private void convert(JCas aJCas, PrintWriter aOut) {
Type chunkType = JCasUtil.getType(aJCas, Chunk.class);
Feature chunkValue = chunkType.getFeatureByBaseName("chunkValue");
for (Sentence sentence : select(aJCas, Sentence.class)) {
HashMap<Token, Row> ctokens = new LinkedHashMap<Token, Row>();
// Tokens
List<Token> tokens = selectCovered(Token.class, sentence);
// Chunks
IobEncoder encoder = new IobEncoder(aJCas.getCas(), chunkType, chunkValue);
for (int i = 0; i < tokens.size(); i++) {
Row row = new Row();
row.id = i + 1;
row.token = tokens.get(i);
row.chunk = encoder.encode(tokens.get(i));
ctokens.put(row.token, row);
}
// Write sentence in CONLL 2006 format
for (Row row : ctokens.values()) {
String pos = UNUSED;
if (writePos && (row.token.getPos() != null)) {
POS posAnno = row.token.getPos();
pos = posAnno.getPosValue();
}
String chunk = UNUSED;
if (writeChunk && (row.chunk != null)) {
chunk = encoder.encode(row.token);
}
aOut.printf("%s %s %s\n", row.token.getCoveredText(), pos, chunk);
}
aOut.println();
}
}
private void convert(JCas aJCas, PrintWriter aOut) {
Map<Token, Collection<SemanticPredicate>> predIdx =
indexCovered(aJCas, Token.class, SemanticPredicate.class);
Map<SemanticArgument, Collection<Token>> argIdx =
indexCovered(aJCas, SemanticArgument.class, Token.class);
for (Sentence sentence : select(aJCas, Sentence.class)) {
HashMap<Token, Row> ctokens = new LinkedHashMap<Token, Row>();
// Tokens
List<Token> tokens = selectCovered(Token.class, sentence);
// Check if we should try to include the FEATS in output
List<MorphologicalFeatures> morphology = selectCovered(MorphologicalFeatures.class, sentence);
boolean useFeats = tokens.size() == morphology.size();
List<SemanticPredicate> preds = selectCovered(SemanticPredicate.class, sentence);
for (int i = 0; i < tokens.size(); i++) {
Row row = new Row();
row.id = i + 1;
row.token = tokens.get(i);
row.args = new SemanticArgument[preds.size()];
if (useFeats) {
row.feats = morphology.get(i);
}
// If there are multiple semantic predicates for the current token, then
// we keep only the first
Collection<SemanticPredicate> predsForToken = predIdx.get(row.token);
if (predsForToken != null && !predsForToken.isEmpty()) {
row.pred = predsForToken.iterator().next();
}
ctokens.put(row.token, row);
}
// Dependencies
for (Dependency rel : selectCovered(Dependency.class, sentence)) {
ctokens.get(rel.getDependent()).deprel = rel;
}
// Semantic arguments
for (int p = 0; p < preds.size(); p++) {
FSArray args = preds.get(p).getArguments();
for (SemanticArgument arg : select(args, SemanticArgument.class)) {
for (Token t : argIdx.get(arg)) {
Row row = ctokens.get(t);
row.args[p] = arg;
}
}
}
// Write sentence in CONLL 2009 format
for (Row row : ctokens.values()) {
int id = row.id;
String form = row.token.getCoveredText();
String lemma = UNUSED;
if (writeLemma && (row.token.getLemma() != null)) {
lemma = row.token.getLemma().getValue();
}
String plemma = lemma;
String pos = UNUSED;
if (writePos && (row.token.getPos() != null)) {
POS posAnno = row.token.getPos();
pos = posAnno.getPosValue();
}
String ppos = pos;
String feat = UNUSED;
if (writeMorph && (row.feats != null)) {
feat = row.feats.getValue();
}
String pfeat = feat;
int headId = UNUSED_INT;
String deprel = UNUSED;
if (writeDependency && (row.deprel != null)) {
deprel = row.deprel.getDependencyType();
headId = ctokens.get(row.deprel.getGovernor()).id;
if (headId == row.id) {
// ROOT dependencies may be modeled as a loop, ignore these.
