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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.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.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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/**
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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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| 284 |
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//TODO: check if we need this anymore. Might be superceded
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| 285 |
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//by MetacatPopulator
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| 286 |
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generateMissingSystemMetadata();
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status = true;
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| 288 |
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}
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else
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|
{
|
| 291 |
|
|
String objectId = request.getPathInfo();
|
| 292 |
|
|
if (objectId != null && objectId.length() > 1)
|
| 293 |
|
|
{
|
| 294 |
|
|
objectId = request.getPathInfo().substring(1);
|
| 295 |
|
|
}
|
| 296 |
|
|
getSystemMetadataObject(objectId);
|
| 297 |
|
|
status = true;
|
| 298 |
|
|
}
|
| 299 |
5211
|
jones
|
|
| 300 |
5446
|
jones
|
} else if (resource.equals(RESOURCE_OBJECTS)) {
|
| 301 |
|
|
logMetacat.debug("D1 Rest: Starting resource processing...");
|
| 302 |
|
|
loadSessionData();
|
| 303 |
5211
|
jones
|
|
| 304 |
5446
|
jones
|
String objectId = request.getPathInfo();
|
| 305 |
|
|
if (objectId != null && objectId.length() > 1)
|
| 306 |
|
|
{
|
| 307 |
|
|
objectId = request.getPathInfo().substring(1);
|
| 308 |
|
|
}
|
| 309 |
|
|
else
|
| 310 |
|
|
{
|
| 311 |
|
|
objectId = null;
|
| 312 |
|
|
}
|
| 313 |
5211
|
jones
|
|
| 314 |
5446
|
jones
|
logMetacat.debug("verb:" + httpVerb);
|
| 315 |
5211
|
jones
|
|
| 316 |
5446
|
jones
|
if (httpVerb == GET) {
|
| 317 |
|
|
getObject(objectId);
|
| 318 |
|
|
status = true;
|
| 319 |
|
|
} else if (httpVerb == POST) {
|
| 320 |
|
|
putObject(objectId, FUNCTION_NAME_INSERT);
|
| 321 |
|
|
status = true;
|
| 322 |
|
|
} else if (httpVerb == PUT) {
|
| 323 |
|
|
putObject(objectId, FUNCTION_NAME_UPDATE);
|
| 324 |
|
|
status = true;
|
| 325 |
|
|
} else if (httpVerb == DELETE) {
|
| 326 |
|
|
deleteObject(objectId);
|
| 327 |
|
|
status = true;
|
| 328 |
|
|
}
|
| 329 |
5211
|
jones
|
|
| 330 |
5446
|
jones
|
} else if (resource.equals(RESOURCE_IDENTIFIER)) {
|
| 331 |
5211
|
jones
|
|
| 332 |
5446
|
jones
|
String identifierId = request.getPathInfo();
|
| 333 |
|
|
if (identifierId != null && identifierId.length() > 1)
|
| 334 |
|
|
identifierId = request.getPathInfo().substring(1); //trim the slash
|
| 335 |
5211
|
jones
|
|
| 336 |
5446
|
jones
|
if (httpVerb == GET) {
|
| 337 |
|
|
String op = params.get(FUNCTION_KEYWORD)[0];
|
| 338 |
|
|
if (op.equals(FUNCTION_NAME_ISREGISTERED)) {
|
| 339 |
|
|
isRegistered(identifierId);
|
| 340 |
|
|
status = true;
|
| 341 |
|
|
} else if (op.equals(FUNCTION_NAME_GETALLDOCS)) {
|
| 342 |
|
|
getAllDocIds();
|
| 343 |
|
|
status = true;
|
| 344 |
|
|
} else if (op.equals(FUNCTION_NAME_GETNEXTREV)) {
|
| 345 |
|
|
getNextRevision(identifierId);
|
| 346 |
|
|
status = true;
|
| 347 |
|
|
} else if (op.equals(FUNCTION_NAME_GETNEXTOBJ)) {
|
| 348 |
|
|
getNextObject();
|
| 349 |
|
|
status = true;
|
| 350 |
|
|
}
|
| 351 |
|
|
|
| 352 |
|
|
} else if (httpVerb == PUT) {
|
| 353 |
|
|
//Earthgrid API > Identifier Service > addLSID Function
|
| 354 |
5512
|
berkley
|
response.setStatus(501);
|
| 355 |
5446
|
jones
|
printError(
|
| 356 |
|
|
"This method is not supported by metacat. To "
|
| 357 |
|
|
+ "add a new LSID, add a document to metacat.",
|
| 358 |
|
|
response);
|
| 359 |
|
|
status = true;
|
| 360 |
|
|
}
|
| 361 |
|
|
|
| 362 |
|
|
} else if (resource.equals(RESOURCE_LOG)) {
|
| 363 |
|
|
//handle log events
|
| 364 |
|
|
if(httpVerb == GET)
|
| 365 |
|
|
{
|
| 366 |
|
|
getLog();
|
| 367 |
|
|
status = true;
|
| 368 |
|
|
}
|
| 369 |
|
|
else
|
| 370 |
|
|
{
|
| 371 |
5481
|
berkley
|
//change to D1 spec for specifying which http methods are allowed for a resource
|
| 372 |
5512
|
berkley
|
response.setStatus(501);
|
| 373 |
5446
|
jones
|
printError("POST, PUT, DELETE is not supported for logs.", response);
|
| 374 |
|
|
status = true;
|
| 375 |
|
|
}
|
| 376 |
|
|
|
| 377 |
|
|
}
|
| 378 |
|
|
|
| 379 |
|
|
if (!status)
|
| 380 |
5512
|
berkley
|
{
|
| 381 |
|
|
response.setStatus(400);
|
| 382 |
5446
|
jones
|
printError("Incorrect parameters!", response);
|
| 383 |
5512
|
berkley
|
}
|
| 384 |
5211
|
jones
|
} else {
|
| 385 |
5512
|
berkley
|
response.setStatus(400);
|
| 386 |
5446
|
jones
|
printError("Incorrect resource!", response);
|
| 387 |
5211
|
jones
|
}
|
| 388 |
|
|
} catch (Exception e) {
|
| 389 |
5446
|
jones
|
logMetacat.error(e.getMessage());
|
| 390 |
|
|
e.printStackTrace();
|
| 391 |
5211
|
jones
|
}
|
| 392 |
|
|
}
|
| 393 |
5374
|
berkley
|
|
| 394 |
|
|
/**
|
| 395 |
5390
|
berkley
|
* get the logs from the CrudService based on passed params. Available
|
| 396 |
|
|
* params are token, fromDate, toDate, event. See
|
| 397 |
|
|
* http://mule1.dataone.org/ArchitectureDocs/mn_api_crud.html#MN_crud.getLogRecords
|
| 398 |
|
|
* for more info
|
| 399 |
|
|
*/
|
| 400 |
|
|
private void getLog()
|
| 401 |
|
|
{
|
| 402 |
|
|
OutputStream out = null;
|
| 403 |
|
|
try
|
| 404 |
|
|
{
|
| 405 |
|
|
out = response.getOutputStream();
|
| 406 |
5515
|
berkley
|
response.setStatus(200);
|
| 407 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 408 |
5390
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
