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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.io.StringBufferInputStream;
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import java.security.MessageDigest;
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import java.sql.SQLException;
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import java.util.*;
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import java.text.DateFormat;
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import java.text.SimpleDateFormat;
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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.*;
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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.IUnmarshallingContext;
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import org.jibx.runtime.JiBXException;
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import org.dataone.service.types.Identifier;
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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.MetacatResultSet;
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import edu.ucsb.nceas.metacat.MetacatResultSet.Document;
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import edu.ucsb.nceas.metacat.DBQuery;
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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.client.rest.MetacatRestClient;
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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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{
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private static CrudService crudService = null;
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private MetacatHandler handler;
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private Hashtable<String, String[]> params;
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private Logger logMetacat = null;
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private Logger logCrud = null;
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private String metacatUrl;
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private static final DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ssZ");
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/**
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* singleton accessor
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*/
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public static CrudService getInstance()
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{
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if(crudService == null)
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{
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crudService = new CrudService();
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}
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return crudService;
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}
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/**
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* Initializes new instance by setting servlet context,request and response.
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*/
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public CrudService() {
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//change crud service into a singleton. dont pass servlet data structures here
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logMetacat = Logger.getLogger(CrudService.class);
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logCrud = Logger.getLogger("DataOneLogger");
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try
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{
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String server = PropertyService.getProperty("server.name");
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String port = PropertyService.getProperty("server.httpPort");
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String context = PropertyService.getProperty("application.context");
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metacatUrl = "http://" + server + ":" + port + "/" + context;
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logMetacat.debug("Initializing CrudService with url " + metacatUrl);
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}
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catch(Exception e)
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{
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logMetacat.error("Could not find servlet url in CrudService: " + e.getMessage());
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e.printStackTrace();
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throw new RuntimeException("Error getting servlet url in CrudService: " + e.getMessage());
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}
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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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params = new Hashtable<String, String[]>();
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handler = new MetacatHandler(new Timer());
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}
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/**
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* return the context url CrudService is using.
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*/
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public String getContextUrl()
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{
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return metacatUrl;
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}
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/**
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* Set the context url that this service uses. It is normally not necessary
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* to call this method unless you are trying to connect to a server other
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* than the one in which this service is installed. Otherwise, this value is
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* taken from the metacat.properties file (server.name, server.port, application.context).
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*/
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public void setContextUrl(String url)
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{
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metacatUrl = url;
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}
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/**
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* set the params for this service from an HttpServletRequest param list
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*/
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public void setParamsFromRequest(HttpServletRequest request)
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{
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Enumeration paramlist = request.getParameterNames();
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while (paramlist.hasMoreElements()) {
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String name = (String) paramlist.nextElement();
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String[] value = (String[])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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* Authenticate against metacat and get a token.
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* @param username
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* @param password
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* @return
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* @throws ServiceFailure
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*/
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public AuthToken authenticate(String username, String password)
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throws ServiceFailure
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{
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/* TODO:
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* This method is not in the original D1 crud spec. It is highly
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* metacat centric. Higher level decisions need to be made on authentication
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* interfaces for D1 nodes.
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*/
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try
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| 200 |
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{
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MetacatRestClient restClient = new MetacatRestClient(getContextUrl());
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String response = restClient.login(username, password);
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String sessionid = restClient.getSessionId();
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SessionService sessionService = SessionService.getInstance();
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sessionService.registerSession(new SessionData(sessionid, username, new String[0], password, "CrudServiceLogin"));
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AuthToken token = new AuthToken(sessionid);
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5383
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EventLog.getInstance().log(metacatUrl,
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5384
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username, null, "authenticate");
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5436
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logCrud.info("authenticate");
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| 210 |
5370
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return token;
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}
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| 212 |
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catch(Exception e)
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| 213 |
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{
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| 214 |
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throw new ServiceFailure("1000", "Error authenticating with metacat: " + e.getMessage());
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| 215 |
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}
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| 216 |
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}
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| 217 |
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| 218 |
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/**
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| 219 |
5337
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* set the parameter values needed for this request
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| 220 |
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*/
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| 221 |
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public void setParameter(String name, String[] value)
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| 222 |
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{
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| 223 |
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params.put(name, value);
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| 224 |
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}
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| 225 |
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| 226 |
5377
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berkley
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/**
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| 227 |
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* Generate SystemMetadata for any object in the object store that does
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| 228 |
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* not already have it. SystemMetadata documents themselves, are, of course,
|
| 229 |
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* exempt. This is a utility method for migration of existing object
|
| 230 |
|
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* stores to DataONE where SystemMetadata is required for all objects. See
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| 231 |
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* https://trac.dataone.org/ticket/591
|
| 232 |
5378
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*
|
| 233 |
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* @param token an authtoken with appropriate permissions to read all
|
| 234 |
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* documents in the object store. To work correctly, this should probably
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| 235 |
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* be an adminstrative credential.
|
| 236 |
5377
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berkley
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*/
|
| 237 |
5378
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berkley
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public void generateMissingSystemMetadata(AuthToken token)
|
| 238 |
5377
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berkley
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{
|
| 239 |
5378
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berkley
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IdentifierManager im = IdentifierManager.getInstance();
|
| 240 |
5377
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berkley
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//get the list of ids with no SM
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| 241 |
5378
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berkley
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List<String> l = im.getLocalIdsWithNoSystemMetadata();
|
| 242 |
5377
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for(int i=0; i<l.size(); i++)
|
| 243 |
|
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{ //for each id, add a system metadata doc
|
| 244 |
5378
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berkley
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String localId = l.get(i);
|
| 245 |
5387
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berkley
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//System.out.println("Creating SystemMetadata for localId " + localId);
|
| 246 |
5378
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berkley
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//get the document
|
| 247 |
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try
|
| 248 |
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{
|
| 249 |
|
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//generate required system metadata fields from the document
|
| 250 |
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SystemMetadata sm = createSystemMetadata(localId, token);
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| 251 |
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//insert the systemmetadata object
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| 252 |
5379
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berkley
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SessionData sessionData = getSessionData(token);
|
| 253 |
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insertSystemMetadata(sm, sessionData);
|
| 254 |
5431
|
berkley
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String username = "public";
|
| 255 |
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if(sessionData != null)
|
| 256 |
|
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{
|
| 257 |
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username = sessionData.getUserName();
|
| 258 |
|
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}
|
| 259 |
5383
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EventLog.getInstance().log(metacatUrl,
|
| 260 |
5384
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username, localId, "generateMissingSystemMetadata");
|
| 261 |
5378
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berkley
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}
|
| 262 |
|
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catch(Exception e)
|
| 263 |
|
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{
|
| 264 |
5379
|
berkley
|
//e.printStackTrace();
|
| 265 |
5378
|
berkley
|
System.out.println("Exception generating missing system metadata: " + e.getMessage());
|
| 266 |
|
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logMetacat.error("Could not generate missing system metadata: " + e.getMessage());
|
| 267 |
|
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}
|
| 268 |
5377
|
berkley
|
}
|
| 269 |
5392
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logCrud.info("generateMissingSystemMetadata");
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| 270 |
5377
|
berkley
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}
|
| 271 |
|
|
|
| 272 |
5378
|
berkley
|
/**
|
| 273 |
5379
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berkley
|
* create an object via the crud interface
|
| 274 |
5378
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berkley
|
*/
|
| 275 |
5320
|
jones
|
public Identifier create(AuthToken token, Identifier guid,
|
| 276 |
5298
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jones
|
InputStream object, SystemMetadata sysmeta) throws InvalidToken,
|
| 277 |
|
|
ServiceFailure, NotAuthorized, IdentifierNotUnique, UnsupportedType,
|
| 278 |
|
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InsufficientResources, InvalidSystemMetadata, NotImplemented {
|
| 279 |
5319
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jones
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logMetacat.debug("Starting CrudService.create()...");
|
| 280 |
|
|
|
| 281 |
5329
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jones
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// authenticate & get user info
|
| 282 |
|
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SessionData sessionData = getSessionData(token);
|
| 283 |
5431
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berkley
|
String username = "public";
|
| 284 |
|
|
String[] groups = null;
|
| 285 |
|
|
if(sessionData != null)
|
| 286 |
|
|
{
|
| 287 |
|
|
username = sessionData.getUserName();
|
| 288 |
|
|
groups = sessionData.getGroupNames();
|
| 289 |
|
|
}
|
| 290 |
5383
|
berkley
|
String localId = null;
|
| 291 |
5319
|
jones
|
|
| 292 |
5376
|
berkley
|
if (username == null || username.equals("public"))
|
| 293 |
|
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{
|
| 294 |
5466
|
berkley
|
//TODO: many of the thrown exceptions do not use the correct error codes
|
| 295 |
|
|
//check these against the docs and correct them
|
| 296 |
5376
|
berkley
|
throw new NotAuthorized("1000", "User " + username + " is not authorized to create content." +
|
| 297 |
|
|
" If you are not logged in, please do so and retry the request.");
|
| 298 |
|
|
}
|
| 299 |
|
|
|
| 300 |
5319
|
jones
|
// verify that guid == SystemMetadata.getIdentifier()
|
| 301 |
5320
|
jones
|
logMetacat.debug("Comparing guid|sysmeta_guid: " + guid.getValue() + "|" + sysmeta.getIdentifier().getValue());
|
| 302 |
5329
|
jones
|
if (!guid.getValue().equals(sysmeta.getIdentifier().getValue())) {
|
| 303 |
5356
|
berkley
|
throw new InvalidSystemMetadata("1180",
|
| 304 |
5329
|
jones
|
"GUID in method call does not match GUID in system metadata.");
|
| 305 |
|
|
}
|
| 306 |
5319
|
jones
|
|
| 307 |
|
|
logMetacat.debug("Checking if identifier exists...");
|
| 308 |
|
|
// Check that the identifier does not already exist
|
| 309 |
5436
|
berkley
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 310 |
5320
|
jones
|
if (im.identifierExists(guid.getValue())) {
|
| 311 |
5356
|
berkley
|
throw new IdentifierNotUnique("1120",
|
| 312 |
5319
|
jones
|
"GUID is already in use by an existing object.");
|
| 313 |
|
|
}
|
| 314 |
|
|
|
| 315 |
5329
|
jones
|
// Check if we are handling metadata or data
|
| 316 |
|
|
boolean isScienceMetadata = isScienceMetadata(sysmeta);
|
| 317 |
5319
|
jones
|
|
| 318 |
5466
|
berkley
|
/* TODO:
|
| 319 |
|
|
* For EML documents, the data url field needs to be checked here
|
| 320 |
|
|
* and the describes and describedBy fields of the system metadata
|
| 321 |
|
|
* need to be set with the appropriate uri. Older EML documents
|
| 322 |
|
|
* maybe have ecogrid:// uri's embedded in them. See bug 618
|
| 323 |
|
|
* (https://trac.dataone.org/ticket/618) for more info on this.
|
| 324 |
|
|
*/
|
| 325 |
5329
|
jones
|
if (isScienceMetadata) {
|
| 326 |
5331
|
jones
|
// CASE METADATA:
|
| 327 |
|
|
try {
|
| 328 |
5466
|
berkley
|
//System.out.println("CrudService: inserting document with guid " + guid.getValue());
|
| 329 |
5350
|
berkley
|
this.insertDocument(object, guid, sessionData);
|
| 330 |
5383
|
berkley
|
localId = im.getLocalId(guid.getValue());
|
| 331 |
5331
|
jones
|
} catch (IOException e) {
|
| 332 |
|
|
String msg = "Could not create string from XML stream: " +
|
| 333 |
|
|
" " + e.getMessage();
|
| 334 |
|
|
logMetacat.debug(msg);
|
| 335 |
5356
|
berkley
|
throw new ServiceFailure("1190", msg);
|
| 336 |
5383
|
berkley
|
} catch(Exception e) {
|
| 337 |
|
|
String msg = "Unexpected error in CrudService.create: " + e.getMessage();
|
| 338 |
|
|
logMetacat.debug(msg);
|
| 339 |
|
|
throw new ServiceFailure("1190", msg);
|
| 340 |
5331
|
jones
|
}
|
| 341 |
5383
|
berkley
|
|
| 342 |
5319
|
jones
|
|
| 343 |
5329
|
jones
|
} else {
|
| 344 |
5331
|
jones
|
// DEFAULT CASE: DATA (needs to be checked and completed)
|
| 345 |
5460
|
berkley
|
localId = insertDataObject(object, guid, sessionData);
|
| 346 |
5331
|
jones
|
|
| 347 |
|
|
}
|
| 348 |
5319
|
jones
|
|
| 349 |
5331
|
jones
|
// For Metadata and Data, insert the system metadata into the object store too
|
| 350 |
5441
|
berkley
|
String sysMetaLocalId = insertSystemMetadata(sysmeta, sessionData);
|
| 351 |
|
|
//get the document info. add any access params for the sysmeta too
|
| 352 |
5466
|
berkley
|
//System.out.println("looking for access records to add for system " +
|
| 353 |
|
|
// "metadata who's parent doc's local id is " + localId);
|
| 354 |
5441
|
berkley
|
try
|
| 355 |
|
|
{
|
| 356 |
5444
|
berkley
|
Hashtable<String, Object> h = im.getDocumentInfo(localId.substring(0, localId.lastIndexOf(".")));
|
| 357 |
5441
|
berkley
|
Vector v = (Vector)h.get("access");
|
| 358 |
|
|
for(int i=0; i<v.size(); i++)
|
| 359 |
|
|
{
|
| 360 |
|
|
Hashtable ah = (Hashtable)v.elementAt(i);
|
| 361 |
|
|
String principal = (String)ah.get("principal_name");
|
| 362 |
|
|
String permission = (String)ah.get("permission");
|
| 363 |
|
|
String permissionType = (String)ah.get("permission_type");
|
| 364 |
|
|
String permissionOrder = (String)ah.get("permission_order");
|
| 365 |
5443
|
berkley
|
int perm = new Integer(permission).intValue();
|
| 366 |
5466
|
berkley
|
//System.out.println("found access record for principal " + principal);
|
| 367 |
|
|
//System.out.println("permission: " + perm + " perm_type: " + permissionType +
|
| 368 |
|
|
// " perm_order: " + permissionOrder);
|
| 369 |
5444
|
berkley
|
this.setAccess(token, guid, principal, perm, permissionType, permissionOrder, true);
|
| 370 |
5441
|
berkley
|
}
|
| 371 |
|
|
}
|
| 372 |
|
|
catch(Exception e)
|
| 373 |
|
|
{
|
| 374 |
|
|
logMetacat.error("Error setting permissions on System Metadata object " +
|
| 375 |
|
|
" with id " + sysMetaLocalId + ": " + e.getMessage());
|
| 376 |
5466
|
berkley
|
//TODO: decide if this error should cancel the entire create or
|
| 377 |
|
|
//if it should continue with just a logged error.
