/**
* tokenizes a given JCas object's document text using the treetagger program and adds the
* recognized tokens to the JCas object.
*
* @param jcas JCas object supplied by the pipeline
*/
private void tokenize(JCas jcas) {
// read tokenized text to add tokens to the jcas
Logger.printDetail(component, "TreeTagger (tokenization) with: " + ttprops.abbFileName);
EnumSet<Flag> flags = Flag.getSet(ttprops.languageSwitch);
TreeTaggerTokenizer ttt;
ttprops.abbFileName = "english-abbreviations";
if (ttprops.abbFileName != null) {
ttt =
new TreeTaggerTokenizer(
ttprops.rootPath
+ ttprops.fileSeparator
+ "lib"
+ ttprops.fileSeparator
+ ttprops.abbFileName,
flags);
} else {
ttt = new TreeTaggerTokenizer(null, flags);
}
String docText = jcas.getDocumentText().replaceAll("\n\n", "\nEMPTYLINE\n");
List<String> tokenized = ttt.tokenize(docText);
int tokenOffset = 0;
// loop through all the lines in the treetagger output
for (String s : tokenized) {
// charset missmatch fallback: signal (invalid) s
if ((!(s.equals("EMPTYLINE"))) && (jcas.getDocumentText().indexOf(s, tokenOffset) < 0))
throw new RuntimeException(
"Opps! Could not find token "
+ s
+ " in JCas after tokenizing with TreeTagger."
+ " Hmm, there may exist a charset missmatch!"
+ " Default encoding is "
+ Charset.defaultCharset().name()
+ " and should always be UTF-8 (use -Dfile.encoding=UTF-8)."
+ " If input document is not UTF-8 use -e option to set it according to the input, additionally.");
// create tokens and add them to the jcas's indexes.
Token newToken = new Token(jcas);
if (s.equals("EMPTYLINE")) {
newToken.setBegin(tokenOffset);
newToken.setEnd(tokenOffset);
newToken.setPos("EMPTYLINE");
if (annotate_partofspeech) {
newToken.addToIndexes();
}
} else {
newToken.setBegin(jcas.getDocumentText().indexOf(s, tokenOffset));
newToken.setEnd(newToken.getBegin() + s.length());
newToken.addToIndexes();
tokenOffset = newToken.getEnd();
}
}
}
/**
* tokenizes a given JCas object's document text using the chinese tokenization script and adds
* the recognized tokens to the JCas object.
*
* @param jcas JCas object supplied by the pipeline
*/
private void tokenizeChinese(JCas jcas) {
try {
// read tokenized text to add tokens to the jcas
Process proc = ttprops.getChineseTokenizationProcess();
Logger.printDetail(component, "Chinese tokenization: " + ttprops.chineseTokenizerPath);
BufferedReader in = new BufferedReader(new InputStreamReader(proc.getInputStream(), "UTF-8"));
BufferedWriter out =
new BufferedWriter(new OutputStreamWriter(proc.getOutputStream(), "UTF-8"));
Integer tokenOffset = 0;
// loop through all the lines in the stdout output
String[] inSplits = jcas.getDocumentText().split("[\\r\\n]+");
for (String inSplit : inSplits) {
out.write(inSplit);
out.newLine();
out.flush();
// do one initial read
String s = in.readLine();
do {
// break out of the loop if we've read a null
if (s == null) break;
String[] outSplits = s.split("\\s+");
for (String tok : outSplits) {
if (jcas.getDocumentText().indexOf(tok, tokenOffset) < 0)
throw new RuntimeException(
"Could not find token "
+ tok
+ " in JCas after tokenizing with Chinese tokenization script.");
// create tokens and add them to the jcas's indexes.
