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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.ByteArrayOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.io.PrintWriter;
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import java.util.Enumeration;
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import java.util.Hashtable;
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import java.util.Timer;
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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 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.AuthToken;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.SystemMetadata;
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import org.jibx.runtime.BindingDirectory;
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import org.jibx.runtime.IBindingFactory;
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import org.jibx.runtime.IMarshallingContext;
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import org.jibx.runtime.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.dataone.CrudService;
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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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/*
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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_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 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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* copies request parameters to a hashtable which is given as argument to native metacathandler functions
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*/
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private void initParams() {
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String name = null;
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String[] value = null;
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Enumeration paramlist = request.getParameterNames();
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while (paramlist.hasMoreElements()) {
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name = (String) paramlist.nextElement();
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value = request.getParameterValues(name);
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System.out.println("adding param: " + name + " = " + value);
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params.put(name, value);
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}
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}
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/**
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*
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* Load user details of metacat session from the request
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*
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*/
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private void loadSessionData() {
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SessionData sessionData = RequestUtil.getSessionData(request);
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// TODO: validate the session before allowing these values to be set
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username = sessionData.getUserName();
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password = sessionData.getPassword();
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groupNames = sessionData.getGroupNames();
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sessionId = sessionData.getId();
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if (username == null) {
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username = "public";
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}
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}
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/**