|
| 378 |
5441
|
berkley
|
}
|
| 379 |
|
|
|
| 380 |
|
|
|
| 381 |
5319
|
jones
|
logMetacat.debug("Returning from CrudService.create()");
|
| 382 |
5383
|
berkley
|
EventLog.getInstance().log(metacatUrl,
|
| 383 |
5384
|
berkley
|
username, localId, "create");
|
| 384 |
5459
|
berkley
|
logCrud.info("create D1GUID:" + guid.getValue() + ":D1SCIMETADATA:" + localId +
|
| 385 |
|
|
":D1SYSMETA:"+ sysMetaLocalId + ":");
|
| 386 |
5319
|
jones
|
return guid;
|
| 387 |
5298
|
jones
|
}
|
| 388 |
5353
|
berkley
|
|
| 389 |
|
|
/**
|
| 390 |
|
|
* update an existing object with a new object. Change the system metadata
|
| 391 |
|
|
* to reflect the changes and update it as well.
|
| 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 |
|
|
try
|
| 399 |
|
|
{
|
| 400 |
|
|
SessionData sessionData = getSessionData(token);
|
| 401 |
|
|
|
| 402 |
|
|
//find the old systemmetadata (sm.old) document id (the one linked to obsoletedGuid)
|
| 403 |
|
|
SystemMetadata sm = getSystemMetadata(token, obsoletedGuid);
|
| 404 |
|
|
//change sm.old's obsoletedBy field
|
| 405 |
|
|
List l = sm.getObsoletedByList();
|
| 406 |
|
|
l.add(guid);
|
| 407 |
|
|
sm.setObsoletedByList(l);
|
| 408 |
|
|
//update sm.old
|
| 409 |
|
|
updateSystemMetadata(sm, sessionData);
|
| 410 |
|
|
|
| 411 |
|
|
//change the obsoletes field of the new systemMetadata (sm.new) to point to the id of the old one
|
| 412 |
|
|
sysmeta.addObsolete(obsoletedGuid);
|
| 413 |
|
|
//insert sm.new
|
| 414 |
5459
|
berkley
|
String sysMetaLocalId = insertSystemMetadata(sysmeta, sessionData);
|
| 415 |
|
|
String localId;
|
| 416 |
5353
|
berkley
|
|
| 417 |
|
|
boolean isScienceMetadata = isScienceMetadata(sysmeta);
|
| 418 |
|
|
if(isScienceMetadata)
|
| 419 |
|
|
{
|
| 420 |
|
|
//update the doc
|
| 421 |
5459
|
berkley
|
localId = updateDocument(object, obsoletedGuid, guid, sessionData, false);
|
| 422 |
5353
|
berkley
|
}
|
| 423 |
|
|
else
|
| 424 |
|
|
{
|
| 425 |
|
|
//update a data file, not xml
|
| 426 |
5459
|
berkley
|
localId = insertDataObject(object, guid, sessionData);
|
| 427 |
5353
|
berkley
|
}
|
| 428 |
5383
|
berkley
|
|
| 429 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 430 |
5431
|
berkley
|
String username = "public";
|
| 431 |
|
|
if(sessionData != null)
|
| 432 |
|
|
{
|
| 433 |
|
|
username = sessionData.getUserName();
|
| 434 |
|
|
}
|
| 435 |
5383
|
berkley
|
EventLog.getInstance().log(metacatUrl,
|
| 436 |
5384
|
berkley
|
username, im.getLocalId(guid.getValue()), "update");
|
| 437 |
5459
|
berkley
|
logCrud.info("update D1GUID:" + guid.getValue() + ":D1SCIMETADATA:" + localId +
|
| 438 |
|
|
":D1SYSMETA:"+ sysMetaLocalId + ":");
|
| 439 |
5353
|
berkley
|
return guid;
|
| 440 |
|
|
}
|
| 441 |
|
|
catch(Exception e)
|
| 442 |
|
|
{
|
| 443 |
5356
|
berkley
|
throw new ServiceFailure("1030", "Error updating document in CrudService: " + e.getMessage());
|
| 444 |
5353
|
berkley
|
}
|
| 445 |
|
|
}
|
| 446 |
5359
|
berkley
|
|
| 447 |
|
|
/**
|
| 448 |
5521
|
berkley
|
* set access permissions on both the science metadata and system metadata
|
| 449 |
|
|
*/
|
| 450 |
|
|
public void setAccess(AuthToken token, Identifier id, String principal, String permission,
|
| 451 |
|
|
String permissionType, String permissionOrder)
|
| 452 |
|
|
throws ServiceFailure
|
| 453 |
|
|
{
|
| 454 |
|
|
setAccess(token, id, principal, permission, permissionType, permissionOrder, true);
|
| 455 |
|
|
}
|
| 456 |
|
|
|
| 457 |
|
|
/**
|
| 458 |
5443
|
berkley
|
* set access control on the doc
|
| 459 |
|
|
* @param token
|
| 460 |
|
|
* @param id
|
| 461 |
|
|
* @param principal
|
| 462 |
|
|
* @param permission
|
| 463 |
|
|
*/
|
| 464 |
|
|
public void setAccess(AuthToken token, Identifier id, String principal, int permission,
|
| 465 |
|
|
String permissionType, String permissionOrder, boolean setSystemMetadata)
|
| 466 |
|
|
throws ServiceFailure
|
| 467 |
|
|
{
|
| 468 |
|
|
String perm = "";
|
| 469 |
5445
|
berkley
|
if(permission >= 4)
|
| 470 |
5443
|
berkley
|
{
|
| 471 |
|
|
perm = "read";
|
| 472 |
|
|
}
|
| 473 |
5445
|
berkley
|
if(permission >= 6)
|
| 474 |
5443
|
berkley
|
{
|
| 475 |
|
|
perm = "write";
|
| 476 |
|
|
}
|
| 477 |
5466
|
berkley
|
//System.out.println("perm in setAccess: " + perm);
|
| 478 |
|
|
//System.out.println("permission in setAccess: " + permission);
|
| 479 |
5443
|
berkley
|
setAccess(token, id, principal, perm, permissionType, permissionOrder,
|
| 480 |
|
|
setSystemMetadata);
|
| 481 |
|
|
|
| 482 |
|
|
}
|
| 483 |
|
|
|
| 484 |
|
|
/**
|
| 485 |
5362
|
berkley
|
* set the permission on the document
|
| 486 |
|
|
* @param token
|
| 487 |
|
|
* @param principal
|
| 488 |
|
|
* @param permission
|
| 489 |
|
|
* @param permissionType
|
| 490 |
|
|
* @param permissionOrder
|
| 491 |
|
|
* @return
|
| 492 |
|
|
*/
|
| 493 |
|
|
public void setAccess(AuthToken token, Identifier id, String principal, String permission,
|
| 494 |
5424
|
berkley
|
String permissionType, String permissionOrder, boolean setSystemMetadata)
|
| 495 |
5362
|
berkley
|
throws ServiceFailure
|
| 496 |
|
|
{
|
| 497 |
5466
|
berkley
|
/* TODO:
|
| 498 |
|
|
* This is also not part of the D1 Crud spec. This method is needed for
|
| 499 |
|
|
* systems such as metacat where access to objects is controlled by
|
| 500 |
|
|
* and ACL. Higher level decisions need to be made about how this
|
| 501 |
|
|
* should work within D1.
|
| 502 |
|
|
*/
|
| 503 |
5362
|
berkley
|
try
|
| 504 |
|
|
{
|
| 505 |
5449
|
berkley
|
final SessionData sessionData = getSessionData(token);
|
| 506 |
|
|
if(sessionData == null)
|
| 507 |
|
|
{
|
| 508 |
|
|
throw new ServiceFailure("1000", "User must be logged in to set access.");
|
| 509 |
|
|
}
|
| 510 |
5362
|
berkley
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 511 |
|
|
String docid = im.getLocalId(id.getValue());
|
| 512 |
5449
|
berkley
|
|
| 513 |
5362
|
berkley
|
String permNum = "0";
|
| 514 |
5370
|
berkley
|
if(permission.equals("read"))
|
| 515 |
5362
|
berkley
|
{
|
| 516 |
|
|
permNum = "4";
|
| 517 |
|
|
}
|
| 518 |
5370
|
berkley
|
else if(permission.equals("write"))
|
| 519 |
5362
|
berkley
|
{
|
| 520 |
|
|
permNum = "6";
|
| 521 |
|
|
}
|
| 522 |
5424
|
berkley
|
System.out.println("user " + sessionData.getUserName() +
|
| 523 |
|
|
" is setting access level " + permNum + " for permission " +
|
| 524 |
|
|
permissionType + " on doc with localid " + docid);
|
| 525 |
5362
|
berkley
|
handler.setAccess(metacatUrl, sessionData.getUserName(), docid,
|
| 526 |
|
|
principal, permNum, permissionType, permissionOrder);
|
| 527 |
5424
|
berkley
|
if(setSystemMetadata)
|
| 528 |
|
|
{
|
| 529 |
|
|
//set the same perms on the system metadata doc
|
| 530 |
|
|
String smlocalid = im.getSystemMetadataLocalId(id.getValue());
|
| 531 |
|
|
System.out.println("setting access on SM doc with localid " + smlocalid);
|
| 532 |
|
|
//cs.setAccess(token, smid, principal, permission, permissionType, permissionOrder);
|
| 533 |
|
|
handler.setAccess(metacatUrl, sessionData.getUserName(), smlocalid,
|
| 534 |
|
|
principal, permNum, permissionType, permissionOrder);
|
| 535 |
|
|
}
|
| 536 |
5431
|
berkley
|
String username = "public";
|
| 537 |
|
|
if(sessionData != null)
|
| 538 |
|
|
{
|
| 539 |
|
|
username = sessionData.getUserName();
|
| 540 |
|
|
}
|
| 541 |
5383
|
berkley
|
EventLog.getInstance().log(metacatUrl,
|
| 542 |
5384
|
berkley
|
username, im.getLocalId(id.getValue()), "setAccess");
|
| 543 |
5392
|
berkley
|
logCrud.info("setAccess");
|
| 544 |
5362
|
berkley
|
}
|
| 545 |
|
|
catch(Exception e)
|
| 546 |
|
|
{
|
| 547 |
5370
|
berkley
|
e.printStackTrace();
|
| 548 |
5362
|
berkley
|
throw new ServiceFailure("1000", "Could not set access on the document with id " + id.getValue());
|
| 549 |
|
|
}
|
| 550 |
|
|
}
|
| 551 |
|
|
|
| 552 |
|
|
/**
|
| 553 |
5359
|
berkley
|
* Retrieve the list of objects present on the MN that match the calling
|
| 554 |
|
|
* parameters. This method is required to support the process of Member
|
| 555 |
|
|
* Node synchronization. At a minimum, this method should be able to
|
| 556 |
|
|
* return a list of objects that match:
|
| 557 |
|
|
* startTime <= SystemMetadata.dateSysMetadataModified
|
| 558 |
|
|
* but is expected to also support date range (by also specifying endTime),
|
| 559 |
|
|
* and should also support slicing of the matching set of records by
|
| 560 |
|
|
* indicating the starting index of the response (where 0 is the index
|
| 561 |
|
|
* of the first item) and the count of elements to be returned.
|
| 562 |
|
|
*
|
| 563 |
5364
|
berkley
|
* If startTime or endTime is null, the query is not restricted by that parameter.
