", "There was a problem archiving the object." + "The error message was: " + e.getMessage());
1590
          }
1591

    
1592
      } else {
1593
          throw new NotAuthorized("1320", "The provided identity does not have " + "permission to archive the object on the Node.");
1594
      }
1595

    
1596
      return pid;
1597
  }
1598

    
1599

    
1600
}
(2-2/7)