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* 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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switch (httpVerb)
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{
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case GET: verb = "GET";
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case POST: verb = "POST";
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case PUT: verb = "PUT";
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case DELETE: verb = "DELETE";
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}
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System.out.println("handling " + verb + " request with resource " + resource);
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boolean status = false;
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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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if (params.get(FUNCTION_KEYWORD)[0]
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.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]
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.equals(FUNCTION_NAME_LOGOUT)) {
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logout();
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status = true;
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}
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} else if (resource.equals(RESOURCE_META)) {
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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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|
|
getSystemMetadataObject(objectId);
|
319 |
5211
|
jones
|
status = true;
|
320 |
5355
|
berkley
|
|
321 |
|
|
} else if (resource.equals(RESOURCE_OBJECTS)) {
|
322 |
5319
|
jones
|
logMetacat.debug("D1 Rest: Starting resource processing...");
|
323 |
5211
|
jones
|
loadSessionData();
|
324 |
|
|
|
325 |
|
|
String objectId = request.getPathInfo();
|
326 |
5355
|
berkley
|
if (objectId != null && objectId.length() > 1)
|
327 |
|
|
{
|
328 |
|
|
objectId = request.getPathInfo().substring(1);
|
329 |
5332
|
jones
|
}
|
330 |
5355
|
berkley
|
|
331 |
5319
|
jones
|
logMetacat.debug("verb:" + httpVerb);
|
332 |
5211
|
jones
|
|
333 |
|
|
if (httpVerb == GET) {
|
334 |
5355
|
berkley
|
getObject(objectId);
|
335 |
5211
|
jones
|
status = true;
|
336 |
|
|
} else if (httpVerb == POST) {
|
337 |
5319
|
jones
|
putObject(objectId, FUNCTION_NAME_INSERT);
|
338 |
5211
|
jones
|
status = true;
|
339 |
|
|
} else if (httpVerb == PUT) {
|
340 |
5319
|
jones
|
putObject(objectId, FUNCTION_NAME_UPDATE);
|
341 |
5211
|
jones
|
status = true;
|
342 |
|
|
} else if (httpVerb == DELETE) {
|
343 |
|
|
deleteObject(objectId);
|
344 |
|
|
status = true;
|
345 |
|
|
}
|
346 |
|
|
|
347 |
|
|
} else if (resource.equals(RESOURCE_IDENTIFIER)) {
|
348 |
|
|
|
349 |
|
|
String identifierId = request.getPathInfo();
|
350 |
|
|
if (identifierId != null && identifierId.length() > 1)
|
351 |
|
|
identifierId = request.getPathInfo().substring(1); //trim the slash
|
352 |
|
|
|
353 |
|
|
if (httpVerb == GET) {
|
354 |
|
|
String op = params.get(FUNCTION_KEYWORD)[0];
|
355 |
|
|
if (op.equals(FUNCTION_NAME_ISREGISTERED)) {
|
356 |
|
|
isRegistered(identifierId);
|
357 |
|
|
status = true;
|
358 |
|
|
} else if (op.equals(FUNCTION_NAME_GETALLDOCS)) {
|
359 |
|
|
getAllDocIds();
|
360 |
|
|
status = true;
|
361 |
|
|
} else if (op.equals(FUNCTION_NAME_GETNEXTREV)) {
|
362 |
|
|
getNextRevision(identifierId);
|
363 |
|
|
status = true;
|
364 |
|
|
} else if (op.equals(FUNCTION_NAME_GETNEXTOBJ)) {
|
365 |
|
|
getNextObject();
|
366 |
|
|
status = true;
|
367 |
|
|
}
|
368 |
|
|
|
369 |
|
|
} else if (httpVerb == PUT) {
|
370 |
|
|
//Earthgrid API > Identifier Service > addLSID Function
|
371 |
|
|
printError(
|
372 |
|
|
"This method is not supported by metacat. To "
|
373 |
|
|
+ "add a new LSID, add a document to metacat.",
|
374 |
|
|
response);
|
375 |
|
|
status = true;
|
376 |
|
|
}
|
377 |
|
|
|
378 |
|
|
}
|
379 |
|
|
if (!status)