| 409 |
|
|
String fromDateS = params.get("fromDate")[0];
|
| 410 |
5418
|
berkley
|
System.out.println("param fromDateS: " + fromDateS);
|
| 411 |
5390
|
berkley
|
Date fromDate = null;
|
| 412 |
|
|
String toDateS = params.get("toDate")[0];
|
| 413 |
5418
|
berkley
|
System.out.println("param toDateS: " + toDateS);
|
| 414 |
5390
|
berkley
|
Date toDate = null;
|
| 415 |
|
|
String eventS = params.get("event")[0];
|
| 416 |
|
|
Event event = null;
|
| 417 |
|
|
if(fromDateS != null)
|
| 418 |
|
|
{
|
| 419 |
5429
|
berkley
|
//fromDate = dateFormat.parse(fromDateS);
|
| 420 |
|
|
fromDate = parseDateAndConvertToGMT(fromDateS);
|
| 421 |
5390
|
berkley
|
}
|
| 422 |
|
|
if(toDateS != null)
|
| 423 |
|
|
{
|
| 424 |
5429
|
berkley
|
//toDate = dateFormat.parse(toDateS);
|
| 425 |
|
|
toDate = parseDateAndConvertToGMT(toDateS);
|
| 426 |
5390
|
berkley
|
}
|
| 427 |
|
|
if(eventS != null)
|
| 428 |
|
|
{
|
| 429 |
|
|
event = Event.convert(eventS);
|
| 430 |
|
|
}
|
| 431 |
5418
|
berkley
|
System.out.println("fromDate: " + fromDate + " toDate: " + toDate);
|
| 432 |
5395
|
berkley
|
|
| 433 |
5418
|
berkley
|
System.out.println("calling crudservice.getLogRecords");
|
| 434 |
5390
|
berkley
|
Log log = CrudService.getInstance().getLogRecords(token, fromDate, toDate, event);
|
| 435 |
|
|
serializeServiceType(Log.class, log, out);
|
| 436 |
|
|
}
|
| 437 |
|
|
catch(Exception e)
|
| 438 |
|
|
{
|
| 439 |
|
|
String msg = "Could not get logs from CrudService: " + e.getMessage();
|
| 440 |
|
|
ServiceFailure sf = new ServiceFailure("1490", msg);
|
| 441 |
|
|
logMetacat.error(msg);
|
| 442 |
|
|
e.printStackTrace();
|
| 443 |
|
|
serializeException(sf, out);
|
| 444 |
|
|
}
|
| 445 |
|
|
}
|
| 446 |
|
|
|
| 447 |
|
|
/**
|
| 448 |
5374
|
berkley
|
* copies request parameters to a hashtable which is given as argument to native metacathandler functions
|
| 449 |
|
|
*/
|
| 450 |
|
|
private void initParams() {
|
| 451 |
5211
|
jones
|
|
| 452 |
5374
|
berkley
|
String name = null;
|
| 453 |
|
|
String[] value = null;
|
| 454 |
|
|
Enumeration paramlist = request.getParameterNames();
|
| 455 |
|
|
while (paramlist.hasMoreElements()) {
|
| 456 |
|
|
name = (String) paramlist.nextElement();
|
| 457 |
|
|
value = request.getParameterValues(name);
|
| 458 |
|
|
params.put(name, value);
|
| 459 |
|
|
}
|
| 460 |
|
|
}
|
| 461 |
|
|
|
| 462 |
5211
|
jones
|
/**
|
| 463 |
5374
|
berkley
|
*
|
| 464 |
|
|
* Load user details of metacat session from the request
|
| 465 |
|
|
*
|
| 466 |
|
|
*/
|
| 467 |
|
|
private void loadSessionData()
|
| 468 |
|
|
throws Exception
|
| 469 |
|
|
{
|
| 470 |
|
|
SessionData sessionData = RequestUtil.getSessionData(request);
|
| 471 |
|
|
try
|
| 472 |
|
|
{
|
| 473 |
|
|
username = null;
|
| 474 |
|
|
password = null;
|
| 475 |
|
|
groupNames = null;
|
| 476 |
|
|
sessionId = null;
|
| 477 |
|
|
|
| 478 |
|
|
boolean validSession = false;
|
| 479 |
|
|
SessionService ss = SessionService.getInstance();
|
| 480 |
5410
|
berkley
|
System.out.println("sessionData: " + sessionData);
|
| 481 |
5423
|
berkley
|
if(sessionData == null)
|
| 482 |
|
|
{
|
| 483 |
|
|
username = "public";
|
| 484 |
|
|
sessionId = "0";
|
| 485 |
|
|
System.out.println("sessiondata is null. Creating a public session.");
|
| 486 |
|
|
return;
|
| 487 |
|
|
}
|
| 488 |
|
|
|
| 489 |
5410
|
berkley
|
System.out.println("username: " + sessionData.getUserName());
|
| 490 |
|
|
System.out.println("sessionid: " + sessionData.getId());
|
| 491 |
5374
|
berkley
|
//validate the session
|
| 492 |
5410
|
berkley
|
if(ss.isSessionRegistered(sessionData.getId()) &&
|
| 493 |
|
|
!(sessionData.getUserName().equals("public") || sessionData.getId().equals("0")))
|
| 494 |
5374
|
berkley
|
{
|
| 495 |
|
|
validSession = true;
|
| 496 |
|
|
}
|
| 497 |
|
|
|
| 498 |
|
|
if(validSession)
|
| 499 |
|
|
{
|
| 500 |
|
|
//if the session is valid, set these variables
|
| 501 |
|
|
username = sessionData.getUserName();
|
| 502 |
|
|
password = sessionData.getPassword();
|
| 503 |
|
|
groupNames = sessionData.getGroupNames();
|
| 504 |
|
|
sessionId = sessionData.getId();
|
| 505 |
5386
|
berkley
|
System.out.println("setting sessionid to " + sessionId);
|
| 506 |
|
|
System.out.println("username: " + username);
|
| 507 |
5374
|
berkley
|
}
|
| 508 |
|
|
|
| 509 |
|
|
//if the session is not valid or the username is null, set
|
| 510 |
|
|
//username to public
|
| 511 |
|
|
if (username == null)
|
| 512 |
|
|
{
|
| 513 |
5386
|
berkley
|
System.out.println("setting username to public.");
|
| 514 |
5374
|
berkley
|
username = "public";
|
| 515 |
|
|
}
|
| 516 |
|
|
}
|
| 517 |
|
|
catch(Exception e)
|
| 518 |
|
|
{
|
| 519 |
5423
|
berkley
|
e.printStackTrace();
|
| 520 |
5374
|
berkley
|
throw new Exception("Could not load the session data: " + e.getMessage());
|
| 521 |
|
|
}
|
| 522 |
|
|
}
|
| 523 |
|
|
|
| 524 |
|
|
/**
|
| 525 |
|
|
* generate missing system metadata for any science metadata objects
|
| 526 |
|
|
* that don't already have it. https://trac.dataone.org/ticket/591
|
| 527 |
5381
|
berkley
|
*
|
| 528 |
|
|
* called with POST meta/?op=generatemissingsystemmetadata
|
| 529 |
5374
|
berkley
|
*/
|
| 530 |
|
|
private void generateMissingSystemMetadata()
|
| 531 |
|
|
{
|
| 532 |
5381
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
| 533 |
|
|
CrudService.getInstance().generateMissingSystemMetadata(token);
|
| 534 |
5374
|
berkley
|
}
|
| 535 |
|
|
|
| 536 |
|
|
/**
|
| 537 |
|
|
* Earthgrid API > Identifier Service > isRegistered Function :
|
| 538 |
|
|
* calls MetacatHandler > handleIdIsRegisteredAction
|
| 539 |
5286
|
jones
|
* @param guid
|
| 540 |
5211
|
jones
|
* @throws IOException
|
| 541 |
|
|
*/
|
| 542 |
5286
|
jones
|
private void isRegistered(String guid) throws IOException
|
| 543 |
|
|
{
|
| 544 |
|
|
|
| 545 |
|
|
