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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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5211
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boolean status = false;
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5424
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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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262 |
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if (resource.equals(RESOURCE_SESSION) &&
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httpVerb == POST &&
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params.get(FUNCTION_KEYWORD) != null) {
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//System.out.println("function_keyword: " + params.get(FUNCTION_KEYWORD)[0]);
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if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_LOGIN)) {
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login();
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status = true;
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} else if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_LOGOUT)) {
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logout();
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status = true;
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} else if (params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_SET_ACCESS)) {
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setaccess();
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status = true;
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//System.out.println("done setting access");
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}
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} else if (resource.equals(RESOURCE_META)) {
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if(params != null && params.get(FUNCTION_KEYWORD) != null &&
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params.get(FUNCTION_KEYWORD)[0].equals(FUNCTION_NAME_GENERATE_MISSING_SYSTEM_METADATA))
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{ //generate system metadata for any object that is
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//a) not system metadata itself
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//b) does not already have a system metadata id in the systemmetadata table
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//c) not a BIN object (data)
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//TODO: check if we need this anymore. Might be superceded
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//by MetacatPopulator
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generateMissingSystemMetadata();
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status = true;
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}
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else
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{
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String objectId = request.getPathInfo();
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if (objectId != null && objectId.length() > 1)
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{
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objectId = request.getPathInfo().substring(1);
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}
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getSystemMetadataObject(objectId);
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status = true;
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}
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} else if (resource.equals(RESOURCE_OBJECTS)) {
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logMetacat.debug("D1 Rest: Starting resource processing...");
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loadSessionData();
|
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 |
|
|
printError(
|
355 |
|
|
"This method is not supported by metacat. To "
|
356 |
|
|
+ "add a new LSID, add a document to metacat.",
|
357 |
|
|
response);
|
358 |
|
|
status = true;
|
359 |
|
|
}
|
360 |
|
|
|
361 |
|
|
} else if (resource.equals(RESOURCE_LOG)) {
|
362 |
|
|
//handle log events
|
363 |
|
|
if(httpVerb == GET)
|
364 |
|
|
{
|
365 |
|
|
getLog();
|
366 |
|
|
status = true;
|
367 |
|
|
}
|
368 |
|
|
else
|
369 |
|
|
{
|
370 |
5481
|
berkley
|
//change to D1 spec for specifying which http methods are allowed for a resource
|
371 |
5446
|
jones
|
printError("POST, PUT, DELETE is not supported for logs.", response);
|
372 |
|
|
status = true;
|
373 |
|
|
}
|
374 |
|
|
|
375 |
|
|
}
|
376 |
|
|
|
377 |
|
|
if (!status)
|
378 |
|
|
printError("Incorrect parameters!", response);
|
379 |
5211
|
jones
|
} else {
|
380 |
5446
|
jones
|
printError("Incorrect resource!", response);
|
381 |
5211
|
jones
|
}
|
382 |
|
|
} catch (Exception e) {
|
383 |
5446
|
jones
|
logMetacat.error(e.getMessage());
|
384 |
|
|
e.printStackTrace();
|
385 |
5211
|
jones
|
}
|
386 |
|
|
}
|
387 |
5374
|
berkley
|
|
388 |
|
|
/**
|
389 |
5390
|
berkley
|
* get the logs from the CrudService based on passed params. Available
|
390 |
|
|
* params are token, fromDate, toDate, event. See
|
391 |
|
|
* http://mule1.dataone.org/ArchitectureDocs/mn_api_crud.html#MN_crud.getLogRecords
|
392 |
|
|
* for more info
|
393 |
|
|
*/
|
394 |
|
|
private void getLog()
|
395 |
|
|
{
|
396 |
|
|
OutputStream out = null;
|
397 |
|
|
try
|
398 |
|
|
{
|
399 |
|
|
