public void annotationUpdated(AnnotationEvent e) {
if (e.getType() == AnnotationEvent.FEATURES_UPDATED) {
if (!disableListener) {
Annotation annot = (Annotation) e.getSource();
// lets find out which annotation set it belongs to
AnnotationSet as = null;
if (getAnnotations().contains(annot)) {
as = getAnnotations();
} else {
Map<String, AnnotationSet> ass = getNamedAnnotationSets();
if (ass == null) return;
Iterator<String> namesIter = getNamedAnnotationSets().keySet().iterator();
while (namesIter.hasNext()) {
String name = namesIter.next();
as = getNamedAnnotationSets().get(name);
if (as.contains(annot)) {
break;
} else as = null;
}
}
if (as == null) return;
for (String docID : combinedDocumentIds) {
OffsetDetails od = getOffsetDetails(docID, as.getName(), annot);
if (od == null) continue;
Annotation toUse = od.getOriginalAnnotation();
toUse.setFeatures(annot.getFeatures());
}
}
}
}
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);
}
}
}
@Override
public void execute() throws ExecutionException {
initBeforeExecute();
AnnotationSet tokensAndDependenciesAS = inputAS;
TreeIndex index =
new GateAwareTreeIndex(
tokensAndDependenciesAS.get(null, Utils.setFromArray(new String[] {"args"})));
QueryData data =
new QueryData(index, new GateAnnotationsNodeAttributes(tokensAndDependenciesAS));
Iterable<QueryMatch> results = queryObject.evaluate(data);
int queryMatchOrd = 0;
for (QueryMatch result : results) {
queryMatchOrd++;
for (NodeMatch match : result.getMatchingNodes()) {
String name = match.getQueryNode().getName();
if (name != null) {
Annotation matchingAnnot = tokensAndDependenciesAS.get(match.getNodeId());
FeatureMap fm = Factory.newFeatureMap();
fm.put("matchingNodeId", match.getNodeId());
fm.put(
"queryMatchId",
String.format("%s_%03d", buildQueryStringHash(getQueryString()), queryMatchOrd));
outputAS.add(matchingAnnot.getStartNode(), matchingAnnot.getEndNode(), name, fm);
}
}
}
}
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");
}
/** Annotation remove event */
public void annotationRemoved(AnnotationSetEvent ase) {
if (!disableListener && ase.getSourceDocument() == this) {
AnnotationSet as = (AnnotationSet) ase.getSource();
Annotation annot = ase.getAnnotation();
FeatureMap features = Factory.newFeatureMap();
features.putAll(annot.getFeatures());
boolean defaultAS = as.getName() == null;
for (String docID : combinedDocumentIds) {
Document aDoc = compoundDocument.getDocument(docID);
// find out the details which refer to the deleted annotation
OffsetDetails od = getOffsetDetails(docID, as.getName(), annot);
if (od == null) continue;
if (defaultAS) {
aDoc.getAnnotations().remove(od.getOriginalAnnotation());
} else {
aDoc.getAnnotations(as.getName()).remove(od.getOriginalAnnotation());
}
removeOffsetDetails(docID, od);
break;
}
}
}
// 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);
}
}
/**
* 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;
}
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);
}
}
protected AnnotationDiffer calculateDocumentDiff(Document document, String annotTypeName) {
AnnotationSet responsesIter = responseAS.get(annotTypeName);
if (getKeyAnnotationsAreInDocumentFeatures()) {
return DocumentFeaturesDiff.computeDiffWithDocFeatures(document, featureNames, responsesIter);
}
AnnotationSet keysIter = keyAS.get(annotTypeName);
AnnotationDiffer differ = new AnnotationDiffer();
differ.setSignificantFeaturesSet(new HashSet<String>(featureNames));
differ.calculateDiff(keysIter, responsesIter); // compare
return differ;
}
/** Annotation added event */
public void annotationAdded(AnnotationSetEvent ase) {
if (!disableListener && ase.getSourceDocument() == this) {
AnnotationSet as = (AnnotationSet) ase.getSource();
Annotation annot = ase.getAnnotation();
annot.addAnnotationListener(this);
FeatureMap features = Factory.newFeatureMap();
features.putAll(annot.getFeatures());
boolean defaultAS = as.getName() == null;
for (String docID : combinedDocumentIds) {
Document aDoc = compoundDocument.getDocument(docID);
long stOffset = getOffsetInSrcDocument(docID, annot.getStartNode().getOffset().longValue());
if (stOffset == -1) continue;
long enOffset = getOffsetInSrcDocument(docID, annot.getEndNode().getOffset().longValue());
