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/**
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* '$RCSfile$'
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* Copyright: 2000 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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*
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* '$Author: $'
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* '$Date: 2009-06-13 15:28:13 +0300 $'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat.dataone;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.io.PrintWriter;
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import java.sql.SQLException;
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import java.util.Date;
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import java.util.Enumeration;
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import java.util.Hashtable;
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import java.util.Timer;
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import javax.servlet.ServletContext;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import org.apache.commons.io.IOUtils;
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import org.apache.log4j.Logger;
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import org.dataone.service.exceptions.IdentifierNotUnique;
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import org.dataone.service.exceptions.InsufficientResources;
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import org.dataone.service.exceptions.InvalidRequest;
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.exceptions.UnsupportedType;
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import org.dataone.service.mn.MemberNodeCrud;
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import org.dataone.service.types.AuthToken;
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import org.dataone.service.types.Checksum;
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import org.dataone.service.types.DescribeResponse;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.LogRecordSet;
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import org.dataone.service.types.SystemMetadata;
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import org.jibx.runtime.BindingDirectory;
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import org.jibx.runtime.IBindingFactory;
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import org.jibx.runtime.IMarshallingContext;
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import org.jibx.runtime.JiBXException;
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import com.gc.iotools.stream.is.InputStreamFromOutputStream;
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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import edu.ucsb.nceas.metacat.DocumentImpl;
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import edu.ucsb.nceas.metacat.EventLog;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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import edu.ucsb.nceas.metacat.McdbException;
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import edu.ucsb.nceas.metacat.MetacatHandler;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler;
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import edu.ucsb.nceas.metacat.service.SessionService;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.metacat.util.SessionData;
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import edu.ucsb.nceas.utilities.ParseLSIDException;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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/**
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*
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* Implements DataONE MemberNode CRUD API for Metacat.
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*
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* @author Matthew Jones
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*/
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public class CrudService implements MemberNodeCrud {
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private ServletContext servletContext;
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private HttpServletRequest request;
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private HttpServletResponse response;
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// private Logger logMetacat;
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private MetacatHandler handler;
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// private String username;
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// private String password;
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// private String sessionId;
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// private String[] groupNames;
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private Hashtable<String, String[]> params;
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Logger logMetacat = null;
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/**
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* Initializes new instance by setting servlet context,request and response.
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* TODO: remove dependency on Servlet infrastructure
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* TODO: Make this a real service, and make it a Singleton
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*/
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public CrudService(ServletContext servletContext,
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HttpServletRequest request, HttpServletResponse response) {
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this.servletContext = servletContext;
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this.request = request;
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this.response = response;
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logMetacat = Logger.getLogger(CrudService.class);
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handler = new MetacatHandler(this.servletContext, new Timer());
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initParams();
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// loadSessionData();
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}
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/**
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* copies request parameters to a Hashtable which is given as argument to
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* native MetacatHandler functions
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*/
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private void initParams() {
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String name = null;
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String[] value = null;
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params = new Hashtable<String, String[]>();
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Enumeration paramlist = request.getParameterNames();
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while (paramlist.hasMoreElements()) {
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name = (String) paramlist.nextElement();
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value = request.getParameterValues(name);
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params.put(name, value);
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}
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}
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/**
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*
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* Load user details of metacat session from the request
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*
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*/
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// private void loadSessionData() {
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// SessionData sessionData = RequestUtil.getSessionData(request);
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//
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// // TODO: validate the session before allowing these values to be set
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// username = sessionData.getUserName();
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// password = sessionData.getPassword();
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// groupNames = sessionData.getGroupNames();
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// sessionId = sessionData.getId();
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//
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// if (username == null) {
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// username = "public";
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// }
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// }
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/*
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* Look up the information on the session using the token provided in
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* the AuthToken. The Session should have all relevant user information.
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* If the session has expired or is invalid, the 'public' session will
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* be returned, giving the user anonymous access.
