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/**
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* '$RCSfile$'
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* Purpose: A Class that implements a metadata catalog as a java Servlet
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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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* Authors: Matt Jones, Dan Higgins, Jivka Bojilova, Chad Berkley
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* Release: @release@
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*
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* '$Author: jones $'
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* '$Date: 2004-03-26 15:25:53 -0800 (Fri, 26 Mar 2004) $'
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* '$Revision: 2067 $'
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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;
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import com.oreilly.servlet.multipart.FilePart;
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import com.oreilly.servlet.multipart.MultipartParser;
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import com.oreilly.servlet.multipart.ParamPart;
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import com.oreilly.servlet.multipart.Part;
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import java.io.File;
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import java.io.PrintWriter;
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import java.io.IOException;
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import java.io.StringReader;
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import java.io.FileInputStream;
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import java.io.BufferedInputStream;
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import java.util.Enumeration;
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import java.util.Hashtable;
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import java.util.ResourceBundle;
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import java.util.Random;
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import java.util.PropertyResourceBundle;
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import java.util.Vector;
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import java.net.URL;
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import java.net.MalformedURLException;
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.Connection;
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import java.sql.SQLException;
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import java.lang.reflect.*;
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import java.net.*;
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import java.util.zip.*;
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import javax.servlet.ServletConfig;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletException;
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import javax.servlet.ServletInputStream;
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import javax.servlet.http.HttpServlet;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import javax.servlet.http.HttpSession;
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import javax.servlet.http.HttpUtils;
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import javax.servlet.ServletOutputStream;
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import org.ecoinformatics.eml.EMLParser;
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import edu.ucsb.nceas.utilities.Options;
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import org.xml.sax.SAXException;
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/**
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* A metadata catalog server implemented as a Java Servlet
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*
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* <p>Valid parameters are:<br>
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* action=query -- query the values of all elements and attributes
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* and return a result set of nodes<br>
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* action=squery -- structured query (see pathquery.dtd)<br>
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* action= -- export a zip format for data packadge<br>
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* action=read -- read any metadata/data file from Metacat and from Internet<br>
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* action=insert -- insert an XML document into the database store<br>
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* action=update -- update an XML document that is in the database store<br>
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* action=delete -- delete an XML document from the database store<br>
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* action=validate -- vallidate the xml contained in valtext<br>
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* doctype -- document type list returned by the query (publicID)<br>
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* qformat=xml -- display resultset from query in XML<br>
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* qformat=html -- display resultset from query in HTML<br>
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* qformat=zip -- zip resultset from query<br>
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* docid=34 -- display the document with the document ID number 34<br>
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* doctext -- XML text of the document to load into the database<br>
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* acltext -- XML access text for a document to load into the database<br>
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* dtdtext -- XML DTD text for a new DTD to load into Metacat XML Catalog<br>
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* query -- actual query text (to go with 'action=query' or 'action=squery')<br>
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* valtext -- XML text to be validated<br>
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* abstractpath -- XPath in metadata document to read from<br>
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* action=getaccesscontrol -- retrieve acl info for Metacat document<br>
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* action=getdoctypes -- retrieve all doctypes (publicID)<br>
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* action=getdtdschema -- retrieve a DTD or Schema file<br>
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* action=getdataguide -- retrieve a Data Guide<br>
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* action=getprincipals -- retrieve a list of principals in XML<br>
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* datadoc -- data document name (id)<br>
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* <p>
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* The particular combination of parameters that are valid for each
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* particular action value is quite specific. This documentation
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* will be reorganized to reflect this information.
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*/
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public class MetaCatServlet extends HttpServlet {
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private ServletConfig config = null;
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private ServletContext context = null;
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private String resultStyleURL = null;
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private String xmlcatalogfile = null;
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private String saxparser = null;
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private String datafilepath = null;
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private File dataDirectory = null;
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private String servletpath = null;
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private String htmlpath = null;
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private PropertyResourceBundle options = null;
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private MetaCatUtil util = null;
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private DBConnectionPool connPool = null;
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private Hashtable sessionHash = new Hashtable();
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private static final String PROLOG = "<?xml version=\"1.0\"?>";
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private static final String SUCCESS = "<success>";
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private static final String SUCCESSCLOSE = "</success>";
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private static final String ERROR = "<error>";
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private static final String ERRORCLOSE = "</error>";
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public static final String SCHEMALOCATIONKEYWORD = ":schemaLocation";
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public static final String NONAMESPACELOCATION = ":noNamespaceSchemaLocation";
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public static final String EML2KEYWORD =":eml";
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private static final String CONFIG_DIR = "WEB-INF";
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private static final String CONFIG_NAME = "metacat.properties";
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/**
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* Initialize the servlet by creating appropriate database connections
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*/
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public void init( ServletConfig config ) throws ServletException {
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try {
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super.init( config );
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this.config = config;
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this.context = config.getServletContext();
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System.out.println("MetaCatServlet Initialize");
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// Initialize the properties file for our options
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String dirPath = context.getRealPath(CONFIG_DIR);
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File propertyFile = new File(dirPath,CONFIG_NAME);
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Options options = null;
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try {
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options = Options.initialize(propertyFile);
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MetaCatUtil.debugMessage("Options configured: " +
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options.getOption("configured"), 20);
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} catch (IOException ioe) {
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MetaCatUtil.debugMessage("Error in loading options: "
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+ioe.getMessage(), 20);
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}
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util = new MetaCatUtil();
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//initial DBConnection pool
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connPool = DBConnectionPool.getInstance();
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// Get the configuration file information
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resultStyleURL = util.getOption("resultStyleURL");
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xmlcatalogfile = util.getOption("xmlcatalogfile");
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saxparser = util.getOption("saxparser");
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datafilepath = util.getOption("datafilepath");
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dataDirectory = new File(datafilepath);
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servletpath = util.getOption("servletpath");
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htmlpath = util.getOption("htmlpath");
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} catch ( ServletException ex ) {
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throw ex;
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} catch (SQLException e) {
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MetaCatUtil.debugMessage("Error in MetacatServlet.init: "
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+e.getMessage(), 20);
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}
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}
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/**
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* Close all db connections from the pool
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*/
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public void destroy() {
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// Close all db connection
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System.out.println("Destroying MetacatServlet");
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connPool.release();
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}
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/** Handle "GET" method requests from HTTP clients */
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public void doGet (HttpServletRequest request, HttpServletResponse response)
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throws ServletException, IOException {
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// Process the data and send back the response
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handleGetOrPost(request, response);
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}
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/** Handle "POST" method requests from HTTP clients */
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public void doPost( HttpServletRequest request, HttpServletResponse response)
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throws ServletException, IOException {
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// Process the data and send back the response
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handleGetOrPost(request, response);
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}
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/**
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* Control servlet response depending on the action parameter specified
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*/
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private void handleGetOrPost(HttpServletRequest request,
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HttpServletResponse response)
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throws ServletException, IOException
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{
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if ( util == null ) {
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util = new MetaCatUtil();
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}
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/*MetaCatUtil.debugMessage("Connection pool size: "
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+connPool.getSizeOfDBConnectionPool(),10);
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MetaCatUtil.debugMessage("Free DBConnection number: "
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+connPool.getFreeDBConnectionNumber(), 10);*/
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//If all DBConnection in the pool are free and DBConnection pool
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//size is greater than initial value, shrink the connection pool
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//size to initial value
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DBConnectionPool.shrinkDBConnectionPoolSize();
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//Debug message to print out the method which have a busy DBConnection
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connPool.printMethodNameHavingBusyDBConnection();
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String ctype = request.getContentType();
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if (ctype != null && ctype.startsWith("multipart/form-data")) {
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handleMultipartForm(request, response);
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} else {
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String name = null;
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String[] value = null;
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String[] docid = new String[3];
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Hashtable params = new Hashtable();
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Enumeration paramlist = request.getParameterNames();
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240
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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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// Decode the docid and mouse click information
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if (name.endsWith(".y")) {
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docid[0] = name.substring(0,name.length()-2);
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params.put("docid", docid);
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name = "ypos";
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}
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if (name.endsWith(".x")) {
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name = "xpos";
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}
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255
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params.put(name,value);
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}
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259
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260
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//handle param is emptpy
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261
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if (params.isEmpty() || params == null)
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262
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{
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return;
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264
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}
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265
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266
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//if the user clicked on the input images, decode which image
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//was clicked then set the action.
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268
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String action = ((String[])params.get("action"))[0];
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util.debugMessage("Line 230: Action is: " + action, 1);
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270
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271
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// This block handles session management for the servlet
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272
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// by looking up the current session information for all actions
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273
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// other than "login" and "logout"
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274
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String username = null;
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275
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String password = null;
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276
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String[] groupnames = null;
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277
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String sess_id = null;
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278
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279
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// handle login action
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280
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if (action.equals("login")) {
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281
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PrintWriter out = response.getWriter();
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282
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handleLoginAction(out, params, request, response);
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283
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out.close();
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284
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285
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// handle logout action
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286
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} else if (action.equals("logout")) {
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287
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PrintWriter out = response.getWriter();
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288
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handleLogoutAction(out, params, request, response);
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289
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out.close();
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290
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291
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// handle shrink DBConnection request
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292
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} else if (action.equals("shrink")) {
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293
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PrintWriter out = response.getWriter();
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294
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boolean success = false;
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295
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//If all DBConnection in the pool are free and DBConnection pool
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296
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//size is greater than initial value, shrink the connection pool
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297
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//size to initial value
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298
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success = DBConnectionPool.shrinkConnectionPoolSize();
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299
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if (success)
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300
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{
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301
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//if successfully shrink the pool size to initial value
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302
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out.println("DBConnection Pool shrink successfully");
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303
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}//if
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304
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else
|
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305
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{
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306
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out.println("DBConnection pool couldn't shrink successfully");
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307
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}
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308
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//close out put
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309
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out.close();
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310
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311
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// aware of session expiration on every request
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312
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}
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313
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else
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314
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{
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315
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HttpSession sess = request.getSession(true);
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316
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if (sess.isNew() && !params.containsKey("sessionid")) {
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317
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// session expired or has not been stored b/w user requests
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318
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MetaCatUtil.debugMessage("in session is new or no sessionid", 40);
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319
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username = "public";
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320
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sess.setAttribute("username", username);
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321
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}
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322
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else
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323
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{
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324
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MetaCatUtil.debugMessage("in session is not new or " +
|
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325
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" has sessionid parameter", 40);
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326
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try
|
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327
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{
|
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328
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if(params.containsKey("sessionid"))
|
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329
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{
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330
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sess_id = ((String[])params.get("sessionid"))[0];
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331
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MetaCatUtil.debugMessage("in has sessionid " + sess_id, 40);
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332
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if(sessionHash.containsKey(sess_id))
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333
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{
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334
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MetaCatUtil.debugMessage("find the id " + sess_id +
|
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335
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" in hash table", 40);
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336
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sess = (HttpSession)sessionHash.get(sess_id);
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337
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}
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338
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}
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339
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else
|
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340
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{
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341
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// we already store the session in login, so we don't need here
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342
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/*MetaCatUtil.debugMessage("in no sessionid parameter ", 40);
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343
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sess_id = (String)sess.getId();
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344
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MetaCatUtil.debugMessage("storing the session id "+ sess_id +
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345
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" which has username " + sess.getAttribute("username") +
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346
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" into session hash in handleGetOrPost method", 35);
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347
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sessionHash.put(sess_id, sess);*/
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348
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}
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349
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}
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|
350
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catch(IllegalStateException ise)
|
|
351
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{
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|
352
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System.out.println("error in handleGetOrPost: this shouldn't " +
|
|
353
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"happen: the session should be valid: " +
|
|
354
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ise.getMessage());
|
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355
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}
|
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356
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|
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357
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username = (String)sess.getAttribute("username");
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358
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MetaCatUtil.debugMessage("The user name from session is: "+
|
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359
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username, 20);
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360
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password = (String)sess.getAttribute("password");
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361
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groupnames = (String[])sess.getAttribute("groupnames");
|
|
362
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}
|
|
363
|
|
|
364
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//make user user username should be public
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|
365
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if (username == null || (username.trim().equals("")))
|
|
366
|
{
|
|
367
|
username = "public";
|
|
368
|
}
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|
369
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MetaCatUtil.debugMessage("The user is : "+ username, 5);
|
|
370
|
}
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|
371
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// Now that we know the session is valid, we can delegate the request
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|
372
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// to a particular action handler
|
|
373
|
if(action.equals("query")) {
|
|
374
|
PrintWriter out = response.getWriter();
|
|
375
|
handleQuery(out,params,response,username,groupnames,sess_id);
|
|
376
|
out.close();
|
|
377
|
} else if(action.equals("squery")) {
|
|
378
|
PrintWriter out = response.getWriter();
|
|
379
|
if(params.containsKey("query")) {
|
|
380
|
handleSQuery(out, params,response,username,groupnames,sess_id);
|
|
381
|
out.close();
|
|
382
|
} else {
|
|
383
|
out.println("Illegal action squery without \"query\" parameter");
|
|
384
|
out.close();
|
|
385
|
}
|
|
386
|
} else if (action.equals("export")) {
|
|
387
|
|
|
388
|
handleExportAction(params, response, username, groupnames, password);
|
|
389
|
} else if (action.equals("read")) {
|
|
390
|
handleReadAction(params, response, username,password, groupnames);
|
|
391
|
} else if (action.equals("readinlinedata")) {
|
|
392
|
handleReadInlineDataAction(params, response, username,
|
|
393
|
password, groupnames);
|
|
394
|
} else if (action.equals("insert") || action.equals("update")) {
|
|
395
|
PrintWriter out = response.getWriter();
|
|
396
|
if ( (username != null) && !username.equals("public") ) {
|
|
397
|
handleInsertOrUpdateAction(out,params,username,groupnames);
|
|
398
|
} else {
|
|
399
|
out.println("Permission denied for user "+username +" " + action);
|
|
400
|
}
|
|
401
|
out.close();
|
|
402
|
} else if (action.equals("delete")) {
|
|
403
|
PrintWriter out = response.getWriter();
|
|
404
|
if ( (username != null) && !username.equals("public") ) {
|
|
405
|
handleDeleteAction(out, params, response, username, groupnames);
|
|
406
|
} else {
|
|
407
|
out.println("Permission denied for " + action);
|
|
408
|
}
|
|
409
|
out.close();
|
|
410
|
} else if (action.equals("validate")) {
|
|
411
|
PrintWriter out = response.getWriter();
|
|
412
|
handleValidateAction(out, params);
|
|
413
|
out.close();
|
|
414
|
} else if (action.equals("setaccess")) {
|
|
415
|
PrintWriter out = response.getWriter();
|
|
416
|
handleSetAccessAction(out, params, username);
|
|
417
|
out.close();
|
|
418
|
} else if (action.equals("getaccesscontrol")) {
|
|
419
|
PrintWriter out = response.getWriter();
|
|
420
|
handleGetAccessControlAction(out,params,response,username,groupnames);
|
|
421
|
out.close();
|
|
422
|
} else if (action.equals("getprincipals")) {
|
|
423
|
PrintWriter out = response.getWriter();
|
|
424
|
handleGetPrincipalsAction(out, username, password);
|
|
425
|
out.close();
|
|
426
|
} else if (action.equals("getdoctypes")) {
|
|
427
|
PrintWriter out = response.getWriter();
|
|
428
|
handleGetDoctypesAction(out, params, response);
|
|
429
|
out.close();
|
|
430
|
} else if (action.equals("getdtdschema")) {
|
|
431
|
PrintWriter out = response.getWriter();
|
|
432
|
handleGetDTDSchemaAction(out, params, response);
|
|
433
|
out.close();
|
|
434
|
} else if (action.equals("getlastdocid")) {
|
|
435
|
PrintWriter out = response.getWriter();
|
|
436
|
handleGetMaxDocidAction(out, params, response);
|
|
437
|
out.close();
|
|
438
|
} else if (action.equals("getrevisionanddoctype")) {
|
|
439
|
PrintWriter out = response.getWriter();
|
|
440
|
handleGetRevisionAndDocTypeAction(out, params);
|
|
441
|
out.close();
|
|
442
|
} else if (action.equals("login") || action.equals("logout")) {
|
|
443
|
} else if (action.equals("protocoltest")) {
|
|
444
|
String testURL = "metacat://dev.nceas.ucsb.edu/NCEAS.897766.9";
|
|
445
|
try {
|
|
446
|
testURL = ((String[])params.get("url"))[0];
|
|
447
|
} catch (Throwable t) {
|
|
448
|
}
|
|
449
|
String phandler = System.getProperty("java.protocol.handler.pkgs");
|
|
450
|
response.setContentType("text/html");
|
|
451
|
PrintWriter out = response.getWriter();
|
|
452
|
out.println("<body bgcolor=\"white\">");
|
|
453
|
out.println("<p>Handler property: <code>" + phandler + "</code></p>");
|
|
454
|
out.println("<p>Starting test for:<br>");
|
|
455
|
out.println(" " + testURL + "</p>");
|
|
456
|
try {
|
|
457
|
URL u = new URL(testURL);
|
|
458
|
out.println("<pre>");
|
|
459
|
out.println("Protocol: " + u.getProtocol());
|
|
460
|
out.println(" Host: " + u.getHost());
|
|
461
|
out.println(" Port: " + u.getPort());
|
|
462
|
out.println(" Path: " + u.getPath());
|
|
463
|
out.println(" Ref: " + u.getRef());
|
|
464
|
String pquery = u.getQuery();
|
|
465
|
out.println(" Query: " + pquery);
|
|
466
|
out.println(" Params: ");
|
|
467
|
if (pquery != null) {
|
|
468
|
Hashtable qparams = util.parseQuery(u.getQuery());
|
|
469
|
for (Enumeration en = qparams.keys(); en.hasMoreElements(); ) {
|
|
470
|
String pname = (String)en.nextElement();
|
|
471
|
String pvalue = (String)qparams.get(pname);
|
|
472
|
out.println(" " + pname + ": " + pvalue);
|
|
473
|
}
|
|
474
|
}
|
|
475
|
out.println("</pre>");
|
|
476
|
out.println("</body>");
|
|
477
|
out.close();
|
|
478
|
} catch (MalformedURLException mue) {
|
|
479
|
System.out.println("bad url from MetacatServlet.handleGetOrPost");
|
|
480
|
out.println(mue.getMessage());
|
|
481
|
mue.printStackTrace(out);
|
|
482
|
out.close();
|
|
483
|
}
|
|
484
|
} else {
|
|
485
|
PrintWriter out = response.getWriter();
|
|
486
|
out.println("<?xml version=\"1.0\"?>");
|
|
487
|
out.println("<error>");
|
|
488
|
out.println("Error: action not registered. Please report this error.");
|
|
489
|
out.println("</error>");
|
|
490
|
out.close();
|
|
491
|
}
|
|
492
|
|
|
493
|
//util.closeConnections();
|
|
494
|
// Close the stream to the client
|
|
495
|
//out.close();
|
|
496
|
}
|
|
497
|
}
|
|
498
|
|
|
499
|
// LOGIN & LOGOUT SECTION
|
|
500
|
/**
|
|
501
|
* Handle the login request. Create a new session object.
