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/**
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* '$RCSfile$'
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* Purpose: A Class that implements org.xml.sax.EntityResolver interface
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* for resolving external entities
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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: Jivka Bojilova, Matt Jones
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*
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* '$Author: tao $'
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* '$Date: 2016-09-13 13:07:09 -0700 (Tue, 13 Sep 2016) $'
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* '$Revision: 9974 $'
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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 org.apache.log4j.Logger;
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import org.xml.sax.*;
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import org.xml.sax.helpers.DefaultHandler;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlList;
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import java.sql.*;
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import java.io.File;
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import java.io.Reader;
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import java.io.BufferedReader;
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import java.io.BufferedInputStream;
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import java.io.FileWriter;
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import java.io.BufferedWriter;
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import java.io.InputStream;
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import java.io.IOException;
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import java.net.URL;
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import java.net.MalformedURLException;
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/**
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* A database aware Class implementing EntityResolver interface for the SAX
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* parser to call when processing the XML stream and intercepting any
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* external entities (including the external DTD subset and external
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* parameter entities, if any) before including them.
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*/
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public class DBEntityResolver implements EntityResolver
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{
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private DBConnection connection = null;
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private DefaultHandler handler = null;
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private String docname = null;
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private String doctype = null;
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private String systemid = null;
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private Reader dtdtext = null;
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private static Logger logMetacat = Logger.getLogger(DBEntityResolver.class);
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/**
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* Construct an instance of the DBEntityResolver class
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*
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* @param conn the JDBC connection to which information is written
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*/
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public DBEntityResolver(DBConnection conn)
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{
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this.connection= conn;
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}
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/**
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* Construct an instance of the DBEntityResolver class
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*
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* @param conn the JDBC connection to which information is written
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* @param handler the SAX handler to determine parsing context
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* @param dtd Reader of new dtd to be uploaded on server's file system
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*/
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public DBEntityResolver(DBConnection conn, DefaultHandler handler, Reader dtd)
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{
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this.connection = conn;
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this.handler = handler;
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this.dtdtext = dtd;
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}
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/**
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* The Parser call this method before opening any external entity
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* except the top-level document entity (including the external DTD subset,
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* external entities referenced within the DTD, and external entities
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* referenced within the document element)
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*/
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public InputSource resolveEntity (String publicId, String systemId)
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throws SAXException
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{
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InputSource dtdSource= null;
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logMetacat.debug("DBEntityResolver.resolveEntity - in resolveEntity "+" the public id is "+publicId+" and systemId is "+systemId);
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String dbSystemID;
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String doctype = null;
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// Won't have a handler under all cases
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if ( handler != null ) {
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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 applied and the document is rejected";
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logMetacat.debug("DBEntityResolver.resolveEntity - the handler class is "+handler.getClass().getCanonicalName());
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if ( handler instanceof DBSAXHandler ) {
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DBSAXHandler dhandler = null;
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dhandler = (DBSAXHandler)handler;
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if ( dhandler.processingDTD() ) {
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logMetacat.debug("DBEntityResolver.resolveEntity - in the branch of the handler class is DBSAXHandler");
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// public ID is doctype
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if (publicId != null) {
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doctype = publicId;
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logMetacat.debug("DBEntityResolver.resolveEntity - the publicId is not null, so the publicId is the doctype. The doctype is: "
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+ doctype);
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// assume public ID (doctype) is docname
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} else {
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doctype = dhandler.getDocname();
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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: "
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+ doctype);
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}
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if(doctype == null || doctype.trim().equals("")) {
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//we can't determine the public id or the name of the root element in for this dtd defined xml document
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logMetacat.error("DBEntityResolver.resolveEntity - "+message);
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throw new SAXException(message);
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} else {
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logMetacat.debug("DBEntityResolver.resolveEntity - the final doctype for DBSAXHandler "+doctype);
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}
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}
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} else if ( handler instanceof AccessControlList ) {
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logMetacat.debug("DBEntityResolver.resolveEntity - in the branch of the handler class is AccessControlList");
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AccessControlList ahandler = null;
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ahandler = (AccessControlList)handler;
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if ( ahandler.processingDTD() ) {
