Metacat

/**

 *  '$RCSfile$'

 *  Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *

 *   '$Author: Serhan AKIN $'

 *     '$Date: 2009-06-13 15:28:13 +0300  $'

 *

 * 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.restservice;

import java.io.*;

import java.util.*;

import javax.mail.BodyPart;

import javax.mail.MessagingException;

import javax.mail.internet.MimeMultipart;

import javax.servlet.ServletContext;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import java.text.DateFormat;

import java.text.ParsePosition;

import java.text.SimpleDateFormat;

import org.apache.commons.httpclient.util.DateParser;

import org.apache.commons.io.IOUtils;

import org.apache.log4j.Logger;

import org.dataone.service.exceptions.BaseException;

import org.dataone.service.exceptions.IdentifierNotUnique;

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.NotImplemented;

import org.dataone.service.exceptions.ServiceFailure;

import org.dataone.service.exceptions.UnsupportedType;

import org.dataone.service.exceptions.NotFound;

import org.dataone.service.types.*;

import org.jibx.runtime.BindingDirectory;

import org.jibx.runtime.IBindingFactory;

import org.jibx.runtime.IMarshallingContext;

import org.jibx.runtime.IUnmarshallingContext;

import org.jibx.runtime.JiBXException;

import edu.ucsb.nceas.metacat.DBUtil;

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.MetacatHandler;

import edu.ucsb.nceas.metacat.dataone.CrudService;

import edu.ucsb.nceas.metacat.service.SessionService;

import edu.ucsb.nceas.metacat.util.RequestUtil;

import edu.ucsb.nceas.metacat.util.SessionData;

/**

 * 

 * Implements Earthgrid REST API to Metacat <br/><br/> 

 * 

 * <ul>

 * <li>

 * <h3> EarthGrid Query Service</h3>

 * <ul><li>

 * <h3>Get & Authenticated Get:</h3> 

 * is equal to Metacat's read action and returns a data file having

 * the specified <doc-id> in the resource path. For authenticated Get service, a session id must be provided 

 * in the query string. <br/><br/>

 * 

 * <b>REST URL:</b>	<code>GET, [context-root]/object/[doc-id]?sessionid=[sessionid] </code><br/>

 * <b>Returns:</b> data file <br/><br/>

 * </li>

 * 

 * <li>

 * <h3>Query & Authenticated Query:</h3> 

 * Metacat's equivalent is squery action but this function 

 * receives a Earthgrid query document and returns Earthgrid resultset document by transforming those documents

 * to Metacat's equivalents by the means of Metacat Implementation in Earthgrid library. For authenticated Query service 

 * a session id must be provided in the query string. See Earthgrid (a.k.a. Ecogrid) project for XSD files of 

 * query and resultset documents<br/><br/>

 * 

 * <b>REST URL:</b>	<code>POST, [context-root]/object?sessionid=[sessionid]</code>    <br/>

 * <b>POST Data:</b> Earthgrid query document , Content-type: <code>text/xml</code><br/>

 * <b>Returns:</b> Earthgrid resultset document<br/><br/>

 * 

 * </li>

 * </ul>

 * 

 * </li>

 * 

 * <li>

 * <h3> EarthGrid Authentication Service</h3>

 * <ul><li>

 * <h3>Login: </h3> 

 * Receives username and password parameters in POST data and 

 * returns SessionId (in XML format) or failure message and uses MetacatHandler's handleLoginAction function<br/><br/>

 *  

 * <b>REST URL:</b> <code>POST, [context-root]/session?op=login</code> <br/>

 * <b>POST Data:</b> username=[username]&password=[password], Content-type: <code>application/x-www-form-urlencoded</code>

 * <b>Returns:</b> sessionId in XML format<br/><br/>

 * </li>

 * 

 * <li>

 * <h3>Logout: </h3> 

 * Receives session Id parameters in querystring and returns xml message, calls 

 * MetacatHandler's handleLogoutAction function<br/><br/>

 *  

 * <b>REST URL:</b>	<code>GET, [context-root]/session?op=logout&sessionid=[sessionid]</code>   <br/>