|
|
502
|
* Do user authentication through the session.
|
|
503
|
*/
|
|
504
|
private void handleLoginAction(PrintWriter out, Hashtable params,
|
|
505
|
HttpServletRequest request, HttpServletResponse response) {
|
|
506
|
|
|
507
|
AuthSession sess = null;
|
|
508
|
String un = ((String[])params.get("username"))[0];
|
|
509
|
MetaCatUtil.debugMessage("user " + un + " try to login", 20);
|
|
510
|
String pw = ((String[])params.get("password"))[0];
|
|
511
|
String action = ((String[])params.get("action"))[0];
|
|
512
|
String qformat = ((String[])params.get("qformat"))[0];
|
|
513
|
|
|
514
|
try {
|
|
515
|
sess = new AuthSession();
|
|
516
|
} catch (Exception e) {
|
|
517
|
System.out.println("error in MetacatServlet.handleLoginAction: " +
|
|
518
|
e.getMessage());
|
|
519
|
out.println(e.getMessage());
|
|
520
|
return;
|
|
521
|
}
|
|
522
|
boolean isValid = sess.authenticate(request, un, pw);
|
|
523
|
|
|
524
|
//if it is authernticate is true, store the session
|
|
525
|
if (isValid)
|
|
526
|
{
|
|
527
|
HttpSession session = sess.getSessions();
|
|
528
|
String id = session.getId();
|
|
529
|
MetaCatUtil.debugMessage("Store session id " + id +
|
|
530
|
"which has username" + session.getAttribute("username")+
|
|
531
|
" into hash in login method", 35);
|
|
532
|
sessionHash.put(id, session);
|
|
533
|
}
|
|
534
|
|
|
535
|
// format and transform the output
|
|
536
|
if (qformat.equals("xml")) {
|
|
537
|
response.setContentType("text/xml");
|
|
538
|
out.println(sess.getMessage());
|
|
539
|
} else {
|
|
540
|
|
|
541
|
try {
|
|
542
|
|
|
543
|
DBTransform trans = new DBTransform();
|
|
544
|
response.setContentType("text/html");
|
|
545
|
trans.transformXMLDocument(sess.getMessage(), "-//NCEAS//login//EN",
|
|
546
|
"-//W3C//HTML//EN", qformat, out, null);
|
|
547
|
|
|
548
|
} catch(Exception e) {
|
|
549
|
|
|
550
|
MetaCatUtil.debugMessage("Error in MetaCatServlet.handleLoginAction: "
|
|
551
|
+e.getMessage(), 30);
|
|
552
|
}
|
|
553
|
|
|
554
|
// any output is returned
|
|
555
|
}
|
|
556
|
}
|
|
557
|
|
|
558
|
/**
|
|
559
|
* Handle the logout request. Close the connection.
|
|
560
|
*/
|
|
561
|
private void handleLogoutAction(PrintWriter out, Hashtable params,
|
|
562
|
HttpServletRequest request, HttpServletResponse response) {
|
|
563
|
|
|
564
|
String qformat = ((String[])params.get("qformat"))[0];
|
|
565
|
|
|
566
|
// close the connection
|
|
567
|
HttpSession sess = request.getSession(false);
|
|
568
|
MetaCatUtil.debugMessage("After get session in logout request", 40);
|
|
569
|
if (sess != null)
|
|
570
|
{
|
|
571
|
MetaCatUtil.debugMessage("The session id " + sess.getId() +
|
|
572
|
" will be invalidate in logout action", 30);
|
|
573
|
MetaCatUtil.debugMessage("The session contains user " +
|
|
574
|
sess.getAttribute("username") +
|
|
575
|
" will be invalidate in logout action", 30);
|
|
576
|
sess.invalidate();
|
|
577
|
}
|
|
578
|
|
|
579
|
// produce output
|
|
580
|
StringBuffer output = new StringBuffer();
|
|
581
|
output.append("<?xml version=\"1.0\"?>");
|
|
582
|
output.append("<logout>");
|
|
583
|
output.append("User logged out");
|
|
584
|
output.append("</logout>");
|
|
585
|
|
|
586
|
//format and transform the output
|
|
587
|
if (qformat.equals("xml")) {
|
|
588
|
response.setContentType("text/xml");
|
|
589
|
out.println(output.toString());
|
|
590
|
} else {
|
|
591
|
|
|
592
|
try {
|
|
593
|
|
|
594
|
DBTransform trans = new DBTransform();
|
|
595
|
response.setContentType("text/html");
|
|
596
|
trans.transformXMLDocument(output.toString(), "-//NCEAS//login//EN",
|
|
597
|
"-//W3C//HTML//EN", qformat, out, null);
|
|
598
|
|
|
599
|
} catch(Exception e) {
|
|
600
|
|
|
601
|
MetaCatUtil.debugMessage("Error in MetaCatServlet.handleLogoutAction"
|
|
602
|
+e.getMessage(), 30);
|
|
603
|
}
|
|
604
|
}
|
|
605
|
}
|
|
606
|
// END OF LOGIN & LOGOUT SECTION
|
|
607
|
|
|
608
|
// SQUERY & QUERY SECTION
|
|
609
|
/**
|
|
610
|
* Retreive the squery xml, execute it and display it
|
|
611
|
*
|
|
612
|
* @param out the output stream to the client
|
|
613
|
* @param params the Hashtable of parameters that should be included
|
|
614
|
* in the squery.
|
|
615
|
* @param response the response object linked to the client
|
|
616
|
* @param conn the database connection
|
|
617
|
*/
|
|
618
|
protected void handleSQuery(PrintWriter out, Hashtable params,
|
|
619
|
HttpServletResponse response, String user, String[] groups,
|
|
620
|
String sessionid)
|
|
621
|
{
|
|
622
|
String xmlquery = ((String[])params.get("query"))[0];
|
|
623
|
String qformat = ((String[])params.get("qformat"))[0];
|
|
624
|
String resultdoc = null;
|
|
625
|
MetaCatUtil.debugMessage("xmlquery: "+xmlquery, 30);
|
|
626
|
double startTime = System.currentTimeMillis()/1000;
|
|
627
|
Hashtable doclist = runQuery(xmlquery, user, groups);
|
|
628
|
double docListTime = System.currentTimeMillis()/1000;
|
|
629
|
MetaCatUtil.debugMessage("Time for getting doc list: "
|
|
630
|
+(docListTime-startTime), 30);
|
|
631
|
|
|
632
|
resultdoc = createResultDocument(doclist, transformQuery(xmlquery));
|
|
633
|
double toStringTime = System.currentTimeMillis()/1000;
|
|
634
|
MetaCatUtil.debugMessage("Time to create xml string: "
|
|
635
|
+(toStringTime-docListTime), 30);
|
|
636
|
//format and transform the results
|
|
637
|
double outPutTime = 0;
|
|
638
|
if(qformat.equals("xml")) {
|
|
639
|
response.setContentType("text/xml");
|
|
640
|
out.println(resultdoc);
|
|
641
|
outPutTime = System.currentTimeMillis()/1000;
|
|
642
|
MetaCatUtil.debugMessage("Output time: "+(outPutTime-toStringTime), 30);
|
|
643
|
} else {
|
|
644
|
transformResultset(resultdoc, response, out, qformat, sessionid, params);
|
|
645
|
outPutTime = System.currentTimeMillis()/1000;
|
|
646
|
MetaCatUtil.debugMessage("Output time: "+(outPutTime-toStringTime), 30);
|
|
647
|
}
|
|
648
|
}
|
|
649
|
|
|
650
|
/**
|
|
651
|
* Create the xml query, execute it and display the results.
|
|
652
|
*
|
|
653
|
* @param out the output stream to the client
|
|
654
|
* @param params the Hashtable of parameters that should be included
|
|
655
|
* in the squery.
|
|
656
|
* @param response the response object linked to the client
|
|
657
|
*/
|
|
658
|
protected void handleQuery(PrintWriter out, Hashtable params,
|
|
659
|
HttpServletResponse response, String user, String[] groups,
|
|
660
|
String sessionid)
|
|
661
|
{
|
|
662
|
//create the query and run it
|
|
663
|
String xmlquery = DBQuery.createSQuery(params);
|
|
664
|
Hashtable doclist = runQuery(xmlquery, user, groups);
|
|
665
|
String qformat = ((String[])params.get("qformat"))[0];
|
|
666
|
String resultdoc = null;
|
|
667
|
|
|
668
|
resultdoc = createResultDocument(doclist, transformQuery(params));
|
|
669
|
|
|
670
|
//format and transform the results
|
|
671
|
if(qformat.equals("xml")) {
|
|
672
|
response.setContentType("text/xml");
|
|
673
|
out.println(resultdoc);
|
|
674
|
} else {
|
|
675
|
transformResultset(resultdoc, response, out, qformat, sessionid, params);
|
|
676
|
}
|
|
677
|
}
|
|
678
|
|
|
679
|
/**
|
|
680
|
* Removes the <?xml version="x"?> tag from the beginning of xmlquery
|
|
681
|
* so it can properly be placed in the <query> tag of the resultset.
|
|
682
|
* This method is overwritable so that other applications can customize
|
|
683
|
* the structure of what is in the <query> tag.
|
|
684
|
*
|
|
685
|
* @param xmlquery is the query to remove the <?xml version="x"?> tag from.
|
|
686
|
*/
|
|
687
|
protected String transformQuery(Hashtable params)
|
|
688
|
{
|
|
689
|
//DBQuery.createSQuery is a re-calling of a previously called
|
|
690
|
//function but it is necessary
|
|
691
|
//so that overriding methods have access to the params hashtable
|
|
692
|
String xmlquery = DBQuery.createSQuery(params);
|
|
693
|
//the <?xml version="1.0"?> tag is the first 22 characters of the
|
|
694
|
xmlquery = xmlquery.trim();
|
|
695
|
int index = xmlquery.indexOf("?>");
|
|
696
|
if ( index != -1 )
|
|
697
|
{
|
|
698
|
//have <?xml version="1.0"?>
|
|
699
|
return xmlquery.substring(index + 2, xmlquery.length());
|
|
700
|
}
|
|
701
|
else
|
|
702
|
{
|
|
703
|
// don't have <?xml version="1.0"?>
|
|
704
|
return xmlquery;
|
|
705
|
}
|
|
706
|
}
|
|
707
|
|
|
708
|
/**
|
|
709
|
* removes the <?xml version="1.0"?> tag from the beginning. This takes a
|
|
710
|
* string as a param instead of a hashtable.
|
|
711
|
*
|
|
712
|
* @param xmlquery a string representing a query.
|
|
713
|
*/
|
|
714
|
protected String transformQuery(String xmlquery)
|
|
715
|
{
|
|
716
|
xmlquery = xmlquery.trim();
|
|
717
|
int index = xmlquery.indexOf("?>");
|
|
718
|
if (index != -1)
|
|
719
|
{
|
|
720
|
return xmlquery.substring(index + 2, xmlquery.length());
|
|
721
|
}
|
|
722
|
else
|
|
723
|
{
|
|
724
|
return xmlquery;
|
|
725
|
}
|
|
726
|
}
|
|
727
|
|
|
728
|
/**
|
|
729
|
* Run the query and return a hashtable of results.