// Look up the localId for this guid
|
| 546 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 547 |
|
|
String localId = "";
|
| 548 |
|
|
try {
|
| 549 |
|
|
localId = im.getLocalId(guid);
|
| 550 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 551 |
|
|
// TODO: Need to return the proper DataONE exception
|
| 552 |
|
|
}
|
| 553 |
|
|
|
| 554 |
|
|
params.put("docid", new String[] { localId });
|
| 555 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
| 556 |
5515
|
berkley
|
response.setStatus(200);
|
| 557 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 558 |
5211
|
jones
|
handler.handleIdIsRegisteredAction(out, params, response);
|
| 559 |
|
|
out.close();
|
| 560 |
|
|
}
|
| 561 |
|
|
|
| 562 |
|
|
/**
|
| 563 |
5374
|
berkley
|
* Earthgrid API > Identifier Service > getAllDocIds Function :
|
| 564 |
|
|
* calls MetacatHandler > handleGetAllDocidsAction
|
| 565 |
5211
|
jones
|
* @throws IOException
|
| 566 |
|
|
*/
|
| 567 |
|
|
private void getAllDocIds() throws IOException {
|
| 568 |
|
|
PrintWriter out = response.getWriter();
|
| 569 |
5515
|
berkley
|
response.setStatus(200);
|
| 570 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 571 |
5211
|
jones
|
handler.handleGetAllDocidsAction(out, params, response);
|
| 572 |
|
|
out.close();
|
| 573 |
|
|
}
|
| 574 |
|
|
|
| 575 |
|
|
/**
|
| 576 |
5374
|
berkley
|
* Earthgrid API > Identifier Service > getNextRevision Function :
|
| 577 |
|
|
* calls MetacatHandler > handleGetRevisionAndDocTypeAction
|
| 578 |
5286
|
jones
|
* @param guid
|
| 579 |
5211
|
jones
|
* @throws IOException
|
| 580 |
|
|
*/
|
| 581 |
5286
|
jones
|
private void getNextRevision(String guid) throws IOException
|
| 582 |
|
|
{
|
| 583 |
|
|
params.put("docid", new String[] { guid });
|
| 584 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
| 585 |
5515
|
berkley
|
response.setStatus(200);
|
| 586 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 587 |
5211
|
jones
|
//handler.handleGetRevisionAndDocTypeAction(out, params);
|
| 588 |
|
|
|
| 589 |
|
|
try {
|
| 590 |
|
|
// Make sure there is a docid
|
| 591 |
5286
|
jones
|
if (guid == null || guid.equals("")) {
|
| 592 |
5211
|
jones
|
throw new Exception("User didn't specify docid!");
|
| 593 |
5286
|
jones
|
}
|
| 594 |
5211
|
jones
|
|
| 595 |
5286
|
jones
|
// Look up the localId for this guid
|
| 596 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 597 |
|
|
String localId = "";
|
| 598 |
|
|
try {
|
| 599 |
|
|
localId = im.getLocalId(guid);
|
| 600 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 601 |
|
|
// TODO: Need to return the proper DataONE exception
|
| 602 |
|
|
}
|
| 603 |
|
|
|
| 604 |
5211
|
jones
|
// Create a DBUtil object
|
| 605 |
|
|
DBUtil dbutil = new DBUtil();
|
| 606 |
|
|
// Get a rev and doctype
|
| 607 |
|
|
String revAndDocType = dbutil
|
| 608 |
5286
|
jones
|
.getCurrentRevisionAndDocTypeForGivenDocument(localId);
|
| 609 |
5211
|
jones
|
int revision = Integer.parseInt(revAndDocType.split(";")[0]) + 1;
|
| 610 |
|
|
|
| 611 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
| 612 |
|
|
out.print("<next-revision>");
|
| 613 |
|
|
out.print(revision);
|
| 614 |
|
|
out.print("</next-revision>");
|
| 615 |
|
|
|
| 616 |
|
|
} catch (Exception e) {
|
| 617 |
|
|
// Handle exception
|
| 618 |
5512
|
berkley
|
response.setStatus(500);
|
| 619 |
5211
|
jones
|
out.println("<?xml version=\"1.0\"?>");
|
| 620 |
|
|
out.println("<error>");
|
| 621 |
|
|
out.println(e.getMessage());
|
| 622 |
|
|
out.println("</error>");
|
| 623 |
|
|
}
|
| 624 |
|
|
|
| 625 |
|
|
out.close();
|
| 626 |
|
|
}
|
| 627 |
|
|
|
| 628 |
|
|
/**
|
| 629 |
5374
|
berkley
|
* Earthgrid API > Identifier Service > getNextObject Function :
|
| 630 |
|
|
* calls MetacatHandler > handleGetMaxDocidAction
|
| 631 |
5211
|
jones
|
* @throws IOException
|
| 632 |
|
|
*/
|
| 633 |
|
|
private void getNextObject() throws IOException {
|
| 634 |
|
|
PrintWriter out = response.getWriter();
|
| 635 |
5515
|
berkley
|
response.setStatus(200);
|
| 636 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 637 |
5211
|
jones
|
handler.handleGetMaxDocidAction(out, params, response);
|
| 638 |
|
|
out.close();
|
| 639 |
|
|
}
|
| 640 |
|
|
|
| 641 |
|
|
/**
|
| 642 |
5299
|
jones
|
* Implements REST version of DataONE CRUD API --> get
|
| 643 |
5282
|
jones
|
* @param guid ID of data object to be read
|
| 644 |
5211
|
jones
|
*/
|
| 645 |
5450
|
berkley
|
private void getObject(String guid) {
|
| 646 |
|
|
CrudService cs = CrudService.getInstance();
|
| 647 |
|
|
cs.setParamsFromRequest(request);
|
| 648 |
|
|
AuthToken token = new AuthToken(sessionId);
|
| 649 |
|
|
OutputStream out = null;
|
| 650 |
|
|
try {
|
| 651 |
|
|
out = response.getOutputStream();
|
| 652 |
5515
|
berkley
|
response.setStatus(200);
|
| 653 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 654 |
|
|
if(guid != null)
|
| 655 |
|
|
{ //get a specific document
|
| 656 |
|
|
Identifier id = new Identifier();
|
| 657 |
|
|
id.setValue(guid);
|
| 658 |
|
|
try
|
| 659 |
|
|
{
|
| 660 |
|
|
if(token == null)
|
| 661 |
|
|
{
|
| 662 |
|
|
token = new AuthToken("Public");
|
| 663 |
|
|
}
|
| 664 |
|
|
InputStream data = cs.get(token, id);
|
| 665 |
|
|
IOUtils.copyLarge(data, response.getOutputStream());
|
| 666 |
|
|
}
|
| 667 |
|
|
catch(InvalidToken it)
|
| 668 |
|
|
{
|
| 669 |
|
|
serializeException(it, out);
|
| 670 |
|
|
}
|
| 671 |
|
|
catch(ServiceFailure sf)
|
| 672 |
|
|
{
|
| 673 |
|
|
serializeException(sf, out);
|
| 674 |
|
|
}
|
| 675 |
|
|
catch(NotAuthorized na)
|
| 676 |
|
|
{
|
| 677 |
|
|
serializeException(na, out);
|
| 678 |
|
|
}
|
| 679 |
|
|
catch(NotFound nf)
|
| 680 |
|
|
{
|
| 681 |
|
|
serializeException(nf, out);
|
| 682 |
|
|
}
|
| 683 |
|
|
catch(NotImplemented ni)
|
| 684 |
|
|
{
|
| 685 |
|
|
serializeException(ni, out);
|
| 686 |
|
|
}
|
| 687 |