|
380 |
|
|
printError("Incorrect parameters!", response);
|
381 |
|
|
} else {
|
382 |
|
|
printError("Incorrect resource!", response);
|
383 |
|
|
}
|
384 |
|
|
} catch (Exception e) {
|
385 |
|
|
logMetacat.error(e.getMessage());
|
386 |
|
|
e.printStackTrace();
|
387 |
|
|
}
|
388 |
|
|
}
|
389 |
|
|
|
390 |
|
|
/**
|
391 |
|
|
* Earthgrid API > Identifier Service > isRegistered Function : calls MetacatHandler > handleIdIsRegisteredAction
|
392 |
5286
|
jones
|
* @param guid
|
393 |
5211
|
jones
|
* @throws IOException
|
394 |
|
|
*/
|
395 |
5286
|
jones
|
private void isRegistered(String guid) throws IOException
|
396 |
|
|
{
|
397 |
|
|
|
398 |
|
|
// Look up the localId for this guid
|
399 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
400 |
|
|
String localId = "";
|
401 |
|
|
try {
|
402 |
|
|
localId = im.getLocalId(guid);
|
403 |
|
|
} catch (McdbDocNotFoundException e) {
|
404 |
|
|
// TODO: Need to return the proper DataONE exception
|
405 |
|
|
}
|
406 |
|
|
|
407 |
|
|
params.put("docid", new String[] { localId });
|
408 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
409 |
|
|
handler.handleIdIsRegisteredAction(out, params, response);
|
410 |
|
|
out.close();
|
411 |
|
|
}
|
412 |
|
|
|
413 |
|
|
/**
|
414 |
|
|
* Earthgrid API > Identifier Service > getAllDocIds Function : calls MetacatHandler > handleGetAllDocidsAction
|
415 |
|
|
* @throws IOException
|
416 |
|
|
*/
|
417 |
|
|
private void getAllDocIds() throws IOException {
|
418 |
|
|
PrintWriter out = response.getWriter();
|
419 |
|
|
handler.handleGetAllDocidsAction(out, params, response);
|
420 |
|
|
out.close();
|
421 |
|
|
}
|
422 |
|
|
|
423 |
|
|
/**
|
424 |
|
|
* Earthgrid API > Identifier Service > getNextRevision Function : calls MetacatHandler > handleGetRevisionAndDocTypeAction
|
425 |
5286
|
jones
|
* @param guid
|
426 |
5211
|
jones
|
* @throws IOException
|
427 |
|
|
*/
|
428 |
5286
|
jones
|
private void getNextRevision(String guid) throws IOException
|
429 |
|
|
{
|
430 |
|
|
params.put("docid", new String[] { guid });
|
431 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
432 |
|
|
//handler.handleGetRevisionAndDocTypeAction(out, params);
|
433 |
|
|
|
434 |
|
|
try {
|
435 |
|
|
// Make sure there is a docid
|
436 |
5286
|
jones
|
if (guid == null || guid.equals("")) {
|
437 |
5211
|
jones
|
throw new Exception("User didn't specify docid!");
|
438 |
5286
|
jones
|
}
|
439 |
5211
|
jones
|
|
440 |
5286
|
jones
|
// Look up the localId for this guid
|
441 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
442 |
|
|
String localId = "";
|
443 |
|
|
try {
|
444 |
|
|
localId = im.getLocalId(guid);
|
445 |
|
|
} catch (McdbDocNotFoundException e) {
|
446 |
|
|
// TODO: Need to return the proper DataONE exception
|
447 |
|
|
}
|
448 |
|
|
|
449 |
5211
|
jones
|
// Create a DBUtil object
|
450 |
|
|
DBUtil dbutil = new DBUtil();
|
451 |
|
|
// Get a rev and doctype
|
452 |
|
|
String revAndDocType = dbutil
|
453 |
5286
|
jones
|
.getCurrentRevisionAndDocTypeForGivenDocument(localId);
|
454 |
5211
|
jones
|
int revision = Integer.parseInt(revAndDocType.split(";")[0]) + 1;
|
455 |
|
|
|
456 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
457 |
|
|
out.print("<next-revision>");
|
458 |
|
|
out.print(revision);
|
459 |
|
|
out.print("</next-revision>");
|
460 |
|
|
|
461 |
|
|
} catch (Exception e) {
|
462 |
|
|
// Handle exception
|
463 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
464 |
|
|
out.println("<error>");
|
465 |
|
|
out.println(e.getMessage());
|
466 |
|
|
out.println("</error>");
|
467 |
|
|
}
|
468 |
|
|
|
469 |
|
|
out.close();
|
470 |
|
|
}
|
471 |
|
|
|
472 |
|
|
/**
|
473 |
|
|
* Earthgrid API > Identifier Service > getNextObject Function : calls MetacatHandler > handleGetMaxDocidAction
|
474 |
|
|
* @throws IOException
|
475 |
|
|
*/
|
476 |
|
|
private void getNextObject() throws IOException {
|
477 |
|
|
PrintWriter out = response.getWriter();
|
478 |
|
|
handler.handleGetMaxDocidAction(out, params, response);