if (enOffset == -1) continue;
Annotation originalAnnot = null;
try {
Integer id = annot.getId();
if (defaultAS) {
aDoc.getAnnotations()
.add(id, new Long(stOffset), new Long(enOffset), annot.getType(), features);
originalAnnot = aDoc.getAnnotations().get(id);
} else {
aDoc.getAnnotations(as.getName())
.add(id, new Long(stOffset), new Long(enOffset), annot.getType(), features);
originalAnnot = aDoc.getAnnotations(as.getName()).get(id);
}
} catch (InvalidOffsetException ioe) {
System.out.println(aDoc.getName() + "=" + stOffset + "=" + enOffset);
throw new GateRuntimeException(ioe);
}
OffsetDetails od = new OffsetDetails();
od.setOldStartOffset(stOffset);
od.setOldEndOffset(enOffset);
od.setNewStartOffset(annot.getStartNode().getOffset().longValue());
od.setNewEndOffset(annot.getEndNode().getOffset().longValue());
od.setOriginalAnnotation(originalAnnot);
od.setNewAnnotation(annot);
addNewOffsetDetails(docID, od);
break;
}
}
}
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");
}
@Override
public void execute() throws ExecutionException {
Document doc = getDocument();
AnnotationSet as = doc.getAnnotations(getAnnotationSetName());
AnnotationSet tocs = as.get(getTokenAnnotationTypeName());
try {
for (Annotation t : tocs) {
String content = Utils.stringFor(doc, t);
String val = getOrthographyValue(content);
if (val != null) t.getFeatures().put("orth", val);
}
} catch (Exception e) {
throw new ExecutionException(e);
}
}
/**
* Sub-range access for annotation sets (mapping to getContained). Allows <code>
* someAnnotationSet[15..20]</code>. This works with ranges whose end points are any numeric type,
* so as well as using integer literals you can do <code>someAnnotationSet[ann.start()..ann.end()]
* </code> (as start and end return Long).
*
* @see AnnotationSet#getContained(Long, Long)
*/
@SuppressWarnings("unchecked")
public static AnnotationSet getAt(AnnotationSet self, Range<?> range) {
if (range.getFrom() instanceof Number) {
return self.getContained(
Long.valueOf(((Number) range.getFrom()).longValue()),
Long.valueOf(((Number) range.getTo()).longValue()));
} else if (range.getFrom() instanceof String) {
return getAt(self, (List<String>) range);
} else {
throw new IllegalArgumentException("AnnotationSet.getAt expects a numeric or string range");
}
}
/**
* Two AnnotationSet are equal if their name, the documents of which belong to the AnnotationSets
* and annotations from the sets are the same
*/
public static boolean annotationSetsEqual(AnnotationSet as1, AnnotationSet as2) {
if (as1 == null ^ as2 == null) return false;
if (as1 == null) return true;
// Sets equality
if (as1.size() != as2.size()) return false;
try {
if (!as1.containsAll(as2)) return false;
} catch (ClassCastException unused) {
return false;
} catch (NullPointerException unused) {
return false;
}
// removed to prevent infinite looping in testDocumentsEqual()
// // verify the documents which they belong to
// if (! check (as1.getDocument(), as2.getDocument())) return false;
// verify the name of the AnnotationSets
if (!check(as1.getName(), as2.getName())) return false;
return true;
} // equals
protected void doExecute(Document theDocument) throws ExecutionException {
interrupted = false;
if (theDocument == null) {
throw new ExecutionException("No document to process!");
}
AnnotationSet outputAS = theDocument.getAnnotations(getOutputAnnotationSet());
if (containingType == null || containingType.isEmpty()) {
annotateText(document, outputAS, 0, document.getContent().size());
} else {
AnnotationSet inputAS = null;
if (inputASName == null || inputASName.isEmpty()) {
inputAS = theDocument.getAnnotations();
} else {
inputAS = theDocument.getAnnotations(inputASName);
}
AnnotationSet containingAnns = inputAS.get(containingType);
for (Annotation containingAnn : containingAnns) {
annotateText(
document, outputAS, gate.Utils.start(containingAnn), gate.Utils.end(containingAnn));
}
}
}
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);
}
}
public void doit(
gate.Document doc,
Map<String, AnnotationSet> bindings,
gate.AnnotationSet annotations,
gate.AnnotationSet inputAS,
gate.AnnotationSet outputAS,
gate.creole.ontology.Ontology ontology)
throws JapeException {
// your RHS Java code will be embedded here ...