out = response.getOutputStream();
|
400 |
5450
|
berkley
|
response.setContentType("text/xml");
|
401 |
5390
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
402 |
|
|
String fromDateS = params.get("fromDate")[0];
|
403 |
5418
|
berkley
|
System.out.println("param fromDateS: " + fromDateS);
|
404 |
5390
|
berkley
|
Date fromDate = null;
|
405 |
|
|
String toDateS = params.get("toDate")[0];
|
406 |
5418
|
berkley
|
System.out.println("param toDateS: " + toDateS);
|
407 |
5390
|
berkley
|
Date toDate = null;
|
408 |
|
|
String eventS = params.get("event")[0];
|
409 |
|
|
Event event = null;
|
410 |
|
|
if(fromDateS != null)
|
411 |
|
|
{
|
412 |
5429
|
berkley
|
//fromDate = dateFormat.parse(fromDateS);
|
413 |
|
|
fromDate = parseDateAndConvertToGMT(fromDateS);
|
414 |
5390
|
berkley
|
}
|
415 |
|
|
if(toDateS != null)
|
416 |
|
|
{
|
417 |
5429
|
berkley
|
//toDate = dateFormat.parse(toDateS);
|
418 |
|
|
toDate = parseDateAndConvertToGMT(toDateS);
|
419 |
5390
|
berkley
|
}
|
420 |
|
|
if(eventS != null)
|
421 |
|
|
{
|
422 |
|
|
event = Event.convert(eventS);
|
423 |
|
|
}
|
424 |
5418
|
berkley
|
System.out.println("fromDate: " + fromDate + " toDate: " + toDate);
|
425 |
5395
|
berkley
|
|
426 |
5418
|
berkley
|
System.out.println("calling crudservice.getLogRecords");
|
427 |
5390
|
berkley
|
Log log = CrudService.getInstance().getLogRecords(token, fromDate, toDate, event);
|
428 |
|
|
serializeServiceType(Log.class, log, out);
|
429 |
|
|
}
|
430 |
|
|
catch(Exception e)
|
431 |
|
|
{
|
432 |
|
|
String msg = "Could not get logs from CrudService: " + e.getMessage();
|
433 |
|
|
ServiceFailure sf = new ServiceFailure("1490", msg);
|
434 |
|
|
logMetacat.error(msg);
|
435 |
|
|
e.printStackTrace();
|
436 |
|
|
serializeException(sf, out);
|
437 |
|
|
}
|
438 |
|
|
}
|
439 |
|
|
|
440 |
|
|
/**
|
441 |
5374
|
berkley
|
* copies request parameters to a hashtable which is given as argument to native metacathandler functions
|
442 |
|
|
*/
|
443 |
|
|
private void initParams() {
|
444 |
5211
|
jones
|
|
445 |
5374
|
berkley
|
String name = null;
|
446 |
|
|
String[] value = null;
|
447 |
|
|
Enumeration paramlist = request.getParameterNames();
|
448 |
|
|
while (paramlist.hasMoreElements()) {
|
449 |
|
|
name = (String) paramlist.nextElement();
|
450 |
|
|
value = request.getParameterValues(name);
|
451 |
|
|
params.put(name, value);
|
452 |
|
|
}
|
453 |
|
|
}
|
454 |
|
|
|
455 |
5211
|
jones
|
/**
|
456 |
5374
|
berkley
|
*
|
457 |
|
|
* Load user details of metacat session from the request
|
458 |
|
|
*
|
459 |
|
|
*/
|
460 |
|
|
private void loadSessionData()
|
461 |
|
|
throws Exception
|
462 |
|
|
{
|
463 |
|
|
SessionData sessionData = RequestUtil.getSessionData(request);
|
464 |
|
|
try
|
465 |
|
|
{
|
466 |
|
|
username = null;
|
467 |
|
|
password = null;
|
468 |
|
|
groupNames = null;
|
469 |
|
|
sessionId = null;
|
470 |
|
|
|
471 |
|
|
boolean validSession = false;
|
472 |
|
|
SessionService ss = SessionService.getInstance();
|
473 |
5410
|
berkley
|
System.out.println("sessionData: " + sessionData);
|
474 |
5423
|
berkley
|
if(sessionData == null)
|
475 |
|
|
{
|
476 |
|
|
username = "public";
|
477 |
|
|
sessionId = "0";
|
478 |
|
|
System.out.println("sessiondata is null. Creating a public session.");
|
479 |
|
|
return;
|
480 |
|
|
}
|
481 |
|
|
|
482 |
5410
|
berkley
|
System.out.println("username: " + sessionData.getUserName());
|
483 |
|
|
System.out.println("sessionid: " + sessionData.getId());
|
484 |
5374
|
berkley
|
//validate the session
|
485 |
5410
|
berkley
|
if(ss.isSessionRegistered(sessionData.getId()) &&
|
486 |
|
|
!(sessionData.getUserName().equals("public") || sessionData.getId().equals("0")))
|
487 |
5374
|
berkley
|
{
|
488 |
|
|
validSession = true;
|
489 |
|
|
}
|
490 |
|
|
|
491 |
|
|
if(validSession)
|
492 |
|
|
{
|
493 |
|
|
//if the session is valid, set these variables
|
494 |
|
|
username = sessionData.getUserName();
|
495 |
|
|
password = sessionData.getPassword();
|
496 |
|
|
groupNames = sessionData.getGroupNames();
|
497 |
|
|
sessionId = sessionData.getId();
|
498 |
5386
|
berkley
|
System.out.println("setting sessionid to " + sessionId);
|
499 |
|
|
System.out.println("username: " + username);
|
500 |
5374
|
berkley
|
}
|
501 |
|
|
|
502 |
|
|
//if the session is not valid or the username is null, set
|
503 |
|
|
//username to public
|
504 |
|
|
if (username == null)
|
505 |
|
|
{
|
506 |
5386
|
berkley
|
System.out.println("setting username to public.");
|
507 |
5374
|
berkley
|
username = "public";
|
508 |
|
|
}
|
509 |
|
|
}
|
510 |
|
|
catch(Exception e)
|
511 |
|
|
{
|
512 |
5423
|
berkley
|
e.printStackTrace();
|
513 |
5374
|
berkley
|
throw new Exception("Could not load the session data: " + e.getMessage());
|
514 |
|
|
}
|
515 |
|
|
}
|
516 |
|
|
|
517 |
|
|
/**
|
518 |
|
|
* generate missing system metadata for any science metadata objects
|
519 |
|
|
* that don't already have it. https://trac.dataone.org/ticket/591
|
520 |
5381
|
berkley
|
*
|
521 |
|
|
* called with POST meta/?op=generatemissingsystemmetadata
|
522 |
5374
|
berkley
|
*/
|
523 |
|
|
private void generateMissingSystemMetadata()
|
524 |
|
|
{
|
525 |
5381
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
526 |
|
|
CrudService.getInstance().generateMissingSystemMetadata(token);
|
527 |
5374
|
berkley
|
}
|
528 |
|
|
|
529 |
|
|
/**
|
530 |
|
|
* Earthgrid API > Identifier Service > isRegistered Function :
|
531 |
|
|
* calls MetacatHandler > handleIdIsRegisteredAction
|
532 |
5286
|
jones
|
* @param guid
|
533 |
5211
|
jones
|