|
479 |
|
|
out.close();
|
480 |
|
|
}
|
481 |
|
|
|
482 |
|
|
/**
|
483 |
5299
|
jones
|
* Implements REST version of DataONE CRUD API --> get
|
484 |
5282
|
jones
|
* @param guid ID of data object to be read
|
485 |
5211
|
jones
|
*/
|
486 |
5282
|
jones
|
private void getObject(String guid) {
|
487 |
5333
|
berkley
|
//hack...fix this
|
488 |
5337
|
berkley
|
//CrudService cs = new CrudService(servletContext, request, response);
|
489 |
|
|
CrudService cs = CrudService.getInstance();
|
490 |
|
|
cs.setParamsFromRequest(request);
|
491 |
5299
|
jones
|
AuthToken token = null;
|
492 |
5319
|
jones
|
OutputStream out = null;
|
493 |
5282
|
jones
|
try {
|
494 |
5319
|
jones
|
out = response.getOutputStream();
|
495 |
5320
|
jones
|
Identifier id = new Identifier();
|
496 |
|
|
id.setValue(guid);
|
497 |
|
|
InputStream data = cs.get(token, id);
|
498 |
5299
|
jones
|
IOUtils.copyLarge(data, response.getOutputStream());
|
499 |
|
|
} catch (BaseException e) {
|
500 |
5319
|
jones
|
serializeException(e, out);
|
501 |
5299
|
jones
|
} catch (IOException e) {
|
502 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
503 |
5319
|
jones
|
serializeException(sf, out);
|
504 |
5282
|
jones
|
}
|
505 |
5211
|
jones
|
}
|
506 |
|
|
|
507 |
|
|
/**
|
508 |
5332
|
jones
|
* Implements REST version of DataONE CRUD API --> getSystemMetadata
|
509 |
|
|
* @param guid ID of data object to be read
|
510 |
|
|
*/
|
511 |
|
|
private void getSystemMetadataObject(String guid) {
|
512 |
5337
|
berkley
|
CrudService cs = CrudService.getInstance();
|
513 |
|
|
cs.setParamsFromRequest(request);
|
514 |
5332
|
jones
|
AuthToken token = null;
|
515 |
|
|
OutputStream out = null;
|
516 |
|
|
try {
|
517 |
|
|
out = response.getOutputStream();
|
518 |
|
|
Identifier id = new Identifier();
|
519 |
|
|
id.setValue(guid);
|
520 |
|
|
SystemMetadata sysmeta = cs.getSystemMetadata(token, id);
|
521 |
|
|
|
522 |
|
|
// Serialize and write it to the output stream
|
523 |
|
|
try {
|
524 |
|
|
IBindingFactory bfact = BindingDirectory.getFactory(SystemMetadata.class);
|
525 |
|
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
526 |
|
|
mctx.marshalDocument(sysmeta, "UTF-8", null, out);
|
527 |
|
|
} catch (JiBXException e) {
|
528 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Failed to serialize SystemMetadata: " + e.getMessage());
|
529 |
5332
|
jones
|
}
|
530 |
|
|
} catch (BaseException e) {
|
531 |
|
|
serializeException(e, out);
|
532 |
|
|
} catch (IOException e) {
|
533 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
534 |
5332
|
jones
|
serializeException(sf, out);
|
535 |
|
|
} finally {
|
536 |
|
|
IOUtils.closeQuietly(out);
|
537 |
|
|
}
|
538 |
|
|
}
|
539 |
|
|
|
540 |
|
|
/**
|
541 |
5211
|
jones
|
* Earthgrid API > Query Service > Query Function : translates ecogrid query document to metacat query
|
542 |
|
|
* then calls DBQuery > createResultDocument function and then again translate resultset to ecogrid resultset
|
543 |
|
|
*
|
544 |
|
|
* NOTE:
|
545 |
|
|
* This is the only method that uses EcoGrid classes for its implementation.
|
546 |
|
|
* It does so because it takes an EcoGrid Query as input, and outputs an
|
547 |
|
|
* EcoGrid ResultSet document. These documents are parsed by the auto-generated
|
548 |
|
|
* EcoGrid classes from axis, and so we link to them here rather than re-inventing them.
|
549 |
|
|
* This creates a circular dependency, because the Metacat classes are needed
|
550 |
|
|
* to build the EcoGrid implementation, and the EcoGrid jars are needed to build this query()
|
551 |
|
|
* method. This circularity could be resolved by moving the EcoGrid classes
|
552 |
|
|
* to Metacat directly. As we transition away from EcoGrid SOAP methods in
|
553 |
|
|
* favor of these REST interfaces, this circular dependency can be eliminated.
|
554 |
|
|
*
|
555 |
|
|
* @throws Exception
|
556 |
|
|
*/
|
557 |
|
|
private void query() throws Exception {
|
558 |
|
|
/* This block commented out because of the EcoGrid circular dependency.
