private void transferAnnotations(List<Annotation> toTransfer, AnnotationSet to, boolean newID)
throws ExecutionException {
for (Annotation annot : toTransfer) {
Mapping m = mappings.get(annot.getType());
String name = (m == null || m.newName == null ? annot.getType() : m.newName);
try {
FeatureMap params = Factory.newFeatureMap();
params.putAll(annot.getFeatures());
if (newID) {
to.add(annot.getStartNode().getOffset(), annot.getEndNode().getOffset(), name, params);
} else {
to.add(
annot.getId(),
annot.getStartNode().getOffset(),
annot.getEndNode().getOffset(),
name,
params);
}
} catch (InvalidOffsetException e) {
throw new ExecutionException(e);
}
}
}
// generate annotations for ngrams over a larger span e.g all couples inside
// a span of 5 tokens
// this allows to match more variants e.g. with adjectives in the middle
// we do not generate intermediate annotations here
// do with only bigrams for the moment
private void generateNGramsOverWindow(List<Annotation> list, AnnotationSet outputAS)
throws ExecutionException {
List<List> boxes = generateBoxes(list, outputAS);
try {
for (int b = 0; b < boxes.size(); b++) {
List<String> tempAnnotationsStartingHere = new ArrayList<String>();
Long loStart = null;
Long hiEnd = null;
// create a temporary list containing all the annotations
// at position 0
List<Annotation> headannots = boxes.get(b);
for (Annotation newAnn : headannots) {
// remembering positions
loStart = newAnn.getStartNode().getOffset();
if (hiEnd == null) hiEnd = newAnn.getEndNode().getOffset();
else if (newAnn.getEndNode().getOffset().longValue() > hiEnd.longValue())
hiEnd = newAnn.getEndNode().getOffset();
String string = (String) newAnn.getFeatures().get(inputAnnotationFeature);
tempAnnotationsStartingHere.add(string);
if (this.generateIntermediateAnnotations) {
FeatureMap fm = Factory.newFeatureMap();
fm.put(this.outputAnnotationFeature, string);
outputAS.add(loStart, hiEnd, outputAnnotationType, fm);
}
}
for (int z = 1; z < window && (b + z < boxes.size()); z++) {
// generate all possible bi-grams
List<Annotation> current = boxes.get(b + z);
for (Annotation newAnn : current) {
// remembering positions
if (hiEnd == null) hiEnd = newAnn.getEndNode().getOffset();
else if (newAnn.getEndNode().getOffset().longValue() > hiEnd.longValue())
hiEnd = newAnn.getEndNode().getOffset();
String newString = (String) newAnn.getFeatures().get(inputAnnotationFeature);
// take what is in the buffer
// and make a new annotation out of that
for (String s : tempAnnotationsStartingHere) {
String combination = s + getNgramSeparator() + newString;
// create an annotation for the combination
FeatureMap fm = Factory.newFeatureMap();
fm.put(this.outputAnnotationFeature, combination);
outputAS.add(loStart, hiEnd, outputAnnotationType, fm);
}
}
}
}
} catch (Exception e) {
throw new ExecutionException(e);
}
}
private void generateNGrams(List<Annotation> list, AnnotationSet outputAS)
throws ExecutionException {
List<List> boxes = generateBoxes(list, outputAS);
try {
// now do the actual n-grams
for (int b = 0; b < boxes.size(); b++) {
List<String> tempAnnotationsStartingHere = new ArrayList<String>();
Long loStart = null;
Long hiEnd = null;
for (int z = 0; z < this.ngram.intValue() && (b + z < boxes.size()); z++) {
// do the combination and dump what we've done at every step
// e.g generate 1 grams as well as 2-grams
List<Annotation> current = boxes.get(b + z);
List<String> temptemp = new ArrayList<String>();
for (Annotation newAnn : current) {
// remembering positions
if (loStart == null) loStart = newAnn.getStartNode().getOffset();
if (hiEnd == null) hiEnd = newAnn.getEndNode().getOffset();
else if (newAnn.getEndNode().getOffset().longValue() > hiEnd.longValue())
hiEnd = newAnn.getEndNode().getOffset();
String newString = (String) newAnn.getFeatures().get(inputAnnotationFeature);
// TODO : what if there is no such value????
