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Apache XML Security for Java supports XML-Signature Syntax and Processing, W3C Recommendation 12 February 2002, and XML Encryption Syntax and Processing, W3C Recommendation 10 December 2002. As of version 1.4, the library supports the standard Java API JSR-105: XML Digital Signature APIs.
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/**
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements. See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership. The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License. You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */
package org.apache.xml.security.stax.config;

import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;

import javax.xml.XMLConstants;
import javax.xml.namespace.NamespaceContext;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMResult;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.sax.SAXResult;
import javax.xml.transform.sax.SAXTransformerFactory;
import javax.xml.transform.sax.TransformerHandler;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import javax.xml.xpath.XPathFactoryConfigurationException;

import org.apache.xml.security.utils.ClassLoaderUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.Attributes;
import org.xml.sax.ContentHandler;
import org.xml.sax.Locator;
import org.xml.sax.SAXException;
import org.xml.sax.SAXParseException;
import org.xml.sax.XMLReader;
import org.xml.sax.helpers.DefaultHandler;
import org.xml.sax.helpers.XMLReaderFactory;

/**
 * Absolutely primitive XInclude#xpointer scheme handling
 *
 */
public class XIncludeHandler extends DefaultHandler {

    private static final transient Logger LOG = LoggerFactory.getLogger(XIncludeHandler.class);

    private static final String xIncludeNS = "http://www.w3.org/2001/XInclude";
    private static final String xIncludeLN = "include";
    private final ContentHandler contentHandler;
    private URL systemId;
    private boolean skipEvents = false;

    private final Map uriDocMap;

    public XIncludeHandler(ContentHandler contentHandler) {
        this(contentHandler, new HashMap<>());
    }

    private XIncludeHandler(ContentHandler contentHandler, Map uriDocMap) {
        this.contentHandler = contentHandler;
        this.uriDocMap = uriDocMap;
    }

    @Override
    public void setDocumentLocator(Locator locator) {
        //this.systemId could already be set when we do a IdentityTransform (@see below)
        if (locator.getSystemId() == null && this.systemId == null) {
            throw new UnsupportedOperationException("Please specify a correct systemId to the sax.parse() method!");
        }
        try {
            if (locator.getSystemId() != null) {
                this.systemId = new URL(locator.getSystemId());
            }
        } catch (MalformedURLException e) {
            throw new IllegalArgumentException(e);
        }
        this.contentHandler.setDocumentLocator(locator);
    }

    @Override
    public void startDocument() throws SAXException {
        if (!skipEvents) {
            this.contentHandler.startDocument();
        }
    }

    @Override
    public void endDocument() throws SAXException {
        if (!skipEvents) {
            this.contentHandler.endDocument();
        }
    }

    @Override
    public void startPrefixMapping(String prefix, String uri) throws SAXException {
        if (!skipEvents) {
            this.contentHandler.startPrefixMapping(prefix, uri);
        }
    }

    @Override
    public void endPrefixMapping(String prefix) throws SAXException {
        if (!skipEvents) {
            this.contentHandler.endPrefixMapping(prefix);
        }
    }

    @Override
    public void startElement(String uri, String localName, String qName, Attributes atts) throws SAXException {
        if (xIncludeNS.equals(uri) && xIncludeLN.equals(localName)) {
            String href = atts.getValue("href");
            if (href == null) {
                throw new SAXException("XInclude href attribute is missing");
            }
            String parse = atts.getValue("parse");
            if (parse != null && !"xml".equals(parse)) {
                throw new UnsupportedOperationException("Only parse=\"xml\" is currently supported");
            }
            String xpointer = atts.getValue("xpointer");

            URL url = ClassLoaderUtils.getResource(href, XIncludeHandler.class);
            if (url == null) {
                throw new SAXException("XML file not found: " + href);
            }
            Document document = null;
            try {
                document = uriDocMap.get(url.toURI());
            } catch (URISyntaxException ex) {
                throw new SAXException(ex);
            }

            if (document == null) {
                DOMResult domResult = new DOMResult();
                try {
                    XMLReader xmlReader = XMLReaderFactory.createXMLReader();
                    SAXTransformerFactory saxTransformerFactory = (SAXTransformerFactory) TransformerFactory.newInstance();
                    saxTransformerFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, Boolean.TRUE);
                    try {
                        saxTransformerFactory.setAttribute(XMLConstants.ACCESS_EXTERNAL_DTD, "");
                        saxTransformerFactory.setAttribute(XMLConstants.ACCESS_EXTERNAL_STYLESHEET, "");
                    } catch (IllegalArgumentException ex) {
                        // ignore
                    }

                    TransformerHandler transformerHandler = saxTransformerFactory.newTransformerHandler();
                    transformerHandler.setResult(domResult);
                    xmlReader.setContentHandler(new XIncludeHandler(transformerHandler, uriDocMap));
                    xmlReader.parse(url.toExternalForm());
                } catch (TransformerConfigurationException e) {
                    throw new SAXException(e);
                } catch (IOException e) {
                    throw new SAXException(e);
                }

                document = (Document) domResult.getNode();
                document.setDocumentURI(url.toExternalForm());
                try {
                    uriDocMap.put(url.toURI(), document);
                } catch (URISyntaxException e) {
                    throw new SAXException(e);
                }
            }

