private void createDbpediaResource(
JCas aJCas, String uri, int begin, String surface, Double sim, String types)
throws UnsupportedEncodingException {
DbpediaAnnotation anno = new DbpediaAnnotation(aJCas);
String abstractText = null;
try {
ArrayListMultimap<String, String> results = DbpediaService.queryDbpediaEnglishAbstract(uri);
for (Entry<String, String> entry : results.entries()) {
abstractText = entry.getValue();
}
} catch (Exception e) {
e.printStackTrace();
System.err.println("Cannot query this uri " + uri);
}
int end = begin + surface.length();
anno.setBegin(begin);
anno.setEnd(end);
anno.setUri(uri);
anno.setAbstract(abstractText);
anno.setSimilarityScore(sim);
List<String> allTypes = Arrays.asList(types.split(","));
anno.setComponentId(ANNOTATOR_COMPONENT_ID);
anno.setResourceType(FSCollectionFactory.createStringList(aJCas, allTypes));
anno.addToIndexes();
}
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
Annotation document = this.processor.process(jCas.getDocumentText());
String lastNETag = "O";
int lastNEBegin = -1;
int lastNEEnd = -1;
for (CoreMap tokenAnn : document.get(TokensAnnotation.class)) {
// create the token annotation
int begin = tokenAnn.get(CharacterOffsetBeginAnnotation.class);
int end = tokenAnn.get(CharacterOffsetEndAnnotation.class);
String pos = tokenAnn.get(PartOfSpeechAnnotation.class);
String lemma = tokenAnn.get(LemmaAnnotation.class);
Token token = new Token(jCas, begin, end);
token.setPos(pos);
token.setLemma(lemma);
token.addToIndexes();
// hackery to convert token-level named entity tag into phrase-level tag
String neTag = tokenAnn.get(NamedEntityTagAnnotation.class);
if (neTag.equals("O") && !lastNETag.equals("O")) {
NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd);
ne.setMentionType(lastNETag);
ne.addToIndexes();
} else {
if (lastNETag.equals("O")) {
lastNEBegin = begin;
} else if (lastNETag.equals(neTag)) {
// do nothing - begin was already set
} else {
NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd);
ne.setMentionType(lastNETag);
ne.addToIndexes();
lastNEBegin = begin;
}
lastNEEnd = end;
}
lastNETag = neTag;
}
if (!lastNETag.equals("O")) {
NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd);
ne.setMentionType(lastNETag);
ne.addToIndexes();
}
// add sentences and trees
for (CoreMap sentenceAnn : document.get(SentencesAnnotation.class)) {
// add the sentence annotation
int sentBegin = sentenceAnn.get(CharacterOffsetBeginAnnotation.class);
int sentEnd = sentenceAnn.get(CharacterOffsetEndAnnotation.class);
Sentence sentence = new Sentence(jCas, sentBegin, sentEnd);
sentence.addToIndexes();
// add the syntactic tree annotation
List<CoreLabel> tokenAnns = sentenceAnn.get(TokensAnnotation.class);
Tree tree = sentenceAnn.get(TreeAnnotation.class);
if (tree.children().length != 1) {
throw new RuntimeException("Expected single root node, found " + tree);
}
tree = tree.firstChild();
tree.indexSpans(0);
TopTreebankNode root = new TopTreebankNode(jCas);
root.setTreebankParse(tree.toString());
// TODO: root.setTerminals(v)
this.addTreebankNodeToIndexes(root, jCas, tree, tokenAnns);
// get the dependencies
SemanticGraph dependencies =
sentenceAnn.get(CollapsedCCProcessedDependenciesAnnotation.class);
// convert Stanford nodes to UIMA annotations
List<Token> tokens = JCasUtil.selectCovered(jCas, Token.class, sentence);
Map<IndexedWord, DependencyNode> stanfordToUima = new HashMap<IndexedWord, DependencyNode>();
for (IndexedWord stanfordNode : dependencies.vertexSet()) {
int indexBegin = stanfordNode.get(BeginIndexAnnotation.class);
int indexEnd = stanfordNode.get(EndIndexAnnotation.class);
int tokenBegin = tokens.get(indexBegin).getBegin();
int tokenEnd = tokens.get(indexEnd - 1).getEnd();
DependencyNode node;
if (dependencies.getRoots().contains(stanfordNode)) {
node = new TopDependencyNode(jCas, tokenBegin, tokenEnd);
} else {
node = new DependencyNode(jCas, tokenBegin, tokenEnd);
}
stanfordToUima.put(stanfordNode, node);
}
// create relation annotations for each Stanford dependency
ArrayListMultimap<DependencyNode, DependencyRelation> headRelations =
ArrayListMultimap.create();
ArrayListMultimap<DependencyNode, DependencyRelation> childRelations =
ArrayListMultimap.create();