if (tempAnnotationsStartingHere.size() == 0) {
// create an annotation for the current annotation
if (this.generateIntermediateAnnotations) {
FeatureMap fm = Factory.newFeatureMap();
fm.put(this.outputAnnotationFeature, newString);
outputAS.add(loStart, hiEnd, outputAnnotationType, fm);
}
// add it to the temp
temptemp.add(newString);
} else
for (String existing : tempAnnotationsStartingHere) {
String combination = existing + getNgramSeparator() + newString;
temptemp.add(combination);
if (this.generateIntermediateAnnotations | z == this.ngram.intValue() - 1) {
// create an annotation for the combination
FeatureMap fm = Factory.newFeatureMap();
fm.put(this.outputAnnotationFeature, combination);
outputAS.add(loStart, hiEnd, outputAnnotationType, fm);
}
}
}
tempAnnotationsStartingHere = temptemp;
}
}
} catch (Exception e) {
throw new ExecutionException(e);
}
}
public void execute() throws ExecutionException {
AnnotationSet outputAS = document.getAnnotations(outputASName);
List<Annotation> tokens =
new ArrayList<Annotation>(
document.getAnnotations(inputASName).get(ANNIEConstants.TOKEN_ANNOTATION_TYPE));
Collections.sort(tokens, new OffsetComparator());
String[] strings = new String[tokens.size()];
for (int i = 0; i < tokens.size(); ++i) {
strings[i] = (String) tokens.get(i).getFeatures().get("string");
}
try {
TagList tags = tagger.tag(strings);
Iterator<Tag> it = tags.iterator();
while (it.hasNext()) {
Tag tag = it.next();
outputAS.add(
tokens.get(tag.getTokenStartIndex()).getStartNode().getOffset(),
tokens.get(tag.getTokenEndIndex()).getEndNode().getOffset(),
tag.getTagname(),
Factory.newFeatureMap());
}
} catch (Exception ioe) {
throw new ExecutionException("Tagger Failed", ioe);
}
}
public void tokenize() {
AnnotationSet tokenizationAs = gateDocument.getAnnotations("Tokenization");
AnnotationSet defaultAs = gateDocument.getAnnotations("");
for (Iterator<Annotation> it = tokenizationAs.iterator(); it.hasNext(); ) {
Annotation currentTokenAnnotation = it.next();
FeatureMap tokenFeaturesMap = currentTokenAnnotation.getFeatures();
FeatureMap curFeaturesMap = Factory.newFeatureMap();
if ("Token".compareToIgnoreCase(currentTokenAnnotation.getType()) == 0) {
curFeaturesMap.put("string", tokenFeaturesMap.get("string"));
curFeaturesMap.put("root", tokenFeaturesMap.get("lemma"));
curFeaturesMap.put("category", tokenFeaturesMap.get("POS"));
// Add the new Token to the Annotation Set
defaultAs.add(
currentTokenAnnotation.getStartNode(),
currentTokenAnnotation.getEndNode(),
currentTokenAnnotation.getType(),
curFeaturesMap);
}
}
gateDocument.removeAnnotationSet("Tokenization");
}
/**
* Generation of a GATE document from a Behemoth one
*
* @param key URL of the input doc
* @param inputDoc
* @return
* @throws ResourceInstantiationException
* @throws InvalidOffsetException
* @throws IOException
*/
public gate.Document generateGATEDoc(BehemothDocument inputDoc)
throws ResourceInstantiationException, InvalidOffsetException, IOException {
gate.Document gatedocument = null;
// if no text is available (e.g. Tika has not extracted it)
// let GATE do the parsing itself from the binary content
if (inputDoc.getText() == null) {
try {
gatedocument = generateGATEDocFromLocalDump(inputDoc);
// transfer the text from GATE to Behemoth
String textContent = gatedocument.getContent().toString();
inputDoc.setText(textContent);
return gatedocument;
} catch (Exception e) {