String category = (String) doc.getFeatures().get("category");
Annotation mention = tagAnnots.iterator().next();
String pName = (String) mention.getFeatures().get("class");
OntoManager om = OntoManager.getInstance();
ProductClass catClass = om.getProductClass(category);
ProductClass pClass = om.getProductClass(pName);
boolean sameCat =
pClass
.getOntClass()
.hasSuperClass(catClass.getOntClass()); // TODO: refactor to used direct method
if (!sameCat) {
outputAS.remove(mention);
}
}
/**
* @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);
}
}
/** Returns a list of annotations to be added to the Behemoth document from the GATE one * */
private List<com.digitalpebble.behemoth.Annotation> convertGATEAnnotationsToBehemoth(
AnnotationSet GATEAnnotionSet, com.digitalpebble.behemoth.BehemothDocument behemoth) {
List<com.digitalpebble.behemoth.Annotation> beheannotations =
new ArrayList<com.digitalpebble.behemoth.Annotation>();
AnnotationSet resultAS = GATEAnnotionSet.get(filters.getTypes());
// sort the GATE annotations
List<gate.Annotation> annotationList = new ArrayList<gate.Annotation>(resultAS);
Collections.sort(annotationList, new OffsetComparator());
Iterator<gate.Annotation> inputASIter = annotationList.iterator();
while (inputASIter.hasNext()) {
gate.Annotation source = inputASIter.next();
com.digitalpebble.behemoth.Annotation target = new com.digitalpebble.behemoth.Annotation();
target.setType(source.getType());
target.setStart(source.getStartNode().getOffset().longValue());
target.setEnd(source.getEndNode().getOffset().longValue());
// now do the features
// is the type listed?
Set<String> expectedfeatnames = filters.getFeatureFilters().get(source.getType());
if (expectedfeatnames != null) {
Iterator featurenames = source.getFeatures().keySet().iterator();
while (featurenames.hasNext()) {
// cast the feature name to a string which will be right in
// 99% of cases
String featurename = featurenames.next().toString();
// if this feature name is not wanted just ignore it
if (expectedfeatnames.contains(featurename) == false) continue;
// we know that we want to keep this feature
// let's see what the best way of representing the value
// would be
// TODO later => find a better way of mapping when not a
// string
Object originalvalue = source.getFeatures().get(featurename);
if (originalvalue == null) originalvalue = "null";
target.getFeatures().put(featurename, originalvalue.toString());
}
}
beheannotations.add(target);
}
return beheannotations;
}
/**
* 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())
}
/**
* 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);
}
}
}
public void execute() throws ExecutionException {
// get all the annotations we need from the input AS
AnnotationSet inputAS =
inputAnnotationSet == null || inputAnnotationSet.trim().length() == 0
? document.getAnnotations()
: document.getAnnotations(inputAnnotationSet);
AnnotationSet outputAS =
outputAnnotationSet == null || outputAnnotationSet.trim().length() == 0
? document.getAnnotations()
: document.getAnnotations(outputAnnotationSet);
// no spans?
if (getSpanAnnotationType() == null | getSpanAnnotationType().equals("")) {
AnnotationSet inputs = inputAS.get(inputAnnotationType);
List<Annotation> list = new ArrayList<Annotation>();
list.addAll(inputs);
Collections.sort(list, new OffsetComparator());
// use window or normal
if (window == -1) generateNGrams(list, outputAS);
else generateNGramsOverWindow(list, outputAS);
} else {
// use the spans
AnnotationSet spans = inputAS.get(getSpanAnnotationType());
Iterator spaniter = spans.iterator();
while (spaniter.hasNext()) {
Annotation span = (Annotation) spaniter.next();
AnnotationSet inputs =
inputAS.get(
inputAnnotationType,
span.getStartNode().getOffset(),
span.getEndNode().getOffset());
List<Annotation> list = new ArrayList<Annotation>();
list.addAll(inputs);
Collections.sort(list, new OffsetComparator());
if (window == -1) generateNGrams(list, outputAS);
else generateNGramsOverWindow(list, outputAS);
}
}
}
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);
}
}
/**
* The main entry point. First we parse the command line options (see usage() method for details),
* then we take all remaining command line parameters to be file names to process. Each file is
* loaded, processed using the application and the results written to the output file
* (inputFile.out.xml).