* @throws IOException
|
534 |
|
|
*/
|
535 |
5286
|
jones
|
private void isRegistered(String guid) throws IOException
|
536 |
|
|
{
|
537 |
|
|
|
538 |
|
|
// Look up the localId for this guid
|
539 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
540 |
|
|
String localId = "";
|
541 |
|
|
try {
|
542 |
|
|
localId = im.getLocalId(guid);
|
543 |
|
|
} catch (McdbDocNotFoundException e) {
|
544 |
|
|
// TODO: Need to return the proper DataONE exception
|
545 |
|
|
}
|
546 |
|
|
|
547 |
|
|
params.put("docid", new String[] { localId });
|
548 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
549 |
5450
|
berkley
|
response.setContentType("text/xml");
|
550 |
5211
|
jones
|
handler.handleIdIsRegisteredAction(out, params, response);
|
551 |
|
|
out.close();
|
552 |
|
|
}
|
553 |
|
|
|
554 |
|
|
/**
|
555 |
5374
|
berkley
|
* Earthgrid API > Identifier Service > getAllDocIds Function :
|
556 |
|
|
* calls MetacatHandler > handleGetAllDocidsAction
|
557 |
5211
|
jones
|
* @throws IOException
|
558 |
|
|
*/
|
559 |
|
|
private void getAllDocIds() throws IOException {
|
560 |
|
|
PrintWriter out = response.getWriter();
|
561 |
5450
|
berkley
|
response.setContentType("text/xml");
|
562 |
5211
|
jones
|
handler.handleGetAllDocidsAction(out, params, response);
|
563 |
|
|
out.close();
|
564 |
|
|
}
|
565 |
|
|
|
566 |
|
|
/**
|
567 |
5374
|
berkley
|
* Earthgrid API > Identifier Service > getNextRevision Function :
|
568 |
|
|
* calls MetacatHandler > handleGetRevisionAndDocTypeAction
|
569 |
5286
|
jones
|
* @param guid
|
570 |
5211
|
jones
|
* @throws IOException
|
571 |
|
|
*/
|
572 |
5286
|
jones
|
private void getNextRevision(String guid) throws IOException
|
573 |
|
|
{
|
574 |
|
|
params.put("docid", new String[] { guid });
|
575 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
576 |
5450
|
berkley
|
response.setContentType("text/xml");
|
577 |
5211
|
jones
|
//handler.handleGetRevisionAndDocTypeAction(out, params);
|
578 |
|
|
|
579 |
|
|
try {
|
580 |
|
|
// Make sure there is a docid
|
581 |
5286
|
jones
|
if (guid == null || guid.equals("")) {
|
582 |
5211
|
jones
|
throw new Exception("User didn't specify docid!");
|
583 |
5286
|
jones
|
}
|
584 |
5211
|
jones
|
|
585 |
5286
|
jones
|
// Look up the localId for this guid
|
586 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
587 |
|
|
String localId = "";
|
588 |
|
|
try {
|
589 |
|
|
localId = im.getLocalId(guid);
|
590 |
|
|
} catch (McdbDocNotFoundException e) {
|
591 |
|
|
// TODO: Need to return the proper DataONE exception
|
592 |
|
|
}
|
593 |
|
|
|
594 |
5211
|
jones
|
// Create a DBUtil object
|
595 |
|
|
DBUtil dbutil = new DBUtil();
|
596 |
|
|
// Get a rev and doctype
|
597 |
|
|
String revAndDocType = dbutil
|
598 |
5286
|
jones
|
.getCurrentRevisionAndDocTypeForGivenDocument(localId);
|
599 |
5211
|
jones
|
int revision = Integer.parseInt(revAndDocType.split(";")[0]) + 1;
|
600 |
|
|
|
601 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
602 |
|
|
out.print("<next-revision>");
|
603 |
|
|
out.print(revision);
|
604 |
|
|
out.print("</next-revision>");
|
605 |
|
|
|
606 |
|
|
} catch (Exception e) {
|
607 |
|
|
// Handle exception
|
608 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
609 |
|
|
out.println("<error>");
|
610 |
|
|
out.println(e.getMessage());
|
611 |
|
|
out.println("</error>");
|
612 |
|
|
}
|
613 |
|
|
|
614 |
|
|
out.close();
|
615 |
|
|
}
|
616 |
|
|
|
617 |
|
|
/**
|
618 |
5374
|
berkley
|
* Earthgrid API > Identifier Service > getNextObject Function :
|
619 |
|
|
* calls MetacatHandler > handleGetMaxDocidAction
|
620 |
5211
|
jones
|
* @throws IOException
|
621 |
|
|
*/
|
622 |
|
|
private void getNextObject() throws IOException {
|
623 |
|
|
PrintWriter out = response.getWriter();
|
624 |
5450
|
berkley
|
response.setContentType("text/xml");
|
625 |
5211
|
jones
|
handler.handleGetMaxDocidAction(out, params, response);
|
626 |
|
|
out.close();
|
627 |
|
|
}
|
628 |
|
|
|
629 |
|
|
/**
|
630 |
5299
|
jones
|
* Implements REST version of DataONE CRUD API --> get
|
631 |
5282
|
jones
|
* @param guid ID of data object to be read
|
632 |
5211
|
jones
|
*/
|
633 |
5450
|
berkley
|
private void getObject(String guid) {
|
634 |
|
|
CrudService cs = CrudService.getInstance();
|
635 |
|
|
cs.setParamsFromRequest(request);
|
636 |
|
|
AuthToken token = new AuthToken(sessionId);
|
637 |
|
|
OutputStream out = null;
|
638 |
|
|
try {
|
639 |
|
|
out = response.getOutputStream();
|
640 |
|
|
response.setContentType("text/xml");
|
641 |
|
|
if(guid != null)
|
642 |
|
|
{ //get a specific document
|
643 |
|
|
Identifier id = new Identifier();
|
644 |
|
|
id.setValue(guid);
|
645 |
|
|
try
|
646 |
|
|
{
|
647 |
|
|
if(token == null)
|
648 |
|
|
{
|
649 |
|
|
token = new AuthToken("Public");
|
650 |
|
|
}
|
651 |
|
|
InputStream data = cs.get(token, id);
|
652 |
|
|
IOUtils.copyLarge(data, response.getOutputStream());
|
653 |
|
|
}
|
654 |
|
|
catch(InvalidToken it)
|
655 |
|
|
{
|
656 |
|
|
serializeException(it, out);
|
657 |
|
|
}
|
658 |
|
|
catch(ServiceFailure sf)
|
659 |
|
|
{
|
660 |
|
|
serializeException(sf, out);
|
661 |
|
|
}
|
662 |
|
|
catch(NotAuthorized na)
|
663 |
|
|
{
|
664 |
|
|
serializeException(na, out);
|
665 |
|
|
}
|
666 |
|
|
catch(NotFound nf)
|
667 |
|
|
{
|
668 |
|
|
serializeException(nf, out);
|
669 |
|
|
}
|
670 |
|
|
catch(NotImplemented ni)
|
671 |
|
|
{
|
672 |
|
|
serializeException(ni, out);
|
673 |
|
|
}
|
674 |
|
|
catch(Exception e)
|
675 |
|
|
{
|
676 |
|
|
System.out.println("Error with Crud.get(). " +
|
677 |
|
|