|
|
catch(Exception e)
|
| 688 |
|
|
{
|
| 689 |
|
|
System.out.println("Error with Crud.get(). " +
|
| 690 |
|
|
"If this is an 'Exception producing data' error, " +
|
| 691 |
|
|
"go to CrudService.get() for better debugging. " +
|
| 692 |
|
|
"Here's the error: " + e.getMessage());
|
| 693 |
|
|
e.printStackTrace();
|
| 694 |
|
|
ServiceFailure sf = new ServiceFailure("1030",
|
| 695 |
|
|
"IO Error in ResourceHandler.getObject: " + e.getMessage());
|
| 696 |
|
|
serializeException(sf, out);
|
| 697 |
|
|
}
|
| 698 |
|
|
}
|
| 699 |
|
|
else
|
| 700 |
|
|
{ //call listObjects with specified params
|
| 701 |
|
|
Date startTime = null;
|
| 702 |
|
|
Date endTime = null;
|
| 703 |
|
|
ObjectFormat objectFormat = null;
|
| 704 |
|
|
boolean replicaStatus = false;
|
| 705 |
|
|
int start = 0;
|
| 706 |
5481
|
berkley
|
//TODO: make the max count into a const
|
| 707 |
5450
|
berkley
|
int count = 1000;
|
| 708 |
|
|
Enumeration paramlist = request.getParameterNames();
|
| 709 |
|
|
while (paramlist.hasMoreElements())
|
| 710 |
|
|
{ //parse the params and make the crud call
|
| 711 |
|
|
String name = (String) paramlist.nextElement();
|
| 712 |
|
|
String[] value = (String[])request.getParameterValues(name);
|
| 713 |
|
|
/*for(int i=0; i<value.length; i++)
|
| 714 |
|
|
{
|
| 715 |
|
|
System.out.println("name: " + name + " value: " + value[i]);
|
| 716 |
|
|
}*/
|
| 717 |
|
|
if(name.equals("startTime") && value != null)
|
| 718 |
|
|
{
|
| 719 |
|
|
try
|
| 720 |
|
|
{
|
| 721 |
|
|
//startTime = dateFormat.parse(value[0]);
|
| 722 |
|
|
startTime = parseDateAndConvertToGMT(value[0]);
|
| 723 |
|
|
}
|
| 724 |
|
|
catch(Exception e)
|
| 725 |
|
|
{ //if we can't parse it, just don't use the startTime param
|
| 726 |
|
|
System.out.println("Could not parse startTime: " + value[0]);
|
| 727 |
|
|
startTime = null;
|
| 728 |
|
|
}
|
| 729 |
|
|
}
|
| 730 |
|
|
else if(name.equals("endTime") && value != null)
|
| 731 |
|
|
{
|
| 732 |
|
|
try
|
| 733 |
|
|
{
|
| 734 |
|
|
//endTime = dateFormat.parse(value[0]);
|
| 735 |
|
|
endTime = parseDateAndConvertToGMT(value[0]);
|
| 736 |
|
|
}
|
| 737 |
|
|
catch(Exception e)
|
| 738 |
|
|
{ //if we can't parse it, just don't use the endTime param
|
| 739 |
|
|
System.out.println("Could not parse endTime: " + value[0]);
|
| 740 |
|
|
endTime = null;
|
| 741 |
|
|
}
|
| 742 |
|
|
}
|
| 743 |
|
|
else if(name.equals("objectFormat") && value != null)
|
| 744 |
|
|
{
|
| 745 |
|
|
objectFormat = ObjectFormat.convert(value[0]);
|
| 746 |
|
|
}
|
| 747 |
|
|
else if(name.equals("replicaStatus") && value != null)
|
| 748 |
|
|
{
|
| 749 |
|
|
if(value != null &&
|
| 750 |
|
|
value.length > 0 &&
|
| 751 |
|
|
(value[0].equals("true") || value[0].equals("TRUE") || value[0].equals("YES")))
|
| 752 |
|
|
{
|
| 753 |
|
|
replicaStatus = true;
|
| 754 |
|
|
}
|
| 755 |
|
|
}
|
| 756 |
|
|
else if(name.equals("start") && value != null)
|
| 757 |
|
|
{
|
| 758 |
|
|
start = new Integer(value[0]).intValue();
|
| 759 |
|
|
}
|
| 760 |
|
|
else if(name.equals("count") && value != null)
|
| 761 |
|
|
{
|
| 762 |
|
|
count = new Integer(value[0]).intValue();
|
| 763 |
|
|
}
|
| 764 |
|
|
}
|
| 765 |
|
|
//make the crud call
|
| 766 |
5510
|
berkley
|
System.out.println("token: " + token + " startTime: " + startTime +
|
| 767 |
5450
|
berkley
|
" endtime: " + endTime + " objectFormat: " +
|
| 768 |
|
|
objectFormat + " replicaStatus: " + replicaStatus +
|
| 769 |
|
|
" start: " + start + " count: " + count);
|
| 770 |
5510
|
berkley
|
|
| 771 |
5450
|
berkley
|
ObjectList ol = cs.listObjects(token, startTime, endTime,
|
| 772 |
|
|
objectFormat, replicaStatus, start, count);
|
| 773 |
|
|
|
| 774 |
|
|
StringReader sr = new StringReader(ol.toString());
|
| 775 |
5515
|
berkley
|
out = response.getOutputStream();
|
| 776 |
|
|
response.setStatus(200);
|
| 777 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 778 |
|
|
// Serialize and write it to the output stream
|
| 779 |
|
|
|
| 780 |
|
|
try {
|
| 781 |
|
|
serializeServiceType(ObjectList.class, ol, out);
|
| 782 |
|
|
} catch (JiBXException e) {
|
| 783 |
|
|
throw new ServiceFailure("1190", "Failed to serialize ObjectList: " + e.getMessage());
|
| 784 |
|
|
}
|
| 785 |
|
|
}
|
| 786 |
|
|
} catch (BaseException e) {
|
| 787 |
|
|
serializeException(e, out);
|
| 788 |
|
|
} catch (IOException e) {
|
| 789 |
|
|
e.printStackTrace();
|
| 790 |
|
|
ServiceFailure sf = new ServiceFailure("1030",
|
| 791 |
|
|
"IO Error in ResourceHandler.getObject: " + e.getMessage());
|
| 792 |
|
|
serializeException(sf, out);
|
| 793 |
|
|
} catch(NumberFormatException ne) {
|
| 794 |
|
|
InvalidRequest ir = new InvalidRequest("1030", "Invalid format for parameter: " + ne.getMessage());
|
| 795 |
|
|
serializeException(ir, out);
|
| 796 |
|
|
} catch (Exception e) {
|
| 797 |
|
|
e.printStackTrace();
|
| 798 |
|
|
ServiceFailure sf = new ServiceFailure("1030",
|
| 799 |
|
|
"Exception " + e.getClass().getName() + " raised while handling listObjects request: " +
|
| 800 |
|
|
e.getMessage());
|
| 801 |
|
|
serializeException(sf, out);
|
| 802 |
|
|
}
|
| 803 |
|
|
}
|
| 804 |
5428
|
berkley
|
|
| 805 |
|
|
/**
|
| 806 |
|
|
* parse a date and return it in GMT if it ends with a 'Z'
|
| 807 |
|
|
* @param date
|
| 808 |
|
|
* @return
|
| 809 |
|
|
* @throws ParseException
|
| 810 |
|
|
*/
|
| 811 |
|
|
private Date parseDateAndConvertToGMT(String date) throws ParseException
|
| 812 |
|
|
{
|
| 813 |
5429
|
berkley
|
try
|
| 814 |
|
|
{ //the format we want
|
| 815 |
|
|
return dateFormat.parse(date);
|
| 816 |
|
|
}
|
| 817 |
|
|
catch(java.text.ParseException pe)
|
| 818 |
|
|
{ //try another legacy format
|
| 819 |
|
|
DateFormat dateFormat2 = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss'Z'");
|
| 820 |
|
|
dateFormat2.setTimeZone(TimeZone.getTimeZone("GMT-0"));
|
| 821 |
|
