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.Calendar;

import org.dataone.client.D1Client;

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.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

   */

    return new CNodeService(request);

  /**

   * Constructor, private for singleton access

   */

    super(request);

  }

   * 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

   *

   */

      InvalidRequest, InvalidToken {

      Subject subject = session.getSubject();

      // 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 " + pid.getValue());

      }

      SystemMetadata systemMetadata = null;

      try {

          lock.lock();

          try {

              if ( HazelcastService.getInstance().getSystemMetadataMap().containsKey(pid) ) {

                  systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);

              }

              // does the request have the most current system metadata?

              if ( systemMetadata.getSerialVersion().longValue() != serialVersion ) {

                 String msg = "The requested system metadata version number " +

                     serialVersion + " differs from the current version at " +

                     systemMetadata.getSerialVersion().longValue() +

                     ". Please get the latest copy in order to modify it.";

                 throw new InvalidRequest("4883", msg);

              }

              throw new NotFound("4884", "No record found for: " + pid.getValue());

          // set the new policy

          systemMetadata.setReplicationPolicy(policy);

          // update the metadata

          try {

              systemMetadata.setSerialVersion(systemMetadata.getSerialVersion().add(BigInteger.ONE));

              systemMetadata.setDateSysMetadataModified(Calendar.getInstance().getTime());

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

          } catch (Exception e) {

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

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

        lock.unlock();

        logMetacat.debug("Unlocked identifier " + pid.getValue());

   * 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

   *

   */

      InvalidRequest, NotFound {

      int replicaEntryIndex = -1;

      List<Replica> replicas = null;

      // get the subject

      Subject subject = session.getSubject();

          " is " + status.toString());

      SystemMetadata systemMetadata = null;

      try {

              systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);

                  logMetacat.debug("systemMetadata is null for " + pid.getValue());

              }

              replicas = systemMetadata.getReplicaList();

              int count = 0;

                  logMetacat.debug("no replicas to evaluate");

                  throw new InvalidRequest("4730", "There are no replicas to update.");

              }

              // find the target replica index in the replica list

              for (Replica replica: replicas) {

                  String replicaNodeStr = replica.getReplicaMemberNode().getValue();

                  String targetNodeStr = targetNode.getValue();

                  logMetacat.debug("Comparing " + replicaNodeStr + " to " + targetNodeStr);

                  if (replicaNodeStr.equals(targetNodeStr)) {

                      replicaEntryIndex = count;

                      logMetacat.debug("replica entry index is: " + replicaEntryIndex);

                      break;

                  }

                  count++;

              }

              // are we allowed to do this? only CNs and target MNs are allowed

              CNode cn = D1Client.getCN();

              List<Node> nodes = cn.listNodes().getNodeList();

              for ( Node node : nodes ) {

                  NodeReference nodeReference = node.getIdentifier();

                  logMetacat.debug("In setReplicationStatus(), Node reference is: " + nodeReference.getValue());

                  // allow target MN certs and CN certs

                  if (targetNode.getValue().equals(nodeReference.getValue()) ||

                      node.getType() == NodeType.CN) {

                      List<Subject> nodeSubjects = node.getSubjectList();

                      // check if the session subject is in the node subject list

                      for (Subject nodeSubject : nodeSubjects) {

                          if ( nodeSubject.equals(subject) ) {

                              allowed = true; // subject of session == target node subject

                              break;

                          }

                      }

                  }

              }

                  String msg = "The subject identified by " + subject.getValue() +

                    " does not have permission to set the replication status for " +

                    "the replica identified by " + targetNode.getValue() + ".";

                  logMetacat.info(msg);

                  throw new NotAuthorized("4720", msg);

              }

              if ( failure != null && status == ReplicationStatus.FAILED ) {

                 String msg = "The replication request of the object identified by " +

                     pid.getValue() + " failed.  The error message was " +

                     failure.getMessage() + ".";

            throw new NotFound("4740", "No record found for: " + pid.getValue() +

                " : " + e.getMessage());

          if ( replicaEntryIndex != -1 ) {

              Replica targetReplica = replicas.get(replicaEntryIndex);

              targetReplica.setReplicationStatus(status);

              logMetacat.debug("Set the replication status for " +

                  targetReplica.getReplicaMemberNode().getValue() + " to " +

                  targetReplica.getReplicationStatus());

              throw new InvalidRequest("4730", "There are no replicas to update.");

          // update the metadata

          try {

              systemMetadata.setSerialVersion(systemMetadata.getSerialVersion().add(BigInteger.ONE));

              systemMetadata.setDateSysMetadataModified(Calendar.getInstance().getTime());

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

              if ( status == ReplicationStatus.FAILED && failure != null ) {

                  logMetacat.warn("Replication failed for identifier " + pid.getValue() +

                      " on target node " + targetNode + ". The exception was: " +

                      failure.getMessage());

              }

          } catch (Exception e) {

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

        lock.unlock();

        logMetacat.debug("Unlocked identifier " + pid.getValue());

   * 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

   */

    String relationship, Identifier pidOfObject)

    throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,

    InvalidRequest, NotImplemented {

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

    SystemMetadata systemMetadata = null;

    try {

        // 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())) {

              asserted = true;

        }

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

        }

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

            Identifier pid = systemMetadata.getObsoletedBy();

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

              asserted = true;

        }

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

        }

        throw new ServiceFailure("4270", "Could not assert relation for: " +

            pidOfSubject.getValue() +

            ". The error message was: " + e.getMessage());

    return asserted;

  /**

   * 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 NotImplemented

   */

    throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,

        checksum = systemMetadata.getChecksum();

    } catch (Exception e) {

        throw new ServiceFailure("1410", "An error occurred getting the checksum for " +

            pid.getValue() + ". The error message was: " + e.getMessage());

    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 InvalidToken

   * @throws ServiceFailure

   * @throws NotAuthorized

   * @throws NotFound

   * @throws 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

   */

    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 ServiceFailure

   * @throws NotFound

   * @throws InsufficientResources

   * @throws NotImplemented

   */

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

  }

   * Format Vocabulary

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

   *                            the DataONE Object Format Vocabulary

   *

   * @throws ServiceFailure

   * @throws NotImplemented

   * @throws InsufficientResources

   */

  }

   * @return nodeList - List of nodes from the registry

   *

   * @throws ServiceFailure

   * @throws NotImplemented

   */

    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

   */

      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: " + pid.getValue() +

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

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

          throw new InvalidRequest("4863",

              "The identifier in method call (" + pid.getValue() +

              ") does not match identifier in system metadata (" +

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

      }

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

          // Check that the identifier does not already exist

          if (HazelcastService.getInstance().getSystemMetadataMap().containsKey(pid)) {

              throw new InvalidRequest("4863",

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

          // insert the system metadata into the object store

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

          try {

              sysmeta.setSerialVersion(BigInteger.ONE);

              sysmeta.setDateSysMetadataModified(Calendar.getInstance().getTime());

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

          } catch (Exception e) {

            logMetacat.error("Problem registering system metadata: " + pid.getValue(), e);

              throw new ServiceFailure("4862", "Error inserting system metadata: " +

                  e.getClass() + ": " + e.getMessage());

          }

          throw new ServiceFailure("4862", "Error inserting system metadata: " +

          lock.unlock();

          logMetacat.debug("Unlocked identifier " + pid.getValue());

      }

      logMetacat.debug("Returning from registerSystemMetadata");

      EventLog.getInstance().log(request.getRemoteAddr(),

          request.getHeader("User-Agent"), session.getSubject().getValue(),

          pid.getValue(), "registerSystemMetadata");

      return pid;

  /**

   * 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

   */

  }