|
|
730
|
*
|
|
731
|
* @param xmlquery the query to run
|
|
732
|
*/
|
|
733
|
private Hashtable runQuery(String xmlquery, String user, String[] groups)
|
|
734
|
{
|
|
735
|
Hashtable doclist=null;
|
|
736
|
|
|
737
|
try
|
|
738
|
{
|
|
739
|
|
|
740
|
DBQuery queryobj = new DBQuery(saxparser);
|
|
741
|
doclist = queryobj.findDocuments(new StringReader(xmlquery),user,groups);
|
|
742
|
|
|
743
|
return doclist;
|
|
744
|
}
|
|
745
|
catch (Exception e)
|
|
746
|
{
|
|
747
|
|
|
748
|
MetaCatUtil.debugMessage("Error in MetacatServlet.runQuery: "
|
|
749
|
+ e.getMessage(), 30);
|
|
750
|
doclist = null;
|
|
751
|
return doclist;
|
|
752
|
}
|
|
753
|
}
|
|
754
|
|
|
755
|
/**
|
|
756
|
* Transorms an xml resultset document to html and sends it to the browser
|
|
757
|
*
|
|
758
|
* @param resultdoc the string representation of the document that needs
|
|
759
|
* to be transformed.
|
|
760
|
* @param response the HttpServletResponse object bound to the client.
|
|
761
|
* @param out the output stream to the client
|
|
762
|
* @param qformat the name of the style-set to use for transformations
|
|
763
|
*/
|
|
764
|
protected void transformResultset(String resultdoc,
|
|
765
|
HttpServletResponse response,
|
|
766
|
PrintWriter out, String qformat,
|
|
767
|
String sessionid, Hashtable params)
|
|
768
|
{
|
|
769
|
|
|
770
|
try {
|
|
771
|
|
|
772
|
DBTransform trans = new DBTransform();
|
|
773
|
response.setContentType("text/html");
|
|
774
|
trans.transformXMLDocument(resultdoc, "-//NCEAS//resultset//EN",
|
|
775
|
"-//W3C//HTML//EN", qformat, out, params,
|
|
776
|
sessionid);
|
|
777
|
|
|
778
|
}
|
|
779
|
catch(Exception e)
|
|
780
|
{
|
|
781
|
|
|
782
|
MetaCatUtil.debugMessage("Error in MetaCatServlet.transformResultset:"
|
|
783
|
+e.getMessage(), 30);
|
|
784
|
}
|
|
785
|
}
|
|
786
|
|
|
787
|
/**
|
|
788
|
* Transforms a hashtable of documents to an xml or html result.
|
|
789
|
*
|
|
790
|
* @param doclist- the hashtable to transform
|
|
791
|
* @param xmlquery- the query that returned the doclist result
|
|
792
|
*/
|
|
793
|
protected String createResultDocument(Hashtable doclist, String xmlquery)
|
|
794
|
{
|
|
795
|
// Create a buffer to hold the xml result
|
|
796
|
StringBuffer resultset = new StringBuffer();
|
|
797
|
|
|
798
|
// Print the resulting root nodes
|
|
799
|
String docid = null;
|
|
800
|
String document = null;
|
|
801
|
resultset.append("<?xml version=\"1.0\"?>\n");
|
|
802
|
resultset.append("<resultset>\n");
|
|
803
|
|
|
804
|
resultset.append(" <query>" + xmlquery + "</query>");
|
|
805
|
|
|
806
|
if(doclist != null)
|
|
807
|
{
|
|
808
|
Enumeration doclistkeys = doclist.keys();
|
|
809
|
while (doclistkeys.hasMoreElements())
|
|
810
|
{
|
|
811
|
docid = (String)doclistkeys.nextElement();
|
|
812
|
document = (String)doclist.get(docid);
|
|
813
|
resultset.append(" <document>" + document + "</document>");
|
|
814
|
}
|
|
815
|
}
|
|
816
|
|
|
817
|
resultset.append("</resultset>");
|
|
818
|
return resultset.toString();
|
|
819
|
}
|
|
820
|
// END OF SQUERY & QUERY SECTION
|
|
821
|
|
|
822
|
//Exoport section
|
|
823
|
/**
|
|
824
|
* Handle the "export" request of data package from Metacat in zip format
|
|
825
|
* @param params the Hashtable of HTTP request parameters
|
|
826
|
* @param response the HTTP response object linked to the client
|
|
827
|
* @param user the username sent the request
|
|
828
|
* @param groups the user's groupnames
|
|
829
|
*/
|
|
830
|
private void handleExportAction(Hashtable params,
|
|
831
|
HttpServletResponse response, String user, String[] groups, String passWord)
|
|
832
|
{
|
|
833
|
// Output stream
|
|
834
|
ServletOutputStream out = null;
|
|
835
|
// Zip output stream
|
|
836
|
ZipOutputStream zOut = null;
|
|
837
|
DocumentImpl docImpls=null;
|
|
838
|
DBQuery queryObj=null;
|
|
839
|
|
|
840
|
String[] docs = new String[10];
|
|
841
|
String docId = "";
|
|
842
|
|
|
843
|
try
|
|
844
|
{
|
|
845
|
// read the params
|
|
846
|
if (params.containsKey("docid"))
|
|
847
|
{
|
|
848
|
docs = (String[])params.get("docid");
|
|
849
|
}//if
|
|
850
|
// Create a DBuery to handle export
|
|
851
|
queryObj = new DBQuery(saxparser);
|
|
852
|
// Get the docid
|
|
853
|
docId=docs[0];
|
|
854
|
// Make sure the client specify docid
|
|
855
|
if (docId == null || docId.equals(""))
|
|
856
|
{
|
|
857
|
response.setContentType("text/xml"); //MIME type
|
|
858
|
// Get a printwriter
|
|
859
|
PrintWriter pw = response.getWriter();
|
|
860
|
// Send back message
|
|
861
|
pw.println("<?xml version=\"1.0\"?>");
|
|
862
|
pw.println("<error>");
|
|
863
|
pw.println("You didn't specify requested docid");
|
|
864
|
pw.println("</error>");
|
|
865
|
// Close printwriter
|
|
866
|
pw.close();
|
|
867
|
return;
|
|
868
|
}//if
|
|
869
|
// Get output stream
|
|
870
|
out = response.getOutputStream();
|
|
871
|
response.setContentType("application/zip"); //MIME type
|
|
872
|
zOut = new ZipOutputStream(out);
|
|
873
|
zOut =queryObj.getZippedPackage(docId, out, user, groups, passWord);
|
|
874
|
zOut.finish(); //terminate the zip file
|
|
875
|
zOut.close(); //close the zip stream
|
|
876
|
|
|
877
|
}//try
|
|
878
|
catch (Exception e)
|
|
879
|
{
|
|
880
|
try
|
|
881
|
{
|
|
882
|
response.setContentType("text/xml"); //MIME type
|
|
883
|
// Send error message back
|
|
884
|
if (out != null)
|
|
885
|
{
|
|
886
|
PrintWriter pw = new PrintWriter(out);
|
|
887
|
pw.println("<?xml version=\"1.0\"?>");
|
|
888
|
pw.println("<error>");
|
|
889
|
pw.println(e.getMessage());
|
|
890
|
pw.println("</error>");
|
|
891
|
// Close printwriter
|
|
892
|
pw.close();
|
|
893
|
// Close output stream
|
|
894
|
out.close();
|
|
895
|
}//if
|
|
896
|
// Close zip output stream
|
|
897
|
if ( zOut != null )
|
|
898
|
{
|
|
899
|
zOut.close();
|
|
900
|
}//if
|
|
901
|
}//try
|
|
902
|
catch (IOException ioe)
|
|
903
|
{
|
|
904
|
MetaCatUtil.debugMessage("Problem with the servlet output " +
|
|
905
|
"in MetacatServlet.handleExportAction: " +
|
|
906
|
ioe.getMessage(), 30);
|
|
907
|
}//catch
|
|
908
|
|
|
909
|
MetaCatUtil.debugMessage("Error in MetacatServlet.handleExportAction: " +
|
|
910
|
e.getMessage(), 30);
|
|
911
|
e.printStackTrace(System.out);
|
|
912
|
|
|
913
|
}//catch
|
|
914
|
|
|
915
|
}//handleExportAction
|
|
916
|
|
|
917
|
|
|
918
|
//read inline data section
|
|
919
|
/**
|
|
920
|
* In eml2 document, the xml can have inline data and data was stripped off
|
|
921
|
* and store in file system. This action can be used to read inline data only
|
|
922
|
* @param params the Hashtable of HTTP request parameters
|
|
923
|
* @param response the HTTP response object linked to the client
|
|
924
|
* @param user the username sent the request
|
|
925
|
* @param groups the user's groupnames
|
|
926
|
*/
|
|
927
|
private void handleReadInlineDataAction(Hashtable params,
|
|
928
|
HttpServletResponse response,
|
|
929
|
String user, String passWord,
|
|
930
|
String[] groups)
|
|
931
|
{
|
|
932
|
String[] docs = new String[10];
|
|
933
|
String inlineDataId = null;
|
|
934
|
String docId = "";
|
|
935
|
ServletOutputStream out = null;
|
|
936
|
|
|
937
|
try
|
|
938
|
{
|
|
939
|
// read the params
|
|
940
|
if (params.containsKey("inlinedataid"))
|
|
941
|
{
|
|
942
|
docs = (String[])params.get("inlinedataid");
|
|
943
|
}//if
|
|
944
|
// Get the docid
|
|
945
|
inlineDataId=docs[0];
|
|
946
|
// Make sure the client specify docid
|
|
947
|
if (inlineDataId == null || inlineDataId.equals(""))
|
|
948
|
{
|
|
949
|
throw new Exception("You didn't specify requested inlinedataid");
|
|
950
|
}//if
|
|
951
|
|
|
952
|
// check for permission
|
|
953
|
docId = MetaCatUtil.getDocIdWithoutRevFromInlineDataID(inlineDataId);
|
|
954
|
PermissionController controller = new PermissionController(docId);
|
|
955
|
// check top level read permission
|
|
956
|
if (!controller.hasPermission(user, groups,
|
|
957
|
AccessControlInterface.READSTRING))
|
|
958
|
{
|
|
959
|
throw new Exception("User "+ user + " doesn't have permission "+
|
|
960
|
" to read document " + docId);
|
|
961
|
}//if
|
|
962
|
// if the document has subtree control, we need to check subtree control
|
|
963
|
else if(controller.hasSubTreeAccessControl())
|
|
964
|
{
|
|
965
|
// get node id for inlinedata
|
|
966
|
long nodeId=getInlineDataNodeId(inlineDataId, docId);
|
|
967
|
if (!controller.hasPermissionForSubTreeNode(user, groups,
|
|
968
|
AccessControlInterface.READSTRING, nodeId))
|
|
969
|
{
|
|
970
|
throw new Exception("User "+ user + " doesn't have permission "+
|
|
971
|
" to read inlinedata " + inlineDataId);
|
|
972
|
}//if
|
|
973
|
|
|
974
|
}//else
|
|
975
|
|
|
976
|
// Get output stream
|
|
977
|
out = response.getOutputStream();
|
|
978
|
// read the inline data from the file
|
|
979
|
String inlinePath = MetaCatUtil.getOption("inlinedatafilepath");
|
|
980
|
File lineData = new File(inlinePath, inlineDataId);
|
|
981
|
FileInputStream input = new FileInputStream(lineData);
|
|
982
|
byte [] buffer = new byte[4*1024];
|
|
983
|
int bytes = input.read(buffer);
|
|
984
|
while (bytes != -1)
|
|
985
|
{
|
|
986
|
out.write(buffer, 0, bytes);
|
|
987
|
bytes = input.read(buffer);
|
|
988
|
}
|
|
989
|
out.close();
|
|
990
|
|
|
991
|
}//try
|
|
992
|
catch (Exception e)
|
|
993
|
{
|
|
994
|
try
|
|
995
|
{
|
|
996
|
PrintWriter pw = null;
|
|
997
|
// Send error message back
|
|
998
|
if (out != null)
|
|
999
|
{
|
|
1000
|
pw = new PrintWriter(out);
|
|
1001
|
}//if
|
|
1002
|
else
|
|
1003
|
{
|
|
1004
|
pw = response.getWriter();
|
|
1005
|
}
|
|
1006
|
pw.println("<?xml version=\"1.0\"?>");
|
|
1007
|
pw.println("<error>");
|
|
1008
|
pw.println(e.getMessage());
|
|
1009
|
pw.println("</error>");
|
|
1010
|
// Close printwriter
|
|
1011
|
pw.close();
|
|
1012
|
// Close output stream if out is not null
|
|
1013
|
if (out != null)
|
|
1014
|
{
|
|
1015
|
out.close();
|
|
1016
|
}
|
|
1017
|
}//try
|
|
1018
|
catch (IOException ioe)
|
|
1019
|
{
|
|
1020
|
MetaCatUtil.debugMessage("Problem with the servlet output " +
|
|
1021
|
"in MetacatServlet.handleExportAction: " +
|
|
1022
|
ioe.getMessage(), 30);
|
|
1023
|
}//catch
|
|
1024
|
|
|
1025
|
MetaCatUtil.debugMessage("Error in MetacatServlet.handleReadInlineDataAction: "
|
|
1026
|
+ e.getMessage(), 30);
|
|
1027
|
|
|
1028
|
}//catch
|
|
1029
|
|
|
1030
|
}//handleReadInlineDataAction
|
|
1031
|
|
|
1032
|
/*
|
|
1033
|
* Get the nodeid from xml_nodes for the inlinedataid
|
|
1034
|
*/
|
|
1035
|
private long getInlineDataNodeId(String inLineDataId, String docId)
|
|
1036
|
throws SQLException
|
|
1037
|
{
|
|
1038
|
long nodeId = 0;
|
|
1039
|
String INLINE = "inline";
|
|
1040
|
boolean hasRow;
|
|
1041
|
PreparedStatement pStmt = null;
|
|
1042
|
DBConnection conn = null;
|
|
1043
|
int serialNumber = -1;
|
|
1044
|
String sql ="SELECT nodeid FROM xml_nodes WHERE docid=? AND nodedata=? " +
|
|
1045
|
"AND nodetype='TEXT' AND parentnodeid IN " +
|
|
1046
|
"(SELECT nodeid FROM xml_nodes WHERE docid=? AND " +
|
|
1047
|
"nodetype='ELEMENT' AND nodename='" + INLINE + "')";
|
|
1048
|
|
|
1049
|
try
|
|
1050
|
{
|
|
1051
|
//check out DBConnection
|
|
1052
|
conn=DBConnectionPool.getDBConnection("AccessControlList.isAllowFirst");
|
|
1053
|
serialNumber=conn.getCheckOutSerialNumber();
|
|
1054
|
|
|
1055
|
pStmt = conn.prepareStatement(sql);
|
|
1056
|
//bind value
|
|
1057
|
pStmt.setString(1, docId);//docid
|
|
1058
|
pStmt.setString(2, inLineDataId);//inlinedataid
|
|
1059
|
pStmt.setString(3, docId);
|
|
1060
|
// excute query
|
|
1061
|
pStmt.execute();
|
|
1062
|
ResultSet rs = pStmt.getResultSet();
|
|
1063
|
hasRow=rs.next();
|
|
1064
|
// get result
|
|
1065
|
if (hasRow)
|
|
1066
|
{
|
|
1067
|
nodeId = rs.getLong(1);
|
|
1068
|
}//if
|
|
1069
|
|
|
1070
|
}//try
|
|
1071
|
catch (SQLException e)
|
|
1072
|
{
|
|
1073
|
throw e;
|
|
1074
|
}
|
|
1075
|
finally
|
|
1076
|
{
|
|
1077
|
try
|
|
1078
|
{
|
|
1079
|
pStmt.close();
|
|
1080
|
}
|
|
1081
|
finally
|
|
1082
|
{
|
|
1083
|
DBConnectionPool.returnDBConnection(conn, serialNumber);
|
|
1084
|
}
|
|
1085
|
}
|
|
1086
|
MetaCatUtil.debugMessage("The nodeid for inlinedataid " + inLineDataId +
|
|
1087
|
" is: "+nodeId, 35);
|
|
1088
|
return nodeId;
|
|
1089
|
}
|
|
1090
|
|
|
1091
|
|
|
1092
|
|
|
1093
|
// READ SECTION
|
|
1094
|
/**
|
|
1095
|
* Handle the "read" request of metadata/data files from Metacat
|
|
1096
|
* or any files from Internet;
|
|
1097
|
* transformed metadata XML document into HTML presentation if requested;
|
|
1098
|
* zip files when more than one were requested.
