gate debug

/*
 *  testApp.java
 *
 * Copyright (c) 2000-2012, The University of Sheffield.
 *
 * This file is part of GATE (see http://gate.ac.uk/), and is free
 * software, licenced under the GNU Library General Public License,
 * Version 3, 29 June 2007.
 *
 * A copy of this licence is included in the distribution in the file
 * licence.html, and is also available at http://gate.ac.uk/gate/licence.html.
 *
 *  sandeepchellappen, 1/6/2016
 *
 * For details on the configuration options, see the user guide:
 * http://gate.ac.uk/cgi-bin/userguide/sec:creole-model:config
 */

package com.mytests;

import gate.*;
import gate.creole.*;
import gate.creole.metadata.*;
import gate.util.*;
import java.util.*;
import java.io.*;
import java.net.*;

import gate.*;
import gate.creole.*;
import gate.util.*;
import gate.util.persistence.PersistenceManager;
import gate.corpora.RepositioningInfo;


/** 
 * This class is the implementation of the resource TESTAPP.
 */
@CreoleResource(name = "testApp",
        comment = "Add a descriptive comment about this resource")
public class testApp   {

	 /** The Corpus Pipeline application to contain ANNIE */
	  private CorpusController annieController;

	  /**
	   * Initialise the ANNIE system. This creates a "corpus pipeline"
	   * application that can be used to run sets of documents through
	   * the extraction system.
	   */
	  public void initAnnie() throws GateException, IOException {
	    Out.prln("Initialising ANNIE...");

	    // load the ANNIE application from the saved state in plugins/ANNIE
	    File pluginsHome = Gate.getPluginsHome();
	    File anniePlugin = new File(pluginsHome, "ANNIE");
//	    File annieGapp = new File(anniePlugin, "ANNIE_with_defaults.gapp");
	    File annieGapp = new File("/Users/sandeepchellappen/Work/Learning/nlp/GateTuorial", "testApp.gapp");
	    annieController =
	      (CorpusController) PersistenceManager.loadObjectFromFile(annieGapp);

	    Out.prln("...ANNIE loaded");
	  } // initAnnie()

	  /** Tell ANNIE's controller about the corpus you want to run on */
	  public void setCorpus(Corpus corpus) {
	    annieController.setCorpus(corpus);
	  } // setCorpus

	  /** Run ANNIE */
	  public void execute() throws GateException {
	    Out.prln("Running ANNIE...");
	    annieController.execute();
	    Out.prln("...ANNIE complete");
	  } // execute()

	  /**
	   * Run from the command-line, with a list of URLs as argument.
	   * <P><B>NOTE:</B><BR>
	   * This code will run with all the documents in memory - if you
	   * want to unload each from memory after use, add code to store
	   * the corpus in a DataStore.
	   */
	  public static void main(String args[]) throws GateException, IOException {
	    // initialise the GATE library
	    Out.prln("Initialising GATE...");
	    Gate.init();
	    Out.prln("...GATE initialised");

	    // initialise ANNIE (this may take several minutes)
	    testApp annie = new testApp();
	    annie.initAnnie();

	    // create a GATE corpus and add a document for each command-line
	    // argument
	    Corpus corpus = Factory.newCorpus("StandAloneAnnie corpus");
	    for(int i = 0; i < args.length; i++) {
	      URL u = new URL(args[i]);
	      FeatureMap params = Factory.newFeatureMap();
	      params.put("sourceUrl", u);
	      params.put("preserveOriginalContent", new Boolean(true));
	      params.put("collectRepositioningInfo", new Boolean(true));
	      Out.prln("Creating doc for " + u);
	      Document doc = (Document)
	        Factory.createResource("gate.corpora.DocumentImpl", params);
	      corpus.add(doc);
	    } // for each of args

	    // tell the pipeline about the corpus and run it
	    annie.setCorpus(corpus);
	    annie.execute();

	    // for each document, get an XML document with the
	    // person and location names added
	    Iterator iter = corpus.iterator();
	    int count = 0;
	    String startTagPart_1 = "<span GateID=\"";
	    String startTagPart_2 = "\" title=\"";
	    String startTagPart_3 = "\" style=\"background:Red;\">";
	    String endTag = "</span>";

	    while(iter.hasNext()) {
	      Document doc = (Document) iter.next();
	      AnnotationSet defaultAnnotSet = doc.getAnnotations();
	      
