/*
* 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.tika.parser.ctakes;
import java.util.Collection;
import java.util.Iterator;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.tika.metadata.Metadata;
import org.apache.tika.sax.ContentHandlerDecorator;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.xml.sax.ContentHandler;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
/**
* Class used to extract biomedical information while parsing.
*
* <p>
* This class relies on <a href="http://ctakes.apache.org/">Apache cTAKES</a>
* that is a natural language processing system for extraction of information
* from electronic medical record clinical free-text.
* </p>
*/
public class CTAKESContentHandler extends ContentHandlerDecorator {
// Prefix used for metadata including cTAKES annotations
public static String CTAKES_META_PREFIX = "ctakes:";
// Configuration object for CTAKESContentHandler
private CTAKESConfig config = null;
// StringBuilder object used to build the clinical free-text for cTAKES
private StringBuilder sb = null;
// Metadata object used for cTAKES annotations
private Metadata metadata = null;
// UIMA Analysis Engine
private AnalysisEngine ae = null;
// JCas object for working with the CAS (Common Analysis System)
private JCas jcas = null;
/**
* Creates a new {@see CTAKESContentHandler} for the given {@see
* ContentHandler} and Metadata objects.
*
* @param handler
* the {@see ContentHandler} object to be decorated.
* @param metadata
* the {@see Metadata} object that will be populated using
* biomedical information extracted by cTAKES.
* @param config
* the {@see CTAKESConfig} object used to configure the handler.
*/
public CTAKESContentHandler(ContentHandler handler, Metadata metadata,
CTAKESConfig config) {
super(handler);
this.metadata = metadata;
this.config = config;
this.sb = new StringBuilder();
}
/**
* Creates a new {@see CTAKESContentHandler} for the given {@see
* ContentHandler} and Metadata objects.
*
* @param handler
* the {@see ContentHandler} object to be decorated.
* @param metadata
* the {@see Metadata} object that will be populated using
* biomedical information extracted by cTAKES.
*/
public CTAKESContentHandler(ContentHandler handler, Metadata metadata) {
this(handler, metadata, new CTAKESConfig());
}
/**
* Default constructor.
*/
public CTAKESContentHandler() {
this(new DefaultHandler(), new Metadata());
}
@Override
public void characters(char[] ch, int start, int length)
throws SAXException {
if (config.isText()) {
sb.append(ch, start, length);
}
super.characters(ch, start, length);
}
@Override
public void endDocument() throws SAXException {
try {
// create an Analysis Engine
if (ae == null) {
ae = CTAKESUtils.getAnalysisEngine(config.getAeDescriptorPath(), config.getUMLSUser(), config.getUMLSPass());
}
// create a JCas, given an AE
if (jcas == null) {
jcas = CTAKESUtils.getJCas(ae);
}
// get metadata to process
StringBuilder metaText = new StringBuilder();
String[] metadataToProcess = config.getMetadata();
if (metadataToProcess != null) {
for (String name : config.getMetadata()) {
for (String value : metadata.getValues(name)) {
metaText.append(value);
metaText.append(System.lineSeparator());
}
}
}
// analyze text
jcas.setDocumentText(metaText.toString() + sb.toString());
ae.process(jcas);
// add annotations to metadata
metadata.add(CTAKES_META_PREFIX + "schema", config.getAnnotationPropsAsString());
CTAKESAnnotationProperty[] annotationPros = config.getAnnotationProps();
Collection<IdentifiedAnnotation> collection = JCasUtil.select(jcas, IdentifiedAnnotation.class);
Iterator<IdentifiedAnnotation> iterator = collection.iterator();
while (iterator.hasNext()) {
IdentifiedAnnotation annotation = iterator.next();
StringBuilder annotationBuilder = new StringBuilder();
annotationBuilder.append(annotation.getCoveredText());
if (annotationPros != null) {
for (CTAKESAnnotationProperty property : annotationPros) {
annotationBuilder.append(config.getSeparatorChar());
annotationBuilder.append(CTAKESUtils.getAnnotationProperty(annotation, property));
}
}
metadata.add(CTAKES_META_PREFIX + annotation.getType().getShortName(), annotationBuilder.toString());
}
if (config.isSerialize()) {
// serialize data
CTAKESUtils.serialize(jcas, config.getSerializerType(), config.isPrettyPrint(), config.getOutputStream());
}
} catch (Exception e) {
throw new SAXException(e.getMessage());
} finally {
CTAKESUtils.resetCAS(jcas);
}
}
/**
* Returns metadata that includes cTAKES annotations.
*
* @return {@Metadata} object that includes cTAKES annotations.
*/
public Metadata getMetadata() {
return metadata;
}
}