 * <b>Returns:</b> message in XML format<br/><br/>

 * </li>

 * </ul>

 * 

 * <li>

 * <h3>EarthGrid Put Service</h3>

 * 

 * <ul>

 * <li><h3>Update/Insert: </h3>		

 * <br/>

 * <b>REST URL:</b>	<code>PUT, [context-root]/object/[doc-id]?op={update|insert}&sessionid=[sessionid]</code>   <br/>

 * <b>POST Data:</b> document object, Content-type: <code>text/xml</code><br/>

 * <b>Returns:</b> message in XML format<br/><br/>

 * </li>

 * 

 * <li><h3>Delete: </h3>		

 * <br/>

 * <b>REST URL:</b>	<code>DELETE, [context-root]/object/[doc-id]?sessionid=[sessionid]</code>   <br/>

 * <b>Returns:</b> message in XML format<br/><br/>

 * </li>

 * </ul>

 * </li>

 * 

 * <li>

 * <h3>EarthGrid Identifier Service</h3><br/>

 * 

 * <ul>

 * <li><h3>isRegistered: </h3>		<br/>

 * <b>REST URL:</b>	<code>GET, [context-root]/identifier/[doc-id]?op=isregistered</code>   <br/>

 * <b>Returns:</b> message in XML format<br/><br/>

 * </li>

 * <li><h3>getAllDocIds:</h3>		<br/>		

 * <b>REST URL:</b>	<code>GET, [context-root]/identifier?op=getalldocids</code>   <br/>

 * <b>Returns:</b> document id list in XML format<br/><br/>

 * </li>

 * 

 * <li><h3>addLSID Function:</h3> 

 * Metacat does not support this function 		<br/>

 * <b>REST URL:</b>	<code>PUT, [context-root]/identifier/[doc-id]</code>   <br/>

 * <b>Returns:</b> error message in XML format<br/><br/>

 * </li>

 * 

 * <li><h3>getNextRevision:</h3>		<br/>

 * <b>REST URL:</b>	<code>GET, [context-root]/identifier/[doc-id]?op=getnextrevision</code>   <br/>

 * <b>Returns:</b> message in XML format<br/><br/>

 * </li>

 * 

 * <li><h3>getNextObject:</h3>		<br/>

 * <b>REST URL:</b>	<code>GET, [context-root]/identifier?op=getnextobject&scope=[scope]</code>   <br/>

 * <b>Returns:</b> message in XML format<br/><br/>

 * </li>

 * 

 * </li>

 * </ul>

 * 

 */

public class ResourceHandler {

    /**HTTP Verb GET*/

    public static final byte GET = 1;

    /**HTTP Verb POST*/

    public static final byte POST = 2;

    /**HTTP Verb PUT*/

    public static final byte PUT = 3;

    /**HTTP Verb DELETE*/

    public static final byte DELETE = 4;

    /*

     * API Resources

     */

    private static final String RESOURCE_OBJECTS = "object";

    private static final String RESOURCE_META = "meta";

    private static final String RESOURCE_SESSION = "session";

    private static final String RESOURCE_IDENTIFIER = "identifier";

    private static final String RESOURCE_LOG = "log";

    /*

     * API Functions used as URL parameters

     */

    private static final String FUNCTION_KEYWORD = "op";

    private static final String FUNCTION_NAME_LOGIN = "login";

    private static final String FUNCTION_NAME_LOGOUT = "logout";

    private static final String FUNCTION_NAME_SET_ACCESS = "setaccess";

    private static final String FUNCTION_NAME_ISREGISTERED = "isregistered";

    private static final String FUNCTION_NAME_GETALLDOCS = "getalldocids";

    private static final String FUNCTION_NAME_GETNEXTREV = "getnextrevision";

    private static final String FUNCTION_NAME_GETNEXTOBJ = "getnextobject";

    private static final String FUNCTION_NAME_INSERT = "insert";

    private static final String FUNCTION_NAME_UPDATE = "update";

    private static final String FUNCTION_NAME_GENERATE_MISSING_SYSTEM_METADATA = "generatemissingsystemmetadata";

    private ServletContext servletContext;

    private Logger logMetacat;

    private MetacatHandler handler;

    private HttpServletRequest request;

    private HttpServletResponse response;

    private String username;

    private String password;

    private String sessionId;

    private String[] groupNames;

    private Hashtable<String, String[]> params;