|
|
1099
|
*
|
|
1100
|
* @param params the Hashtable of HTTP request parameters
|
|
1101
|
* @param response the HTTP response object linked to the client
|
|
1102
|
* @param user the username sent the request
|
|
1103
|
* @param groups the user's groupnames
|
|
1104
|
*/
|
|
1105
|
private void handleReadAction(Hashtable params, HttpServletResponse response,
|
|
1106
|
String user, String passWord, String[] groups)
|
|
1107
|
{
|
|
1108
|
ServletOutputStream out = null;
|
|
1109
|
ZipOutputStream zout = null;
|
|
1110
|
PrintWriter pw = null;
|
|
1111
|
boolean zip = false;
|
|
1112
|
boolean withInlineData = true;
|
|
1113
|
|
|
1114
|
try {
|
|
1115
|
String[] docs = new String[0];
|
|
1116
|
String docid = "";
|
|
1117
|
String qformat = "";
|
|
1118
|
String abstrpath = null;
|
|
1119
|
|
|
1120
|
// read the params
|
|
1121
|
if (params.containsKey("docid")) {
|
|
1122
|
docs = (String[])params.get("docid");
|
|
1123
|
}
|
|
1124
|
if (params.containsKey("qformat")) {
|
|
1125
|
qformat = ((String[])params.get("qformat"))[0];
|
|
1126
|
}
|
|
1127
|
// the param for only metadata (eml)
|
|
1128
|
if (params.containsKey("inlinedata"))
|
|
1129
|
{
|
|
1130
|
|
|
1131
|
String inlineData = ((String[])params.get("inlinedata"))[0];
|
|
1132
|
if (inlineData.equalsIgnoreCase("false"))
|
|
1133
|
{
|
|
1134
|
withInlineData = false;
|
|
1135
|
}
|
|
1136
|
}
|
|
1137
|
if (params.containsKey("abstractpath")) {
|
|
1138
|
abstrpath = ((String[])params.get("abstractpath"))[0];
|
|
1139
|
if ( !abstrpath.equals("") && (abstrpath != null) ) {
|
|
1140
|
viewAbstract(response, abstrpath, docs[0]);
|
|
1141
|
return;
|
|
1142
|
}
|
|
1143
|
}
|
|
1144
|
if ( (docs.length > 1) || qformat.equals("zip") ) {
|
|
1145
|
zip = true;
|
|
1146
|
out = response.getOutputStream();
|
|
1147
|
response.setContentType("application/zip"); //MIME type
|
|
1148
|
zout = new ZipOutputStream(out);
|
|
1149
|
}
|
|
1150
|
// go through the list of docs to read
|
|
1151
|
for (int i=0; i < docs.length; i++ ) {
|
|
1152
|
try {
|
|
1153
|
|
|
1154
|
URL murl = new URL(docs[i]);
|
|
1155
|
Hashtable murlQueryStr = util.parseQuery(murl.getQuery());
|
|
1156
|
// case docid="http://.../?docid=aaa"
|
|
1157
|
// or docid="metacat://.../?docid=bbb"
|
|
1158
|
if (murlQueryStr.containsKey("docid")) {
|
|
1159
|
// get only docid, eliminate the rest
|
|
1160
|
docid = (String)murlQueryStr.get("docid");
|
|
1161
|
if ( zip ) {
|
|
1162
|
addDocToZip(docid, zout, user, groups);
|
|
1163
|
} else {
|
|
1164
|
readFromMetacat(response, docid, qformat, abstrpath,
|
|
1165
|
user, groups, zip, zout, withInlineData, params);
|
|
1166
|
}
|
|
1167
|
|
|
1168
|
// case docid="http://.../filename"
|
|
1169
|
} else {
|
|
1170
|
docid = docs[i];
|
|
1171
|
if ( zip ) {
|
|
1172
|
addDocToZip(docid, zout, user, groups);
|
|
1173
|
} else {
|
|
1174
|
readFromURLConnection(response, docid);
|
|
1175
|
}
|
|
1176
|
}
|
|
1177
|
|
|
1178
|
// case docid="ccc"
|
|
1179
|
} catch (MalformedURLException mue) {
|
|
1180
|
docid = docs[i];
|
|
1181
|
if ( zip ) {
|
|
1182
|
addDocToZip(docid, zout, user, groups);
|
|
1183
|
} else {
|
|
1184
|
readFromMetacat(response, docid, qformat, abstrpath,
|
|
1185
|
user, groups, zip, zout, withInlineData, params);
|
|
1186
|
}
|
|
1187
|
}
|
|
1188
|
|
|
1189
|
} /* end for */
|
|
1190
|
|
|
1191
|
if ( zip ) {
|
|
1192
|
zout.finish(); //terminate the zip file
|
|
1193
|
zout.close(); //close the zip stream
|
|
1194
|
}
|
|
1195
|
|
|
1196
|
|
|
1197
|
}
|
|
1198
|
// To handle doc not found exception
|
|
1199
|
catch (McdbDocNotFoundException notFoundE)
|
|
1200
|
{
|
|
1201
|
// the docid which didn't be found
|
|
1202
|
String notFoundDocId = notFoundE.getUnfoundDocId();
|
|
1203
|
String notFoundRevision = notFoundE.getUnfoundRevision();
|
|
1204
|
MetaCatUtil.debugMessage("Missed id: "+ notFoundDocId, 30);
|
|
1205
|
MetaCatUtil.debugMessage("Missed rev: "+ notFoundRevision, 30);
|
|
1206
|
try
|
|
1207
|
{
|
|
1208
|
// read docid from remote server
|
|
1209
|
readFromRemoteMetaCat(response, notFoundDocId, notFoundRevision,
|
|
1210
|
user, passWord, out, zip, zout);
|
|
1211
|
// Close zout outputstream
|
|
1212
|
if ( zout != null)
|
|
1213
|
{
|
|
1214
|
zout.close();
|
|
1215
|
}
|
|
1216
|
// close output stream
|
|
1217
|
if (out != null)
|
|
1218
|
{
|
|
1219
|
out.close();
|
|
1220
|
}
|
|
1221
|
|
|
1222
|
}//try
|
|
1223
|
catch ( Exception exc)
|
|
1224
|
{
|
|
1225
|
MetaCatUtil.debugMessage("Erorr in MetacatServlet.hanldReadAction: "+
|
|
1226
|
exc.getMessage(), 30);
|
|
1227
|
try
|
|
1228
|
{
|
|
1229
|
if (out != null)
|
|
1230
|
{
|
|
1231
|
response.setContentType("text/xml");
|
|
1232
|
// Send back error message by printWriter
|
|
1233
|
pw = new PrintWriter(out);
|
|
1234
|
pw.println("<?xml version=\"1.0\"?>");
|
|
1235
|
pw.println("<error>");
|
|
1236
|
pw.println(notFoundE.getMessage());
|
|
1237
|
pw.println("</error>");
|
|
1238
|
pw.close();
|
|
1239
|
out.close();
|
|
1240
|
|
|
1241
|
}
|
|
1242
|
else
|
|
1243
|
{
|
|
1244
|
response.setContentType("text/xml"); //MIME type
|
|
1245
|
// Send back error message if out = null
|
|
1246
|
if (pw == null)
|
|
1247
|
{
|
|
1248
|
// If pw is null, open the respnose
|
|
1249
|
pw = response.getWriter();
|
|
1250
|
}
|
|
1251
|
pw.println("<?xml version=\"1.0\"?>");
|
|
1252
|
pw.println("<error>");
|
|
1253
|
pw.println(notFoundE.getMessage());
|
|
1254
|
pw.println("</error>");
|
|
1255
|
pw.close();
|
|
1256
|
}
|
|
1257
|
// close zout
|
|
1258
|
if ( zout != null )
|
|
1259
|
{
|
|
1260
|
zout.close();
|
|
1261
|
}
|
|
1262
|
}//try
|
|
1263
|
catch (IOException ie)
|
|
1264
|
{
|
|
1265
|
MetaCatUtil.debugMessage("Problem with the servlet output " +
|
|
1266
|
"in MetacatServlet.handleReadAction: " +
|
|
1267
|
ie.getMessage(), 30);
|
|
1268
|
}//cathch
|
|
1269
|
}//catch
|
|
1270
|
}// catch McdbDocNotFoundException
|
|
1271
|
catch (Exception e)
|
|
1272
|
{
|
|
1273
|
try {
|
|
1274
|
|
|
1275
|
if (out != null) {
|
|
1276
|
response.setContentType("text/xml"); //MIME type
|
|
1277
|
pw = new PrintWriter(out);
|
|
1278
|
pw.println("<?xml version=\"1.0\"?>");
|
|
1279
|
pw.println("<error>");
|
|
1280
|
pw.println(e.getMessage());
|
|
1281
|
pw.println("</error>");
|
|
1282
|
pw.close();
|
|
1283
|
out.close();
|
|
1284
|
}
|
|
1285
|
else
|
|
1286
|
{
|
|
1287
|
response.setContentType("text/xml"); //MIME type
|
|
1288
|
// Send back error message if out = null
|
|
1289
|
if ( pw == null)
|
|
1290
|
{
|
|
1291
|
pw = response.getWriter();
|
|
1292
|
}
|
|
1293
|
pw.println("<?xml version=\"1.0\"?>");
|
|
1294
|
pw.println("<error>");
|
|
1295
|
pw.println(e.getMessage());
|
|
1296
|
pw.println("</error>");
|
|
1297
|
pw.close();
|
|
1298
|
|
|
1299
|
}
|
|
1300
|
// Close zip output stream
|
|
1301
|
if ( zout != null ) { zout.close(); }
|
|
1302
|
|
|
1303
|
} catch (IOException ioe) {
|
|
1304
|
MetaCatUtil.debugMessage("Problem with the servlet output " +
|
|
1305
|
"in MetacatServlet.handleReadAction: " +
|
|
1306
|
ioe.getMessage(), 30);
|
|
1307
|
ioe.printStackTrace(System.out);
|
|
1308
|
|
|
1309
|
}
|
|
1310
|
|
|
1311
|
MetaCatUtil.debugMessage("Error in MetacatServlet.handleReadAction: " +
|
|
1312
|
e.getMessage(), 30);
|
|
1313
|
//e.printStackTrace(System.out);
|
|
1314
|
}
|
|
1315
|
|
|
1316
|
}
|
|
1317
|
|
|
1318
|
// read metadata or data from Metacat
|
|
1319
|
private void readFromMetacat(HttpServletResponse response, String docid,
|
|
1320
|
String qformat, String abstrpath, String user,
|
|
1321
|
String[] groups, boolean zip,
|
|
1322
|
ZipOutputStream zout, boolean withInlineData,
|
|
1323
|
Hashtable params)
|
|
1324
|
throws ClassNotFoundException, IOException, SQLException,
|
|
1325
|
McdbException, Exception
|
|
1326
|
{
|
|
1327
|
|
|
1328
|
try {
|
|
1329
|
|
|
1330
|
|
|
1331
|
DocumentImpl doc = new DocumentImpl(docid);
|
|
1332
|
|
|
1333
|
//check the permission for read
|
|
1334
|
if (!doc.hasReadPermission(user, groups, docid))
|
|
1335
|
{
|
|
1336
|
Exception e = new Exception("User " + user + " does not have permission"
|
|
1337
|
+" to read the document with the docid " + docid);
|
|
1338
|
|
|
1339
|
throw e;
|
|
1340
|
}
|
|
1341
|
|
|
1342
|
if ( doc.getRootNodeID() == 0 ) {
|
|
1343
|
// this is data file
|
|
1344
|
String filepath = util.getOption("datafilepath");
|
|
1345
|
if(!filepath.endsWith("/")) {
|
|
1346
|
filepath += "/";
|
|
1347
|
}
|
|
1348
|
String filename = filepath + docid;
|
|
1349
|
FileInputStream fin = null;
|
|
1350
|
fin = new FileInputStream(filename);
|
|
1351
|
|
|
1352
|
//MIME type
|
|
1353
|
String contentType = getServletContext().getMimeType(filename);
|
|
1354
|
if (contentType == null)
|
|
1355
|
{
|
|
1356
|
ContentTypeProvider provider = new ContentTypeProvider(docid);
|
|
1357
|
contentType = provider.getContentType();
|
|
1358
|
MetaCatUtil.debugMessage("Final contenttype is: "+ contentType, 30);
|
|
1359
|
}
|
|
1360
|
|
|
1361
|
response.setContentType(contentType);
|
|
1362
|
// if we decide to use "application/octet-stream" for all data returns
|
|
1363
|
// response.setContentType("application/octet-stream");
|
|
1364
|
|
|
1365
|
try {
|
|
1366
|
|
|
1367
|
ServletOutputStream out = response.getOutputStream();
|
|
1368
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1369
|
int b = fin.read(buf);
|
|
1370
|
while (b != -1) {
|
|
1371
|
out.write(buf, 0, b);
|
|
1372
|
b = fin.read(buf);
|
|
1373
|
}
|
|
1374
|
} finally {
|
|
1375
|
if (fin != null) fin.close();
|
|
1376
|
}
|
|
1377
|
|
|
1378
|
} else {
|
|
1379
|
// this is metadata doc
|
|
1380
|
if ( qformat.equals("xml") ) {
|
|
1381
|
|
|
1382
|
// set content type first
|
|
1383
|
response.setContentType("text/xml"); //MIME type
|
|
1384
|
PrintWriter out = response.getWriter();
|
|
1385
|
doc.toXml(out, user, groups, withInlineData);
|
|
1386
|
} else {
|
|
1387
|
response.setContentType("text/html"); //MIME type
|
|
1388
|
PrintWriter out = response.getWriter();
|
|
1389
|
|
|
1390
|
// Look up the document type
|
|
1391
|
String doctype = doc.getDoctype();
|
|
1392
|
// Transform the document to the new doctype
|
|
1393
|
DBTransform dbt = new DBTransform();
|
|
1394
|
dbt.transformXMLDocument(doc.toString(user, groups, withInlineData),