|
return dateFormat2.parse(date);
|
| 822 |
|
|
}
|
| 823 |
|
|
|
| 824 |
|
|
/*System.out.println("Parsing date " + date);
|
| 825 |
5428
|
berkley
|
Date d = dateFormat.parse(date);
|
| 826 |
|
|
|
| 827 |
|
|
if(date.endsWith("Z"))
|
| 828 |
|
|
{
|
| 829 |
|
|
Calendar lTime = Calendar.getInstance();
|
| 830 |
|
|
lTime.setTime(d);
|
| 831 |
|
|
Calendar zTime = Calendar.getInstance(TimeZone.getTimeZone("GMT-0"));
|
| 832 |
|
|
zTime.set(Calendar.MONTH, lTime.get(Calendar.MONTH));
|
| 833 |
|
|
zTime.set(Calendar.DATE, lTime.get(Calendar.DATE));
|
| 834 |
|
|
zTime.set(Calendar.YEAR, lTime.get(Calendar.YEAR));
|
| 835 |
|
|
zTime.set(Calendar.HOUR, lTime.get(Calendar.HOUR));
|
| 836 |
|
|
zTime.set(Calendar.MINUTE, lTime.get(Calendar.MINUTE));
|
| 837 |
|
|
zTime.set(Calendar.SECOND, lTime.get(Calendar.SECOND));
|
| 838 |
|
|
|
| 839 |
|
|
System.out.println("date parsed to " + zTime.getTime());
|
| 840 |
|
|
return zTime.getTime();
|
| 841 |
|
|
}
|
| 842 |
|
|
|
| 843 |
|
|
System.out.println("date parsed, but not converted. returned as " + d);
|
| 844 |
5429
|
berkley
|
return d;*/
|
| 845 |
5428
|
berkley
|
}
|
| 846 |
5211
|
jones
|
|
| 847 |
|
|
/**
|
| 848 |
5332
|
jones
|
* Implements REST version of DataONE CRUD API --> getSystemMetadata
|
| 849 |
|
|
* @param guid ID of data object to be read
|
| 850 |
|
|
*/
|
| 851 |
|
|
private void getSystemMetadataObject(String guid) {
|
| 852 |
5337
|
berkley
|
CrudService cs = CrudService.getInstance();
|
| 853 |
|
|
cs.setParamsFromRequest(request);
|
| 854 |
5386
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
| 855 |
5332
|
jones
|
OutputStream out = null;
|
| 856 |
|
|
try {
|
| 857 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 858 |
5515
|
berkley
|
response.setStatus(200);
|
| 859 |
5332
|
jones
|
out = response.getOutputStream();
|
| 860 |
|
|
Identifier id = new Identifier();
|
| 861 |
|
|
id.setValue(guid);
|
| 862 |
|
|
SystemMetadata sysmeta = cs.getSystemMetadata(token, id);
|
| 863 |
|
|
|
| 864 |
|
|
// Serialize and write it to the output stream
|
| 865 |
|
|
try {
|
| 866 |
5481
|
berkley
|
//TODO: look at the efficiency of this method. The system metadata
|
| 867 |
|
|
//is read from metacat (in CrudService) as xml, then serialized
|
| 868 |
|
|
//to a SystemMetadat object, then returned here, then serizlized
|
| 869 |
|
|
//back to XML to be sent to the response.
|
| 870 |
5390
|
berkley
|
serializeServiceType(SystemMetadata.class, sysmeta, out);
|
| 871 |
5332
|
jones
|
} catch (JiBXException e) {
|
| 872 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Failed to serialize SystemMetadata: " + e.getMessage());
|
| 873 |
5332
|
jones
|
}
|
| 874 |
|
|
} catch (BaseException e) {
|
| 875 |
|
|
serializeException(e, out);
|
| 876 |
|
|
} catch (IOException e) {
|
| 877 |
5414
|
berkley
|
ServiceFailure sf = new ServiceFailure("1030",
|
| 878 |
|
|
"Error in ResourceHandler.getSystemMetadataObject: " + e.getMessage());
|
| 879 |
5332
|
jones
|
serializeException(sf, out);
|
| 880 |
|
|
} finally {
|
| 881 |
|
|
IOUtils.closeQuietly(out);
|
| 882 |
|
|
}
|
| 883 |
|
|
}
|
| 884 |
|
|
|
| 885 |
|
|
/**
|
| 886 |
5390
|
berkley
|
* serialize an object of type to out
|
| 887 |
|
|
* @param type the class of the object to serialize (i.e. SystemMetadata.class)
|
| 888 |
|
|
* @param object the object to serialize
|
| 889 |
|
|
* @param out the stream to serialize it to
|
| 890 |
|
|
* @throws JiBXException
|
| 891 |
|
|
*/
|
| 892 |
|
|
private void serializeServiceType(Class type, Object object, OutputStream out)
|
| 893 |
|
|
throws JiBXException
|
| 894 |
|
|
{
|
| 895 |
|
|
IBindingFactory bfact = BindingDirectory.getFactory(type);
|
| 896 |
|
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
| 897 |
|
|
mctx.marshalDocument(object, "UTF-8", null, out);
|
| 898 |
|
|
}
|
| 899 |
|
|
|
| 900 |
|
|
/**
|
| 901 |
|
|
* deserialize an object of type from is
|
| 902 |
|
|
* @param type the class of the object to serialize (i.e. SystemMetadata.class)
|
| 903 |
|
|
* @param is the stream to deserialize from
|
| 904 |
|
|
* @throws JiBXException
|
| 905 |
|
|
*/
|
| 906 |
|
|
private Object deserializeServiceType(Class type, InputStream is)
|
| 907 |
|
|
throws JiBXException
|
| 908 |
|
|
{
|
| 909 |
|
|
IBindingFactory bfact = BindingDirectory.getFactory(type);
|
| 910 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
| 911 |
|
|
Object o = (Object) uctx.unmarshalDocument(is, null);
|
| 912 |
|
|
return o;
|
| 913 |
|
|
}
|
| 914 |
|
|
|
| 915 |
|
|
/**
|
| 916 |
5211
|
jones
|
* Earthgrid API > Query Service > Query Function : translates ecogrid query document to metacat query
|
| 917 |
|
|
* then calls DBQuery > createResultDocument function and then again translate resultset to ecogrid resultset
|
| 918 |
|
|
*
|
| 919 |
|
|
* NOTE:
|
| 920 |
|
|
* This is the only method that uses EcoGrid classes for its implementation.
|
| 921 |
|
|
* It does so because it takes an EcoGrid Query as input, and outputs an
|
| 922 |
|
|
* EcoGrid ResultSet document. These documents are parsed by the auto-generated
|
| 923 |
|
|
* EcoGrid classes from axis, and so we link to them here rather than re-inventing them.
|
| 924 |
|
|
* This creates a circular dependency, because the Metacat classes are needed
|
| 925 |
|
|
* to build the EcoGrid implementation, and the EcoGrid jars are needed to build this query()
|
| 926 |
|
|
* method. This circularity could be resolved by moving the EcoGrid classes
|
| 927 |
|
|
* to Metacat directly. As we transition away from EcoGrid SOAP methods in
|
| 928 |
|
|
* favor of these REST interfaces, this circular dependency can be eliminated.
|
| 929 |
|
|
*
|
| 930 |
|
|
* @throws Exception
|
| 931 |
|
|
*/
|
| 932 |
|
|
private void query() throws Exception {
|
| 933 |
|
|
/* This block commented out because of the EcoGrid circular dependency.