|
| 564 |
|
|
*
|
| 565 |
5359
|
berkley
|
* @see http://mule1.dataone.org/ArchitectureDocs/mn_api_replication.html#MN_replication.listObjects
|
| 566 |
|
|
* @param token
|
| 567 |
|
|
* @param startTime
|
| 568 |
|
|
* @param endTime
|
| 569 |
|
|
* @param objectFormat
|
| 570 |
|
|
* @param replicaStatus
|
| 571 |
|
|
* @param start
|
| 572 |
|
|
* @param count
|
| 573 |
|
|
* @return ObjectList
|
| 574 |
|
|
* @throws NotAuthorized
|
| 575 |
|
|
* @throws InvalidRequest
|
| 576 |
|
|
* @throws NotImplemented
|
| 577 |
|
|
* @throws ServiceFailure
|
| 578 |
|
|
* @throws InvalidToken
|
| 579 |
|
|
*/
|
| 580 |
|
|
public ObjectList listObjects(AuthToken token, Date startTime, Date endTime,
|
| 581 |
|
|
ObjectFormat objectFormat, boolean replicaStatus, int start, int count)
|
| 582 |
|
|
throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken
|
| 583 |
|
|
{
|
| 584 |
|
|
ObjectList ol = new ObjectList();
|
| 585 |
5362
|
berkley
|
final SessionData sessionData = getSessionData(token);
|
| 586 |
5413
|
berkley
|
int totalAfterQuery = 0;
|
| 587 |
5510
|
berkley
|
|
| 588 |
5362
|
berkley
|
try
|
| 589 |
|
|
{
|
| 590 |
5510
|
berkley
|
if (PropertyService.getProperty("database.queryCacheOn").equals("true"))
|
| 591 |
|
|
{
|
| 592 |
|
|
//System.out.println("the string stored into cache is "+ resultsetBuffer.toString());
|
| 593 |
|
|
DBQuery.clearQueryResultCache();
|
| 594 |
|
|
}
|
| 595 |
|
|
}
|
| 596 |
|
|
catch (PropertyNotFoundException e1)
|
| 597 |
|
|
{
|
| 598 |
|
|
//just don't do anything
|
| 599 |
|
|
}
|
| 600 |
|
|
|
| 601 |
|
|
try
|
| 602 |
|
|
{
|
| 603 |
5466
|
berkley
|
//TODO: Milliseconds need to be added to the dateFormat
|
| 604 |
5430
|
berkley
|
System.out.println("=========== Listing Objects =============");
|
| 605 |
|
|
System.out.println("Current server time is: " + new Date());
|
| 606 |
|
|
if(startTime != null)
|
| 607 |
|
|
{
|
| 608 |
|
|
System.out.println("query start time is " + startTime);
|
| 609 |
|
|
}
|
| 610 |
|
|
if(endTime != null)
|
| 611 |
|
|
{
|
| 612 |
|
|
System.out.println("query end time is " + endTime);
|
| 613 |
|
|
}
|
| 614 |
5362
|
berkley
|
params.clear();
|
| 615 |
5466
|
berkley
|
/* TODO:
|
| 616 |
|
|
* These metacat queries should not be hard coded here. They
|
| 617 |
|
|
* should be accessed from within a .properties file
|
| 618 |
|
|
*/
|
| 619 |
5362
|
berkley
|
params.put("returndoctype", new String[] {"http://dataone.org/service/types/SystemMetadata/0.1"});
|
| 620 |
|
|
params.put("qformat", new String[] {"xml"});
|
| 621 |
5364
|
berkley
|
params.put("returnfield", new String[] {"size", "originMemberNode",
|
| 622 |
5387
|
berkley
|
"identifier", "objectFormat", "dateSysMetadataModified", "checksum", "checksum/@algorithm"});
|
| 623 |
5362
|
berkley
|
params.put("anyfield", new String[] {"%"});
|
| 624 |
5363
|
berkley
|
|
| 625 |
5411
|
berkley
|
//System.out.println("query is: metacatUrl: " + metacatUrl + " user: " + sessionData.getUserName() +
|
| 626 |
|
|
// " sessionid: " + sessionData.getId() + " params: " + params.toString());
|
| 627 |
5426
|
berkley
|
String username = "public";
|
| 628 |
|
|
String[] groups = null;
|
| 629 |
|
|
String sessionid = "";
|
| 630 |
|
|
if(sessionData != null)
|
| 631 |
|
|
{
|
| 632 |
|
|
username = sessionData.getUserName();
|
| 633 |
|
|
groups = sessionData.getGroupNames();
|
| 634 |
|
|
sessionid = sessionData.getId();
|
| 635 |
|
|
}
|
| 636 |
5408
|
berkley
|
|
| 637 |
5426
|
berkley
|
MetacatResultSet rs = handler.query(metacatUrl, params, username,
|
| 638 |
|
|
groups, sessionid);
|
| 639 |
5363
|
berkley
|
List docs = rs.getDocuments();
|
| 640 |
5403
|
berkley
|
|
| 641 |
5510
|
berkley
|
System.out.println("query returned " + docs.size() + " documents.");
|
| 642 |
5413
|
berkley
|
Vector<Document> docCopy = new Vector<Document>();
|
| 643 |
5408
|
berkley
|
|
| 644 |
5413
|
berkley
|
//preparse the list to remove any that don't match the query params
|
| 645 |
5466
|
berkley
|
/* TODO: this type of query/subquery processing is probably not scalable
|
| 646 |
|
|
* to larger object stores. This code should be revisited. The metacat
|
| 647 |
|
|
* query handler should probably be altered to handle the type of query
|
| 648 |
|
|
* done here.
|
| 649 |
|
|
*/
|
| 650 |
5413
|
berkley
|
for(int i=0; i<docs.size(); i++)
|
| 651 |
5369
|
berkley
|
{
|
| 652 |
5363
|
berkley
|
Document d = (Document)docs.get(i);
|
| 653 |
5364
|
berkley
|
ObjectFormat returnedObjectFormat = ObjectFormat.convert(d.getField("objectFormat"));
|
| 654 |
5413
|
berkley
|
|
| 655 |
|
|
if(returnedObjectFormat != null &&
|
| 656 |
|
|
objectFormat != null &&
|
| 657 |
|
|
!objectFormat.toString().trim().equals(returnedObjectFormat.toString().trim()))
|
| 658 |
5364
|
berkley
|
{ //make sure the objectFormat is the one specified
|
| 659 |
|
|
continue;
|
| 660 |
|
|
}
|
| 661 |
5384
|
berkley
|
|
| 662 |
|
|
String dateSMM = d.getField("dateSysMetadataModified");
|
| 663 |
5413
|
berkley
|
if((startTime != null || endTime != null) && dateSMM == null)
|
| 664 |
|
|
{ //if startTime or endTime are not null, we need a date to compare to
|
| 665 |
5384
|
berkley
|
continue;
|
| 666 |
|
|
}
|
| 667 |
5413
|
berkley
|
|
| 668 |
|
|
//date parse
|
| 669 |
|
|
Date dateSysMetadataModified = null;
|
| 670 |
|
|
if(dateSMM != null)
|
| 671 |
|
|
{
|
| 672 |
5420
|
berkley
|
//dateSysMetadataModified = parseDate(dateSMM);
|
| 673 |
|
|
if(dateSMM.indexOf(".") != -1)
|
| 674 |
|
|
{ //strip the milliseconds
|
| 675 |
5466
|
berkley
|
//TODO: don't do this. we need milliseconds now.
|
| 676 |
5481
|
berkley
|
//TODO: explore ISO 8601 to figure out milliseconds
|
| 677 |
5420
|
berkley
|
dateSMM = dateSMM.substring(0, dateSMM.indexOf(".")) + 'Z';
|
| 678 |
|
|
}
|
| 679 |
|
|
//System.out.println("dateSMM: " + dateSMM);
|
| 680 |
5428
|
berkley
|
//dateFormat.setTimeZone(TimeZone.getTimeZone("GMT-0"));
|
| 681 |
|
|
try
|
| 682 |
|
|
{ //the format we want
|
| 683 |
|
|
dateSysMetadataModified = dateFormat.parse(dateSMM);
|
| 684 |
|
|
}
|
| 685 |
|
|
catch(java.text.ParseException pe)
|
| 686 |
|
|
{ //try another legacy format
|
| 687 |
|
|
DateFormat dateFormat2 = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss'Z'");
|
| 688 |
|
|
dateFormat2.setTimeZone(TimeZone.getTimeZone("GMT-0"));
|
| 689 |
|
|
dateSysMetadataModified = dateFormat2.parse(dateSMM);
|
| 690 |
|
|
}
|
| 691 |
5413
|
berkley
|
}
|
| 692 |
5428
|
berkley
|
|
| 693 |
5510
|
berkley
|
/*System.out.println("====================================");
|
| 694 |
|
|
System.out.println("doc number " + i);
|
| 695 |
|
|
System.out.println("docid: " + d.docid);
|
| 696 |
5420
|
berkley
|
System.out.println("dateSysMetadataModified: " + dateSysMetadataModified);
|
| 697 |
|
|
System.out.println("startTime: " + startTime);
|
| 698 |
|
|
System.out.println("endtime: " + endTime);*/
|
| 699 |
5427
|
berkley
|
|
| 700 |
5364
|
berkley
|
int startDateComparison = 0;
|
| 701 |
|
|
int endDateComparison = 0;
|
| 702 |
|
|
if(startTime != null)
|
| 703 |
|
|
{
|
| 704 |
5427
|
berkley
|
Calendar zTime = Calendar.getInstance(TimeZone.getTimeZone("GMT-0"));
|
| 705 |
|
|
zTime.setTime(startTime);
|
| 706 |
|
|
startTime = zTime.getTime();
|
| 707 |
|
|
|
| 708 |
5413
|
berkley
|
if(dateSysMetadataModified == null)
|
| 709 |
|
|
{
|
| 710 |
|
|
startDateComparison = -1;
|
| 711 |
|
|
}
|
| 712 |
|
|
else
|
| 713 |
|
|
{
|
| 714 |
|
|
startDateComparison = dateSysMetadataModified.compareTo(startTime);
|
| 715 |
|
|
}
|
| 716 |
|
|
//System.out.println("startDateCom: " + startDateComparison);
|
| 717 |
5364
|
berkley
|
}
|
| 718 |
5413
|
berkley
|
else
|
| 719 |
|
|
{
|
| 720 |
|
|
startDateComparison = 1;
|
| 721 |
|
|
}
|
| 722 |
5364
|
berkley
|
|
| 723 |
|
|
if(endTime != null)
|
| 724 |
|
|
{
|
| 725 |
5427
|
berkley
|
Calendar zTime = Calendar.getInstance(TimeZone.getTimeZone("GMT-0"));
|
| 726 |
|
|
zTime.setTime(endTime);
|
| 727 |
|
|
endTime = zTime.getTime();
|
| 728 |
|
|
|
| 729 |
5413
|
berkley
|
if(dateSysMetadataModified == null)
|
| 730 |
|
|
{
|
| 731 |
|
|
endDateComparison = 1;
|
| 732 |
|
|
}
|
| 733 |
|
|
else
|
| 734 |
|
|
{
|
| 735 |
|
|
endDateComparison = dateSysMetadataModified.compareTo(endTime);
|
| 736 |
|
|
}
|
| 737 |
|
|
//System.out.println("endDateCom: " + endDateComparison);
|
| 738 |
5364
|
berkley
|
}
|
| 739 |
5413
|
berkley
|
else
|
| 740 |
|
|
{
|
| 741 |
|
|
endDateComparison = -1;
|
| 742 |
|
|
}
|
| 743 |
5364
|
berkley
|
|
| 744 |
5413
|
berkley
|
|
| 745 |
5364
|
berkley
|
if(startDateComparison < 0 || endDateComparison > 0)
|
| 746 |
5413
|
berkley
|
{
|
| 747 |
5364
|
berkley
|
continue;
|
| 748 |
|
|
}
|
| 749 |
|
|
|
| 750 |
5413
|
berkley
|
docCopy.add((Document)docs.get(i));
|
| 751 |
|
|
} //end pre-parse
|
| 752 |
|
|
|
| 753 |
|
|
docs = docCopy;
|
| 754 |
|
|
totalAfterQuery = docs.size();
|
| 755 |
5428
|
berkley
|
//System.out.println("total after subquery: " + totalAfterQuery);
|
| 756 |
5413
|
berkley
|
|
| 757 |
|
|
//make sure we don't run over the end
|
| 758 |
|
|
int end = start + count;
|
| 759 |
|
|
if(end > docs.size())
|
| 760 |
|
|
{
|
| 761 |
|
|
end = docs.size();
|
| 762 |
|
|
}
|
| 763 |
|
|
|
| 764 |
|
|
for(int i=start; i<end; i++)
|
| 765 |
|
|
{
|
| 766 |
|
|
//get the document from the result
|
| 767 |
|
|
Document d = (Document)docs.get(i);
|
| 768 |
|
|
//System.out.println("processing doc " + d.docid);
|
| 769 |
|
|
|
| 770 |
|
|
String dateSMM = d.getField("dateSysMetadataModified");
|
| 771 |
|
|
Date dateSysMetadataModified = null;
|
| 772 |
|
|
if(dateSMM != null)
|
| 773 |
|
|
{
|
| 774 |
|
|
try
|
| 775 |
|
|
{
|
| 776 |
|
|
dateSysMetadataModified = parseDate(dateSMM);
|
| 777 |
|
|
}
|
| 778 |
|
|
catch(Exception e)
|
| 779 |
|
|
{ //if we fail to parse the date, just ignore the value
|
| 780 |
|
|
dateSysMetadataModified = null;
|
| 781 |
|
|
}
|
| 782 |
|
|
}
|
| 783 |
|
|
ObjectFormat returnedObjectFormat = ObjectFormat.convert(d.getField("objectFormat"));
|
| 784 |
|
|
|
| 785 |
|
|
|
| 786 |
5364
|
berkley
|
ObjectInfo info = new ObjectInfo();
|
| 787 |
|
|
//add the fields to the info object
|
| 788 |
|
|
Checksum cs = new Checksum();
|
| 789 |
|
|
cs.setValue(d.getField("checksum"));
|
| 790 |
5370
|
berkley
|
String csalg = d.getField("algorithm");
|
| 791 |
|
|
if(csalg == null)
|
| 792 |
|
|
{
|
| 793 |
|
|
csalg = "MD5";
|
| 794 |
|
|
}
|
| 795 |
|
|
ChecksumAlgorithm ca = ChecksumAlgorithm.convert(csalg);
|
| 796 |
|
|
cs.setAlgorithm(ca);
|
| 797 |
5364
|
berkley
|
info.setChecksum(cs);
|
| 798 |
|
|
info.setDateSysMetadataModified(dateSysMetadataModified);
|
| 799 |
|
|
Identifier id = new Identifier();
|
| 800 |
5445
|
berkley
|
id.setValue(d.getField("identifier").trim());
|
| 801 |
5364
|
berkley
|
info.setIdentifier(id);
|
| 802 |
|
|
info.setObjectFormat(returnedObjectFormat);
|
| 803 |
5413
|
berkley
|
String size = d.getField("size");
|
| 804 |
|
|
if(size != null)
|
| 805 |
|
|
{
|
| 806 |
|
|
info.setSize(new Long(size.trim()).longValue());
|
| 807 |
|
|
}
|
| 808 |
5364
|
berkley
|
//add the ObjectInfo to the ObjectList
|
| 809 |
5557
|
berkley
|
//logCrud.info("objectFormat: " + info.getObjectFormat().toString());
|
| 810 |
|
|
//logCrud.info("id: " + info.getIdentifier().getValue());
|
| 811 |
|
|
|
| 812 |
5555
|
berkley
|
if(info.getIdentifier().getValue() != null)
|
| 813 |
5414
|
berkley
|
{ //id can be null from tests. should not happen in production.