Token newToken = new Token(jcas);
newToken.setBegin(jcas.getDocumentText().indexOf(tok, tokenOffset));
newToken.setEnd(newToken.getBegin() + tok.length());
newToken.addToIndexes();
tokenOffset = newToken.getEnd();
}
// break out of the loop if the next read will block
if (!in.ready()) break;
s = in.readLine();
} while (true);
}
// clean up
in.close();
proc.destroy();
} catch (Exception e) {
e.printStackTrace();
}
}
private void populateFileList(String dirPath) throws ResourceInitializationException {
ArrayList<File> myFiles = new ArrayList<File>();
File dir = new File(dirPath);
// check if the given directory path is valid
if (!dir.exists() || !dir.isDirectory()) throw new ResourceInitializationException();
else myFiles.addAll(Arrays.asList(dir.listFiles()));
// check for existence and readability; add handle to the list
for (File f : myFiles) {
if (!f.exists() || !f.isFile() || !f.canRead()) {
Logger.printDetail(
component,
"File \""
+ f.getAbsolutePath()
+ "\" was ignored because it either didn't exist, wasn't a file or wasn't readable.");
} else {
files.add(f);
}
}
numberOfDocuments = files.size();
}
/**
* based on tokens from the jcas object, adds part of speech (POS) and sentence tags to the jcas
* object using the treetagger program.
*
* @param jcas JCas object supplied by the pipeline
*/
private void doTreeTag(JCas jcas) {
File tmpDocument = null;
BufferedWriter tmpFileWriter;
ArrayList<Token> tokens = new ArrayList<Token>();
try {
// create a temporary file and write our pre-existing tokens to it.
tmpDocument = File.createTempFile("postokens", null);
tmpFileWriter =
new BufferedWriter(new OutputStreamWriter(new FileOutputStream(tmpDocument), "UTF-8"));
// iterate over existing tokens
FSIterator ai = jcas.getAnnotationIndex(Token.type).iterator();
while (ai.hasNext()) {
Token t = (Token) ai.next();
tokens.add(t);
if (!(t.getBegin() == t.getEnd())) {
tmpFileWriter.write(t.getCoveredText() + ttprops.newLineSeparator);
}
}
tmpFileWriter.close();
} catch (IOException e) {
Logger.printError(
"Something went wrong creating a temporary file for the treetagger to process.");
System.exit(-1);
}
// Possible End-of-Sentence Tags
HashSet<String> hsEndOfSentenceTag = new HashSet<String>();
hsEndOfSentenceTag.add("SENT"); // ENGLISH, FRENCH, GREEK,
hsEndOfSentenceTag.add("$."); // GERMAN, DUTCH
hsEndOfSentenceTag.add("FS"); // SPANISH
hsEndOfSentenceTag.add("_Z_Fst"); // ESTONIAN
hsEndOfSentenceTag.add("_Z_Int"); // ESTONIAN
hsEndOfSentenceTag.add("_Z_Exc"); // ESTONIAN
hsEndOfSentenceTag.add("ew"); // CHINESE
try {
Process p = ttprops.getTreeTaggingProcess(tmpDocument);
Logger.printDetail(component, "TreeTagger (pos tagging) with: " + ttprops.parFileName);
BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream(), "UTF-8"));
Sentence sentence = null;
// iterate over all the output lines and tokens array (which have the same source and are
// hence symmetric)
int i = 0;
String s = null;
while ((s = in.readLine()) != null) {
// grab a token
Token token = tokens.get(i++);
// modified (Aug 29, 2011): Handle empty tokens (such as empty lines) in input file
while (token.getCoveredText().equals("")) {
// if part of the configuration, also add sentences to the jcas document
if ((annotate_sentences)
&& (token.getPos() != null && token.getPos().equals("EMPTYLINE"))) {
// Establish sentence structure
if (sentence == null) {
sentence = new Sentence(jcas);
sentence.setBegin(token.getBegin());
}
// Finish current sentence if end-of-sentence pos was found or document ended
sentence.setEnd(token.getEnd());
if (sentence.getBegin() < sentence.getEnd()) {
sentence.addToIndexes();
}
// Make sure current sentence is not active anymore so that a new one might be created
sentence = null;
// sentence = new Sentence(jcas);
}
token.removeFromIndexes();
token = tokens.get(i++);
}
// remove tokens, otherwise they are in the index twice
token.removeFromIndexes();
// set part of speech tag and add to indexes again
if (!(token.getCoveredText().equals(""))) {
token.setPos(s);
token.addToIndexes();
}
// if part of the configuration, also add sentences to the jcas document
if (annotate_sentences) {
