Metacat

import org.dataone.service.types.NodeReference;

import org.dataone.service.types.Subject;

    public SystemMetadata asSystemMetadata(Date dateUploaded, String rightsHolder,

            String checksum, String checksumAlgorithm, String originMemberNode,

            String authoritativeMemberNode, Date dateModified, String submitter, 

            String guid, String objectFormat, long size) {

        SystemMetadata sysMeta = new SystemMetadata();

        Identifier sysMetaId = new Identifier();

        sysMetaId.setValue(guid);

        sysMeta.setIdentifier(sysMetaId);

        sysMeta.setDateUploaded(dateUploaded);

        Subject rightsHolderSubject = new Subject();

        rightsHolderSubject.setValue(rightsHolder);

        sysMeta.setRightsHolder(rightsHolderSubject);

        Checksum checksumObject = new Checksum();

        checksumObject.setValue(checksum);

        checksumObject.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));

        sysMeta.setChecksum(checksumObject);

        NodeReference omn = new NodeReference();

        omn.setValue(originMemberNode);

        sysMeta.setOriginMemberNode(omn);

        NodeReference amn = new NodeReference();

        amn.setValue(authoritativeMemberNode);

        sysMeta.setAuthoritativeMemberNode(amn);

        sysMeta.setDateSysMetadataModified(dateModified);

        Subject submitterSubject = new Subject();

        submitterSubject.setValue(submitter);

        sysMeta.setSubmitter(submitterSubject);

        sysMeta.setObjectFormat(ObjectFormat.convert(objectFormat));

        sysMeta.setSize(size);

        return sysMeta;

    }

     * return a hash of all of the info that is in the systemmetadata table

     * @param localId

     * @return

     */

    public SystemMetadata getSystemMetadata(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

        }

        SystemMetadata sysMeta = new SystemMetadata();

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

          "origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size " +

          "from systemmetadata where docid = ?";

        DBConnection dbConn = null;

        int serialNumber = -1;

        try 

        {

            // Get a database connection from the pool

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

            serialNumber = dbConn.getCheckOutSerialNumber();

            // Execute the 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);

                String objectFormat = rs.getString(10);

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

                Identifier sysMetaId = new Identifier();

                sysMetaId.setValue(guid);

                sysMeta.setIdentifier(sysMetaId);

                sysMeta.setDateUploaded(dateUploaded);

                Subject rightsHolderSubject = new Subject();

                rightsHolderSubject.setValue(rightsHolder);

                sysMeta.setRightsHolder(rightsHolderSubject);

                Checksum checksumObject = new Checksum();

                checksumObject.setValue(checksum);

                checksumObject.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));

                sysMeta.setChecksum(checksumObject);

                NodeReference omn = new NodeReference();

                omn.setValue(originMemberNode);

                sysMeta.setOriginMemberNode(omn);

                NodeReference amn = new NodeReference();

                amn.setValue(authoritativeMemberNode);

                sysMeta.setAuthoritativeMemberNode(amn);

                sysMeta.setDateSysMetadataModified(dateModified);

                Subject submitterSubject = new Subject();

                submitterSubject.setValue(submitter);

                sysMeta.setSubmitter(submitterSubject);

                sysMeta.setObjectFormat(ObjectFormat.convert(objectFormat));

                sysMeta.setSize(size);

                stmt.close();

            } 

            else

            {

                stmt.close();

                DBConnectionPool.returnDBConnection(dbConn, serialNumber);

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

            }

        } 

        catch (SQLException e) 

        {

            e.printStackTrace();

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

                    + e.getMessage());

        } 

        finally 

        {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

        // look up provenance information

        sysMeta.setObsoleteList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "obsoletes"));

        sysMeta.setObsoletedByList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "obsoletedBy"));

        sysMeta.setDescribeList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "describes"));

        sysMeta.setDescribedByList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "describedBy"));

        sysMeta.setDerivedFromList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "derivedFrom"));

        return sysMeta;

    }

    private List<Identifier> getSystemMetadataProvenance(String guid, String relationship)

    	throws McdbDocNotFoundException {

    	List<Identifier> identifiers = new ArrayList<Identifier>();

