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 org.dataone.service.cn.v1.CNCore;

import org.dataone.service.cn.v1.CNRead;

import org.dataone.service.cn.v1.CNReplication;

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.v1.Identifier;

import org.dataone.service.types.v1.ObjectFormatIdentifier;

import org.dataone.service.types.v1.ObjectFormatList;

import org.dataone.service.types.v1.ObjectList;

import org.dataone.service.types.v1.ObjectLocationList;

import org.dataone.service.types.v1.Permission;

import org.dataone.service.types.v1.Replica;

import org.dataone.service.types.v1.ReplicationPolicy;

import org.dataone.service.types.v1.ReplicationStatus;

import org.dataone.service.types.v1.Session;

import org.dataone.service.types.v1.Subject;

import org.dataone.service.types.v1.SystemMetadata;

import edu.ucsb.nceas.metacat.IdentifierManager;

 * Represents Metacat's implementation of the DataONE Coordinating Node

 * D1NodeService super class.

 *

 */

public class CNodeService extends D1NodeService implements CNAuthorization,

  private Logger logMetacat = null;

   * singleton accessor

   */

  }

  /**

   * Constructor, private for singleton access

   */

  }

   * 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

   *

   */

  public boolean setReplicationPolicy(Session session, Identifier pid,

    ReplicationPolicy policy)

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

    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

	    HazelcastService.getInstance().getSystemMetadataMap().lock(systemMetadata.getIdentifier());

	    HazelcastService.getInstance().getSystemMetadataMap().put(systemMetadata.getIdentifier(), systemMetadata);

	    HazelcastService.getInstance().getSystemMetadataMap().unlock(systemMetadata.getIdentifier());

    } catch (Exception e) {

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

	} finally {

	    HazelcastService.getInstance().getSystemMetadataMap().unlock(systemMetadata.getIdentifier());

	}

  }

   * 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

   *

   */

  public boolean setReplicationStatus(Session session, Identifier pid,

    NodeReference targetNode, ReplicationStatus status)

    throws ServiceFailure, NotImplemented, InvalidToken, NotAuthorized,

    InvalidRequest, NotFound {

    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

	    HazelcastService.getInstance().getSystemMetadataMap().lock(systemMetadata.getIdentifier());

	    HazelcastService.getInstance().getSystemMetadataMap().put(systemMetadata.getIdentifier(), systemMetadata);

	    HazelcastService.getInstance().getSystemMetadataMap().unlock(systemMetadata.getIdentifier());

    } catch (Exception e) {

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

	} finally {

	    HazelcastService.getInstance().getSystemMetadataMap().unlock(systemMetadata.getIdentifier());

	}

  }

   * 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

   */

  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: use ORE map

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

    }

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

    }

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

    }

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

      Identifier pid = systemMetadata.getObsoletes();

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

        return true;

      }

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

    }

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

      Identifier pid = systemMetadata.getObsoletedBy();

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

        return true;

      }

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

    }

  }

  /**

   * 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

   */

  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

   */

  public ObjectLocationList resolve(Session session, Identifier pid)

    throws InvalidRequest, InvalidToken, ServiceFailure, NotAuthorized,

    NotFound, NotImplemented {

   * 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

   */

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

    throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,

    NotImplemented {

    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());

    }

    //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.

         *  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);

            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

   */

  public ObjectFormat getFormat(ObjectFormatIdentifier fmtid)

    throws InvalidRequest, ServiceFailure, NotFound, InsufficientResources,

    NotImplemented {

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

  }

   * 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

   */

  public ObjectFormatList listFormats()

    throws InvalidRequest, ServiceFailure, NotFound, InsufficientResources,

    NotImplemented {

  }

   * @return nodeList - List of nodes from the registry

   *

   * @throws ServiceFailure

   * @throws NotImplemented

   */

  public NodeList listNodes()

    throws NotImplemented, ServiceFailure {

  }

   * 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

   */

  public Identifier registerSystemMetadata(Session session, Identifier guid,

    SystemMetadata sysmeta)

    throws NotImplemented, NotAuthorized, ServiceFailure, InvalidRequest,

    InvalidSystemMetadata {

        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() + ").");

        }

        // Check that the identifier does not already exist

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

            throw new InvalidRequest("4863",

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

        }

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

        sysmeta.setDateSysMetadataModified(new Date());

        try {

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

          HazelcastService.getInstance().getSystemMetadataMap().unlock(sysmeta.getIdentifier());

        logMetacat.debug("Returning from registerSystemMetadata");