*/
public static void main(String[] args) throws Exception {
parseCommandLine(args);
// initialise GATE - this must be done before calling any GATE APIs
Gate.init();
// load the saved application
CorpusController application =
(CorpusController) PersistenceManager.loadObjectFromFile(gappFile);
// Create a Corpus to use. We recycle the same Corpus object for each
// iteration. The string parameter to newCorpus() is simply the
// GATE-internal name to use for the corpus. It has no particular
// significance.
ArrayList<String> files = getFilesFromDir(inputDir);
gate.Corpus corpus = createCorpus(files);
// Corpus corpus = Factory.newCorpus("BatchProcessApp Corpus");
application.setCorpus(corpus);
System.out.println("Processing " + files.size() + " files");
// process the files one by one
for (int i = 0; i < files.size(); i++) {
// load the document (using the specified encoding if one was given)
File docFile = new File(files.get(i));
System.out.print("Processing document " + docFile + " (" + i + ") ...");
Document doc = Factory.newDocument(docFile.toURL(), encoding);
// put the document in the corpus
corpus.add(doc);
// run the application
application.execute();
// remove the document from the corpus again
corpus.clear();
String docXMLString = null;
// if we want to just write out specific annotation types, we must
// extract the annotations into a Set
if (annotTypesToWrite != null) {
// Create a temporary Set to hold the annotations we wish to write out
Set annotationsToWrite = new HashSet();
// we only extract annotations from the default (unnamed) AnnotationSet
// in this example
AnnotationSet defaultAnnots = doc.getAnnotations("Output");
Iterator annotTypesIt = annotTypesToWrite.iterator();
while (annotTypesIt.hasNext()) {
// extract all the annotations of each requested type and add them to
// the temporary set
AnnotationSet annotsOfThisType = defaultAnnots.get((String) annotTypesIt.next());
if (annotsOfThisType != null) {
annotationsToWrite.addAll(annotsOfThisType);
}
}
// create the XML string using these annotations
docXMLString = doc.toXml(annotationsToWrite, true);
}
// otherwise, just write out the whole document as GateXML
else {
docXMLString = doc.toXml();
}
// Release the document, as it is no longer needed
Factory.deleteResource(doc);
// output the XML to <inputFile>.out.xml
System.out.println("Writing file " + docFile.getName());
String outputFileName = docFile.getName() + ".out.xml";
// File outputFile = new File(docFile.getParentFile(), outputFileName);
File outputFile = new File(new File(outputDir).getAbsolutePath(), outputFileName);
// Write output files using the same encoding as the original
FileOutputStream fos = new FileOutputStream(outputFile);
BufferedOutputStream bos = new BufferedOutputStream(fos);
OutputStreamWriter out;
if (encoding == null) {
out = new OutputStreamWriter(bos);
} else {
out = new OutputStreamWriter(bos, encoding);
}
out.write(docXMLString);
out.close();
System.out.println("done");
} // for each file
System.out.println("All done");
} // void main(String[] args)
@Override
public void execute() throws ExecutionException {
interrupted = false;
// quit if setup failed
if (gracefulExit) {
gracefulExit("Plugin was not initialised correctly. Exiting gracefully ... ");
return;
}
AnnotationSet inputAS =
(inputASName == null || inputASName.trim().length() == 0)
? document.getAnnotations()
: document.getAnnotations(inputASName);
AnnotationSet outputAS =
(outputASName == null || outputASName.trim().length() == 0)
? document.getAnnotations()
: document.getAnnotations(outputASName);
AnnotationSet sentenceAS = null;
if (sentenceType != null && !sentenceType.isEmpty()) {
sentenceAS = inputAS.get(sentenceType);
}
// Document content
String docContent = document.getContent().toString();
int docLen = docContent.length();
// For matching purposes replace all whitespace characters with a single space
docContent = docContent.replaceAll("[\\s\\xA0\\u2007\\u202F]", " ");
fireStatusChanged("Locating anatomy, disease and procedure mentions in " + document.getName());
fireProgressChanged(0);
if (sentenceAS != null) {
for (Annotation sentence : sentenceAS) {