headId = 0;
}
}
String head = UNUSED;
if (headId != UNUSED_INT) {
head = Integer.toString(headId);
}
String phead = head;
String pdeprel = deprel;
String fillpred = UNUSED;
String pred = UNUSED;
StringBuilder apreds = new StringBuilder();
if (writeSemanticPredicate) {
if (row.pred != null) {
fillpred = "Y";
pred = row.pred.getCategory();
}
for (SemanticArgument arg : row.args) {
if (apreds.length() > 0) {
apreds.append('\t');
}
apreds.append(arg != null ? arg.getRole() : UNUSED);
}
}
aOut.printf(
"%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
id, form, lemma, plemma, pos, ppos, feat, pfeat, head, phead, deprel, pdeprel, fillpred,
pred, apreds);
}
aOut.println();
}
}
public void convert(JCas aJCas, BufferedReader aReader) throws IOException {
if (readPos) {
try {
posMappingProvider.configure(aJCas.getCas());
} catch (AnalysisEngineProcessException e) {
throw new IOException(e);
}
}
JCasBuilder doc = new JCasBuilder(aJCas);
List<String[]> words;
while ((words = readSentence(aReader)) != null) {
if (words.isEmpty()) {
// Ignore empty sentences. This can happen when there are multiple end-of-sentence
// markers following each other.
continue;
}
int sentenceBegin = doc.getPosition();
int sentenceEnd = sentenceBegin;
// Tokens, Lemma, POS
Map<Integer, Token> tokens = new HashMap<Integer, Token>();
List<SemanticPredicate> preds = new ArrayList<>();
for (String[] word : words) {
// Read token
Token token = doc.add(word[FORM], Token.class);
tokens.put(Integer.valueOf(word[ID]), token);
doc.add(" ");
// Read lemma
if (!UNUSED.equals(word[LEMMA]) && readLemma) {
Lemma lemma = new Lemma(aJCas, token.getBegin(), token.getEnd());
lemma.setValue(word[LEMMA]);
lemma.addToIndexes();
token.setLemma(lemma);
}
// Read part-of-speech tag
if (!UNUSED.equals(word[POS]) && readPos) {
Type posTag = posMappingProvider.getTagType(word[POS]);
POS pos = (POS) aJCas.getCas().createAnnotation(posTag, token.getBegin(), token.getEnd());
pos.setPosValue(word[POS]);
pos.addToIndexes();
token.setPos(pos);
}
// Read morphological features
if (!UNUSED.equals(word[FEAT]) && readMorph) {
MorphologicalFeatures morphtag =
new MorphologicalFeatures(aJCas, token.getBegin(), token.getEnd());
morphtag.setValue(word[FEAT]);
morphtag.addToIndexes();
}
if (!UNUSED.equals(word[PRED]) && readSemanticPredicate) {
SemanticPredicate pred = new SemanticPredicate(aJCas, token.getBegin(), token.getEnd());
pred.setCategory(word[PRED]);
pred.addToIndexes();
preds.add(pred);
}
sentenceEnd = token.getEnd();
}
// Dependencies
if (readDependency) {
for (String[] word : words) {
if (!UNUSED.equals(word[DEPREL])) {
int depId = Integer.valueOf(word[ID]);
int govId = Integer.valueOf(word[HEAD]);
// Model the root as a loop onto itself
if (govId == 0) {
Dependency rel = new ROOT(aJCas);
rel.setGovernor(tokens.get(depId));
rel.setDependent(tokens.get(depId));
rel.setDependencyType(word[DEPREL]);
rel.setBegin(rel.getDependent().getBegin());
rel.setEnd(rel.getDependent().getEnd());
rel.addToIndexes();
} else {
Dependency rel = new Dependency(aJCas);
rel.setGovernor(tokens.get(govId));
rel.setDependent(tokens.get(depId));
rel.setDependencyType(word[DEPREL]);
rel.setBegin(rel.getDependent().getBegin());
rel.setEnd(rel.getDependent().getEnd());
rel.addToIndexes();
}
}
}
}
// Semantic arguments
if (readSemanticPredicate) {
// Get arguments for one predicate at a time
for (int p = 0; p < preds.size(); p++) {
List<SemanticArgument> args = new ArrayList<SemanticArgument>();
for (String[] word : words) {
if (!UNUSED.equals(word[APRED + p])) {
Token token = tokens.get(Integer.valueOf(word[ID]));
SemanticArgument arg = new SemanticArgument(aJCas, token.getBegin(), token.getEnd());
arg.setRole(word[APRED + p]);
arg.addToIndexes();
args.add(arg);
}
}
SemanticPredicate pred = preds.get(p);
pred.setArguments(FSCollectionFactory.createFSArray(aJCas, args));
}
}
// Sentence
Sentence sentence = new Sentence(aJCas, sentenceBegin, sentenceEnd);
sentence.addToIndexes();
// Once sentence per line.
