Metacat

/**

 *  '$RCSfile$'

 *  Copyright: 2000-2011 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *

 *   '$Author:  $'

 *     '$Date:  $'

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat.dataone;

import java.util.Date;

import java.util.List;

import org.apache.log4j.Logger;

import org.dataone.service.cn.CNAuthorization;

import org.dataone.service.cn.CNCore;

import org.dataone.service.cn.CNRead;

import org.dataone.service.cn.CNReplication;

import org.dataone.service.exceptions.IdentifierNotUnique;

import org.dataone.service.exceptions.InsufficientResources;

import org.dataone.service.exceptions.InvalidRequest;

import org.dataone.service.exceptions.InvalidSystemMetadata;

import org.dataone.service.exceptions.InvalidToken;

import org.dataone.service.exceptions.NotAuthorized;

import org.dataone.service.exceptions.NotFound;

import org.dataone.service.exceptions.NotImplemented;

import org.dataone.service.exceptions.ServiceFailure;

import org.dataone.service.types.Checksum;

import org.dataone.service.types.Identifier;

import org.dataone.service.types.NodeList;

import org.dataone.service.types.ObjectFormat;

import org.dataone.service.types.ObjectFormatIdentifier;

import org.dataone.service.types.ObjectFormatList;

import org.dataone.service.types.ObjectList;

import org.dataone.service.types.ObjectLocationList;

import org.dataone.service.types.Permission;

import org.dataone.service.types.QueryType;

import org.dataone.service.types.Replica;

import org.dataone.service.types.ReplicationPolicy;

import org.dataone.service.types.ReplicationStatus;

import org.dataone.service.types.Session;

import org.dataone.service.types.Subject;

import org.dataone.service.types.SystemMetadata;

import edu.ucsb.nceas.metacat.EventLog;

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.replication.ForceReplicationSystemMetadataHandler;

/**

 * Represents Metacat's implementation of the DataONE Coordinating Node 

 * service API. Methods implement the various CN* interfaces, and methods common

 * to both Member Node and Coordinating Node interfaces are found in the

 * D1NodeService super class.

 *

 */

public class CNodeService extends D1NodeService implements CNAuthorization,

    CNCore, CNRead, CNReplication {

	/* the instance of the CNodeService object */

  private static CNodeService instance = null;

  /* the logger instance */

  private Logger logMetacat = null;

  /**

   * singleton accessor

   */

  public static CNodeService getInstance() { 

    if (instance == null) {

      instance = new CNodeService();

    }

    return instance;

  }

  /**

   * Constructor, private for singleton access

   */

  private CNodeService() {

  	super();

    logMetacat = Logger.getLogger(CNodeService.class);

  }

	/**

	 * Set the replication policy for an object given the object identifier

	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param pid - the object identifier for the given object

	 * @param policy - the replication policy to be applied

	 * 

	 * @return true or false

	 * 

	 * @throws NotImplemented

	 * @throws NotAuthorized

	 * @throws ServiceFailure

	 * @throws InvalidRequest

	 * 

	 */

	@Override

	public boolean setReplicationPolicy(Session session, Identifier pid,

	  ReplicationPolicy policy) 

	  throws NotImplemented, NotFound, NotAuthorized, ServiceFailure, InvalidRequest, InvalidToken {

		// get the subject

		Subject subject = session.getSubject();

		// get the system metadata

		String guid = pid.getValue();

		// are we allowed to do this?

		if (!isAuthorized(session, pid, Permission.CHANGE_PERMISSION)) {

			throw new NotAuthorized("4881", Permission.CHANGE_PERMISSION + " not allowed by " + subject.getValue() + " on " + guid);	

		}

		SystemMetadata systemMetadata = null;

		try {

			systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);

		} catch (McdbDocNotFoundException e) {

			throw new NotFound("4884", "No record found for: " + guid);

		}

		// set the new policy

		systemMetadata.setReplicationPolicy(policy);

		// update the metadata

		try {

			IdentifierManager.getInstance().updateSystemMetadata(systemMetadata);

		} catch (McdbDocNotFoundException e) {

			throw new ServiceFailure("4882", e.getMessage());

		}

		return true;

	}

	/**

	 * Set the replication status for an object given the object identifier

	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param pid - the object identifier for the given object

