/** Performs name finding on the given cas object. */
public final void process(CAS cas) {
if (isRemoveExistingAnnotations) {
final AnnotationComboIterator sentenceNameCombo =
new AnnotationComboIterator(cas, mSentenceType, mNameType);
List<AnnotationFS> removeAnnotations = new LinkedList<AnnotationFS>();
for (AnnotationIteratorPair annotationIteratorPair : sentenceNameCombo) {
for (AnnotationFS nameAnnotation : annotationIteratorPair.getSubIterator()) {
removeAnnotations.add(nameAnnotation);
}
}
for (AnnotationFS annotation : removeAnnotations) {
cas.removeFsFromIndexes(annotation);
}
}
final AnnotationComboIterator sentenceTokenCombo =
new AnnotationComboIterator(cas, mSentenceType, mTokenType);
for (AnnotationIteratorPair annotationIteratorPair : sentenceTokenCombo) {
final List<AnnotationFS> sentenceTokenAnnotationList = new LinkedList<AnnotationFS>();
final List<String> sentenceTokenList = new LinkedList<String>();
for (AnnotationFS tokenAnnotation : annotationIteratorPair.getSubIterator()) {
sentenceTokenAnnotationList.add(tokenAnnotation);
sentenceTokenList.add(tokenAnnotation.getCoveredText());
}
Span[] names =
find(cas, (String[]) sentenceTokenList.toArray(new String[sentenceTokenList.size()]));
AnnotationFS nameAnnotations[] = new AnnotationFS[names.length];
for (int i = 0; i < names.length; i++) {
int startIndex =
((AnnotationFS) sentenceTokenAnnotationList.get(names[i].getStart())).getBegin();
int endIndex =
((AnnotationFS) sentenceTokenAnnotationList.get(names[i].getEnd() - 1)).getEnd();
nameAnnotations[i] = cas.createAnnotation(mNameType, startIndex, endIndex);
cas.getIndexRepository().addFS(nameAnnotations[i]);
}
postProcessAnnotations(names, nameAnnotations);
}
documentDone(cas);
}
/**
* Called when the processing of a Document is completed. <br>
* The process status can be looked at and corresponding actions taken.
*
* @param aCas CAS corresponding to the completed processing
* @param aStatus EntityProcessStatus that holds the status of all the events for aEntity
*/
public void entityProcessComplete(CAS aCas, EntityProcessStatus aStatus) {
if (aStatus != null) {
if (aStatus.isException()) {
System.err.println("Error on process CAS call to remote service:");
List exceptions = aStatus.getExceptions();
for (int i = 0; i < exceptions.size(); i++) {
((Throwable) exceptions.get(i)).printStackTrace();
}
if (!ignoreErrors) {
System.err.println("Terminating Client...");
stop();
}
}
if (logCas) {
String ip = "no IP";
List eList = aStatus.getProcessTrace().getEventsByComponentName("UimaEE", false);
for (int e = 0; e < eList.size(); e++) {
ProcessTraceEvent event = (ProcessTraceEvent) eList.get(e);
if (event.getDescription().equals("Service IP")) {
ip = event.getResultMessage();
}
}
String casId = ((UimaASProcessStatus) aStatus).getCasReferenceId();
if (casId != null) {
long current = System.nanoTime() / 1000000 - mStartTime;
if (casMap.containsKey(casId)) {
Object value = casMap.get(casId);
if (value != null && value instanceof Long) {
long start = ((Long) value).longValue();
System.out.println(ip + "\t" + start + "\t" + (current - start));
}
}
}
} else {
System.out.print(".");
if (0 == (entityCount + 1) % 50) {
System.out.print((entityCount + 1) + " processed\n");
}
}
}
// if output dir specified, dump CAS to XMI
if (outputDir != null) {
// try to retrieve the filename of the input file from the CAS
File outFile = null;
Type srcDocInfoType =
aCas.getTypeSystem().getType("org.apache.uima.examples.SourceDocumentInformation");
if (srcDocInfoType != null) {
FSIterator it = aCas.getIndexRepository().getAllIndexedFS(srcDocInfoType);
if (it.hasNext()) {
FeatureStructure srcDocInfoFs = it.get();
Feature uriFeat = srcDocInfoType.getFeatureByBaseName("uri");
Feature offsetInSourceFeat = srcDocInfoType.getFeatureByBaseName("offsetInSource");
String uri = srcDocInfoFs.getStringValue(uriFeat);
int offsetInSource = srcDocInfoFs.getIntValue(offsetInSourceFeat);
File inFile;
try {
inFile = new File(new URL(uri).getPath());
String outFileName = inFile.getName();
if (offsetInSource > 0) {
outFileName += ("_" + offsetInSource);
}
outFileName += ".xmi";
outFile = new File((String) outputDir, outFileName);
} catch (MalformedURLException e1) {
// invalid URI, use default processing below
}
}
}
if (outFile == null) {
outFile = new File((String) outputDir, "doc" + entityCount);
}
try {
FileOutputStream outStream = new FileOutputStream(outFile);
try {
XmiCasSerializer.serialize(aCas, outStream);
} finally {
outStream.close();
}
} catch (Exception e) {
System.err.println("Could not save CAS to XMI file");
e.printStackTrace();
}
}
// update stats
entityCount++;
String docText = aCas.getDocumentText();
if (docText != null) {
size += docText.length();
}
// Called just before sendCas with next CAS from collection reader
}