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// public ID is doctype
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if (publicId != null) {
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doctype = publicId;
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logMetacat.debug("DBEntityResolver.resolveEntity - the publicId is not null, so the publicId is the doctype. The doctype in AccessControlList is: "
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+ doctype);
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// assume public ID (doctype) is docname
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} else {
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doctype = ahandler.getDocname();
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logMetacat.debug("DBEntityResolver.resolveEntity - the publicId is null and we treat the doc name(the root element name) as the doc type. The doctype in AccessControlList is: "
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+ doctype);
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}
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if(doctype == null || doctype.trim().equals("")) {
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//we can't determine the public id or the name of the root element in for this dtd defined xml document
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logMetacat.error("DBEntityResolver.resolveEntity - "+message);
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throw new SAXException(message);
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} else {
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logMetacat.debug("DBEntityResolver.resolveEntity - the final doctype for AccessControList "+doctype);
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}
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} else {
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logMetacat.debug("DBEntityResolver.resolveEntity - the method resolverEntity for the AccessControList class is not processing a dtd");
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}
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} else {
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logMetacat.debug("DBEntityResolver.resolveEntity - in the branch of the other handler class");
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}
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} else {
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logMetacat.debug("DBEntityResolver.resolveEntity - the xml handler is null. So we can't find the doctype.");
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}
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// get System ID for doctype
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if (doctype != null) {
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// look at db XML Catalog for System ID
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logMetacat.info("DBEntityResolver.resolveEntity - get systemId from doctype: " + doctype);
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dbSystemID = getDTDSystemID(doctype);
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logMetacat.info("DBEntityResolver.resolveEntity - The Systemid from xml_catalog table is: " + dbSystemID);
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if(dbSystemID == null) {
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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");
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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");
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}
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// check that it is accessible on our system before getting too far
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try {
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InputStream in = checkURLConnection(dbSystemID);
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dtdSource = new InputSource(in);
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} catch (SAXException se) {
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se.printStackTrace();
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throw se;
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// after an upgrade, the dtd will not exist on disk, but it is in xml catalog. The db system id may be pointing
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// back at this system Try and download it from the original system id and see if we still have a problem
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// checking the URL connection.
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/*logMetacat.warn("DBEntityResolver.resolveEntity - Problem when checking URL Connection: " + se.getMessage());
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logMetacat.warn("DBEntityResolver.resolveEntity - Probably, dtd for doc type " + doctype + " existed in xml catalog, but not on disk. Uploading from: " + systemId);
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InputStream istream = checkURLConnection(systemId);
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uploadDTDFromURL(istream, systemId);
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try {
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Thread.currentThread().sleep(6000);
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checkURLConnection(dbSystemID);
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} catch (Exception e2) {
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logMetacat.error("DBEntityResolver.resolveEntity - still could not find dtd for doc type " + doctype + " at "
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+ dbSystemID + " : " + e2.getMessage());
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dbSystemID = null;
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}*/
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}
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/*boolean doctypeIsInDB = true;
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// no System ID found in db XML Catalog
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if (dbSystemID == null) {
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doctypeIsInDB = false;
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// use the provided System ID
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if (systemId != null) {
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dbSystemID = systemId;
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}
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logMetacat.info("DBEntityResolver.resolveEntity - If above Systemid is null, then get "
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+ "system id from file: " + dbSystemID);
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}
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// there are dtd text provided; try to upload on Metacat
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if ( dtdtext != null ) {
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dbSystemID = uploadDTD(dbSystemID);
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}
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// open URLConnection to check first
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InputStream istream = checkURLConnection(dbSystemID);
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// need to register System ID in db XML Catalog if not yet
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if ( !doctypeIsInDB ) {
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// new DTD from outside URL location; try to upload on Metacat
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if ( dtdtext == null ) {
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dbSystemID = uploadDTDFromURL(istream, dbSystemID);
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}
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registerDTD(doctype, dbSystemID);
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}
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// return a byte-input stream for use
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InputSource is = new InputSource(dbSystemID);
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// close and open URLConnection again
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try {
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istream.close();
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} catch (IOException e) {
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throw new SAXException
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("DBEntityResolver.resolveEntity - I/O issue when resolving entity: " + e.getMessage());
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}
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istream = checkURLConnection(dbSystemID);
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is.setByteStream(istream);
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return is;*/
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} else {
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//InputStream istream = checkURLConnection(systemId);
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//return null;
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}
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return dtdSource;
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}
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249
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/**
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* Look at db XML Catalog to get System ID (if any) for @doctype.