Long sentStartOffset = sentence.getStartNode().getOffset();
Long sentEndOffset = sentence.getEndNode().getOffset();
// Converting the sentence to lower case prevents the need to use case-insenstive regex
// matching, which should give a small performance boost
String sentenceContent =
docContent
.substring(sentStartOffset.intValue(), sentEndOffset.intValue())
.toLowerCase(Locale.ENGLISH);
if (diseaseType != null && !diseaseType.isEmpty()) {
doMatch(
patternMap.get("disease_suffix"),
sentenceContent,
inputAS,
outputAS,
"suffDisease",
sentStartOffset,
docLen);
doMatch(
patternMap.get("disease_abbrevs"),
sentenceContent,
inputAS,
outputAS,
"preDisease",
sentStartOffset,
docLen);
doMatch(
patternMap.get("disease_named_syndrome"),
sentenceContent,
inputAS,
outputAS,
"namedDisease",
sentStartOffset,
docLen);
doMatch(
patternMap.get("disease_sense"),
sentenceContent,
inputAS,
outputAS,
"tmpDiseaseSense",
sentStartOffset,
docLen);
doMatch(
patternMap.get("disease_sense_context"),
sentenceContent,
inputAS,
outputAS,
"tmpDiseaseSenseContext",
sentStartOffset,
docLen);
doMatch(
patternMap.get("disease_generic_context"),
sentenceContent,
inputAS,
outputAS,
"poDisease",
sentStartOffset,
docLen);
doMatch(
patternMap.get("disease_anatomy_context"),
sentenceContent,
inputAS,
outputAS,
"tmpDisease",
sentStartOffset,
docLen);
}
if (procedureType != null && !procedureType.isEmpty()) {
doMatch(
patternMap.get("procedure_suffix"),
sentenceContent,
inputAS,
outputAS,
"poProcedure",
sentStartOffset,
docLen);
doMatch(
patternMap.get("procedure_key"),
sentenceContent,
inputAS,
outputAS,
"poProcedure",
sentStartOffset,
docLen);
doMatch(
patternMap.get("procedure_anatomy_context"),
sentenceContent,
inputAS,
outputAS,
"tmpProcedure",
sentStartOffset,
docLen);
}
if (symptomType != null && !symptomType.isEmpty()) {
doMatch(
patternMap.get("symptom_key"),
sentenceContent,
inputAS,
outputAS,
"poSymptom",
sentStartOffset,
docLen);
}
if (testType != null && !testType.isEmpty()) {
doMatch(
patternMap.get("test_key"),
sentenceContent,
inputAS,
outputAS,
"poTest",
sentStartOffset,
docLen);
}
if (anatomyType != null && !anatomyType.isEmpty()) {
doMatch(
patternMap.get("anatomy_suffix_adjective"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatSuffAdj",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_suffix"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatSuff",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_prefix"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatPre",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_position"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatPos",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_space_region_junction"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatSpace",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_part_adjective"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatAdj",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_latin_noun"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatLatin",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_muscle"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatMuscle",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_part"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatPart",
sentStartOffset,
docLen);
doMatch(
patternMap.get("anatomy_fluid"),
sentenceContent,
inputAS,
outputAS,
"tmpAnatFluid",
sentStartOffset,
docLen);
}
}
// Run JAPE transducer to clean up the output
fireStatusChanged(
"Processing anatomical, disease and procedure mentions in " + document.getName());
try {
japeTransducer.setDocument(document);
japeTransducer.setInputASName(inputASName);
japeTransducer.setOutputASName(outputASName);
japeTransducer.addProgressListener(this);
japeTransducer.execute();
} catch (ExecutionException re) {
gate.util.Err.println("Unable to run " + japeURL);
gracefulExit = true;
} finally {
japeTransducer.setDocument(null);
}
// rename temporary annotations
if (!debug) {
renameAnnotations(outputAS, "tmpAnatomicalTerm", anatomyType);
renameAnnotations(outputAS, "suffDisease", diseaseType);
renameAnnotations(outputAS, "poDisease", diseaseType);
renameAnnotations(outputAS, "preDisease", diseaseType);