|
559 |
|
|
* For now, query will not be supported until the circularity can be
|
560 |
5286
|
jones
|
* resolved, probably by moving the ecogrid query syntax transformers
|
561 |
5211
|
jones
|
* directly into the Metacat codebase. MBJ 2010-02-03
|
562 |
|
|
|
563 |
|
|
try {
|
564 |
|
|
EcogridQueryParser parser = new EcogridQueryParser(request
|
565 |
|
|
.getReader());
|
566 |
|
|
parser.parseXML();
|
567 |
|
|
QueryType queryType = parser.getEcogridQuery();
|
568 |
|
|
EcogridJavaToMetacatJavaQueryTransformer queryTransformer =
|
569 |
|
|
new EcogridJavaToMetacatJavaQueryTransformer();
|
570 |
|
|
QuerySpecification metacatQuery = queryTransformer
|
571 |
|
|
.transform(queryType);
|
572 |
|
|
|
573 |
|
|
DBQuery metacat = new DBQuery();
|
574 |
|
|
|
575 |
|
|
boolean useXMLIndex = (new Boolean(PropertyService
|
576 |
|
|
.getProperty("database.usexmlindex"))).booleanValue();
|
577 |
|
|
String xmlquery = "query"; // we don't care the query in resultset,
|
578 |
|
|
// the query can be anything
|
579 |
|
|
PrintWriter out = null; // we don't want metacat result, so set out null
|
580 |
|
|
|
581 |
|
|
// parameter: queryspecification, user, group, usingIndexOrNot
|
582 |
|
|
StringBuffer result = metacat.createResultDocument(xmlquery,
|
583 |
|
|
metacatQuery, out, username, groupNames, useXMLIndex);
|
584 |
|
|
|
585 |
|
|
// create result set transfer
|
586 |
|
|
String saxparser = PropertyService.getProperty("xml.saxparser");
|
587 |
|
|
MetacatResultsetParser metacatResultsetParser = new MetacatResultsetParser(
|
588 |
|
|
new StringReader(result.toString()), saxparser, queryType
|
589 |
|
|
.getNamespace().get_value());
|
590 |
|
|
ResultsetType records = metacatResultsetParser.getEcogridResult();
|
591 |
|
|
|
592 |
|
|
System.out
|
593 |
|
|
.println(EcogridResultsetTransformer.toXMLString(records));
|
594 |
|
|
response.setContentType("text/xml");
|
595 |
|
|
out = response.getWriter();
|
596 |
|
|
out.print(EcogridResultsetTransformer.toXMLString(records));
|
597 |
|
|
|
598 |
|
|
} catch (Exception e) {
|
599 |
|
|
e.printStackTrace();
|
600 |
|
|
}*/
|
601 |
|
|
response.setContentType("text/xml");
|
602 |
|
|
PrintWriter out = response.getWriter();
|
603 |
|
|
out.print("<error>Query operation not yet supported by Metacat.</error>");
|
604 |
|
|
out.close();
|
605 |
|
|
}
|
606 |
5319
|
jones
|
|
607 |
5211
|
jones
|
/**
|
608 |
|
|
* Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
|
609 |
|
|
*
|
610 |
5319
|
jones
|
* @param guid ID of data object to be inserted or updated
|
611 |
5211
|
jones
|
* @throws IOException
|
612 |
|
|
*/
|
613 |
5319
|
jones
|
private void putObject(String guid, String action) {
|
614 |
|
|
logMetacat.debug("Entering putObject: " + guid + "/" + action);
|
615 |
|
|
|
616 |
5286
|
jones
|
// TODO: This function lacks proper handling of authz and authn, so it
|
617 |
|
|
// seems that anyone can insert or update; interacts with
|
618 |
5319
|
jones
|
// loadSessionData(), which doesn't validate the session
|
619 |
5286
|
jones
|
|
620 |
5319
|
jones
|
// Get an output stream for handling errors; this should really be passed in as