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* Return null if there are no System ID found for @doctype
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*/
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public static String getDTDSystemID( String doctype )
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throws SAXException
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{
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String systemid = null;
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PreparedStatement pstmt = null;
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DBConnection conn = null;
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int serialNumber = -1;
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ResultSet rs = null;
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try {
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//check out DBConnection
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conn=DBConnectionPool.getDBConnection("DBEntityResolver.getDTDSystemID");
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serialNumber=conn.getCheckOutSerialNumber();
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String sql = "SELECT system_id FROM xml_catalog " +
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"WHERE entry_type = 'DTD' AND public_id = ?";
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pstmt = conn.prepareStatement(sql);
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pstmt.setString(1, doctype);
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pstmt.execute();
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rs = pstmt.getResultSet();
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boolean tableHasRows = rs.next();
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if (tableHasRows) {
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systemid = rs.getString(1);
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// system id may not have server url on front. Add it if not.
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if (!systemid.startsWith("http://")) {
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279
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systemid = SystemUtil.getContextURL() + systemid;
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}
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}
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282
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//pstmt.close();
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} catch (SQLException e) {
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284
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throw new SAXException
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285
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("DBEntityResolver.getDTDSystemID - SQL error when getting DTD system ID: " + e.getMessage());
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286
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} catch (PropertyNotFoundException pnfe) {
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287
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throw new SAXException
|
288
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("DBEntityResolver.getDTDSystemID - Property error when getting DTD system ID: " + pnfe.getMessage());
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289
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}
|
290
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finally
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291
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{
|
292
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try
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293
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{
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if(rs != null) {
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295
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rs.close();
|
296
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}
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297
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if(pstmt != null) {
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298
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pstmt.close();
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299
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}
|
300
|
|
301
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}//try
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302
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catch (SQLException sqlE)
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{
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logMetacat.error("DBEntityResolver.getDTDSystemId - SQL error: " + sqlE.getMessage());
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305
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}//catch
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306
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finally
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307
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{
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308
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DBConnectionPool.returnDBConnection(conn, serialNumber);
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309
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}//finally
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310
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}//finally
|
311
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|
312
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// return the selected System ID
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313