renameAnnotations(outputAS, "poProcedure", procedureType);
renameAnnotations(outputAS, "poSymptom", symptomType);
renameAnnotations(outputAS, "poTest", testType);
}
} else {
gracefulExit("No sentences to process!");
}
// want list of disease key words plus symptoms such as oedema? or just diseases
fireProcessFinished();
} // end 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)
StandAloneAnnie annie = new StandAloneAnnie();
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();
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
@Override
public void execute() throws ExecutionException {
AnnotationSet inputAS = document.getAnnotations(inputASName);
AnnotationSet outputAS = document.getAnnotations(outputASName);
AnnotationSet tagAS = document.getAnnotations(tagASName);
AnnotationSet annotsToTransfer = null;
boolean newID = copyAnnotations && inputAS.equals(outputAS);
mappings.clear();
// TODO clean this up so we don't have to repeat ourselves
if (configURL != null) {
BufferedReader in = null;
try {
in = new BomStrippingInputStreamReader(configURL.openStream());
String line = in.readLine();
while (line != null) {
if (!line.trim().equals("")) {
String[] data = line.split("=", 2);
String oldName = data[0].trim();
String newName = data.length == 2 ? data[1].trim() : null;
mappings.put(oldName, new Mapping(oldName, newName));
}
line = in.readLine();
}
} catch (IOException ioe) {
ioe.printStackTrace();
} finally {
IOUtils.closeQuietly(in);
}
} else if (annotationTypes != null) {
for (String type : annotationTypes) {
String[] data = type.split("=", 2);
String oldName = data[0].trim();
String newName = data.length == 2 ? data[1].trim() : null;
mappings.put(oldName, new Mapping(oldName, newName));
}
}
// else
// throw new
// ExecutionException("The annotation list and URL cannot both be null");
if (mappings.size() > 0) {
annotsToTransfer = inputAS.get(mappings.keySet());
} else {
// transfer everything
annotsToTransfer = inputAS.get();
}
// in case of no one annotation from some of annotationTypes
if (annotsToTransfer == null || annotsToTransfer.size() == 0) return;
// check if we have a BODY annotation
// if not, just copy all
if (textTagName == null || textTagName.equals("")) {
// remove from input set unless we copy only
if (!copyAnnotations) inputAS.removeAll(annotsToTransfer);
transferAnnotations(new ArrayList<Annotation>(annotsToTransfer), outputAS, newID);
return;
}
// get the BODY annotation
bodyAnnotations = tagAS.get(textTagName);
if (bodyAnnotations == null || bodyAnnotations.isEmpty()) {
// outputAS.addAll(inputAS);
if (transferAllUnlessFound) {
// remove from input set unless we copy only
if (!copyAnnotations) inputAS.removeAll(annotsToTransfer);
transferAnnotations(new ArrayList<Annotation>(annotsToTransfer), outputAS, newID);
}
return;
}
List<Annotation> annots2Move = new ArrayList<Annotation>();
Iterator<Annotation> bodyIter = bodyAnnotations.iterator();
while (bodyIter.hasNext()) {
Annotation bodyAnn = bodyIter.next();
Long start = bodyAnn.getStartNode().getOffset();
Long end = bodyAnn.getEndNode().getOffset();
// get all annotations we want transferred
AnnotationSet annots2Copy = annotsToTransfer.getContained(start, end);
// copy them to the new set and delete them from the old one
annots2Move.addAll(annots2Copy);
}
if (!copyAnnotations) inputAS.removeAll(annots2Move);
transferAnnotations(annots2Move, outputAS, newID);
}
/**
* 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();
private RetObj ProcessRecords() throws Exception {
// Create a Corpus to use. We recycle the same Corpus object for each
// iteration.
Corpus corpus = Factory.newCorpus("BatchProcessApp Corpus");
this.application.setCorpus(corpus);
// object for returned data
List<String> processedlines = new ArrayList<String>();
List<String> processedText = new ArrayList<String>();
for (int record_num = 0; record_num < this.recs.size(); ++record_num) {
/*if( record_num % Math.ceil(((double) this.recs.size())/10.0) == 0)
System.out.println("Thread " + this.threadID + ": "+ ((int) ((double)record_num)/((double) this.recs.size())*100.0 ) +"% complete.");
*/
// first, split title from body and get embedded age in title..
