Metacat

/**

 *  '$RCSfile$'

 *  Copyright: 2010 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *

 *   '$Author: jones $'

 *     '$Date: 2010-02-03 17:58:12 -0900 (Wed, 03 Feb 2010) $'

 * '$Revision: 5211 $'

 *

 * 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;

import java.sql.ResultSet;

import java.sql.SQLException;

import org.apache.log4j.Logger;

import org.dataone.service.types.ChecksumAlgorithm;

import org.dataone.service.types.ObjectFormat;

import org.dataone.service.types.ObjectInfo;

import org.dataone.service.types.ObjectList;

import edu.ucsb.nceas.metacat.database.DBConnection;

import edu.ucsb.nceas.metacat.database.DBConnectionPool;

/**

 * Manage the relationship between Metacat local identifiers (LocalIDs) that are

 * codified as the (docid, rev) pair with globally uniqe string identifiers

 * (GUIDs) that are opaque strings.  This class provides methods to manage these

 * identifiers, and to search for and look up LocalIDs based on their GUID and

 * vice versa. IdentifierManager is a singleton.

 *

 * @author Matthew Jones

 */

public class IdentifierManager {

    public static final String TYPE_IDENTIFIER = "identifier";

     * The single instance of the manager that is always returned.

     */

    private static IdentifierManager self = null;

    private Logger logMetacat = Logger.getLogger(EventLog.class);

    /**

     * A private constructor that initializes the class when getInstance() is

     * called.

     */

    private IdentifierManager()

    {

        {

            DATAONE_SM_DOCTYPE = PropertyService.getProperty("crudService.listObjects.ReturnDoctype");

        }

        catch(Exception e)

        {

            throw new RuntimeException("Error getting System Metadata doctype from " +

                    "the properties file.  Please make sure crudService.listObjects.ReturnDoctype " +

                    "exists in metacat.properties.");

        }

    /**

     * Return the single instance of the manager after initializing it if it

     * wasn't previously initialized.

     *

     * @return the single IdentifierManager instance

     */

    public static IdentifierManager getInstance()

    {

        if (self == null) {

            self = new IdentifierManager();

        }

        return self;

    }

    /**

     * @param localId

     * @return

     */

    public Hashtable<String, String> getSystemMetadataInfo(String localId)

    throws McdbDocNotFoundException

    {

        try

        {

            AccessionNumber acc = new AccessionNumber(localId, "NONE");

            localId = acc.getDocid();

        }

        catch(Exception e)

        {

            //do nothing. just try the localId as it is

        }

        Hashtable<String, String> h = new Hashtable<String, String>();

        String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +

        DBConnection dbConn = null;

        int serialNumber = -1;

        try

        {

            // Get a database connection from the pool

            dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getDocumentInfo");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            PreparedStatement stmt = dbConn.prepareStatement(sql);

            stmt.setString(1, localId);

            ResultSet rs = stmt.executeQuery();

            if (rs.next())

            {

                String guid = rs.getString(1);

                Timestamp dateUploaded = rs.getTimestamp(2);

                String rightsHolder = rs.getString(3);

                String checksum = rs.getString(4);

                String checksumAlgorithm = rs.getString(5);

                String originMemberNode = rs.getString(6);

                String authoritativeMemberNode = rs.getString(7);

                Timestamp dateModified = rs.getTimestamp(8);

                String submitter = rs.getString(9);

                long size = new Long(rs.getString(11)).longValue();

                h.put("guid", guid);

                h.put("date_uploaded", new Long(dateUploaded.getTime()).toString());

                h.put("rights_holder", rightsHolder);

                h.put("checksum", checksum);

                h.put("checksum_algorithm", checksumAlgorithm);

                h.put("origin_member_node", originMemberNode);

                h.put("authoritative_member_node", authoritativeMemberNode);

                h.put("date_modified", new Long(dateModified.getTime()).toString());

                h.put("submitter", submitter);

                h.put("size", new Long(size).toString());

                stmt.close();

            }

            else

            {

                stmt.close();

                DBConnectionPool.returnDBConnection(dbConn, serialNumber);

                throw new McdbDocNotFoundException("2Could not find document " + localId);

            }

        }

        catch (SQLException e)

        {

            e.printStackTrace();

            logMetacat.error("Error while getting system metadata info for localid " + localId + " : "

                    + e.getMessage());

        }

        finally

        {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        return h;

    }

    /**

     * from the xml_documents table.  They can be used to contstruct metadata

     * about the object that is stored.