    /**Initializes new instance by setting servlet context,request and response*/

    public ResourceHandler(ServletContext servletContext,

            HttpServletRequest request, HttpServletResponse response) {

        this.servletContext = servletContext;

        this.request = request;

        this.response = response;

    }

    /**

     * This function is called from REST APU servlet and handles each request to the servlet 

     * 

     * @param httpVerb (GET, POST, PUT or DELETE)

     */

    public void handle(byte httpVerb) {

        logMetacat = Logger.getLogger(ResourceHandler.class);

        try {

            String resource = request.getServletPath();

            String verb = "";

            //System.out.println("handling verb " + httpVerb + " request with resource " + resource);

            boolean status = false;

            if (resource != null) {

                resource = request.getServletPath().substring(1);

                params = new Hashtable<String, String[]>();

                initParams();

                Timer timer = new Timer();

                handler = new MetacatHandler(timer);

                if (resource.equals(RESOURCE_SESSION) && 

                    httpVerb == POST && 

                    params.get(FUNCTION_KEYWORD) != null) {

                    //System.out.println("function_keyword: " + params.get(FUNCTION_KEYWORD)[0]);

                    //System.out.println("function set access: " + FUNCTION_NAME_SET_ACCESS);

                        if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_LOGIN)) {

                            login();

                            status = true;

                        } else if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_LOGOUT)) {

                            logout();

                            status = true;

                        } else if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_SET_ACCESS)) {

                            //System.out.println("setting access in resourceHandler");

                            setaccess();

                            status = true;

                            //System.out.println("done setting access");

                        }

                    } else if (resource.equals(RESOURCE_META)) {

                        if(params != null && params.get(FUNCTION_KEYWORD) != null &&

                           params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_GENERATE_MISSING_SYSTEM_METADATA))

                        { //generate system metadata for any object that is

                          //a) not system metadata itself

                          //b) does not already have a system metadata id in the systemmetadata table

                          //c) not a BIN object (data)

                            generateMissingSystemMetadata();

                            status = true;

                        }

                        else

                        {

                            loadSessionData();

                            String objectId = request.getPathInfo();

                            if (objectId != null && objectId.length() > 1) 

                            {

                                objectId = request.getPathInfo().substring(1);

                            }

                            getSystemMetadataObject(objectId);

                            status = true;

                        }

                    } else if (resource.equals(RESOURCE_OBJECTS)) {

                    logMetacat.debug("D1 Rest: Starting resource processing...");

                    loadSessionData();

                    String objectId = request.getPathInfo();

                    if (objectId != null && objectId.length() > 1) 

                    {

                        objectId = request.getPathInfo().substring(1);

                    }

                    else

                    {

                        objectId = null;

                    }

                    logMetacat.debug("verb:" + httpVerb);

                    if (httpVerb == GET) {

                        getObject(objectId);

                        status = true;

                    } else if (httpVerb == POST) {

                        putObject(objectId, FUNCTION_NAME_INSERT);

                        status = true;

                    } else if (httpVerb == PUT) {

                        putObject(objectId, FUNCTION_NAME_UPDATE);

                        status = true;

                    } else if (httpVerb == DELETE) {

                        deleteObject(objectId);

                        status = true;

                    }

                } else if (resource.equals(RESOURCE_IDENTIFIER)) {

                    String identifierId = request.getPathInfo();

                    if (identifierId != null && identifierId.length() > 1)

                        identifierId = request.getPathInfo().substring(1); //trim the slash

                    if (httpVerb == GET) {

                        String op = params.get(FUNCTION_KEYWORD)[0];

                        if (op.equals(FUNCTION_NAME_ISREGISTERED)) {

                            isRegistered(identifierId);

                            status = true;

                        } else if (op.equals(FUNCTION_NAME_GETALLDOCS)) {

                            getAllDocIds();

                            status = true;

                        } else if (op.equals(FUNCTION_NAME_GETNEXTREV)) {

                            getNextRevision(identifierId);

                            status = true;

                        } else if (op.equals(FUNCTION_NAME_GETNEXTOBJ)) {

                            getNextObject();

                            status = true;

                        } 

                    } else if (httpVerb == PUT) {

                        //Earthgrid API > Identifier Service > addLSID Function 

                        printError(

                                "This method is not supported by metacat.  To "

                                        + "add a new LSID, add a document to metacat.",

                                response);

                        status = true;