|
|
1395
|
doctype,"-//W3C//HTML//EN",
|
|
1396
|
qformat, out, params);
|
|
1397
|
}
|
|
1398
|
|
|
1399
|
}
|
|
1400
|
}
|
|
1401
|
catch (Exception except)
|
|
1402
|
{
|
|
1403
|
throw except;
|
|
1404
|
|
|
1405
|
}
|
|
1406
|
|
|
1407
|
}
|
|
1408
|
|
|
1409
|
// read data from URLConnection
|
|
1410
|
private void readFromURLConnection(HttpServletResponse response, String docid)
|
|
1411
|
throws IOException, MalformedURLException
|
|
1412
|
{
|
|
1413
|
ServletOutputStream out = response.getOutputStream();
|
|
1414
|
String contentType = getServletContext().getMimeType(docid); //MIME type
|
|
1415
|
if (contentType == null) {
|
|
1416
|
if (docid.endsWith(".xml")) {
|
|
1417
|
contentType="text/xml";
|
|
1418
|
} else if (docid.endsWith(".css")) {
|
|
1419
|
contentType="text/css";
|
|
1420
|
} else if (docid.endsWith(".dtd")) {
|
|
1421
|
contentType="text/plain";
|
|
1422
|
} else if (docid.endsWith(".xsd")) {
|
|
1423
|
contentType="text/xml";
|
|
1424
|
} else if (docid.endsWith("/")) {
|
|
1425
|
contentType="text/html";
|
|
1426
|
} else {
|
|
1427
|
File f = new File(docid);
|
|
1428
|
if ( f.isDirectory() ) {
|
|
1429
|
contentType="text/html";
|
|
1430
|
} else {
|
|
1431
|
contentType="application/octet-stream";
|
|
1432
|
}
|
|
1433
|
}
|
|
1434
|
}
|
|
1435
|
response.setContentType(contentType);
|
|
1436
|
// if we decide to use "application/octet-stream" for all data returns
|
|
1437
|
// response.setContentType("application/octet-stream");
|
|
1438
|
|
|
1439
|
// this is http url
|
|
1440
|
URL url = new URL(docid);
|
|
1441
|
BufferedInputStream bis = null;
|
|
1442
|
try {
|
|
1443
|
bis = new BufferedInputStream(url.openStream());
|
|
1444
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1445
|
int b = bis.read(buf);
|
|
1446
|
while (b != -1) {
|
|
1447
|
out.write(buf, 0, b);
|
|
1448
|
b = bis.read(buf);
|
|
1449
|
}
|
|
1450
|
} finally {
|
|
1451
|
if (bis != null) bis.close();
|
|
1452
|
}
|
|
1453
|
|
|
1454
|
}
|
|
1455
|
|
|
1456
|
// read file/doc and write to ZipOutputStream
|
|
1457
|
private void addDocToZip(String docid, ZipOutputStream zout,
|
|
1458
|
String user, String[] groups)
|
|
1459
|
throws ClassNotFoundException, IOException, SQLException,
|
|
1460
|
McdbException, Exception
|
|
1461
|
{
|
|
1462
|
byte[] bytestring = null;
|
|
1463
|
ZipEntry zentry = null;
|
|
1464
|
|
|
1465
|
try {
|
|
1466
|
URL url = new URL(docid);
|
|
1467
|
|
|
1468
|
// this http url; read from URLConnection; add to zip
|
|
1469
|
zentry = new ZipEntry(docid);
|
|
1470
|
zout.putNextEntry(zentry);
|
|
1471
|
BufferedInputStream bis = null;
|
|
1472
|
try {
|
|
1473
|
bis = new BufferedInputStream(url.openStream());
|
|
1474
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1475
|
int b = bis.read(buf);
|
|
1476
|
while(b != -1) {
|
|
1477
|
zout.write(buf, 0, b);
|
|
1478
|
b = bis.read(buf);
|
|
1479
|
}
|
|
1480
|
} finally {
|
|
1481
|
if (bis != null) bis.close();
|
|
1482
|
}
|
|
1483
|
zout.closeEntry();
|
|
1484
|
|
|
1485
|
} catch (MalformedURLException mue) {
|
|
1486
|
|
|
1487
|
// this is metacat doc (data file or metadata doc)
|
|
1488
|
|
|
1489
|
try {
|
|
1490
|
|
|
1491
|
DocumentImpl doc = new DocumentImpl(docid);
|
|
1492
|
|
|
1493
|
//check the permission for read
|
|
1494
|
if (!doc.hasReadPermission(user, groups, docid))
|
|
1495
|
{
|
|
1496
|
Exception e = new Exception("User " + user + " does not have "
|
|
1497
|
+"permission to read the document with the docid " + docid);
|
|
1498
|
|
|
1499
|
throw e;
|
|
1500
|
}
|
|
1501
|
|
|
1502
|
if ( doc.getRootNodeID() == 0 ) {
|
|
1503
|
// this is data file; add file to zip
|
|
1504
|
String filepath = util.getOption("datafilepath");
|
|
1505
|
if(!filepath.endsWith("/")) {
|
|
1506
|
filepath += "/";
|
|
1507
|
}
|
|
1508
|
String filename = filepath + docid;
|
|
1509
|
FileInputStream fin = null;
|
|
1510
|
fin = new FileInputStream(filename);
|
|
1511
|
try {
|
|
1512
|
|
|
1513
|
zentry = new ZipEntry(docid);
|
|
1514
|
zout.putNextEntry(zentry);
|
|
1515
|
byte[] buf = new byte[4 * 1024]; // 4K buffer
|
|
1516
|
int b = fin.read(buf);
|
|
1517
|
while (b != -1) {
|
|
1518
|
zout.write(buf, 0, b);
|
|
1519
|
b = fin.read(buf);
|
|
1520
|
}
|
|
1521
|
} finally {
|
|
1522
|
if (fin != null) fin.close();
|
|
1523
|
}
|
|
1524
|
zout.closeEntry();
|
|
1525
|
|
|
1526
|
} else {
|
|
1527
|
// this is metadata doc; add doc to zip
|
|
1528
|
bytestring = doc.toString().getBytes();
|
|
1529
|
zentry = new ZipEntry(docid + ".xml");
|
|
1530
|
zentry.setSize(bytestring.length);
|
|
1531
|
zout.putNextEntry(zentry);
|
|
1532
|
zout.write(bytestring, 0, bytestring.length);
|
|
1533
|
zout.closeEntry();
|
|
1534
|
}
|
|
1535
|
} catch (Exception except) {
|
|
1536
|
throw except;
|
|
1537
|
|
|
1538
|
}
|
|
1539
|
|
|
1540
|
}
|
|
1541
|
|
|
1542
|
}
|
|
1543
|
|
|
1544
|
// view abstract within document
|
|
1545
|
private void viewAbstract(HttpServletResponse response,
|
|
1546
|
String abstractpath, String docid)
|
|
1547
|
throws ClassNotFoundException, IOException, SQLException,
|
|
1548
|
McdbException, Exception
|
|
1549
|
{
|
|
1550
|
|
|
1551
|
PrintWriter out =null;
|
|
1552
|
try {
|
|
1553
|
|
|
1554
|
response.setContentType("text/html"); //MIME type
|
|
1555
|
out = response.getWriter();
|
|
1556
|
Object[] abstracts = DBQuery.getNodeContent(abstractpath, docid);
|
|
1557
|
out.println("<html><head><title>Abstract</title></head>");
|
|
1558
|
out.println("<body bgcolor=\"white\"><h1>Abstract</h1>");
|
|
1559
|
for (int i=0; i<abstracts.length; i++) {
|
|
1560
|
out.println("<p>" + (String)abstracts[i] + "</p>");
|
|
1561
|
}
|
|
1562
|
out.println("</body></html>");
|
|
1563
|
|
|
1564
|
} catch (Exception e) {
|
|
1565
|
out.println("<?xml version=\"1.0\"?>");
|
|
1566
|
out.println("<error>");
|
|
1567
|
out.println(e.getMessage());
|
|
1568
|
out.println("</error>");
|
|
1569
|
|
|
1570
|
|
|
1571
|
}
|
|
1572
|
}
|
|
1573
|
/**
|
|
1574
|
* If metacat couldn't find a data file or document locally, it will read this
|
|
1575
|
* docid from its home server. This is for the replication feature
|
|
1576
|
*/
|
|
1577
|
private void readFromRemoteMetaCat(HttpServletResponse response, String docid,
|
|
1578
|
String rev, String user, String password,
|
|
1579
|
ServletOutputStream out, boolean zip, ZipOutputStream zout)
|
|
1580
|
throws Exception
|
|
1581
|
{
|
|
1582
|
// Create a object of RemoteDocument, "" is for zipEntryPath
|
|
1583
|
RemoteDocument remoteDoc =
|
|
1584
|
new RemoteDocument (docid, rev,user, password, "");
|
|
1585
|
String docType = remoteDoc.getDocType();
|
|
1586
|
// Only read data file
|
|
1587
|
if (docType.equals("BIN"))
|
|
1588
|
{
|
|
1589
|
// If it is zip format
|
|
1590
|
if (zip)
|
|
1591
|
{
|
|
1592
|
remoteDoc.readDocumentFromRemoteServerByZip(zout);
|
|
1593
|
}//if
|
|
1594
|
else
|
|
1595
|
{
|
|
1596
|
if (out == null)
|
|
1597
|
{
|
|
1598
|
out = response.getOutputStream();
|
|
1599
|
}//if
|
|
1600
|
response.setContentType("application/octet-stream");
|
|
1601
|
remoteDoc.readDocumentFromRemoteServer(out);
|
|
1602
|
}//else (not zip)
|
|
1603
|
}//if doctype=bin
|
|
1604
|
else
|
|
1605
|
{
|
|
1606
|
throw new Exception("Docid: "+docid+"."+rev+" couldn't find");
|
|
1607
|
}//else
|
|
1608
|
}//readFromRemoteMetaCat
|
|
1609
|
|
|
1610
|
// END OF READ SECTION
|
|
1611
|
|
|
1612
|
|
|
1613
|
|
|
1614
|
// INSERT/UPDATE SECTION
|
|
1615
|
/**
|
|
1616
|
* Handle the database putdocument request and write an XML document
|
|
1617
|
* to the database connection
|
|
1618
|
*/
|
|
1619
|
private void handleInsertOrUpdateAction(PrintWriter out, Hashtable params,
|
|
1620
|
String user, String[] groups) {
|
|
1621
|
|
|
1622
|
DBConnection dbConn = null;
|
|
1623
|
int serialNumber = -1;
|
|
1624
|
|
|
1625
|
try {
|
|
1626
|
// Get the document indicated
|
|
1627
|
String[] doctext = (String[])params.get("doctext");
|
|
1628
|
|
|
1629
|
String pub = null;
|
|
1630
|
if (params.containsKey("public")) {
|
|
1631
|
pub = ((String[])params.get("public"))[0];
|
|
1632
|
}
|
|
1633
|
|
|
1634
|
StringReader dtd = null;
|
|
1635
|
if (params.containsKey("dtdtext")) {
|
|
1636
|
String[] dtdtext = (String[])params.get("dtdtext");
|
|
1637
|
try {
|
|
1638
|
if ( !dtdtext[0].equals("") ) {
|
|
1639
|
dtd = new StringReader(dtdtext[0]);
|
|
1640
|
}
|
|
1641
|
} catch (NullPointerException npe) {}
|
|
1642
|
}
|
|
1643
|
|
|
1644
|
StringReader xml = new StringReader(doctext[0]);
|
|
1645
|
boolean validate = false;
|
|
1646
|
DocumentImplWrapper documentWrapper = null;
|
|
1647
|
try {
|
|
1648
|
// look inside XML Document for <!DOCTYPE ... PUBLIC/SYSTEM ... >
|
|
1649
|
// in order to decide whether to use validation parser
|
|
1650
|
validate = needDTDValidation(xml);
|
|
1651
|
if (validate)
|
|
1652
|
{
|
|
1653
|
// set a dtd base validation parser
|
|
1654
|
String rule = DocumentImpl.DTD;
|
|
1655
|
documentWrapper = new DocumentImplWrapper(rule, validate);
|
|
1656
|
}
|
|
1657
|
else if (needSchemaValidation(xml))
|
|
1658
|
{
|
|
1659
|
// for eml2
|
|
1660
|
if (needEml2Validation(xml))
|
|
1661
|
{
|
|
1662
|
// set eml2 base validation parser
|
|
1663
|
String rule = DocumentImpl.EML2;
|
|
1664
|
// using emlparser to check id validation
|
|
1665
|
EMLParser parser = new EMLParser(doctext[0]);
|
|
1666
|
documentWrapper = new DocumentImplWrapper(rule, true);
|
|
1667
|
}
|
|
1668
|
else
|
|
1669
|
{
|
|
1670
|
// set schema base validation parser
|
|
1671
|
String rule = DocumentImpl.SCHEMA;
|
|
1672
|
documentWrapper = new DocumentImplWrapper(rule, true);
|
|
1673
|
}
|
|
1674
|
}
|
|
1675
|
else
|
|
1676
|
{
|
|
1677
|
documentWrapper = new DocumentImplWrapper("", false);
|
|
1678
|
}
|
|
1679
|
|
|
1680
|
String[] action = (String[])params.get("action");
|
|
1681
|
String[] docid = (String[])params.get("docid");
|
|
1682
|
String newdocid = null;
|
|
1683
|
|
|
1684
|
String doAction = null;
|
|
1685
|
if (action[0].equals("insert")) {
|
|
1686
|
doAction = "INSERT";
|
|
1687
|
} else if (action[0].equals("update")) {
|
|
1688
|
doAction = "UPDATE";
|
|
1689
|
}
|
|
1690
|
|
|
1691
|
try
|
|
1692
|
{
|
|
1693
|
// get a connection from the pool
|
|
1694
|
dbConn=DBConnectionPool.