     * @param localId

     * @return

     * @throws McdbDocNotFoundException

     */

    {

        {

            AccessionNumber acc = new AccessionNumber(localId, "NONE");

            localId = acc.getDocid();

        }

        catch(Exception e)

        {

            //do nothing. just try the localId as it is

        }

            "server_location, rev, date_created, date_updated from " +

            "xml_documents where docid like '" + localId + "'";

        DBConnection dbConn = null;

        int serialNumber = -1;

        try

        {

            // Get a database connection from the pool

            dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getDocumentInfo");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            PreparedStatement stmt = dbConn.prepareStatement(sql);

            ResultSet rs = stmt.executeQuery();

            if (rs.next())

            {

                String docname = rs.getString(1);

                String doctype = rs.getString(2);

                String user_owner = rs.getString(3);

                String user_updated = rs.getString(4);

                String server_location = rs.getString(5);

                int rev = rs.getInt(6);

                String date_created = rs.getString(7);

                String date_updated = rs.getString(8);

                h.put("doctype", doctype);

                h.put("user_owner", user_owner);

                h.put("user_updated", user_updated);

                h.put("server_location", server_location);

                h.put("rev", new Integer(rev).toString());

                h.put("date_created", date_created);

                h.put("date_updated", date_updated);

                stmt.close();

            }

            else

            {

                stmt.close();

                DBConnectionPool.returnDBConnection(dbConn, serialNumber);

                Hashtable accessHash = new Hashtable();

                String principal_name = rs.getString(1);

                String permission = rs.getString(2);

                String permissionType = rs.getString(3);

                String permissionOrder = rs.getString(4);

                accessHash.put("principal_name", principal_name);

                accessHash.put("permission", permission);

                accessHash.put("permission_type", permissionType);

                accessHash.put("permission_order", permissionOrder);

            }

            h.put("access", accessVector);

        catch (SQLException e)

        {

                    + e.getMessage());

        }

        finally

        {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        return h;

    }

    /**

     * return the newest rev for a given localId

     * @param localId

     * @return

     */

    public int getLatestRevForLocalId(String localId)

        throws McdbDocNotFoundException

    {

        {

            AccessionNumber acc = new AccessionNumber(localId, "NONE");

            localId = acc.getDocid();

        }

        catch(Exception e)

        {

            //do nothing. just try the localId as it is

        }

        String sql = "select rev from xml_documents where docid like '" + localId + "'";

        DBConnection dbConn = null;

        int serialNumber = -1;

        try

        {

            // Get a database connection from the pool

            dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLatestRevForLocalId");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            PreparedStatement stmt = dbConn.prepareStatement(sql);

            ResultSet rs = stmt.executeQuery();

            if (rs.next())

            {

                rev = rs.getInt(1);

                stmt.close();

            }

            else

            {

                stmt.close();

                DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        catch (SQLException e)

        {

            logMetacat.error("Error while looking up the guid: "

                    + e.getMessage());

        }

        finally

        {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        return rev;

    }

    /**

     * system metadata and are not themselves system metadata

     */

    public List<String> getLocalIdsWithNoSystemMetadata()

    {

        Vector<String> ids = new Vector<String>();

        //String sql = "select docid from identifier where guid in (select guid from systemmetadata)";

        //    "in (select docid from identifier where guid in (select guid from systemmetadata)) " +

        //    "and doctype not like '" + DATAONE_SM_DOCTYPE + "'";

            "(select docid from identifier where guid in (select guid from systemmetadata)))";

        int serialNumber = -1;

        try

        {

            // Get a database connection from the pool

            dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLocalIdsWithNoSystemMetadata");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            PreparedStatement stmt = dbConn.prepareStatement(sql);

            ResultSet rs = stmt.executeQuery();

            while (rs.next())

            {

                String localid = rs.getString(1);

                localid += "." + rev;