|
| 814 |
5555
|
berkley
|
if((info.getObjectFormat() != null && !info.getObjectFormat().toString().trim().equals("")))
|
| 815 |
|
|
{ //objectFormat needs to not be null and not be an empty string
|
| 816 |
|
|
ol.addObjectInfo(info);
|
| 817 |
|
|
}
|
| 818 |
5557
|
berkley
|
else
|
| 819 |
|
|
{
|
| 820 |
|
|
logCrud.info("Not adding object " + info.getIdentifier().toString());
|
| 821 |
|
|
}
|
| 822 |
5414
|
berkley
|
}
|
| 823 |
5424
|
berkley
|
|
| 824 |
5363
|
berkley
|
}
|
| 825 |
5362
|
berkley
|
}
|
| 826 |
|
|
catch(Exception e)
|
| 827 |
|
|
{
|
| 828 |
|
|
e.printStackTrace();
|
| 829 |
5557
|
berkley
|
logCrud.error("Error creating ObjectList: " + e.getMessage() + " cause: " + e.getCause());
|
| 830 |
5362
|
berkley
|
throw new ServiceFailure("1580", "Error retrieving ObjectList: " + e.getMessage());
|
| 831 |
|
|
}
|
| 832 |
5430
|
berkley
|
String username = "public";
|
| 833 |
|
|
if(sessionData != null)
|
| 834 |
|
|
{
|
| 835 |
|
|
username = sessionData.getUserName();
|
| 836 |
|
|
}
|
| 837 |
5383
|
berkley
|
EventLog.getInstance().log(metacatUrl,
|
| 838 |
5384
|
berkley
|
username, null, "read");
|
| 839 |
5392
|
berkley
|
logCrud.info("listObjects");
|
| 840 |
5413
|
berkley
|
ol.setCount(count);
|
| 841 |
|
|
ol.setStart(start);
|
| 842 |
|
|
ol.setTotal(totalAfterQuery);
|
| 843 |
5359
|
berkley
|
return ol;
|
| 844 |
|
|
}
|
| 845 |
|
|
|
| 846 |
|
|
/**
|
| 847 |
|
|
* Call listObjects with the default values for replicaStatus (true), start (0),
|
| 848 |
|
|
* and count (1000).
|
| 849 |
|
|
* @param token
|
| 850 |
|
|
* @param startTime
|
| 851 |
|
|
* @param endTime
|
| 852 |
|
|
* @param objectFormat
|
| 853 |
|
|
* @return
|
| 854 |
|
|
* @throws NotAuthorized
|
| 855 |
|
|
* @throws InvalidRequest
|
| 856 |
|
|
* @throws NotImplemented
|
| 857 |
|
|
* @throws ServiceFailure
|
| 858 |
|
|
* @throws InvalidToken
|
| 859 |
|
|
*/
|
| 860 |
|
|
public ObjectList listObjects(AuthToken token, Date startTime, Date endTime,
|
| 861 |
|
|
ObjectFormat objectFormat)
|
| 862 |
|
|
throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken
|
| 863 |
|
|
{
|
| 864 |
|
|
return listObjects(token, startTime, endTime, objectFormat, true, 0, 1000);
|
| 865 |
|
|
}
|
| 866 |
5298
|
jones
|
|
| 867 |
5359
|
berkley
|
/**
|
| 868 |
|
|
* Delete a document. NOT IMPLEMENTED
|
| 869 |
|
|
*/
|
| 870 |
5320
|
jones
|
public Identifier delete(AuthToken token, Identifier guid)
|
| 871 |
5298
|
jones
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 872 |
|
|
NotImplemented {
|
| 873 |
5392
|
berkley
|
logCrud.info("delete");
|
| 874 |
5356
|
berkley
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
| 875 |
5298
|
jones
|
}
|
| 876 |
|
|
|
| 877 |
5359
|
berkley
|
/**
|
| 878 |
|
|
* describe a document. NOT IMPLEMENTED
|
| 879 |
|
|
*/
|
| 880 |
5320
|
jones
|
public DescribeResponse describe(AuthToken token, Identifier guid)
|
| 881 |
5298
|
jones
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 882 |
|
|
NotImplemented {
|
| 883 |
5392
|
berkley
|
logCrud.info("describe");
|
| 884 |
5356
|
berkley
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
| 885 |
5298
|
jones
|
}
|
| 886 |
|
|
|
| 887 |
5359
|
berkley
|
/**
|
| 888 |
|
|
* get a document with a specified guid.
|
| 889 |
|
|
*/
|
| 890 |
5320
|
jones
|
public InputStream get(AuthToken token, Identifier guid)
|
| 891 |
5298
|
jones
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 892 |
|
|
NotImplemented {
|
| 893 |
|
|
|
| 894 |
|
|
// Retrieve the session information from the AuthToken
|
| 895 |
|
|
// If the session is expired, then the user is 'public'
|
| 896 |
5436
|
berkley
|
if(token == null)
|
| 897 |
|
|
{
|
| 898 |
|
|
token = new AuthToken("Public");
|
| 899 |
|
|
}
|
| 900 |
5298
|
jones
|
final SessionData sessionData = getSessionData(token);
|
| 901 |
|
|
|
| 902 |
|
|
// Look up the localId for this global identifier
|
| 903 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 904 |
|
|
try {
|
| 905 |
5320
|
jones
|
final String localId = im.getLocalId(guid.getValue());
|
| 906 |
5298
|
jones
|
|
| 907 |
|
|
final InputStreamFromOutputStream<String> objectStream =
|
| 908 |
|
|
new InputStreamFromOutputStream<String>() {
|
| 909 |
|
|
|
| 910 |
|
|
@Override
|
| 911 |
|
|
public String produce(final OutputStream dataSink) throws Exception {
|
| 912 |
|
|
|
| 913 |
|
|
try {
|
| 914 |
5439
|
berkley
|
String username = "public";
|
| 915 |
|
|
String[] groups = new String[0];
|
| 916 |
|
|
if(sessionData != null)
|
| 917 |
|
|
{
|
| 918 |
|
|
username = sessionData.getUserName();
|
| 919 |
|
|
groups = sessionData.getGroupNames();
|
| 920 |
|
|
}
|
| 921 |
|
|
/*System.out.println("metacatUrl: " + metacatUrl +
|
| 922 |
|
|
" dataSink: " + dataSink + " localId: " + localId +
|
| 923 |
|
|
" username: " + username + " params: " + params.toString());
|
| 924 |
|
|
*/
|
| 925 |
5466
|
berkley
|
/* TODO:
|
| 926 |
|
|
* This multithreaded approach to getting data without
|
| 927 |
|
|
* being memory bound causes problems with exception
|
| 928 |
|
|
* handling. The only exception the produce method
|
| 929 |
|
|
* will return is an IOException, rendering all of the
|
| 930 |
|
|
* catch blocks below mute. This should probably be changed
|
| 931 |
|
|
* to use a memory mapped solution instead so that we
|
| 932 |
|
|
* can properly pass exceptions to the client.
|
| 933 |
|
|
* see https://trac.dataone.org/ticket/706
|
| 934 |
|
|
*/
|
| 935 |
5344
|
berkley
|
handler.readFromMetacat(metacatUrl, null,
|
| 936 |
5298
|
jones
|
dataSink, localId, "xml",
|
| 937 |
5439
|
berkley
|
username,
|
| 938 |
|
|
groups, true, params);
|
| 939 |
5298
|
jones
|
} catch (PropertyNotFoundException e) {
|
| 940 |
5382
|
berkley
|
e.printStackTrace();
|
| 941 |
|
|
throw new ServiceFailure("1030", "Error getting property from metacat: " + e.getMessage());
|
| 942 |
5298
|
jones
|
} catch (ClassNotFoundException e) {
|
| 943 |
5382
|
berkley
|
e.printStackTrace();
|
| 944 |
|
|
throw new ServiceFailure("1030", "Class not found error when reading from metacat: " + e.getMessage());
|
| 945 |
5298
|
jones
|
} catch (IOException e) {
|
| 946 |
5382
|
berkley
|
e.printStackTrace();
|
| 947 |
|
|
throw new ServiceFailure("1030", "IOException while reading from metacat: " + e.getMessage());
|
| 948 |
5298
|
jones
|
} catch (SQLException e) {
|
| 949 |
5382
|
berkley
|
e.printStackTrace();
|
| 950 |
|
|
throw new ServiceFailure("1030", "SQLException while reading from metacat: " + e.getMessage());
|
| 951 |
5298
|
jones
|
} catch (McdbException e) {
|
| 952 |
5382
|
berkley
|
e.printStackTrace();
|
| 953 |
|
|
throw new ServiceFailure("1030", "Metacat DB exception while reading from metacat: " + e.getMessage());
|
| 954 |
5298
|
jones
|
} catch (ParseLSIDException e) {
|
| 955 |
5382
|
berkley
|
e.printStackTrace();
|
| 956 |
|
|
throw new NotFound("1020", "LSID parsing exception while reading from metacat: " + e.getMessage());
|
| 957 |
5298
|
jones
|
} catch (InsufficientKarmaException e) {
|
| 958 |
5382
|
berkley
|
e.printStackTrace();
|
| 959 |
|
|
throw new NotAuthorized("1000", "User not authorized for get(): " + e.getMessage());
|
| 960 |
5298
|
jones
|
}
|
| 961 |
|
|
|
| 962 |
|
|
return "Completed";
|
| 963 |
|
|
}
|
| 964 |
|
|
};
|
| 965 |
5431
|
berkley
|
String username = "public";
|
| 966 |
|
|
if(sessionData != null)
|
| 967 |
|
|
{
|
| 968 |
|
|
username = sessionData.getUserName();
|
| 969 |
|
|
}
|
| 970 |
|
|
|
| 971 |
5383
|
berkley
|
EventLog.getInstance().log(metacatUrl,
|
| 972 |
5384
|
berkley
|
username, im.getLocalId(guid.getValue()), "read");
|
| 973 |
5459
|
berkley
|
logCrud.info("get D1GUID:" + guid.getValue() + ":D1SCIMETADATA:" + localId +
|
| 974 |
|
|
":");
|
| 975 |
5298
|
jones
|
return objectStream;
|
| 976 |
|
|
|
| 977 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 978 |
5356
|
berkley
|
throw new NotFound("1020", e.getMessage());
|
| 979 |
5298
|
jones
|
}
|
| 980 |
|
|
}
|
| 981 |
|
|
|
| 982 |
5359
|
berkley
|
/**
|
| 983 |
|
|
* get the checksum for a document. NOT IMPLEMENTED
|
| 984 |
|
|
*/
|
| 985 |
5320
|
jones
|
public Checksum getChecksum(AuthToken token, Identifier guid)
|
| 986 |
5298
|
jones
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 987 |
|
|
InvalidRequest, NotImplemented {
|
| 988 |
5392
|
berkley
|
logCrud.info("getChecksum");
|
| 989 |
5466
|
berkley
|
//TODO: this could now easily be implemented
|
| 990 |
5356
|
berkley
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
| 991 |
5298
|
jones
|
}
|
| 992 |
|
|
|
| 993 |
5359
|
berkley
|
/**
|
| 994 |
|
|
* get the checksum for a document. NOT IMPLEMENTED
|
| 995 |
|
|
*/
|
| 996 |
5320
|
jones
|
public Checksum getChecksum(AuthToken token, Identifier guid,
|
| 997 |
5298
|
jones
|
String checksumAlgorithm) throws InvalidToken, ServiceFailure,
|
| 998 |
|
|
NotAuthorized, NotFound, InvalidRequest, NotImplemented {
|
| 999 |
5392
|
berkley
|
logCrud.info("getChecksum");
|
| 1000 |
5466
|
berkley
|
//TODO: this could now easily be implemented
|
| 1001 |
5356
|
berkley
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
| 1002 |
5298
|
jones
|
}
|
| 1003 |
|
|
|
| 1004 |
5359
|
berkley
|
/**
|
| 1005 |
5384
|
berkley
|
* get log records.
