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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: Serhan AKIN $'
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* '$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.restservice;
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import java.io.*;
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import java.util.*;
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import javax.mail.BodyPart;
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import javax.mail.MessagingException;
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import javax.mail.internet.MimeMultipart;
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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 java.text.DateFormat;
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import java.text.ParseException;
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import java.text.ParsePosition;
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import java.text.SimpleDateFormat;
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import org.apache.commons.httpclient.util.DateParser;
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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.apache.maven.artifact.ant.shaded.IOUtil;
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import org.dataone.service.exceptions.BaseException;
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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.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.exceptions.NotFound;
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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 edu.ucsb.nceas.metacat.DBUtil;
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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.MetacatHandler;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.dataone.CrudService;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.service.SessionService;
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import edu.ucsb.nceas.metacat.util.RequestUtil;
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import edu.ucsb.nceas.metacat.util.SessionData;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import org.dataone.service.streaming.util.StreamUtil;
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import com.gc.iotools.stream.is.InputStreamFromOutputStream;
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/**
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*
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* Implements Earthgrid REST API to Metacat <br/><br/>
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*
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* <ul>
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* <li>
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* <h3> EarthGrid Query Service</h3>
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* <ul><li>
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* <h3>Get & Authenticated Get:</h3>
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* is equal to Metacat's read action and returns a data file having
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* the specified <doc-id> in the resource path. For authenticated Get service, a session id must be provided
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* in the query string. <br/><br/>
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*
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* <b>REST URL:</b> <code>GET, [context-root]/object/[doc-id]?sessionid=[sessionid] </code><br/>
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* <b>Returns:</b> data file <br/><br/>
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* </li>
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*
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* <li>
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* <h3>Query & Authenticated Query:</h3>
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* Metacat's equivalent is squery action but this function
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* receives a Earthgrid query document and returns Earthgrid resultset document by transforming those documents
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* to Metacat's equivalents by the means of Metacat Implementation in Earthgrid library. For authenticated Query service
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* a session id must be provided in the query string. See Earthgrid (a.k.a. Ecogrid) project for XSD files of
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* query and resultset documents<br/><br/>
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*
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* <b>REST URL:</b> <code>POST, [context-root]/object?sessionid=[sessionid]</code> <br/>
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* <b>POST Data:</b> Earthgrid query document , Content-type: <code>text/xml</code><br/>
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* <b>Returns:</b> Earthgrid resultset document<br/><br/>
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*
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* </li>
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* </ul>
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*
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* </li>
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*
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* <li>
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* <h3> EarthGrid Authentication Service</h3>
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* <ul><li>
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* <h3>Login: </h3>
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* Receives username and password parameters in POST data and
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* returns SessionId (in XML format) or failure message and uses MetacatHandler's handleLoginAction function<br/><br/>
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*
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* <b>REST URL:</b> <code>POST, [context-root]/session?op=login</code> <br/>
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* <b>POST Data:</b> username=[username]&password=[password], Content-type: <code>application/x-www-form-urlencoded</code>
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* <b>Returns:</b> sessionId in XML format<br/><br/>
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* </li>
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*
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* <li>
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* <h3>Logout: </h3>
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* Receives session Id parameters in querystring and returns xml message, calls
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* MetacatHandler's handleLogoutAction function<br/><br/>
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*
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* <b>REST URL:</b> <code>GET, [context-root]/session?op=logout&sessionid=[sessionid]</code> <br/>
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* <b>Returns:</b> message in XML format<br/><br/>
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* </li>
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* </ul>
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*
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* <li>
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* <h3>EarthGrid Put Service</h3>
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*
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* <ul>
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* <li><h3>Update/Insert: </h3>
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* <br/>
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* <b>REST URL:</b> <code>PUT, [context-root]/object/[doc-id]?op={update|insert}&sessionid=[sessionid]</code> <br/>
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* <b>POST Data:</b> document object, Content-type: <code>text/xml</code><br/>
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* <b>Returns:</b> message in XML format<br/><br/>
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* </li>
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*
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* <li><h3>Delete: </h3>
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* <br/>
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* <b>REST URL:</b> <code>DELETE, [context-root]/object/[doc-id]?sessionid=[sessionid]</code> <br/>
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* <b>Returns:</b> message in XML format<br/><br/>
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* </li>
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* </ul>
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* </li>
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*
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* <li>
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* <h3>EarthGrid Identifier Service</h3><br/>
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*
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* <ul>
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* <li><h3>isRegistered: </h3> <br/>
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* <b>REST URL:</b> <code>GET, [context-root]/identifier/[doc-id]?op=isregistered</code> <br/>
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* <b>Returns:</b> message in XML format<br/><br/>
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* </li>
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* <li><h3>getAllDocIds:</h3> <br/>
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* <b>REST URL:</b> <code>GET, [context-root]/identifier?op=getalldocids</code> <br/>
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* <b>Returns:</b> document id list in XML format<br/><br/>
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* </li>
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*
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* <li><h3>addLSID Function:</h3>
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* Metacat does not support this function <br/>
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* <b>REST URL:</b> <code>PUT, [context-root]/identifier/[doc-id]</code> <br/>
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* <b>Returns:</b> error message in XML format<br/><br/>
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* </li>
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*
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* <li><h3>getNextRevision:</h3> <br/>
