// todo: initialize document language from article metadata
private void initializeCas(JCas jCas, PubmedArticle article) {
JCasBuilder builder = new JCasBuilder(jCas);
jCas.setDocumentLanguage("en");
if (article.getMedlineCitation().getArticle().getAbstract() != null) {
String abstractText =
article.getMedlineCitation().getArticle().getAbstract().getAbstractText();
builder.add(abstractText);
}
String articleTitle = article.getMedlineCitation().getArticle().getArticleTitle();
builder.add(articleTitle);
builder.close();
}
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();
}