"If this is an 'Exception producing data' error, " +
|
678 |
|
|
"go to CrudService.get() for better debugging. " +
|
679 |
|
|
"Here's the error: " + e.getMessage());
|
680 |
|
|
e.printStackTrace();
|
681 |
|
|
ServiceFailure sf = new ServiceFailure("1030",
|
682 |
|
|
"IO Error in ResourceHandler.getObject: " + e.getMessage());
|
683 |
|
|
serializeException(sf, out);
|
684 |
|
|
}
|
685 |
|
|
}
|
686 |
|
|
else
|
687 |
|
|
{ //call listObjects with specified params
|
688 |
|
|
Date startTime = null;
|
689 |
|
|
Date endTime = null;
|
690 |
|
|
ObjectFormat objectFormat = null;
|
691 |
|
|
boolean replicaStatus = false;
|
692 |
|
|
int start = 0;
|
693 |
5481
|
berkley
|
//TODO: make the max count into a const
|
694 |
5450
|
berkley
|
int count = 1000;
|
695 |
|
|
Enumeration paramlist = request.getParameterNames();
|
696 |
|
|
while (paramlist.hasMoreElements())
|
697 |
|
|
{ //parse the params and make the crud call
|
698 |
|
|
String name = (String) paramlist.nextElement();
|
699 |
|
|
String[] value = (String[])request.getParameterValues(name);
|
700 |
|
|
/*for(int i=0; i<value.length; i++)
|
701 |
|
|
{
|
702 |
|
|
System.out.println("name: " + name + " value: " + value[i]);
|
703 |
|
|
}*/
|
704 |
|
|
if(name.equals("startTime") && value != null)
|
705 |
|
|
{
|
706 |
|
|
try
|
707 |
|
|
{
|
708 |
|
|
//startTime = dateFormat.parse(value[0]);
|
709 |
|
|
startTime = parseDateAndConvertToGMT(value[0]);
|
710 |
|
|
}
|
711 |
|
|
catch(Exception e)
|
712 |
|
|
{ //if we can't parse it, just don't use the startTime param
|
713 |
|
|
System.out.println("Could not parse startTime: " + value[0]);
|
714 |
|
|
startTime = null;
|
715 |
|
|
}
|
716 |
|
|
}
|
717 |
|
|
else if(name.equals("endTime") && value != null)
|
718 |
|
|
{
|
719 |
|
|
try
|
720 |
|
|
{
|
721 |
|
|
//endTime = dateFormat.parse(value[0]);
|
722 |
|
|
endTime = parseDateAndConvertToGMT(value[0]);
|
723 |
|
|
}
|
724 |
|
|
catch(Exception e)
|
725 |
|
|
{ //if we can't parse it, just don't use the endTime param
|
726 |
|
|
System.out.println("Could not parse endTime: " + value[0]);
|
727 |
|
|
endTime = null;
|
728 |
|
|
}
|
729 |
|
|
}
|
730 |
|
|
else if(name.equals("objectFormat") && value != null)
|
731 |
|
|
{
|
732 |
|
|
objectFormat = ObjectFormat.convert(value[0]);
|
733 |
|
|
}
|
734 |
|
|
else if(name.equals("replicaStatus") && value != null)
|
735 |
|
|
{
|
736 |
|
|
if(value != null &&
|
737 |
|
|
value.length > 0 &&
|
738 |
|
|
(value[0].equals("true") || value[0].equals("TRUE") || value[0].equals("YES")))
|
739 |
|
|
{
|
740 |
|
|
replicaStatus = true;
|
741 |
|
|
}
|
742 |
|
|
}
|
743 |
|
|
else if(name.equals("start") && value != null)
|
744 |
|
|
{
|
745 |
|
|
start = new Integer(value[0]).intValue();
|
746 |
|
|
}
|
747 |
|
|
else if(name.equals("count") && value != null)
|
748 |
|
|
{
|
749 |
|
|
count = new Integer(value[0]).intValue();
|
750 |
|
|
}
|
751 |
|
|
}
|
752 |
|
|
//make the crud call
|
753 |
|
|
/*System.out.println("token: " + token + " startTime: " + startTime +
|
754 |
|
|
" endtime: " + endTime + " objectFormat: " +
|
755 |
|
|
objectFormat + " replicaStatus: " + replicaStatus +
|
756 |
|
|
" start: " + start + " count: " + count);
|
757 |
|
|
*/
|
758 |
|
|
ObjectList ol = cs.listObjects(token, startTime, endTime,
|
759 |
|
|
objectFormat, replicaStatus, start, count);
|
760 |
5481
|
berkley
|
//TODO: why is this calling this twice?
|
761 |
|
|
//ol = cs.listObjects(token, startTime, endTime, objectFormat, replicaStatus, start, count);
|
762 |
5450
|
berkley
|
|
763 |
|
|
StringReader sr = new StringReader(ol.toString());
|
764 |
|
|
out = response.getOutputStream();
|
765 |
|
|
response.setContentType("text/xml");
|
766 |
|
|
// Serialize and write it to the output stream
|
767 |
|
|
|
768 |
|
|
try {
|
769 |
|
|
serializeServiceType(ObjectList.class, ol, out);
|
770 |
|
|
} catch (JiBXException e) {
|
771 |
|
|
throw new ServiceFailure("1190", "Failed to serialize ObjectList: " + e.getMessage());
|
772 |
|
|
}
|
773 |
|
|
}
|
774 |
|
|
} catch (BaseException e) {
|
775 |
|
|
serializeException(e, out);
|
776 |
|
|
} catch (IOException e) {
|
777 |
|
|
e.printStackTrace();
|
778 |
|
|
ServiceFailure sf = new ServiceFailure("1030",
|
779 |
|
|
"IO Error in ResourceHandler.getObject: " + e.getMessage());
|
780 |
|
|
serializeException(sf, out);
|
781 |
|
|
} catch(NumberFormatException ne) {
|
782 |
|
|
InvalidRequest ir = new InvalidRequest("1030", "Invalid format for parameter: " + ne.getMessage());
|
783 |
|
|
serializeException(ir, out);
|
784 |
|
|
} catch (Exception e) {
|
785 |
|
|
e.printStackTrace();
|
786 |
|
|
ServiceFailure sf = new ServiceFailure("1030",
|
787 |
|
|
"Exception " + e.getClass().getName() + " raised while handling listObjects request: " +
|
788 |
|
|
e.getMessage());
|
789 |
|
|
serializeException(sf, out);
|
790 |
|
|
}
|
791 |
|
|
}
|
792 |
5428
|
berkley
|
|
793 |
|
|
/**
|
794 |
|
|
* parse a date and return it in GMT if it ends with a 'Z'
|
795 |
|
|
* @param date
|
796 |
|
|
* @return
|
797 |
|
|
* @throws ParseException
|
798 |
|
|
*/
|
799 |
|
|
private Date parseDateAndConvertToGMT(String date) throws ParseException
|
800 |
|
|
{
|
801 |
5429
|
berkley
|
try
|
802 |
|
|
{ //the format we want
|
803 |
|
|
return dateFormat.parse(date);
|
804 |
|
|
}
|
805 |
|
|
catch(java.text.ParseException pe)
|
806 |
|
|
{ //try another legacy format
|
807 |
|
|
DateFormat dateFormat2 = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss'Z'");
|
808 |
|
|
dateFormat2.setTimeZone(TimeZone.getTimeZone("GMT-0"));
|
809 |
|
|
return dateFormat2.parse(date);