	 * @param status - the replication status to be applied

	 * 

	 * @return true or false

	 * 

	 * @throws NotImplemented

	 * @throws NotAuthorized

	 * @throws ServiceFailure

	 * @throws InvalidRequest

	 * @throws InvalidToken

	 * @throws NotFound

	 * 

	 */

	@Override

	public boolean setReplicationStatus(Session session, Identifier pid,

	  ReplicationStatus status) 

	  throws ServiceFailure, NotImplemented, InvalidToken, NotAuthorized, 

	  InvalidRequest, NotFound {

		// get the subject

		Subject subject = session.getSubject();

		// get the system metadata

		String guid = pid.getValue();

		// are we allowed to do this?

		if (!isAuthorized(session, pid, Permission.WRITE)) {

			throw new NotAuthorized("4720", Permission.WRITE + " not allowed by " + subject.getValue() + " on " + guid);	

		}

		SystemMetadata systemMetadata = null;

		try {

			systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);

		} catch (McdbDocNotFoundException e) {

			throw new NotFound("4740", "No record found for: " + guid);

		}

		// set the status for each replica

		// TODO: should this method select a certain replica?

		List<Replica> replicas = systemMetadata.getReplicaList();

		for (Replica replica: replicas) {

			replica.setReplicationStatus(status);

		}

		// [re]set the list -- redundant?

		systemMetadata.setReplicaList(replicas);

		// update the metadata

		try {

			IdentifierManager.getInstance().updateSystemMetadata(systemMetadata);

		} catch (McdbDocNotFoundException e) {

			throw new ServiceFailure("4700", e.getMessage());

		}

		return true;

	}

	/**

	 * Test that the specified relationship between pidOfSubject and pidOfObject exists

	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param node - the node information for the given node be modified

	 * 

	 * @return true if the relationship exists

	 * 

	 * @throws InvalidToken

	 * @throws ServiceFailure

	 * @throws NotAuthorized

	 * @throws NotFound

	 * @throws InvalidRequest

	 * @throws NotImplemented

	 */

	@Override

	public boolean assertRelation(Session session, Identifier pidOfSubject, 

		String relationship, Identifier pidOfObject) 

	  throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 

	  InvalidRequest, NotImplemented {

		// get the system metadata

		String guid1 = pidOfSubject.getValue();

		// are we allowed to do this?

		if (!isAuthorized(session, pidOfSubject, Permission.READ)) {

			throw new NotAuthorized("4881", Permission.READ + " not allowed on " + guid1);	

		}

		SystemMetadata systemMetadata = null;

		try {

			systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid1);

		} catch (McdbDocNotFoundException e) {

			throw new NotFound("4884", "No record found for: " + guid1);

		}

		// check relationships

		// TODO: make this more strongly typed?

		if (relationship.equalsIgnoreCase("describes")) {

			for (Identifier pid: systemMetadata.getDescribeList()) {

				if (pid.getValue().equals(pidOfObject.getValue())) {

					return true;

				}

			}

			//return systemMetadata.getDescribeList().contains(pidOfObject);

		}

		if (relationship.equalsIgnoreCase("describedBy")) {

			for (Identifier pid: systemMetadata.getDescribedByList()) {

				if (pid.getValue().equals(pidOfObject.getValue())) {

					return true;

				}

			}

			//return systemMetadata.getDescribedByList().contains(pidOfObject);

		}

		if (relationship.equalsIgnoreCase("derivedFrom")) {

			for (Identifier pid: systemMetadata.getDerivedFromList()) {

				if (pid.getValue().equals(pidOfObject.getValue())) {

					return true;

				}

			}

			//return systemMetadata.getDerivedFromList().contains(pidOfObject);

		}

		if (relationship.equalsIgnoreCase("obsoletes")) {

			for (Identifier pid: systemMetadata.getObsoleteList()) {

				if (pid.getValue().equals(pidOfObject.getValue())) {

					return true;

				}

			}

			//return systemMetadata.getObsoleteList().contains(pidOfObject);

		}

		if (relationship.equalsIgnoreCase("obsoletedBy")) {

			for (Identifier pid: systemMetadata.getObsoletedByList()) {

				if (pid.getValue().equals(pidOfObject.getValue())) {

					return true;

				}

			}

			//return systemMetadata.getObsoletedByList().contains(pidOfObject);

		}

		return false;

	}

	/**

	 * Return the checksum of the object given the identifier 

	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param pid - the object identifier for the given object

