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.metacattest;

import java.sql.SQLException;

import edu.ucsb.nceas.MCTestCase;

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.client.MetacatAuthException;

import edu.ucsb.nceas.metacat.client.MetacatInaccessibleException;

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

public class IdentifierManagerTest extends MCTestCase {

    private String badGuid = "test:testIdThatDoesNotExist";

    /**

     * Initialize the connection to metacat, and insert a document to be 

     * used for testing with a known docid.

     */

    public void setUp() {

        metacatConnectionNeeded = true;

        try {

            DBConnectionPool pool = DBConnectionPool.getInstance();

        } catch (SQLException e2) {

            fail(e2.getMessage());

        }

        try {

            super.setUp();

        } catch (Exception e1) {

            fail(e1.getMessage());

        }

    }

    /** Test that IM instances can be created. */

    public void testGetInstance() {

        IdentifierManager im = IdentifierManager.getInstance();

        assertNotNull(im);

    }

    /** Test that known LocalId's can be looked up from GUIDs. */

    public void testGetLocalId() {

        IdentifierManager im = IdentifierManager.getInstance();

        String docid = insertTestDocument();

        String goodGuid = "test:" + docid;

        im.createMapping(goodGuid, docid);

        String idReturned;

        try {

            idReturned = im.getLocalId(goodGuid);

            assertEquals(docid, idReturned);

        } catch (McdbDocNotFoundException e) {

            fail(e.getMessage());

        }

    }

    /** Test that unknown LocalId's return the proper exception. */

    public void testGetLocalIdNotFound() {

        IdentifierManager im = IdentifierManager.getInstance();

        String idReturned;

        try {

            idReturned = im.getLocalId(badGuid);

            fail("Failed: getLocalID() should have returned an document not " + 

                 "found exception but did not.");

        } catch (McdbDocNotFoundException e) {

            assertNotNull(e);

        }

    }

    /** 

     * Test that an identifier is present in the system when it should

     *  be, and that it is not present when it shouldn't be. 

     */

    public void testIdentifierExists() {

        IdentifierManager im = IdentifierManager.getInstance();

        String docid = insertTestDocument();

        im.createMapping("test:"+docid, docid);

        String goodGuid = "test:" + docid;

        assertTrue(im.identifierExists(goodGuid));

        assertFalse(im.identifierExists(badGuid));

    }

    /**

     * Test that we are able to create mappings from guids to localIds, and that

     * improperly formatted docids generate the proper exceptions.

     */

    public void testCreateMapping() {

        IdentifierManager im = IdentifierManager.getInstance();

        String docid = insertTestDocument();

        im.createMapping("test:"+docid, docid);

        try {

            assertEquals(im.getLocalId("test:"+docid), docid);

        } catch (McdbDocNotFoundException e) {

            fail("createMapping failed to create proper localId from guid.");

        }

    }

    /** Insert a test document, returning the docid that was used. */

    private String insertTestDocument() {

        String accessBlock = getAccessBlock("public", true, true,

                false, false, false);

        String emldoc = getTestEmlDoc("Test identifier manager", EML2_1_0, null,

                null, "http://fake.example.com/somedata", null,

                accessBlock, null, null,

                null, null);

        String docid = generateDocumentId() + ".1";

        try {

            m.login(username, password);

            String response = insertDocumentId(docid, emldoc, true, false);

        } catch (MetacatAuthException e) {

            fail(e.getMessage());

        } catch (MetacatInaccessibleException e) {

            fail(e.getMessage());

        }

        return docid;

    }

}

    private static final String public_doc_id = "doi:12345.5/playing/in/dirt/rev1";

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

     * @param guid ID of data object to be read

    private void getObject(String guid) {

        // Look up the localId for this global identifier

        IdentifierManager im = IdentifierManager.getInstance();

        String localId = "";

        try {

            localId = im.getLocalId(guid);

        } catch (McdbDocNotFoundException e) {

            // Need to return the proper DataONE exception

        }

        // Now use that localId to read the object and return it

        params.put("docid", new String[] { localId });

            //

            // WARNING: This should not be a Reader if we are inserting data

            // Nor should it be read into a String

            // so this seems like a latent bug to me (MBJ; 16Mar2010)

	public static final String RESOURCE_OBJECTS = "object";

/**

 *  '$RCSfile$'

 *  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.PreparedStatement;

import java.sql.ResultSet;

import java.sql.SQLException;

import org.apache.log4j.Logger;

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 {

    /**

     * 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()

    {

    }

    /**

     * 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;

    }

    /**

     * Lookup a GUID from the database, and return the associated LocalID. If

     * 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

    {

        String db_guid = "";

        String docid = "";

        int rev = 0;

        String query = "select guid, docid, rev from identifier where guid = ?";

        DBConnection dbConn = null;

        int serialNumber = -1;

        try {

            // Get a database connection from the pool

            dbConn = DBConnectionPool.getDBConnection("Identifier.getLocalId");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            PreparedStatement stmt = dbConn.prepareStatement(query);

            stmt.setString(1, guid);

            ResultSet rs = stmt.executeQuery();

            if (rs.next()) {

                db_guid = rs.getString(1);

                docid = rs.getString(2);

                rev = rs.getInt(3);

                assert(db_guid.equals(guid));

            } else {

                throw new McdbDocNotFoundException("Document not found:" + guid);

            }

            stmt.close();

        } catch (SQLException e) {

            logMetacat.error("Error while looking up the local identifier: " 

                    + e.getMessage());

        } finally {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        return docid + "." + rev;

    }

    /**

     * 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)

    {   

        int serialNumber = -1;

        DBConnection dbConn = null;

        try {

            // Parse the localId into scope and rev parts

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

            String docid = acc.getDocid();

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

            // Get a database connection from the pool

            dbConn = 

                DBConnectionPool.getDBConnection("Identifier.createMapping");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the insert statement

            String query = "insert into identifier (guid, docid, rev) values (?, ?, ?)";            

            PreparedStatement stmt = dbConn.prepareStatement(query);

            stmt.setString(1, guid);

            stmt.setString(2, docid);

            stmt.setInt(3, rev);

            int rows = stmt.executeUpdate();

            stmt.close();

        } catch (SQLException e) {

            logMetacat.error("SQL error while creating a mapping to the local identifier: " 

                    + e.getMessage());

        } catch (NumberFormatException e) {

            logMetacat.error("NumberFormat error while creating a mapping to the local identifier: " 

                    + e.getMessage());

        } catch (AccessionNumberException e) {

            logMetacat.error("AccessionNumber error while creating a mapping to the local identifier: " 

                    + e.getMessage());

        } finally {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

    }

}

   * Create a new exception but only set the message.

   * @param message a message giving information about why the document was not found

   */

  public McdbDocNotFoundException(String message) {

      super(message);

  }

  /**