LOG.error("Can't generate GATE doc from byte dump", e);
}
}
// if the input document does not have any text -> create a doc with an
// empty text
String text = inputDoc.getText();
if (inputDoc.getText() == null) text = "";
else text = inputDoc.getText();
gatedocument = Factory.newDocument(text);
// then the metadata as document features
FeatureMap docFeatures = gatedocument.getFeatures();
String docUrl = inputDoc.getUrl();
if (docUrl != null) docFeatures.put("gate.SourceURL", docUrl);
if (inputDoc.getMetadata() != null) {
Iterator<Entry<Writable, Writable>> iter = inputDoc.getMetadata().entrySet().iterator();
while (iter.hasNext()) {
Entry<Writable, Writable> entry = iter.next();
String skey = entry.getKey().toString().trim();
String svalue = null;
if (entry.getValue() != null) svalue = entry.getValue().toString().trim();
docFeatures.put(skey, svalue);
}
}
// finally the annotations as original markups
// TODO change the name of the annotation set via config
AnnotationSet outputAS = gatedocument.getAnnotations("Original markups");
for (Annotation annot : inputDoc.getAnnotations()) {
// add to outputAS as a GATE annotation
FeatureMap features = Factory.newFeatureMap();
features.putAll(annot.getFeatures());
outputAS.add(annot.getStart(), annot.getEnd(), annot.getType(), features);
}
return gatedocument;
}
public void splitter() {
AnnotationSet sDetectionAS = gateDocument.getAnnotations("SentenceDetection");
AnnotationSet defaultAs = gateDocument.getAnnotations("");
for (Iterator<Annotation> it = sDetectionAS.iterator(); it.hasNext(); ) {
Annotation currentSentenceAnnotation = it.next();
// Add the Sentence to the Annotation Set
defaultAs.add(
currentSentenceAnnotation.getStartNode(),
currentSentenceAnnotation.getEndNode(),
"Sentence",
null);
}
gateDocument.removeAnnotationSet("SentenceDetection");
}
/**
* Creates the Lookup annotations according to a gazetteer match.
*
* @param matchingState the final FSMState that was reached while matching.
* @param matchedRegionStart the start of the matched text region.
* @param matchedRegionEnd the end of the matched text region.
* @param annotationSet the annotation set where the new annotations should be added.
*/
protected void createLookups(
FSMState matchingState,
long matchedRegionStart,
long matchedRegionEnd,
AnnotationSet annotationSet) {
Iterator lookupIter = matchingState.getLookupSet().iterator();
while (lookupIter.hasNext()) {
Lookup currentLookup = (Lookup) lookupIter.next();
FeatureMap fm = Factory.newFeatureMap();
fm.put(LOOKUP_MAJOR_TYPE_FEATURE_NAME, currentLookup.majorType);
if (null != currentLookup.oClass && null != currentLookup.ontology) {
fm.put(LOOKUP_CLASS_FEATURE_NAME, currentLookup.oClass);
fm.put(LOOKUP_ONTOLOGY_FEATURE_NAME, currentLookup.ontology);
}
if (null != currentLookup.minorType)
fm.put(LOOKUP_MINOR_TYPE_FEATURE_NAME, currentLookup.minorType);
if (null != currentLookup.languages)
fm.put(LOOKUP_LANGUAGE_FEATURE_NAME, currentLookup.languages);
if (null != currentLookup.features) {
fm.putAll(currentLookup.features);
}
try {
// if(currentLookup.annotationType==null || "".equals(currentLookup.annotationType)){
// annotationSet.add(new Long(matchedRegionStart),
// new Long(matchedRegionEnd + 1),
// LOOKUP_ANNOTATION_TYPE,
// fm);
// }else{
annotationSet.add(
new Long(matchedRegionStart),
new Long(matchedRegionEnd + 1),
currentLookup.annotationType, // this pojo attribute will have Lookup as a default tag.
