/**
* 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.ctakes.preprocessor.test;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
import org.apache.ctakes.preprocessor.ClinicalNotePreProcessor;
import org.apache.ctakes.preprocessor.DocumentMetaData;
import org.apache.ctakes.preprocessor.PreProcessor;
import org.apache.ctakes.preprocessor.SegmentMetaData;
/**
*
* @author Mayo Clinic
*/
public class TestDriver
{
public static void main(String[] args)
{
if (args.length < 1 || args.length > 2)
{
System.out.println("Usage: TestDriver <input file> [<dtd file>]");
// example parameters: "test/data/testpatient_cn_1.xml"
// example parameters: "test/data/testpatient_cn_1.xml" "resources/cda/NotesIIST_RTF.DTD"
System.exit(1);
}
try
{
String hl7Text = load(args[0]);
String dtdFilename = "resources/cda/NotesIIST_RTF.DTD";
if (args.length > 1) {
dtdFilename = args[1];
}
long timestamp, elapsedTime;
Set sectionNames;
Iterator snItr;
File dtdFile = new File(dtdFilename);
if (!exists(dtdFile)) {
System.exit(-1);
}
PreProcessor pp = new ClinicalNotePreProcessor(dtdFile, false);
timestamp = System.currentTimeMillis();
DocumentMetaData dmd = pp.process(hl7Text);
elapsedTime = System.currentTimeMillis() - timestamp;
System.out.println("PreProcessor Took " + elapsedTime + "ms");
System.out.println("Plain Text Start");
System.out.println(dmd.getText());
System.out.println("Plain Text End");
sectionNames = dmd.getSegmentIdentifiers();
snItr = sectionNames.iterator();
while (snItr.hasNext())
{
String sectionId = (String) snItr.next();
SegmentMetaData smd = dmd.getSegment(sectionId);
System.out.println("SECTION="
+ sectionId
+ "\tSTART_OFFSET="
+ smd.span.start
+ "\tEND_OFFSET="
+ smd.span.end);
//System.out.println(dmd.getText().substring(smd.span.start, smd.span.end));
}
Map metaDataMap = dmd.getMetaData();
Iterator keyItr = metaDataMap.keySet().iterator();
while (keyItr.hasNext())
{
Object key = keyItr.next();
Object value = metaDataMap.get(key);
System.out.println("MetaData KEY="
+ key.toString()
+ " VALUE="
+ value.toString());
}
}
catch (Exception e)
{
e.printStackTrace();
}
}
/**
* Loads text from a file.
*
* @param filename
* @return
* @throws FileNotFoundException
* @throws IOException
*/
public static String load(String filename)
throws FileNotFoundException, IOException
{
String msg = "";
File f = new File(filename);
exists(f); // output error message if file does not exist
BufferedReader br = new BufferedReader(new FileReader(f));
String line = br.readLine();
while (line != null)
{
msg += line + "\n";
line = br.readLine();
}
br.close();
return msg;
}
public static boolean exists(File f) {
if (f.exists()) {
return true;
}
System.out.println("cwd = " + new File(".").getAbsolutePath());
System.out.println("File " + f + " does not exist.");
return false;
}
}