|
621 |
|
|
// a parameter
|
622 |
|
|
OutputStream out = null;
|
623 |
|
|
try {
|
624 |
|
|
out = response.getOutputStream();
|
625 |
|
|
} catch (IOException e1) {
|
626 |
|
|
logMetacat.error("Could not get the output stream for writing in putObject");
|
627 |
|
|
}
|
628 |
|
|
try {
|
629 |
5353
|
berkley
|
|
630 |
|
|
// Read the incoming data from its Mime Multipart encoding
|
631 |
|
|
logMetacat.debug("Disassembling MIME multipart form");
|
632 |
|
|
InputStream object = null;
|
633 |
|
|
InputStream sysmeta = null;
|
634 |
|
|
MimeMultipart mmp = new MimeMultipart(new InputStreamDataSource("message", request.getInputStream()));
|
635 |
|
|
logMetacat.debug("MMP created.");
|
636 |
|
|
mmp.writeTo(System.out);
|
637 |
|
|
for (int i = 0; i < mmp.getCount(); i++) {
|
638 |
|
|
BodyPart part = mmp.getBodyPart(i);
|
639 |
|
|
String name = part.getFileName();
|
640 |
|
|
logMetacat.debug("Part name is: " + name);
|
641 |
|
|
logMetacat.debug("Part has class name: " + part.getClass().getName());
|
642 |
|
|
if (name.equals("object")) {
|
643 |
|
|
object = part.getInputStream();
|
644 |
|
|
logMetacat.debug("Found object part, size is: " + part.getSize());
|
645 |
|
|
} else if (name.equals("systemmetadata")) {
|
646 |
|
|
sysmeta = part.getInputStream();
|
647 |
|
|
logMetacat.debug("Found sysmeta part, size is: " + part.getSize());
|
648 |
|
|
} else {
|
649 |
5356
|
berkley
|
throw new InvalidRequest("1000", "Request had malformed MIME part with name: " + name);
|
650 |
5353
|
berkley
|
}
|
651 |
|
|
}
|
652 |
|
|
|
653 |
|
|
if ( action.equals(FUNCTION_NAME_INSERT)) { //handle inserts
|
654 |
5211
|
jones
|
|
655 |
5319
|
jones
|
// Check if the objectId exists
|
656 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
657 |
|
|
if (im.identifierExists(guid)) {
|
658 |
5356
|
berkley
|
throw new IdentifierNotUnique("1000", "Identifier is already in use: " + guid);
|
659 |
5319
|
jones
|
}
|
660 |
5211
|
jones
|
|
661 |
5327
|
jones
|
// TODO: access control -- should be in CrudService et al. I think
|
662 |
5319
|
jones
|
//if (username != null && !username.equals("public")) {
|
663 |
|
|
if (username != null) {
|
664 |
|
|
logMetacat.debug("Commence creation...");
|
665 |
|
|
AuthToken token = null;
|
666 |
5320
|
jones
|
IBindingFactory bfact =
|
667 |
|
|
BindingDirectory.getFactory(SystemMetadata.class);
|
668 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
669 |
|
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
670 |
5355
|
berkley
|
|
671 |
5337
|
berkley
|
CrudService cs = CrudService.getInstance();
|
672 |
|
|
cs.setParamsFromRequest(request);
|
673 |
5320
|
jones
|
Identifier id = new Identifier();
|
674 |
|
|
id.setValue(guid);
|
675 |
|
|
cs.create(token, id, object, m);
|
676 |
5319
|
jones
|
|
677 |
|
|
} else {
|
678 |
|
|
logMetacat.debug("Unauthorized to create.");
|
679 |
5356
|
berkley
|
throw new NotAuthorized("1000", "Permission denied for user " + username);
|
680 |
5319
|
jones
|
}
|
681 |
5353
|
berkley
|
} else if (action.equals(FUNCTION_NAME_UPDATE)) { //handle updates