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* <b>REST URL:</b> <code>GET, [context-root]/identifier/[doc-id]?op=getnextrevision</code> <br/>
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* <b>Returns:</b> message in XML format<br/><br/>
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* </li>
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*
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* <li><h3>getNextObject:</h3> <br/>
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* <b>REST URL:</b> <code>GET, [context-root]/identifier?op=getnextobject&scope=[scope]</code> <br/>
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* <b>Returns:</b> message in XML format<br/><br/>
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* </li>
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*
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* </li>
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* </ul>
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*
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*/
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public class ResourceHandler {
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/**HTTP Verb GET*/
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public static final byte GET = 1;
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/**HTTP Verb POST*/
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public static final byte POST = 2;
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/**HTTP Verb PUT*/
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public static final byte PUT = 3;
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/**HTTP Verb DELETE*/
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public static final byte DELETE = 4;
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/*
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* API Resources
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*/
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private static final String RESOURCE_OBJECTS = "object";
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private static final String RESOURCE_META = "meta";
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private static final String RESOURCE_SESSION = "session";
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private static final String RESOURCE_IDENTIFIER = "identifier";
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private static final String RESOURCE_LOG = "log";
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/*
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* API Functions used as URL parameters
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*/
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private static final String FUNCTION_KEYWORD = "op";
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private static final String FUNCTION_NAME_LOGIN = "login";
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private static final String FUNCTION_NAME_LOGOUT = "logout";
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private static final String FUNCTION_NAME_SET_ACCESS = "setaccess";
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private static final String FUNCTION_NAME_ISREGISTERED = "isregistered";
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private static final String FUNCTION_NAME_GETALLDOCS = "getalldocids";
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private static final String FUNCTION_NAME_GETNEXTREV = "getnextrevision";
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private static final String FUNCTION_NAME_GETNEXTOBJ = "getnextobject";
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private static final String FUNCTION_NAME_INSERT = "insert";
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private static final String FUNCTION_NAME_UPDATE = "update";
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private static final String FUNCTION_NAME_GENERATE_MISSING_SYSTEM_METADATA = "generatemissingsystemmetadata";
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private static final DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ");
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private ServletContext servletContext;
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private Logger logMetacat;
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private MetacatHandler handler;
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private HttpServletRequest request;
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private HttpServletResponse response;
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private String username;
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private String password;
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private String sessionId;
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private String[] groupNames;
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private Hashtable<String, String[]> params;
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/**Initializes new instance by setting servlet context,request and response*/
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public ResourceHandler(ServletContext servletContext,
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HttpServletRequest request, HttpServletResponse response) {
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this.servletContext = servletContext;
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this.request = request;
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this.response = response;
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}
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/**
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* This function is called from REST APU servlet and handles each request to the servlet
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*
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* @param httpVerb (GET, POST, PUT or DELETE)
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*/
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public void handle(byte httpVerb) {
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logMetacat = Logger.getLogger(ResourceHandler.class);
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try {
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String resource = request.getServletPath();
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String verb = "";
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System.out.println("handling verb " + httpVerb + " request with resource " + resource);
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boolean status = false;
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loadSessionData();
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if (resource != null) {
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resource = request.getServletPath().substring(1);
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params = new Hashtable<String, String[]>();
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initParams();
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Timer timer = new Timer();
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handler = new MetacatHandler(timer);
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if (resource.equals(RESOURCE_SESSION) &&
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httpVerb == POST &&
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params.get(FUNCTION_KEYWORD) != null) {
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//System.out.println("function_keyword: " + params.get(FUNCTION_KEYWORD)[0]);
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if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_LOGIN)) {
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login();
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status = true;
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} else if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_LOGOUT)) {
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logout();
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status = true;
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} else if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_SET_ACCESS)) {
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setaccess();
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status = true;
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//System.out.println("done setting access");
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}
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} else if (resource.equals(RESOURCE_META)) {
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if(params != null && params.get(FUNCTION_KEYWORD) != null &&
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params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_GENERATE_MISSING_SYSTEM_METADATA))
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{ //generate system metadata for any object that is
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//a) not system metadata itself
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//b) does not already have a system metadata id in the systemmetadata table
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//c) not a BIN object (data)
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//TODO: check if we need this anymore. Might be superceded
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//by MetacatPopulator
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generateMissingSystemMetadata();
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status = true;
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}
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else
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{
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String objectId = request.getPathInfo();
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if (objectId != null && objectId.length() > 1)
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{
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objectId = request.getPathInfo().substring(1);
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}
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getSystemMetadataObject(objectId);
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status = true;
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}
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} else if (resource.equals(RESOURCE_OBJECTS)) {
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logMetacat.debug("D1 Rest: Starting resource processing...");
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loadSessionData();
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String objectId = request.getPathInfo();
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if (objectId != null && objectId.length() > 1)