doc.add("\n");
}
doc.close();
}
public void convert(JCas aJCas, BufferedReader aReader) throws IOException {
try {
if (readPos) {
posMappingProvider.configure(aJCas.getCas());
}
if (readConstituent) {
constituentMappingProvider.configure(aJCas.getCas());
}
} catch (AnalysisEngineProcessException e) {
throw new IOException(e);
}
Map<String, CoreferenceLink> chains = new HashMap<>();
JCasBuilder doc = new JCasBuilder(aJCas);
List<String[]> words;
while ((words = readSentence(aJCas, aReader)) != null) {
if (words.isEmpty()) {
// Ignore empty sentences. This can happen when there are multiple end-of-sentence
// markers following each other.
continue;
}
int sentenceBegin = doc.getPosition();
int sentenceEnd = sentenceBegin;
StringBuilder parse = new StringBuilder();
// Tokens, Lemma, POS
Map<Integer, Token> tokenById = new HashMap<Integer, Token>();
List<SemPred> preds = new ArrayList<>();
for (String[] word : words) {
// Read token
Token token = doc.add(word[FORM], Token.class);
tokenById.put(Integer.valueOf(word[ID]), token);
doc.add(" ");
// Read lemma
if (!UNUSED.equals(word[LEMMA]) && readLemma) {
Lemma lemma = new Lemma(aJCas, token.getBegin(), token.getEnd());
lemma.setValue(word[LEMMA]);
lemma.addToIndexes();
token.setLemma(lemma);
}
// Read part-of-speech tag
if (!UNUSED.equals(word[POS]) && readPos) {
Type posTag = posMappingProvider.getTagType(word[POS]);
POS pos = (POS) aJCas.getCas().createAnnotation(posTag, token.getBegin(), token.getEnd());
pos.setPosValue(word[POS]);
pos.addToIndexes();
token.setPos(pos);
}
if (!UNUSED.equals(word[PRED]) && readSemanticPredicate) {
SemPred pred = new SemPred(aJCas, token.getBegin(), token.getEnd());
pred.setCategory(word[PRED]);
pred.addToIndexes();
preds.add(pred);
}
if (!UNUSED.equals(word[PARSE]) && readConstituent) {
String fixed = word[PARSE].replace("*", "(" + word[POS] + " " + word[FORM] + ")");
parse.append(fixed);
}
if (!UNUSED.equals(word[WORD_SENSE]) && readWordSense) {
WordSense wordSense = new WordSense(aJCas, token.getBegin(), token.getEnd());
wordSense.setValue(word[WORD_SENSE]);
wordSense.addToIndexes();
}
if (!UNUSED.equals(word[word.length - 1]) && readCoreference) {
String[] chainFragments = word[word.length - 1].split("\\|");
for (String chainFragment : chainFragments) {
boolean beginning = chainFragment.startsWith("(");
boolean ending = chainFragment.endsWith(")");
String chainId =
chainFragment.substring(
beginning ? 1 : 0,
ending ? chainFragment.length() - 1 : chainFragment.length());
CoreferenceLink link = chains.get(chainId);
if (beginning) {
if (link == null) {
link = new CoreferenceLink(aJCas);
CoreferenceChain chain = new CoreferenceChain(aJCas);
chain.setFirst(link);
chain.addToIndexes();
} else {
CoreferenceLink newLink = new CoreferenceLink(aJCas);
link.setNext(newLink);
link = newLink;
}
link.setReferenceType(chainId);
link.setBegin(token.getBegin());
}
if (ending) {
link.setEnd(token.getEnd());
link.addToIndexes();
}
chains.put(chainId, link);
}
}
sentenceEnd = token.getEnd();
}
// Named entities
if (readNamedEntity) {
int currentNeBegin = -1;
String currentNeType = null;
for (int i = 0; i < words.size(); i++) {
String ne = words.get(i)[NAMED_ENTITIES];
boolean beginning = ne.startsWith("(");
boolean ending = ne.endsWith(")");
// When a NE is beginning, we remember what the NE is and where it began
if (beginning) {
// The NE is beginning with "(" and either ending with "(" or "*", so we trim
// the first and last character
currentNeType = ne.substring(1, ne.length() - 1);
currentNeBegin = i;
}
// We need to create an annotation if the current token is the end of an annotation
if (ending) {
// Determine begin and end of named entity
int begin = tokenById.get(currentNeBegin).getBegin();
int end = tokenById.get(i).getEnd();
// Add named entity
NamedEntity namedEntity = new NamedEntity(aJCas, begin, end);
namedEntity.setValue(currentNeType);
namedEntity.addToIndexes();
// Forget remembered named entity
currentNeBegin = -1;
currentNeType = null;
}
}
}
// Semantic arguments
if (readSemanticPredicate) {
// Get arguments for one predicate at a time
for (int p = 0; p < preds.size(); p++) {
SemPred pred = preds.get(p);
List<SemArgLink> args = new ArrayList<>();
int currentArgBegin = -1;
String currentArgType = null;