|
682 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
683 |
|
|
CrudService cs = CrudService.getInstance();
|
684 |
|
|
Identifier obsoletedGuid = new Identifier();
|
685 |
|
|
Identifier id = new Identifier();
|
686 |
|
|
id.setValue(guid);
|
687 |
|
|
AuthToken token = null;
|
688 |
|
|
|
689 |
|
|
//do some checks
|
690 |
|
|
if(params.get("obsoletedGuid") == null)
|
691 |
|
|
{
|
692 |
5356
|
berkley
|
throw new InvalidRequest("1202", "obsoletedGuid must be contained in the request parameters.");
|
693 |
5353
|
berkley
|
}
|
694 |
|
|
//get the obsoletedGuid
|
695 |
|
|
String[] obsGuidS = params.get("obsoletedGuid");
|
696 |
|
|
obsoletedGuid.setValue(obsGuidS[0]);
|
697 |
|
|
|
698 |
|
|
if (!im.identifierExists(obsoletedGuid.getValue()))
|
699 |
|
|
{
|
700 |
5356
|
berkley
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
701 |
5353
|
berkley
|
}
|
702 |
|
|
|
703 |
|
|
|
704 |
|
|
logMetacat.debug("Commence update...");
|
705 |
|
|
|
706 |
|
|
//get the systemmetadata
|
707 |
|
|
IBindingFactory bfact =
|
708 |
|
|
BindingDirectory.getFactory(SystemMetadata.class);
|
709 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
710 |
|
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
711 |
|
|
|
712 |
|
|
//do the update
|
713 |
|
|
try
|
714 |
|
|
{
|
715 |
|
|
cs.setParamsFromRequest(request);
|
716 |
|
|
Identifier rId = cs.update(token, id, object, obsoletedGuid, m);
|
717 |
|
|
}
|
718 |
|
|
catch(NotFound e)
|
719 |
|
|
{
|
720 |
5356
|
berkley
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
721 |
5353
|
berkley
|
}
|
722 |
|
|
|
723 |
5211
|
jones
|
} else {
|
724 |
5356
|
berkley
|
throw new InvalidRequest("1000", "Operation must be create or update.");
|
725 |
5211
|
jones
|
}
|
726 |
5319
|
jones
|
} catch (NotAuthorized e) {
|
727 |
|
|
serializeException(e, out);
|
728 |
|
|
} catch (InvalidToken e) {
|
729 |
|
|
serializeException(e, out);
|
730 |
|
|
} catch (ServiceFailure e) {
|
731 |
|
|
serializeException(e, out);
|
732 |
|
|
} catch (IdentifierNotUnique e) {
|
733 |
|
|
serializeException(e, out);
|
734 |
|
|
} catch (UnsupportedType e) {
|
735 |
|
|
serializeException(e, out);
|
736 |
|
|
} catch (InsufficientResources e) {
|
737 |
|
|
serializeException(e, out);
|
738 |
|
|
} catch (InvalidSystemMetadata e) {
|
739 |
|
|
serializeException(e, out);
|
740 |
|
|
} catch (NotImplemented e) {
|
741 |
|
|
serializeException(e, out);
|
742 |
|
|
} catch (InvalidRequest e) {
|
743 |
|
|
serializeException(e, out);
|
744 |
|
|
} catch (MessagingException e) {
|
745 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
746 |
5319
|
jones
|
serializeException(sf, out);
|
747 |
|
|
} catch (IOException e) {
|
748 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
749 |
5319
|
jones
|
serializeException(sf, out);
|
750 |
5320
|
jones
|
} catch (JiBXException e) {
|
751 |
|
|
e.printStackTrace(System.out);
|
752 |
5356
|
berkley
|
InvalidSystemMetadata ism = new InvalidSystemMetadata("1080", e.getMessage());
|
753 |
5320
|
jones
|
serializeException(ism, out);
|
754 |
5211
|
jones
|
}
|
755 |
|
|
}
|
756 |