    	String sql = "select guid, relationship, target_guid " +

    		"from systemMetadataProvenance where guid = ? and relationship = ?";

    DBConnection dbConn = null;

    int serialNumber = -1;

    try 

    {

        // Get a database connection from the pool

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

        serialNumber = dbConn.getCheckOutSerialNumber();

        // Execute the statement

        PreparedStatement stmt = dbConn.prepareStatement(sql);

        stmt.setString(1, guid);

        stmt.setString(2, relationship);

        ResultSet rs = stmt.executeQuery();

        while (rs.next()) 

        {

            String targetGuid = rs.getString(3);

            Identifier id = new Identifier();

            id.setValue(targetGuid);

            identifiers.add(id);

        } 

        stmt.close();

    } 

    catch (SQLException e) 

    {

        logMetacat.error("Error while getting system metadata provenance for guid " + guid, e);

    } 

    finally 

    {

        // Return database connection to the pool

        DBConnectionPool.returnDBConnection(dbConn, serialNumber);

    }

    return identifiers;

}

    /**

    private void insertAdditionalSystemMetadataFields(long dateUploaded, String rightsHolder,

    private void insertSystemMetadataProvenance(String guid, String relationship, List<String> targetGuids)

    {

        DBConnection dbConn = null;

        int serialNumber = -1;

        try {

            // Get a database connection from the pool

            dbConn = 

                DBConnectionPool.getDBConnection("IdentifierManager.createMapping");

            serialNumber = dbConn.getCheckOutSerialNumber();

            // remove existing values first

            String delete = "delete from systemMetadataProvenance " + 

            "where guid = ? and relationship = ?";

	        PreparedStatement stmt = dbConn.prepareStatement(delete);

	        //data values

	        stmt.setString(1, guid);

	        stmt.setString(2, relationship);

	        //execute

	        int deletedCount = stmt.executeUpdate();

	        stmt.close();

            for (String targetGuid: targetGuids) {

	            // Execute the insert statement

	            String insert = "insert into systemMetadataProvenance " + 

	                "(guid, relationship, target_guid) " +

	                "values (?, ?, ?)";

	            PreparedStatement insertStatement = dbConn.prepareStatement(insert);

	            //data values

	            insertStatement.setString(1, guid);

	            insertStatement.setString(2, relationship);

	            insertStatement.setString(3, targetGuid);

	            //execute

	            int rows = insertStatement.executeUpdate();

	            insertStatement.close();

            }

        } catch (SQLException e) {

            logMetacat.error("SQL error while adding systemMetadataProvenance for: " + guid, e); 

        } finally {

            // Return database connection to the pool

            DBConnectionPool.returnDBConnection(dbConn, serialNumber);

        }

    }

        // add provenance information

        String guid = sm.getIdentifier().getValue();

        List<String> targetGuids = null;

        String relationship = null;

        relationship = "obsoletedBy";

        targetGuids = new ArrayList<String>();

        for (Identifier id: sm.getObsoletedByList()) {

        	targetGuids.add(id.getValue());

        }

        this.insertSystemMetadataProvenance(guid, relationship, targetGuids);

        relationship = "obsoletes";

        targetGuids = new ArrayList<String>();

        for (Identifier id: sm.getObsoleteList()) {

        	targetGuids.add(id.getValue());

        }

        this.insertSystemMetadataProvenance(guid, relationship, targetGuids);

        relationship = "describes";

        targetGuids = new ArrayList<String>();

        for (Identifier id: sm.getDescribeList()) {

        	targetGuids.add(id.getValue());

        }

        this.insertSystemMetadataProvenance(guid, relationship, targetGuids);

        relationship = "describedBy";

        targetGuids = new ArrayList<String>();

        for (Identifier id: sm.getDescribedByList()) {

        	targetGuids.add(id.getValue());

        }

        this.insertSystemMetadataProvenance(guid, relationship, targetGuids);

        relationship = "derivedFrom";

        targetGuids = new ArrayList<String>();

        for (Identifier id: sm.getDerivedFromList()) {

        	targetGuids.add(id.getValue());

        }

        this.insertSystemMetadataProvenance(guid, relationship, targetGuids);