Metacat

/**

 *  '$RCSfile$'

 *    Purpose: A Class that implements org.xml.sax.EntityResolver interface

 *             for resolving external entities

 *  Copyright: 2000 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *    Authors: Jivka Bojilova, Matt Jones

 *

 *   '$Author: tao $'

 *     '$Date: 2016-09-02 18:20:44 -0700 (Fri, 02 Sep 2016) $'

 * '$Revision: 9916 $'

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat;

import org.apache.log4j.Logger;

import org.xml.sax.*;

import org.xml.sax.helpers.DefaultHandler;

import edu.ucsb.nceas.metacat.accesscontrol.AccessControlList;

import edu.ucsb.nceas.metacat.database.DBConnection;

import edu.ucsb.nceas.metacat.database.DBConnectionPool;

import edu.ucsb.nceas.metacat.util.SystemUtil;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

import java.sql.*;

import java.io.File;

import java.io.Reader;

import java.io.BufferedReader;

import java.io.BufferedInputStream;

import java.io.FileWriter;

import java.io.BufferedWriter;

import java.io.InputStream;

import java.io.IOException;

import java.net.URL;

import java.net.MalformedURLException;

/**

 * A database aware Class implementing EntityResolver interface for the SAX

 * parser to call when processing the XML stream and intercepting any

 * external entities (including the external DTD subset and external

 * parameter entities, if any) before including them.

 */

public class DBEntityResolver implements EntityResolver

{

  private DBConnection connection = null;

  private DefaultHandler handler = null;

  private String docname = null;

  private String doctype = null;

  private String systemid = null;

  private Reader dtdtext = null;

  private static Logger logMetacat = Logger.getLogger(DBEntityResolver.class);

  /**

   * Construct an instance of the DBEntityResolver class

   *

   * @param conn the JDBC connection to which information is written

   */

  public DBEntityResolver(DBConnection conn)

  {

    this.connection= conn;

  }

  /**

   * Construct an instance of the DBEntityResolver class

   *

   * @param conn the JDBC connection to which information is written

   * @param handler the SAX handler to determine parsing context

   * @param dtd Reader of new dtd to be uploaded on server's file system

   */

  public DBEntityResolver(DBConnection conn, DefaultHandler handler, Reader dtd)

  {

    this.connection = conn;

    this.handler = handler;

    this.dtdtext = dtd;

  }

  /**

   * The Parser call this method before opening any external entity

   * except the top-level document entity (including the external DTD subset,

   * external entities referenced within the DTD, and external entities

   * referenced within the document element)

   */

  public InputSource resolveEntity (String publicId, String systemId)

                     throws SAXException

  {

    InputSource dtdSource= null;

    logMetacat.debug("DBEntityResolver.resolveEntity - in resolveEntity "+" the public id is "+publicId+" and systemId is "+systemId);

    String dbSystemID;

    String doctype = null;

    // Won't have a handler under all cases

    if ( handler != null ) {

      if ( handler instanceof DBSAXHandler ) {

        DBSAXHandler dhandler = null;

        dhandler = (DBSAXHandler)handler;

        if ( dhandler.processingDTD() ) {

          // public ID is doctype

          if (publicId != null) {

            doctype = publicId;

            logMetacat.debug("DBEntityResolver.resolveEntity - the publicId is not null, so the publicId is the doctype. The doctype is: "

                                     + doctype);

          // assume public ID (doctype) is docname

          } else {

            doctype = dhandler.getDocname();

            logMetacat.debug("DBEntityResolver.resolveEntity - the publicId is null and we treat the doc name(the root element name) as the doc type. The doctype is: "

                    + doctype);

          }

        }

      } else if ( handler instanceof AccessControlList ) {

        AccessControlList ahandler = null;

        ahandler = (AccessControlList)handler;

        if ( ahandler.processingDTD() ) {

          // public ID is doctype

          if (publicId != null) {

            doctype = publicId;

          // assume public ID (doctype) is docname

          } else {

            doctype = ahandler.getDocname();

          }

        }

      }

    } else {

        logMetacat.debug("DBEntityResolver.resolveEntity - the xml handler is null. So we can't find the doctype.");

    }

    // get System ID for doctype

    if (doctype != null) {

      // look at db XML Catalog for System ID

      logMetacat.info("DBEntityResolver.resolveEntity - get systemId from doctype: " + doctype);

      dbSystemID = getDTDSystemID(doctype);

      logMetacat.info("DBEntityResolver.resolveEntity - The Systemid from xml_catalog table is: " + dbSystemID);

      if(dbSystemID == null) {

          logMetacat.error("DBEntityResolver.resolveEntity - "+"The doctype: "+doctype+" , which was defined by a DTD document, isn't registered in Metacat. Please contact the operator of the Metacat");

          throw new SAXException("The doctype: "+doctype+" , which was defined by a DTD document, isn't registered in Metacat. Please contact the operator of the Metacat");