|
|
|
757 |
|
|
/**
|
758 |
|
|
* Earthgrid API > Put Service > Delete Function : calls MetacatHandler > handleDeleteAction
|
759 |
|
|
*
|
760 |
5287
|
jones
|
* @param guid ID of data object to be deleted
|
761 |
5211
|
jones
|
* @throws IOException
|
762 |
|
|
*/
|
763 |
5287
|
jones
|
private void deleteObject(String guid) throws IOException
|
764 |
|
|
{
|
765 |
|
|
// Look up the localId for this global identifier
|
766 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
767 |
|
|
String localId = "";
|
768 |
|
|
try {
|
769 |
|
|
localId = im.getLocalId(guid);
|
770 |
|
|
} catch (McdbDocNotFoundException e) {
|
771 |
|
|
// TODO: Need to return the proper DataONE exception
|
772 |
|
|
}
|
773 |
|
|
|
774 |
|
|
params.put("docid", new String[] { localId });
|
775 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
776 |
|
|
handler.handleDeleteAction(out, params, request, response, username,
|
777 |
|
|
groupNames);
|
778 |
|
|
out.close();
|
779 |
|
|
}
|
780 |
|
|
|
781 |
|
|
/**
|
782 |
|
|
* Earthgrid API > Authentication Service > Login Function : calls MetacatHandler > handleLoginAction
|
783 |
|
|
*
|
784 |
|
|
* @throws IOException
|
785 |
|
|
*/
|
786 |
|
|
private void login() throws IOException {
|
787 |
|
|
PrintWriter out = response.getWriter();
|
788 |
|
|
handler.handleLoginAction(out, params, request, response);
|
789 |
|
|
out.close();
|
790 |
|
|
}
|
791 |
|
|
|
792 |
|
|
/**
|
793 |
|
|
* Earthgrid API > Authentication Service > Logout Function : calls MetacatHandler > handleLogoutAction
|
794 |
|
|
*
|
795 |
|
|
* @throws IOException
|
796 |
|
|
*/
|
797 |
|
|
private void logout() throws IOException {
|
798 |
|
|
PrintWriter out = response.getWriter();
|
799 |
|
|
handler.handleLogoutAction(out, params, request, response);
|
800 |
|
|
out.close();
|
801 |
|
|
}
|
802 |
|
|
|
803 |
|
|
/**
|
804 |
|
|
* Prints xml response
|
805 |
|
|
* @param message Message to be displayed
|
806 |
|
|
* @param response Servlet response that xml message will be printed
|
807 |
|
|
* */
|
808 |
|
|
private void printError(String message, HttpServletResponse response) {
|
809 |
|
|
try {
|
810 |
|
|
PrintWriter out = response.getWriter();
|
811 |
|
|
response.setContentType("text/xml");
|
812 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
813 |
|
|
out.println("<error>");
|
814 |
|
|
out.println(message);
|
815 |
|
|
out.println("</error>");
|
816 |
|
|
out.close();
|
817 |
|
|
} catch (IOException e) {
|
818 |
|
|
e.printStackTrace();
|
819 |
|
|
}
|
820 |
|
|
}
|
821 |
|
|
|
822 |
5319
|
jones
|
private void serializeException(BaseException e, OutputStream out) {
|
823 |
|
|
// TODO: Use content negotiation to determine which return format to use
|
824 |
|
|
response.setContentType("text/xml");
|
825 |
|
|
response.setStatus(e.getCode());
|
826 |
|
|
try {
|
827 |
|
|
IOUtils.write(e.serialize(BaseException.FMT_XML), out);
|
828 |
|
|
} catch (IOException e1) {
|
829 |
|
|
logMetacat.error("Error writing exception to stream. "
|
830 |
|
|
+ e1.getMessage());
|
831 |
|
|
}
|
832 |
|
|
}
|
833 |
|
|
|
834 |
5211
|
jones
|
}
|