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return systemid;
|
314
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}
|
315
|
|
316
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/**
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317
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* Register new DTD identified by @systemId in Metacat XML Catalog
|
318
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* . make a reference with @systemId for @doctype in Metacat DB
|
319
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*/
|
320
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private void registerDTD ( String doctype, String systemId )
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321
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throws SAXException
|
322
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{
|
323
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String existingSystemId = getDTDSystemID(doctype);
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324
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if (existingSystemId != null && existingSystemId.equals(systemId)) {
|
325
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logMetacat.warn("DBEntityResolver.registerDTD - doctype/systemId already registered in DB: " + doctype);
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326
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return;
|
327
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}
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328
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//DBConnection conn = null;
|
329
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//int serialNumber = -1;
|
330
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PreparedStatement pstmt = null;
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331
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// make a reference in db catalog table with @systemId for @doctype
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332
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try {
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333
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//check out DBConnection
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334
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//conn=DBConnectionPool.getDBConnection("DBEntityResolver.registerDTD");
|
335
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//serialNumber=conn.getCheckOutSerialNumber();
|
336
|
|
337
|
|
338
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pstmt = connection.prepareStatement(
|
339
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"INSERT INTO xml_catalog " +
|
340
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"(entry_type, public_id, system_id) " +
|
341
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"VALUES ('DTD', ?, ?)");
|
342
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// Increase usage count
|
343
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connection.increaseUsageCount(1);
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344
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// Bind the values to the query
|
345
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pstmt.setString(1, doctype);
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346
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pstmt.setString(2, systemId);
|
347
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// Do the insertion
|
348
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pstmt.execute();
|
349
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int updateCnt = pstmt.getUpdateCount();
|
350
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logMetacat.debug("DBEntityReolver.registerDTD - DTDs registered: " + updateCnt);
|
351
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pstmt.close();
|
352
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} catch (SQLException e) {
|
353
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throw new SAXException
|
354
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("DBEntityResolver.registerDTD - SQL issue when registering DTD: " + e.getMessage());
|
355
|
}
|
356
|
finally
|
357
|
{
|
358
|
try
|
359
|
{
|
360
|
pstmt.close();
|
361
|
}//try
|
362
|
catch (SQLException sqlE)
|
363
|
{
|
364
|
logMetacat.error("DBEntityResolver.registerDTD - SQL error: " + sqlE.getMessage());
|
365
|
}//catch
|
366
|
//DBConnectionPool.returnDBConnection(conn, serialNumber);
|
367
|
}//finally
|
368
|
|
369
|
}
|
370
|
|
371
|
/**
|
372
|
* Upload new DTD text identified by
|
373
|
*
|
374
|
* @systemId to Metacat file system
|
375
|
*/
|
376
|
private String uploadDTD(String systemId) throws SAXException {
|
377
|
String dtdPath = null;
|
378
|
String dtdURL = null;
|
379
|
try {
|
380
|
dtdPath = SystemUtil.getContextDir() + "/dtd/";
|
381
|
dtdURL = SystemUtil.getContextURL() + "/dtd/";
|
382
|
} catch (PropertyNotFoundException pnfe) {
|
383
|
throw new SAXException("DBEntityResolver.uploadDTD: " + pnfe.getMessage());
|
384
|
}
|
385
|
|
386
|
// get filename from systemId
|
387
|
String filename = systemId;
|
388
|
int slash = Math.max(filename.lastIndexOf('/'), filename.lastIndexOf('\\'));
|
389
|
if (slash > -1) {
|
390
|
filename = filename.substring(slash + 1);
|
391
|
}
|
392
|
|
393
|
// writing dtd text on Metacat file system as filename
|
394
|
try {
|
395
|
// create a buffering character-input stream
|
396
|
// that uses a default-sized input buffer
|
397
|
BufferedReader in = new BufferedReader(dtdtext);
|
398
|
|
399
|
// open file writer to write the input into it
|
400
|
// String dtdPath = "/opt/tomcat/webapps/bojilova/dtd/";
|
401
|
File f = new File(dtdPath, filename);
|
402
|
synchronized (f) {
|
403
