org.openscience.cdk.io.CMLReader Maven / Gradle / Ivy
/* Copyright (C) 2001-2007 Egon Willighagen
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
package org.openscience.cdk.io;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.util.HashMap;
import java.util.Map;
import javax.xml.parsers.ParserConfigurationException;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.io.cml.CMLErrorHandler;
import org.openscience.cdk.io.cml.CMLHandler;
import org.openscience.cdk.io.cml.CMLResolver;
import org.openscience.cdk.io.cml.ICMLModule;
import org.openscience.cdk.io.formats.CMLFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.SAXParseException;
import org.xml.sax.XMLReader;
/**
* Reads a molecule in CML 1.x and 2.0 format.
* CML is an XML based application {@cdk.cite PMR99}, and this Reader
* applies the method described in {@cdk.cite WIL01}.
*
* @author Egon L. Willighagen
* @cdk.created 2001-02-01
* @cdk.module io
* @cdk.githash
* @cdk.keyword file format, CML
* @cdk.bug 1544406
* @cdk.iooptions
*/
public class CMLReader extends DefaultChemObjectReader {
private XMLReader parser;
private InputStream input;
private String url;
private Map userConventions = new HashMap();
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(CMLReader.class);
/**
* Reads CML from an java.io.InputStream, for example the FileInputStream.
*
* @param input InputStream type input
*/
public CMLReader(InputStream input) {
this.input = input;
init();
}
public CMLReader() {
this(new ByteArrayInputStream(new byte[0]));
}
public void registerConvention(String convention, ICMLModule conv) {
userConventions.put(convention, conv);
}
/**
* Define this CMLReader to take the input from a java.io.Reader
* class. Possible readers are (among others) StringReader and FileReader.
*
* @param url String url which points to the file to be read
*/
public CMLReader(String url) {
this.init();
this.url = url;
}
@Override
public IResourceFormat getFormat() {
return CMLFormat.getInstance();
}
/**
* This method must not be used; XML reading requires the use of an InputStream.
* Use setReader(InputStream) instead.
*/
@Override
public void setReader(Reader reader) throws CDKException {
throw new CDKException("Invalid method call; use SetReader(InputStream) instead.");
}
@Override
public void setReader(InputStream input) throws CDKException {
this.input = input;
}
private void init() {
url = ""; // make sure it is not null
boolean success = false;
// If JAXP is prefered (comes with Sun JVM 1.4.0 and higher)
if (!success) {
try {
javax.xml.parsers.SAXParserFactory spf = javax.xml.parsers.SAXParserFactory.newInstance();
spf.setNamespaceAware(true);
javax.xml.parsers.SAXParser saxParser = spf.newSAXParser();
parser = saxParser.getXMLReader();
logger.info("Using JAXP/SAX XML parser.");
success = true;
} catch (ParserConfigurationException | SAXException e) {
logger.warn("Could not instantiate JAXP/SAX XML reader: ", e.getMessage());
logger.debug(e);
}
}
// Aelfred is first alternative.
if (!success) {
try {
parser = (XMLReader) this.getClass().getClassLoader().loadClass("gnu.xml.aelfred2.XmlReader")
.newInstance();
logger.info("Using Aelfred2 XML parser.");
success = true;
} catch (ClassNotFoundException | InstantiationException | IllegalAccessException e) {
logger.warn("Could not instantiate Aelfred2 XML reader!");
logger.debug(e);
}
}
// Xerces is second alternative
if (!success) {
try {
parser = (XMLReader) this.getClass().getClassLoader().loadClass("org.apache.xerces.parsers.SAXParser")
.newInstance();
logger.info("Using Xerces XML parser.");
success = true;
} catch (ClassNotFoundException | InstantiationException | IllegalAccessException e) {
logger.warn("Could not instantiate Xerces XML reader!");
logger.debug(e);
}
}
if (!success) {
logger.error("Could not instantiate any XML parser!");
}
}
@Override
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (int i = 0; i < interfaces.length; i++) {
if (IChemFile.class.equals(interfaces[i])) return true;
}
if (IChemFile.class.equals(classObject)) return true;
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Read a IChemObject from input.
*
* @return the content in a ChemFile object
*/
@Override
public T read(T object) throws CDKException {
if (object instanceof IChemFile) {
return (T) readChemFile((IChemFile) object);
} else {
throw new CDKException("Only supported is reading of ChemFile objects.");
}
}
// private functions
private IChemFile readChemFile(IChemFile file) throws CDKException {
logger.debug("Started parsing from input...");
try {
parser.setFeature("http://xml.org/sax/features/validation", false);
logger.info("Deactivated validation");
} catch (SAXException e) {
logger.warn("Cannot deactivate validation.");
return null;
}
CMLHandler handler = new CMLHandler(file);
// copy the manually added conventions
for (String conv : userConventions.keySet()) {
handler.registerConvention(conv, userConventions.get(conv));
}
parser.setContentHandler(handler);
parser.setEntityResolver(new CMLResolver());
parser.setErrorHandler(new CMLErrorHandler());
try {
if (input == null) {
logger.debug("Parsing from URL: ", url);
parser.parse(url);
} else {
logger.debug("Parsing from Reader");
parser.parse(new InputSource(input));
}
} catch (IOException e) {
String error = "Error while reading file: " + e.getMessage();
logger.error(error);
logger.debug(e);
throw new CDKException(error, e);
} catch (SAXParseException saxe) {
SAXParseException spe = (SAXParseException) saxe;
String error = "Found well-formedness error in line " + spe.getLineNumber();
logger.error(error);
logger.debug(saxe);
throw new CDKException(error, saxe);
} catch (SAXException saxe) {
String error = "Error while parsing XML: " + saxe.getMessage();
logger.error(error);
logger.debug(saxe);
throw new CDKException(error, saxe);
}
return file;
}
@Override
public void close() throws IOException {
if (input != null) input.close();
}
}
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