|
| 1006 |
5359
|
berkley
|
*/
|
| 1007 |
5390
|
berkley
|
public Log getLogRecords(AuthToken token, Date fromDate, Date toDate, Event event)
|
| 1008 |
5298
|
jones
|
throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,
|
| 1009 |
5384
|
berkley
|
NotImplemented
|
| 1010 |
|
|
{
|
| 1011 |
5430
|
berkley
|
System.out.println("=================== Getting log records ===================");
|
| 1012 |
|
|
System.out.println("Current server time is: " + new Date());
|
| 1013 |
|
|
if(fromDate != null)
|
| 1014 |
|
|
{
|
| 1015 |
|
|
System.out.println("query start time is " + fromDate);
|
| 1016 |
|
|
}
|
| 1017 |
|
|
if(toDate != null)
|
| 1018 |
|
|
{
|
| 1019 |
|
|
System.out.println("query end time is " + toDate);
|
| 1020 |
|
|
}
|
| 1021 |
5389
|
berkley
|
Log log = new Log();
|
| 1022 |
|
|
Vector<LogEntry> logs = new Vector<LogEntry>();
|
| 1023 |
5384
|
berkley
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1024 |
|
|
EventLog el = EventLog.getInstance();
|
| 1025 |
5391
|
berkley
|
if(fromDate == null)
|
| 1026 |
|
|
{
|
| 1027 |
5418
|
berkley
|
System.out.println("setting fromdate from null");
|
| 1028 |
5391
|
berkley
|
fromDate = new Date(1);
|
| 1029 |
|
|
}
|
| 1030 |
|
|
if(toDate == null)
|
| 1031 |
|
|
{
|
| 1032 |
5418
|
berkley
|
System.out.println("setting todate from null");
|
| 1033 |
5391
|
berkley
|
toDate = new Date();
|
| 1034 |
|
|
}
|
| 1035 |
5418
|
berkley
|
|
| 1036 |
|
|
System.out.println("fromDate: " + fromDate);
|
| 1037 |
|
|
System.out.println("toDate: " + toDate);
|
| 1038 |
|
|
|
| 1039 |
5384
|
berkley
|
String report = el.getReport(null, null, null, null,
|
| 1040 |
|
|
new java.sql.Timestamp(fromDate.getTime()),
|
| 1041 |
|
|
new java.sql.Timestamp(toDate.getTime()));
|
| 1042 |
|
|
|
| 1043 |
5418
|
berkley
|
//System.out.println("report: " + report);
|
| 1044 |
|
|
|
| 1045 |
5384
|
berkley
|
String logEntry = "<logEntry>";
|
| 1046 |
|
|
String endLogEntry = "</logEntry>";
|
| 1047 |
|
|
int startIndex = 0;
|
| 1048 |
|
|
int foundIndex = report.indexOf(logEntry, startIndex);
|
| 1049 |
|
|
while(foundIndex != -1)
|
| 1050 |
|
|
{
|
| 1051 |
|
|
//parse out each entry
|
| 1052 |
|
|
int endEntryIndex = report.indexOf(endLogEntry, foundIndex);
|
| 1053 |
|
|
String entry = report.substring(foundIndex, endEntryIndex);
|
| 1054 |
|
|
//System.out.println("entry: " + entry);
|
| 1055 |
|
|
startIndex = endEntryIndex + endLogEntry.length();
|
| 1056 |
|
|
foundIndex = report.indexOf(logEntry, startIndex);
|
| 1057 |
|
|
|
| 1058 |
|
|
String entryId = getLogEntryField("entryid", entry);
|
| 1059 |
|
|
String ipAddress = getLogEntryField("ipAddress", entry);
|
| 1060 |
|
|
String principal = getLogEntryField("principal", entry);
|
| 1061 |
|
|
String docid = getLogEntryField("docid", entry);
|
| 1062 |
5390
|
berkley
|
String eventS = getLogEntryField("event", entry);
|
| 1063 |
5384
|
berkley
|
String dateLogged = getLogEntryField("dateLogged", entry);
|
| 1064 |
|
|
|
| 1065 |
5389
|
berkley
|
LogEntry le = new LogEntry();
|
| 1066 |
5384
|
berkley
|
|
| 1067 |
5390
|
berkley
|
Event e = Event.convert(eventS);
|
| 1068 |
5384
|
berkley
|
if(e == null)
|
| 1069 |
|
|
{ //skip any events that are not Dataone Crud events
|
| 1070 |
|
|
continue;
|
| 1071 |
|
|
}
|
| 1072 |
5389
|
berkley
|
le.setEvent(e);
|
| 1073 |
5384
|
berkley
|
Identifier entryid = new Identifier();
|
| 1074 |
|
|
entryid.setValue(entryId);
|
| 1075 |
5389
|
berkley
|
le.setEntryId(entryid);
|
| 1076 |
5384
|
berkley
|
Identifier identifier = new Identifier();
|
| 1077 |
|
|
try
|
| 1078 |
|
|
{
|
| 1079 |
5432
|
berkley
|
//System.out.println("converting docid '" + docid + "' to a guid.");
|
| 1080 |
5417
|
berkley
|
if(docid == null || docid.trim().equals("") || docid.trim().equals("null"))
|
| 1081 |
|
|
{
|
| 1082 |
|
|
continue;
|
| 1083 |
|
|
}
|
| 1084 |
5416
|
berkley
|
docid = docid.substring(0, docid.lastIndexOf("."));
|
| 1085 |
5384
|
berkley
|
identifier.setValue(im.getGUID(docid, im.getLatestRevForLocalId(docid)));
|
| 1086 |
|
|
}
|
| 1087 |
|
|
catch(Exception ex)
|
| 1088 |
|
|
{ //try to get the guid, if that doesn't work, just use the local id
|
| 1089 |
5419
|
berkley
|
//throw new ServiceFailure("1030", "Error getting guid for localId " +
|
| 1090 |
5424
|
berkley
|
// docid + ": " + ex.getMessage());\
|
| 1091 |
|
|
|
| 1092 |
|
|
//skip it if the guid can't be found
|
| 1093 |
5419
|
berkley
|
continue;
|
| 1094 |
5384
|
berkley
|
}
|
| 1095 |
|
|
|
| 1096 |
5389
|
berkley
|
le.setIdentifier(identifier);
|
| 1097 |
|
|
le.setIpAddress(ipAddress);
|
| 1098 |
5384
|
berkley
|
Calendar c = Calendar.getInstance();
|
| 1099 |
|
|
String year = dateLogged.substring(0, 4);
|
| 1100 |
|
|
String month = dateLogged.substring(5, 7);
|
| 1101 |
|
|
String date = dateLogged.substring(8, 10);
|
| 1102 |
|
|
//System.out.println("year: " + year + " month: " + month + " day: " + date);
|
| 1103 |
|
|
c.set(new Integer(year).intValue(), new Integer(month).intValue(), new Integer(date).intValue());
|
| 1104 |
|
|
Date logDate = c.getTime();
|
| 1105 |
5389
|
berkley
|
le.setDateLogged(logDate);
|
| 1106 |
5384
|
berkley
|
NodeReference memberNode = new NodeReference();
|
| 1107 |
|
|
memberNode.setValue(ipAddress);
|
| 1108 |
5389
|
berkley
|
le.setMemberNode(memberNode);
|
| 1109 |
5384
|
berkley
|
Principal princ = new Principal();
|
| 1110 |
|
|
princ.setValue(principal);
|
| 1111 |
5389
|
berkley
|
le.setPrincipal(princ);
|
| 1112 |
|
|
le.setUserAgent("metacat/RESTService");
|
| 1113 |
5390
|
berkley
|
|
| 1114 |
|
|
if(event == null)
|
| 1115 |
|
|
{
|
| 1116 |
|
|
logs.add(le);
|
| 1117 |
|
|
}
|
| 1118 |
|
|
|
| 1119 |
|
|
if(event != null &&
|
| 1120 |
|
|
e.toString().toLowerCase().trim().equals(event.toString().toLowerCase().trim()))
|
| 1121 |
|
|
{
|
| 1122 |
|
|
logs.add(le);
|
| 1123 |
|
|
}
|
| 1124 |
5384
|
berkley
|
}
|
| 1125 |
|
|
|
| 1126 |
5389
|
berkley
|
log.setLogEntryList(logs);
|
| 1127 |
5392
|
berkley
|
logCrud.info("getLogRecords");
|
| 1128 |
5389
|
berkley
|
return log;
|
| 1129 |
5298
|
jones
|
}
|
| 1130 |
5384
|
berkley
|
|
| 1131 |
|
|
/**
|
| 1132 |
|
|
* parse a logEntry and get the relavent field from it
|
| 1133 |
|
|
* @param fieldname
|
| 1134 |
|
|
* @param entry
|
| 1135 |
|
|
* @return
|
| 1136 |
|
|
*/
|
| 1137 |
|
|
private String getLogEntryField(String fieldname, String entry)
|
| 1138 |
|
|
{
|
| 1139 |
|
|
String begin = "<" + fieldname + ">";
|
| 1140 |
|
|
String end = "</" + fieldname + ">";
|
| 1141 |
|
|
//System.out.println("looking for " + begin + " and " + end + " in entry " + entry);
|
| 1142 |
|
|
String s = entry.substring(entry.indexOf(begin) + begin.length(), entry.indexOf(end));
|
| 1143 |
|
|
//System.out.println("entry " + fieldname + " : " + s);
|
| 1144 |
|
|
return s;
|
| 1145 |
|
|
}
|
| 1146 |
5298
|
jones
|
|
| 1147 |
5359
|
berkley
|
/**
|
| 1148 |
|
|
* get the system metadata for a document with a specified guid.
|
| 1149 |
|
|
*/
|
| 1150 |
5481
|
berkley
|
public SystemMetadata getSystemMetadata(AuthToken token, Identifier guid)
|
| 1151 |
5298
|
jones
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 1152 |
|
|
InvalidRequest, NotImplemented {
|
| 1153 |
5319
|
jones
|
|
| 1154 |
5332
|
jones
|
logMetacat.debug("CrudService.getSystemMetadata - for guid: " + guid.getValue());
|
| 1155 |
|
|
|
| 1156 |
|
|
// Retrieve the session information from the AuthToken
|
| 1157 |
|
|
// If the session is expired, then the user is 'public'
|
| 1158 |
|
|
final SessionData sessionData = getSessionData(token);
|
| 1159 |
|
|
|
| 1160 |
|
|
try {
|
| 1161 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1162 |
5424
|
berkley
|
final String localId = im.getSystemMetadataLocalId(guid.getValue());
|
| 1163 |
5332
|
jones
|
|
| 1164 |
|
|
// Read system metadata from metacat's db
|
| 1165 |
|
|
final InputStreamFromOutputStream<String> objectStream =
|
| 1166 |
|
|
new InputStreamFromOutputStream<String>() {
|
| 1167 |
|
|
|
| 1168 |
|
|
@Override
|
| 1169 |
|
|
public String produce(final OutputStream dataSink) throws Exception {
|
| 1170 |
5481
|
berkley
|
//TODO: change to memory mapped IO so that exceptions get
|
| 1171 |
|
|
//passed to the response correctly.
|
| 1172 |
5332
|
jones
|
try {
|
| 1173 |
5449
|
berkley
|
String username = "public";
|
| 1174 |
|
|
String[] groupnames = null;
|
| 1175 |
|
|
if(sessionData != null)
|
| 1176 |
|
|
{
|
| 1177 |
|
|
username = sessionData.getUserName();
|
| 1178 |
|
|
groupnames = sessionData.getGroupNames();
|
| 1179 |
|
|
}
|
| 1180 |
|
|
|
| 1181 |
5344
|
berkley
|
handler.readFromMetacat(metacatUrl, null,
|
| 1182 |
5332
|
jones
|
dataSink, localId, "xml",
|
| 1183 |
5449
|
berkley
|
username,
|
| 1184 |
|
|
groupnames, true, params);
|
| 1185 |
5332
|
jones
|
} catch (PropertyNotFoundException e) {
|
| 1186 |
5382
|
berkley
|
e.printStackTrace();
|
| 1187 |
|
|
throw new ServiceFailure("1030", "Property not found while reading system metadata from metacat: " + e.getMessage());
|
| 1188 |
5332
|
jones
|
} catch (ClassNotFoundException e) {
|
| 1189 |
5382
|
berkley
|
e.printStackTrace();
|
| 1190 |
|
|
throw new ServiceFailure("1030", "Class not found while reading system metadata from metacat: " + e.getMessage());
|
| 1191 |
5332
|
jones
|
} catch (IOException e) {
|
| 1192 |
5382
|
berkley
|
e.printStackTrace();
|
| 1193 |
|
|
throw new ServiceFailure("1030", "IOException while reading system metadata from metacat: " + e.getMessage());
|
| 1194 |
5332
|
jones
|
} catch (SQLException e) {
|
| 1195 |
5382
|
berkley
|
e.printStackTrace();
|
| 1196 |
|
|
throw new ServiceFailure("1030", "SQLException while reading system metadata from metacat: " + e.getMessage());
|
| 1197 |
5332
|
jones
|
} catch (McdbException e) {
|
| 1198 |
5382
|
berkley
|
e.printStackTrace();
|
| 1199 |
|
|
throw new ServiceFailure("1030", "Metacat DB Exception while reading system metadata from metacat: " + e.getMessage());
|
| 1200 |
5332
|
jones
|
} catch (ParseLSIDException e) {
|
| 1201 |
5382
|
berkley
|
e.printStackTrace();
|
| 1202 |
|
|
throw new NotFound("1020", "Error parsing LSID while reading system metadata from metacat: " + e.getMessage());
|
| 1203 |
5332
|
jones
|
} catch (InsufficientKarmaException e) {
|
| 1204 |
5382
|
berkley
|
e.printStackTrace();
|
| 1205 |
|
|
throw new NotAuthorized("1000", "User not authorized for get() on system metadata: " + e.getMessage());
|
| 1206 |
5332
|
jones
|
}
|
| 1207 |
|
|
|
| 1208 |
|
|
return "Completed";
|
| 1209 |
|
|
}
|
| 1210 |
|
|
};
|
| 1211 |
|
|
|
| 1212 |
|
|