                    }

                } else if (resource.equals(RESOURCE_LOG)) {

                    //handle log events

                    if(httpVerb == GET)

                    {

                        getLog();

                        status = true;

                    }

                    else

                    {

                        printError("POST, PUT, DELETE is not supported for logs.", response);

                        status = true;

                    }

                }

                if (!status)

                    printError("Incorrect parameters!", response);

            } else {

                printError("Incorrect resource!", response);

            }

        } catch (Exception e) {

            logMetacat.error(e.getMessage());

            e.printStackTrace();

        }

    }

    /**

     * get the logs from the CrudService based on passed params.  Available 

     * params are token, fromDate, toDate, event.  See 

     * http://mule1.dataone.org/ArchitectureDocs/mn_api_crud.html#MN_crud.getLogRecords

     * for more info

     */

    private void getLog()

    {

        OutputStream out = null;

        try

        {

            out = response.getOutputStream();

            AuthToken token = new AuthToken(sessionId);

            String fromDateS = params.get("fromDate")[0];

            Date fromDate = null;

            String toDateS = params.get("toDate")[0];

            Date toDate = null;

            String eventS = params.get("event")[0];

            Event event = null;

            SimpleDateFormat sdf = new SimpleDateFormat();

            if(fromDateS != null)

            {

                fromDate = new Date(new Long(fromDateS).longValue());//sdf.parse(fromDateS, new ParsePosition(0));

            }

            if(toDateS != null)

            {

                toDate = new Date(new Long(toDateS).longValue());//sdf.parse(toDateS, new ParsePosition(0));

            }

            if(eventS != null)

            {

                event = Event.convert(eventS);

            }

            Log log = CrudService.getInstance().getLogRecords(token, fromDate, toDate, event);

            serializeServiceType(Log.class, log, out);

        }

        catch(Exception e)

        {

            String msg = "Could not get logs from CrudService: " + e.getMessage();

            ServiceFailure sf = new ServiceFailure("1490", msg);

            logMetacat.error(msg);

            e.printStackTrace();

            serializeException(sf, out);

        }

    }

    /**

     *  copies request parameters to a hashtable which is given as argument to native metacathandler functions  

     */

    private void initParams() {

        String name = null;

        String[] value = null;

        Enumeration paramlist = request.getParameterNames();

        while (paramlist.hasMoreElements()) {

            name = (String) paramlist.nextElement();

            value = request.getParameterValues(name);

            params.put(name, value);

        }

    }

    /**

     * 

     * Load user details of metacat session from the request 

     * 

     */

    private void loadSessionData()

      throws Exception

    {

        SessionData sessionData = RequestUtil.getSessionData(request);

        try

        {

            username = null;

            password = null;

            groupNames = null;

            sessionId = null;

            boolean validSession = false;

            SessionService ss = SessionService.getInstance();

            System.out.println("sessionData: " + sessionData);

            System.out.println("username: " + sessionData.getUserName());

            System.out.println("sessionid: " + sessionData.getId());

            //validate the session

            if(ss.isSessionRegistered(sessionData.getId()) && 

               !(sessionData.getUserName().equals("public") || sessionData.getId().equals("0")))

            {

                validSession = true;

            }

            if(validSession)

            {

                //if the session is valid, set these variables

                username = sessionData.getUserName();

                password = sessionData.getPassword();

                groupNames = sessionData.getGroupNames();

                sessionId = sessionData.getId();

                System.out.println("setting sessionid to " + sessionId);

                System.out.println("username: " + username);

            }

            //if the session is not valid or the username is null, set

            //username to public

            if (username == null) 

            {

                System.out.println("setting username to public.");

                username = "public";

            }

        }

        catch(Exception e)

        {

            throw new Exception("Could not load the session data: " + e.getMessage());

        }

    }

    /**

     * generate missing system metadata for any science metadata objects

     * that don't already have it. https://trac.dataone.org/ticket/591

     * 

     * called with POST meta/?op=generatemissingsystemmetadata

     */

    private void generateMissingSystemMetadata()

    {

        AuthToken token = new AuthToken(sessionId);

        CrudService.getInstance().generateMissingSystemMetadata(token);

    }

    /**

     *  Earthgrid API > Identifier Service > isRegistered Function : 