// Establish sentence structure
if (sentence == null) {
sentence = new Sentence(jcas);
sentence.setBegin(token.getBegin());
}
// Finish current sentence if end-of-sentence pos was found or document ended
if (hsEndOfSentenceTag.contains(s) || i == tokens.size()) {
sentence.setEnd(token.getEnd());
sentence.addToIndexes();
// Make sure current sentence is not active anymore so that a new one might be created
sentence = null;
// sentence = new Sentence(jcas);
}
}
}
while (i < tokens.size()) {
if (!(sentence == null)) {
sentence.setEnd(tokens.get(tokens.size() - 1).getEnd());
sentence.addToIndexes();
}
Token token = tokens.get(i++);
if (token.getPos() != null && token.getPos().equals("EMPTYLINE")) {
token.removeFromIndexes();
}
}
in.close();
p.destroy();
} catch (Exception e) {
e.printStackTrace();
} finally {
// Delete temporary files
tmpDocument.delete();
}
}
/** initialization method where we fill configuration values and check some prerequisites */
public void initialize(UimaContext aContext) {
// check if the supplied language is one that we can currently handle
this.language =
Language.getLanguageFromString((String) aContext.getConfigParameterValue(PARAM_LANGUAGE));
// get configuration from the descriptor
annotate_tokens = (Boolean) aContext.getConfigParameterValue(PARAM_ANNOTATE_TOKENS);
annotate_sentences = (Boolean) aContext.getConfigParameterValue(PARAM_ANNOTATE_SENTENCES);
annotate_partofspeech = (Boolean) aContext.getConfigParameterValue(PARAM_ANNOTATE_PARTOFSPEECH);
String cnTokPath = (String) aContext.getConfigParameterValue(PARAM_CHINESE_TOKENIZER_PATH);
// set some configuration based upon these values
ttprops.languageName = language.getTreeTaggerLangName();
if (ttprops.rootPath == null) ttprops.rootPath = System.getenv("TREETAGGER_HOME");
ttprops.tokScriptName = "utf8-tokenize.perl";
// parameter file
if (!(new File(
ttprops.rootPath + ttprops.fileSeparator + "lib", ttprops.languageName + "-utf8.par")
.exists())) // get UTF8 version if it exists
ttprops.parFileName = ttprops.languageName + ".par";
else ttprops.parFileName = ttprops.languageName + "-utf8.par";
// abbreviation file
if (new File(
ttprops.rootPath + ttprops.fileSeparator + "lib",
ttprops.languageName + "-abbreviations-utf8")
.exists()) { // get UTF8 version if it exists
ttprops.abbFileName = ttprops.languageName + "-abbreviations-utf8";
} else {
ttprops.abbFileName = ttprops.languageName + "-abbreviations";
}
ttprops.languageSwitch = language.getTreeTaggerSwitch();
if (cnTokPath != null && !cnTokPath.equals(""))
ttprops.chineseTokenizerPath = new File(cnTokPath);
else ttprops.chineseTokenizerPath = new File(ttprops.rootPath, "cmd");
// handle the treetagger path from the environment variables
if (ttprops.rootPath == null) {
Logger.printError("TreeTagger environment variable is not present, aborting.");
System.exit(-1);
}
// Check for whether the required treetagger parameter files are present
Boolean abbFileFlag = true;
Boolean parFileFlag = true;
Boolean tokScriptFlag = true;
File abbFile = new File(ttprops.rootPath + ttprops.fileSeparator + "lib", ttprops.abbFileName);
File parFile = new File(ttprops.rootPath + ttprops.fileSeparator + "lib", ttprops.parFileName);
File tokFile =
new File(ttprops.rootPath + ttprops.fileSeparator + "cmd", ttprops.tokScriptName);
if (!(abbFileFlag = abbFile.exists())) {
if (language.equals(Language.CHINESE) || language.equals(Language.RUSSIAN)) {
abbFileFlag = true;
ttprops.abbFileName = null;
} else {
Logger.printError(
component, "File missing to use TreeTagger tokenizer: " + ttprops.abbFileName);
}
}
if (!(parFileFlag = parFile.exists())) {
Logger.printError(
component, "File missing to use TreeTagger tokenizer: " + ttprops.parFileName);
}
if (!(tokScriptFlag = tokFile.exists())) {
if (language.equals(Language.CHINESE)) tokScriptFlag = true;
else
Logger.printError(
component, "File missing to use TreeTagger tokenizer: " + ttprops.tokScriptName);
}
if (!abbFileFlag || !parFileFlag || !tokScriptFlag) {
Logger.printError(
component,
"Cannot find tree tagger ("
+ ttprops.rootPath
+ ttprops.fileSeparator
+ "cmd"
+ ttprops.fileSeparator
+ ttprops.tokScriptName
+ ")."