for (SemanticGraphEdge stanfordEdge : dependencies.edgeIterable()) {
DependencyRelation relation = new DependencyRelation(jCas);
DependencyNode head = stanfordToUima.get(stanfordEdge.getGovernor());
DependencyNode child = stanfordToUima.get(stanfordEdge.getDependent());
String relationType = stanfordEdge.getRelation().toString();
if (head == null || child == null || relationType == null) {
throw new RuntimeException(
String.format(
"null elements not allowed in relation:\nrelation=%s\nchild=%s\nhead=%s\n",
relation, child, head));
}
relation.setHead(head);
relation.setChild(child);
relation.setRelation(relationType);
relation.addToIndexes();
headRelations.put(child, relation);
childRelations.put(head, relation);
}
// set the relations for each node annotation
for (DependencyNode node : stanfordToUima.values()) {
List<DependencyRelation> heads = headRelations.get(node);
node.setHeadRelations(new FSArray(jCas, heads == null ? 0 : heads.size()));
if (heads != null) {
FSCollectionFactory.fillArrayFS(node.getHeadRelations(), heads);
}
List<DependencyRelation> children = childRelations.get(node);
node.setChildRelations(new FSArray(jCas, children == null ? 0 : children.size()));
if (children != null) {
FSCollectionFactory.fillArrayFS(node.getChildRelations(), children);
}
node.addToIndexes();
}
}
// map from spans to named entity mentions
Map<Span, NamedEntityMention> spanMentionMap = new HashMap<Span, NamedEntityMention>();
for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) {
spanMentionMap.put(new Span(mention.getBegin(), mention.getEnd()), mention);
}
// add mentions for all entities identified by the coreference system
List<NamedEntity> entities = new ArrayList<NamedEntity>();
List<List<Token>> sentenceTokens = new ArrayList<List<Token>>();
for (Sentence sentence : JCasUtil.select(jCas, Sentence.class)) {
sentenceTokens.add(JCasUtil.selectCovered(jCas, Token.class, sentence));
}
Map<Integer, CorefChain> corefChains = document.get(CorefChainAnnotation.class);
for (CorefChain chain : corefChains.values()) {
List<NamedEntityMention> mentions = new ArrayList<NamedEntityMention>();
for (CorefMention corefMention : chain.getMentionsInTextualOrder()) {
// figure out the character span of the token
List<Token> tokens = sentenceTokens.get(corefMention.sentNum - 1);
int begin = tokens.get(corefMention.startIndex - 1).getBegin();
int end = tokens.get(corefMention.endIndex - 2).getEnd();
// use an existing named entity mention when possible; otherwise create a new one
NamedEntityMention mention = spanMentionMap.get(new Span(begin, end));
if (mention == null) {
mention = new NamedEntityMention(jCas, begin, end);
mention.addToIndexes();
}
mentions.add(mention);
}
// create an entity for the mentions
Collections.sort(
mentions,
new Comparator<NamedEntityMention>() {
@Override
public int compare(NamedEntityMention m1, NamedEntityMention m2) {
return m1.getBegin() - m2.getBegin();
}
});
// create mentions and add them to entity
NamedEntity entity = new NamedEntity(jCas);
entity.setMentions(new FSArray(jCas, mentions.size()));
int index = 0;
for (NamedEntityMention mention : mentions) {
mention.setMentionedEntity(entity);
entity.setMentions(index, mention);
index += 1;
}
entities.add(entity);
}
// add singleton entities for any named entities not picked up by coreference system
for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) {
if (mention.getMentionedEntity() == null) {
NamedEntity entity = new NamedEntity(jCas);
entity.setMentions(new FSArray(jCas, 1));
entity.setMentions(0, mention);
mention.setMentionedEntity(entity);
entity.getMentions();
entities.add(entity);
}
}
// sort entities by document order
Collections.sort(
entities,
new Comparator<NamedEntity>() {
@Override
public int compare(NamedEntity o1, NamedEntity o2) {
return getFirstBegin(o1) - getFirstBegin(o2);
}
private int getFirstBegin(NamedEntity entity) {
int min = Integer.MAX_VALUE;
for (NamedEntityMention mention :
JCasUtil.select(entity.getMentions(), NamedEntityMention.class)) {
if (mention.getBegin() < min) {
min = mention.getBegin();
}
}
return min;
}
});
// add entities to document
for (NamedEntity entity : entities) {
entity.addToIndexes();
}
}