String title_age = "-1";
String sep = "..THIS IS MY SEPARATION STRING..";
String title = "";
String body = this.recs.get(record_num);
Boolean trimmed = false;
int age_end = body.indexOf(",> ");
if (age_end >= 0 && age_end < body.length()) {
int age_start = body.lastIndexOf("-", age_end);
if (age_start >= 0 && age_start < age_end) {
title_age = body.substring(age_start + 1, age_end).trim();
if (!isInteger(title_age)) title_age = "-1";
else {
title = body.substring(0, age_start);
body = body.substring(age_end + 2, body.length());
body = title + sep + body;
trimmed = true;
}
}
if (!trimmed) {
title = body.substring(0, age_end);
body = body.substring(age_end + 2, body.length());
body = title + sep + body;
trimmed = true;
}
}
// --------------------
org.jsoup.nodes.Document htmldoc =
Jsoup.parseBodyFragment(body.replaceAll("COMMA_GOES_HERE", ","));
Elements links = htmldoc.select("a[href]");
Elements media = htmldoc.select("[src]");
Elements imports = htmldoc.select("link[href]");
processedText.add(htmldoc.text().replace(sep, " "));
Document doc = Factory.newDocument(htmldoc.text());
// put the document in the corpus
corpus.add(doc);
// run the application
this.application.execute();
// remove the document from the corpus again
corpus.clear();
// extract annotations
String line = "";
AnnotationSet Annots = doc.getAnnotations("");
Integer FirstPersonCount = 0, ThirdPersonCount = 0;
AnnotationSet FirstPerson = Annots.get("FirstPerson");
if (FirstPerson != null) FirstPersonCount = FirstPerson.size();
AnnotationSet ThirdPerson = Annots.get("ThirdPerson");
if (ThirdPerson != null) ThirdPersonCount = ThirdPerson.size();
line += FirstPersonCount.toString() + "," + ThirdPersonCount.toString() + ",";
AnnotationSet Names = Annots.get("Name");
if (Names == null || Names.size() < 1) line += ",";
else {
Iterator<Annotation> Iter = Names.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("name");
if (Feat != null) line += Feat.toString();
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet Age = Annots.get("Age");
if (Age == null || Age.size() < 1) line += title_age + ",";
else {
Iterator<Annotation> Iter = Age.inDocumentOrder().iterator();
line += title_age + ";";
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("age");
if (Feat != null) line += Feat.toString();
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet Cost = Annots.get("Cost");
if (Cost == null || Cost.size() < 1) line += ",";
else {
Iterator<Annotation> Iter = Cost.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("value");
if (Feat != null) line += Feat.toString();
else line += "none";
line += "/";
Feat = Ann.getFeatures().get("target_value");
if (Feat != null) line += Feat.toString();
else line += "none";
line += "/";
Feat = Ann.getFeatures().get("target_type");
if (Feat != null) line += Feat.toString();
else line += "none";
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet height = Annots.get("height");
if (height == null || height.size() < 1) line += ",,";
else {
String ft = "";
String inch = "";
Iterator<Annotation> Iter = height.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("feet");
if (Feat != null) ft += Feat.toString();
else ft += "none";
Feat = Ann.getFeatures().get("inches");
if (Feat != null) inch += Feat.toString();
else inch += "none";
if (Iter.hasNext()) {
ft += ";";
inch += ";";
}
}
line += ft + "," + inch + ",";
}
AnnotationSet weight = Annots.get("weight");
if (weight == null || weight.size() < 1) line += ",";
else {
Iterator<Annotation> Iter = weight.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("pounds");
if (Feat != null) line += Feat.toString();
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet measurement = Annots.get("measurement");
if (measurement == null || measurement.size() < 1) line += ",,,,";
else {
String cup = "";
String chest = "";
String waist = "";
String hip = "";
Iterator<Annotation> Iter = measurement.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("cup");
if (Feat != null) cup += Feat.toString();
else cup += "none";
Feat = Ann.getFeatures().get("chest");
if (Feat != null) chest += Feat.toString();
else chest += "none";
Feat = Ann.getFeatures().get("waist");
if (Feat != null) waist += Feat.toString();
else waist += "none";
Feat = Ann.getFeatures().get("hip");
if (Feat != null) hip += Feat.toString();
else hip += "none";
if (Iter.hasNext()) {
cup += ";";
chest += ";";
waist += ";";
hip += ";";
}
}
line += cup + "," + chest + "," + waist + "," + hip + ",";
}
AnnotationSet Ethnicity = Annots.get("Ethnicity");
if (Ethnicity == null || Ethnicity.size() < 1) line += ",";
else {
Iterator<Annotation> Iter = Ethnicity.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("ethnicity");
if (Feat != null)
line += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ");