|
|
1695
|
getDBConnection("MetaCatServlet.handleInsertOrUpdateAction");
|
|
1696
|
serialNumber=dbConn.getCheckOutSerialNumber();
|
|
1697
|
|
|
1698
|
// write the document to the database
|
|
1699
|
try
|
|
1700
|
{
|
|
1701
|
String accNumber = docid[0];
|
|
1702
|
MetaCatUtil.debugMessage(""+ doAction + " " + accNumber +"...", 10);
|
|
1703
|
if (accNumber.equals(""))
|
|
1704
|
{
|
|
1705
|
accNumber = null;
|
|
1706
|
}//if
|
|
1707
|
newdocid = documentWrapper.write(dbConn, xml, pub, dtd, doAction,
|
|
1708
|
accNumber, user, groups);
|
|
1709
|
|
|
1710
|
}//try
|
|
1711
|
catch (NullPointerException npe)
|
|
1712
|
{
|
|
1713
|
newdocid = documentWrapper.write(dbConn, xml, pub, dtd, doAction,
|
|
1714
|
null, user, groups);
|
|
1715
|
}//catch
|
|
1716
|
|
|
1717
|
}//try
|
|
1718
|
finally
|
|
1719
|
{
|
|
1720
|
// Return db connection
|
|
1721
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1722
|
}
|
|
1723
|
|
|
1724
|
// set content type and other response header fields first
|
|
1725
|
//response.setContentType("text/xml");
|
|
1726
|
out.println("<?xml version=\"1.0\"?>");
|
|
1727
|
out.println("<success>");
|
|
1728
|
out.println("<docid>" + newdocid + "</docid>");
|
|
1729
|
out.println("</success>");
|
|
1730
|
|
|
1731
|
}
|
|
1732
|
catch (NullPointerException npe)
|
|
1733
|
{
|
|
1734
|
//response.setContentType("text/xml");
|
|
1735
|
out.println("<?xml version=\"1.0\"?>");
|
|
1736
|
out.println("<error>");
|
|
1737
|
out.println(npe.getMessage());
|
|
1738
|
out.println("</error>");
|
|
1739
|
}
|
|
1740
|
}
|
|
1741
|
catch (Exception e)
|
|
1742
|
{
|
|
1743
|
//response.setContentType("text/xml");
|
|
1744
|
out.println("<?xml version=\"1.0\"?>");
|
|
1745
|
out.println("<error>");
|
|
1746
|
out.println(e.getMessage());
|
|
1747
|
out.println("</error>");
|
|
1748
|
}
|
|
1749
|
}
|
|
1750
|
|
|
1751
|
/**
|
|
1752
|
* Parse XML Document to look for <!DOCTYPE ... PUBLIC/SYSTEM ... >
|
|
1753
|
* in order to decide whether to use validation parser
|
|
1754
|
*/
|
|
1755
|
private static boolean needDTDValidation(StringReader xmlreader) throws
|
|
1756
|
IOException
|
|
1757
|
{
|
|
1758
|
|
|
1759
|
|
|
1760
|
StringBuffer cbuff = new StringBuffer();
|
|
1761
|
java.util.Stack st = new java.util.Stack();
|
|
1762
|
boolean validate = false;
|
|
1763
|
int c;
|
|
1764
|
int inx;
|
|
1765
|
|
|
1766
|
// read from the stream until find the keywords
|
|
1767
|
while ( (st.empty() || st.size()<4) && ((c = xmlreader.read()) != -1) ) {
|
|
1768
|
cbuff.append((char)c);
|
|
1769
|
|
|
1770
|
// "<!DOCTYPE" keyword is found; put it in the stack
|
|
1771
|
if ( (inx = cbuff.toString().indexOf("<!DOCTYPE")) != -1 ) {
|
|
1772
|
cbuff = new StringBuffer();
|
|
1773
|
st.push("<!DOCTYPE");
|
|
1774
|
}
|
|
1775
|
// "PUBLIC" keyword is found; put it in the stack
|
|
1776
|
if ( (inx = cbuff.toString().indexOf("PUBLIC")) != -1 ) {
|
|
1777
|
cbuff = new StringBuffer();
|
|
1778
|
st.push("PUBLIC");
|
|
1779
|
}
|
|
1780
|
// "SYSTEM" keyword is found; put it in the stack
|
|
1781
|
if ( (inx = cbuff.toString().indexOf("SYSTEM")) != -1 ) {
|
|
1782
|
cbuff = new StringBuffer();
|
|
1783
|
st.push("SYSTEM");
|
|
1784
|
}
|
|
1785
|
// ">" character is found; put it in the stack
|
|
1786
|
// ">" is found twice: fisrt from <?xml ...?>
|
|
1787
|
// and second from <!DOCTYPE ... >
|
|
1788
|
if ( (inx = cbuff.toString().indexOf(">")) != -1 ) {
|
|
1789
|
cbuff = new StringBuffer();
|
|
1790
|
st.push(">");
|
|
1791
|
}
|
|
1792
|
}
|
|
1793
|
|
|
1794
|
// close the stream
|
|
1795
|
xmlreader.reset();
|
|
1796
|
|
|
1797
|
// check the stack whether it contains the keywords:
|
|
1798
|
// "<!DOCTYPE", "PUBLIC" or "SYSTEM", and ">" in this order
|
|
1799
|
if ( st.size() == 4 ) {
|
|
1800
|
if ( ((String)st.pop()).equals(">") &&
|
|
1801
|
( ((String)st.peek()).equals("PUBLIC") |
|
|
1802
|
((String)st.pop()).equals("SYSTEM") ) &&
|
|
1803
|
((String)st.pop()).equals("<!DOCTYPE") ) {
|
|
1804
|
validate = true;
|
|
1805
|
}
|
|
1806
|
}
|
|
1807
|
|
|
1808
|
MetaCatUtil.debugMessage("Validation for dtd is " + validate, 10);
|
|
1809
|
return validate;
|
|
1810
|
}
|
|
1811
|
// END OF INSERT/UPDATE SECTION
|
|
1812
|
|
|
1813
|
/* check if the xml string contains key words to specify schema loocation*/
|
|
1814
|
private boolean needSchemaValidation(StringReader xml) throws IOException
|
|
1815
|
{
|
|
1816
|
boolean needSchemaValidate =false;
|
|
1817
|
if (xml == null)
|
|
1818
|
{
|
|
1819
|
MetaCatUtil.debugMessage("Validation for schema is " +
|
|
1820
|
needSchemaValidate, 10);
|
|
1821
|
return needSchemaValidate;
|
|
1822
|
}
|
|
1823
|
System.out.println("before get target line");
|
|
1824
|
String targetLine = getSchemaLine(xml);
|
|
1825
|
System.out.println("before get target line");
|
|
1826
|
// to see if the second line contain some keywords
|
|
1827
|
if (targetLine != null && (targetLine.indexOf(SCHEMALOCATIONKEYWORD) != -1||
|
|
1828
|
targetLine.indexOf(NONAMESPACELOCATION) != -1 ))
|
|
1829
|
{
|
|
1830
|
// if contains schema location key word, should be validate
|
|
1831
|
needSchemaValidate = true;
|
|
1832
|
}
|
|
1833
|
|
|
1834
|
MetaCatUtil.debugMessage("Validation for schema is " +
|
|
1835
|
needSchemaValidate, 10);
|
|
1836
|
return needSchemaValidate;
|
|
1837
|
|
|
1838
|
}
|
|
1839
|
|
|
1840
|
/* check if the xml string contains key words to specify schema loocation*/
|
|
1841
|
private boolean needEml2Validation(StringReader xml) throws IOException
|
|
1842
|
{
|
|
1843
|
boolean needEml2Validate =false;
|
|
1844
|
String emlNameSpace =DocumentImpl.EMLNAMESPACE;
|
|
1845
|
String schemaLocationContent = null;
|
|
1846
|
if (xml == null)
|
|
1847
|
{
|
|
1848
|
MetaCatUtil.debugMessage("Validation for schema is " +
|
|
1849
|
needEml2Validate, 10);
|
|
1850
|
return needEml2Validate;
|
|
1851
|
}
|
|
1852
|
String targetLine = getSchemaLine(xml);
|
|
1853
|
|
|
1854
|
if (targetLine != null)
|
|
1855
|
{
|
|
1856
|
|
|
1857
|
int startIndex = targetLine.indexOf(SCHEMALOCATIONKEYWORD);
|
|
1858
|
int start = 1;
|
|
1859
|
int end = 1;
|
|
1860
|
String schemaLocation = null;
|
|
1861
|
int count = 0;
|
|
1862
|
if (startIndex != -1)
|
|
1863
|
{
|
|
1864
|
for ( int i=startIndex; i<targetLine.length(); i++)
|
|
1865
|
{
|
|
1866
|
if (targetLine.charAt(i) =='"')
|
|
1867
|
{
|
|
1868
|
count ++;
|
|
1869
|
}
|
|
1870
|
if (targetLine.charAt(i) =='"' && count == 1)
|
|
1871
|
{
|
|
1872
|
start = i;
|
|
1873
|
}
|
|
1874
|
if (targetLine.charAt(i) =='"' && count == 2)
|
|
1875
|
{
|
|
1876
|
end = i;
|
|
1877
|
break;
|
|
1878
|
}
|
|
1879
|
}
|
|
1880
|
}
|
|
1881
|
schemaLocation = targetLine.substring(start+1, end);
|
|
1882
|
MetaCatUtil.debugMessage("schemaLocation in xml is: "+schemaLocation, 30);
|
|
1883
|
if ( schemaLocation.indexOf(emlNameSpace) != -1)
|
|
1884
|
{
|
|
1885
|
needEml2Validate = true;
|
|
1886
|
}
|
|
1887
|
}
|
|
1888
|
|
|
1889
|
MetaCatUtil.debugMessage("Validation for eml is " +
|
|
1890
|
needEml2Validate, 10);
|
|
1891
|
return needEml2Validate;
|
|
1892
|
|
|
1893
|
}
|
|
1894
|
|
|
1895
|
private String getSchemaLine(StringReader xml) throws IOException
|
|
1896
|
{
|
|
1897
|
// find the line
|
|
1898
|
String secondLine = null;
|
|
1899
|
int count =0;
|
|
1900
|
int endIndex = 0;
|
|
1901
|
int startIndex = 0;
|
|
1902
|
final int TARGETNUM = 2;
|
|
1903
|
StringBuffer buffer = new StringBuffer();
|
|
1904
|
boolean comment =false;
|
|
1905
|
char thirdPreviousCharacter = '?';
|
|
1906
|
char secondPreviousCharacter ='?';
|
|
1907
|
char previousCharacter = '?';
|
|
1908
|
char currentCharacter = '?';
|
|
1909
|
|
|
1910
|
while ( (currentCharacter = (char) xml.read()) != -1)
|
|
1911
|
{
|
|
1912
|
//in a comment
|
|
1913
|
if (currentCharacter =='-' && previousCharacter == '-' &&
|
|
1914
|
secondPreviousCharacter =='!' && thirdPreviousCharacter == '<')
|
|
1915
|
{
|
|
1916
|
comment = true;
|
|
1917
|
}
|
|
1918
|
//out of comment
|
|
1919
|
if (comment && currentCharacter == '>' && previousCharacter == '-' &&
|
|
1920
|
secondPreviousCharacter =='-')
|
|
1921
|
{
|
|
1922
|
comment = false;
|
|
1923
|
}
|
|
1924
|
|
|
1925
|
//this is not comment
|
|
1926
|
if (currentCharacter !='!' && previousCharacter == '<' && !comment)
|
|
1927
|
{
|
|
1928
|
count ++;
|
|
1929
|
}
|
|
1930
|
// get target line
|
|
1931
|
if (count == TARGETNUM && currentCharacter !='>')
|
|
1932
|
{
|
|
1933
|
buffer.append(currentCharacter);
|
|
1934
|
}
|
|
1935
|
if (count == TARGETNUM && currentCharacter == '>')
|
|
1936
|
{
|
|
1937
|
break;
|
|
1938
|
}
|
|
1939
|
thirdPreviousCharacter = secondPreviousCharacter;
|
|
1940
|
secondPreviousCharacter = previousCharacter;
|
|
1941
|
previousCharacter = currentCharacter;
|
|
1942
|
|
|
1943
|
}
|
|
1944
|
secondLine = buffer.toString();
|
|
1945
|
MetaCatUtil.debugMessage("the second line string is: "+secondLine, 25);
|
|
1946
|
xml.reset();
|
|
1947
|
return secondLine;
|
|
1948
|
}
|
|
1949
|
|
|
1950
|
// DELETE SECTION
|
|
1951
|
/**
|
|
1952
|
* Handle the database delete request and delete an XML document
|
|
1953
|
* from the database connection
|
|
1954
|
*/
|
|
1955
|
private void handleDeleteAction(PrintWriter out, Hashtable params,
|
|
1956
|
HttpServletResponse response, String user, String[] groups) {
|
|
1957
|
|
|
1958
|
String[] docid = (String[])params.get("docid");
|
|
1959
|
|
|
1960
|
// delete the document from the database
|
|
1961
|
try {
|
|
1962
|
|
|
1963
|
// NOTE -- NEED TO TEST HERE
|
|
1964
|
// FOR EXISTENCE OF DOCID PARAM
|
|
1965
|
// BEFORE ACCESSING ARRAY
|
|
1966
|
try {
|
|
1967
|
DocumentImpl.delete(docid[0], user, groups);
|
|
1968
|
response.setContentType("text/xml");
|
|
1969
|
out.println("<?xml version=\"1.0\"?>");
|
|
1970
|
out.println("<success>");
|
|
1971
|
out.println("Document deleted.");
|
|
1972
|
out.println("</success>");
|
|
1973
|
} catch (AccessionNumberException ane) {
|
|
1974
|
response.setContentType("text/xml");
|
|
1975
|
out.println("<?xml version=\"1.0\"?>");
|
|
1976
|
out.println("<error>");
|
|
1977
|
out.println("Error deleting document!!!");
|
|
1978
|
out.println(ane.getMessage());
|
|
1979
|
out.println("</error>");
|
|
1980
|
}
|
|
1981
|
} catch (Exception e) {
|
|
1982
|
response.setContentType("text/xml");
|
|
1983
|
out.println("<?xml version=\"1.0\"?>");
|
|
1984
|
out.println("<error>");
|
|
1985
|
out.println(e.getMessage());
|
|
1986
|
out.println("</error>");
|
|
1987
|
}
|
|
1988
|
}
|
|
1989
|
// END OF DELETE SECTION
|
|
1990
|
|
|
1991
|
// VALIDATE SECTION
|
|
1992
|
/**
|
|
1993
|
* Handle the validation request and return the results to the requestor
|
|
1994
|
*/
|
|
1995
|
private void handleValidateAction(PrintWriter out, Hashtable params) {
|
|
1996
|
|
|
1997
|
// Get the document indicated
|
|
1998
|
String valtext = null;
|
|
1999
|
DBConnection dbConn = null;
|
|
2000
|
int serialNumber = -1;
|
|
2001
|
|
|
2002
|
try {
|
|
2003
|
valtext = ((String[])params.get("valtext"))[0];
|
|
2004
|
} catch (Exception nullpe) {
|
|
2005
|
|
|
2006
|
|
|
2007
|
String docid = null;
|
|
2008
|
try {
|
|
2009
|
// Find the document id number
|
|
2010
|
docid = ((String[])params.get("docid"))[0];
|
|
2011
|
|
|
2012
|
|
|
2013
|
// Get the document indicated from the db
|
|
2014
|
DocumentImpl xmldoc = new DocumentImpl(docid);
|
|
2015
|
valtext = xmldoc.toString();
|
|
2016
|
|
|
2017
|
} catch (NullPointerException npe) {
|
|
2018
|
|
|
2019
|
out.println("<error>Error getting document ID: " + docid + "</error>");
|
|
2020
|
//if ( conn != null ) { util.returnConnection(conn); }
|
|
2021
|
return;
|
|
2022
|
} catch (Exception e) {
|
|
2023
|
|
|
2024
|
out.println(e.getMessage());
|
|
2025
|
}
|
|
2026
|
}
|
|
2027
|
|
|
2028
|
|
|
2029
|
try {
|
|
2030
|
// get a connection from the pool
|
|
2031
|
dbConn=DBConnectionPool.