	 * 

	 * @return checksum - the checksum of the object

	 * 

	 * @throws InvalidToken

	 * @throws ServiceFailure

	 * @throws NotAuthorized

	 * @throws NotFound

	 * @throws InvalidRequest

	 * @throws NotImplemented

	 */

	@Override

	public Checksum getChecksum(Session session, Identifier pid)

	  throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 

	  InvalidRequest, NotImplemented {

		if (!isAuthorized(session, pid, Permission.READ)) {

			throw new NotAuthorized("1400", Permission.READ + " not allowed on " + pid.getValue());	

		}

		SystemMetadata systemMetadata = null;

		try {

			systemMetadata = IdentifierManager.getInstance().getSystemMetadata(pid.getValue());

		} catch (McdbDocNotFoundException e) {

			throw new NotFound("1420", "No record found for: " + pid.getValue());

		}

		Checksum checksum = systemMetadata.getChecksum();

		return checksum;

	}

	/**

	 * Resolve the location of a given object

	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param pid - the object identifier for the given object

	 * 

	 * @return objectLocationList - the list of nodes known to contain the object

	 * 

	 * @throws InvalidRequest

	 * @throws InvalidToken

	 * @throws ServiceFailure

	 * @throws NotAuthorized

	 * @throws NotFound

	 * @throws NotImplemented

	 */

	@Override

	public ObjectLocationList resolve(Session session, Identifier pid)

	  throws InvalidRequest, InvalidToken, ServiceFailure, NotAuthorized,

	  NotFound, NotImplemented {

		throw new NotImplemented("4131", "resolve not implemented");

	}

	/**

	 * Search the metadata catalog for identifiers that match the criteria

	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param queryType - An identifier for the type of query expression 

	 *                    provided in the query

	 * @param query -  The criteria for matching the characteristics of the 

	 *                 metadata objects of interest

	 * 

	 * @return objectList - the list of objects matching the criteria

	 * 

	 * @throws InvalidToken

	 * @throws ServiceFailure

	 * @throws NotAuthorized

	 * @throws InvalidRequest

	 * @throws NotImplemented

	 */

	@Override

	public ObjectList search(Session session, QueryType queryType, String query)

	  throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,

	  NotImplemented {

		ObjectList objectList = null;

		try {

		    objectList = 

		    	IdentifierManager.getInstance().querySystemMetadata(

		    			null, //startTime, 

		    			null, //endTime,

		    			null, //objectFormat, 

		    			false, //replicaStatus, 

		    			0, //start, 

		    			-1 //count

		    			);

		} catch (Exception e) {

			throw new ServiceFailure("4310", "Error querying system metadata: " + e.getMessage());

		}

	    return objectList;

		//throw new NotImplemented("4281", "search not implemented");

		// the code block below is from an older implementation

		/*  This block commented out because of the EcoGrid circular dependency.

         *  For now, query will not be supported until the circularity can be

         *  resolved, probably by moving the ecogrid query syntax transformers

         *  directly into the Metacat codebase.  MBJ 2010-02-03

        try {

            EcogridQueryParser parser = new EcogridQueryParser(request

                    .getReader());

            parser.parseXML();

            QueryType queryType = parser.getEcogridQuery();

            EcogridJavaToMetacatJavaQueryTransformer queryTransformer = 

                new EcogridJavaToMetacatJavaQueryTransformer();

            QuerySpecification metacatQuery = queryTransformer

                    .transform(queryType);

            DBQuery metacat = new DBQuery();

            boolean useXMLIndex = (new Boolean(PropertyService

                    .getProperty("database.usexmlindex"))).booleanValue();

            String xmlquery = "query"; // we don't care the query in resultset,

            // the query can be anything

            PrintWriter out = null; // we don't want metacat result, so set out null

            // parameter: queryspecification, user, group, usingIndexOrNot

            StringBuffer result = metacat.createResultDocument(xmlquery,

                    metacatQuery, out, username, groupNames, useXMLIndex);

            // create result set transfer       

            String saxparser = PropertyService.getProperty("xml.saxparser");

            MetacatResultsetParser metacatResultsetParser = new MetacatResultsetParser(

                    new StringReader(result.toString()), saxparser, queryType

                            .getNamespace().get_value());

            ResultsetType records = metacatResultsetParser.getEcogridResult();

            System.out

                    .println(EcogridResultsetTransformer.toXMLString(records));

            response.setContentType("text/xml");

            out = response.getWriter();

            out.print(EcogridResultsetTransformer.toXMLString(records));