            }

            stmt.close();

        }

        catch (SQLException e)

        {

            logMetacat.error("Error while looking up the guid: "

                    + e.getMessage());

        }

        finally

        {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        return ids;

    }

    /**

     * return a listing of all local ids in the object store

     * @return a list of all local ids in metacat

     */

    public List<String> getAllLocalIds()

       throws Exception

    {

        Vector<String> ids = new Vector<String>();

        String sql = "select docid from xml_documents";

        DBConnection dbConn = null;

        int serialNumber = -1;

        try

        {

            // Get a database connection from the pool

            dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllLocalIds");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            PreparedStatement stmt = dbConn.prepareStatement(sql);

            ResultSet rs = stmt.executeQuery();

            while (rs.next())

            {

                String localid = rs.getString(1);

                ids.add(localid);

            }

            stmt.close();

        }

        catch (SQLException e)

        {

            logMetacat.error("Error while looking up the guid: "

                    + e.getMessage());

        }

        finally

        {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        return ids;

    }

    /**

     * the identifier is not found, throw an exception.

     *

     * @param guid the global identifier to look up

     * @return String containing the corresponding LocalId

     * @throws McdbDocNotFoundException if the identifier is not found

     */

    public String getLocalId(String guid) throws McdbDocNotFoundException

    {

    /**

     * Determine if an identifier exists already, returning true if so.

     *

     * @param guid the global identifier to look up

     * @return boolean true if the identifier exists

     */

    public boolean identifierExists(String guid)

    {

        boolean idExists = false;

        try {

            String id = getLocalId(guid);

            if (id != null) {

                idExists = true;

            }

        } catch (McdbDocNotFoundException e) {

            idExists = false;

        }

        return idExists;

    }

    /**

     * Create a mapping between two identifiers, one representing an

     * unconstrained, globally unique string (guid), and one a localId

     * in the Metacat docid format (scope.id.revision).

     * This mapping allows one to find the global id (guid) from the localId.

     *

     * @param guid the global string identifier to be mapped

     * @param localId the local identifier to be mapped

     */

    public void createMapping(String guid, String localId)

    {

    /**

     *

     * @param guid

     * @param rev

     * @return

     */

    public String generateLocalId(String guid, int rev)

    {

        return generateLocalId(guid, rev, false);

    }

    /**

     * Given a global identifier (guid), create a suitable local identifier that

     * follows Metacat's docid semantics and format (scope.id.rev), and create

     * a mapping between these two identifiers.  This effectively reserves both

     * the global and the local identifier, as they will now be present in the

     * identifier mapping table.  If the incoming guid has the syntax of a

     * Metacat docid (scope.id.rev), then simply use it.

     *

     * @param guid the global string identifier

     * @param rev the revision number to be used in the localId

     * @return String containing the localId to be used for Metacat operations

     */

        String localId = "";

        boolean conformsToDocidFormat = false;

        // Check if the guid passed in is already in docid (scope.id.rev) format

        try {

            AccessionNumber acc = new AccessionNumber(guid, "NONE");

            if (new Integer(acc.getRev()).intValue() > 0) {

                conformsToDocidFormat = true;

            }

        } catch (NumberFormatException e) {

            // No action needed, simply detecting invalid AccessionNumbers

        } catch (AccessionNumberException e) {

            // No action needed, simply detecting invalid AccessionNumbers

        } catch (SQLException e) {

            // No action needed, simply detecting invalid AccessionNumbers

        }

        if (conformsToDocidFormat) {

            // if it conforms, use it for both guid and localId

            localId = guid;

        } else {

            // if not, then generate a new unique localId

            localId = DocumentUtil.generateDocumentId(rev);

        }

        // Register this new pair in the identifier mapping table

        if(!isSystemMetadata)

        { //don't do this if we're generating for system metadata

            createMapping(guid, localId);

        }

        return localId;

    }

    /**

     * given a local identifer, look up the guid.  Throw McdbDocNotFoundException

     * @param docid the docid to look up

     * @param rev the revision of the docid to look up

     * @return String containing the mapped guid

     * @throws McdbDocNotFoundException if the docid, rev is not found

     */

    public String getGUID(String docid, int rev)

      throws McdbDocNotFoundException

    {

        String guid = null;