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*/
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private static SessionData getSessionData(AuthToken token) {
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SessionData sessionData = null;
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String sessionId = "PUBLIC";
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if (token != null) {
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sessionId = token.getToken();
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}
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// if the session id is registered in SessionService, get the
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// SessionData for it. Otherwise, use the public session.
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if (SessionService.isSessionRegistered(sessionId)) {
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sessionData = SessionService.getRegisteredSession(sessionId);
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} else {
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sessionData = SessionService.getPublicSession();
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}
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return sessionData;
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}
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public Identifier create(AuthToken token, Identifier guid,
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InputStream object, SystemMetadata sysmeta) throws InvalidToken,
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ServiceFailure, NotAuthorized, IdentifierNotUnique, UnsupportedType,
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InsufficientResources, InvalidSystemMetadata, NotImplemented {
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logMetacat.debug("Starting CrudService.create()...");
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// authenticate & get user info
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SessionData sessionData = getSessionData(token);
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String username = sessionData.getUserName();
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String[] groups = sessionData.getGroupNames();
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// verify that guid == SystemMetadata.getIdentifier()
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logMetacat.debug("Comparing guid|sysmeta_guid: " + guid.getValue() + "|" + sysmeta.getIdentifier().getValue());
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if (!guid.getValue().equals(sysmeta.getIdentifier().getValue())) {
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throw new InvalidSystemMetadata(1180,
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"GUID in method call does not match GUID in system metadata.");
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}
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logMetacat.debug("Checking if identifier exists...");
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// Check that the identifier does not already exist
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IdentifierManager im = IdentifierManager.getInstance();
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if (im.identifierExists(guid.getValue())) {
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throw new IdentifierNotUnique(1120,
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"GUID is already in use by an existing object.");
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}
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// generate guid/localId pair for object
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logMetacat.debug("Generating a guid/localId mapping");
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String localId = im.generateLocalId(guid.getValue(), 1);
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// Check if we are handling metadata or data
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boolean isScienceMetadata = isScienceMetadata(sysmeta);
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if (isScienceMetadata) {
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// TODO: CASE METADATA:
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// Setup and call handleInsertOrUpdate()
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} else {
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// TODO: DEFAULT CASE: DATA (needs to be checked and completed)
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try {
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logMetacat.debug("Case DATA: starting to write to disk.");
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if (DocumentImpl.getDataFileLockGrant(localId)) {
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// Save the data file to disk using "localId" as the name
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try {
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String datafilepath = PropertyService.getProperty("application.datafilepath");
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File dataDirectory = new File(datafilepath);
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dataDirectory.mkdirs();
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File newFile = writeStreamToFile(dataDirectory, localId, object);
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// TODO: Check that the file size matches SystemMetadata
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// long size = newFile.length();
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// if (size == 0) {
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// throw new IOException("Uploaded file is 0 bytes!");
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// }
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//register the file in the database (which generates an exception
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// if the docid is not acceptable or other untoward things happen
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try {
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logMetacat.debug("Registering document...");
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DocumentImpl.registerDocument(localId, "BIN", localId,
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username, groups);
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logMetacat.debug("Registrtion step completed.");
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} catch (SQLException e) {
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//newFile.delete();
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logMetacat.debug("SQLE: " + e.getMessage());
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e.printStackTrace(System.out);
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throw new ServiceFailure(1190, "Registration failed: " + e.getMessage());
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} catch (AccessionNumberException e) {
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//newFile.delete();
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logMetacat.debug("ANE: " + e.getMessage());
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e.printStackTrace(System.out);
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throw new ServiceFailure(1190, "Registration failed: " + e.getMessage());
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} catch (Exception e) {
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//newFile.delete();
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logMetacat.debug("Exception: " + e.getMessage());
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e.printStackTrace(System.out);
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throw new ServiceFailure(1190, "Registration failed: " + e.getMessage());
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}
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logMetacat.debug("Logging the creation event.");
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EventLog.getInstance().log(request.getRemoteAddr(),
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username, localId, "create");
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// Force replication this data file
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// To data file, "insert" and update is same
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// The fourth parameter is null. Because it is notification
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// server and this method is in MetaCatServerlet. It is