     *  calls MetacatHandler > handleIdIsRegisteredAction

     * @param guid

     * @throws IOException

     */

    private void isRegistered(String guid) throws IOException

    {

        // Look up the localId for this guid

        IdentifierManager im = IdentifierManager.getInstance();

        String localId = "";

        try {

            localId = im.getLocalId(guid);

        } catch (McdbDocNotFoundException e) {

            // TODO: Need to return the proper DataONE exception

        }

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

        PrintWriter out = response.getWriter();

        handler.handleIdIsRegisteredAction(out, params, response);

        out.close();

    }

    /**

     * Earthgrid API > Identifier Service > getAllDocIds Function : 

     * calls MetacatHandler > handleGetAllDocidsAction

     * @throws IOException

     */

    private void getAllDocIds() throws IOException {

        PrintWriter out = response.getWriter();

        handler.handleGetAllDocidsAction(out, params, response);

        out.close();

    }

    /**

     * Earthgrid API > Identifier Service > getNextRevision Function : 

     * calls MetacatHandler > handleGetRevisionAndDocTypeAction

     * @param guid

     * @throws IOException

     */

    private void getNextRevision(String guid) throws IOException 

    {

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

        PrintWriter out = response.getWriter();

        //handler.handleGetRevisionAndDocTypeAction(out, params);

        try {

            // Make sure there is a docid

            if (guid == null || guid.equals("")) {

                throw new Exception("User didn't specify docid!");

            }

            // Look up the localId for this guid

            IdentifierManager im = IdentifierManager.getInstance();

            String localId = "";

            try {

                localId = im.getLocalId(guid);

            } catch (McdbDocNotFoundException e) {

                // TODO: Need to return the proper DataONE exception

            }

            // Create a DBUtil object

            DBUtil dbutil = new DBUtil();

            // Get a rev and doctype

            String revAndDocType = dbutil

                    .getCurrentRevisionAndDocTypeForGivenDocument(localId);

            int revision = Integer.parseInt(revAndDocType.split(";")[0]) + 1;

            out.println("<?xml version=\"1.0\"?>");

            out.print("<next-revision>");

            out.print(revision);

            out.print("</next-revision>");

        } catch (Exception e) {

            // Handle exception

            out.println("<?xml version=\"1.0\"?>");

            out.println("<error>");

            out.println(e.getMessage());

            out.println("</error>");

        }

        out.close();

    }

    /**

     * Earthgrid API > Identifier Service > getNextObject Function : 

     * calls MetacatHandler > handleGetMaxDocidAction

     * @throws IOException

     */

    private void getNextObject() throws IOException {

        PrintWriter out = response.getWriter();

        handler.handleGetMaxDocidAction(out, params, response);

        out.close();

    }

    /**

     * Implements REST version of DataONE CRUD API --> get

     * @param guid ID of data object to be read

     */

    private void getObject(String guid) {

        CrudService cs = CrudService.getInstance();

        cs.setParamsFromRequest(request);

        AuthToken token = new AuthToken(sessionId);

        OutputStream out = null;

        try {

            out = response.getOutputStream();

            if(guid != null)

            { //get a specific document

                Identifier id = new Identifier();

                id.setValue(guid);

                InputStream data = cs.get(token, id);

                IOUtils.copyLarge(data, response.getOutputStream());

            }

            else

            { //call listObjects with specified params

                Date startTime = null;

                Date endTime = null;

                ObjectFormat objectFormat = null;

                boolean replicaStatus = false;

                int start = 0;

                int count = 1000;

                Enumeration paramlist = request.getParameterNames();

                while (paramlist.hasMoreElements()) 

                { //parse the params and make the crud call

                    String name = (String) paramlist.nextElement();

                    String[] value = (String[])request.getParameterValues(name);

                    System.out.println("name: " + name + " value: " + value);

                    if(name.equals("startTime") && value != null)

                    {

                        try

                        {

                          startTime = DateFormat.getDateTimeInstance().parse(value[0]);

                        }

                        catch(Exception e)

                        {  //if we can't parse it, just don't use the startTime param

                            System.out.println("Could not parse startTime: " + value[0]);

                            startTime = null;

                        }

                    }

                    else if(name.equals("endTime") && value != null)

                    {

                        try

                        {

                          endTime = DateFormat.getDateTimeInstance().parse(value[0]);

                        }

                        catch(Exception e)