// Deserialize the xml to create a SystemMetadata object
|
| 1213 |
|
|
SystemMetadata sysmeta = deserializeSystemMetadata(objectStream);
|
| 1214 |
5431
|
berkley
|
String username = "public";
|
| 1215 |
|
|
if(sessionData != null)
|
| 1216 |
|
|
{
|
| 1217 |
|
|
username = sessionData.getUserName();
|
| 1218 |
|
|
}
|
| 1219 |
5383
|
berkley
|
EventLog.getInstance().log(metacatUrl,
|
| 1220 |
5384
|
berkley
|
username, im.getLocalId(guid.getValue()), "read");
|
| 1221 |
5459
|
berkley
|
logCrud.info("getsystemmetadata D1GUID:" + guid.getValue() +
|
| 1222 |
|
|
":D1SYSMETA:"+ localId + ":");
|
| 1223 |
5332
|
jones
|
return sysmeta;
|
| 1224 |
|
|
|
| 1225 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 1226 |
5348
|
berkley
|
//e.printStackTrace();
|
| 1227 |
5356
|
berkley
|
throw new NotFound("1000", e.getMessage());
|
| 1228 |
5332
|
jones
|
}
|
| 1229 |
5298
|
jones
|
}
|
| 1230 |
5366
|
berkley
|
|
| 1231 |
|
|
/**
|
| 1232 |
|
|
* parse the date in the systemMetadata
|
| 1233 |
|
|
* @param s
|
| 1234 |
|
|
* @return
|
| 1235 |
|
|
* @throws Exception
|
| 1236 |
|
|
*/
|
| 1237 |
5418
|
berkley
|
public Date parseDate(String s)
|
| 1238 |
5366
|
berkley
|
throws Exception
|
| 1239 |
|
|
{
|
| 1240 |
5466
|
berkley
|
/* TODO:
|
| 1241 |
|
|
* This method should be replaced by a DateFormatter
|
| 1242 |
|
|
*/
|
| 1243 |
5366
|
berkley
|
Date d = null;
|
| 1244 |
|
|
int tIndex = s.indexOf("T");
|
| 1245 |
|
|
int zIndex = s.indexOf("Z");
|
| 1246 |
|
|
if(tIndex != -1 && zIndex != -1)
|
| 1247 |
|
|
{ //parse a date that looks like 2010-05-18T21:12:54.362Z
|
| 1248 |
|
|
//System.out.println("original date: " + s);
|
| 1249 |
|
|
|
| 1250 |
|
|
String date = s.substring(0, tIndex);
|
| 1251 |
|
|
String year = date.substring(0, date.indexOf("-"));
|
| 1252 |
|
|
String month = date.substring(date.indexOf("-") + 1, date.lastIndexOf("-"));
|
| 1253 |
|
|
String day = date.substring(date.lastIndexOf("-") + 1, date.length());
|
| 1254 |
|
|
/*System.out.println("date: " + "year: " + new Integer(year).intValue() +
|
| 1255 |
|
|
" month: " + new Integer(month).intValue() + " day: " +
|
| 1256 |
|
|
new Integer(day).intValue());
|
| 1257 |
|
|
*/
|
| 1258 |
|
|
String time = s.substring(tIndex + 1, zIndex);
|
| 1259 |
|
|
String hour = time.substring(0, time.indexOf(":"));
|
| 1260 |
|
|
String minute = time.substring(time.indexOf(":") + 1, time.lastIndexOf(":"));
|
| 1261 |
|
|
String seconds = "00";
|
| 1262 |
|
|
String milliseconds = "00";
|
| 1263 |
|
|
if(time.indexOf(".") != -1)
|
| 1264 |
|
|
{
|
| 1265 |
|
|
seconds = time.substring(time.lastIndexOf(":") + 1, time.indexOf("."));
|
| 1266 |
|
|
milliseconds = time.substring(time.indexOf(".") + 1, time.length());
|
| 1267 |
|
|
}
|
| 1268 |
5418
|
berkley
|
else
|
| 1269 |
|
|
{
|
| 1270 |
|
|
seconds = time.substring(time.lastIndexOf(":") + 1, time.length());
|
| 1271 |
|
|
}
|
| 1272 |
5366
|
berkley
|
/*System.out.println("time: " + "hour: " + new Integer(hour).intValue() +
|
| 1273 |
|
|
" minute: " + new Integer(minute).intValue() + " seconds: " +
|
| 1274 |
|
|
new Integer(seconds).intValue() + " milli: " +
|
| 1275 |
|
|
new Integer(milliseconds).intValue());*/
|
| 1276 |
|
|
|
| 1277 |
|
|
//d = DateFormat.getDateTimeInstance().parse(date + " " + time);
|
| 1278 |
5418
|
berkley
|
Calendar c = Calendar.getInstance(/*TimeZone.getTimeZone("GMT-0")*/TimeZone.getDefault());
|
| 1279 |
5366
|
berkley
|
c.set(new Integer(year).intValue(), new Integer(month).intValue() - 1,
|
| 1280 |
|
|
new Integer(day).intValue(), new Integer(hour).intValue(),
|
| 1281 |
|
|
new Integer(minute).intValue(), new Integer(seconds).intValue());
|
| 1282 |
|
|
c.set(Calendar.MILLISECOND, new Integer(milliseconds).intValue());
|
| 1283 |
|
|
d = new Date(c.getTimeInMillis());
|
| 1284 |
|
|
//System.out.println("d: " + d);
|
| 1285 |
|
|
return d;
|
| 1286 |
|
|
}
|
| 1287 |
|
|
else
|
| 1288 |
|
|
{ //if it's not in the expected format, try the formatter
|
| 1289 |
|
|
return DateFormat.getDateTimeInstance().parse(s);
|
| 1290 |
|
|
}
|
| 1291 |
|
|
}
|
| 1292 |
5298
|
jones
|
|
| 1293 |
5331
|
jones
|
/*
|
| 1294 |
|
|
* Look up the information on the session using the token provided in
|
| 1295 |
|
|
* the AuthToken. The Session should have all relevant user information.
|
| 1296 |
|
|
* If the session has expired or is invalid, the 'public' session will
|
| 1297 |
|
|
* be returned, giving the user anonymous access.
|
| 1298 |
|
|
*/
|
| 1299 |
5394
|
berkley
|
public static SessionData getSessionData(AuthToken token) {
|
| 1300 |
5331
|
jones
|
SessionData sessionData = null;
|
| 1301 |
|
|
String sessionId = "PUBLIC";
|
| 1302 |
|
|
if (token != null) {
|
| 1303 |
|
|
sessionId = token.getToken();
|
| 1304 |
|
|
}
|
| 1305 |
|
|
|
| 1306 |
|
|
// if the session id is registered in SessionService, get the
|
| 1307 |
|
|
// SessionData for it. Otherwise, use the public session.
|
| 1308 |
5411
|
berkley
|
//System.out.println("sessionid: " + sessionId);
|
| 1309 |
5403
|
berkley
|
if (sessionId != null &&
|
| 1310 |
5406
|
berkley
|
!sessionId.toLowerCase().equals("public") &&
|
| 1311 |
5403
|
berkley
|
SessionService.getInstance().isSessionRegistered(sessionId))
|
| 1312 |
|
|
{
|
| 1313 |
5374
|
berkley
|
sessionData = SessionService.getInstance().getRegisteredSession(sessionId);
|
| 1314 |
5331
|
jones
|
} else {
|
| 1315 |
5374
|
berkley
|
sessionData = SessionService.getInstance().getPublicSession();
|
| 1316 |
5331
|
jones
|
}
|
| 1317 |
5411
|
berkley
|
|
| 1318 |
5331
|
jones
|
return sessionData;
|
| 1319 |
|
|
}
|
| 1320 |
|
|
|
| 1321 |
|
|
/**
|
| 1322 |
|
|
* Determine if a given object should be treated as an XML science metadata
|
| 1323 |
|
|
* object.
|
| 1324 |
|
|
*
|
| 1325 |
|
|
* TODO: This test should be externalized in a configuration dictionary rather than being hardcoded.
|
| 1326 |
|
|
*
|
| 1327 |
|
|
* @param sysmeta the SystemMetadata describig the object
|
| 1328 |
|
|
* @return true if the object should be treated as science metadata
|
| 1329 |
|
|
*/
|
| 1330 |
|
|
private boolean isScienceMetadata(SystemMetadata sysmeta) {
|
| 1331 |
5523
|
berkley
|
/*boolean scimeta = false;
|
| 1332 |
5466
|
berkley
|
//TODO: this should be read from a .properties file instead of being hard coded
|
| 1333 |
5331
|
jones
|
switch (sysmeta.getObjectFormat()) {
|
| 1334 |
|
|
case EML_2_1_0: scimeta = true; break;
|
| 1335 |
|
|
case EML_2_0_1: scimeta = true; break;
|
| 1336 |
|
|
case EML_2_0_0: scimeta = true; break;
|
| 1337 |
|
|
case FGDC_STD_001_1_1999: scimeta = true; break;
|
| 1338 |
|
|
case FGDC_STD_001_1998: scimeta = true; break;
|
| 1339 |
|
|
case NCML_2_2: scimeta = true; break;
|
| 1340 |
5521
|
berkley
|
case DSPACE_METS_SIP_1_0: scimeta = true; break;
|
| 1341 |
5331
|
jones
|
}
|
| 1342 |
|
|
|
| 1343 |
5523
|
berkley
|
return scimeta;*/
|
| 1344 |
|
|
|
| 1345 |
|
|
return MetadataTypeRegister.isMetadataType(sysmeta.getObjectFormat());
|
| 1346 |
5331
|
jones
|
}
|
| 1347 |
|
|
|
| 1348 |
5359
|
berkley
|
/**
|
| 1349 |
|
|
* insert a data doc
|
| 1350 |
|
|
* @param object
|
| 1351 |
|
|
* @param guid
|
| 1352 |
|
|
* @param sessionData
|
| 1353 |
|
|
* @throws ServiceFailure
|
| 1354 |
5459
|
berkley
|
* @returns localId of the data object inserted
|
| 1355 |
5359
|
berkley
|
*/
|
| 1356 |
5459
|
berkley
|
private String insertDataObject(InputStream object, Identifier guid,
|
| 1357 |
5331
|
jones
|
SessionData sessionData) throws ServiceFailure {
|
| 1358 |
|
|
|
| 1359 |
5431
|
berkley
|
String username = "public";
|
| 1360 |
|
|
String[] groups = null;
|
| 1361 |
|
|
if(sessionData != null)
|
| 1362 |
|
|
{
|
| 1363 |
|
|
username = sessionData.getUserName();
|
| 1364 |
|
|
groups = sessionData.getGroupNames();
|
| 1365 |
|
|
}
|
| 1366 |
5331
|
jones
|
|
| 1367 |
|
|
// generate guid/localId pair for object
|
| 1368 |
|
|
logMetacat.debug("Generating a guid/localId mapping");
|
| 1369 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1370 |
|
|
String localId = im.generateLocalId(guid.getValue(), 1);
|
| 1371 |
|
|
|
| 1372 |
|
|
try {
|
| 1373 |
|
|
logMetacat.debug("Case DATA: starting to write to disk.");
|
| 1374 |
|
|
if (DocumentImpl.getDataFileLockGrant(localId)) {
|
| 1375 |
|
|
|
| 1376 |
|
|
// Save the data file to disk using "localId" as the name
|
| 1377 |
|
|
try {
|
| 1378 |
|
|
String datafilepath = PropertyService.getProperty("application.datafilepath");
|
| 1379 |
|
|
|
| 1380 |
|
|
File dataDirectory = new File(datafilepath);
|
| 1381 |
|
|
dataDirectory.mkdirs();
|
| 1382 |
|
|
|
| 1383 |
|
|
File newFile = writeStreamToFile(dataDirectory, localId, object);
|
| 1384 |
|
|
|
| 1385 |
|
|
// TODO: Check that the file size matches SystemMetadata
|
| 1386 |
|
|
// long size = newFile.length();
|
| 1387 |
|
|
// if (size == 0) {
|
| 1388 |
|
|
// throw new IOException("Uploaded file is 0 bytes!");
|
| 1389 |
|
|
// }
|
| 1390 |
|
|
|
| 1391 |
|
|
// Register the file in the database (which generates an exception
|
| 1392 |
|
|
// if the localId is not acceptable or other untoward things happen
|
| 1393 |
|
|
try {
|
| 1394 |
|
|
logMetacat.debug("Registering document...");
|
| 1395 |
|
|
DocumentImpl.registerDocument(localId, "BIN", localId,
|
| 1396 |
|
|
username, groups);
|
| 1397 |
|
|
logMetacat.debug("Registration step completed.");
|
| 1398 |
|
|
} catch (SQLException e) {
|
| 1399 |
|
|
//newFile.delete();
|
| 1400 |
|
|
logMetacat.debug("SQLE: " + e.getMessage());
|
| 1401 |
|
|
e.printStackTrace(System.out);
|
| 1402 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());
|
| 1403 |
5331
|
jones
|
} catch (AccessionNumberException e) {
|
| 1404 |
|
|
//newFile.delete();
|
| 1405 |
|
|
logMetacat.debug("ANE: " + e.getMessage());
|
| 1406 |
|
|
e.printStackTrace(System.out);
|
| 1407 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());
|
| 1408 |
5331
|
jones
|
} catch (Exception e) {
|
| 1409 |
|
|
//newFile.delete();
|
| 1410 |
|
|
logMetacat.debug("Exception: " + e.getMessage());
|
| 1411 |
|
|
e.printStackTrace(System.out);
|
| 1412 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());
|
| 1413 |
5331
|
jones
|
}
|
| 1414 |
|
|
|
| 1415 |
|
|
logMetacat.debug("Logging the creation event.");
|
| 1416 |
5344
|
berkley
|
EventLog.getInstance().log(metacatUrl,
|
| 1417 |
5384
|
berkley
|
username, localId, "create");
|
| 1418 |
5331
|
jones
|
|
| 1419 |
|
|
// Schedule replication for this data file
|
| 1420 |
|
|
logMetacat.debug("Scheduling replication.");
|
| 1421 |
|
|
ForceReplicationHandler frh = new ForceReplicationHandler(
|
| 1422 |