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{
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objectId = request.getPathInfo().substring(1);
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}
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else
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{
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objectId = null;
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}
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logMetacat.debug("verb:" + httpVerb);
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if (httpVerb == GET) {
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getObject(objectId);
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status = true;
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} else if (httpVerb == POST) {
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putObject(objectId, FUNCTION_NAME_INSERT);
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status = true;
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} else if (httpVerb == PUT) {
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putObject(objectId, FUNCTION_NAME_UPDATE);
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status = true;
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} else if (httpVerb == DELETE) {
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deleteObject(objectId);
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status = true;
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}
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} else if (resource.equals(RESOURCE_IDENTIFIER)) {
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String identifierId = request.getPathInfo();
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if (identifierId != null && identifierId.length() > 1)
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identifierId = request.getPathInfo().substring(1); //trim the slash
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|
if (httpVerb == GET) {
|
|
343
|
String op = params.get(FUNCTION_KEYWORD)[0];
|
|
344
|
if (op.equals(FUNCTION_NAME_ISREGISTERED)) {
|
|
345
|
isRegistered(identifierId);
|
|
346
|
status = true;
|
|
347
|
} else if (op.equals(FUNCTION_NAME_GETALLDOCS)) {
|
|
348
|
getAllDocIds();
|
|
349
|
status = true;
|
|
350
|
} else if (op.equals(FUNCTION_NAME_GETNEXTREV)) {
|
|
351
|
getNextRevision(identifierId);
|
|
352
|
status = true;
|
|
353
|
} else if (op.equals(FUNCTION_NAME_GETNEXTOBJ)) {
|
|
354
|
getNextObject();
|
|
355
|
status = true;
|
|
356
|
}
|
|
357
|
|
|
358
|
} else if (httpVerb == PUT) {
|
|
359
|
//Earthgrid API > Identifier Service > addLSID Function
|
|
360
|
response.setStatus(501);
|
|
361
|
printError(
|
|
362
|
"This method is not supported by metacat. To "
|
|
363
|
+ "add a new LSID, add a document to metacat.",
|
|
364
|
response);
|
|
365
|
status = true;
|
|
366
|
}
|
|
367
|
|
|
368
|
} else if (resource.equals(RESOURCE_LOG)) {
|
|
369
|
//handle log events
|
|
370
|
if(httpVerb == GET)
|
|
371
|
{
|
|
372
|
getLog();
|
|
373
|
status = true;
|
|
374
|
}
|
|
375
|
else
|
|
376
|
{
|
|
377
|
//change to D1 spec for specifying which http methods are allowed for a resource
|
|
378
|
response.setStatus(501);
|
|
379
|
printError("POST, PUT, DELETE is not supported for logs.", response);
|
|
380
|
status = true;
|
|
381
|
}
|
|
382
|
|
|
383
|
}
|
|
384
|
|
|
385
|
if (!status)
|
|
386
|
{
|
|
387
|
response.setStatus(400);
|
|
388
|
printError("Incorrect parameters!", response);
|
|
389
|
}
|
|
390
|
} else {
|
|
391
|
response.setStatus(400);
|
|
392
|
printError("Incorrect resource!", response);
|
|
393
|
}
|
|
394
|
} catch (Exception e) {
|
|
395
|
logMetacat.error(e.getMessage());
|
|
396
|
e.printStackTrace();
|
|
397
|
}
|
|
398
|
}
|
|
399
|
|
|
400
|
/**
|
|
401
|
* get the logs from the CrudService based on passed params. Available
|
|
402
|
* params are token, fromDate, toDate, event. See
|
|
403
|
* http://mule1.dataone.org/ArchitectureDocs/mn_api_crud.html#MN_crud.getLogRecords
|
|
404
|
* for more info
|
|
405
|
*/
|
|
406
|
private void getLog()
|
|
407
|
{
|
|
408
|
OutputStream out = null;
|
|
409
|
try
|
|
410
|
{
|
|
411
|
out = response.getOutputStream();
|
|
412
|
response.setStatus(200);
|
|
413
|
response.setContentType("text/xml");
|
|
414
|
AuthToken token = new AuthToken(sessionId);
|
|
415
|
String fromDateS = params.get("fromDate")[0];
|
|
416
|
System.out.println("param fromDateS: " + fromDateS);
|
|
417
|
Date fromDate = null;
|
|
418
|
String toDateS = params.get("toDate")[0];
|
|
419
|
System.out.println("param toDateS: " + toDateS);
|
|
420
|
Date toDate = null;
|
|
421
|
String eventS = params.get("event")[0];
|
|
422
|
Event event = null;
|
|
423
|
if(fromDateS != null)
|
|
424
|
{
|
|
425
|
//fromDate = dateFormat.parse(fromDateS);
|
|
426
|
fromDate = parseDateAndConvertToGMT(fromDateS);
|
|
427
|
}
|
|
428
|
if(toDateS != null)
|
|
429
|
{
|
|
430
|
//toDate = dateFormat.parse(toDateS);
|
|
431
|
toDate = parseDateAndConvertToGMT(toDateS);
|
|
432
|
}
|
|
433
|
if(eventS != null)
|
|
434
|
{
|
|
435
|
event = Event.convert(eventS);
|
|
436
|
}
|
|
437
|
System.out.println("fromDate: " + fromDate + " toDate: " + toDate);
|
|
438
|
|
|
439
|
System.out.println("calling crudservice.getLogRecords");
|
|
440
|
Log log = CrudService.getInstance().getLogRecords(token, fromDate, toDate, event);
|
|
441
|
serializeServiceType(Log.class, log, out);
|
|
442
|
}
|
|
443
|
catch(Exception e)
|
|
444
|
{
|
|
445
|
String msg = "Could not get logs from CrudService: " + e.getMessage();
|
|
446
|
response.setStatus(500);
|
|
447
|
ServiceFailure sf = new ServiceFailure("1490", msg);
|
|
448
|
logMetacat.error(msg);
|
|
449
|
e.printStackTrace();
|
|
450
|
serializeException(sf, out);
|
|
451
|
}
|
|
452
|
}
|
|
453
|
|
|
454
|
/**
|
|
455
|
* copies request parameters to a hashtable which is given as argument to native metacathandler functions
|
|
456
|
*/
|
|
457
|
private void initParams() {
|
|
458
|
|
|
459
|
String name = null;
|
|
460
|
String[] value = null;
|
|
461
|
Enumeration paramlist = request.getParameterNames();
|
|
462
|
while (paramlist.hasMoreElements()) {
|
|
463
|
name = (String) paramlist.nextElement();
|
|
464
|
value = request.getParameterValues(name);
|
|
465
|
params.put(name, value);
|
|
466
|
}
|
|
467
|
}
|
|
468
|
|
|
469
|
/**
|
|
470
|
*
|
|
471
|
* Load user details of metacat session from the request
|
|
472
|
*
|
|
473
|
*/
|
|
474
|
private void loadSessionData()
|
|
475
|
throws Exception
|
|
476
|
{
|
|
477
|
SessionData sessionData = RequestUtil.getSessionData(request);
|
|
478
|
try
|
|
479
|
{
|
|
480
|
username = null;
|
|
481
|
password = null;
|
|
482
|
groupNames = null;
|
|
483
|
sessionId = null;
|
|
484
|
|
|
485
|
boolean validSession = false;
|
|
486
|
SessionService ss = SessionService.getInstance();
|
|
487
|
System.out.println("sessionData: " + sessionData);
|
|
488
|
if(sessionData == null)
|
|
489
|
{
|
|
490
|
username = "public";
|
|
491
|
sessionId = "0";
|
|
492
|
System.out.println("sessiondata is null. Creating a public session.");
|
|
493
|
return;
|
|
494
|
}
|
|
495
|
|
|
496
|
System.out.println("username: " + sessionData.getUserName());
|
|
497
|
System.out.println("sessionid: " + sessionData.getId());
|
|
498
|
//validate the session
|
|
499
|
if(ss.isSessionRegistered(sessionData.getId()) &&
|
|
500
|
!(sessionData.getUserName().equals("public") || sessionData.getId().equals("0")))
|
|
501
|
{
|
|
502
|
validSession = true;
|
|
503
|
}
|
|
504
|
|
|
505
|
if(validSession)
|
|
506
|
{
|
|
507
|
//if the session is valid, set these variables
|
|
508
|
username = sessionData.getUserName();
|
|
509
|
password = sessionData.getPassword();
|
|
510
|
groupNames = sessionData.getGroupNames();
|
|
511
|
sessionId = sessionData.getId();
|
|
512
|
System.out.println("setting sessionid to " + sessionId);
|
|
513
|
System.out.println("username: " + username);
|
|
514
|
}
|
|
515
|
|
|
516
|
//if the session is not valid or the username is null, set
|
|
517
|
//username to public
|
|
518
|
if (username == null)
|
|
519
|
{
|
|
520
|
System.out.println("setting username to public.");
|
|
521
|
username = "public";
|
|
522
|
}
|
|
523
|
}
|
|
524
|
catch(Exception e)
|
|
525
|
{
|
|
526
|
e.printStackTrace();
|
|
527
|
throw new Exception("Could not load the session data: " + e.getMessage());
|
|
528
|
}
|
|
529
|
}
|
|
530
|
|
|
531
|
/**
|
|
532
|
* generate missing system metadata for any science metadata objects
|
|
533
|
* that don't already have it. https://trac.dataone.org/ticket/591
|
|
534
|
*
|
|
535
|
* called with POST meta/?op=generatemissingsystemmetadata
|
|
536
|
*/
|
|
537
|
private void generateMissingSystemMetadata()
|
|
538
|
{
|
|
539
|
AuthToken token = new AuthToken(sessionId);
|
|
540
|
CrudService.getInstance().generateMissingSystemMetadata(token);
|
|
541
|
}
|
|
542
|
|
|
543
|
/**
|
|
544
|
* Earthgrid API > Identifier Service > isRegistered Function :
|
|
545
|
* calls MetacatHandler > handleIdIsRegisteredAction
|
|
546
|
* @param guid
|
|
547
|
* @throws IOException
|
|
548
|
*/
|
|
549
|
private void isRegistered(String guid) throws IOException
|
|
550
|
{
|
|
551
|
|
|
552
|
// Look up the localId for this guid
|
|
553
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
554
|
String localId = "";
|
|
555
|
try {
|
|
556
|
localId = im.getLocalId(guid);
|
|
557
|
} catch (McdbDocNotFoundException e) {
|
|
558
|
// TODO: Need to return the proper DataONE exception
|
|
559
|
}
|
|
560
|
|
|
561
|
params.put("docid", new String[] { localId });
|
|
562
|
PrintWriter out = response.getWriter();
|
|
563
|
response.setStatus(200);
|
|
564
|
response.setContentType("text/xml");
|
|
565
|
handler.handleIdIsRegisteredAction(out, params, response);
|
|
566
|
out.close();
|
|
567
|
}
|
|
568
|
|
|
569
|
/**
|
|
570
|
* Earthgrid API > Identifier Service > getAllDocIds Function :
|
|
571
|
* calls MetacatHandler > handleGetAllDocidsAction
|
|
572
|
* @throws IOException
|
|
573
|
*/
|
|
574
|
private void getAllDocIds() throws IOException {
|
|
575
|
PrintWriter out = response.getWriter();
|
|
576
|
response.setStatus(200);
|
|
577
|
response.setContentType("text/xml");
|
|
578
|
handler.handleGetAllDocidsAction(out, params, response);
|
|
579
|
out.close();
|
|
580
|
}
|
|
581
|
|
|
582
|
/**
|
|
583
|
* Earthgrid API > Identifier Service > getNextRevision Function :
|
|
584
|
* calls MetacatHandler > handleGetRevisionAndDocTypeAction
|
|
585
|
* @param guid
|
|
586
|
* @throws IOException
|
|
587
|
*/
|
|
588
|
private void getNextRevision(String guid) throws IOException
|
|
589
|
{
|
|
590
|
params.put("docid", new String[] { guid });
|
|
591
|
PrintWriter out = response.getWriter();
|
|
592
|
response.setStatus(200);
|
|
593
|