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// original command, not get force replication info from
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// another metacat
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// TODO: note that GUID mapping is not being replicated
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logMetacat.debug("Scheduling replication.");
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ForceReplicationHandler frh = new ForceReplicationHandler(
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localId, "insert", false, null);
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} catch (PropertyNotFoundException e) {
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throw new ServiceFailure(1190, "Could not lock file for writing:" + e.getMessage());
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}
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}
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} catch (Exception e) {
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// Could not get a lock on the document, so we can not update the file now
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throw new ServiceFailure(1190, "Failed to lock file: " + e.getMessage());
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}
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// Insert the system metadata into the object store
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insertSystemMetadata(sysmeta, sessionData);
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}
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logMetacat.debug("Returning from CrudService.create()");
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return guid;
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}
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298
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299
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public Identifier delete(AuthToken token, Identifier guid)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
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NotImplemented {
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throw new NotImplemented(1000, "This method not yet implemented.");
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}
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304
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305
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public DescribeResponse describe(AuthToken token, Identifier guid)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
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NotImplemented {
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308
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throw new NotImplemented(1000, "This method not yet implemented.");
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309
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}
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310
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311
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public InputStream get(AuthToken token, Identifier guid)
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312
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
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NotImplemented {
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314
|
|
315
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// Retrieve the session information from the AuthToken
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// If the session is expired, then the user is 'public'
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final SessionData sessionData = getSessionData(token);
|
318
|
|
319
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// Look up the localId for this global identifier
|
320
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IdentifierManager im = IdentifierManager.getInstance();
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try {
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322
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final String localId = im.getLocalId(guid.getValue());
|
323
|
|
324
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final InputStreamFromOutputStream<String> objectStream =
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325
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new InputStreamFromOutputStream<String>() {
|
326
|
|
327
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@Override
|
328
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public String produce(final OutputStream dataSink) throws Exception {
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329
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330
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try {
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331
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handler.readFromMetacat(request.getRemoteAddr(), null,
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dataSink, localId, "xml",
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sessionData.getUserName(),
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sessionData.getGroupNames(), true, params);
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335
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} catch (PropertyNotFoundException e) {
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336
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throw new ServiceFailure(1030, e.getMessage());
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337
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} catch (ClassNotFoundException e) {
|
338
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throw new ServiceFailure(1030, e.getMessage());
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339
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} catch (IOException e) {
|
340
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throw new ServiceFailure(1030, e.getMessage());
|
341
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} catch (SQLException e) {
|
342
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throw new ServiceFailure(1030, e.getMessage());
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343
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} catch (McdbException e) {
|
344
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throw new ServiceFailure(1030, e.getMessage());
|
345
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} catch (ParseLSIDException e) {
|
346
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throw new NotFound(1020, e.getMessage());
|
347
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} catch (InsufficientKarmaException e) {
|
348
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throw new NotAuthorized(1000, "Not authorized for get().");
|
349
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}
|
350
|
|
351
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return "Completed";
|
352
|
}
|
353
|
};
|
354
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return objectStream;
|
355
|
|
356
|
} catch (McdbDocNotFoundException e) {
|
357
|
throw new NotFound(1020, e.getMessage());
|
358
|
}
|
359
|
}
|
360
|
|
361
|
public Checksum getChecksum(AuthToken token, Identifier guid)
|
362
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
363
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InvalidRequest, NotImplemented {
|
364
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throw new NotImplemented(1000, "This method not yet implemented.");
|
365
|
}
|
366
|
|
367
|
public Checksum getChecksum(AuthToken token, Identifier guid,
|
368
|
String checksumAlgorithm) throws InvalidToken, ServiceFailure,
|
369
|
NotAuthorized, NotFound, InvalidRequest, NotImplemented {
|
370
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throw new NotImplemented(1000, "This method not yet implemented.");
|
371
|
}
|
372
|
|
373
|
public LogRecordSet getLogRecords(AuthToken token, Date fromDate, Date toDate)
|
374
|
throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,
|
375
|
NotImplemented {
|
376
|
throw new NotImplemented(1000, "This method not yet implemented.");
|
377
|
}
|
378
|
|
379
|
public SystemMetadata getSystemMetadata(AuthToken token, Identifier guid)
|
380
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
381
|
InvalidRequest, NotImplemented {
|
382
|
|
383
|
// TODO: Look up ID of system metadata based on guid
|
384
|
// TODO: Initially from document, later from entry in table?