        } catch (Exception e) {

            e.printStackTrace();

        }*/

	}

	/**

	 * Returns the object format registered in the DataONE Object Format 

	 * Vocabulary for the given format identifier

	 * 

	 * @param fmtid - the identifier of the format requested

	 * 

	 * @return objectFormat - the object format requested

	 * 

	 * @throws InvalidRequest

	 * @throws ServiceFailure

	 * @throws NotFound

	 * @throws InsufficientResources

	 * @throws NotImplemented

	 */

	@Override

	public ObjectFormat getFormat(ObjectFormatIdentifier fmtid)

	  throws InvalidRequest, ServiceFailure, NotFound, InsufficientResources,

	  NotImplemented {

	  	return ObjectFormatService.getInstance().getFormat(fmtid);

	}

	/**

   * Returns a list of all object formats registered in the DataONE Object 

   * Format Vocabulary

 	 * 

	 * @return objectFormatList - The list of object formats registered in 

	 *                            the DataONE Object Format Vocabulary

	 * 

	 * @throws InvalidRequest

	 * @throws ServiceFailure

	 * @throws NotImplemented

	 * @throws NotFound

	 * @throws InsufficientResources

	 */

	@Override

	public ObjectFormatList listFormats() 

	  throws InvalidRequest, ServiceFailure, NotFound, InsufficientResources, 

	  NotImplemented {

		return ObjectFormatService.getInstance().listFormats();

	}

	/**

   * Returns a list of nodes that have been registered with the DataONE infrastructure

 	 * 

	 * @return nodeList - List of nodes from the registry

	 * 

	 * @throws ServiceFailure

	 * @throws NotImplemented

	 */

	@Override

	public NodeList listNodes() 

	  throws NotImplemented, ServiceFailure {

		throw new NotImplemented("4800", "listNodes not implemented");

	}

	/**

   * Provides a mechanism for adding system metadata independently of its 

   * associated object, such as when adding system metadata for data objects.

 	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param pid - The identifier of the object to register the system metadata against

	 * @param sysmeta - The system metadata to be registered

	 * 

	 * @return true if the registration succeeds

	 * 

	 * @throws NotImplemented

	 * @throws NotAuthorized

	 * @throws ServiceFailure

	 * @throws InvalidRequest

	 * @throws InvalidSystemMetadata

	 */

	@Override

	public boolean registerSystemMetadata(Session session, Identifier guid,

	  SystemMetadata sysmeta) 

	  throws NotImplemented, NotAuthorized, ServiceFailure, InvalidRequest, 

	  InvalidSystemMetadata {

		// TODO: control who can call this?

	      if (session == null) {

	          //TODO: many of the thrown exceptions do not use the correct error codes

	          //check these against the docs and correct them

	          throw new NotAuthorized("4861", "No Session - could not authorize for registration." +

	                  "  If you are not logged in, please do so and retry the request.");

	      }

	      // verify that guid == SystemMetadata.getIdentifier()

	      logMetacat.debug("Comparing guid|sysmeta_guid: " + guid.getValue() + "|" + sysmeta.getIdentifier().getValue());

	      if (!guid.getValue().equals(sysmeta.getIdentifier().getValue())) {

	          throw new InvalidRequest("4863", 

	              "GUID in method call (" + guid.getValue() + ") does not match GUID in system metadata (" +

	              sysmeta.getIdentifier().getValue() + ").");

	      }

	      logMetacat.debug("Checking if identifier exists...");

	      // Check that the identifier does not already exist

	      if (IdentifierManager.getInstance().identifierExists(guid.getValue())) {

			// check if we reserved the id

			boolean reserved = IdentifierManager.getInstance().hasReservation(guid, session);

			// throw an exception if not

			if (!reserved) {

	          throw new InvalidRequest("4863", 

	              "GUID is already in use by an existing object.");

			}

	      }

	      // insert the system metadata into the object store

	      logMetacat.debug("Starting to insert SystemMetadata...");

	      sysmeta.setDateSysMetadataModified(new Date());

	      try {

			    IdentifierManager.getInstance().createSystemMetadata(sysmeta);

			    // force replication of this record

			    ForceReplicationSystemMetadataHandler forceReplication = 

			    	new ForceReplicationSystemMetadataHandler(guid.getValue(), null);

		    } catch (Exception e) {

	          throw new ServiceFailure("4862", "Error inserting system metadata: " + e.getClass() + ": " + e.getMessage());

		    }

	      logMetacat.debug("Returning from registerSystemMetadata");

	      EventLog.getInstance().log(null, session.getSubject().getValue(), guid.getValue(), "registerSystemMetadata");

	      return true;

	}

	/**

   * Given an optional scope and format, reserves and returns an identifier 

   * within that scope and format that is unique and will not be 

   * used by any other sessions. 