            SAXResult saxResult = new SAXResult(this);
            skipEvents = true;
            try {
                TransformerFactory transformerFactory = TransformerFactory.newInstance();
                transformerFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, Boolean.TRUE);
                try {
                    transformerFactory.setAttribute(XMLConstants.ACCESS_EXTERNAL_DTD, "");
                    transformerFactory.setAttribute(XMLConstants.ACCESS_EXTERNAL_STYLESHEET, "");
                } catch (IllegalArgumentException ex) {
                    // ignore
                }

                Transformer transformer = transformerFactory.newTransformer();
                if (xpointer == null) {
                    transformer.transform(new DOMSource(document, document.getDocumentURI()), saxResult);
                } else {
                    NodeList nodeList = evaluateXPointer(xpointer, document);
                    int length = nodeList.getLength();
                    for (int i = 0; i < length; i++) {
                        Node node = nodeList.item(i);
                        transformer.transform(new DOMSource(node, document.getDocumentURI()), saxResult);
                    }
                }
            } catch (TransformerConfigurationException e) {
                throw new SAXException(e);
            } catch (TransformerException e) {
                throw new SAXException(e);
            } finally {
                skipEvents = false;
            }

        } else {
            this.contentHandler.startElement(uri, localName, qName, atts);
        }
    }

    @Override
    public void endElement(String uri, String localName, String qName) throws SAXException {
        if (!(xIncludeNS.equals(uri) && xIncludeLN.equals(localName))) {
            this.contentHandler.endElement(uri, localName, qName);
        }
    }

    @Override
    public void characters(char[] ch, int start, int length) throws SAXException {
        this.contentHandler.characters(ch, start, length);
    }

    @Override
    public void ignorableWhitespace(char[] ch, int start, int length) throws SAXException {
        this.contentHandler.ignorableWhitespace(ch, start, length);
    }

    @Override
    public void processingInstruction(String target, String data) throws SAXException {
        this.contentHandler.processingInstruction(target, data);
    }

    @Override
    public void skippedEntity(String name) throws SAXException {
        this.contentHandler.skippedEntity(name);
    }

    @Override
    public void warning(SAXParseException e) throws SAXException {
        LOG.warn(e.getMessage(), e);
    }

    @Override
    public void error(SAXParseException e) throws SAXException {
        LOG.error(e.getMessage(), e);
    }

    @Override
    public void fatalError(SAXParseException e) throws SAXException {
        LOG.error(e.getMessage(), e);
    }

    private NodeList evaluateXPointer(String xpointer, Node node) throws SAXException {
        final String xPointerSchemeString = "xpointer(";
        final String xmlnsSchemeString = "xmlns(";
        int xPointerSchemeIndex = xpointer.indexOf(xPointerSchemeString);
        if (xPointerSchemeIndex < 0) {
            throw new SAXException("Only xpointer scheme is supported ATM");
        }
        xPointerSchemeIndex += xPointerSchemeString.length();
        int xPointerSchemeEndIndex = this.findBalancedEndIndex(xpointer, xPointerSchemeIndex, '(', ')');
        XPathFactory xPathFactory = XPathFactory.newInstance();
        try {
            xPathFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, Boolean.TRUE);
        } catch (XPathFactoryConfigurationException ex) {
            throw new SAXException(ex);
        }
        XPath xPath = xPathFactory.newXPath();

        int xmlnsSchemeIndex = xpointer.indexOf(xmlnsSchemeString);
        if (xmlnsSchemeIndex >= 0) {
            xmlnsSchemeIndex += xmlnsSchemeString.length();
            int xmlnsSchemeEndIndex = this.findBalancedEndIndex(xpointer, xmlnsSchemeIndex, '(', ')');
            String namespaceScheme = xpointer.substring(xmlnsSchemeIndex, xmlnsSchemeEndIndex);
            final String[] namespaceSplit = namespaceScheme.split("=");
            xPath.setNamespaceContext(new NamespaceContext() {
                @Override
                public String getNamespaceURI(String prefix) {
                    if (prefix.equals(namespaceSplit[0])) {
                        return namespaceSplit[1];
                    }
                    return null;
                }

                @Override
                public String getPrefix(String namespaceURI) {
                    if (namespaceURI.equals(namespaceSplit[1])) {
                        return namespaceSplit[0];
                    }
                    return null;
                }

                @Override
                public Iterator getPrefixes(String namespaceURI) {
                    return null;
                }
            });
        }
        try {
            return (NodeList) xPath.evaluate(xpointer.substring(xPointerSchemeIndex, xPointerSchemeEndIndex), node, XPathConstants.NODESET);
        } catch (XPathExpressionException e) {
            throw new SAXException(e);
        }
    }

    private int findBalancedEndIndex(String string, int startIndex, char opening, char ending) {
        int endIndex = -1;
        int openPar = 1;
        int length = string.length();
        for (int i = startIndex; i < length; i++) {
            char curChar = string.charAt(i);
            if (curChar == opening) {
                openPar++;
            } else if (curChar == ending) {
                openPar--;
            }
            if (openPar == 0) {
                endIndex = i;
                break;
            }
        }
        return endIndex;
    }
}