|
| 934 |
|
|
* For now, query will not be supported until the circularity can be
|
| 935 |
5286
|
jones
|
* resolved, probably by moving the ecogrid query syntax transformers
|
| 936 |
5211
|
jones
|
* directly into the Metacat codebase. MBJ 2010-02-03
|
| 937 |
|
|
|
| 938 |
|
|
try {
|
| 939 |
|
|
EcogridQueryParser parser = new EcogridQueryParser(request
|
| 940 |
|
|
.getReader());
|
| 941 |
|
|
parser.parseXML();
|
| 942 |
|
|
QueryType queryType = parser.getEcogridQuery();
|
| 943 |
|
|
EcogridJavaToMetacatJavaQueryTransformer queryTransformer =
|
| 944 |
|
|
new EcogridJavaToMetacatJavaQueryTransformer();
|
| 945 |
|
|
QuerySpecification metacatQuery = queryTransformer
|
| 946 |
|
|
.transform(queryType);
|
| 947 |
|
|
|
| 948 |
|
|
DBQuery metacat = new DBQuery();
|
| 949 |
|
|
|
| 950 |
|
|
boolean useXMLIndex = (new Boolean(PropertyService
|
| 951 |
|
|
.getProperty("database.usexmlindex"))).booleanValue();
|
| 952 |
|
|
String xmlquery = "query"; // we don't care the query in resultset,
|
| 953 |
|
|
// the query can be anything
|
| 954 |
|
|
PrintWriter out = null; // we don't want metacat result, so set out null
|
| 955 |
|
|
|
| 956 |
|
|
// parameter: queryspecification, user, group, usingIndexOrNot
|
| 957 |
|
|
StringBuffer result = metacat.createResultDocument(xmlquery,
|
| 958 |
|
|
metacatQuery, out, username, groupNames, useXMLIndex);
|
| 959 |
|
|
|
| 960 |
|
|
// create result set transfer
|
| 961 |
|
|
String saxparser = PropertyService.getProperty("xml.saxparser");
|
| 962 |
|
|
MetacatResultsetParser metacatResultsetParser = new MetacatResultsetParser(
|
| 963 |
|
|
new StringReader(result.toString()), saxparser, queryType
|
| 964 |
|
|
.getNamespace().get_value());
|
| 965 |
|
|
ResultsetType records = metacatResultsetParser.getEcogridResult();
|
| 966 |
|
|
|
| 967 |
|
|
System.out
|
| 968 |
|
|
.println(EcogridResultsetTransformer.toXMLString(records));
|
| 969 |
|
|
response.setContentType("text/xml");
|
| 970 |
|
|
out = response.getWriter();
|
| 971 |
|
|
out.print(EcogridResultsetTransformer.toXMLString(records));
|
| 972 |
|
|
|
| 973 |
|
|
} catch (Exception e) {
|
| 974 |
|
|
e.printStackTrace();
|
| 975 |
|
|
}*/
|
| 976 |
|
|
response.setContentType("text/xml");
|
| 977 |
5512
|
berkley
|
response.setStatus(501);
|
| 978 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
| 979 |
|
|
out.print("<error>Query operation not yet supported by Metacat.</error>");
|
| 980 |
|
|
out.close();
|
| 981 |
|
|
}
|
| 982 |
5319
|
jones
|
|
| 983 |
5394
|
berkley
|
private String streamToString(InputStream is)
|
| 984 |
|
|
throws IOException
|
| 985 |
|
|
{
|
| 986 |
|
|
byte b[] = new byte[1024];
|
| 987 |
|
|
int numread = is.read(b, 0, 1024);
|
| 988 |
|
|
String response = new String();
|
| 989 |
|
|
while(numread != -1)
|
| 990 |
|
|
{
|
| 991 |
|
|
response += new String(b, 0, numread);
|
| 992 |
|
|
numread = is.read(b, 0, 1024);
|
| 993 |
|
|
}
|
| 994 |
|
|
return response;
|
| 995 |
|
|
}
|
| 996 |
|
|
|
| 997 |
|
|
private InputStream stringToStream(String s)
|
| 998 |
|
|
throws IOException
|
| 999 |
|
|
{
|
| 1000 |
|
|
ByteArrayInputStream bais = new ByteArrayInputStream(s.getBytes());
|
| 1001 |
|
|
return bais;
|
| 1002 |
|
|
}
|
| 1003 |
|
|
|
| 1004 |
5462
|
berkley
|
/**
|
| 1005 |
|
|
* process a mime multipart message
|
| 1006 |
|
|
* @param is
|
| 1007 |
|
|
* @return
|
| 1008 |
|
|
*/
|
| 1009 |
|
|
private Hashtable processMMP(InputStream is)
|
| 1010 |
|
|
throws IOException
|
| 1011 |
|
|
{
|
| 1012 |
5481
|
berkley
|
//TODO: verify that this is how the RFC for MMP should work
|
| 1013 |
|
|
//SORTAHACK: Since mmp seems to have a bug where large object parts get truncated,
|
| 1014 |
5462
|
berkley
|
//parse the stream here. This has the disavantage of putting the
|
| 1015 |
|
|
//stream into memory.
|
| 1016 |
|
|
InputStream object = null;
|
| 1017 |
|
|
InputStream sysmeta = null;
|
| 1018 |
5616
|
berkley
|
String s = IOUtils.toString(is);
|
| 1019 |
|
|
System.out.println("mime: " + s);
|
| 1020 |
5462
|
berkley
|
//figure out what the boundary marker is
|
| 1021 |
|
|
String searchString = "boundary=";
|
| 1022 |
|
|
int searchStringIndex = s.indexOf(searchString);
|
| 1023 |
|
|
String boundary = s.substring(searchStringIndex + searchString.length() + 1,
|
| 1024 |
|
|
s.indexOf("\"", searchStringIndex + searchString.length() + 1));
|
| 1025 |
|
|
boundary = "--" + boundary;
|
| 1026 |
|
|
//System.out.println("boundary is " + boundary);
|
| 1027 |
|
|
|
| 1028 |
|
|
//find the system metadata
|
| 1029 |
|
|
searchString = "Content-Disposition: attachment; filename=systemmetadata";
|
| 1030 |
|
|
searchStringIndex = s.indexOf(searchString);
|
| 1031 |
5616
|
berkley
|
String sm = s.substring(searchStringIndex +
|
| 1032 |
|
|
searchString.length() + 2,
|
| 1033 |
|
|
s.indexOf(boundary, searchStringIndex));
|
| 1034 |
|
|
sysmeta = new ByteArrayInputStream(sm.getBytes());
|
| 1035 |
5462
|
berkley
|
|
| 1036 |
|
|
//find the object
|
| 1037 |
|
|
searchString = "Content-Disposition: attachment; filename=object";
|
| 1038 |
|
|
searchStringIndex = s.indexOf(searchString);
|
| 1039 |
5616
|
berkley
|
String o = s.substring(searchStringIndex +
|
| 1040 |
|
|
searchString.length() + 2,
|
| 1041 |
|
|
s.indexOf(boundary, searchStringIndex));
|
| 1042 |
|
|
object = new ByteArrayInputStream(o.getBytes());
|
| 1043 |
5462
|
berkley
|
|
| 1044 |
|
|
Hashtable h = new Hashtable();
|
| 1045 |
|
|
h.put("object", object);
|
| 1046 |
|
|
h.put("systemmetadata", sysmeta);
|
| 1047 |
5616
|
berkley
|
|
| 1048 |
|
|
System.out.println("o: \"" + o + "\"");
|
| 1049 |
|
|
System.out.println("sm: \"" + sm + "\"");
|
| 1050 |
5462
|
berkley
|
return h;
|
| 1051 |
|
|
}
|
| 1052 |
5394
|
berkley
|
|
| 1053 |
5462
|
berkley
|
|
| 1054 |
5211
|
jones
|
/**
|
| 1055 |
|
|
* Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
