Metacat

import java.io.IOException;

import java.io.PipedInputStream;

import java.io.PipedOutputStream;

import java.lang.reflect.InvocationTargetException;

import org.apache.commons.beanutils.BeanUtils;

import org.dataone.client.v2.MNode;

import org.dataone.service.types.v1_1.QueryEngineDescription;

import org.dataone.service.types.v1_1.QueryEngineList;

import org.dataone.service.types.v2.Node;

import org.dataone.service.types.v2.NodeList;

import org.dataone.service.types.v2.ObjectFormat;

import org.dataone.service.types.v2.ObjectFormatList;

import org.dataone.service.util.TypeMarshaller;

import org.jibx.runtime.JiBXException;

import edu.ucsb.nceas.metacat.DBUtil;

import edu.ucsb.nceas.metacat.properties.PropertyService;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

    @Override

    public ObjectFormatIdentifier addFormat(Session session, ObjectFormatIdentifier formatId, ObjectFormat format)

            throws ServiceFailure, NotFound, NotImplemented, NotAuthorized, InvalidToken {

        logMetacat.debug("CNodeService.addFormat() called.\n" + 

                "format ID: " + format.getFormatId() + "\n" + 

                "format name: " + format.getFormatName() + "\n" + 

                "format type: " + format.getFormatType() );

        // FIXME remove:

        if (true)

            throw new NotImplemented("0000", "Implementation underway... Will need testing too...");

        if (!isAdminAuthorized(session))

            throw new NotAuthorized("0000", "Not authorized to call addFormat()");

        String separator = ".";

        try {

            separator = PropertyService.getProperty("document.accNumSeparator");

        } catch (PropertyNotFoundException e) {

            logMetacat.warn("Unable to find property \"document.accNumSeparator\"\n" + e.getMessage());

        }

        // find pids of last and next ObjectFormatList

        String OBJECT_FORMAT_DOCID = ObjectFormatService.OBJECT_FORMAT_DOCID;

        int lastRev = -1;

        try {

            lastRev = DBUtil.getLatestRevisionInDocumentTable(OBJECT_FORMAT_DOCID);

        } catch (SQLException e) {

            throw new ServiceFailure("0000", "Unable to locate last revision of the object format list.\n" + e.getMessage());

        }

        int nextRev = lastRev + 1;

        String lastDocID = OBJECT_FORMAT_DOCID + separator + lastRev;

        String nextDocID = OBJECT_FORMAT_DOCID + separator + nextRev;

        Identifier lastPid = new Identifier();

        lastPid.setValue(lastDocID);

        Identifier nextPid = new Identifier();

        nextPid.setValue(nextDocID);

        logMetacat.debug("Last ObjectFormatList document ID: " + lastDocID + "\n" 

                + "Next ObjectFormatList document ID: " + nextDocID);

        // add new format to the current ObjectFormatList

        ObjectFormatList objectFormatList = ObjectFormatService.getInstance().listFormats();

        List<ObjectFormat> innerList = objectFormatList.getObjectFormatList();

        innerList.add(format);

        // get existing (last) sysmeta and make a copy

        SystemMetadata lastSysmeta = getSystemMetadata(session, lastPid);

        SystemMetadata nextSysmeta = new SystemMetadata();

        try {

            BeanUtils.copyProperties(nextSysmeta, lastSysmeta);

        } catch (IllegalAccessException | InvocationTargetException e) {

            throw new ServiceFailure("0000", "Unable to create system metadata for updated object format list.\n" + e.getMessage());

        }

        // create the new object format list, and update the old sysmeta with obsoletedBy

        createNewObjectFormatList(session, lastPid, nextPid, objectFormatList, nextSysmeta);

        updateOldObjectFormatList(session, lastPid, nextPid, lastSysmeta);

        // TODO add to ObjectFormatService local cache?

        return formatId;

    }

    /**

     * Creates the object for the next / updated version of the ObjectFormatList.