      }

      // check that it is accessible on our system before getting too far

      try {

    	  InputStream in = checkURLConnection(dbSystemID);

    	  dtdSource = new InputSource(in);

	  } catch (SAXException se) {

	      se.printStackTrace();

	      throw se;

		  // after an upgrade, the dtd will not exist on disk, but it is in xml catalog.  The db system id may be pointing 

		  // back at this system  Try and download it from the original system id and see if we still have a problem

		  // checking the URL connection.

		  /*logMetacat.warn("DBEntityResolver.resolveEntity - Problem when checking URL Connection: " + se.getMessage());

		  logMetacat.warn("DBEntityResolver.resolveEntity - Probably, dtd for doc type " + doctype + " existed in xml catalog, but not on disk.  Uploading from: " + systemId);

		  InputStream istream = checkURLConnection(systemId);

		  uploadDTDFromURL(istream, systemId);

		  try {

			  Thread.currentThread().sleep(6000);

			  checkURLConnection(dbSystemID);

		  } catch (Exception e2) {

			  logMetacat.error("DBEntityResolver.resolveEntity - still could not find dtd for doc type " + doctype + " at " 

					  + dbSystemID + " : " + e2.getMessage());

			  dbSystemID = null;

		  }*/

	  } 

      /*boolean doctypeIsInDB = true;

      // no System ID found in db XML Catalog

      if (dbSystemID == null) {

        doctypeIsInDB = false;

        // use the provided System ID

        if (systemId != null) {

          dbSystemID = systemId;

        }

        logMetacat.info("DBEntityResolver.resolveEntity - If above Systemid is null, then get "

                                 + "system id from file: " + dbSystemID);

      }

      // there are dtd text provided; try to upload on Metacat

      if ( dtdtext != null ) {

        dbSystemID = uploadDTD(dbSystemID);

      }

      // open URLConnection to check first

      InputStream istream = checkURLConnection(dbSystemID);

      // need to register System ID in db XML Catalog if not yet

      if ( !doctypeIsInDB ) {

        // new DTD from outside URL location; try to upload on Metacat

        if ( dtdtext == null ) {

          dbSystemID = uploadDTDFromURL(istream, dbSystemID);

        }

        registerDTD(doctype, dbSystemID);

      }

      // return a byte-input stream for use

      InputSource is = new InputSource(dbSystemID);

      // close and open URLConnection again

      try {

        istream.close();

      } catch (IOException e) {

        throw new SAXException

        ("DBEntityResolver.resolveEntity - I/O issue when resolving entity: " + e.getMessage());

      }

      istream = checkURLConnection(dbSystemID);

      is.setByteStream(istream);

      return is;*/

    } else {

      //we can't determine the public id or the name of the root element in for this dtd defined xml document

      String message = "Metacat can't determine the public id or the name of the root element of the document, so the validation can't be imposed and the document is rejected";

      logMetacat.error("DBEntityResolver.resolveEntity - "+message);

      throw new SAXException(message);

      //InputStream istream = checkURLConnection(systemId);

      //return null;

    }

    return dtdSource;

  }

  /**

   * Look at db XML Catalog to get System ID (if any) for @doctype.

   * Return null if there are no System ID found for @doctype

   */

  public static String getDTDSystemID( String doctype )

                 throws SAXException

  {

    String systemid = null;

    PreparedStatement pstmt = null;

    DBConnection conn = null;

    int serialNumber = -1;

    ResultSet rs = null;

    try {

      //check out DBConnection

      conn=DBConnectionPool.getDBConnection("DBEntityResolver.getDTDSystemID");

      serialNumber=conn.getCheckOutSerialNumber();

      String sql = "SELECT system_id FROM xml_catalog " +

      "WHERE entry_type = 'DTD' AND public_id = ?";

      pstmt = conn.prepareStatement(sql);

      pstmt.setString(1, doctype);

      pstmt.execute();

      rs = pstmt.getResultSet();

      boolean tableHasRows = rs.next();

      if (tableHasRows) {

        systemid = rs.getString(1);

        // system id may not have server url on front.  Add it if not.

        if (!systemid.startsWith("http://")) {

        	systemid = SystemUtil.getContextURL() + systemid;

        }

      }

      //pstmt.close();