|
385
|
|
386
|
// TODO: Read system metadata from disk and create SystemMetadata object
|
387
|
// TODO: Follows same implementation plan as get()
|
388
|
|
389
|
// TODO: return it
|
390
|
throw new NotImplemented(1000, "This method not yet implemented.");
|
391
|
}
|
392
|
|
393
|
public Identifier update(AuthToken token, Identifier guid,
|
394
|
InputStream object, Identifier obsoletedGuid, SystemMetadata sysmeta)
|
395
|
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
|
396
|
UnsupportedType, InsufficientResources, NotFound, InvalidSystemMetadata,
|
397
|
NotImplemented {
|
398
|
throw new NotImplemented(1000, "This method not yet implemented.");
|
399
|
}
|
400
|
|
401
|
private File writeStreamToFile(File dir, String fileName, InputStream data)
|
402
|
throws ServiceFailure {
|
403
|
// logMetacat.debug("***********************************************");
|
404
|
// logMetacat.debug("** FILE TEST FROM CS **");
|
405
|
// logMetacat.debug("***********************************************");
|
406
|
|
407
|
File newFile = new File(dir, fileName);
|
408
|
logMetacat.debug("Filename for write is: " + newFile.getAbsolutePath());
|
409
|
|
410
|
try {
|
411
|
if (newFile.createNewFile()) {
|
412
|
// logMetacat.debug("File doesn't yet exist, so write to it.");
|
413
|
// logMetacat.debug("Creating file stream...");
|
414
|
|
415
|
// write data stream to desired file
|
416
|
OutputStream os = new FileOutputStream(newFile);
|
417
|
// logMetacat.debug("Copying file stream...");
|
418
|
long length = IOUtils.copyLarge(data, os);
|
419
|
os.flush();
|
420
|
// logMetacat.debug("Closing file stream...");
|
421
|
os.close();
|
422
|
// logMetacat.debug("Done with file stream...");
|
423
|
} else {
|
424
|
logMetacat.debug("File creation failed, or file already exists.");
|
425
|
throw new ServiceFailure(1190, "File already exists: " + fileName);
|
426
|
}
|
427
|
} catch (FileNotFoundException e) {
|
428
|
logMetacat.debug("FNF: " + e.getMessage());
|
429
|
throw new ServiceFailure(1190, "File not found: " + fileName + " "
|
430
|
+ e.getMessage());
|
431
|
} catch (IOException e) {
|
432
|
logMetacat.debug("IOE: " + e.getMessage());
|
433
|
throw new ServiceFailure(1190, "File was not written: " + fileName
|
434
|
+ " " + e.getMessage());
|
435
|
}
|
436
|
|
437
|
// logMetacat.debug("***********************************************");
|
438
|
// logMetacat.debug("** END FILE TEST **");
|
439
|
// logMetacat.debug("***********************************************");
|
440
|
|
441
|
return newFile;
|
442
|
}
|
443
|
|
444
|
/**
|
445
|
* Determine if a given object should be treated as an XML science metadata
|
446
|
* object.
|
447
|
*
|
448
|
* TODO: This test should be externalized in a configuration dictionary rather than being hardcoded.