for (int i = 0; i < words.size(); i++) {
String ne = words.get(i)[APRED + p];
boolean beginning = ne.startsWith("(");
boolean ending = ne.endsWith(")");
// When a arg is beginning, we remember what the NE is and where it began
if (beginning) {
// The arg is beginning with "(" and either ending with "(" or "*", so
// we trim the first and last character
currentArgType = ne.substring(1, ne.length() - 1);
currentArgBegin = i;
}
// We need to create an annotation if the current token is the end of an
// annotation
if (ending) {
// Determine begin and end of argument
int begin = tokenById.get(currentArgBegin).getBegin();
int end = tokenById.get(i).getEnd();
// Add named entity unless it is a (V*) which has the same offsets as
// the predicate
if (!(pred.getBegin() == begin && pred.getEnd() == end)) {
SemArg arg = new SemArg(aJCas, begin, end);
arg.addToIndexes();
SemArgLink link = new SemArgLink(aJCas);
link.setRole(currentArgType);
link.setTarget(arg);
args.add(link);
}
// Forget remembered arg
currentArgBegin = -1;
currentArgType = null;
}
}
pred.setArguments(FSCollectionFactory.createFSArray(aJCas, args));
}
}
// Sentence
Sentence sentence = new Sentence(aJCas, sentenceBegin, sentenceEnd);
sentence.addToIndexes();
converter.convertPennTree(sentence, PennTreeUtils.parsePennTree(parse.toString()));
// Once sentence per line.
doc.add("\n");
}
doc.close();
}
public static Tree createStanfordTree(Annotation root, TreeFactory tFact) {
JCas aJCas;
try {
aJCas = root.getCAS().getJCas();
} catch (CASException e) {
throw new IllegalStateException("Unable to get JCas from JCas wrapper");
}
// define the new (root) node
Tree rootNode;
// before we can create a node, we must check if we have any children (we have to know
// whether to create a node or a leaf - not very dynamic)
if (root instanceof Constituent && !isLeaf((Constituent) root)) {
Constituent node = (Constituent) root;
List<Tree> childNodes = new ArrayList<Tree>();
// get childNodes from child annotations
FSArray children = node.getChildren();
for (int i = 0; i < children.size(); i++) {
childNodes.add(createStanfordTree(node.getChildren(i), tFact));
}
// now create the node with its children
rootNode = tFact.newTreeNode(node.getConstituentType(), childNodes);
} else {
// Handle leaf annotations
// Leafs are always Token-annotations
// We also have to insert a Preterminal node with the value of the
// POS-Annotation on the token
// because the POS is not directly stored within the treee
Token wordAnnotation = (Token) root;
// create leaf-node for the tree
Tree wordNode = tFact.newLeaf(wordAnnotation.getCoveredText());
// create information about preceding and trailing whitespaces in the leaf node
StringBuilder preWhitespaces = new StringBuilder();
StringBuilder trailWhitespaces = new StringBuilder();
List<Token> precedingTokenList = selectPreceding(aJCas, Token.class, wordAnnotation, 1);
List<Token> followingTokenList = selectFollowing(aJCas, Token.class, wordAnnotation, 1);
if (precedingTokenList.size() > 0) {
Token precedingToken = precedingTokenList.get(0);
int precedingWhitespaces = wordAnnotation.getBegin() - precedingToken.getEnd();
for (int i = 0; i < precedingWhitespaces; i++) {
preWhitespaces.append(" ");
}
}
if (followingTokenList.size() > 0) {
Token followingToken = followingTokenList.get(0);
int trailingWhitespaces = followingToken.getBegin() - wordAnnotation.getEnd();
for (int i = 0; i < trailingWhitespaces; i++) {
trailWhitespaces.append(" ");
}
}
// write whitespace information as CoreAnnotation.BeforeAnnotation and
// CoreAnnotation.AfterAnnotation to the node add annotation to list and write back to
// node label
((CoreLabel) wordNode.label())
.set(CoreAnnotations.BeforeAnnotation.class, preWhitespaces.toString());
((CoreLabel) wordNode.label())
.set(CoreAnnotations.AfterAnnotation.class, trailWhitespaces.toString());
// get POS-annotation
// get the token that is covered by the POS
List<POS> coveredPos = JCasUtil.selectCovered(aJCas, POS.class, wordAnnotation);
// the POS should only cover one token
assert coveredPos.size() == 1;
POS pos = coveredPos.get(0);
// create POS-Node in the tree and attach word-node to it
rootNode = tFact.newTreeNode(pos.getPosValue(), Arrays.asList((new Tree[] {wordNode})));
}
return rootNode;
}