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet SkinColor = Annots.get("SkinColor");
if (SkinColor == null || SkinColor.size() < 1) line += ",";
else {
Iterator<Annotation> Iter = SkinColor.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("color");
if (Feat != null)
line += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ");
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet EyeColor = Annots.get("EyeColor");
if (EyeColor == null || EyeColor.size() < 1) line += ",";
else {
Iterator<Annotation> Iter = EyeColor.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("color");
if (Feat != null)
line += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ");
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet HairColor = Annots.get("HairColor");
if (HairColor == null || HairColor.size() < 1) line += ",";
else {
Iterator<Annotation> Iter = HairColor.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("color");
if (Feat != null)
line += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ");
if (Iter.hasNext()) line += ";";
}
line += ",";
}
AnnotationSet Restriction = Annots.get("Restriction");
if (Restriction == null || Restriction.size() < 1) line += ",,,";
else {
String type = "";
String ethnicity = "";
String age = "";
Iterator<Annotation> Iter = Restriction.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("type");
if (Feat != null) type += Feat.toString();
else type += "none";
Feat = Ann.getFeatures().get("ethnicity");
if (Feat != null)
ethnicity += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ");
else ethnicity += "none";
Feat = Ann.getFeatures().get("age");
if (Feat != null) age += Feat.toString();
else age += "none";
if (Iter.hasNext()) {
type += ";";
ethnicity += ";";
age += ";";
}
}
line += type + "," + ethnicity + "," + age + ",";
}
AnnotationSet Phone = Annots.get("PhoneNumber");
if (Phone == null || Phone.size() < 1) line += ",,,";
else {
String value = "";
String state = "";
String city = "";
Iterator<Annotation> Iter = Phone.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("value");
if (Feat != null) value += Feat.toString();
else value += "none";
Feat = Ann.getFeatures().get("state");
if (Feat != null) state += Feat.toString();
else state += "none";
Feat = Ann.getFeatures().get("area");
if (Feat != null)
city += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ");
else city += "none";
if (Iter.hasNext()) {
value += ";";
state += ";";
city += ";";
}
}
line += value + "," + state + "," + city + ",";
}
String Emails = "";
AnnotationSet Email = Annots.get("Email");
if (Email == null || Email.size() < 1) Emails = "";
else {
Iterator<Annotation> Iter = Email.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("email");
if (Feat != null)
Emails += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ") + ";";
}
}
if (links != null) {
for (Element l : links) {
String href = l.attr("abs:href");
if (href == null) continue;
if (href.length() > 7 && href.substring(0, 7).toLowerCase().equals("mailto:")) {
Emails +=
href.substring(7, href.length()).replaceAll(",", " ").replaceAll(";", " ") + ";";
}
}
}
if (Emails.length() > 0 && Emails.substring(Emails.length() - 1, Emails.length()).equals(";"))
Emails = Emails.substring(0, Emails.length() - 1);
line += Emails + ",";
String Urls = "";
AnnotationSet Url = Annots.get("Url");
if (Url == null || Url.size() < 1) Urls = "";
else {
Iterator<Annotation> Iter = Url.inDocumentOrder().iterator();
while (Iter.hasNext()) {
Annotation Ann = Iter.next();
Object Feat = Ann.getFeatures().get("url");
if (Feat != null)
Urls += Feat.toString().toLowerCase().replaceAll(",", " ").replaceAll(";", " ") + ";";
}
}
if (links != null) {
for (Element l : links) {
String href = l.attr("abs:href");
if (href == null) continue;
if (href.length() <= 7 || !href.substring(0, 7).toLowerCase().equals("mailto:")) {
Urls += href.replaceAll(",", " ").replaceAll(";", " ") + ";";
}
}
}
if (imports != null) {
for (Element l : imports) {
String href = l.attr("abs:href");
if (href == null) continue;
Urls += href.replaceAll(",", " ").replaceAll(";", " ") + ";";
}
}
if (Urls.length() > 0 && Urls.substring(Urls.length() - 1, Urls.length()).equals(";"))
Urls = Urls.substring(0, Urls.length() - 1);
line += Urls + ",";
String Medias = "";
if (media != null) {
for (Element l : media) {
String src = l.attr("abs:src");
if (src == null) continue;
Medias += src.replaceAll(",", " ").replaceAll(";", " ") + ";";
}
}
if (Medias.length() > 0 && Medias.substring(Medias.length() - 1, Medias.length()).equals(";"))
Medias = Medias.substring(0, Medias.length() - 1);
line += Medias;
processedlines.add(line);
// Release the document, as it is no longer needed
Factory.deleteResource(doc);
}
Factory.deleteResource(corpus);
RetObj out = new RetObj(processedlines, processedText);
return out;
}