5384
|
berkley
|
localId, "create", false, null);
|
| 1423 |
5331
|
jones
|
|
| 1424 |
|
|
} catch (PropertyNotFoundException e) {
|
| 1425 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Could not lock file for writing:" + e.getMessage());
|
| 1426 |
5331
|
jones
|
}
|
| 1427 |
|
|
}
|
| 1428 |
5459
|
berkley
|
return localId;
|
| 1429 |
5331
|
jones
|
} catch (Exception e) {
|
| 1430 |
|
|
// Could not get a lock on the document, so we can not update the file now
|
| 1431 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Failed to lock file: " + e.getMessage());
|
| 1432 |
5331
|
jones
|
}
|
| 1433 |
|
|
}
|
| 1434 |
|
|
|
| 1435 |
5359
|
berkley
|
/**
|
| 1436 |
|
|
* write a file to a stream
|
| 1437 |
|
|
* @param dir
|
| 1438 |
|
|
* @param fileName
|
| 1439 |
|
|
* @param data
|
| 1440 |
|
|
* @return
|
| 1441 |
|
|
* @throws ServiceFailure
|
| 1442 |
|
|
*/
|
| 1443 |
5319
|
jones
|
private File writeStreamToFile(File dir, String fileName, InputStream data)
|
| 1444 |
|
|
throws ServiceFailure {
|
| 1445 |
|
|
|
| 1446 |
|
|
File newFile = new File(dir, fileName);
|
| 1447 |
|
|
logMetacat.debug("Filename for write is: " + newFile.getAbsolutePath());
|
| 1448 |
|
|
|
| 1449 |
|
|
try {
|
| 1450 |
|
|
if (newFile.createNewFile()) {
|
| 1451 |
|
|
// write data stream to desired file
|
| 1452 |
|
|
OutputStream os = new FileOutputStream(newFile);
|
| 1453 |
|
|
long length = IOUtils.copyLarge(data, os);
|
| 1454 |
|
|
os.flush();
|
| 1455 |
|
|
os.close();
|
| 1456 |
|
|
} else {
|
| 1457 |
|
|
logMetacat.debug("File creation failed, or file already exists.");
|
| 1458 |
5356
|
berkley
|
throw new ServiceFailure("1190", "File already exists: " + fileName);
|
| 1459 |
5319
|
jones
|
}
|
| 1460 |
|
|
} catch (FileNotFoundException e) {
|
| 1461 |
|
|
logMetacat.debug("FNF: " + e.getMessage());
|
| 1462 |
5356
|
berkley
|
throw new ServiceFailure("1190", "File not found: " + fileName + " "
|
| 1463 |
5319
|
jones
|
+ e.getMessage());
|
| 1464 |
|
|
} catch (IOException e) {
|
| 1465 |
|
|
logMetacat.debug("IOE: " + e.getMessage());
|
| 1466 |
5356
|
berkley
|
throw new ServiceFailure("1190", "File was not written: " + fileName
|
| 1467 |
5319
|
jones
|
+ " " + e.getMessage());
|
| 1468 |
|
|
}
|
| 1469 |
|
|
|
| 1470 |
|
|
return newFile;
|
| 1471 |
5329
|
jones
|
}
|
| 1472 |
|
|
|
| 1473 |
5350
|
berkley
|
/**
|
| 1474 |
5441
|
berkley
|
* insert a systemMetadata doc, return the localId of the sysmeta
|
| 1475 |
5350
|
berkley
|
*/
|
| 1476 |
5441
|
berkley
|
private String insertSystemMetadata(SystemMetadata sysmeta, SessionData sessionData)
|
| 1477 |
5377
|
berkley
|
throws ServiceFailure
|
| 1478 |
|
|
{
|
| 1479 |
5329
|
jones
|
logMetacat.debug("Starting to insert SystemMetadata...");
|
| 1480 |
|
|
|
| 1481 |
|
|
// generate guid/localId pair for sysmeta
|
| 1482 |
5331
|
jones
|
Identifier sysMetaGuid = new Identifier();
|
| 1483 |
|
|
sysMetaGuid.setValue(DocumentUtil.generateDocumentId(1));
|
| 1484 |
5329
|
jones
|
sysmeta.setDateSysMetadataModified(new Date());
|
| 1485 |
5453
|
berkley
|
System.out.println("****inserting new system metadata with modified date " +
|
| 1486 |
|
|
sysmeta.getDateSysMetadataModified());
|
| 1487 |
5329
|
jones
|
|
| 1488 |
|
|
String xml = new String(serializeSystemMetadata(sysmeta).toByteArray());
|
| 1489 |
5444
|
berkley
|
System.out.println("sysmeta: " + xml);
|
| 1490 |
5453
|
berkley
|
String localId = insertDocument(xml, sysMetaGuid, sessionData, true);
|
| 1491 |
5420
|
berkley
|
System.out.println("sysmeta inserted with localId " + localId);
|
| 1492 |
5453
|
berkley
|
//insert the system metadata doc id into the systemmetadata table to
|
| 1493 |
5333
|
berkley
|
//link it to the data or metadata document
|
| 1494 |
5377
|
berkley
|
IdentifierManager.getInstance().createSystemMetadataMapping(
|
| 1495 |
|
|
sysmeta.getIdentifier().getValue(), sysMetaGuid.getValue());
|
| 1496 |
5441
|
berkley
|
return localId;
|
| 1497 |
5329
|
jones
|
}
|
| 1498 |
|
|
|
| 1499 |
5333
|
berkley
|
/**
|
| 1500 |
5350
|
berkley
|
* update a systemMetadata doc
|
| 1501 |
|
|
*/
|
| 1502 |
|
|
private void updateSystemMetadata(SystemMetadata sm, SessionData sessionData)
|
| 1503 |
|
|
throws ServiceFailure
|
| 1504 |
|
|
{
|
| 1505 |
|
|
try
|
| 1506 |
|
|
{
|
| 1507 |
5424
|
berkley
|
String smId = IdentifierManager.getInstance().getSystemMetadataLocalId(sm.getIdentifier().getValue());
|
| 1508 |
5350
|
berkley
|
sm.setDateSysMetadataModified(new Date());
|
| 1509 |
|
|
String xml = new String(serializeSystemMetadata(sm).toByteArray());
|
| 1510 |
5456
|
berkley
|
String localId = updateDocument(xml, sm.getIdentifier(), null, sessionData, true);
|
| 1511 |
5350
|
berkley
|
IdentifierManager.getInstance().updateSystemMetadataMapping(sm.getIdentifier().getValue(), localId);
|
| 1512 |
|
|
}
|
| 1513 |
|
|
catch(Exception e)
|
| 1514 |
|
|
{
|
| 1515 |
5356
|
berkley
|
throw new ServiceFailure("1030", "Error updating system metadata: " + e.getMessage());
|
| 1516 |
5350
|
berkley
|
}
|
| 1517 |
|
|
}
|
| 1518 |
|
|
|
| 1519 |
5453
|
berkley
|
private String insertDocument(String xml, Identifier guid, SessionData sessionData)
|
| 1520 |
|
|
throws ServiceFailure
|
| 1521 |
|
|
{
|
| 1522 |
|
|
return insertDocument(xml, guid, sessionData, false);
|
| 1523 |
|
|
}
|
| 1524 |
|
|
|
| 1525 |
5350
|
berkley
|
/**
|
| 1526 |
|
|
* insert a document
|
| 1527 |
|
|
* NOTE: this method shouldn't be used from the update or create() methods.
|
| 1528 |
|
|
* we shouldn't be putting the science metadata or data objects into memory.
|
| 1529 |
|
|
*/
|
| 1530 |
5453
|
berkley
|
private String insertDocument(String xml, Identifier guid, SessionData sessionData,
|
| 1531 |
|
|
boolean isSystemMetadata)
|
| 1532 |
5350
|
berkley
|
throws ServiceFailure
|
| 1533 |
|
|
{
|
| 1534 |
5453
|
berkley
|
return insertOrUpdateDocument(xml, guid, sessionData, "insert", isSystemMetadata);
|
| 1535 |
5350
|
berkley
|
}
|
| 1536 |
|
|
|
| 1537 |
|
|
/**
|
| 1538 |
|
|
* insert a document from a stream
|
| 1539 |
|
|
*/
|
| 1540 |
|
|
private String insertDocument(InputStream is, Identifier guid, SessionData sessionData)
|
| 1541 |
|
|
throws IOException, ServiceFailure
|
| 1542 |
|
|
{
|
| 1543 |
|
|
//HACK: change this eventually. we should not be converting the stream to a string
|
| 1544 |
|
|
String xml = IOUtils.toString(is);
|
| 1545 |
|
|
return insertDocument(xml, guid, sessionData);
|
| 1546 |
|
|
}
|
| 1547 |
|
|
|
| 1548 |
|
|
/**
|
| 1549 |
|
|
* update a document
|
| 1550 |
|
|
* NOTE: this method shouldn't be used from the update or create() methods.
|
| 1551 |
|
|
* we shouldn't be putting the science metadata or data objects into memory.
|
| 1552 |
|
|
*/
|
| 1553 |
5453
|
berkley
|
private String updateDocument(String xml, Identifier obsoleteGuid,
|
| 1554 |
|
|
Identifier guid, SessionData sessionData, boolean isSystemMetadata)
|
| 1555 |
5350
|
berkley
|
throws ServiceFailure
|
| 1556 |
|
|
{
|
| 1557 |
5453
|
berkley
|
return insertOrUpdateDocument(xml, obsoleteGuid, sessionData, "update", isSystemMetadata);
|
| 1558 |
5350
|
berkley
|
}
|
| 1559 |
|
|
|
| 1560 |
|
|
/**
|
| 1561 |
|
|
* update a document from a stream
|
| 1562 |
|
|
*/
|
| 1563 |
5453
|
berkley
|
private String updateDocument(InputStream is, Identifier obsoleteGuid,
|
| 1564 |
|
|
Identifier guid, SessionData sessionData, boolean isSystemMetadata)
|
| 1565 |
5350
|
berkley
|
throws IOException, ServiceFailure
|
| 1566 |
|
|
{
|
| 1567 |
|
|
//HACK: change this eventually. we should not be converting the stream to a string
|
| 1568 |
|
|
String xml = IOUtils.toString(is);
|
| 1569 |
5453
|
berkley
|
String localId = updateDocument(xml, obsoleteGuid, guid, sessionData, isSystemMetadata);
|
| 1570 |
5350
|
berkley
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1571 |
|
|
if(guid != null)
|
| 1572 |
|
|
{
|
| 1573 |
|
|
im.createMapping(guid.getValue(), localId);
|
| 1574 |
|
|
}
|
| 1575 |
|
|
return localId;
|
| 1576 |
|
|
}
|
| 1577 |
|
|
|
| 1578 |
|
|
/**
|
| 1579 |
5333
|
berkley
|
* insert a document, return the id of the document that was inserted
|
| 1580 |
|
|
*/
|
| 1581 |
5453
|
berkley
|
protected String insertOrUpdateDocument(String xml, Identifier guid,
|
| 1582 |
|
|
SessionData sessionData, String insertOrUpdate, boolean isSystemMetadata)
|
| 1583 |
5329
|
jones
|
throws ServiceFailure {
|
| 1584 |
|
|
logMetacat.debug("Starting to insert xml document...");
|
| 1585 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1586 |
|
|
|
| 1587 |
|
|
// generate guid/localId pair for sysmeta
|
| 1588 |
5350
|
berkley
|
String localId = null;
|
| 1589 |
|
|
if(insertOrUpdate.equals("insert"))
|
| 1590 |
|
|
{
|
| 1591 |
5453
|
berkley
|
localId = im.generateLocalId(guid.getValue(), 1, isSystemMetadata);
|
| 1592 |
5350
|
berkley
|
}
|
| 1593 |
|
|
else
|
| 1594 |
|
|
{
|
| 1595 |
|
|
//localid should already exist in the identifier table, so just find it
|
| 1596 |
|
|
try
|
| 1597 |
|
|
{
|
| 1598 |
5456
|
berkley
|
System.out.println("updating guid " + guid.getValue());
|
| 1599 |
|
|
if(!isSystemMetadata)
|
| 1600 |
|
|
{
|
| 1601 |
|
|
System.out.println("looking in identifier table for guid " + guid.getValue());
|
| 1602 |
|
|
localId = im.getLocalId(guid.getValue());
|
| 1603 |
|
|
}
|
| 1604 |
|
|
else
|
| 1605 |
|
|
{
|
| 1606 |
|
|
System.out.println("looking in systemmetadata table for guid " + guid.getValue());
|
| 1607 |
|
|
localId = im.getSystemMetadataLocalId(guid.getValue());
|
| 1608 |
|
|
}
|
| 1609 |
|
|
System.out.println("localId: " + localId);
|
| 1610 |
5350
|
berkley
|
//increment the revision
|
| 1611 |
|
|
String docid = localId.substring(0, localId.lastIndexOf("."));
|
| 1612 |
|
|
String revS = localId.substring(localId.lastIndexOf(".") + 1, localId.length());
|
| 1613 |
|
|
int rev = new Integer(revS).intValue();
|
| 1614 |
|
|
rev++;
|
| 1615 |
|
|
docid = docid + "." + rev;
|
| 1616 |
|
|
localId = docid;
|
| 1617 |
5456
|
berkley
|
System.out.println("incremented localId: " + localId);
|
| 1618 |
5350
|
berkley
|
}
|
| 1619 |
|
|
catch(McdbDocNotFoundException e)
|
| 1620 |
|
|
{
|
| 1621 |
5356
|
berkley
|
throw new ServiceFailure("1030", "CrudService.insertOrUpdateDocument(): " +
|
| 1622 |
5350
|
berkley
|
"guid " + guid.getValue() + " should have been in the identifier table, but it wasn't: " + e.getMessage());
|
| 1623 |
|
|
}
|
| 1624 |
|
|
}
|
| 1625 |
5331
|
jones
|
logMetacat.debug("Metadata guid|localId: " + guid.getValue() + "|" +
|
| 1626 |
5329
|
jones
|
localId);
|
| 1627 |
|
|
|
| 1628 |
|
|
