/** Test the default tokeniser */
public void testHashGazetteer() throws Exception {
// get a document
Document doc =
Factory.newDocument(new URL(TestDocument.getTestServerName() + "tests/doc0.html"));
System.out.println(doc.getFeatures().get("gate.SourceURL"));
// create a default gazetteer
FeatureMap params = Factory.newFeatureMap();
HashGazetteer gaz =
(HashGazetteer) Factory.createResource("com.ontotext.gate.gazetteer.HashGazetteer", params);
// runtime stuff
gaz.setDocument(doc);
gaz.setAnnotationSetName(GAZ_AS);
gaz.execute();
assertTrue(
"the Annotation set resulting of the execution of the OntoText "
+ "Natural Gazetteer is empty.",
!doc.getAnnotations(GAZ_AS).isEmpty());
// check whether the annotations are as expected
assertEquals("wrong number of lookup annotations found", 76, doc.getAnnotations(GAZ_AS).size());
} // testHashGazetteer();
@Override
public Document get(int index) {
if (index >= docDataList.size()) return null;
Document res = documents.get(index);
if (DEBUG) Out.prln("SerialCorpusImpl: get(): index " + index + "result: " + res);
// if the document is null, then I must get it from the DS
if (res == null) {
FeatureMap parameters = Factory.newFeatureMap();
parameters.put(DataStore.DATASTORE_FEATURE_NAME, this.dataStore);
try {
parameters.put(DataStore.LR_ID_FEATURE_NAME, docDataList.get(index).getPersistentID());
Document lr =
(Document) Factory.createResource(docDataList.get(index).getClassType(), parameters);
if (DEBUG) Out.prln("Loaded document :" + lr.getName());
// change the result to the newly loaded doc
res = lr;
// finally replace the doc with the instantiated version
documents.set(index, lr);
} catch (ResourceInstantiationException ex) {
Err.prln("Error reading document inside a serialised corpus.");
throw new GateRuntimeException(ex);
}
}
return res;
}
/**
* Use a {@link SharedDefaultGazetteer} to duplicate this gazetteer by sharing the internal FSM
* rather than re-loading the lists.
*/
@Override
public Resource duplicate(Factory.DuplicationContext ctx) throws ResourceInstantiationException {
return Factory.createResource(
SharedDefaultGazetteer.class.getName(),
Utils.featureMap(SharedDefaultGazetteer.SDEF_GAZ_BOOTSTRAP_GAZETTEER_PROPERTY_NAME, this),
Factory.duplicate(this.getFeatures(), ctx),
this.getName());
}
/**
* Loading the configurationg file and corpus for testing. And make settings as in the GATE Gui.
*/
void loadSettings(String configFileName, String corpusDirName, String inputasN, String outputasN)
throws GateException, IOException {
LogService.minVerbosityLevel = 0;
if (LogService.minVerbosityLevel > 0)
System.out.println("Learning Home : " + learningHome.getAbsolutePath());
FeatureMap parameters = Factory.newFeatureMap();
URL configFileURL = new File(configFileName).toURI().toURL();
parameters.put("configFileURL", configFileURL);
learningApi =
(LearningAPIMain) Factory.createResource("gate.learning.LearningAPIMain", parameters);
// Load the corpus
corpus = Factory.newCorpus("DataSet");
ExtensionFileFilter fileFilter = new ExtensionFileFilter();
fileFilter.addExtension("xml");
File[] xmlFiles = new File(corpusDirName).listFiles(fileFilter);
Arrays.sort(
xmlFiles,
new Comparator<File>() {
public int compare(File a, File b) {
return a.getName().compareTo(b.getName());
}
});
for (File f : xmlFiles) {
if (!f.isDirectory()) {
Document doc = Factory.newDocument(f.toURI().toURL(), "UTF-8");
doc.setName(f.getName());
corpus.add(doc);
}
}
// URL tempURL = new File(corpusDirName).toURI().toURL();
// corpus.populate(tempURL, fileFilter, "UTF-8", false);
// Set the inputAS
learningApi.setInputASName(inputasN);
learningApi.setOutputASName(outputasN);
controller =
(gate.creole.SerialAnalyserController)
Factory.createResource("gate.creole.SerialAnalyserController");
controller.setCorpus(corpus);
controller.add(learningApi);
}
private static Document readDocument(String gateDocumentString)
throws ResourceInstantiationException {
Document gateDocument =
(Document)
Factory.createResource(
"gate.corpora.DocumentImpl",
Utils.featureMap(
"stringContent",
gateDocumentString,
"mimeType",
"text/xml",
"encoding",
"UTF-8"));
return gateDocument;
}
private gate.Document generateGATEDocFromLocalDump(BehemothDocument inputDoc)