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

        return guid;

  }

   * Provides a mechanism for updating system metadata independently of its

   * associated object

    *

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

   * @param pid - The identifier of the system metadata

   * @param sysmeta - The system metadata to be registered

   *

   * @return true if the update succeeds

   *

   * @throws NotImplemented

   * @throws NotAuthorized

   * @throws ServiceFailure

   * @throws InvalidRequest

   * @throws InvalidSystemMetadata

   * @throws NotFound

   */

  public boolean updateSystemMetadata(Session session, Identifier guid,

    SystemMetadata sysmeta)

    throws NotImplemented, NotAuthorized, ServiceFailure, InvalidRequest,

    InvalidSystemMetadata, NotFound {

        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 update." +

                    "  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() + ").");

        }

        // Check that the identifier exists

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

            throw new NotFound("000",

                "GUID does not exist");

        }

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

        sysmeta.setDateSysMetadataModified(new Date());

        try {

    	    HazelcastService.getInstance().getSystemMetadataMap().lock(sysmeta.getIdentifier());

    	    HazelcastService.getInstance().getSystemMetadataMap().put(sysmeta.getIdentifier(), sysmeta);

    	    HazelcastService.getInstance().getSystemMetadataMap().unlock(sysmeta.getIdentifier());

        } catch (Exception e) {

    		throw new ServiceFailure("4852", e.getMessage());

    	} finally {

    	    HazelcastService.getInstance().getSystemMetadataMap().unlock(sysmeta.getIdentifier());

    	}

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

        return true;

  }

  /**

   * 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

   */

  public boolean reserveIdentifier(Session session, Identifier pid)

  throws InvalidToken, ServiceFailure,

  }

  public Identifier generateIdentifier(Session session, String scheme, String fragment)

  throws InvalidToken, ServiceFailure,

  }

  /**

    * Checks whether the pid is reserved by the subject in the session param

    * If the reservation is held on the pid by the subject, we return true.

    *

   * @param session - the Session object containing the Subject

   * @param pid - The identifier to check

   *

   * @return true if the reservation exists for the subject/pid

   *

   * @throws InvalidToken

   * @throws ServiceFailure

   * @throws NotFound - when the pid is not found (in use or in reservation)

   * @throws NotAuthorized - when the subject does not hold a reservation on the pid

   * @throws IdentifierNotUnique - when the pid is in use

   * @throws NotImplemented

   */

      throws InvalidToken, ServiceFailure, NotFound, NotAuthorized, IdentifierNotUnique,

      NotImplemented, InvalidRequest {

      throw new NotImplemented("4191", "hasReservation not implemented on this node");

  }

   * 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

   */

  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

	    HazelcastService.getInstance().getSystemMetadataMap().lock(systemMetadata.getIdentifier());

	    HazelcastService.getInstance().getSystemMetadataMap().put(systemMetadata.getIdentifier(), systemMetadata);

	    HazelcastService.getInstance().getSystemMetadataMap().unlock(systemMetadata.getIdentifier());

    } catch (Exception e) {

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

	} finally {

	    HazelcastService.getInstance().getSystemMetadataMap().unlock(systemMetadata.getIdentifier());

	}

  }

   * Verify that a replication task is authorized by comparing the target node's

   * Subject (from the X.509 certificate-derived Session) with the list of

   * subjects in the known, pending replication tasks map.

   *

   * @param originatingNodeSession - Session information that contains the

   *                                 identity of the calling user

   * @param targetNodeSubject - Subject identifying the target node

   * @param pid - the identifier of the object to be replicated

   * @param replicatePermission - the execute permission to be granted

   *

   * @throws ServiceFailure

   * @throws NotImplemented

   * @throws InvalidToken

   * @throws NotAuthorized

   * @throws InvalidRequest

   * @throws NotFound

   */

    NotFound, InvalidRequest {

	  SystemMetadata sysmeta = null;

    String query = "subject = '" + targetNodeSubject + "'";

    NodeReference targetNode = null;

	  try {

	    // get the target node reference from the hzNodes map

	    Set<Node> nodeList = (Set<Node>)

	      HazelcastService.getInstance().getNodesMap().values(new SqlPredicate(query));

	    for (Node node : nodeList) {

	      targetNode = node.getIdentifier();

	      break;

      }