|
try {
|
404
|
if (f.exists()) {
|
405
|
throw new IOException("File already exist: "
|
406
|
+ f.getCanonicalFile());
|
407
|
// if ( f.exists() && !f.canWrite() ) {
|
408
|
// throw new IOException("Not writable: " +
|
409
|
// f.getCanonicalFile());
|
410
|
}
|
411
|
} catch (SecurityException se) {
|
412
|
// if a security manager exists,
|
413
|
// its checkRead method is called for f.exist()
|
414
|
// or checkWrite method is called for f.canWrite()
|
415
|
throw se;
|
416
|
}
|
417
|
// create a buffered character-output stream
|
418
|
// that uses a default-sized output buffer
|
419
|
FileWriter fw = new FileWriter(f);
|
420
|
BufferedWriter out = new BufferedWriter(fw);
|
421
|
|
422
|
// read the input and write into the file writer
|
423
|
String inputLine;
|
424
|
while ((inputLine = in.readLine()) != null) {
|
425
|
out.write(inputLine, 0, inputLine.length());
|
426
|
out.newLine(); // instead of out.write('\r\n');
|
427
|
}
|
428
|
|
429
|
// the input and the output streams must be closed
|
430
|
in.close();
|
431
|
out.flush();
|
432
|
out.close();
|
433
|
fw.close();
|
434
|
} // end of synchronized
|
435
|
} catch (MalformedURLException e) {
|
436
|
throw new SAXException("DBEntityResolver.uploadDTD() - Malformed URL when uploading DTD: " + e.getMessage());
|
437
|
} catch (IOException e) {
|
438
|
throw new SAXException("DBEntityResolver.uploadDTD - I/O issue when uploading DTD: " + e.getMessage());
|
439
|
} catch (SecurityException e) {
|
440
|
throw new SAXException("DBEntityResolver.uploadDTD() - Security issue when uploading DTD: " + e.getMessage());
|
441
|
}
|
442
|
|
443
|
// String dtdURL = "http://dev.nceas.ucsb.edu/bojilova/dtd/";
|
444
|
return dtdURL + filename;
|
445
|
}
|
446
|
|
447
|
|
448
|
/**
|
449
|
* Upload new DTD located at outside URL to Metacat file system
|
450
|
*/
|
451
|
private String uploadDTDFromURL(InputStream istream, String systemId)
|
452
|
throws SAXException {
|
453
|
String dtdPath = null;
|
454
|
String dtdURL = null;
|
455
|
try {
|
456
|
dtdPath = SystemUtil.getContextDir() + "/dtd/";
|
457
|
dtdURL = SystemUtil.getContextURL() + "/dtd/";
|
458
|
} catch (PropertyNotFoundException pnfe) {
|
459
|
throw new SAXException("DBEntityResolver.uploadDTDFromURL - Property issue when uploading DTD from URL: "
|
460
|
+ pnfe.getMessage());
|
461
|
}
|
462
|
|
463
|
// get filename from systemId
|
464
|
String filename = systemId;
|
465
|
int slash = Math.max(filename.lastIndexOf('/'), filename.lastIndexOf('\\'));
|
466
|
if (slash > -1) {
|
467
|
filename = filename.substring(slash + 1);
|
468
|
}
|
469
|
|
470
|
// writing dtd text on Metacat file system as filename
|
471
|
try {
|
472
|
// create a buffering character-input stream
|
473
|
// that uses a default-sized input buffer
|
474
|
BufferedInputStream in = new BufferedInputStream(istream);
|
475
|
|
476
|
// open file writer to write the input into it
|
477
|
//String dtdPath = "/opt/tomcat/webapps/bojilova/dtd/";
|
478
|
File f = new File(dtdPath, filename);
|
479
|
synchronized (f) {
|
480
|
try {
|
481
|
if (f.exists()) {
|
482
|
logMetacat.warn("DBEntityResolver.uploadDTDFromURL - File already exists: " + f.getCanonicalFile());
|
483
|
//return dtdURL + filename;
|
484
|
//throw new IOException("File already exist: "
|
485
|
// + f.getCanonicalFile());
|
486
|
//if ( f.exists() && !f.canWrite() ) {
|
487
|
// throw new IOException("Not writable: " + f.getCanonicalFile());
|
488
|
}
|
489
|
} catch (SecurityException se) {
|
490
|
// if a security manager exists,
|
491
|
// its checkRead method is called for f.exist()
|
492
|
// or checkWrite method is called for f.canWrite()
|
493
|
throw se;
|
494
|
}
|
495
|
// create a buffered character-output stream
|
496
|
// that uses a default-sized output buffer
|
497
|
FileWriter fw = new FileWriter(f);
|
498
|
BufferedWriter out = new BufferedWriter(fw);
|
499
|
|
500
|
// read the input and write into the file writer
|
501
|
int inputByte;
|
502
|
while ((inputByte = in.read()) != -1) {
|
503
|
out.write(inputByte);
|
504
|
//out.newLine(); //instead of out.write('\r\n');
|
505
|
}
|
506
|
|
507
|
// the input and the output streams must be closed
|
508
|
in.close();
|
509
|
out.flush();
|
510
|
out.close();
|
511
|
fw.close();
|
512
|
} // end of synchronized
|
513
|
} catch (MalformedURLException e) {
|
514
|
throw new SAXException("DBEntityResolver.uploadDTDFromURL - Malformed URL when uploading DTD from URL: "
|
515
|
+ e.getMessage());
|
516
|
} catch (IOException e) {
|
517
|
throw new SAXException("DBEntityResolver.uploadDTDFromURL - I/O issue when uploading DTD from URL: "
|
518
|
+ e.getMessage());
|
519
|
} catch (SecurityException e) {
|
520
|
throw new SAXException("DBEntityResolver.uploadDTDFromURL - Security issue when uploading DTD from URL: "
|
521
|
+ e.getMessage());
|
522
|
}
|
523
|
|
524
|
//String dtdURL = "http://dev.nceas.ucsb.edu/bojilova/dtd/";
|
525
|
return dtdURL + filename;
|
526
|
}
|
527
|
|
528
|
/**
|
529
|
* Check URL Connection for @systemId, and return an InputStream
|
530
|
* that can be used to read from the systemId URL. The parser ends
|
531
|
* up using this via the InputSource to read the DTD.
|
532
|
*
|
533
|
* @param systemId a URI (in practice URL) to be checked and opened
|
534
|
*/
|
535
|
public static InputStream checkURLConnection(String systemId) throws SAXException {
|
536
|
try {
|
537
|
return (new URL(systemId).openStream());
|
538
|
|
539
|
} catch (MalformedURLException e) {
|
540
|
throw new SAXException("DBEntityResolver.checkURLConnection - Malformed URL when checking URL Connection: "
|
541
|
+ e.getMessage());
|
542
|
} catch (IOException e) {
|
543
|
throw new SAXException("DBEntityResolver.checkURLConnection - I/O issue when checking URL Connection: "
|
544
|
+ e.getMessage());
|
545
|
}
|
546
|
}
|
547
|
}
|