                        {  //if we can't parse it, just don't use the endTime param

                            System.out.println("Could not parse endTime: " + value[0]);

                            endTime = null;

                        }

                    }

                    else if(name.equals("objectFormat") && value != null)

                    {

                        objectFormat = ObjectFormat.convert(value[0]);

                    }

                    else if(name.equals("replicaStatus") && value != null)

                    {

                        if(value != null && 

                           value.length > 0 && 

                           (value[0].equals("true") || value[0].equals("TRUE") || value[0].equals("YES")))

                        {

                            replicaStatus = true;

                        }

                    }

                    else if(name.equals("start") && value != null)

                    {

                        start = new Integer(value[0]).intValue();

                    }

                    else if(name.equals("count") && value != null)

                    {

                        count = new Integer(value[0]).intValue();

                    }

                }

                //make the crud call

                /*System.out.println("token: " + token + " startTime: " + startTime +

                        " endtime: " + endTime + " objectFormat: " + 

                        objectFormat + " replicaStatus: " + replicaStatus + 

                        " start: " + start + " count: " + count);

                */

                ObjectList ol = cs.listObjects(token, startTime, endTime, 

                        objectFormat, replicaStatus, start, count);

                ol = cs.listObjects(token, null, null, null, false, 0, 1000);

                StringReader sr = new StringReader(ol.toString());                

                out = response.getOutputStream();                

                // Serialize and write it to the output stream

                try {

                    serializeServiceType(ObjectList.class, ol, out);

                } catch (JiBXException e) {

                    throw new ServiceFailure("1190", "Failed to serialize ObjectList: " + e.getMessage());

                }

            }

        } catch (BaseException e) {

                serializeException(e, out);

        } catch (IOException e) {

            ServiceFailure sf = new ServiceFailure("1030", e.getMessage());

            serializeException(sf, out);

        }

    }

    /**

     * Implements REST version of DataONE CRUD API --> getSystemMetadata

     * @param guid ID of data object to be read

     */

    private void getSystemMetadataObject(String guid) {

        CrudService cs = CrudService.getInstance();

        cs.setParamsFromRequest(request);

        AuthToken token = new AuthToken(sessionId);

        OutputStream out = null;

        try {

            out = response.getOutputStream();

            Identifier id = new Identifier();

            id.setValue(guid);

            SystemMetadata sysmeta = cs.getSystemMetadata(token, id);

            // Serialize and write it to the output stream

            try {

                serializeServiceType(SystemMetadata.class, sysmeta, out);

            } catch (JiBXException e) {

                throw new ServiceFailure("1190", "Failed to serialize SystemMetadata: " + e.getMessage());

            }

        } catch (BaseException e) {

                serializeException(e, out);

        } catch (IOException e) {

            ServiceFailure sf = new ServiceFailure("1030", e.getMessage());

            serializeException(sf, out);

        } finally {

            IOUtils.closeQuietly(out);

        }

    }

    /**

     * serialize an object of type to out

     * @param type the class of the object to serialize (i.e. SystemMetadata.class)

     * @param object the object to serialize

     * @param out the stream to serialize it to

     * @throws JiBXException

     */

    private void serializeServiceType(Class type, Object object, OutputStream out)

      throws JiBXException

    {

        IBindingFactory bfact = BindingDirectory.getFactory(type);

        IMarshallingContext mctx = bfact.createMarshallingContext();

        mctx.marshalDocument(object, "UTF-8", null, out);

    }

    /**

     * deserialize an object of type from is

     * @param type the class of the object to serialize (i.e. SystemMetadata.class)

     * @param is the stream to deserialize from

     * @throws JiBXException

     */

    private Object deserializeServiceType(Class type, InputStream is)

      throws JiBXException

    {

        IBindingFactory bfact = BindingDirectory.getFactory(type);

        IUnmarshallingContext uctx = bfact.createUnmarshallingContext();

        Object o = (Object) uctx.unmarshalDocument(is, null);

        return o;

    }

    /**

     * Earthgrid API > Query Service > Query Function : translates ecogrid query document to metacat query 

     * then calls DBQuery > createResultDocument function and then again translate resultset to ecogrid resultset

     * 

     * NOTE:

     *      This is the only method that uses EcoGrid classes for its implementation.  