response.setContentType("text/xml");
|
|
594
|
//handler.handleGetRevisionAndDocTypeAction(out, params);
|
|
595
|
|
|
596
|
try {
|
|
597
|
// Make sure there is a docid
|
|
598
|
if (guid == null || guid.equals("")) {
|
|
599
|
throw new Exception("User didn't specify docid!");
|
|
600
|
}
|
|
601
|
|
|
602
|
// Look up the localId for this guid
|
|
603
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
604
|
String localId = "";
|
|
605
|
try {
|
|
606
|
localId = im.getLocalId(guid);
|
|
607
|
} catch (McdbDocNotFoundException e) {
|
|
608
|
// TODO: Need to return the proper DataONE exception
|
|
609
|
}
|
|
610
|
|
|
611
|
// Create a DBUtil object
|
|
612
|
DBUtil dbutil = new DBUtil();
|
|
613
|
// Get a rev and doctype
|
|
614
|
String revAndDocType = dbutil
|
|
615
|
.getCurrentRevisionAndDocTypeForGivenDocument(localId);
|
|
616
|
int revision = Integer.parseInt(revAndDocType.split(";")[0]) + 1;
|
|
617
|
|
|
618
|
out.println("<?xml version=\"1.0\"?>");
|
|
619
|
out.print("<next-revision>");
|
|
620
|
out.print(revision);
|
|
621
|
out.print("</next-revision>");
|
|
622
|
|
|
623
|
} catch (Exception e) {
|
|
624
|
// Handle exception
|
|
625
|
response.setStatus(500);
|
|
626
|
out.println("<?xml version=\"1.0\"?>");
|
|
627
|
out.println("<error>");
|
|
628
|
out.println(e.getMessage());
|
|
629
|
out.println("</error>");
|
|
630
|
}
|
|
631
|
|
|
632
|
out.close();
|
|
633
|
}
|
|
634
|
|
|
635
|
/**
|
|
636
|
* Earthgrid API > Identifier Service > getNextObject Function :
|
|
637
|
* calls MetacatHandler > handleGetMaxDocidAction
|
|
638
|
* @throws IOException
|
|
639
|
*/
|
|
640
|
private void getNextObject() throws IOException {
|
|
641
|
PrintWriter out = response.getWriter();
|
|
642
|
response.setStatus(200);
|
|
643
|
response.setContentType("text/xml");
|
|
644
|
handler.handleGetMaxDocidAction(out, params, response);
|
|
645
|
out.close();
|
|
646
|
}
|
|
647
|
|
|
648
|
/**
|
|
649
|
* Implements REST version of DataONE CRUD API --> get
|
|
650
|
* @param guid ID of data object to be read
|
|
651
|
*/
|
|
652
|
private void getObject(String guid) {
|
|
653
|
CrudService cs = CrudService.getInstance();
|
|
654
|
cs.setParamsFromRequest(request);
|
|
655
|
AuthToken token = new AuthToken(sessionId);
|
|
656
|
OutputStream out = null;
|
|
657
|
try {
|
|
658
|
out = response.getOutputStream();
|
|
659
|
response.setStatus(200);
|
|
660
|
response.setContentType("text/xml");
|
|
661
|
if(guid != null)
|
|
662
|
{ //get a specific document
|
|
663
|
Identifier id = new Identifier();
|
|
664
|
id.setValue(guid);
|
|
665
|
try
|
|
666
|
{
|
|
667
|
if(token == null)
|
|
668
|
{
|
|
669
|
token = new AuthToken("Public");
|
|
670
|
}
|
|
671
|
InputStream data = cs.get(token, id);
|
|
672
|
IOUtils.copyLarge(data, response.getOutputStream());
|
|
673
|
}
|
|
674
|
catch(InvalidToken it)
|
|
675
|
{
|
|
676
|
response.setStatus(500);
|
|
677
|
serializeException(it, out);
|
|
678
|
}
|
|
679
|
catch(ServiceFailure sf)
|
|
680
|
{
|
|
681
|
response.setStatus(500);
|
|
682
|
serializeException(sf, out);
|
|
683
|
}
|
|
684
|
catch(NotAuthorized na)
|
|
685
|
{
|
|
686
|
response.setStatus(500);
|
|
687
|
serializeException(na, out);
|
|
688
|
}
|
|
689
|
catch(NotFound nf)
|
|
690
|
{
|
|
691
|
response.setStatus(500);
|
|
692
|
serializeException(nf, out);
|
|
693
|
}
|
|
694
|
catch(NotImplemented ni)
|
|
695
|
{
|
|
696
|
response.setStatus(500);
|
|
697
|
serializeException(ni, out);
|
|
698
|
}
|
|
699
|
catch(Exception e)
|
|
700
|
{
|
|
701
|
response.setStatus(500);
|
|
702
|
System.out.println("Error with Crud.get(). " +
|
|
703
|
"If this is an 'Exception producing data' error, " +
|
|
704
|
"go to CrudService.get() for better debugging. " +
|
|
705
|
"Here's the error: " + e.getMessage());
|
|
706
|
e.printStackTrace();
|
|
707
|
ServiceFailure sf = new ServiceFailure("1030",
|
|
708
|
"IO Error in ResourceHandler.getObject: " + e.getMessage());
|
|
709
|
serializeException(sf, out);
|
|
710
|
}
|
|
711
|
}
|
|
712
|
else
|
|
713
|
{ //call listObjects with specified params
|
|
714
|
Date startTime = null;
|
|
715
|
Date endTime = null;
|
|
716
|
ObjectFormat objectFormat = null;
|
|
717
|
boolean replicaStatus = false;
|
|
718
|
int start = 0;
|
|
719
|
//TODO: make the max count into a const
|
|
720
|
int count = 1000;
|
|
721
|
Enumeration paramlist = request.getParameterNames();
|
|
722
|
while (paramlist.hasMoreElements())
|
|
723
|
{ //parse the params and make the crud call
|
|
724
|
String name = (String) paramlist.nextElement();
|
|
725
|
String[] value = (String[])request.getParameterValues(name);
|
|
726
|
/*for(int i=0; i<value.length; i++)
|
|
727
|
{
|
|
728
|
System.out.println("name: " + name + " value: " + value[i]);
|
|
729
|
}*/
|
|
730
|
if(name.equals("startTime") && value != null)
|
|
731
|
{
|
|
732
|
try
|
|
733
|
{
|
|
734
|
//startTime = dateFormat.parse(value[0]);
|
|
735
|
startTime = parseDateAndConvertToGMT(value[0]);
|
|
736
|
}
|
|
737
|
catch(Exception e)
|
|
738
|
{ //if we can't parse it, just don't use the startTime param
|
|
739
|
System.out.println("Could not parse startTime: " + value[0]);
|
|
740
|
startTime = null;
|
|
741
|
}
|
|
742
|
}
|
|
743
|
else if(name.equals("endTime") && value != null)
|
|
744
|
{
|
|
745
|
try
|
|
746
|
{
|
|
747
|
//endTime = dateFormat.parse(value[0]);
|
|
748
|
endTime = parseDateAndConvertToGMT(value[0]);
|
|
749
|
}
|
|
750
|
catch(Exception e)
|
|
751
|
{ //if we can't parse it, just don't use the endTime param
|
|
752
|
System.out.println("Could not parse endTime: " + value[0]);
|
|
753
|
endTime = null;
|
|
754
|
}
|
|
755
|
}
|
|
756
|
else if(name.equals("objectFormat") && value != null)
|
|
757
|
{
|
|
758
|
objectFormat = ObjectFormat.convert(value[0]);
|
|
759
|
}
|
|
760
|
else if(name.equals("replicaStatus") && value != null)
|
|
761
|
{
|
|
762
|
if(value != null &&
|
|
763
|
value.length > 0 &&
|
|
764
|
(value[0].equals("true") || value[0].equals("TRUE") || value[0].equals("YES")))
|
|
765
|
{
|
|
766
|
replicaStatus = true;
|
|
767
|
}
|
|
768
|
}
|
|
769
|
else if(name.equals("start") && value != null)
|
|
770
|
{
|
|
771
|
start = new Integer(value[0]).intValue();
|
|
772
|
}
|
|
773
|
else if(name.equals("count") && value != null)
|
|
774
|
{
|
|
775
|
count = new Integer(value[0]).intValue();
|
|
776
|
}
|
|
777
|
}
|
|
778
|
//make the crud call
|
|
779
|
System.out.println("token: " + token + " startTime: " + startTime +
|
|
780
|
" endtime: " + endTime + " objectFormat: " +
|
|
781
|
objectFormat + " replicaStatus: " + replicaStatus +
|
|
782
|
" start: " + start + " count: " + count);
|
|
783
|
|
|
784
|
ObjectList ol = cs.listObjects(token, startTime, endTime,
|
|
785
|
objectFormat, replicaStatus, start, count);
|
|
786
|
|
|
787
|
StringReader sr = new StringReader(ol.toString());
|
|
788
|
out = response.getOutputStream();
|
|
789
|
response.setStatus(200);
|
|
790
|
response.setContentType("text/xml");
|
|
791
|
// Serialize and write it to the output stream
|
|
792
|
|
|
793
|
try {
|
|
794
|
serializeServiceType(ObjectList.class, ol, out);
|
|
795
|
} catch (JiBXException e) {
|
|
796
|
throw new ServiceFailure("1190", "Failed to serialize ObjectList: " + e.getMessage());
|
|
797
|
}
|
|
798
|
}
|
|
799
|
} catch (BaseException e) {
|
|
800
|
response.setStatus(500);
|
|
801
|
serializeException(e, out);
|
|
802
|
} catch (IOException e) {
|
|
803
|
e.printStackTrace();
|
|
804
|
response.setStatus(500);
|
|
805
|
ServiceFailure sf = new ServiceFailure("1030",
|
|
806
|
"IO Error in ResourceHandler.getObject: " + e.getMessage());
|
|
807
|
serializeException(sf, out);
|
|
808
|
} catch(NumberFormatException ne) {
|
|
809
|
response.setStatus(500);
|
|
810
|
InvalidRequest ir = new InvalidRequest("1030", "Invalid format for parameter: " + ne.getMessage());
|
|
811
|
serializeException(ir, out);
|
|
812
|
} catch (Exception e) {
|
|
813
|
e.printStackTrace();
|
|
814
|
response.setStatus(500);
|
|
815
|
ServiceFailure sf = new ServiceFailure("1030",
|
|
816
|
"Exception " + e.getClass().getName() + " raised while handling listObjects request: " +
|
|
817
|
e.getMessage());
|
|
818
|
serializeException(sf, out);
|
|
819
|
}
|
|
820
|
}
|
|
821
|
|
|
822
|
/**
|
|
823
|
* parse a date and return it in GMT if it ends with a 'Z'
|
|
824
|
* @param date
|
|
825
|
* @return
|
|
826
|
* @throws ParseException
|
|
827
|
*/
|
|
828
|
private Date parseDateAndConvertToGMT(String date) throws ParseException
|
|
829
|
{
|
|
830
|
try
|
|
831
|
{ //the format we want
|
|
832
|
return dateFormat.parse(date);
|
|
833
|
}
|
|
834
|
catch(java.text.ParseException pe)
|
|
835
|
{ //try another legacy format
|
|
836
|
DateFormat dateFormat2 = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss'Z'");
|
|
837
|
dateFormat2.setTimeZone(TimeZone.getTimeZone("GMT-0"));
|
|
838
|
return dateFormat2.parse(date);
|
|
839
|
}
|
|
840
|
|
|
841
|
/*System.out.println("Parsing date " + date);
|
|
842
|
Date d = dateFormat.parse(date);
|
|
843
|
|
|
844
|
if(date.endsWith("Z"))
|
|
845
|
{
|
|
846
|
Calendar lTime = Calendar.getInstance();
|
|
847
|
lTime.setTime(d);
|
|
848
|
Calendar zTime = Calendar.getInstance(TimeZone.getTimeZone("GMT-0"));
|
|
849
|
zTime.set(Calendar.MONTH, lTime.get(Calendar.MONTH));
|
|
850
|
zTime.set(Calendar.DATE, lTime.get(Calendar.DATE));
|
|
851
|
zTime.set(Calendar.YEAR, lTime.get(Calendar.YEAR));
|
|
852
|
zTime.set(Calendar.HOUR, lTime.get(Calendar.HOUR));
|
|
853
|
zTime.set(Calendar.MINUTE, lTime.get(Calendar.MINUTE));
|
|
854
|
zTime.set(Calendar.SECOND, lTime.get(Calendar.SECOND));
|
|
855
|
|
|
856
|
System.out.println("date parsed to " + zTime.getTime());
|
|
857
|
return zTime.getTime();
|
|
858
|
}
|
|
859
|
|
|
860
|
System.out.println("date parsed, but not converted. returned as " + d);
|
|
861
|
return d;*/
|
|
862
|
}
|
|
863
|
|
|
864
|
/**
|
|
865
|
* Implements REST version of DataONE CRUD API --> getSystemMetadata
|
|
866
|
* @param guid ID of data object to be read
|
|
867
|
*/
|
|
868
|
private void getSystemMetadataObject(String guid) {
|
|
869
|
CrudService cs = CrudService.getInstance();
|
|
870
|
cs.setParamsFromRequest(request);
|
|
871
|
AuthToken token = new AuthToken(sessionId);
|
|
872
|
OutputStream out = null;
|
|
873
|
try {
|
|
874
|
response.setContentType("text/xml");
|
|
875
|
response.setStatus(200);
|
|
876
|
out = response.getOutputStream();
|
|
877
|
Identifier id = new Identifier();
|
|
878
|
id.setValue(guid);
|
|
879
|
SystemMetadata sysmeta = cs.getSystemMetadata(token, id);
|
|
880
|
|
|
881
|
// Serialize and write it to the output stream
|
|
882
|
try {
|
|
883
|
//TODO: look at the efficiency of this method. The system metadata
|
|
884
|
//is read from metacat (in CrudService) as xml, then serialized
|
|
885
|
//to a SystemMetadat object, then returned here, then serizlized
|
|
886
|
//back to XML to be sent to the response.
