org.apache.tika.parser.ctakes.CTAKESContentHandler Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of aem-sdk-api Show documentation
The Adobe Experience Manager SDK
There is a newer version: 2024.11.18751.20241128T090041Z-241100
/*
 * 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.
 *
 * 
 * This class relies on Apache cTAKES
 * that is a natural language processing system for extraction of information
 * from electronic medical record clinical free-text.
 * 
 */
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 {@link CTAKESContentHandler} for the given {@link ContentHandler} and Metadata objects.
	 * 
	 * @param handler
	 *            the {@link ContentHandler} object to be decorated.
	 * @param metadata
	 *            the {@link Metadata} object that will be populated using
	 *            biomedical information extracted by cTAKES.
	 * @param config
	 *            the {@link 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 {@link CTAKESContentHandler} for the given {@link
	 * ContentHandler} and Metadata objects.
	 * 
	 * @param handler
	 *            the {@link ContentHandler} object to be decorated.
	 * @param metadata
	 *            the {@link 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 collection = JCasUtil.select(jcas, IdentifiedAnnotation.class);
            Iterator 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 {@link Metadata} object that includes cTAKES annotations.
	 */
	public Metadata getMetadata() {
		return metadata;
	}
}