     *      It does so because it takes an EcoGrid Query as input, and outputs an

     *      EcoGrid ResultSet document.  These documents are parsed by the auto-generated

     *      EcoGrid classes from axis, and so we link to them here rather than re-inventing them.

     *      This creates a circular dependency, because the Metacat classes are needed

     *      to build the EcoGrid implementation, and the EcoGrid jars are needed to build this query()

     *      method.  This circularity could be resolved by moving the EcoGrid classes

     *      to Metacat directly.  As we transition away from EcoGrid SOAP methods in

     *      favor of these REST interfaces, this circular dependency can be eliminated.

     *        

     * @throws Exception

     */

    private void query() throws Exception {

        /*  This block commented out because of the EcoGrid circular dependency.

         *  For now, query will not be supported until the circularity can be

         *  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);

            DBQuery metacat = new DBQuery();

            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();

        }*/

        response.setContentType("text/xml");

        PrintWriter out = response.getWriter();

        out.print("<error>Query operation not yet supported by Metacat.</error>");

        out.close();

    }

    private String streamToString(InputStream is)

    throws IOException

    {

        byte b[] = new byte[1024];

        int numread = is.read(b, 0, 1024);

        String response = new String();

        while(numread != -1)

        {

            response += new String(b, 0, numread);

            numread = is.read(b, 0, 1024);

        }

        return response;

    }

    private InputStream stringToStream(String s)

    throws IOException

    {

        ByteArrayInputStream bais = new ByteArrayInputStream(s.getBytes());

        return bais;

    }

    /**

     * Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction 

     * 

     * @param guid ID of data object to be inserted or updated

     * @throws IOException

     */

    private void putObject(String guid, String action) {

        logMetacat.debug("Entering putObject: " + guid + "/" + action);

        OutputStream out = null;

        try {

            out = response.getOutputStream();

        } catch (IOException e1) {

            logMetacat.error("Could not get the output stream for writing in putObject");

        }

        try {

            // Read the incoming data from its Mime Multipart encoding

            logMetacat.debug("Disassembling MIME multipart form");

            InputStream object = null;

            InputStream sysmeta = null;

            //HACK: Since mmp seems to have a bug where large object parts get truncated,

            //parse the stream here.  This has the disavantage of putting the

            //stream into memory.

            String s = streamToString(request.getInputStream());

            String searchString = "Content-Disposition: attachment; filename=systemmetadata";

            String endString = "------=_Part";

            int searchStringIndex = s.indexOf(searchString);

            sysmeta = new ByteArrayInputStream(

                    s.substring(searchStringIndex +

                            searchString.length(), 

                            s.indexOf(endString, searchStringIndex)).trim().getBytes());

            searchString = "Content-Disposition: attachment; filename=object";

            searchStringIndex = s.indexOf(searchString);

            object = new ByteArrayInputStream(

                    s.substring(searchStringIndex +

                            searchString.length(), 

                            s.indexOf(endString, searchStringIndex)).trim().getBytes());

            /*

            //This code should work, however there seems to be a bug in part.getInputStream()

            //where it does not return the entire stream.  Only about the first 6kB 

            //are actually returned.

            MimeMultipart mmp = new MimeMultipart(new InputStreamDataSource("message", request.getInputStream()));

            logMetacat.debug("MMP created.");

            //mmp.writeTo(System.out);

            for (int i = 0; i < mmp.getCount(); i++) {

                BodyPart part = mmp.getBodyPart(i);

                String name = part.getFileName();

                logMetacat.debug("Part name is: " + name);

                logMetacat.debug("Part has class name: " + part.getClass().getName());

                if (name.equals("object")) {

                    object = part.getInputStream();

                    try

                    {

                        String s = streamToString(object);

                        System.out.println("doc text: " + s);

                        System.out.println("size of doc text is: " + s.getBytes().length);

                        object = stringToStream(s);

                    }

                    catch(Exception e)

                    {}

                    System.out.println("Found object part, size is: " + part.getSize());

                } else if (name.equals("systemmetadata")) {

                    sysmeta = part.getInputStream();

                    try

                    {

                      String s = streamToString(sysmeta);

                      System.out.println("system metadata part: " + s);

                      sysmeta = stringToStream(s);

                    }

                    catch(Exception e){}

                    System.out.println("system metadata part, size is " + part.getSize());