fm);
// }
} catch (InvalidOffsetException ioe) {
throw new GateRuntimeException(ioe.toString());
}
} // while(lookupIter.hasNext())
}
public void execute() throws ExecutionException {
AnnotationSet outputAS = document.getAnnotations(annotationSetName);
String text = document.getContent().toString();
Span[] tokens = tokenizer.getTokens(text);
try {
for (Span token : tokens) {
FeatureMap features = Factory.newFeatureMap();
features.put(
ANNIEConstants.TOKEN_STRING_FEATURE_NAME,
text.substring(token.getStart(), token.getEnd()));
outputAS.add(
(long) token.getStart(),
(long) token.getEnd(),
ANNIEConstants.TOKEN_ANNOTATION_TYPE,
features);
}
} catch (Exception e) {
throw new ExecutionException("error running tokenizer", e);
}
}
/**
* Rename annotation
*
* @param outputAS output annotation set
* @param oldType old annotation name
* @param newType new annotation name
*/
private void renameAnnotations(AnnotationSet outputAS, String oldType, String newType) {
AnnotationSet tmpAnatomyAS = outputAS.get(oldType);
for (Annotation tmpAnn : tmpAnatomyAS) {
Long startOffset = tmpAnn.getStartNode().getOffset();
Long endOffset = tmpAnn.getEndNode().getOffset();
AnnotationSet existingAS = outputAS.getCovering(newType, startOffset, endOffset);
// If we've already got an annotation of the same name in the same place, don't add a new one
// just delete the old one
if (existingAS.isEmpty()) {
FeatureMap tmpFm = tmpAnn.getFeatures();
FeatureMap fm = Factory.newFeatureMap();
fm.putAll(tmpFm);
try {
outputAS.add(startOffset, endOffset, newType, fm);
outputAS.remove(tmpAnn);
} catch (InvalidOffsetException ie) {
// shouldn't happen
}
} else {
outputAS.remove(tmpAnn);
}
}
}
/**
* @param inputAS input annotation set
* @param outputAS output annotation set
* @param term String matched
* @param startOffset match start offset
* @param endOffset match end offset
*/
private void addLookup(
AnnotationSet inputAS,
AnnotationSet outputAS,
String term,
String outputASType,
Long startOffset,
Long endOffset,
boolean useNounChunk) {
if (useNounChunk && nounChunkType != null && !nounChunkType.isEmpty()) {
AnnotationSet nounChunkAS = inputAS.getCovering(nounChunkType, startOffset, endOffset);
if (!nounChunkAS.isEmpty()) {
startOffset = nounChunkAS.firstNode().getOffset();
endOffset = nounChunkAS.lastNode().getOffset();
}
}
try {
AnnotationSet diseaseAS = inputAS.get(outputASType, startOffset, endOffset);
if (diseaseAS.isEmpty()) {
FeatureMap fm = Factory.newFeatureMap();
fm.put("match", term);
outputAS.add(startOffset, endOffset, outputASType, fm);
} else {
Annotation disease = diseaseAS.iterator().next();
FeatureMap fm = disease.getFeatures();
String meta = (String) fm.get("match");
if (meta != null) {
meta = meta + " " + term;
}
fm.put("match", meta);
}
} catch (InvalidOffsetException ie) {
// shouldn't happen
gate.util.Err.println(ie);
}
}
public void execute() throws ExecutionException {
// get the sentence splitter file from the URL provided
File splitter = Files.fileFromURL(splitterBinary);
// get the document content and replace non-breaking spaces with spaces
// TODO replace new-lines with spaces so we don't get a sentence per line
String docContent = document.getContent().toString().replace((char) 160, ' ');
try {
// create temporary files to use with the external sentence splitter
File tmpIn = File.createTempFile("GENIA", ".txt");
File tmpOut = File.createTempFile("GENIA", ".txt");
// store the document content in the input file
FileOutputStream fos = new FileOutputStream(tmpIn);
fos.write(docContent.getBytes("utf8"));
fos.close();
// setup the command line to run the sentence splitter
String[] args =
new String[] {
splitter.getAbsolutePath(), tmpIn.getAbsolutePath(), tmpOut.getAbsolutePath()
};
// run the sentence splitter over the docuement
manager.runProcess(
args, splitter.getParentFile(), (debug ? System.out : null), (debug ? System.err : null));
// get the annotation set we are going to store results in
AnnotationSet annotationSet = document.getAnnotations(annotationSetName);
// we haven't found any sentence yet so start looking for the next one
// from the beginning of the document
int end = 0;
// read in the output from the sentence splitter one line at a time
BufferedReader in = new BufferedReader(new FileReader(tmpOut));
String sentence = in.readLine();
while (sentence != null) {
// trim the sentence so we don't annotate extranious white space,
// this isn't python code after all :)
sentence = sentence.trim();
// find the start of the sentence
// TODO throw a sensible exception if the sentence can't be found?
