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TeXoo module for Named Entity Recognition
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package de.datexis.ner.eval;

import de.datexis.common.Resource;
import de.datexis.model.Annotation;
import de.datexis.model.Dataset;
import de.datexis.model.Document;
import de.datexis.model.Sentence;
import de.datexis.model.Token;
import de.datexis.model.tag.BIO2Tag;
import de.datexis.model.tag.BIOESTag;
import de.datexis.model.tag.Tag;
import de.datexis.ner.MentionAnnotation;
import java.io.IOException;
import java.util.Arrays;
import java.util.Locale;
import org.apache.commons.io.FileUtils;
import org.nd4j.linalg.api.ndarray.INDArray;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Export a Document with MentionAnnotations as HTML
 * @author sarnold
 */
public class HTMLExport {
  
  protected static final Logger log = LoggerFactory.getLogger(HTMLExport.class);
  
  StringBuilder html;
  
  public HTMLExport(Dataset data, Class tagset) {
    this(data.getDocuments(), tagset, Annotation.Source.GOLD, Annotation.Source.PRED);
  }
  
  public HTMLExport(Document doc, Class tagset, Annotation.Source source) {
    this(Arrays.asList(doc), tagset, source, source);
  }

  public HTMLExport(Iterable docs, Class tagset) {
   this(docs, tagset, Annotation.Source.GOLD, Annotation.Source.PRED);
  }
  
  public HTMLExport(Iterable docs, Class tagset, Annotation.Source expected) {
   this(docs, tagset, expected, Annotation.Source.PRED);
  }
  
  public HTMLExport(Iterable docs, Class tagset, Annotation.Source expected, Annotation.Source predicted) {
    log.info("Exporting HTML...");
    html = new StringBuilder();
    appendHeader();
    for(Document doc : docs) {
      if(!doc.isTagAvaliable(expected, tagset)) MentionAnnotation.createTagsFromAnnotations(doc, expected, tagset);
      if(!doc.isTagAvaliable(predicted, tagset)) MentionAnnotation.createTagsFromAnnotations(doc, predicted, tagset);
      appendDocumentLabels(doc, tagset, expected, predicted);
    }
    appendFooter();
  }

  public String getHTML() {
    return html.toString();
  }
  
  protected void appendDocumentLabels(Document doc, Class target, Annotation.Source expected, Annotation.Source predicted) {
    if(expected.equals(predicted)) {
      html.append(annotateDocumentLabels(doc, target, expected));
    } else {
      html.append(annotateDocumentLabelsDiff(doc, target, expected, predicted));
    }
  }
  
  protected String annotateDocumentLabelsDiff(Document doc, Class target) {
    return annotateDocumentLabelsDiff(doc, target, Annotation.Source.GOLD, Annotation.Source.PRED);
  }

  protected String annotateDocumentLabelsDiff(Document doc, Class target, Annotation.Source expected, Annotation.Source predicted) {
    StringBuilder html = new StringBuilder();
    html.append("");
    int cursor = doc.getBegin();
    for(Sentence s : doc.getSentences()) {
      String last = "";
      for(Token t : s.getTokens()) {
        Tag gold = t.getTag(expected, target);
        Tag pred = t.getTag(predicted, target);
        
        //if(!ELStringUtils.skipSpaceAfter.contains(last) && !ELStringUtils.skipSpaceBefore.contains(t.getText())) html.append(" ");
        if(t.isEmpty()) continue;
        if(cursor > t.getBegin()) {
          // reset in case of wrong offsets
          html.append(" ");
          cursor = t.getBegin();
        }
        while(cursor < t.getBegin()) {
          html.append(" ");
          cursor++;
        }
        cursor = t.getEnd();
        
        if(!gold.getTag().equals("O") || !pred.getTag().equals("O")) {
          // positive - labels
          html.append("")
              .append("");
          INDArray vector = pred.getVector();
          if(gold.getTag().equals("O") && !pred.getTag().equals("O")) {
            // false positive - blue
            html.append("")
                .append(t.getText())
                .append("");
          } else if(!gold.getTag().equals("O") && !pred.getTag().equals("O")) {
            if(gold.getTag().equals(pred.getTag())) {
              // true positive - green
              html.append("")
                  .append(t.getText())
                  .append("");
            } else {
              // boundary error - yellow
              html.append("")
                  .append(t.getText())
                  .append("");
            }
          } else if(!gold.getTag().equals("O") && pred.getTag().equals("O")) {
            // false negative - red
            html.append("")
                .append(t.getText())
                .append("");
          }
          html.append("")
              .append("");
        } else {
          // true negative - white
          html.append("")
              .append(t.getText())
              .append("");
        }
        last = t.getText();
      }
      html.append("\n");
    }
    html.append("\n");
    return html.toString();
  }
  
  protected String annotateDocumentLabels(Document doc, Class tagset) {
    return annotateDocumentLabels(doc, tagset, Annotation.Source.PRED);
  }

  protected String annotateDocumentLabels(Document doc, Class tagset, Annotation.Source source) {
    StringBuilder html = new StringBuilder();
    html.append("");
    int cursor = doc.getBegin();
    for(Sentence s : doc.getSentences()) {
      for(Token t : s.getTokens()) {
        Tag pred = t.getTag(source, tagset);
        if(t.isEmpty()) continue;
        if(cursor > t.getBegin()) {
          // reset in case of wrong offsets
          html.append(" ");
          cursor = t.getBegin();
        }
        while(cursor < t.getBegin()) {
          html.append(" ");
          cursor++;
        }
        cursor = t.getEnd();
        
        if(!pred.getTag().equals("O")) {
          INDArray vector = pred.getVector();
          html.append("");
          html.append(t.getText());
          html.append("");
        } else {
          html.append("");
          html.append(t.getText());
          html.append("");
        }
      }
      html.append("\n");
    }
    html.append("\n");
    return html.toString();
  }
  
  protected void appendHeader() {
    html.append("\n\n\n  \n");
    //html.append("\n");
    html.append("\n");
    html.append("\n\n");
    
  }
  
  private void appendFooter() {
    html.append("\n");
  }
  
  public void saveHTML(Resource path, String name) {
    Resource file = path.resolve(name + ".html");
    try {
      FileUtils.writeStringToFile(file.toFile(), getHTML());
    } catch(IOException ex) {
      log.error("Could not write output: " + ex.toString());
    }
  }
  
}