|
| 1056 |
|
|
*
|
| 1057 |
5319
|
jones
|
* @param guid ID of data object to be inserted or updated
|
| 1058 |
5211
|
jones
|
* @throws IOException
|
| 1059 |
|
|
*/
|
| 1060 |
5319
|
jones
|
private void putObject(String guid, String action) {
|
| 1061 |
|
|
logMetacat.debug("Entering putObject: " + guid + "/" + action);
|
| 1062 |
|
|
OutputStream out = null;
|
| 1063 |
|
|
try {
|
| 1064 |
|
|
out = response.getOutputStream();
|
| 1065 |
5515
|
berkley
|
response.setStatus(200);
|
| 1066 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 1067 |
5319
|
jones
|
} catch (IOException e1) {
|
| 1068 |
|
|
logMetacat.error("Could not get the output stream for writing in putObject");
|
| 1069 |
|
|
}
|
| 1070 |
|
|
try {
|
| 1071 |
5353
|
berkley
|
|
| 1072 |
|
|
// Read the incoming data from its Mime Multipart encoding
|
| 1073 |
|
|
logMetacat.debug("Disassembling MIME multipart form");
|
| 1074 |
|
|
InputStream object = null;
|
| 1075 |
|
|
InputStream sysmeta = null;
|
| 1076 |
5394
|
berkley
|
|
| 1077 |
5462
|
berkley
|
Hashtable parts = processMMP(request.getInputStream());
|
| 1078 |
|
|
object = (InputStream)parts.get("object");
|
| 1079 |
5616
|
berkley
|
|
| 1080 |
5462
|
berkley
|
sysmeta = (InputStream)parts.get("systemmetadata");
|
| 1081 |
5394
|
berkley
|
|
| 1082 |
5353
|
berkley
|
if ( action.equals(FUNCTION_NAME_INSERT)) { //handle inserts
|
| 1083 |
5211
|
jones
|
|
| 1084 |
5319
|
jones
|
// Check if the objectId exists
|
| 1085 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1086 |
|
|
if (im.identifierExists(guid)) {
|
| 1087 |
5356
|
berkley
|
throw new IdentifierNotUnique("1000", "Identifier is already in use: " + guid);
|
| 1088 |
5319
|
jones
|
}
|
| 1089 |
5211
|
jones
|
|
| 1090 |
5376
|
berkley
|
logMetacat.debug("Commence creation...");
|
| 1091 |
|
|
IBindingFactory bfact =
|
| 1092 |
|
|
BindingDirectory.getFactory(SystemMetadata.class);
|
| 1093 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
| 1094 |
|
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
| 1095 |
|
|
|
| 1096 |
|
|
CrudService cs = CrudService.getInstance();
|
| 1097 |
5386
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
| 1098 |
5376
|
berkley
|
cs.setParamsFromRequest(request);
|
| 1099 |
|
|
Identifier id = new Identifier();
|
| 1100 |
|
|
id.setValue(guid);
|
| 1101 |
|
|
cs.create(token, id, object, m);
|
| 1102 |
5386
|
berkley
|
|
| 1103 |
5353
|
berkley
|
} else if (action.equals(FUNCTION_NAME_UPDATE)) { //handle updates
|
| 1104 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1105 |
|
|
CrudService cs = CrudService.getInstance();
|
| 1106 |
|
|
Identifier obsoletedGuid = new Identifier();
|
| 1107 |
|
|
Identifier id = new Identifier();
|
| 1108 |
|
|
id.setValue(guid);
|
| 1109 |
5386
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
| 1110 |
5353
|
berkley
|
|
| 1111 |
|
|
//do some checks
|
| 1112 |
|
|
if(params.get("obsoletedGuid") == null)
|
| 1113 |
|
|
{
|
| 1114 |
5356
|
berkley
|
throw new InvalidRequest("1202", "obsoletedGuid must be contained in the request parameters.");
|
| 1115 |
5353
|
berkley
|
}
|
| 1116 |
|
|
//get the obsoletedGuid
|
| 1117 |
|
|
String[] obsGuidS = params.get("obsoletedGuid");
|
| 1118 |
|
|
obsoletedGuid.setValue(obsGuidS[0]);
|
| 1119 |
|
|
|
| 1120 |
|
|
if (!im.identifierExists(obsoletedGuid.getValue()))
|
| 1121 |
|
|
{
|
| 1122 |
5356
|
berkley
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
| 1123 |
5353
|
berkley
|
}
|
| 1124 |
|
|
|
| 1125 |
|
|
|
| 1126 |
|
|
logMetacat.debug("Commence update...");
|
| 1127 |
|
|
|
| 1128 |
|
|
//get the systemmetadata
|
| 1129 |
|
|
IBindingFactory bfact =
|
| 1130 |
|
|
BindingDirectory.getFactory(SystemMetadata.class);
|
| 1131 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
| 1132 |
|
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
| 1133 |
|
|
|
| 1134 |
|
|
//do the update
|
| 1135 |
|
|
try
|
| 1136 |
|
|
{
|
| 1137 |
|
|
cs.setParamsFromRequest(request);
|
| 1138 |
|
|
Identifier rId = cs.update(token, id, object, obsoletedGuid, m);
|
| 1139 |
|
|
}
|
| 1140 |
|
|
catch(NotFound e)
|
| 1141 |
|
|
{
|
| 1142 |
5356
|
berkley
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
| 1143 |
5353
|
berkley
|
}
|
| 1144 |
|
|
|
| 1145 |
5211
|
jones
|
} else {
|
| 1146 |
5356
|
berkley
|
throw new InvalidRequest("1000", "Operation must be create or update.");
|
| 1147 |
5211
|
jones
|
}
|
| 1148 |
5319
|
jones
|
} catch (NotAuthorized e) {
|
| 1149 |
|
|
serializeException(e, out);
|
| 1150 |
|
|
} catch (InvalidToken e) {
|
| 1151 |
|
|
serializeException(e, out);
|
| 1152 |
|
|
} catch (ServiceFailure e) {
|
| 1153 |
|
|
serializeException(e, out);
|
| 1154 |
|
|
} catch (IdentifierNotUnique e) {
|
| 1155 |
|
|
serializeException(e, out);
|
| 1156 |
|
|
} catch (UnsupportedType e) {
|
| 1157 |
|
|
serializeException(e, out);
|
| 1158 |
|
|
} catch (InsufficientResources e) {
|
| 1159 |
|
|
serializeException(e, out);
|
| 1160 |
|
|
} catch (InvalidSystemMetadata e) {
|
| 1161 |
|
|
serializeException(e, out);
|
| 1162 |
|
|
} catch (NotImplemented e) {
|
| 1163 |
|
|
serializeException(e, out);
|
| 1164 |
|
|
} catch (InvalidRequest e) {
|
| 1165 |
|
|
serializeException(e, out);
|
| 1166 |
5394
|
berkley
|
} /*catch (MessagingException e) {
|
| 1167 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
| 1168 |
5319
|
jones
|
serializeException(sf, out);
|
| 1169 |
5394
|
berkley
|
}*/ catch (IOException e) {
|
| 1170 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
| 1171 |
5319
|
jones
|
serializeException(sf, out);
|
| 1172 |
5320
|
jones
|
} catch (JiBXException e) {
|
| 1173 |
|
|
e.printStackTrace(System.out);
|
| 1174 |
5356
|
berkley
|
InvalidSystemMetadata ism = new InvalidSystemMetadata("1080", e.getMessage());
|
| 1175 |
5320
|
jones
|
serializeException(ism, out);
|
| 1176 |
5211
|
jones