	      // Get all the sentence annotations and for each sentence
	      // print all the tokens and their associated annotation
	     
	      String[] reqTypes = {"Sentence"};
	     AnnotationSet sentAnns = annie.getAllAnnotationForTypes(defaultAnnotSet ,reqTypes); 
	    
	     for(Annotation sent: sentAnns){
	    	Long startOffset = sent.getStartNode().getOffset();
	    	Long endOffset = sent.getEndNode().getOffset();
	    	
	    	// Get the annotation set within this range
	    	
	    	String[] reqTypes1 = {"Location"};
	    	Set<Annotation> anns = annie.getAllAnnotationForTypesWithinOffset(defaultAnnotSet ,reqTypes1,startOffset,endOffset); 
	    	
	    	for(Annotation ann: anns){
	    		String word = gate.Utils.stringFor(doc,ann);
	    		String type = ann.getType();
	    		System.out.println(word + " : " + type);
	    	}
	     }
	     
//	      Set annotTypesRequired = new HashSet();
//	      annotTypesRequired.add("Person");
//	      annotTypesRequired.add("Location");
//	      Set<Annotation> peopleAndPlaces =
//	        new HashSet<Annotation>(defaultAnnotSet.get(annotTypesRequired));
//
//	      FeatureMap features = doc.getFeatures();
//	      String originalContent = (String)
//	        features.get(GateConstants.ORIGINAL_DOCUMENT_CONTENT_FEATURE_NAME);
//	      RepositioningInfo info = (RepositioningInfo)
//	        features.get(GateConstants.DOCUMENT_REPOSITIONING_INFO_FEATURE_NAME);
//
//	      ++count;
//	      File file = new File("StANNIE_" + count + ".HTML");
//	      Out.prln("File name: '"+file.getAbsolutePath()+"'");
//	      if(originalContent != null && info != null) {
//	        Out.prln("OrigContent and reposInfo existing. Generate file...");
//
//	        Iterator it = peopleAndPlaces.iterator();
//	        Annotation currAnnot;
//	        SortedAnnotationList sortedAnnotations = new SortedAnnotationList();
//
//	        while(it.hasNext()) {
//	          currAnnot = (Annotation) it.next();
//	          sortedAnnotations.addSortedExclusive(currAnnot);
//	        } // while
//
//	        StringBuffer editableContent = new StringBuffer(originalContent);
//	        long insertPositionEnd;
//	        long insertPositionStart;
//	        // insert anotation tags backward
//	        Out.prln("Unsorted annotations count: "+peopleAndPlaces.size());
//	        Out.prln("Sorted annotations count: "+sortedAnnotations.size());
//	        for(int i=sortedAnnotations.size()-1; i>=0; --i) {
//	          currAnnot = (Annotation) sortedAnnotations.get(i);
//	          insertPositionStart =
//	            currAnnot.getStartNode().getOffset().longValue();
//	          insertPositionStart = info.getOriginalPos(insertPositionStart);
//	          insertPositionEnd = currAnnot.getEndNode().getOffset().longValue();
//	          insertPositionEnd = info.getOriginalPos(insertPositionEnd, true);
//	          if(insertPositionEnd != -1 && insertPositionStart != -1) {
//	            editableContent.insert((int)insertPositionEnd, endTag);
//	            editableContent.insert((int)insertPositionStart, startTagPart_3);
//	            editableContent.insert((int)insertPositionStart,
//	                                                          currAnnot.getType());
//	            editableContent.insert((int)insertPositionStart, startTagPart_2);
//	            editableContent.insert((int)insertPositionStart,
//	                                                  currAnnot.getId().toString());
//	            editableContent.insert((int)insertPositionStart, startTagPart_1);
//	          } // if
//	        } // for
//
//	        FileWriter writer = new FileWriter(file);
//	        writer.write(editableContent.toString());
//	        writer.close();
//	      } // if - should generate
//	      else if (originalContent != null) {
//	        Out.prln("OrigContent existing. Generate file...");
//
//	        Iterator it = peopleAndPlaces.iterator();
//	        Annotation currAnnot;
//	        SortedAnnotationList sortedAnnotations = new SortedAnnotationList();
//
//	        while(it.hasNext()) {
//	          currAnnot = (Annotation) it.next();
//	          sortedAnnotations.addSortedExclusive(currAnnot);
//	        } // while
//
//	        StringBuffer editableContent = new StringBuffer(originalContent);
//	        long insertPositionEnd;
//	        long insertPositionStart;
//	        // insert anotation tags backward
//	        Out.prln("Unsorted annotations count: "+peopleAndPlaces.size());
//	        Out.prln("Sorted annotations count: "+sortedAnnotations.size());
//	        for(int i=sortedAnnotations.size()-1; i>=0; --i) {
//	          currAnnot = (Annotation) sortedAnnotations.get(i);
//	          insertPositionStart =
//	            currAnnot.getStartNode().getOffset().longValue();
//	          insertPositionEnd = currAnnot.getEndNode().getOffset().longValue();
//	          if(insertPositionEnd != -1 && insertPositionStart != -1) {
//	            editableContent.insert((int)insertPositionEnd, endTag);
//	            editableContent.insert((int)insertPositionStart, startTagPart_3);
//	            editableContent.insert((int)insertPositionStart,
//	                                                          currAnnot.getType());
//	            editableContent.insert((int)insertPositionStart, startTagPart_2);
//	            editableContent.insert((int)insertPositionStart,
//	                                                  currAnnot.getId().toString());
//	            editableContent.insert((int)insertPositionStart, startTagPart_1);
//	          } // if
//	        } // for
//
//	        FileWriter writer = new FileWriter(file);
//	        writer.write(editableContent.toString());
//	        writer.close();
//	      }
//	      else {
//	        Out.prln("Content : "+originalContent);
//	        Out.prln("Repositioning: "+info);
//	      }
//
//	      String xmlDocument = doc.toXml(peopleAndPlaces, false);
//	      String fileName = new String("StANNIE_toXML_" + count + ".HTML");
//	      FileWriter writer = new FileWriter(fileName);
//	      writer.write(xmlDocument);
//	      writer.close();