|
449
|
*
|
450
|
* @param sysmeta the SystemMetadata describig the object
|
451
|
* @return true if the object should be treated as science metadata
|
452
|
*/
|
453
|
private boolean isScienceMetadata(SystemMetadata sysmeta) {
|
454
|
boolean scimeta = false;
|
455
|
switch (sysmeta.getObjectFormat()) {
|
456
|
case EML_2_1_0: scimeta = true; break;
|
457
|
case EML_2_0_1: scimeta = true; break;
|
458
|
case EML_2_0_0: scimeta = true; break;
|
459
|
case FGDC_STD_001_1_1999: scimeta = true; break;
|
460
|
case FGDC_STD_001_1998: scimeta = true; break;
|
461
|
case NCML_2_2: scimeta = true; break;
|
462
|
}
|
463
|
|
464
|
return scimeta;
|
465
|
}
|
466
|
|
467
|
private void insertSystemMetadata(SystemMetadata sysmeta, SessionData sessionData)
|
468
|
throws ServiceFailure {
|
469
|
logMetacat.debug("Starting to insert SystemMetadata...");
|
470
|
IdentifierManager im = IdentifierManager.getInstance();
|
471
|
|
472
|
// generate guid/localId pair for sysmeta
|
473
|
String sysMetaGuid = DocumentUtil.generateDocumentId(1);
|
474
|
sysmeta.setDateSysMetadataModified(new Date());
|
475
|
|
476
|
String xml = new String(serializeSystemMetadata(sysmeta).toByteArray());
|
477
|
insertDocument(xml, sysMetaGuid, sessionData);
|
478
|
}
|
479
|
|
480
|
private void insertDocument(String xml, String guid, SessionData sessionData)
|
481
|
throws ServiceFailure {
|
482
|
logMetacat.debug("Starting to insert xml document...");
|
483
|
IdentifierManager im = IdentifierManager.getInstance();
|
484
|
|
485
|
// generate guid/localId pair for sysmeta
|
486
|
String localId = im.generateLocalId(guid, 1);
|
487
|
logMetacat.debug("Metadata guid|localId: " + guid + "|" +
|
488
|
localId);
|
489
|
|
490
|
// TODO: insert system metadata to metacat (probably at end)
|
491
|
// TODO: can't pass in the out PrintWriter, as we don't want to write
|
492
|
// error info on this stream -- need to be able to return to process
|
493
|
// the real object. So, need to:
|
494
|
// TODO: refactor handleInsertOrUpdateAction() to not output XML directly
|
495
|
// onto output stream, or alternatively, capture that and parse it to
|
496
|
// generate the right exceptions
|
497
|
String[] action = new String[1];
|
498
|
action[0] = "insert";
|
499
|
params.put("action", action);
|
500
|
String[] docid = new String[1];
|
501
|
docid[0] = localId;
|
502
|
params.put("docid", docid);
|
503
|
String[] doctext = new String[1];
|
504
|
doctext[0] = xml;
|
505
|
logMetacat.debug(doctext[0]);
|
506
|
params.put("doctext", doctext);
|
507
|
ByteArrayOutputStream output = new ByteArrayOutputStream();
|
508
|
PrintWriter pw = new PrintWriter(output);
|
509
|
handler.handleInsertOrUpdateAction(request.getRemoteAddr(), response,
|
510
|
pw, params, sessionData.getUserName(),
|
511
|
sessionData.getGroupNames());
|
512
|
logMetacat.debug(new String(output.toByteArray()));
|
513
|
logMetacat.debug("Finsihed inserting xml document.");
|
514
|
}
|
515
|
|
516
|
private ByteArrayOutputStream serializeSystemMetadata(SystemMetadata sysmeta)
|
517
|
throws ServiceFailure {
|
518
|
IBindingFactory bfact;
|
519
|
ByteArrayOutputStream sysmetaOut = null;
|
520
|
try {
|
521
|
bfact = BindingDirectory.getFactory(SystemMetadata.class);
|
522
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
523
|
sysmetaOut = new ByteArrayOutputStream();
|
524
|
mctx.marshalDocument(sysmeta, "UTF-8", null, sysmetaOut);
|
525
|
} catch (JiBXException e) {
|
526
|
throw new ServiceFailure(1190, "Failed to serialize and insert SystemMetadata: " + e.getMessage());
|
527
|
}
|
528
|
|
529
|
return sysmetaOut;
|
530
|
}
|
531
|
}
|