|
|
887
|
serializeServiceType(SystemMetadata.class, sysmeta, out);
|
|
888
|
} catch (JiBXException e) {
|
|
889
|
throw new ServiceFailure("1190", "Failed to serialize SystemMetadata: " + e.getMessage());
|
|
890
|
}
|
|
891
|
} catch (BaseException e) {
|
|
892
|
response.setStatus(500);
|
|
893
|
serializeException(e, out);
|
|
894
|
} catch (IOException e) {
|
|
895
|
response.setStatus(500);
|
|
896
|
ServiceFailure sf = new ServiceFailure("1030",
|
|
897
|
"Error in ResourceHandler.getSystemMetadataObject: " + e.getMessage());
|
|
898
|
serializeException(sf, out);
|
|
899
|
} finally {
|
|
900
|
IOUtils.closeQuietly(out);
|
|
901
|
}
|
|
902
|
}
|
|
903
|
|
|
904
|
/**
|
|
905
|
* serialize an object of type to out
|
|
906
|
* @param type the class of the object to serialize (i.e. SystemMetadata.class)
|
|
907
|
* @param object the object to serialize
|
|
908
|
* @param out the stream to serialize it to
|
|
909
|
* @throws JiBXException
|
|
910
|
*/
|
|
911
|
private void serializeServiceType(Class type, Object object, OutputStream out)
|
|
912
|
throws JiBXException
|
|
913
|
{
|
|
914
|
IBindingFactory bfact = BindingDirectory.getFactory(type);
|
|
915
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
|
916
|
mctx.marshalDocument(object, "UTF-8", null, out);
|
|
917
|
}
|
|
918
|
|
|
919
|
/**
|
|
920
|
* deserialize an object of type from is
|
|
921
|
* @param type the class of the object to serialize (i.e. SystemMetadata.class)
|
|
922
|
* @param is the stream to deserialize from
|
|
923
|
* @throws JiBXException
|
|
924
|
*/
|
|
925
|
private Object deserializeServiceType(Class type, InputStream is)
|
|
926
|
throws JiBXException
|
|
927
|
{
|
|
928
|
IBindingFactory bfact = BindingDirectory.getFactory(type);
|
|
929
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
|
930
|
Object o = (Object) uctx.unmarshalDocument(is, null);
|
|
931
|
return o;
|
|
932
|
}
|
|
933
|
|
|
934
|
/**
|
|
935
|
* Earthgrid API > Query Service > Query Function : translates ecogrid query document to metacat query
|
|
936
|
* then calls DBQuery > createResultDocument function and then again translate resultset to ecogrid resultset
|
|
937
|
*
|
|
938
|
* NOTE:
|
|
939
|
* This is the only method that uses EcoGrid classes for its implementation.
|
|
940
|
* It does so because it takes an EcoGrid Query as input, and outputs an
|
|
941
|
* EcoGrid ResultSet document. These documents are parsed by the auto-generated
|
|
942
|
* EcoGrid classes from axis, and so we link to them here rather than re-inventing them.
|
|
943
|
* This creates a circular dependency, because the Metacat classes are needed
|
|
944
|
* to build the EcoGrid implementation, and the EcoGrid jars are needed to build this query()
|
|
945
|
* method. This circularity could be resolved by moving the EcoGrid classes
|
|
946
|
* to Metacat directly. As we transition away from EcoGrid SOAP methods in
|
|
947
|
* favor of these REST interfaces, this circular dependency can be eliminated.
|
|
948
|
*
|
|
949
|
* @throws Exception
|
|
950
|
*/
|
|
951
|
private void query() throws Exception {
|
|
952
|
/* This block commented out because of the EcoGrid circular dependency.
|
|
953
|
* For now, query will not be supported until the circularity can be
|
|
954
|
* resolved, probably by moving the ecogrid query syntax transformers
|
|
955
|
* directly into the Metacat codebase. MBJ 2010-02-03
|
|
956
|
|
|
957
|
try {
|
|
958
|
EcogridQueryParser parser = new EcogridQueryParser(request
|
|
959
|
.getReader());
|
|
960
|
parser.parseXML();
|
|
961
|
QueryType queryType = parser.getEcogridQuery();
|
|
962
|
EcogridJavaToMetacatJavaQueryTransformer queryTransformer =
|
|
963
|
new EcogridJavaToMetacatJavaQueryTransformer();
|
|
964
|
QuerySpecification metacatQuery = queryTransformer
|
|
965
|
.transform(queryType);
|
|
966
|
|
|
967
|
DBQuery metacat = new DBQuery();
|
|
968
|
|
|
969
|
boolean useXMLIndex = (new Boolean(PropertyService
|
|
970
|
.getProperty("database.usexmlindex"))).booleanValue();
|
|
971
|
String xmlquery = "query"; // we don't care the query in resultset,
|
|
972
|
// the query can be anything
|
|
973
|
PrintWriter out = null; // we don't want metacat result, so set out null
|
|
974
|
|
|
975
|
// parameter: queryspecification, user, group, usingIndexOrNot
|
|
976
|
StringBuffer result = metacat.createResultDocument(xmlquery,
|
|
977
|
metacatQuery, out, username, groupNames, useXMLIndex);
|
|
978
|
|
|
979
|
// create result set transfer
|
|
980
|
String saxparser = PropertyService.getProperty("xml.saxparser");
|
|
981
|
MetacatResultsetParser metacatResultsetParser = new MetacatResultsetParser(
|
|
982
|
new StringReader(result.toString()), saxparser, queryType
|
|
983
|
.getNamespace().get_value());
|
|
984
|
ResultsetType records = metacatResultsetParser.getEcogridResult();
|
|
985
|
|
|
986
|
System.out
|
|
987
|
.println(EcogridResultsetTransformer.toXMLString(records));
|
|
988
|
response.setContentType("text/xml");
|
|
989
|
out = response.getWriter();
|
|
990
|
out.print(EcogridResultsetTransformer.toXMLString(records));
|
|
991
|
|
|
992
|
} catch (Exception e) {
|
|
993
|
e.printStackTrace();
|
|
994
|
}*/
|
|
995
|
response.setContentType("text/xml");
|
|
996
|
response.setStatus(501);
|
|
997
|
PrintWriter out = response.getWriter();
|
|
998
|
out.print("<error>Query operation not yet supported by Metacat.</error>");
|
|
999
|
out.close();
|
|
1000
|
}
|
|
1001
|
|
|
1002
|
private String streamToString(InputStream is)
|
|
1003
|
throws IOException
|
|
1004
|
{
|
|
1005
|
return IOUtil.toString(is);
|
|
1006
|
}
|
|
1007
|
|
|
1008
|
private InputStream stringToStream(String s)
|
|
1009
|
throws IOException
|
|
1010
|
{
|
|
1011
|
ByteArrayInputStream bais = new ByteArrayInputStream(s.getBytes());
|
|
1012
|
return bais;
|
|
1013
|
}
|
|
1014
|
|
|
1015
|
/**
|
|
1016
|
* process a mime multipart message
|
|
1017
|
* @param is
|
|
1018
|
* @return
|
|
1019
|
*/
|
|
1020
|
/*private Hashtable processMMP(InputStream is)
|
|
1021
|
throws IOException
|
|
1022
|
{
|
|
1023
|
//TODO: verify that this is how the RFC for MMP should work
|
|
1024
|
//SORTAHACK: Since mmp seems to have a bug where large object parts get truncated,
|
|
1025
|
//parse the stream here. This has the disavantage of putting the
|
|
1026
|
//stream into memory.