     * 

     * @param session

     * @param lastPid

     * @param nextPid

     * @param objectFormatList

     * @param lastSysmeta

     */

    private void createNewObjectFormatList(Session session, Identifier lastPid, Identifier nextPid,

            ObjectFormatList objectFormatList, SystemMetadata lastSysmeta) 

                    throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented {

        PipedInputStream is = new PipedInputStream();

        PipedOutputStream os = null;

        try {

            os = new PipedOutputStream(is);

            TypeMarshaller.marshalTypeToOutputStream(objectFormatList, os);

        } catch (JiBXException | IOException e) {

            throw new ServiceFailure("0000", "Unable to marshal object format list.\n" + e.getMessage());

        } finally {

            try {

                os.flush();

                os.close();

            } catch (IOException ioe) {

                throw new ServiceFailure("0000", "Unable to marshal object format list.\n" + ioe.getMessage());

            }

        }

        BigInteger docSize = lastSysmeta.getSize();

        try {

            docSize = BigInteger.valueOf(is.available());

        } catch (IOException e) {

            logMetacat.warn("Unable to set an accurate size for the new object format list.", e);

        }

        lastSysmeta.setIdentifier(nextPid);

        lastSysmeta.setObsoletes(lastPid);

        lastSysmeta.setSize(docSize); 

        lastSysmeta.setSubmitter(session.getSubject());

        lastSysmeta.setDateUploaded(new Date());

        // create new object format list

        try {

            create(session, nextPid, is, lastSysmeta);

        } catch (IdentifierNotUnique | UnsupportedType | InsufficientResources

                | InvalidSystemMetadata | InvalidRequest e) {

            throw new ServiceFailure("0000", "Unable to create() new object format list" + e.getMessage());

        }

    }

    /**

     * Updates the SystemMetadata for the old version of the ObjectFormatList

     * by setting the obsoletedBy value to the pid of the new version of the 

     * ObjectFormatList.

     * 

     * @param session

     * @param lastPid

     * @param obsoletedByPid

     * @param lastSysmeta

     * @throws ServiceFailure

     */

    private void updateOldObjectFormatList(Session session, Identifier lastPid, Identifier obsoletedByPid, SystemMetadata lastSysmeta) 

            throws ServiceFailure {

        lastSysmeta.setObsoletedBy(obsoletedByPid);

        try {

            this.updateSystemMetadata(session, lastPid, lastSysmeta);

        } catch (NotImplemented | NotAuthorized | ServiceFailure | InvalidRequest

                | InvalidSystemMetadata | InvalidToken e) {

            throw new ServiceFailure("0000", "Unable to update metadata of old object format list.\n" + e.getMessage());

        }

    }

    @Override

    public boolean synchronize(Session session, Identifier pid) throws NotAuthorized, InvalidRequest, NotImplemented{

        throw new NotImplemented("0000", "CN query services are not implemented in Metacat.");

                    } else if (httpVerb == PUT) {

                        addFormat(extra);

     * Adds a new {@link ObjectFormat} to the object format list.

     * 

     * @param formatIdStr the format identifier

     * 

     * @throws NotImplemented 

     * @throws InvalidRequest 

     * @throws ServiceFailure 

     * @throws JiBXException 

     * @throws IOException 

     * @throws IllegalAccessException 

     * @throws InstantiationException 

     * @throws NotFound 

     * @throws NotAuthorized 

     * @throws InvalidToken 

     */

    private void addFormat(String formatIdStr) 

            throws NotImplemented, ServiceFailure, InvalidRequest, InstantiationException, 

            IllegalAccessException, IOException, JiBXException, NotFound, NotAuthorized, InvalidToken {

        logMetacat.debug("addFormat: " + formatIdStr);

        Map<String, File> files = collectMultipartFiles();

        File formatFile = files.get("format");

        FileInputStream formatStream = new FileInputStream(formatFile);

        ObjectFormat objectFormat = TypeMarshaller.unmarshalTypeFromStream(ObjectFormat.class, formatStream);

        ObjectFormatIdentifier formatId = new ObjectFormatIdentifier();

        formatId.setValue(formatIdStr);

        ObjectFormatIdentifier formatID = CNodeService.getInstance(request).addFormat(session, formatId, objectFormat);

        OutputStream out = response.getOutputStream();

        response.setStatus(200);

        response.setContentType("text/xml");

        TypeMarshaller.marshalTypeToOutputStream(formatID, out);

    }

    /**