        DBConnection dbConn = null;

        int serialNumber = -1;

        try {

            // Get a database connection from the pool

            // Execute the insert statement

            PreparedStatement stmt = dbConn.prepareStatement(query);

            stmt.setString(1, docid);

            stmt.setInt(2, rev);

            ResultSet rs = stmt.executeQuery();

            {

            else

            {

                query = "select guid from systemmetadata where docid = ? and rev = ?";

                stmt = dbConn.prepareStatement(query);

                stmt.setString(1, docid);

                stmt.setInt(2, rev);

                {

                    guid = rs.getString(1);

                }

                else

                {

                    throw new McdbDocNotFoundException("No guid registered for docid " + docid + "." + rev);

                }

            logMetacat.error("Error while looking up the guid: "

                    + e.getMessage());

        } finally {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        return guid;

    }

    /**

     * of the extra system metadata information to the table.  You must call

     * insertAdditionalSystemMetadataFields to complete the entry

     * @param guid the id to insert

     * @param localId the systemMetadata object to get the local id for

     */

    public void createSystemMetadataMapping(String guid, String localId)

    {

    }

     * to the table for quick searching.

     *

     * @param guid the id to insert

     * @param localId the systemMetadata object to get the local id for

     */

    public void createSystemMetadataMapping(SystemMetadata sysmeta, String localId)

    {

        createGenericMapping(sysmeta.getIdentifier().getValue(), localId, TYPE_SYSTEM_METADATA);

        insertAdditionalSystemMetadataFields(sysmeta);

    }

    /**

     * @param guid

     * @param localId

     */

    {

        DBConnection dbConn = null;

        try {

            // Parse the localId into scope and rev parts

            AccessionNumber acc = new AccessionNumber(localId, "NOACTION");

            String docid = acc.getDocid();

            int rev = 1;

            if(acc.getRev() != null)

            {

              rev = (new Integer(acc.getRev()).intValue());

            }

            // Get a database connection from the pool

            dbConn =

            // Execute the insert statement

            String query = "update systemmetadata set (docid, rev) = (?, ?) where guid='" + guid + "'";

            stmt.setString(1, docid);

            stmt.setInt(2, rev);

            int rows = stmt.executeUpdate();

            stmt.close();

        } catch (SQLException e) {

            e.printStackTrace();

            logMetacat.error("SQL error while updating a mapping to the system metadata identifier: "

                    + e.getMessage());

        } catch (NumberFormatException e) {

            e.printStackTrace();

            logMetacat.error("NumberFormat error while updating a mapping to the system metadata identifier: "

                    + e.getMessage());

        } catch (AccessionNumberException e) {

            e.printStackTrace();

            logMetacat.error("AccessionNumber error while updating a mapping to the system metadata identifier: "

                    + e.getMessage());

        } finally {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

    /**

     * return the localId of a system metadata document based on its guid

     */

    {

            String checksum, String checksumAlgorithm, String originMemberNode,

            String guid, String objectFormat, long size)

        DBConnection dbConn = null;

        int serialNumber = -1;

            // Get a database connection from the pool

            dbConn =

                DBConnectionPool.getDBConnection("IdentifierManager.createMapping");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            String query = "update " + TYPE_SYSTEM_METADATA +

                " set (date_uploaded, rights_holder, checksum, checksum_algorithm, " +

                "submitter, object_format, size) " +

                "= (?, ?, ?, ?, ?, ?, ?, ?, ?, ?) where guid = ?";

            //data values

            stmt.setTimestamp(1, new java.sql.Timestamp(dateUploaded));

            stmt.setString(2, rightsHolder);

            stmt.setString(3, checksum);

            stmt.setString(4, checksumAlgorithm);

            stmt.setString(5, originMemberNode);

            stmt.setString(6, authoritativeMemberNode);

            stmt.setTimestamp(7, new java.sql.Timestamp(modifiedDate));

            stmt.setString(8, submitter);

            stmt.setString(10, new Long(size).toString());

            //execute

            int rows = stmt.executeUpdate();

            stmt.close();

        } catch (SQLException e) {

            e.printStackTrace();