    } catch (SQLException e) {

      throw new SAXException

      ("DBEntityResolver.getDTDSystemID - SQL error when getting DTD system ID: " + e.getMessage());

    } catch (PropertyNotFoundException pnfe) {

        throw new SAXException

        ("DBEntityResolver.getDTDSystemID - Property error when getting DTD system ID:  " + pnfe.getMessage());

      }

    finally

    {

      try

      {

          if(rs != null) {

              rs.close();

          }

          if(pstmt != null) {

              pstmt.close();

          }

      }//try

      catch (SQLException sqlE)

      {

        logMetacat.error("DBEntityResolver.getDTDSystemId - SQL error: " + sqlE.getMessage());

      }//catch

      finally

      {

        DBConnectionPool.returnDBConnection(conn, serialNumber);

      }//finally

    }//finally

    // return the selected System ID

    return systemid;

  }

  /**

   * Register new DTD identified by @systemId in Metacat XML Catalog

   * . make a reference with @systemId for @doctype in Metacat DB

   */

  private void registerDTD ( String doctype, String systemId )

                 throws SAXException

  {

	  String existingSystemId = getDTDSystemID(doctype);

	  if (existingSystemId != null && existingSystemId.equals(systemId)) {

		  logMetacat.warn("DBEntityResolver.registerDTD - doctype/systemId already registered in DB: " + doctype);

		  return;

	  }

    //DBConnection conn = null;

    //int serialNumber = -1;

    PreparedStatement pstmt = null;

    // make a reference in db catalog table with @systemId for @doctype

    try {

      //check out DBConnection

      //conn=DBConnectionPool.getDBConnection("DBEntityResolver.registerDTD");

      //serialNumber=conn.getCheckOutSerialNumber();

      pstmt = connection.prepareStatement(

             "INSERT INTO xml_catalog " +

             "(entry_type, public_id, system_id) " +

             "VALUES ('DTD', ?, ?)");

      // Increase usage count

      connection.increaseUsageCount(1);

      // Bind the values to the query

      pstmt.setString(1, doctype);

      pstmt.setString(2, systemId);

      // Do the insertion

      pstmt.execute();

      int updateCnt = pstmt.getUpdateCount();

      logMetacat.debug("DBEntityReolver.registerDTD - DTDs registered: " + updateCnt);

      pstmt.close();

    } catch (SQLException e) {

      throw new SAXException

      ("DBEntityResolver.registerDTD - SQL issue when registering DTD: " + e.getMessage());

    }

    finally

    {

      try

      {

        pstmt.close();

      }//try

      catch (SQLException sqlE)

      {

        logMetacat.error("DBEntityResolver.registerDTD - SQL error: " + sqlE.getMessage());

      }//catch

      //DBConnectionPool.returnDBConnection(conn, serialNumber);

    }//finally

  }

  /**

	 * Upload new DTD text identified by

	 * 

	 * @systemId to Metacat file system

	 */

	private String uploadDTD(String systemId) throws SAXException {

		String dtdPath = null;

		String dtdURL = null;

		try {

			dtdPath = SystemUtil.getContextDir() + "/dtd/";

			dtdURL = SystemUtil.getContextURL() + "/dtd/";

		} catch (PropertyNotFoundException pnfe) {

			throw new SAXException("DBEntityResolver.uploadDTD: " + pnfe.getMessage());

		}

		// get filename from systemId

		String filename = systemId;

		int slash = Math.max(filename.lastIndexOf('/'), filename.lastIndexOf('\\'));

		if (slash > -1) {

			filename = filename.substring(slash + 1);

		}

		// writing dtd text on Metacat file system as filename

		try {

			// create a buffering character-input stream

			// that uses a default-sized input buffer

			BufferedReader in = new BufferedReader(dtdtext);

			// open file writer to write the input into it

			// String dtdPath = "/opt/tomcat/webapps/bojilova/dtd/";

			File f = new File(dtdPath, filename);

			synchronized (f) {

				try {

					if (f.exists()) {

						throw new IOException("File already exist: "

								+ f.getCanonicalFile());

						// if ( f.exists() && !f.canWrite() ) {

						// throw new IOException("Not writable: " +

						// f.getCanonicalFile());

					}

				} catch (SecurityException se) {

					// if a security manager exists,

					// its checkRead method is called for f.exist()

					// or checkWrite method is called for f.canWrite()

					throw se;

				}

				// create a buffered character-output stream

				// that uses a default-sized output buffer

				FileWriter fw = new FileWriter(f);

				BufferedWriter out = new BufferedWriter(fw);