|
810 |
|
|
}
|
811 |
|
|
|
812 |
|
|
/*System.out.println("Parsing date " + date);
|
813 |
5428
|
berkley
|
Date d = dateFormat.parse(date);
|
814 |
|
|
|
815 |
|
|
if(date.endsWith("Z"))
|
816 |
|
|
{
|
817 |
|
|
Calendar lTime = Calendar.getInstance();
|
818 |
|
|
lTime.setTime(d);
|
819 |
|
|
Calendar zTime = Calendar.getInstance(TimeZone.getTimeZone("GMT-0"));
|
820 |
|
|
zTime.set(Calendar.MONTH, lTime.get(Calendar.MONTH));
|
821 |
|
|
zTime.set(Calendar.DATE, lTime.get(Calendar.DATE));
|
822 |
|
|
zTime.set(Calendar.YEAR, lTime.get(Calendar.YEAR));
|
823 |
|
|
zTime.set(Calendar.HOUR, lTime.get(Calendar.HOUR));
|
824 |
|
|
zTime.set(Calendar.MINUTE, lTime.get(Calendar.MINUTE));
|
825 |
|
|
zTime.set(Calendar.SECOND, lTime.get(Calendar.SECOND));
|
826 |
|
|
|
827 |
|
|
System.out.println("date parsed to " + zTime.getTime());
|
828 |
|
|
return zTime.getTime();
|
829 |
|
|
}
|
830 |
|
|
|
831 |
|
|
System.out.println("date parsed, but not converted. returned as " + d);
|
832 |
5429
|
berkley
|
return d;*/
|
833 |
5428
|
berkley
|
}
|
834 |
5211
|
jones
|
|
835 |
|
|
/**
|
836 |
5332
|
jones
|
* Implements REST version of DataONE CRUD API --> getSystemMetadata
|
837 |
|
|
* @param guid ID of data object to be read
|
838 |
|
|
*/
|
839 |
|
|
private void getSystemMetadataObject(String guid) {
|
840 |
5337
|
berkley
|
CrudService cs = CrudService.getInstance();
|
841 |
|
|
cs.setParamsFromRequest(request);
|
842 |
5386
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
843 |
5332
|
jones
|
OutputStream out = null;
|
844 |
|
|
try {
|
845 |
5450
|
berkley
|
response.setContentType("text/xml");
|
846 |
5332
|
jones
|
out = response.getOutputStream();
|
847 |
|
|
Identifier id = new Identifier();
|
848 |
|
|
id.setValue(guid);
|
849 |
|
|
SystemMetadata sysmeta = cs.getSystemMetadata(token, id);
|
850 |
|
|
|
851 |
|
|
// Serialize and write it to the output stream
|
852 |
|
|
try {
|
853 |
5481
|
berkley
|
//TODO: look at the efficiency of this method. The system metadata
|
854 |
|
|
//is read from metacat (in CrudService) as xml, then serialized
|
855 |
|
|
//to a SystemMetadat object, then returned here, then serizlized
|
856 |
|
|
//back to XML to be sent to the response.
|
857 |
5390
|
berkley
|
serializeServiceType(SystemMetadata.class, sysmeta, out);
|
858 |
5332
|
jones
|
} catch (JiBXException e) {
|
859 |
5356
|
berkley
|
throw new ServiceFailure("1190", "Failed to serialize SystemMetadata: " + e.getMessage());
|
860 |
5332
|
jones
|
}
|
861 |
|
|
} catch (BaseException e) {
|
862 |
|
|
serializeException(e, out);
|
863 |
|
|
} catch (IOException e) {
|
864 |
5414
|
berkley
|
ServiceFailure sf = new ServiceFailure("1030",
|
865 |
|
|
"Error in ResourceHandler.getSystemMetadataObject: " + e.getMessage());
|
866 |
5332
|
jones
|
serializeException(sf, out);
|
867 |
|
|
} finally {
|
868 |
|
|
IOUtils.closeQuietly(out);
|
869 |
|
|
}
|
870 |
|
|
}
|
871 |
|
|
|
872 |
|
|
/**
|
873 |
5390
|
berkley
|
* serialize an object of type to out
|
874 |
|
|
* @param type the class of the object to serialize (i.e. SystemMetadata.class)
|
875 |
|
|
* @param object the object to serialize
|
876 |
|
|
* @param out the stream to serialize it to
|
877 |
|
|
* @throws JiBXException
|
878 |
|
|
*/
|
879 |
|
|
private void serializeServiceType(Class type, Object object, OutputStream out)
|
880 |
|
|
throws JiBXException
|
881 |
|
|
{
|
882 |
|
|
IBindingFactory bfact = BindingDirectory.getFactory(type);
|
883 |
|
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
884 |
|
|
mctx.marshalDocument(object, "UTF-8", null, out);
|
885 |
|
|
}
|
886 |
|
|
|
887 |
|
|
/**
|
888 |
|
|
* deserialize an object of type from is
|
889 |
|
|
* @param type the class of the object to serialize (i.e. SystemMetadata.class)
|
890 |
|
|
* @param is the stream to deserialize from
|
891 |
|
|
* @throws JiBXException
|
892 |
|
|
*/
|
893 |
|
|
private Object deserializeServiceType(Class type, InputStream is)
|
894 |
|
|
throws JiBXException
|
895 |
|
|
{
|
896 |
|
|
IBindingFactory bfact = BindingDirectory.getFactory(type);
|
897 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
898 |
|
|
Object o = (Object) uctx.unmarshalDocument(is, null);
|
899 |
|
|
return o;
|
900 |
|
|
}
|
901 |
|
|
|
902 |
|
|
/**
|
903 |
5211
|
jones
|
* Earthgrid API > Query Service > Query Function : translates ecogrid query document to metacat query
|
904 |
|
|
* then calls DBQuery > createResultDocument function and then again translate resultset to ecogrid resultset
|
905 |
|
|
*
|
906 |
|
|
* NOTE:
|
907 |
|
|
* This is the only method that uses EcoGrid classes for its implementation.
|
908 |
|
|
* It does so because it takes an EcoGrid Query as input, and outputs an
|
909 |
|
|
* EcoGrid ResultSet document. These documents are parsed by the auto-generated
|
910 |
|
|
* EcoGrid classes from axis, and so we link to them here rather than re-inventing them.
|
911 |
|
|
* This creates a circular dependency, because the Metacat classes are needed
|
912 |
|
|
* to build the EcoGrid implementation, and the EcoGrid jars are needed to build this query()
|
913 |
|
|
* method. This circularity could be resolved by moving the EcoGrid classes
|
914 |
|
|
* to Metacat directly. As we transition away from EcoGrid SOAP methods in
|
915 |
|
|
* favor of these REST interfaces, this circular dependency can be eliminated.
|
916 |
|
|
*
|
917 |
|
|
* @throws Exception
|
918 |
|
|
*/
|
919 |
|
|
private void query() throws Exception {
|
920 |
|
|
/* This block commented out because of the EcoGrid circular dependency.