+ " Make sure that path to tree tagger is set correctly in config.props!");
Logger.printError(component, "If path is set correctly:");
Logger.printError(
component, "Maybe you need to download the TreeTagger tagger-scripts.tar.gz");
Logger.printError(
component,
"from http://www.cis.uni-muenchen.de/~schmid/tools/TreeTagger/data/tagger-scripts.tar.gz");
Logger.printError(
component,
"Extract this file and copy the missing file into the corresponding TreeTagger directories.");
Logger.printError(
component,
"If missing, copy "
+ ttprops.abbFileName
+ " into "
+ ttprops.rootPath
+ ttprops.fileSeparator
+ "lib");
Logger.printError(
component,
"If missing, copy "
+ ttprops.parFileName
+ " into "
+ ttprops.rootPath
+ ttprops.fileSeparator
+ "lib");
Logger.printError(
component,
"If missing, copy "
+ ttprops.tokScriptName
+ " into "
+ ttprops.rootPath
+ ttprops.fileSeparator
+ "cmd");
System.exit(-1);
}
}
private void fillJCas(JCas jcas) {
// grab a file to process
File f = files.poll();
try {
// create xml parsing facilities
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
// parse input xml file
Document doc = db.parse(f);
doc.getDocumentElement().normalize();
// get the <text> tag's content to set the document text
NodeList nList = doc.getElementsByTagName("TEXT");
Node textNode = nList.item(0);
String text = textNode.getTextContent();
jcas.setDocumentText(text);
// get the <dct> timex tag's value attribute for the dct
Boolean gotDCT = false;
String dctText = null;
try {
nList = doc.getDocumentElement().getElementsByTagName("DCT");
nList = ((Element) nList.item(0)).getElementsByTagName("TIMEX3"); // timex3 tag
Node dctTimex = nList.item(0);
NamedNodeMap dctTimexAttr = dctTimex.getAttributes();
Node dctValue = dctTimexAttr.getNamedItem("value");
dctText = dctValue.getTextContent();
gotDCT = true;
} catch (Exception e) {
gotDCT = false;
}
if (!gotDCT)
try { // try a different location for the DCT timex element
nList = doc.getDocumentElement().getElementsByTagName("TEXT");
nList = ((Element) nList.item(0)).getElementsByTagName("TIMEX3"); // timex3 tag
Node dctTimex = nList.item(0);
NamedNodeMap dctTimexAttr = dctTimex.getAttributes();
if (dctTimexAttr.getNamedItem("functionInDocument") != null
&& dctTimexAttr
.getNamedItem("functionInDocument")
.getTextContent()
.equals("CREATION_TIME")) {
Node dctValue = dctTimexAttr.getNamedItem("value");
dctText = dctValue.getTextContent();
}
gotDCT = true;
} catch (Exception e) {
gotDCT = false;
}
// get the document id
nList = doc.getElementsByTagName("DOCID");
String filename = null;
if (nList != null && nList.getLength() > 0) filename = nList.item(0).getTextContent();
else filename = f.getName().replaceAll("\\.[^\\.]+$", "");
Dct dct = new Dct(jcas);
dct.setBegin(0);
dct.setEnd(text.length());
dct.setFilename(filename);
dct.setValue(dctText);
dct.setTimexId("t0");
dct.addToIndexes();
} catch (Exception e) {
e.printStackTrace();
Logger.printError(
component, "File " + f.getAbsolutePath() + " could not be properly parsed.");
}
}