				// read the input and write into the file writer

				String inputLine;

				while ((inputLine = in.readLine()) != null) {

					out.write(inputLine, 0, inputLine.length());

					out.newLine(); // instead of out.write('\r\n');

				}

				// the input and the output streams must be closed

				in.close();

				out.flush();

				out.close();

				fw.close();

			} // end of synchronized

		} catch (MalformedURLException e) {

			throw new SAXException("DBEntityResolver.uploadDTD() - Malformed URL when uploading DTD: " + e.getMessage());

		} catch (IOException e) {

			throw new SAXException("DBEntityResolver.uploadDTD - I/O issue when uploading DTD: " + e.getMessage());

		} catch (SecurityException e) {

			throw new SAXException("DBEntityResolver.uploadDTD() - Security issue when uploading DTD: " + e.getMessage());

		}

		// String dtdURL = "http://dev.nceas.ucsb.edu/bojilova/dtd/";

		return dtdURL + filename;

	}

  /**

	 * Upload new DTD located at outside URL to Metacat file system

	 */

	private String uploadDTDFromURL(InputStream istream, String systemId)

			throws SAXException {

		String dtdPath = null;

		String dtdURL = null;

		try {

			dtdPath = SystemUtil.getContextDir() + "/dtd/";

			dtdURL = SystemUtil.getContextURL() + "/dtd/";

		} catch (PropertyNotFoundException pnfe) {

			throw new SAXException("DBEntityResolver.uploadDTDFromURL - Property issue when uploading DTD from URL: "

					+ pnfe.getMessage());

		}

		// get filename from systemId

		String filename = systemId;

		int slash = Math.max(filename.lastIndexOf('/'), filename.lastIndexOf('\\'));

		if (slash > -1) {

			filename = filename.substring(slash + 1);

		}

		// writing dtd text on Metacat file system as filename

		try {

			// create a buffering character-input stream

			// that uses a default-sized input buffer

			BufferedInputStream in = new BufferedInputStream(istream);

			// open file writer to write the input into it

			//String dtdPath = "/opt/tomcat/webapps/bojilova/dtd/";

			File f = new File(dtdPath, filename);

			synchronized (f) {

				try {

					if (f.exists()) {

						logMetacat.warn("DBEntityResolver.uploadDTDFromURL - File already exists: " + f.getCanonicalFile());

						//return dtdURL + filename;

						//throw new IOException("File already exist: "

						//		+ f.getCanonicalFile());

						//if ( f.exists() && !f.canWrite() ) {

						//  throw new IOException("Not writable: " + f.getCanonicalFile());

					}

				} catch (SecurityException se) {

					// if a security manager exists,

					// its checkRead method is called for f.exist()

					// or checkWrite method is called for f.canWrite()

					throw se;

				}

				// create a buffered character-output stream

				// that uses a default-sized output buffer

				FileWriter fw = new FileWriter(f);

				BufferedWriter out = new BufferedWriter(fw);

				// read the input and write into the file writer

				int inputByte;

				while ((inputByte = in.read()) != -1) {

					out.write(inputByte);

					//out.newLine(); //instead of out.write('\r\n');

				}

				// the input and the output streams must be closed

				in.close();

				out.flush();

				out.close();

				fw.close();

			} // end of synchronized

		} catch (MalformedURLException e) {

			throw new SAXException("DBEntityResolver.uploadDTDFromURL - Malformed URL when uploading DTD from URL: "

					+ e.getMessage());

		} catch (IOException e) {

			throw new SAXException("DBEntityResolver.uploadDTDFromURL - I/O issue when uploading DTD from URL:  "

					+ e.getMessage());

		} catch (SecurityException e) {

			throw new SAXException("DBEntityResolver.uploadDTDFromURL - Security issue when uploading DTD from URL:  "

					+ e.getMessage());

		}

		//String dtdURL = "http://dev.nceas.ucsb.edu/bojilova/dtd/";

		return dtdURL + filename;

	}

	/**

	 * Check URL Connection for @systemId, and return an InputStream

	 * that can be used to read from the systemId URL.  The parser ends

	 * up using this via the InputSource to read the DTD.

	 *

	 * @param systemId a URI (in practice URL) to be checked and opened

	 */

	public static InputStream checkURLConnection(String systemId) throws SAXException {

		try {

			return (new URL(systemId).openStream());

		} catch (MalformedURLException e) {

			throw new SAXException("DBEntityResolver.checkURLConnection - Malformed URL when checking URL Connection: "

					+ e.getMessage());

		} catch (IOException e) {

			throw new SAXException("DBEntityResolver.checkURLConnection - I/O issue when checking URL Connection: "

					+ e.getMessage());

		}

	}

}