|
921 |
|
|
* For now, query will not be supported until the circularity can be
|
922 |
5286
|
jones
|
* resolved, probably by moving the ecogrid query syntax transformers
|
923 |
5211
|
jones
|
* directly into the Metacat codebase. MBJ 2010-02-03
|
924 |
|
|
|
925 |
|
|
try {
|
926 |
|
|
EcogridQueryParser parser = new EcogridQueryParser(request
|
927 |
|
|
.getReader());
|
928 |
|
|
parser.parseXML();
|
929 |
|
|
QueryType queryType = parser.getEcogridQuery();
|
930 |
|
|
EcogridJavaToMetacatJavaQueryTransformer queryTransformer =
|
931 |
|
|
new EcogridJavaToMetacatJavaQueryTransformer();
|
932 |
|
|
QuerySpecification metacatQuery = queryTransformer
|
933 |
|
|
.transform(queryType);
|
934 |
|
|
|
935 |
|
|
DBQuery metacat = new DBQuery();
|
936 |
|
|
|
937 |
|
|
boolean useXMLIndex = (new Boolean(PropertyService
|
938 |
|
|
.getProperty("database.usexmlindex"))).booleanValue();
|
939 |
|
|
String xmlquery = "query"; // we don't care the query in resultset,
|
940 |
|
|
// the query can be anything
|
941 |
|
|
PrintWriter out = null; // we don't want metacat result, so set out null
|
942 |
|
|
|
943 |
|
|
// parameter: queryspecification, user, group, usingIndexOrNot
|
944 |
|
|
StringBuffer result = metacat.createResultDocument(xmlquery,
|
945 |
|
|
metacatQuery, out, username, groupNames, useXMLIndex);
|
946 |
|
|
|
947 |
|
|
// create result set transfer
|
948 |
|
|
String saxparser = PropertyService.getProperty("xml.saxparser");
|
949 |
|
|
MetacatResultsetParser metacatResultsetParser = new MetacatResultsetParser(
|
950 |
|
|
new StringReader(result.toString()), saxparser, queryType
|
951 |
|
|
.getNamespace().get_value());
|
952 |
|
|
ResultsetType records = metacatResultsetParser.getEcogridResult();
|
953 |
|
|
|
954 |
|
|
System.out
|
955 |
|
|
.println(EcogridResultsetTransformer.toXMLString(records));
|
956 |
|
|
response.setContentType("text/xml");
|
957 |
|
|
out = response.getWriter();
|
958 |
|
|
out.print(EcogridResultsetTransformer.toXMLString(records));
|
959 |
|
|
|
960 |
|
|
} catch (Exception e) {
|
961 |
|
|
e.printStackTrace();
|
962 |
|
|
}*/
|
963 |
|
|
response.setContentType("text/xml");
|
964 |
|
|
PrintWriter out = response.getWriter();
|
965 |
|
|
out.print("<error>Query operation not yet supported by Metacat.</error>");
|
966 |
|
|
out.close();
|
967 |
|
|
}
|
968 |
5319
|
jones
|
|
969 |
5394
|
berkley
|
private String streamToString(InputStream is)
|
970 |
|
|
throws IOException
|
971 |
|
|
{
|
972 |
|
|
byte b[] = new byte[1024];
|
973 |
|
|
int numread = is.read(b, 0, 1024);
|
974 |
|
|
String response = new String();
|
975 |
|
|
while(numread != -1)
|
976 |
|
|
{
|
977 |
|
|
response += new String(b, 0, numread);
|
978 |
|
|
numread = is.read(b, 0, 1024);
|
979 |
|
|
}
|
980 |
|
|
return response;
|
981 |
|
|
}
|
982 |
|
|
|
983 |
|
|
private InputStream stringToStream(String s)
|
984 |
|
|
throws IOException
|
985 |
|
|
{
|
986 |
|
|
ByteArrayInputStream bais = new ByteArrayInputStream(s.getBytes());
|
987 |
|
|
return bais;
|
988 |
|
|
}
|
989 |
|
|
|
990 |
5462
|
berkley
|
/**
|
991 |
|
|
* process a mime multipart message
|
992 |
|
|
* @param is
|
993 |
|
|
* @return
|
994 |
|
|
*/
|
995 |
|
|
private Hashtable processMMP(InputStream is)
|
996 |
|
|
throws IOException
|
997 |
|
|
{
|
998 |
5481
|
berkley
|
//TODO: verify that this is how the RFC for MMP should work
|
999 |
|
|
//SORTAHACK: Since mmp seems to have a bug where large object parts get truncated,
|
1000 |
5462
|
berkley
|
//parse the stream here. This has the disavantage of putting the
|
1001 |
|
|
//stream into memory.
|
1002 |
|
|
InputStream object = null;
|
1003 |
|
|
InputStream sysmeta = null;
|
1004 |
|
|
String s = streamToString(is);
|
1005 |
|
|
//System.out.println("s: " + s);
|
1006 |
|
|
//figure out what the boundary marker is
|
1007 |
|
|
String searchString = "boundary=";
|
1008 |
|
|
int searchStringIndex = s.indexOf(searchString);
|
1009 |
|
|
String boundary = s.substring(searchStringIndex + searchString.length() + 1,
|
1010 |
|
|
s.indexOf("\"", searchStringIndex + searchString.length() + 1));
|
1011 |
|
|
boundary = "--" + boundary;
|
1012 |
|
|
//System.out.println("boundary is " + boundary);
|
1013 |
|
|
|
1014 |
|
|
//find the system metadata
|
1015 |
|
|
searchString = "Content-Disposition: attachment; filename=systemmetadata";
|
1016 |
|
|
searchStringIndex = s.indexOf(searchString);
|
1017 |
|
|
sysmeta = new ByteArrayInputStream(
|
1018 |
|
|
s.substring(searchStringIndex +
|
1019 |
|
|
searchString.length(),
|
1020 |
|
|
s.indexOf(boundary, searchStringIndex)).trim().getBytes());
|
1021 |
|
|
|
1022 |
|
|
//find the object
|
1023 |
|
|
searchString = "Content-Disposition: attachment; filename=object";
|
1024 |
|
|
searchStringIndex = s.indexOf(searchString);
|
1025 |
|
|
object = new ByteArrayInputStream(
|
1026 |
|
|
s.substring(searchStringIndex +
|
1027 |
|
|
searchString.length(),
|
1028 |
|
|
s.indexOf(boundary, searchStringIndex)).trim().getBytes());
|
1029 |
|
|
|
1030 |
|
|
Hashtable h = new Hashtable();
|
1031 |
|
|
h.put("object", object);
|
1032 |
|
|
h.put("systemmetadata", sysmeta);
|
1033 |
|
|
return h;
|
1034 |
|
|
}
|
1035 |
5394
|
berkley
|
|
1036 |
5462
|
berkley
|
|
1037 |
5211
|
jones
|
/**
|
1038 |
|
|
* Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