|
|
2032
|
getDBConnection("MetaCatServlet.handleValidateAction");
|
|
2033
|
serialNumber=dbConn.getCheckOutSerialNumber();
|
|
2034
|
DBValidate valobj = new DBValidate(saxparser,dbConn);
|
|
2035
|
boolean valid = valobj.validateString(valtext);
|
|
2036
|
|
|
2037
|
// set content type and other response header fields first
|
|
2038
|
|
|
2039
|
out.println(valobj.returnErrors());
|
|
2040
|
|
|
2041
|
} catch (NullPointerException npe2) {
|
|
2042
|
// set content type and other response header fields first
|
|
2043
|
|
|
2044
|
out.println("<error>Error validating document.</error>");
|
|
2045
|
} catch (Exception e) {
|
|
2046
|
|
|
2047
|
out.println(e.getMessage());
|
|
2048
|
} finally {
|
|
2049
|
// Return db connection
|
|
2050
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2051
|
}
|
|
2052
|
}
|
|
2053
|
// END OF VALIDATE SECTION
|
|
2054
|
|
|
2055
|
// OTHER ACTION HANDLERS
|
|
2056
|
|
|
2057
|
/**
|
|
2058
|
* Handle "getrevsionanddoctype" action
|
|
2059
|
* Given a docid, return it's current revision and doctype from data base
|
|
2060
|
* The output is String look like "rev;doctype"
|
|
2061
|
*/
|
|
2062
|
private void handleGetRevisionAndDocTypeAction(PrintWriter out,
|
|
2063
|
Hashtable params)
|
|
2064
|
{
|
|
2065
|
// To store doc parameter
|
|
2066
|
String [] docs = new String[10];
|
|
2067
|
// Store a single doc id
|
|
2068
|
String givenDocId = null;
|
|
2069
|
// Get docid from parameters
|
|
2070
|
if (params.containsKey("docid"))
|
|
2071
|
{
|
|
2072
|
docs = (String[])params.get("docid");
|
|
2073
|
}
|
|
2074
|
// Get first docid form string array
|
|
2075
|
givenDocId = docs[0];
|
|
2076
|
|
|
2077
|
try
|
|
2078
|
{
|
|
2079
|
// Make sure there is a docid
|
|
2080
|
if (givenDocId == null || givenDocId.equals(""))
|
|
2081
|
{
|
|
2082
|
throw new Exception("User didn't specify docid!");
|
|
2083
|
}//if
|
|
2084
|
|
|
2085
|
// Create a DBUtil object
|
|
2086
|
DBUtil dbutil = new DBUtil();
|
|
2087
|
// Get a rev and doctype
|
|
2088
|
String revAndDocType =
|
|
2089
|
dbutil.getCurrentRevisionAndDocTypeForGivenDocument(givenDocId);
|
|
2090
|
out.println(revAndDocType);
|
|
2091
|
|
|
2092
|
}//try
|
|
2093
|
catch (Exception e)
|
|
2094
|
{
|
|
2095
|
// Handle exception
|
|
2096
|
out.println("<?xml version=\"1.0\"?>");
|
|
2097
|
out.println("<error>");
|
|
2098
|
out.println(e.getMessage());
|
|
2099
|
out.println("</error>");
|
|
2100
|
}//catch
|
|
2101
|
|
|
2102
|
}//handleGetRevisionAndDocTypeAction
|
|
2103
|
|
|
2104
|
/**
|
|
2105
|
* Handle "getaccesscontrol" action.
|
|
2106
|
* Read Access Control List from db connection in XML format
|
|
2107
|
*/
|
|
2108
|
private void handleGetAccessControlAction(PrintWriter out, Hashtable params,
|
|
2109
|
HttpServletResponse response,
|
|
2110
|
String username, String[] groupnames) {
|
|
2111
|
|
|
2112
|
DBConnection dbConn = null;
|
|
2113
|
int serialNumber = -1;
|
|
2114
|
String docid = ((String[])params.get("docid"))[0];
|
|
2115
|
|
|
2116
|
try {
|
|
2117
|
|
|
2118
|
// get connection from the pool
|
|
2119
|
dbConn=DBConnectionPool.
|
|
2120
|
getDBConnection("MetaCatServlet.handleGetAccessControlAction");
|
|
2121
|
serialNumber=dbConn.getCheckOutSerialNumber();
|
|
2122
|
AccessControlList aclobj = new AccessControlList(dbConn);
|
|
2123
|
String acltext = aclobj.getACL(docid, username, groupnames);
|
|
2124
|
out.println(acltext);
|
|
2125
|
|
|
2126
|
} catch (Exception e) {
|
|
2127
|
out.println("<?xml version=\"1.0\"?>");
|
|
2128
|
out.println("<error>");
|
|
2129
|
out.println(e.getMessage());
|
|
2130
|
out.println("</error>");
|
|
2131
|
} finally {
|
|
2132
|
// Retrun db connection to pool
|
|
2133
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2134
|
}
|
|
2135
|
|
|
2136
|
}
|
|
2137
|
|
|
2138
|
/**
|
|
2139
|
* Handle the "getprincipals" action.
|
|
2140
|
* Read all principals from authentication scheme in XML format
|
|
2141
|
*/
|
|
2142
|
private void handleGetPrincipalsAction(PrintWriter out, String user,
|
|
2143
|
String password) {
|
|
2144
|
|
|
2145
|
|
|
2146
|
try {
|
|
2147
|
|
|
2148
|
|
|
2149
|
AuthSession auth = new AuthSession();
|
|
2150
|
String principals = auth.getPrincipals(user, password);
|
|
2151
|
out.println(principals);
|
|
2152
|
|
|
2153
|
} catch (Exception e) {
|
|
2154
|
out.println("<?xml version=\"1.0\"?>");
|
|
2155
|
out.println("<error>");
|
|
2156
|
out.println(e.getMessage());
|
|
2157
|
out.println("</error>");
|
|
2158
|
}
|
|
2159
|
|
|
2160
|
}
|
|
2161
|
|
|
2162
|
/**
|
|
2163
|
* Handle "getdoctypes" action.
|
|
2164
|
* Read all doctypes from db connection in XML format
|
|
2165
|
*/
|
|
2166
|
private void handleGetDoctypesAction(PrintWriter out, Hashtable params,
|
|
2167
|
HttpServletResponse response) {
|
|
2168
|
|
|
2169
|
|
|
2170
|
try {
|
|
2171
|
|
|
2172
|
|
|
2173
|
DBUtil dbutil = new DBUtil();
|
|
2174
|
String doctypes = dbutil.readDoctypes();
|
|
2175
|
out.println(doctypes);
|
|
2176
|
|
|
2177
|
} catch (Exception e) {
|
|
2178
|
out.println("<?xml version=\"1.0\"?>");
|
|
2179
|
out.println("<error>");
|
|
2180
|
out.println(e.getMessage());
|
|
2181
|
out.println("</error>");
|
|
2182
|
}
|
|
2183
|
|
|
2184
|
}
|
|
2185
|
|
|
2186
|
/**
|
|
2187
|
* Handle the "getdtdschema" action.
|
|
2188
|
* Read DTD or Schema file for a given doctype from Metacat catalog system
|
|
2189
|
*/
|
|
2190
|
private void handleGetDTDSchemaAction(PrintWriter out, Hashtable params,
|
|
2191
|
HttpServletResponse response) {
|
|
2192
|
|
|
2193
|
|
|
2194
|
String doctype = null;
|
|
2195
|
String[] doctypeArr = (String[])params.get("doctype");
|
|
2196
|
|
|
2197
|
// get only the first doctype specified in the list of doctypes
|
|
2198
|
// it could be done for all doctypes in that list
|
|
2199
|
if (doctypeArr != null) {
|
|
2200
|
doctype = ((String[])params.get("doctype"))[0];
|
|
2201
|
}
|
|
2202
|
|
|
2203
|
try {
|
|
2204
|
|
|
2205
|
|
|
2206
|
DBUtil dbutil = new DBUtil();
|
|
2207
|
String dtdschema = dbutil.readDTDSchema(doctype);
|
|
2208
|
out.println(dtdschema);
|
|
2209
|
|
|
2210
|
} catch (Exception e) {
|
|
2211
|
out.println("<?xml version=\"1.0\"?>");
|
|
2212
|
out.println("<error>");
|
|
2213
|
out.println(e.getMessage());
|
|
2214
|
out.println("</error>");
|
|
2215
|
}
|
|
2216
|
|
|
2217
|
}
|
|
2218
|
|
|
2219
|
/**
|
|
2220
|
* Handle the "getlastdocid" action.
|
|
2221
|
* Get the latest docid with rev number from db connection in XML format
|
|
2222
|
*/
|
|
2223
|
private void handleGetMaxDocidAction(PrintWriter out, Hashtable params,
|
|
2224
|
HttpServletResponse response) {
|
|
2225
|
|
|
2226
|
|
|
2227
|
String scope = ((String[])params.get("scope"))[0];
|
|
2228
|
if (scope == null) {
|
|
2229
|
scope = ((String[])params.get("username"))[0];
|
|
2230
|
}
|
|
2231
|
|
|
2232
|
try {
|
|
2233
|
|
|
2234
|
|
|
2235
|
DBUtil dbutil = new DBUtil();
|
|
2236
|
String lastDocid = dbutil.getMaxDocid(scope);
|
|
2237
|
out.println("<?xml version=\"1.0\"?>");
|
|
2238
|
out.println("<lastDocid>");
|
|
2239
|
out.println(" <scope>" + scope + "</scope>");
|
|
2240
|
out.println(" <docid>" + lastDocid + "</docid>");
|
|
2241
|
out.println("</lastDocid>");
|
|
2242
|
|
|
2243
|
} catch (Exception e) {
|
|
2244
|
out.println("<?xml version=\"1.0\"?>");
|
|
2245
|
out.println("<error>");
|
|
2246
|
out.println(e.getMessage());
|
|
2247
|
out.println("</error>");
|
|
2248
|
}
|
|
2249
|
|
|
2250
|
}
|
|
2251
|
|
|
2252
|
/**
|
|
2253
|
* Handle documents passed to metacat that are encoded using the
|
|
2254
|
* "multipart/form-data" mime type. This is typically used for uploading
|
|
2255
|
* data files which may be binary and large.
|
|
2256
|
*/
|
|
2257
|
private void handleMultipartForm(HttpServletRequest request,
|
|
2258
|
HttpServletResponse response)
|
|
2259
|
{
|
|
2260
|
PrintWriter out = null;
|
|
2261
|
String action = null;
|
|
2262
|
|
|
2263
|
// Parse the multipart form, and save the parameters in a Hashtable and
|
|
2264
|
// save the FileParts in a hashtable
|
|
2265
|
|
|
2266
|
Hashtable params = new Hashtable();
|
|
2267
|
Hashtable fileList = new Hashtable();
|
|
2268
|
int sizeLimit = (new Integer(MetaCatUtil.getOption("datafilesizelimit")))
|
|
2269
|
.intValue();
|
|
2270
|
MetaCatUtil.debugMessage("The limit size of data file is: "+sizeLimit, 50);
|
|
2271
|
|
|
2272
|
try {
|
|
2273
|
// MBJ: need to put filesize limit in Metacat config (metacat.properties)
|
|
2274
|
MultipartParser mp = new MultipartParser(request, sizeLimit*1024*1024);
|
|
2275
|
Part part;
|
|
2276
|
while ((part = mp.readNextPart()) != null) {
|
|
2277
|
String name = part.getName();
|
|
2278
|
|
|
2279
|
if (part.isParam()) {
|
|
2280
|
// it's a parameter part
|
|
2281
|
ParamPart paramPart = (ParamPart) part;
|
|
2282
|
String value = paramPart.getStringValue();
|
|
2283
|
params.put(name, value);
|
|
2284
|
if (name.equals("action")) {
|
|
2285
|
action = value;
|
|
2286
|
}
|
|
2287
|
} else if (part.isFile()) {
|
|
2288
|
// it's a file part
|
|
2289
|
FilePart filePart = (FilePart) part;
|
|
2290
|
fileList.put(name, filePart);
|
|
2291
|
|
|
2292
|
// Stop once the first file part is found, otherwise going onto the
|
|
2293
|
// next part prevents access to the file contents. So...for upload
|
|
2294
|
// to work, the datafile must be the last part
|
|
2295
|
break;
|
|
2296
|
}
|
|
2297
|
}
|
|
2298
|
} catch (IOException ioe) {
|
|
2299
|
try {
|
|
2300
|
out = response.getWriter();
|
|
2301
|
} catch (IOException ioe2) {
|
|
2302
|
System.err.println("Fatal Error: couldn't get response output stream.");
|
|
2303
|
}
|
|
2304
|
out.println("<?xml version=\"1.0\"?>");
|
|
2305
|
out.println("<error>");
|
|
2306
|
out.println("Error: problem reading multipart data.");
|
|
2307
|
out.println("</error>");
|
|
2308
|
}
|
|
2309
|
|
|
2310
|
// Get the session information
|
|
2311
|
String username = null;
|
|
2312
|
String password = null;
|
|
2313
|
String[] groupnames = null;
|
|
2314
|
String sess_id = null;
|
|
2315
|
|
|
2316
|
// be aware of session expiration on every request
|
|
2317
|
HttpSession sess = request.getSession(true);
|
|
2318
|
if (sess.isNew()) {
|
|
2319
|
// session expired or has not been stored b/w user requests
|
|
2320
|
username = "public";
|
|
2321
|
sess.setAttribute("username", username);
|
|
2322
|
} else {
|
|
2323
|
username = (String)sess.getAttribute("username");
|
|
2324
|
password = (String)sess.getAttribute("password");
|
|
2325
|
groupnames = (String[])sess.getAttribute("groupnames");
|
|
2326
|
try {
|
|
2327
|
sess_id = (String)sess.getId();
|
|
2328
|
} catch(IllegalStateException ise) {
|
|
2329
|
System.out.println("error in handleMultipartForm: this shouldn't " +
|
|
2330
|
"happen: the session should be valid: " +
|
|
2331
|
ise.getMessage());
|
|
2332
|
}
|
|
2333
|
}
|
|
2334
|
|
|
2335
|
// Get the out stream
|
|
2336
|
try {
|
|
2337
|
out = response.getWriter();
|
|
2338
|
} catch (IOException ioe2) {
|
|
2339
|
util.debugMessage("Fatal Error: couldn't get response "+
|
|
2340
|
"output stream.", 30);
|
|
2341
|
}
|
|
2342
|
|
|
2343
|
if ( action.equals("upload")) {
|
|
2344
|
if (username != null && !username.equals("public")) {
|
|
2345
|
handleUploadAction(request, out, params, fileList,
|
|
2346
|
username, groupnames);
|
|
2347
|
} else {
|
|
2348
|
|
|
2349
|
out.println("<?xml version=\"1.0\"?>");
|
|
2350
|
out.println("<error>");
|
|
2351
|
out.println("Permission denied for " + action);
|
|
2352
|
out.println("</error>");
|
|
2353
|
}
|
|
2354
|
} else {
|
|
2355
|
/*try {
|
|
2356
|
out = response.getWriter();
|
|
2357
|
} catch (IOException ioe2) {
|
|
2358
|
System.err.println("Fatal Error: couldn't get response output stream.");
|
|
2359
|
}*/
|
|
2360
|
out.println("<?xml version=\"1.0\"?>");
|
|
2361
|
out.println("<error>");
|
|
2362
|
out.println("Error: action not registered. Please report this error.");
|
|
2363
|
out.println("</error>");
|
|
2364
|
}
|
|
2365
|
out.close();
|
|
2366
|
}
|
|
2367
|
|
|
2368
|
/**
|
|
2369
|
* Handle the upload action by saving the attached file to disk and
|
|
2370
|
* registering it in the Metacat db
|
|
2371
|
*/
|
|
2372
|
private void handleUploadAction(HttpServletRequest request,
|
|
2373
|
PrintWriter out,
|
|
2374
|
Hashtable params, Hashtable fileList,
|
|
2375
|
String username, String[] groupnames)
|
|
2376
|
{
|
|
2377
|
//PrintWriter out = null;
|
|