String[] action = new String[1];
|
| 1629 |
5350
|
berkley
|
action[0] = insertOrUpdate;
|
| 1630 |
5329
|
jones
|
params.put("action", action);
|
| 1631 |
|
|
String[] docid = new String[1];
|
| 1632 |
|
|
docid[0] = localId;
|
| 1633 |
|
|
params.put("docid", docid);
|
| 1634 |
|
|
String[] doctext = new String[1];
|
| 1635 |
|
|
doctext[0] = xml;
|
| 1636 |
|
|
logMetacat.debug(doctext[0]);
|
| 1637 |
|
|
params.put("doctext", doctext);
|
| 1638 |
5331
|
jones
|
|
| 1639 |
|
|
// TODO: refactor handleInsertOrUpdateAction() to not output XML directly
|
| 1640 |
|
|
// onto output stream, or alternatively, capture that and parse it to
|
| 1641 |
|
|
// generate the right exceptions
|
| 1642 |
5337
|
berkley
|
//ByteArrayOutputStream output = new ByteArrayOutputStream();
|
| 1643 |
|
|
//PrintWriter pw = new PrintWriter(output);
|
| 1644 |
5449
|
berkley
|
String username = "public";
|
| 1645 |
|
|
String[] groupnames = null;
|
| 1646 |
|
|
if(sessionData != null)
|
| 1647 |
|
|
{
|
| 1648 |
|
|
username = sessionData.getUserName();
|
| 1649 |
|
|
groupnames = sessionData.getGroupNames();
|
| 1650 |
|
|
}
|
| 1651 |
5344
|
berkley
|
String result = handler.handleInsertOrUpdateAction(metacatUrl, null,
|
| 1652 |
5449
|
berkley
|
null, params, username, groupnames);
|
| 1653 |
5461
|
berkley
|
if(result.indexOf("<error>") != -1)
|
| 1654 |
|
|
{
|
| 1655 |
|
|
throw new ServiceFailure("1000", "Error inserting or updating document: " + result);
|
| 1656 |
|
|
}
|
| 1657 |
5337
|
berkley
|
//String outputS = new String(output.toByteArray());
|
| 1658 |
|
|
logMetacat.debug("CrudService.insertDocument - Metacat returned: " + result);
|
| 1659 |
5333
|
berkley
|
logMetacat.debug("Finsished inserting xml document with id " + localId);
|
| 1660 |
|
|
return localId;
|
| 1661 |
5329
|
jones
|
}
|
| 1662 |
|
|
|
| 1663 |
5359
|
berkley
|
/**
|
| 1664 |
5555
|
berkley
|
* serialize a dataone type
|
| 1665 |
5550
|
berkley
|
*/
|
| 1666 |
5555
|
berkley
|
private void serializeServiceType(Class type, Object object, OutputStream out)
|
| 1667 |
|
|
throws JiBXException
|
| 1668 |
5550
|
berkley
|
{
|
| 1669 |
5555
|
berkley
|
IBindingFactory bfact = BindingDirectory.getFactory(type);
|
| 1670 |
|
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
| 1671 |
|
|
mctx.marshalDocument(object, "UTF-8", null, out);
|
| 1672 |
5550
|
berkley
|
}
|
| 1673 |
|
|
|
| 1674 |
|
|
/**
|
| 1675 |
5359
|
berkley
|
* serialize a system metadata doc
|
| 1676 |
|
|
* @param sysmeta
|
| 1677 |
|
|
* @return
|
| 1678 |
|
|
* @throws ServiceFailure
|
| 1679 |
|
|
*/
|
| 1680 |
5332
|
jones
|
public static ByteArrayOutputStream serializeSystemMetadata(SystemMetadata sysmeta)
|
| 1681 |
5329
|
jones
|
throws ServiceFailure {
|
| 1682 |
|
|
IBindingFactory bfact;
|
| 1683 |
|
|
ByteArrayOutputStream sysmetaOut = null;
|
| 1684 |
|
|
try {
|
| 1685 |
|
|
bfact = BindingDirectory.getFactory(SystemMetadata.class);
|
| 1686 |
|
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
| 1687 |
|
|
sysmetaOut = new ByteArrayOutputStream();
|
| 1688 |
|
|
mctx.marshalDocument(sysmeta, "UTF-8", null, sysmetaOut);
|
| 1689 |
|
|
} catch (JiBXException e) {
|
| 1690 |
5382
|
berkley
|
e.printStackTrace();
|
| 1691 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Failed to serialize and insert SystemMetadata: " + e.getMessage());
|
| 1692 |
5329
|
jones
|
}
|
| 1693 |
|
|
|
| 1694 |
|
|
return sysmetaOut;
|
| 1695 |
|
|
}
|
| 1696 |
5332
|
jones
|
|
| 1697 |
5359
|
berkley
|
/**
|
| 1698 |
|
|
* deserialize a system metadata doc
|
| 1699 |
|
|
* @param xml
|
| 1700 |
|
|
* @return
|
| 1701 |
|
|
* @throws ServiceFailure
|
| 1702 |
|
|
*/
|
| 1703 |
5332
|
jones
|
public static SystemMetadata deserializeSystemMetadata(InputStream xml)
|
| 1704 |
|
|
throws ServiceFailure {
|
| 1705 |
|
|
try {
|
| 1706 |
|
|
IBindingFactory bfact = BindingDirectory.getFactory(SystemMetadata.class);
|
| 1707 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
| 1708 |
|
|
SystemMetadata sysmeta = (SystemMetadata) uctx.unmarshalDocument(xml, null);
|
| 1709 |
|
|
return sysmeta;
|
| 1710 |
|
|
} catch (JiBXException e) {
|
| 1711 |
5382
|
berkley
|
e.printStackTrace();
|
| 1712 |
|
|
throw new ServiceFailure("1190", "Failed to deserialize and insert SystemMetadata: " + e.getMessage());
|
| 1713 |
5332
|
jones
|
}
|
| 1714 |
|
|
}
|
| 1715 |
5378
|
berkley
|
|
| 1716 |
|
|
/**
|
| 1717 |
|
|
* produce an md5 checksum for item
|
| 1718 |
|
|
*/
|
| 1719 |
|
|
private String checksum(InputStream is)
|
| 1720 |
|
|
throws Exception
|
| 1721 |
|
|
{
|
| 1722 |
|
|
byte[] buffer = new byte[1024];
|
| 1723 |
|
|
MessageDigest complete = MessageDigest.getInstance("MD5");
|
| 1724 |
|
|
int numRead;
|
| 1725 |
|
|
|
| 1726 |
|
|
do
|
| 1727 |
|
|
{
|
| 1728 |
|
|
numRead = is.read(buffer);
|
| 1729 |
|
|
if (numRead > 0)
|
| 1730 |
|
|
{
|
| 1731 |
|
|
complete.update(buffer, 0, numRead);
|
| 1732 |
|
|
}
|
| 1733 |
|
|
} while (numRead != -1);
|
| 1734 |
|
|
|
| 1735 |
|
|
|
| 1736 |
|
|
return getHex(complete.digest());
|
| 1737 |
|
|
}
|
| 1738 |
|
|
|
| 1739 |
|
|
/**
|
| 1740 |
|
|
* convert a byte array to a hex string
|
| 1741 |
|
|
*/
|
| 1742 |
|
|
private static String getHex( byte [] raw )
|
| 1743 |
|
|
{
|
| 1744 |
|
|
final String HEXES = "0123456789ABCDEF";
|
| 1745 |
|
|
if ( raw == null ) {
|
| 1746 |
|
|
return null;
|
| 1747 |
|
|
}
|
| 1748 |
|
|
final StringBuilder hex = new StringBuilder( 2 * raw.length );
|
| 1749 |
|
|
for ( final byte b : raw ) {
|
| 1750 |
|
|
hex.append(HEXES.charAt((b & 0xF0) >> 4))
|
| 1751 |
|
|
.append(HEXES.charAt((b & 0x0F)));
|
| 1752 |
|
|
}
|
| 1753 |
|
|
return hex.toString();
|
| 1754 |
|
|
}
|
| 1755 |
|
|
|
| 1756 |
|
|
/**
|
| 1757 |
|
|
* parse the metacat date which looks like 2010-06-08 (YYYY-MM-DD) into
|
| 1758 |
|
|
* a proper date object
|
| 1759 |
|
|
* @param date
|
| 1760 |
|
|
* @return
|
| 1761 |
|
|
*/
|
| 1762 |
|
|
private Date parseMetacatDate(String date)
|
| 1763 |
|
|
{
|
| 1764 |
|
|
String year = date.substring(0, 4);
|
| 1765 |
|
|
String month = date.substring(5, 7);
|
| 1766 |
|
|
String day = date.substring(8, 10);
|
| 1767 |
5420
|
berkley
|
Calendar c = Calendar.getInstance(TimeZone.getDefault());
|
| 1768 |
5378
|
berkley
|
c.set(new Integer(year).intValue(),
|
| 1769 |
|
|
new Integer(month).intValue(),
|
| 1770 |
|
|
new Integer(day).intValue());
|
| 1771 |
5420
|
berkley
|
System.out.println("time in parseMetacatDate: " + c.getTime());
|
| 1772 |
5378
|
berkley
|
return c.getTime();
|
| 1773 |
|
|
}
|
| 1774 |
|
|
|
| 1775 |
|
|
/**
|
| 1776 |
|
|
* find the size (in bytes) of a stream
|
| 1777 |
|
|
* @param is
|
| 1778 |
|
|
* @return
|
| 1779 |
|
|
* @throws IOException
|
| 1780 |
|
|
*/
|
| 1781 |
|
|
private long sizeOfStream(InputStream is)
|
| 1782 |
|
|
throws IOException
|
| 1783 |
|
|
{
|
| 1784 |
|
|
long size = 0;
|
| 1785 |
|
|
byte[] b = new byte[1024];
|
| 1786 |
|
|
int numread = is.read(b, 0, 1024);
|
| 1787 |
|
|
while(numread != -1)
|
| 1788 |
|
|
{
|
| 1789 |
|
|
size += numread;
|
| 1790 |
|
|
numread = is.read(b, 0, 1024);
|
| 1791 |
|
|
}
|
| 1792 |
|
|
return size;
|
| 1793 |
|
|
}
|
| 1794 |
5379
|
berkley
|
|
| 1795 |
|
|
/**
|
| 1796 |
|
|
* create system metadata with a specified id, doc and format
|
| 1797 |
|
|
*/
|
| 1798 |
|
|
private SystemMetadata createSystemMetadata(String localId, AuthToken token)
|
| 1799 |
|
|
throws Exception
|
| 1800 |
|
|
{
|
| 1801 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1802 |
5441
|
berkley
|
Hashtable<String, Object> docInfo = im.getDocumentInfo(localId);
|
| 1803 |
5379
|
berkley
|
|
| 1804 |
|
|
//get the document text
|
| 1805 |
|
|
int rev = im.getLatestRevForLocalId(localId);
|
| 1806 |
|
|
Identifier identifier = new Identifier();
|
| 1807 |
|
|
identifier.setValue(im.getGUID(localId, rev));
|
| 1808 |
|
|
InputStream is = this.get(token, identifier);
|
| 1809 |
|
|
|
| 1810 |
|
|
SystemMetadata sm = new SystemMetadata();
|
| 1811 |
|
|
//set the id
|
| 1812 |
|
|
sm.setIdentifier(identifier);
|
| 1813 |
|
|
|
| 1814 |
|
|
//set the object format
|
| 1815 |
5441
|
berkley
|
String doctype = (String)docInfo.get("doctype");
|
| 1816 |
|
|
ObjectFormat format = ObjectFormat.convert((String)docInfo.get("doctype"));
|
| 1817 |
5379
|
berkley
|
if(format == null)
|
| 1818 |
|
|
{
|
| 1819 |
|
|
if(doctype.trim().equals("BIN"))
|
| 1820 |
|
|
{
|
| 1821 |
5521
|
berkley
|
format = ObjectFormat.OCTET_STREAM;
|
| 1822 |
5379
|
berkley
|
}
|
| 1823 |
|
|
else
|
| 1824 |
|
|
{
|
| 1825 |
|
|
format = ObjectFormat.convert("text/plain");
|
| 1826 |
|
|
}
|
| 1827 |
|
|
}
|
| 1828 |
|
|
sm.setObjectFormat(format);
|
| 1829 |
|
|
|
| 1830 |
|
|
//create the checksum
|
| 1831 |
|
|
String checksumS = checksum(is);
|
| 1832 |
|
|
ChecksumAlgorithm ca = ChecksumAlgorithm.convert("MD5");
|
| 1833 |
|
|
Checksum checksum = new Checksum();
|
| 1834 |
|
|
checksum.setValue(checksumS);
|
| 1835 |
|
|
checksum.setAlgorithm(ca);
|
| 1836 |
|
|
sm.setChecksum(checksum);
|
| 1837 |
|
|
|
| 1838 |
|
|
//set the size
|
| 1839 |
|
|
is = this.get(token, identifier);
|
| 1840 |
|
|
sm.setSize(sizeOfStream(is));
|
| 1841 |
|
|
|
| 1842 |
|
|
//submitter
|
| 1843 |
|
|
Principal p = new Principal();
|
| 1844 |
5441
|
berkley
|
p.setValue((String)docInfo.get("user_owner"));
|
| 1845 |
5379
|
berkley
|
sm.setSubmitter(p);
|
| 1846 |
|
|
sm.setRightsHolder(p);
|
| 1847 |
|
|
try
|
| 1848 |
|
|
{
|
| 1849 |
5441
|
berkley
|
Date dateCreated = parseMetacatDate((String)docInfo.get("date_created"));
|
| 1850 |
5379
|
berkley
|
sm.setDateUploaded(dateCreated);
|
| 1851 |
5441
|
berkley
|
Date dateUpdated = parseMetacatDate((String)docInfo.get("date_updated"));
|
| 1852 |
5379
|
berkley
|
sm.setDateSysMetadataModified(dateUpdated);
|
| 1853 |
|
|
}
|
| 1854 |
|
|
catch(Exception e)
|
| 1855 |
|
|
{
|
| 1856 |
5428
|
berkley
|
System.out.println("POSSIBLE ERROR: couldn't parse a date: " + e.getMessage());
|
| 1857 |
5379
|
berkley
|
Date dateCreated = new Date();
|
| 1858 |
|
|
sm.setDateUploaded(dateCreated);
|
| 1859 |
|
|
Date dateUpdated = new Date();
|
| 1860 |
|
|
sm.setDateSysMetadataModified(dateUpdated);
|
| 1861 |
|
|
}
|
| 1862 |
|
|
NodeReference nr = new NodeReference();
|
| 1863 |
5466
|
berkley
|
//TODO: this should be set to be something more meaningful once the registry is up
|
| 1864 |
5379
|
berkley
|
nr.setValue("metacat");
|
| 1865 |
|
|
sm.setOriginMemberNode(nr);
|
| 1866 |
|
|
sm.setAuthoritativeMemberNode(nr);
|
| 1867 |
|
|
return sm;
|
| 1868 |
|
|
}
|
| 1869 |
5298
|
jones
|
}
|