|
1039 |
|
|
*
|
1040 |
5319
|
jones
|
* @param guid ID of data object to be inserted or updated
|
1041 |
5211
|
jones
|
* @throws IOException
|
1042 |
|
|
*/
|
1043 |
5319
|
jones
|
private void putObject(String guid, String action) {
|
1044 |
|
|
logMetacat.debug("Entering putObject: " + guid + "/" + action);
|
1045 |
|
|
OutputStream out = null;
|
1046 |
|
|
try {
|
1047 |
|
|
out = response.getOutputStream();
|
1048 |
5450
|
berkley
|
response.setContentType("text/xml");
|
1049 |
5319
|
jones
|
} catch (IOException e1) {
|
1050 |
|
|
logMetacat.error("Could not get the output stream for writing in putObject");
|
1051 |
|
|
}
|
1052 |
|
|
try {
|
1053 |
5353
|
berkley
|
|
1054 |
|
|
// Read the incoming data from its Mime Multipart encoding
|
1055 |
|
|
logMetacat.debug("Disassembling MIME multipart form");
|
1056 |
|
|
InputStream object = null;
|
1057 |
|
|
InputStream sysmeta = null;
|
1058 |
5394
|
berkley
|
|
1059 |
5462
|
berkley
|
Hashtable parts = processMMP(request.getInputStream());
|
1060 |
|
|
object = (InputStream)parts.get("object");
|
1061 |
|
|
sysmeta = (InputStream)parts.get("systemmetadata");
|
1062 |
5394
|
berkley
|
|
1063 |
5353
|
berkley
|
if ( action.equals(FUNCTION_NAME_INSERT)) { //handle inserts
|
1064 |
5211
|
jones
|
|
1065 |
5319
|
jones
|
// Check if the objectId exists
|
1066 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
1067 |
|
|
if (im.identifierExists(guid)) {
|
1068 |
5356
|
berkley
|
throw new IdentifierNotUnique("1000", "Identifier is already in use: " + guid);
|
1069 |
5319
|
jones
|
}
|
1070 |
5211
|
jones
|
|
1071 |
5376
|
berkley
|
logMetacat.debug("Commence creation...");
|
1072 |
|
|
IBindingFactory bfact =
|
1073 |
|
|
BindingDirectory.getFactory(SystemMetadata.class);
|
1074 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
1075 |
|
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
1076 |
|
|
|
1077 |
|
|
CrudService cs = CrudService.getInstance();
|
1078 |
5386
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
1079 |
5376
|
berkley
|
cs.setParamsFromRequest(request);
|
1080 |
|
|
Identifier id = new Identifier();
|
1081 |
|
|
id.setValue(guid);
|
1082 |
|
|
cs.create(token, id, object, m);
|
1083 |
5386
|
berkley
|
|
1084 |
5353
|
berkley
|
} else if (action.equals(FUNCTION_NAME_UPDATE)) { //handle updates
|
1085 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
1086 |
|
|
CrudService cs = CrudService.getInstance();
|
1087 |
|
|
Identifier obsoletedGuid = new Identifier();
|
1088 |
|
|
Identifier id = new Identifier();
|
1089 |
|
|
id.setValue(guid);
|
1090 |
5386
|
berkley
|
AuthToken token = new AuthToken(sessionId);
|
1091 |
5353
|
berkley
|
|
1092 |
|
|
//do some checks
|
1093 |
|
|
if(params.get("obsoletedGuid") == null)
|
1094 |
|
|
{
|
1095 |
5356
|
berkley
|
throw new InvalidRequest("1202", "obsoletedGuid must be contained in the request parameters.");
|
1096 |
5353
|
berkley
|
}
|
1097 |
|
|
//get the obsoletedGuid
|
1098 |
|
|
String[] obsGuidS = params.get("obsoletedGuid");
|
1099 |
|
|
obsoletedGuid.setValue(obsGuidS[0]);
|
1100 |
|
|
|
1101 |
|
|
if (!im.identifierExists(obsoletedGuid.getValue()))
|
1102 |
|
|
{
|
1103 |
5356
|
berkley
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
1104 |
5353
|
berkley
|
}
|
1105 |
|
|
|
1106 |
|
|
|
1107 |
|
|
logMetacat.debug("Commence update...");
|
1108 |
|
|
|
1109 |
|
|
//get the systemmetadata
|
1110 |
|
|
IBindingFactory bfact =
|
1111 |
|
|
BindingDirectory.getFactory(SystemMetadata.class);
|
1112 |
|
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
1113 |
|
|
SystemMetadata m = (SystemMetadata) uctx.unmarshalDocument(sysmeta, null);
|
1114 |
|
|
|
1115 |
|
|
//do the update
|
1116 |
|
|
try
|
1117 |
|
|
{
|
1118 |
|
|
cs.setParamsFromRequest(request);
|
1119 |
|
|
Identifier rId = cs.update(token, id, object, obsoletedGuid, m);
|
1120 |
|
|
}
|
1121 |
|
|
catch(NotFound e)
|
1122 |
|
|
{
|
1123 |
5356
|
berkley
|
throw new InvalidRequest("1202", "The guid you are trying to update does not exist.");
|
1124 |
5353
|
berkley
|
}
|
1125 |
|
|
|
1126 |
5211
|
jones
|
} else {
|
1127 |
5356
|
berkley
|
throw new InvalidRequest("1000", "Operation must be create or update.");
|
1128 |
5211
|
jones
|
}
|
1129 |
5319
|
jones
|
} catch (NotAuthorized e) {
|
1130 |
|
|
serializeException(e, out);
|
1131 |
|
|
} catch (InvalidToken e) {
|
1132 |
|
|
serializeException(e, out);
|
1133 |
|
|
} catch (ServiceFailure e) {
|
1134 |
|
|
serializeException(e, out);
|
1135 |
|
|
} catch (IdentifierNotUnique e) {
|
1136 |
|
|
serializeException(e, out);
|
1137 |
|
|
} catch (UnsupportedType e) {
|
1138 |
|
|
serializeException(e, out);
|
1139 |
|
|
} catch (InsufficientResources e) {
|
1140 |
|
|
serializeException(e, out);
|
1141 |
|
|
} catch (InvalidSystemMetadata e) {
|
1142 |
|
|
serializeException(e, out);
|
1143 |
|
|
} catch (NotImplemented e) {
|
1144 |
|
|
serializeException(e, out);
|
1145 |
|
|
} catch (InvalidRequest e) {
|
1146 |
|
|
serializeException(e, out);
|
1147 |
5394
|
berkley
|
} /*catch (MessagingException e) {
|
1148 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
1149 |
5319
|
jones
|
serializeException(sf, out);
|
1150 |
5394
|
berkley
|
}*/ catch (IOException e) {
|
1151 |
5356
|
berkley
|
ServiceFailure sf = new ServiceFailure("1000", e.getMessage());