int start = docContent.indexOf(sentence, end);
// work out where the sentence ends
end = start + sentence.length();
if (end > start) {
// the sentence has a length so annotate it
annotationSet.add((long) start, (long) end, "Sentence", Factory.newFeatureMap());
}
// get the next line from the output from the tagger
sentence = in.readLine();
}
// delete the temp files
if (!debug && !tmpIn.delete()) tmpIn.deleteOnExit();
if (!debug && !tmpOut.delete()) tmpOut.deleteOnExit();
} catch (Exception ioe) {
throw new ExecutionException("An error occured running the splitter", ioe);
}
}
/**
* This method annotates paragraphs in a GATE document. The investigated text spans beetween start
* and end offsets and the paragraph annotations are created in the annotSetName. If annotSetName
* is null then they are creted in the default annotation set.
*
* @param aDoc is the gate document on which the paragraph detection would be performed.If it is
* null or its content it's null then the method woul simply return doing nothing.
* @param startOffset is the index form the document content from which the paragraph detection
* will start
* @param endOffset is the offset where the detection will end.
* @param annotSetName is the name of the set in which paragraph annotation would be created.The
* annotation type created will be "paragraph"
*/
public void annotateParagraphs(Document aDoc, int startOffset, int endOffset, String annotSetName)
throws DocumentFormatException {
// Simply return if the document is null or its content
if (aDoc == null || aDoc.getContent() == null) return;
// Simply return if the start is > than the end
if (startOffset > endOffset) return;
// Decide where to put the newly detected annotations
AnnotationSet annotSet = null;
if (annotSetName == null) annotSet = aDoc.getAnnotations();
else annotSet = aDoc.getAnnotations(annotSetName);
// Extract the document content
String content = aDoc.getContent().toString();
// This is the offset marking the start of a para
int startOffsetPara = startOffset;
// This marks the ned of a para
int endOffsetPara = endOffset;
// The initial sate of the FSA
int state = 1;
// This field marks that a BR entity was read
// A BR entity can be NL or NL CR, depending on the operating system (UNIX
// or DOS)
boolean readBR = false;
int index = startOffset;
while (index < endOffset) {
// Read the current char
char ch = content.charAt(index);
// Test if a BR entity was read
if (ch == '\n') {
readBR = true;
// If \n is followed by a \r then advance the index in order to read a
// BR entity
while ((index + 1 < endOffset) && (content.charAt(index + 1) == '\r')) index++;
} // End if
switch (state) {
// It is the initial and also a final state
// Stay in state 1 while it reads whitespaces
case 1:
{
// If reads a non whitespace char then move to state 2 and record
// the beggining of a paragraph
if (!Character.isWhitespace(ch)) {
state = 2;
startOffsetPara = index;
} // End if
}
break;
// It can be also a final state.
case 2:
{
// Stay in state 2 while reading chars != BR entities
if (readBR) {
// If you find a BR char go to state 3. The possible end of the para
// can be index. This will be confirmed by state 3. So, this is why
// the end of a para is recorded here.
readBR = false;
endOffsetPara = index;
state = 3;
} // End if
}
break;
// It can be also a final state
// From state 3 there are only 2 possible ways: (state 2 or state1)
// In state 1 it needs to read a BR
// For state 2 it nead to read something different then a BR
case 3:
{
if (readBR) {
// A BR was read. Go to state 1
readBR = false;
state = 1;
// Create an annotation type paragraph
try {
annotSet.add(
new Long(startOffsetPara),
new Long(endOffsetPara),
"paragraph",
Factory.newFeatureMap());
} catch (gate.util.InvalidOffsetException ioe) {
throw new DocumentFormatException(
"Coudn't create a paragraph" + " annotation", ioe);
} // End try
} else {
// Go to state 2 an keep reading chars
state = 2;
} // End if
}
break;
} // End switch
// Prepare to read the next char.
index++;
} // End while
endOffsetPara = index;
// Investigate where the finite automata has stoped
if (state == 2 || state == 3) {
// Create an annotation type paragraph
try {
annotSet.add(
new Long(startOffsetPara),
// Create the final annotation using the endOffset
new Long(endOffsetPara),
"paragraph",
Factory.newFeatureMap());
} catch (gate.util.InvalidOffsetException ioe) {
throw new DocumentFormatException("Coudn't create a paragraph" + " annotation", ioe);
} // End try
} // End if
} // End annotateParagraphs();
