code: /**
   * Copyright 2012 Lezan Hawizy, David M. Jessop, Daniel Lowe and Peter Murray-Rust
   *
   * Licensed 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 uk.ac.cam.ch.wwmm.chemicaltagger;
  
  import java.util.Arrays;
  import java.util.List;
  
  import org.junit.Assert;
  
  import org.junit.AfterClass;
  import org.junit.BeforeClass;
  import org.junit.Test;
  
  import uk.ac.cam.ch.wwmm.oscar.document.Token;
  
  /************************************
   * Tests the RecombineTokens Class.
   * @author lh359
   ************************************/
  public class RecombineTokensTest {
  
  	private static OscarTagger oscarTagger;
  	private static RegexTagger regexTagger;
  	private static OpenNLPTagger openNLPTagger;
  	private static OscarTokeniser oscarTokeniser;
  	@BeforeClass
  	public static void setup(){
  		ChemistryPOSTagger posTagger = ChemistryPOSTagger.getDefaultInstance();
  		oscarTokeniser = (OscarTokeniser)posTagger.getCTTokeniser();
  		oscarTagger = posTagger.getOscarTagger();
  		regexTagger = posTagger.getRegexTagger();
  		openNLPTagger = posTagger.getOpenNLPTagger();
  	    
  	}
  	
  	@AfterClass
  	public static void cleanUp(){
  		oscarTokeniser = null;
  		oscarTagger = null;
  		regexTagger = null;
  		openNLPTagger = null;
  	}
  	
  	@Test
  	public void testRecombineSentence1() {
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/sentence1.txt");
  		String expectedOutput = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/ref1.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.combineTaggers();
  		int beforeRecombined = posContainer.getCombinedTagsList().size();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		int afterRecombined = posContainer.getCombinedTagsList().size();
  		Assert.assertNotSame("Different Size of combined List",
  				beforeRecombined, afterRecombined);
  		Assert.assertEquals("Combined all the hyphenated words",expectedOutput, posContainer.getTokenTagTupleAsString());
  
  	}
  
  	@Test
  	public void testRecombineSentence2() {
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/sentence2.txt");
  		String expectedOutput = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/ref2.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.combineTaggers();
  		int beforeRecombined = posContainer.getCombinedTagsList().size();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		int afterRecombined = posContainer.getCombinedTagsList().size();
  		Assert.assertNotSame(beforeRecombined, afterRecombined);
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals("Combined all the hyphenated words",expectedOutput, posContainer.getTokenTagTupleAsString());
  	}
  	
  	@Test
  	public void testRecombineSentence3() {
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/sentence3.txt");
  		String expectedOutput = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/ref3.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.combineTaggers();
  		int beforeRecombined = posContainer.getCombinedTagsList().size();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		int afterRecombined = posContainer.getCombinedTagsList().size();
  		Assert.assertNotSame(beforeRecombined, afterRecombined);
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals("Combined all the hyphenated words",expectedOutput, posContainer.getTokenTagTupleAsString());
  	}
  
  
  
  	@Test
  	public void testRecombineSentence4() {
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/sentence4.txt");
  		String expectedOutput = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/ref4.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.combineTaggers();
  		int beforeRecombined = posContainer.getCombinedTagsList().size();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		int afterRecombined = posContainer.getCombinedTagsList().size();
  		Assert.assertNotSame(beforeRecombined, afterRecombined);
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals("Combined all the hyphenated words",expectedOutput, posContainer.getTokenTagTupleAsString());
  	}
  
  	@Test
  	public void testRecombineSentence5() {
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/sentence5.txt");
  		String expectedOutput = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/ref5.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.combineTaggers();
  		int beforeRecombined = posContainer.getCombinedTagsList().size();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		int afterRecombined = posContainer.getCombinedTagsList().size();
  		Assert.assertNotSame(beforeRecombined, afterRecombined);
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals("Combined all the hyphenated words",expectedOutput, posContainer.getTokenTagTupleAsString());
  	}
  	
  	
  	
  	@Test
  	public void testCelciusDotRecombination() {//recombine 50C . to 50C.
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/celciusDot.txt");
  		String expectedOutput = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/celciusDotRef.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.combineTaggers();
  		int beforeRecombined = posContainer.getCombinedTagsList().size();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		int afterRecombined = posContainer.getCombinedTagsList().size();
  		Assert.assertNotSame(beforeRecombined, afterRecombined);
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals("Combined all the hyphenated words",expectedOutput, posContainer.getTokenTagTupleAsString());
  	}
  	
  	
  	@Test
  	public void testOxidationRecombineSentence() {
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/oxidation.txt");
  		String expectedOutput = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/oxidationRef.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		posContainer.combineTaggers();
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals("Combined all the hyphenated words",expectedOutput, posContainer.getTokenTagTupleAsString());
  	}
  	
  	@Test
  	public void testForMissingInput1() {
  		POSContainer posContainer = new POSContainer();
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/missingInput1.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  		posContainer.combineTaggers();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  	
  
  	}
  	@Test
  	public void testForMissingInput2() {
  		POSContainer posContainer = new POSContainer();
  		
  		String inputSentence = Utils.readSentence("uk/ac/cam/ch/wwmm/chemicaltagger/recombineTokens/missingInput2.txt");
  		inputSentence = Formatter.normaliseText(inputSentence);
          posContainer.setInputText(inputSentence);
          
  		posContainer.setWordTokenList(Formatter.subTokeniseTokens(oscarTokeniser.tokenise(inputSentence)));
  		posContainer.registerTagList(oscarTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  		posContainer.registerTagList(regexTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  		posContainer.registerTagList(openNLPTagger.runTagger(posContainer.getWordTokenList(), inputSentence));
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  		posContainer.combineTaggers();
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		new PostProcessTags(posContainer).correctCombinedTagsList();
  		Assert.assertEquals(inputSentence.replace(" ", ""), tokenListToConcatenatedString(posContainer.getWordTokenList()));
  	}
  	
  	
  	@Test
  	public void testMolPerVolumeRecombination() {//e.g. recombine mol / L
  		POSContainer posContainer = new POSContainer();
          posContainer.setInputText("5 mol/L");
  		posContainer.setWordTokenList(oscarTokeniser.tokenise("5 mol / L"));
  		posContainer.setCombinedTagsList(Arrays.asList("CD", "NN-AMOUNT", "DASH", "NN-VOL"));
  		posContainer = RecombineTokens.recombineTokens(posContainer);
  		Assert.assertEquals("CD 5 NN-MOLAR mol/L", posContainer.getTokenTagTupleAsString());
  	}
  	
  	private String tokenListToConcatenatedString(List<Token> tokens){
  		StringBuilder sb = new StringBuilder();
  		for (Token token : tokens) {
  			sb.append(token.getSurface());
  		}
  		return sb.toString();
  	}
  }
  