2378
|
//Connection conn = null;
|
|
2379
|
String action = null;
|
|
2380
|
String docid = null;
|
|
2381
|
|
|
2382
|
/*response.setContentType("text/xml");
|
|
2383
|
try
|
|
2384
|
{
|
|
2385
|
out = response.getWriter();
|
|
2386
|
}
|
|
2387
|
catch (IOException ioe2)
|
|
2388
|
{
|
|
2389
|
System.err.println("Fatal Error: couldn't get response output stream.");
|
|
2390
|
}*/
|
|
2391
|
|
|
2392
|
if (params.containsKey("docid"))
|
|
2393
|
{
|
|
2394
|
docid = (String)params.get("docid");
|
|
2395
|
}
|
|
2396
|
|
|
2397
|
// Make sure we have a docid and datafile
|
|
2398
|
if (docid != null && fileList.containsKey("datafile")) {
|
|
2399
|
|
|
2400
|
// Get a reference to the file part of the form
|
|
2401
|
FilePart filePart = (FilePart)fileList.get("datafile");
|
|
2402
|
String fileName = filePart.getFileName();
|
|
2403
|
MetaCatUtil.debugMessage("Uploading filename: " + fileName, 10);
|
|
2404
|
|
|
2405
|
// Check if the right file existed in the uploaded data
|
|
2406
|
if (fileName != null) {
|
|
2407
|
|
|
2408
|
try
|
|
2409
|
{
|
|
2410
|
//MetaCatUtil.debugMessage("Upload datafile " + docid +"...", 10);
|
|
2411
|
//If document get lock data file grant
|
|
2412
|
if (DocumentImpl.getDataFileLockGrant(docid))
|
|
2413
|
{
|
|
2414
|
// register the file in the database (which generates an exception
|
|
2415
|
//if the docid is not acceptable or other untoward things happen
|
|
2416
|
DocumentImpl.registerDocument(fileName, "BIN", docid, username);
|
|
2417
|
|
|
2418
|
// Save the data file to disk using "docid" as the name
|
|
2419
|
dataDirectory.mkdirs();
|
|
2420
|
File newFile = new File(dataDirectory, docid);
|
|
2421
|
long size = filePart.writeTo(newFile);
|
|
2422
|
|
|
2423
|
// Force replication this data file
|
|
2424
|
// To data file, "insert" and update is same
|
|
2425
|
// The fourth parameter is null. Because it is notification server
|
|
2426
|
// and this method is in MetaCatServerlet. It is original command,
|
|
2427
|
// not get force replication info from another metacat
|
|
2428
|
ForceReplicationHandler frh = new ForceReplicationHandler
|
|
2429
|
(docid, "insert", false, null);
|
|
2430
|
|
|
2431
|
// set content type and other response header fields first
|
|
2432
|
out.println("<?xml version=\"1.0\"?>");
|
|
2433
|
out.println("<success>");
|
|
2434
|
out.println("<docid>" + docid + "</docid>");
|
|
2435
|
out.println("<size>" + size + "</size>");
|
|
2436
|
out.println("</success>");
|
|
2437
|
}//if
|
|
2438
|
|
|
2439
|
} //try
|
|
2440
|
catch (Exception e)
|
|
2441
|
{
|
|
2442
|
out.println("<?xml version=\"1.0\"?>");
|
|
2443
|
out.println("<error>");
|
|
2444
|
out.println(e.getMessage());
|
|
2445
|
out.println("</error>");
|
|
2446
|
}
|
|
2447
|
|
|
2448
|
}
|
|
2449
|
else
|
|
2450
|
{
|
|
2451
|
// the field did not contain a file
|
|
2452
|
out.println("<?xml version=\"1.0\"?>");
|
|
2453
|
out.println("<error>");
|
|
2454
|
out.println("The uploaded data did not contain a valid file.");
|
|
2455
|
out.println("</error>");
|
|
2456
|
}
|
|
2457
|
}
|
|
2458
|
else
|
|
2459
|
{
|
|
2460
|
// Error bcse docid missing or file missing
|
|
2461
|
out.println("<?xml version=\"1.0\"?>");
|
|
2462
|
out.println("<error>");
|
|
2463
|
out.println("The uploaded data did not contain a valid docid " +
|
|
2464
|
"or valid file.");
|
|
2465
|
out.println("</error>");
|
|
2466
|
}
|
|
2467
|
}
|
|
2468
|
|
|
2469
|
/*
|
|
2470
|
* A method to handle set access action
|
|
2471
|
*/
|
|
2472
|
private void handleSetAccessAction(PrintWriter out,
|
|
2473
|
Hashtable params,
|
|
2474
|
String username)
|
|
2475
|
{
|
|
2476
|
String [] docList = null;
|
|
2477
|
String [] principalList = null;
|
|
2478
|
String [] permissionList = null;
|
|
2479
|
String [] permTypeList = null;
|
|
2480
|
String [] permOrderList = null;
|
|
2481
|
String permission = null;
|
|
2482
|
String permType = null;
|
|
2483
|
String permOrder = null;
|
|
2484
|
Vector errorList = new Vector();
|
|
2485
|
String error = null;
|
|
2486
|
Vector successList = new Vector();
|
|
2487
|
String success = null;
|
|
2488
|
|
|
2489
|
|
|
2490
|
// Get parameters
|
|
2491
|
if (params.containsKey("docid"))
|
|
2492
|
{
|
|
2493
|
docList = (String[])params.get("docid");
|
|
2494
|
}
|
|
2495
|
if (params.containsKey("principal"))
|
|
2496
|
{
|
|
2497
|
principalList = (String[])params.get("principal");
|
|
2498
|
}
|
|
2499
|
if (params.containsKey("permission"))
|
|
2500
|
{
|
|
2501
|
permissionList = (String[])params.get("permission");
|
|
2502
|
|
|
2503
|
}
|
|
2504
|
if (params.containsKey("permType"))
|
|
2505
|
{
|
|
2506
|
permTypeList = (String[])params.get("permType");
|
|
2507
|
|
|
2508
|
}
|
|
2509
|
if (params.containsKey("permOrder"))
|
|
2510
|
{
|
|
2511
|
permOrderList = (String[])params.get("permOrder");
|
|
2512
|
|
|
2513
|
}
|
|
2514
|
|
|
2515
|
// Make sure the parameter is not null
|
|
2516
|
if (docList == null || principalList == null || permTypeList == null ||
|
|
2517
|
permissionList == null)
|
|
2518
|
{
|
|
2519
|
error = "Please check your parameter list, it should look like: "+
|
|
2520
|
"?action=setaccess&docid=pipeline.1.1&principal=public" +
|
|
2521
|
"&permission=read&permType=allow&permOrder=allowFirst";
|
|
2522
|
errorList.addElement(error);
|
|
2523
|
outputResponse(successList, errorList, out);
|
|
2524
|
return;
|
|
2525
|
}
|
|
2526
|
|
|
2527
|
// Only select first element for permission, type and order
|
|
2528
|
permission = permissionList[0];
|
|
2529
|
permType = permTypeList[0];
|
|
2530
|
if (permOrderList != null)
|
|
2531
|
{
|
|
2532
|
permOrder = permOrderList[0];
|
|
2533
|
}
|
|
2534
|
|
|
2535
|
// Get package doctype set
|
|
2536
|
Vector packageSet =MetaCatUtil.getOptionList(
|
|
2537
|
MetaCatUtil.getOption("packagedoctypeset"));
|
|
2538
|
//debug
|
|
2539
|
if (packageSet != null)
|
|
2540
|
{
|
|
2541
|
for (int i = 0; i<packageSet.size(); i++)
|
|
2542
|
{
|
|
2543
|
MetaCatUtil.debugMessage("doctype in package set: " +
|
|
2544
|
(String)packageSet.elementAt(i), 34);
|
|
2545
|
}
|
|
2546
|
}//if
|
|
2547
|
|
|
2548
|
// handle every accessionNumber
|
|
2549
|
for (int i=0; i <docList.length; i++)
|
|
2550
|
{
|
|
2551
|
String accessionNumber = docList[i];
|
|
2552
|
String owner = null;
|
|
2553
|
String publicId = null;
|
|
2554
|
// Get document owner and public id
|
|
2555
|
try
|
|
2556
|
{
|
|
2557
|
owner = getFieldValueForDoc(accessionNumber, "user_owner");
|
|
2558
|
publicId = getFieldValueForDoc(accessionNumber, "doctype");
|
|
2559
|
}//try
|
|
2560
|
catch (Exception e)
|
|
2561
|
{
|
|
2562
|
MetaCatUtil.debugMessage("Error in handleSetAccessAction: " +
|
|
2563
|
e.getMessage(), 30);
|
|
2564
|
error = "Error in set access control for document - " + accessionNumber+
|
|
2565
|
e.getMessage();
|
|
2566
|
errorList.addElement(error);
|
|
2567
|
continue;
|
|
2568
|
}
|
|
2569
|
//check if user is the owner. Only owner can do owner
|
|
2570
|
if (username == null || owner == null || !username.equals(owner))
|
|
2571
|
{
|
|
2572
|
error = "User - " + username + " does not have permission to set " +
|
|
2573
|
"access control for docid - " + accessionNumber;
|
|
2574
|
errorList.addElement(error);
|
|
2575
|
continue;
|
|
2576
|
}
|
|
2577
|
|
|
2578
|
// If docid publicid is BIN data file or other beta4, 6 package document
|
|
2579
|
// we could not do set access control. Because we don't want inconsistent
|
|
2580
|
// to its access docuemnt
|
|
2581
|
if (publicId!=null && packageSet!=null && packageSet.contains(publicId))
|
|
2582
|
{
|
|
2583
|
error = "Could not set access control to document "+ accessionNumber +
|
|
2584
|
"because it is in a pakcage and it has a access file for it";
|
|
2585
|
errorList.addElement(error);
|
|
2586
|
continue;
|
|
2587
|
}
|
|
2588
|
|
|
2589
|
// for every principle
|
|
2590
|
for (int j = 0; j<principalList.length; j++)
|
|
2591
|
{
|
|
2592
|
String principal = principalList[j];
|
|
2593
|
try
|
|
2594
|
{
|
|
2595
|
//insert permission
|
|
2596
|
AccessControlForSingleFile accessControl = new
|
|
2597
|
AccessControlForSingleFile(accessionNumber,
|
|
2598
|
principal, permission, permType, permOrder);
|
|
2599
|
accessControl.insertPermissions();
|
|
2600
|
success = "Set access control to document "+ accessionNumber +
|
|
2601
|
" successfully";
|
|
2602
|
successList.addElement(success);
|
|
2603
|
}
|
|
2604
|
catch (Exception ee)
|
|
2605
|
{
|
|
2606
|
MetaCatUtil.debugMessage("Erorr in handleSetAccessAction2: " +
|
|
2607
|
ee.getMessage(), 30);
|
|
2608
|
error = "Faild to set access control for document " +
|
|
2609
|
accessionNumber + " because " + ee.getMessage();
|
|
2610
|
errorList.addElement(error);
|
|
2611
|
continue;
|
|
2612
|
}
|
|
2613
|
}//for every principle
|
|
2614
|
}//for every document
|
|
2615
|
outputResponse(successList, errorList, out);
|
|
2616
|
}//handleSetAccessAction
|
|
2617
|
|
|
2618
|
|
|
2619
|
/*
|
|
2620
|
* A method try to determin a docid's public id, if couldn't find null
|
|
2621
|
* will be returned.
|
|
2622
|
*/
|
|
2623
|
private String getFieldValueForDoc(String accessionNumber, String fieldName)
|
|
2624
|
throws Exception
|
|
2625
|
{
|
|
2626
|
if (accessionNumber==null || accessionNumber.equals("") ||fieldName == null
|
|
2627
|
|| fieldName.equals(""))
|
|
2628
|
{
|
|
2629
|
throw new Exception("Docid or field name was not specified");
|
|
2630
|
}
|
|
2631
|
|
|
2632
|
PreparedStatement pstmt = null;
|
|
2633
|
ResultSet rs = null;
|
|
2634
|
String fieldValue = null;
|
|
2635
|
String docId = null;
|
|
2636
|
DBConnection conn = null;
|
|
2637
|
int serialNumber = -1;
|
|
2638
|
|
|
2639
|
// get rid of revision if access number has
|
|
2640
|
docId = MetaCatUtil.getDocIdFromString(accessionNumber);
|
|
2641
|
try
|
|
2642
|
{
|
|
2643
|
//check out DBConnection
|
|
2644
|
conn=DBConnectionPool.getDBConnection("MetaCatServlet.getPublicIdForDoc");
|
|
2645
|
serialNumber=conn.getCheckOutSerialNumber();
|
|
2646
|
pstmt = conn.prepareStatement(
|
|
2647
|
"SELECT " + fieldName + " FROM xml_documents " +
|
|
2648
|
"WHERE docid = ? ");
|
|
2649
|
|
|
2650
|
pstmt.setString(1, docId);
|
|
2651
|
pstmt.execute();
|
|
2652
|
rs = pstmt.getResultSet();
|
|
2653
|
boolean hasRow = rs.next();
|
|
2654
|
int perm = 0;
|
|
2655
|
if ( hasRow )
|
|
2656
|
{
|
|
2657
|
fieldValue = rs.getString(1);
|
|
2658
|
}
|
|
2659
|
else
|
|
2660
|
{
|
|
2661
|
throw new Exception("Could not find document: "+accessionNumber);
|
|
2662
|
}
|
|
2663
|
}//try
|
|
2664
|
catch (Exception e)
|
|
2665
|
{
|
|
2666
|
MetaCatUtil.debugMessage("Exception in MetacatServlet.getPublicIdForDoc: "
|
|
2667
|
+ e.getMessage(), 30);
|
|
2668
|
throw e;
|
|
2669
|
}
|
|
2670
|
finally
|
|
2671
|
{
|
|
2672
|
try
|
|
2673
|
{
|
|
2674
|
rs.close();
|
|
2675
|
pstmt.close();
|
|
2676
|
|
|
2677
|
}
|
|
2678
|
finally
|
|
2679
|
{
|
|
2680
|
DBConnectionPool.returnDBConnection(conn, serialNumber);
|
|
2681
|
}
|
|
2682
|
}
|
|
2683
|
return fieldValue;
|
|
2684
|
}//getFieldValueForDoc
|
|
2685
|
|
|
2686
|
/*
|
|
2687
|
* A method to output setAccess action result
|
|
2688
|
*/
|
|
2689
|
private void outputResponse(Vector successList,
|
|
2690
|
Vector errorList,
|
|
2691
|
PrintWriter out)
|
|
2692
|
{
|
|
2693
|
boolean error = false;
|
|
2694
|
boolean success = false;
|
|
2695
|
// Output prolog
|
|
2696
|
out.println(PROLOG);
|
|
2697
|
// output success message
|
|
2698
|
if ( successList != null)
|
|
2699
|
{
|
|
2700
|
for (int i = 0; i<successList.size(); i++)
|
|
2701
|
{
|
|
2702
|
out.println(SUCCESS);
|
|
2703
|
out.println((String)successList.elementAt(i));
|
|
2704
|
out.println(SUCCESSCLOSE);
|
|
2705
|
success = true;
|
|
2706
|
}//for
|
|
2707
|
}//if
|
|
2708
|
// output error message
|
|
2709
|
if (errorList != null)
|
|
2710
|
{
|
|
2711
|
for (int i = 0; i<errorList.size(); i++)
|
|
2712
|
{
|
|
2713
|
out.println(ERROR);
|
|
2714
|
out.println((String)errorList.elementAt(i));
|
|
2715
|
out.println(ERRORCLOSE);
|
|
2716
|
error = true;
|
|
2717
|
}//for
|
|
2718
|
}//if
|
|
2719
|
|
|
2720
|
// if no error and no success info, send a error that nothing happened
|
|
2721
|
if( !error && !success)
|
|
2722
|
{
|
|
2723
|
out.println(ERROR);
|
|
2724
|
out.println("Nothing happend for setaccess action");
|
|
2725
|
out.println(ERRORCLOSE);
|
|
2726
|
}
|
|
2727
|
|
|
2728
|
}//outputResponse
|
|
2729
|
}
|