|
|
1027
|
InputStream object = null;
|
|
1028
|
InputStream sysmeta = null;
|
|
1029
|
String s = IOUtils.toString(is);
|
|
1030
|
System.out.println("mime: " + s);
|
|
1031
|
//figure out what the boundary marker is
|
|
1032
|
String searchString = "boundary=";
|
|
1033
|
int searchStringIndex = s.indexOf(searchString);
|
|
1034
|
String boundary = s.substring(searchStringIndex + searchString.length() + 1,
|
|
1035
|
s.indexOf("\"", searchStringIndex + searchString.length() + 1));
|
|
1036
|
boundary = "--" + boundary;
|
|
1037
|
//System.out.println("boundary is " + boundary);
|
|
1038
|
|
|
1039
|
//find the system metadata
|
|
1040
|
searchString = "Content-Disposition: attachment; filename=systemmetadata";
|
|
1041
|
searchStringIndex = s.indexOf(searchString);
|
|
1042
|
String sm = s.substring(searchStringIndex +
|
|
1043
|
searchString.length() + 2,
|
|
1044
|
s.indexOf(boundary, searchStringIndex));
|
|
1045
|
sysmeta = new ByteArrayInputStream(sm.getBytes());
|
|
1046
|
|
|
1047
|
//find the object
|
|
1048
|
searchString = "Content-Disposition: attachment; filename=object";
|
|
1049
|
searchStringIndex = s.indexOf(searchString);
|
|
1050
|
String o = s.substring(searchStringIndex +
|
|
1051
|
searchString.length() + 2,
|
|
1052
|
s.indexOf(boundary, searchStringIndex));
|
|
1053
|
object = new ByteArrayInputStream(o.getBytes());
|
|
1054
|
|
|
1055
|
Hashtable h = new Hashtable();
|
|
1056
|
h.put("object", object);
|
|
1057
|
h.put("systemmetadata", sysmeta);
|
|
1058
|
|
|
1059
|
//System.out.println("o: \"" + o + "\"");
|
|
1060
|
//System.out.println("sm: \"" + sm + "\"");
|
|
1061
|
return h;
|
|
1062
|
}
|
|
1063
|
*/
|
|
1064
|
|
|
1065
|
protected static String[] findBoundaryString(InputStream is)
|
|
1066
|
throws IOException
|
|
1067
|
{
|
|
1068
|
String[] endResult = new String[2];
|
|
1069
|
String boundary = "";
|
|
1070
|
String searchString = "boundary=";
|
|
1071
|
boolean doneWithCurrentArray = false;
|
|
1072
|
byte[] b = new byte[1024];
|
|
1073
|
int numbytes = is.read(b, 0, 1024);
|
|
1074
|
while(numbytes != -1)
|
|
1075
|
{
|
|
1076
|
String s = new String(b, 0, numbytes);
|
|
1077
|
|
|
1078
|
int[] result = StreamUtil.lookForMatch(searchString, s);
|
|
1079
|
int searchStringIndex = s.indexOf(searchString);
|
|
1080
|
if(s.indexOf("\"", searchStringIndex + searchString.length() + 1) == -1)
|
|
1081
|
{ //the end of the boundary is in the next byte array
|
|
1082
|
boundary = s.substring(searchStringIndex + searchString.length() + 1, s.length());
|
|
1083
|
}
|
|
1084
|
else if(!boundary.startsWith("--"))
|
|
1085
|
{ //we can read the whole boundary from this byte array
|
|
1086
|
boundary = s.substring(searchStringIndex + searchString.length() + 1,
|
|
1087
|
s.indexOf("\"", searchStringIndex + searchString.length() + 1));
|
|
1088
|
boundary = "--" + boundary;
|
|
1089
|
endResult[0] = boundary;
|
|
1090
|
endResult[1] = s.substring(s.indexOf("\"", searchStringIndex + searchString.length() + 1) + 1,
|
|
1091
|
s.length());
|
|
1092
|
break;
|
|
1093
|
}
|
|
1094
|
else
|
|
1095
|
{ //we're now reading the 2nd byte array to get the rest of the boundary
|
|
1096
|
searchString = "\"";
|
|
1097
|
searchStringIndex = s.indexOf(searchString);
|
|
1098
|
boundary += s.substring(0, searchStringIndex);
|
|
1099
|
boundary = "--" + boundary;
|
|
1100
|
endResult[0] = boundary;
|
|
1101
|
endResult[1] = s.substring(s.indexOf("\"", searchStringIndex + searchString.length() + 1) + 1,
|
|
1102
|
s.length());
|
|
1103
|
break;
|
|
1104
|
}
|
|
1105
|
}
|
|
1106
|
System.out.println("boundary is: " + boundary);
|
|
1107
|
return endResult;
|
|
1108
|
}
|
|
1109
|
|
|
1110
|
protected String writeMMPPartToFile(String beginSearch,
|
|
1111
|
InputStream is, String boundary, String searchString, File f)
|
|
1112
|
throws IOException
|
|
1113
|
{
|
|
1114
|
Logger logMetacat = Logger.getLogger(ResourceHandler.class);
|
|
1115
|
logMetacat.info("writing MMP parts");
|
|
1116
|
String s = beginSearch;
|
|
1117
|
FileOutputStream fos = new FileOutputStream(f);
|
|
1118
|
int numread = 0;
|
|
1119
|
byte[] b = new byte[1024];
|
|
1120
|
String writeString = "";
|
|
1121
|
|
|
1122
|
if(s == null)
|
|
1123
|
{ //starting with the first part of the stream
|
|
1124
|
numread = is.read(b, 0, 1024);
|
|
1125
|
s = new String(b, 0, numread);
|
|
1126
|
}
|
|
1127
|
|
|
1128
|
boolean useCurrentS = true;
|
|
1129
|
boolean searchForBoundary = false;
|
|
1130
|
String seekString = searchString;
|
|
1131
|
|
|
1132
|
while(numread != -1)
|
|
1133
|
{
|
|
1134
|
logMetacat.info("////////////////////////iterating");
|
|
1135
|
logMetacat.info("searchForBoundary: " + searchForBoundary);
|
|
1136
|
logMetacat.info("useCurrentS: " + useCurrentS);
|
|
1137
|
if(searchForBoundary)
|
|
1138
|
{
|
|
1139
|
seekString = boundary;
|
|
1140
|
}
|
|
1141
|
else
|
|
1142
|
{
|
|
1143
|
seekString = searchString;
|
|
1144
|
}
|
|
1145
|
|
|
1146
|
int[] result = StreamUtil.lookForMatch(seekString, s);
|
|
1147
|
if(!useCurrentS)
|
|
1148
|
{
|
|
1149
|
numread = is.read(b, 0, 1024);
|
|
1150
|
if(numread != -1)
|
|
1151
|
{
|
|
1152
|
s = new String(b, 0, numread);
|
|
1153
|
}
|
|
1154
|
else
|
|
1155
|
{
|
|
1156
|
break;
|
|
1157
|
}
|
|
1158
|
}
|
|
1159
|
|
|
1160
|
logMetacat.info("seekString: " + seekString);
|
|
1161
|
logMetacat.info("in string: " + s);
|
|
1162
|
|
|
1163
|
if(result[0] >= 0 && result[1] == seekString.length())
|
|
1164
|
{
|
|
1165
|
//searchString is full in s
|
|
1166
|
logMetacat.info("seekstring is fully in s");
|
|
1167
|
if(!searchForBoundary)
|
|
1168
|
{ //we're looking for searchString and we found it
|
|
1169
|
//chop off the searchString itself and start writing
|
|
1170
|
//until we find boundary
|
|
1171
|
s = s.substring(result[0] + result[1], s.length());
|
|
1172
|
if(s.length() > 0)
|
|
1173
|
{
|
|
1174
|
useCurrentS = true;
|
|
1175
|
}
|
|
1176
|
else
|
|
1177
|
{
|
|
1178
|
useCurrentS = false;
|
|
1179
|
}
|
|
1180
|
searchForBoundary = true;
|
|
1181
|
}
|
|
1182
|
else
|
|
1183
|
{ //we're writing, but we found the boundary in this chunk
|
|
1184
|
|
|
1185
|
writeString = s.substring(0, result[0]);
|
|
1186
|
System.out.println("writing1: " + writeString);
|
|
1187
|
fos.write(writeString.getBytes());
|
|
1188
|
//we're done. break and return;
|
|
1189
|
return s.substring(result[0] + result[1], s.length());
|
|
1190
|
}
|
|
1191
|
}
|
|
1192
|
else if(result[0] > 0 && result[1] != seekString.length())
|
|
1193
|
{
|
|
1194
|
logMetacat.info("seekstring is partially in s");
|
|
1195
|
//seekString is partially in s
|
|
1196
|
//more specifically, the beginning of seekString is at the end
|
|
1197
|
//of s
|
|
1198
|
|
|
1199
|
//get the next chunk right now, see if the beginning matches
|
|
1200
|
numread = is.read(b, 0, 1024);
|
|
1201
|
String s2 = new String(b, 0, numread);
|
|
1202
|
s += s2;
|
|
1203
|
useCurrentS = true;
|
|
1204
|
}
|
|
1205
|
else
|
|
1206
|
{
|
|
1207
|
