001 /*
002 Copyright (c) 2012, Regents of the University of Colorado
003 All rights reserved.
004
005 Redistribution and use in source and binary forms, with or without modification,
006 are permitted provided that the following conditions are met:
007
008 * Redistributions of source code must retain the above copyright notice, this
009 list of conditions and the following disclaimer.
010
011 * Redistributions in binary form must reproduce the above copyright notice,
012 this list of conditions and the following disclaimer in the documentation
013 and/or other materials provided with the distribution.
014
015 * Neither the name of the University of Colorado nor the names of its
016 contributors may be used to endorse or promote products derived from this
017 software without specific prior written permission.
018
019 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
020 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
021 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
022 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
023 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
024 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
025 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
026 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
027 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
028 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
029 */
030 package edu.ucdenver.ccp.medline.parser;
031
032 import java.io.EOFException;
033 import java.io.FileNotFoundException;
034 import java.io.IOException;
035 import java.io.InputStream;
036 import java.io.ObjectInputStream;
037 import java.util.Iterator;
038 import java.util.NoSuchElementException;
039
040 import com.thoughtworks.xstream.XStream;
041 import com.thoughtworks.xstream.io.xml.StaxDriver;
042
043 import edu.ucdenver.ccp.common.file.CharacterEncoding;
044 import edu.ucdenver.ccp.common.file.FileReaderUtil;
045
046 /**
047 * @author Center for Computational Pharmacology, UC Denver; ccpsupport@ucdenver.edu
048 *
049 */
050 public class MedlineXmlDeserializer implements Iterator<Object> {
051
052 private Object nextCitation = null;
053 private final ObjectInputStream in;
054
055 public MedlineXmlDeserializer(InputStream medlineXmlFileStream) throws FileNotFoundException, IOException {
056 XStream xstream = new XStream(new StaxDriver());
057 xstream.processAnnotations(MedlineCitationSet.class);
058 xstream.processAnnotations(MedlineCitation.class);
059
060 in = xstream.createObjectInputStream(FileReaderUtil.initBufferedReader(medlineXmlFileStream,
061 CharacterEncoding.UTF_8));
062 }
063
064 /*
065 * (non-Javadoc)
066 *
067 * @see java.util.Iterator#hasNext()
068 */
069 public boolean hasNext() {
070 if (nextCitation == null) {
071 try {
072 Object citation = in.readObject();
073 nextCitation = citation;
074 } catch (EOFException e) {
075 return false;
076 } catch (IOException e) {
077 throw new RuntimeException(e);
078 } catch (ClassNotFoundException e) {
079 throw new RuntimeException(e);
080 }
081 }
082 return true;
083 }
084
085 /*
086 * (non-Javadoc)
087 *
088 * @see java.util.Iterator#next()
089 */
090 public Object next() {
091 if (!hasNext())
092 throw new NoSuchElementException();
093
094 Object citationToReturn = nextCitation;
095 nextCitation = null;
096 return citationToReturn;
097 }
098
099 /*
100 * (non-Javadoc)
101 *
102 * @see java.util.Iterator#remove()
103 */
104 public void remove() {
105 throw new UnsupportedOperationException("The remove() method is not supported for this iterator.");
106 }
107
108 }