 	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param pid - The identifier of the object to register the system metadata against

	 * @param scope - An optional string to be used to qualify the scope of 

	 *                the identifier namespace, which is applied differently 

	 *                depending on the format requested. If scope is not 

	 *                supplied, a default scope will be used.

	 * @param format - The optional name of the identifier format to be used, 

	 * 								 drawn from a DataONE-specific vocabulary of identifier 

	 *                 format names, including several common syntaxes such 

	 *                 as DOI, LSID, UUID, and LSRN, among others. If the 

	 *                 format is not supplied by the caller, the CN service 

	 *                 will use a default identifier format, which may change 

	 *                 over time.

	 * 

	 * @return true if the registration succeeds

	 * 

	 * @throws InvalidToken

	 * @throws ServiceFailure

	 * @throws NotAuthorized

	 * @throws IdentifierNotUnique

	 * @throws NotImplemented

	 */

	@Override

	public Identifier reserveIdentifier(Session session, Identifier pid,

	  String scope, String format) 

	  throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique, 

	  NotImplemented, InvalidRequest {

		// generate a pid if not provided

		if (pid == null) {

			pid = new Identifier();

			// TODO: go to EZID

			StringBuffer sb = new StringBuffer();

			if (scope != null) {

				sb.append(scope);

				sb.append(".");

			}

			sb.append(System.currentTimeMillis());

			pid.setValue(sb.toString());

		}

		// does this identifier exist?

		if (IdentifierManager.getInstance().identifierExists(pid.getValue())) {

			// check if it was reserved already

			if (IdentifierManager.getInstance().hasReservation(pid, session)) {

				throw new IdentifierNotUnique("4210", "Identifier already reserved: " + pid.getValue());

			}

			throw new IdentifierNotUnique("4210", "Identifier already exists: " + pid.getValue());

		}

		// if we got this far, save it

		SystemMetadata provisoinalSystemMetadata = new SystemMetadata();

		provisoinalSystemMetadata.setIdentifier(pid);

		provisoinalSystemMetadata.setRightsHolder(session.getSubject());

		try {

			IdentifierManager.getInstance().createSystemMetadata(provisoinalSystemMetadata);

		} catch (McdbDocNotFoundException e) {

			throw new ServiceFailure("4210", e.getMessage());

		}

		return pid;

	}

	/**

   * Changes ownership (RightsHolder) of the specified object to the 

   * subject specified by userId

 	 * 

	 * @param session - the Session object containing the credentials for the Subject

	 * @param pid - Identifier of the object to be modified

	 * @param userId - The subject that will be taking ownership of the specified object.

	 *

	 * @return pid - the identifier of the modified object

	 * 

	 * @throws ServiceFailure

	 * @throws InvalidToken

	 * @throws NotFound

	 * @throws NotAuthorized

	 * @throws NotImplemented

	 * @throws InvalidRequest

	 */	

	@Override

	public Identifier setOwner(Session session, Identifier pid, Subject userId)

	  throws InvalidToken, ServiceFailure, NotFound, NotAuthorized,

	  NotImplemented, InvalidRequest {

		// get the subject

		Subject subject = session.getSubject();

		// get the system metadata

		String guid = pid.getValue();

		// are we allowed to do this?

		if (!isAuthorized(session, pid, Permission.CHANGE_PERMISSION)) {

			throw new NotAuthorized("4440", "not allowed by " + subject.getValue() + " on " + guid);	

		}

		SystemMetadata systemMetadata = null;

		try {

			systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);

		} catch (McdbDocNotFoundException e) {

			throw new NotFound("4460", "No record found for: " + guid);

		}

		// set the new rights holder

		systemMetadata.setRightsHolder(userId);

		// update the metadata

		try {

			IdentifierManager.getInstance().updateSystemMetadata(systemMetadata);

		} catch (McdbDocNotFoundException e) {

			throw new ServiceFailure("4490", e.getMessage());

		}

		return pid;

	}

}