logMetacat.info("seekstring is not in s");
|
|
1208
|
//searchString is not in s
|
|
1209
|
if(searchForBoundary)
|
|
1210
|
{
|
|
1211
|
System.out.println("writing2: " + s);
|
|
1212
|
fos.write(s.getBytes());
|
|
1213
|
}
|
|
1214
|
numread = is.read(b, 0, 1024);
|
|
1215
|
if(numread != -1)
|
|
1216
|
{
|
|
1217
|
s = new String(b, 0, numread);
|
|
1218
|
}
|
|
1219
|
else
|
|
1220
|
{
|
|
1221
|
break;
|
|
1222
|
}
|
|
1223
|
useCurrentS = true;
|
|
1224
|
}
|
|
1225
|
}
|
|
1226
|
return "";
|
|
1227
|
}
|
|
1228
|
|
|
1229
|
protected Hashtable<String, File> writeMMPPartsToFiles(InputStream is)
|
|
1230
|
throws IOException
|
|
1231
|
{
|
|
1232
|
Logger logMetacat = Logger.getLogger(ResourceHandler.class);
|
|
1233
|
logMetacat.info("Processing Mime Multipart");
|
|
1234
|
String[] boundaryResults = findBoundaryString(is);
|
|
1235
|
String boundary = boundaryResults[0];
|
|
1236
|
String s = boundaryResults[1];
|
|
1237
|
String[] searchStrings = {
|
|
1238
|
"Content-Disposition: attachment; filename=systemmetadata\n\n",
|
|
1239
|
"Content-Disposition: attachment; filename=object\n\n"};
|
|
1240
|
|
|
1241
|
File[] fileArr = getMMPTempFiles();
|
|
1242
|
Hashtable<String, File> h = new Hashtable<String, File>();
|
|
1243
|
//System.out.println("==========================Looking for SM");
|
|
1244
|
//System.out.println("writing sm to " + fileArr[0].getAbsolutePath());
|
|
1245
|
logMetacat.info("writing mime system metadata to " + fileArr[0].getAbsolutePath());
|
|
1246
|
s = writeMMPPartToFile(s, is, boundary, searchStrings[0], fileArr[0]);
|
|
1247
|
//System.out.println("==========================Looking for Object");
|
|
1248
|
//System.out.println("writing obj to " + fileArr[1].getAbsolutePath());
|
|
1249
|
logMetacat.info("writing mime object to " + fileArr[1].getAbsolutePath());
|
|
1250
|
writeMMPPartToFile(s, is, boundary, searchStrings[1], fileArr[1]);
|
|
1251
|
h.put("sysmeta", fileArr[0]);
|
|
1252
|
h.put("object", fileArr[1]);
|
|
1253
|
return h;
|
|
1254
|
}
|
|
1255
|
|
|
1256
|
private static File[] getMMPTempFiles()
|
|
1257
|
throws IOException
|
|
1258
|
{
|
|
1259
|
Logger logMetacat = Logger.getLogger(ResourceHandler.class);
|
|
1260
|
File tmpDir;
|
|
1261
|
try
|
|
1262
|
{
|
|
1263
|
tmpDir = new File(PropertyService.getProperty("application.tempDir"));
|
|
1264
|
}
|
|
1265
|
catch(PropertyNotFoundException pnfe)
|
|
1266
|
{
|
|
1267
|
logMetacat.error("ResourceHandler.writeMMPPartstoFiles: " +
|
|
1268
|
"application.tmpDir not found. Using /tmp instead.");
|
|
1269
|
tmpDir = new File("/tmp");
|
|
1270
|
}
|
|
1271
|
long datetimetag = new Date().getTime();
|
|
1272
|
File smFile = new File(tmpDir, "sm." + datetimetag + ".tmp");
|
|
1273
|
File objFile = new File(tmpDir, "obj." + datetimetag + ".tmp");
|
|
1274
|
File[] fileArr = {smFile, objFile};
|
|
1275
|
return fileArr;
|
|
1276
|
}
|
|
1277
|
|
|
1278
|
/**
|
|
1279
|
* return a vector where the first element is a string that represents the system
|
|
1280
|
* metadata and the 2nd element is an InputStream that is the object
|
|
1281
|
*/
|
|
1282
|
protected Hashtable<String, File> processMMP(final InputStream is)
|
|
1283
|
throws IOException
|
|
1284
|
{
|
|
1285
|
return writeMMPPartsToFiles(is);
|
|
1286
|
}
|
|
1287
|
|
|
1288
|
/**
|
|
1289
|
* Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
|
|
1290
|
*
|
|
1291
|
* @param guid ID of data object to be inserted or updated
|
|
1292
|
* @throws IOException
|
|
1293
|
*/
|
|
1294
|
private void putObject(String guid, String action) {
|
|
1295
|
logMetacat.debug("Entering putObject: " + guid + "/" + action);
|
|
1296
|
OutputStream out = null;
|
|
1297
|
try {
|
|
1298
|
out = response.getOutputStream();
|
|
1299
|
response.setStatus(200);
|
|
1300
|
response.setContentType("text/xml");
|
|
1301
|
} catch (IOException e1) {
|
|
1302
|
logMetacat.error("Could not get the output stream for writing in putObject");
|
|
1303
|
}
|
|
1304
|
try {
|
|
1305
|
|
|
1306
|
// Read the incoming data from its Mime Multipart encoding
|
|
1307
|
logMetacat.debug("Disassembling MIME multipart form");
|
|
1308
|
InputStream object = null;
|
|
1309
|
InputStream sysmeta = null;
|
|
1310
|
Hashtable<String, File> parts;
|
|
1311
|
|
|
1312
|
try
|
|
1313
|
{
|
|
1314
|
parts = processMMP(request.getInputStream());
|
|
1315
|
object = new FileInputStream(parts.get("object"));
|
|
1316
|
sysmeta = new FileInputStream(parts.get("sysmeta"));
|
|
1317
|
}
|
|
1318
|
catch(IOException ioe)
|
|
1319
|
{
|
|
1320
|
throw new ServiceFailure("1202",
|
|
1321
|
"IOException when processing Mime Multipart: " + ioe.getMessage());
|
|
1322
|
}
|
|
1323
|
|
|
1324
|
if ( action.equals(FUNCTION_NAME_INSERT)) { //handle inserts
|
|
1325
|
|
|
1326
|
// Check if the objectId exists
|
|
1327
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
1328
|
if (im.identifierExists(guid)) {
|
|
1329
|
throw new IdentifierNotUnique("1000", "Identifier is already in use: " + guid);
|
|
1330
|
}
|
|
1331
|
|
|
1332
|
logMetacat.debug("Commence creation...");
|
|
1333
|
IBindingFactory bfact =
|
|
1334
|
BindingDirectory.getFactory(SystemMetadata.class);
|
|
1335
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
|
1336
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
|
1337
|
|
|
1338
|
CrudService cs = CrudService.getInstance();
|
|
1339
|
AuthToken token = new AuthToken(sessionId);
|
|
1340
|
cs.setParamsFromRequest(request);
|
|
1341
|
Identifier id = new Identifier();
|
|
1342
|
id.setValue(guid);
|
|
1343
|
cs.create(token, id, object, m);
|
|
1344
|
|
|
1345
|
} else if (action.equals(FUNCTION_NAME_UPDATE)) { //handle updates
|
|
1346
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
1347
|
CrudService cs = CrudService.getInstance();
|
|
1348
|
Identifier obsoletedGuid = new Identifier();
|
|
1349
|
Identifier id = new Identifier();
|
|
1350
|
id.setValue(guid);
|
|
1351
|
AuthToken token = new AuthToken(sessionId);
|
|
1352
|
|
|
1353
|
//do some checks
|
|
1354
|
if(params.get("obsoletedGuid") == null)
|
|
1355
|
{
|
|
1356
|
throw new InvalidRequest("1202", "obsoletedGuid must be contained in the request parameters.");
|
|
1357
|
}
|
|
1358
|
//get the obsoletedGuid
|
|
1359
|
String[] obsGuidS = params.get("obsoletedGuid");
|
|
1360
|
obsoletedGuid.setValue(obsGuidS[0]);
|
|
1361
|
|
|
1362
|
if (!im.identifierExists(obsoletedGuid.getValue()))
|
|
1363
|
{
|
|
1364
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
|
1365
|
}
|
|
1366
|
|
|
1367
|
|
|
1368
|
logMetacat.debug("Commence update...");
|
|
1369
|
|
|
1370
|
//get the systemmetadata
|
|
1371
|
IBindingFactory bfact =
|
|
1372
|
BindingDirectory.getFactory(SystemMetadata.class);
|
|
1373
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
|
1374
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
|
1375
|
|
|
1376
|
//do the update
|
|
1377
|
try
|
|
1378
|
{
|
|
1379
|
cs.setParamsFromRequest(request);
|
|
1380
|
Identifier rId = cs.update(token, id, object, obsoletedGuid, m);