|
1152 |
5319
|
jones
|
serializeException(sf, out);
|
1153 |
5320
|
jones
|
} catch (JiBXException e) {
|
1154 |
|
|
e.printStackTrace(System.out);
|
1155 |
5356
|
berkley
|
InvalidSystemMetadata ism = new InvalidSystemMetadata("1080", e.getMessage());
|
1156 |
5320
|
jones
|
serializeException(ism, out);
|
1157 |
5211
|
jones
|
}
|
1158 |
|
|
}
|
1159 |
|
|
|
1160 |
|
|
/**
|
1161 |
|
|
* Earthgrid API > Put Service > Delete Function : calls MetacatHandler > handleDeleteAction
|
1162 |
|
|
*
|
1163 |
5287
|
jones
|
* @param guid ID of data object to be deleted
|
1164 |
5211
|
jones
|
* @throws IOException
|
1165 |
|
|
*/
|
1166 |
5287
|
jones
|
private void deleteObject(String guid) throws IOException
|
1167 |
|
|
{
|
1168 |
|
|
// Look up the localId for this global identifier
|
1169 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
1170 |
|
|
String localId = "";
|
1171 |
|
|
try {
|
1172 |
|
|
localId = im.getLocalId(guid);
|
1173 |
|
|
} catch (McdbDocNotFoundException e) {
|
1174 |
|
|
// TODO: Need to return the proper DataONE exception
|
1175 |
|
|
}
|
1176 |
|
|
|
1177 |
|
|
params.put("docid", new String[] { localId });
|
1178 |
5211
|
jones
|
PrintWriter out = response.getWriter();
|
1179 |
5450
|
berkley
|
response.setContentType("text/xml");
|
1180 |
5211
|
jones
|
handler.handleDeleteAction(out, params, request, response, username,
|
1181 |
|
|
groupNames);
|
1182 |
|
|
out.close();
|
1183 |
|
|
}
|
1184 |
5370
|
berkley
|
|
1185 |
|
|
/**
|
1186 |
|
|
* set the access perms on a document
|
1187 |
|
|
* @throws IOException
|
1188 |
|
|
*/
|
1189 |
5424
|
berkley
|
private void setaccess() throws Exception
|
1190 |
5370
|
berkley
|
{
|
1191 |
|
|
try
|
1192 |
|
|
{
|
1193 |
|
|
String guid = params.get("guid")[0];
|
1194 |
|
|
Identifier id = new Identifier();
|
1195 |
|
|
id.setValue(guid);
|
1196 |
|
|
AuthToken token = new AuthToken(sessionId);
|
1197 |
|
|
String principal = params.get("principal")[0];
|
1198 |
|
|
String permission = params.get("permission")[0];
|
1199 |
|
|
String permissionType = params.get("permissionType")[0];
|
1200 |
|
|
String permissionOrder = params.get("permissionOrder")[0];
|
1201 |
|
|
String setSystemMetadata = params.get("setsystemmetadata")[0];
|
1202 |
5424
|
berkley
|
boolean ssm = false;
|
1203 |
5370
|
berkley
|
if(setSystemMetadata.equals("true") || setSystemMetadata.equals("TRUE") ||
|
1204 |
5424
|
berkley
|
setSystemMetadata.equals("yes"))
|
1205 |
|
|
{
|
1206 |
|
|
ssm = true;
|
1207 |
5370
|
berkley
|
}
|
1208 |
5424
|
berkley
|
CrudService cs = CrudService.getInstance();
|
1209 |
|
|
cs.setAccess(token, id, principal, permission, permissionType, permissionOrder, ssm);
|
1210 |
5370
|
berkley
|
}
|
1211 |
|
|
catch(Exception e)
|
1212 |
|
|
{
|
1213 |
|
|
printError("Error setting access in ResourceHandler: " + e.getMessage(), response);
|
1214 |
5424
|
berkley
|
throw e;
|
1215 |
5370
|
berkley
|
}
|
1216 |
|
|
}
|
1217 |
5211
|
jones
|
|
1218 |
|
|
/**
|
1219 |
|
|
* Earthgrid API > Authentication Service > Login Function : calls MetacatHandler > handleLoginAction
|
1220 |
|
|
*
|
1221 |
|
|
* @throws IOException
|
1222 |
|
|
*/
|
1223 |
|
|
private void login() throws IOException {
|
1224 |
|
|
PrintWriter out = response.getWriter();
|
1225 |
5450
|
berkley
|
response.setContentType("text/xml");
|
1226 |
5211
|
jones
|
handler.handleLoginAction(out, params, request, response);
|
1227 |
|
|
out.close();
|
1228 |
|
|
}
|
1229 |
|
|
|
1230 |
|
|
/**
|
1231 |
|
|
* Earthgrid API > Authentication Service > Logout Function : calls MetacatHandler > handleLogoutAction
|
1232 |
|
|
*
|
1233 |
|
|
* @throws IOException
|
1234 |
|
|
*/
|
1235 |
|
|
private void logout() throws IOException {
|
1236 |
|
|
PrintWriter out = response.getWriter();
|
1237 |
5450
|
berkley
|
response.setContentType("text/xml");
|
1238 |
5211
|
jones
|
handler.handleLogoutAction(out, params, request, response);
|
1239 |
|
|
out.close();
|
1240 |
|
|
}
|
1241 |
|
|
|
1242 |
|
|
/**
|
1243 |
|
|
* Prints xml response
|
1244 |
|
|
* @param message Message to be displayed
|
1245 |
|
|
* @param response Servlet response that xml message will be printed
|
1246 |
|
|
* */
|
1247 |
|
|
private void printError(String message, HttpServletResponse response) {
|
1248 |
|
|
try {
|
1249 |
|
|
PrintWriter out = response.getWriter();
|
1250 |
|
|
response.setContentType("text/xml");
|
1251 |
|
|
out.println("<?xml version=\"1.0\"?>");
|
1252 |
|
|
out.println("<error>");
|
1253 |
|
|
out.println(message);
|
1254 |
|
|
out.println("</error>");
|
1255 |
|
|
out.close();
|
1256 |
|
|
} catch (IOException e) {
|
1257 |
|
|
e.printStackTrace();
|
1258 |
|
|
}
|
1259 |
|
|
}
|
1260 |
5370
|
berkley
|
|
1261 |
5319
|
jones
|
private void serializeException(BaseException e, OutputStream out) {
|
1262 |
|
|
// TODO: Use content negotiation to determine which return format to use
|
1263 |
|
|
response.setContentType("text/xml");
|
1264 |
|
|
response.setStatus(e.getCode());
|
1265 |
|
|
try {
|
1266 |
|
|
IOUtils.write(e.serialize(BaseException.FMT_XML), out);
|
1267 |
|
|
} catch (IOException e1) {
|
1268 |
|
|
logMetacat.error("Error writing exception to stream. "
|
1269 |
|
|
+ e1.getMessage());
|
1270 |
|
|
}
|
1271 |
|
|
}
|
1272 |
|
|
|
1273 |
5211
|
jones
|
}
|