	    } // for each doc
	  } // main

	  private Set<Annotation> getAllAnnotationForTypesWithinOffset(AnnotationSet defaultAnnotSet, String[] reqTypes,
			Long startOffset, Long endOffset) {
		  Set<Annotation> annotTypesRequired = Collections.emptySet();
		  
//	      Set<Annotation> peopleAndPlaces =
//	        new HashSet<Annotation>(defaultAnnotSet.get(annotTypesRequired));
		  for(String type: reqTypes){
			  Set<Annotation> annSet = defaultAnnotSet.get(type,startOffset,endOffset);
			  annotTypesRequired.addAll(annSet);
		  }
	       return annotTypesRequired;

	}

	private AnnotationSet getAllAnnotationForTypes(AnnotationSet aSet ,String[] reqTypes) {
		  
		  Set annotTypesRequired = new HashSet();
		  for(String type: reqTypes){
			  annotTypesRequired.add(type);
		  }
	       return (AnnotationSet) aSet.get(annotTypesRequired);
	}

	/**
	   *
	   */
	  public static class SortedAnnotationList extends Vector {
	    public SortedAnnotationList() {
	      super();
	    } // SortedAnnotationList

	    public boolean addSortedExclusive(Annotation annot) {
	      Annotation currAnot = null;

	      // overlapping check
	      for (int i=0; i<size(); ++i) {
	        currAnot = (Annotation) get(i);
	        if(annot.overlaps(currAnot)) {
	          return false;
	        } // if
	      } // for

	      long annotStart = annot.getStartNode().getOffset().longValue();
	      long currStart;
	      // insert
	      for (int i=0; i < size(); ++i) {
	        currAnot = (Annotation) get(i);
	        currStart = currAnot.getStartNode().getOffset().longValue();
	        if(annotStart < currStart) {
	          insertElementAt(annot, i);
	          /*
	           Out.prln("Insert start: "+annotStart+" at position: "+i+" size="+size());
	           Out.prln("Current start: "+currStart);
	           */
	          return true;
	        } // if
	      } // for

	      int size = size();
	      insertElementAt(annot, size);
	//Out.prln("Insert start: "+annotStart+" at size position: "+size);
	      return true;
	    } // addSorted
	  } // SortedAnnotationList

} // class testApp