|
|
1381
|
}
|
|
1382
|
catch(NotFound e)
|
|
1383
|
{
|
|
1384
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
|
1385
|
}
|
|
1386
|
|
|
1387
|
} else {
|
|
1388
|
throw new InvalidRequest("1000", "Operation must be create or update.");
|
|
1389
|
}
|
|
1390
|
|
|
1391
|
//clean up the MMP files
|
|
1392
|
//parts.get("sysmeta").delete();
|
|
1393
|
//parts.get("object").delete();
|
|
1394
|
} catch (NotAuthorized e) {
|
|
1395
|
response.setStatus(500);
|
|
1396
|
serializeException(e, out);
|
|
1397
|
} catch (InvalidToken e) {
|
|
1398
|
response.setStatus(500);
|
|
1399
|
serializeException(e, out);
|
|
1400
|
} catch (ServiceFailure e) {
|
|
1401
|
response.setStatus(500);
|
|
1402
|
serializeException(e, out);
|
|
1403
|
} catch (IdentifierNotUnique e) {
|
|
1404
|
response.setStatus(500);
|
|
1405
|
serializeException(e, out);
|
|
1406
|
} catch (UnsupportedType e) {
|
|
1407
|
response.setStatus(500);
|
|
1408
|
serializeException(e, out);
|
|
1409
|
} catch (InsufficientResources e) {
|
|
1410
|
response.setStatus(500);
|
|
1411
|
serializeException(e, out);
|
|
1412
|
} catch (InvalidSystemMetadata e) {
|
|
1413
|
response.setStatus(500);
|
|
1414
|
serializeException(e, out);
|
|
1415
|
} catch (NotImplemented e) {
|
|
1416
|
response.setStatus(500);
|
|
1417
|
serializeException(e, out);
|
|
1418
|
} catch (InvalidRequest e) {
|
|
1419
|
response.setStatus(500);
|
|
1420
|
serializeException(e, out);
|
|
1421
|
} /*catch (MessagingException e) {
|
|
1422
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
|
1423
|
serializeException(sf, out);
|
|
1424
|
} catch (IOException e) {
|
|
1425
|
response.setStatus(500);
|
|
1426
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
|
1427
|
serializeException(sf, out);
|
|
1428
|
}*/ catch (JiBXException e) {
|
|
1429
|
response.setStatus(500);
|
|
1430
|
e.printStackTrace(System.out);
|
|
1431
|
InvalidSystemMetadata ism = new InvalidSystemMetadata("1080", e.getMessage());
|
|
1432
|
serializeException(ism, out);
|
|
1433
|
}
|
|
1434
|
}
|
|
1435
|
|
|
1436
|
/**
|
|
1437
|
* Earthgrid API > Put Service > Delete Function : calls MetacatHandler > handleDeleteAction
|
|
1438
|
*
|
|
1439
|
* @param guid ID of data object to be deleted
|
|
1440
|
* @throws IOException
|
|
1441
|
*/
|
|
1442
|
private void deleteObject(String guid) throws IOException
|
|
1443
|
{
|
|
1444
|
// Look up the localId for this global identifier
|
|
1445
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
1446
|
String localId = "";
|
|
1447
|
try {
|
|
1448
|
localId = im.getLocalId(guid);
|
|
1449
|
} catch (McdbDocNotFoundException e) {
|
|
1450
|
// TODO: Need to return the proper DataONE exception
|
|
1451
|
}
|
|
1452
|
|
|
1453
|
params.put("docid", new String[] { localId });
|
|
1454
|
PrintWriter out = response.getWriter();
|
|
1455
|
response.setStatus(200);
|
|
1456
|
response.setContentType("text/xml");
|
|
1457
|
handler.handleDeleteAction(out, params, request, response, username,
|
|
1458
|
groupNames);
|
|
1459
|
out.close();
|
|
1460
|
}
|
|
1461
|
|
|
1462
|
/**
|
|
1463
|
* set the access perms on a document
|
|
1464
|
* @throws IOException
|
|
1465
|
*/
|
|
1466
|
private void setaccess() throws Exception
|
|
1467
|
{
|
|
1468
|
try
|
|
1469
|
{
|
|
1470
|
String guid = params.get("guid")[0];
|
|
1471
|
Identifier id = new Identifier();
|
|
1472
|
id.setValue(guid);
|
|
1473
|
AuthToken token = new AuthToken(sessionId);
|
|
1474
|
String principal = params.get("principal")[0];
|
|
1475
|
String permission = params.get("permission")[0];
|
|
1476
|
String permissionType = params.get("permissionType")[0];
|
|
1477
|
String permissionOrder = params.get("permissionOrder")[0];
|
|
1478
|
String setSystemMetadata = params.get("setsystemmetadata")[0];
|
|
1479
|
boolean ssm = false;
|
|
1480
|
if(setSystemMetadata.equals("true") || setSystemMetadata.equals("TRUE") ||
|
|
1481
|
setSystemMetadata.equals("yes"))
|
|
1482
|
{
|
|
1483
|
ssm = true;
|
|
1484
|
}
|
|
1485
|
CrudService cs = CrudService.getInstance();
|
|
1486
|
//TODO: remove the setsystemmetadata param and set this so the systemmetadata always gets set
|
|
1487
|
cs.setAccess(token, id, principal, permission, permissionType, permissionOrder, ssm);
|
|
1488
|
}
|
|
1489
|
catch(Exception e)
|
|
1490
|
{
|
|
1491
|
response.setStatus(500);
|
|
1492
|
printError("Error setting access in ResourceHandler: " + e.getMessage(), response);
|
|
1493
|
throw e;
|
|
1494
|
}
|
|
1495
|
}
|
|
1496
|
|
|
1497
|
/**
|
|
1498
|
* Earthgrid API > Authentication Service > Login Function : calls MetacatHandler > handleLoginAction
|
|
1499
|
*
|
|
1500
|
* @throws IOException
|
|
1501
|
*/
|
|
1502
|
private void login() throws IOException {
|
|
1503
|
PrintWriter out = response.getWriter();
|
|
1504
|
response.setStatus(200);
|
|
1505
|
response.setContentType("text/xml");
|
|
1506
|
handler.handleLoginAction(out, params, request, response);
|
|
1507
|
out.close();
|
|
1508
|
}
|
|
1509
|
|
|
1510
|
/**
|
|
1511
|
* Earthgrid API > Authentication Service > Logout Function : calls MetacatHandler > handleLogoutAction
|
|
1512
|
*
|
|
1513
|
* @throws IOException
|
|
1514
|
*/
|
|
1515
|
private void logout() throws IOException {
|
|
1516
|
PrintWriter out = response.getWriter();
|
|
1517
|
response.setStatus(200);
|
|
1518
|
response.setContentType("text/xml");
|
|
1519
|
handler.handleLogoutAction(out, params, request, response);
|
|
1520
|
out.close();
|
|
1521
|
}
|
|
1522
|
|
|
1523
|
/**
|
|
1524
|
* Prints xml response
|
|
1525
|
* @param message Message to be displayed
|
|
1526
|
* @param response Servlet response that xml message will be printed
|
|
1527
|
* */
|
|
1528
|
private void printError(String message, HttpServletResponse response) {
|
|
1529
|
try {
|
|
1530
|
logMetacat.error("ResourceHandler: Printing error to servlet response: " + message);
|
|
1531
|
PrintWriter out = response.getWriter();
|
|
1532
|
response.setContentType("text/xml");
|
|
1533
|
out.println("<?xml version=\"1.0\"?>");
|
|
1534
|
out.println("<error>");
|
|
1535
|
out.println(message);
|
|
1536
|
out.println("</error>");
|
|
1537
|
out.close();
|
|
1538
|
} catch (IOException e) {
|
|
1539
|
e.printStackTrace();
|
|
1540
|
}
|
|
1541
|
}
|
|
1542
|
|
|
1543
|
private void serializeException(BaseException e, OutputStream out) {
|
|
1544
|
// TODO: Use content negotiation to determine which return format to use
|
|
1545
|
response.setContentType("text/xml");
|
|
1546
|
response.setStatus(e.getCode());
|
|
1547
|
|
|
1548
|
logMetacat.error("ResourceHandler: Serializing exception with code " + e.getCode() + ": " + e.getMessage());
|
|
1549
|
e.printStackTrace();
|
|
1550
|
|
|
1551
|
try {
|
|
1552
|
IOUtils.write(e.serialize(BaseException.FMT_XML), out);
|
|
1553
|
} catch (IOException e1) {
|
|
1554
|
logMetacat.error("Error writing exception to stream. "
|
|
1555
|
+ e1.getMessage());
|
|
1556
|
}
|
|
1557
|
}
|
|
1558
|
|
|
1559
|
}
|