|
}
|
| 1177 |
|
|
}
|
| 1178 |
|
|
|
| 1179 |
|
|
/**
|
| 1180 |
|
|
* Earthgrid API > Put Service > Delete Function : calls MetacatHandler > handleDeleteAction
|
| 1181 |
|
|
*
|
| 1182 |
5287
|
jones
|
* @param guid ID of data object to be deleted
|
| 1183 |
5211
|
jones
|
* @throws IOException
|
| 1184 |
|
|
*/
|
| 1185 |
5287
|
jones
|
private void deleteObject(String guid) throws IOException
|
| 1186 |
|
|
{
|
| 1187 |
|
|
// Look up the localId for this global identifier
|
| 1188 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
| 1189 |
|
|
String localId = "";
|
| 1190 |
|
|
try {
|
| 1191 |
|
|
localId = im.getLocalId(guid);
|
| 1192 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 1193 |
|
|
// TODO: Need to return the proper DataONE exception
|
| 1194 |
|
|
}
|
| 1195 |
|
|
|
| 1196 |
|
|
params.put("docid", new String[] { localId });
|
| 1197 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
| 1198 |
5515
|
berkley
|
response.setStatus(200);
|
| 1199 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 1200 |
5211
|
jones
|
handler.handleDeleteAction(out, params, request, response, username,
|
| 1201 |
|
|
groupNames);
|
| 1202 |
|
|
out.close();
|
| 1203 |
|
|
}
|
| 1204 |
5370
|
berkley
|
|
| 1205 |
|
|
/**
|
| 1206 |
|
|
* set the access perms on a document
|
| 1207 |
|
|
* @throws IOException
|
| 1208 |
|
|
*/
|
| 1209 |
5424
|
berkley
|
private void setaccess() throws Exception
|
| 1210 |
5370
|
berkley
|
{
|
| 1211 |
|
|
try
|
| 1212 |
|
|
{
|
| 1213 |
|
|
String guid = params.get("guid")[0];
|
| 1214 |
|
|
Identifier id = new Identifier();
|
| 1215 |
|
|
id.setValue(guid);
|
| 1216 |
|
|
AuthToken token = new AuthToken(sessionId);
|
| 1217 |
|
|
String principal = params.get("principal")[0];
|
| 1218 |
|
|
String permission = params.get("permission")[0];
|
| 1219 |
|
|
String permissionType = params.get("permissionType")[0];
|
| 1220 |
|
|
String permissionOrder = params.get("permissionOrder")[0];
|
| 1221 |
|
|
String setSystemMetadata = params.get("setsystemmetadata")[0];
|
| 1222 |
5424
|
berkley
|
boolean ssm = false;
|
| 1223 |
5370
|
berkley
|
if(setSystemMetadata.equals("true") || setSystemMetadata.equals("TRUE") ||
|
| 1224 |
5424
|
berkley
|
setSystemMetadata.equals("yes"))
|
| 1225 |
|
|
{
|
| 1226 |
|
|
ssm = true;
|
| 1227 |
5370
|
berkley
|
}
|
| 1228 |
5424
|
berkley
|
CrudService cs = CrudService.getInstance();
|
| 1229 |
5484
|
berkley
|
//TODO: remove the setsystemmetadata param and set this so the systemmetadata always gets set
|
| 1230 |
5424
|
berkley
|
cs.setAccess(token, id, principal, permission, permissionType, permissionOrder, ssm);
|
| 1231 |
5370
|
berkley
|
}
|
| 1232 |
|
|
catch(Exception e)
|
| 1233 |
|
|
{
|
| 1234 |
5512
|
berkley
|
response.setStatus(500);
|
| 1235 |
5370
|
berkley
|
printError("Error setting access in ResourceHandler: " + e.getMessage(), response);
|
| 1236 |
5424
|
berkley
|
throw e;
|
| 1237 |
5370
|
berkley
|
}
|
| 1238 |
|
|
}
|
| 1239 |
5211
|
jones
|
|
| 1240 |
|
|
/**
|
| 1241 |
|
|
* Earthgrid API > Authentication Service > Login Function : calls MetacatHandler > handleLoginAction
|
| 1242 |
|
|
*
|
| 1243 |
|
|
* @throws IOException
|
| 1244 |
|
|
*/
|
| 1245 |
|
|
private void login() throws IOException {
|
| 1246 |
|
|
PrintWriter out = response.getWriter();
|
| 1247 |
5515
|
berkley
|
response.setStatus(200);
|
| 1248 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 1249 |
5211
|
jones
|
handler.handleLoginAction(out, params, request, response);
|
| 1250 |
|
|
out.close();
|
| 1251 |
|
|
}
|
| 1252 |
|
|
|
| 1253 |
|
|
/**
|
| 1254 |
|
|
* Earthgrid API > Authentication Service > Logout Function : calls MetacatHandler > handleLogoutAction
|
| 1255 |
|
|
*
|
| 1256 |
|
|
* @throws IOException
|
| 1257 |
|
|
*/
|
| 1258 |
|
|
private void logout() throws IOException {
|
| 1259 |
|
|
PrintWriter out = response.getWriter();
|
| 1260 |
5515
|
berkley
|
response.setStatus(200);
|
| 1261 |
5450
|
berkley
|
response.setContentType("text/xml");
|
| 1262 |
5211
|
jones
|
handler.handleLogoutAction(out, params, request, response);
|
| 1263 |
|
|
out.close();
|
| 1264 |
|
|
}
|
| 1265 |
|
|
|
| 1266 |
|
|
/**
|
| 1267 |
|
|
* Prints xml response
|
| 1268 |
|
|
* @param message Message to be displayed
|
| 1269 |
|
|
* @param response Servlet response that xml message will be printed
|
| 1270 |
|
|
* */
|
| 1271 |
|
|
private void printError(String message, HttpServletResponse response) {
|
| 1272 |
|
|
try {
|
| 1273 |
5512
|
berkley
|
logMetacat.error("ResourceHandler: Printing error to servlet response: " + message);
|
| 1274 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
| 1275 |
|
|
response.setContentType("text/xml");
|
| 1276 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
| 1277 |
|
|
out.println("<error>");
|
| 1278 |
|
|
out.println(message);
|
| 1279 |
|
|
out.println("</error>");
|
| 1280 |
|
|
out.close();
|
| 1281 |
|
|
} catch (IOException e) {
|
| 1282 |
|
|
e.printStackTrace();
|
| 1283 |
|
|
}
|
| 1284 |
|
|
}
|
| 1285 |
5370
|
berkley
|
|
| 1286 |
5319
|
jones
|
private void serializeException(BaseException e, OutputStream out) {
|
| 1287 |
|
|
// TODO: Use content negotiation to determine which return format to use
|
| 1288 |
|
|
response.setContentType("text/xml");
|
| 1289 |
|
|
response.setStatus(e.getCode());
|
| 1290 |
5512
|
berkley
|
|
| 1291 |
|
|
logMetacat.error("ResourceHandler: Serializing exception with code " + e.getCode() + ": " + e.getMessage());
|
| 1292 |
|
|
e.printStackTrace();
|
| 1293 |
|
|
|
| 1294 |
5319
|
jones
|
try {
|
| 1295 |
|
|
IOUtils.write(e.serialize(BaseException.FMT_XML), out);
|
| 1296 |
|
|
} catch (IOException e1) {
|
| 1297 |
|
|
logMetacat.error("Error writing exception to stream. "
|
| 1298 |
|
|
+ e1.getMessage());
|
| 1299 |
|
|
}
|
| 1300 |
|
|
}
|
| 1301 |
|
|
|
| 1302 |
5211
|
jones
|
}
|