throws ResourceInstantiationException, IOException {
// can't get that to work
// File tempDirectory = new
// File(this.config.get("hadoop.tmp.dir","/tmp"),this.config.get("user.name",
// "./tmp"));
// LOG.info("tempDirectory "+tempDirectory);
//
// tempDirectory.mkdirs();
//
// File tempInputFile = File.createTempFile("gateInput-",
// inputDoc.getUrl(),tempDirectory);
//
// FileOutputStream fos = new FileOutputStream(tempInputFile);
// OutputStream bout = new BufferedOutputStream(fos);
// bout.write(inputDoc.getContent());
// bout.flush();
// bout.close();
//
// URL url;
// try {
// url = tempInputFile.toURI().toURL();
// } catch (MalformedURLException e) {
// // delete the input doc
// tempInputFile.delete();
// throw e;
// }
FeatureMap params = Factory.newFeatureMap();
params.put(Document.DOCUMENT_STRING_CONTENT_PARAMETER_NAME, new String(inputDoc.getContent()));
String ct = inputDoc.getContentType();
if (ct != null) params.put(Document.DOCUMENT_MIME_TYPE_PARAMETER_NAME, ct);
gate.Document gatedocument;
try {
gatedocument = (Document) Factory.createResource("gate.corpora.DocumentImpl", params);
} finally {
// delete the input doc
// tempInputFile.delete();
}
return gatedocument;
}
public static void main(String[] args) throws Exception {
// Logger.getLogger(DocumentFeaturesDiff.class).setLevel(Level.ALL);
GateUtils.initGateKeepLog();
GateUtils.registerCzsemPlugin();
ProcessingResource eval =
new PRSetup.SinglePRSetup(LearningEvaluator.class)
.putFeature("keyASName", ":-)")
// .putFeature("responseASName", "lemma_flex")
.putFeature("responseASName", "flex")
.putFeature("keyAnnotationsAreInDocumentFeatures", true)
.putFeatureList("annotationTypes", "Lookup")
.putFeatureList("featureNames", "meshID")
.createPR();
SerialAnalyserController controller =
(SerialAnalyserController)
Factory.createResource(SerialAnalyserController.class.getCanonicalName());
controller.add(eval);
Corpus corpus = Factory.newCorpus(null);
corpus.populate(
new File("C:\\Users\\dedek\\Desktop\\bmc\\experiment\\analyzed").toURI().toURL(),
// new File("C:\\Users\\dedek\\Desktop\\bmca_devel").toURI().toURL(),
null,
"utf8",
false);
System.err.println("populated");
controller.setCorpus(corpus);
controller.execute();
}
@Override
public Resource init() throws ResourceInstantiationException {
gracefulExit = false;
if (configFileURL == null) {
gracefulExit = true;
gate.util.Err.println("No configuration file provided!");
}
if (japeURL == null) {
gracefulExit = true;
gate.util.Err.println("No JAPE grammar file provided!");
}
// create the init params for the JAPE transducer
FeatureMap params = Factory.newFeatureMap();
params.put(Transducer.TRANSD_GRAMMAR_URL_PARAMETER_NAME, japeURL);
// Code borrowed from Mark Greenwood's Measurements PR
if (japeTransducer == null) {
// if this is the first time we are running init then actually create a
// new transducer as we don't already have one
FeatureMap hidden = Factory.newFeatureMap();
Gate.setHiddenAttribute(hidden, true);
japeTransducer =
(Transducer) Factory.createResource("gate.creole.Transducer", params, hidden);
} else {
// we are being run through a call to reInit so simply re-init the
// underlying JAPE transducer
japeTransducer.setParameterValues(params);
japeTransducer.reInit();
}
ConfigReader config = new ConfigReader(configFileURL);
gracefulExit = config.config();
try {
HashMap<String, String> options = config.getOptions();
patternMap = new HashMap<String, Pattern>();
addSuffixPattern("disease_suffix", options);
addWordPattern("disease_abbrevs", options);
addWordPattern("disease_sense", options);
addWordExtraPattern("disease_sense_context", options);
addPossessiveWordPattern("disease_named_syndrome", options);
addWordExtraPattern("disease_generic_context", options);
addWordExtraPattern("disease_anatomy_context", options);
addSuffixPluralPattern("procedure_suffix", options);
addWordPluralPattern("procedure_key", options);
addWordExtraPattern("procedure_anatomy_context", options);
addWordPluralPattern("symptom_key", options);
addWordPattern("test_key", options);
addSuffixPattern("anatomy_suffix_adjective", options);
addSuffixPattern("anatomy_suffix", options);
addPrefixPattern("anatomy_prefix", options);
addWordPattern("anatomy_position", options);
addWordPluralPattern("anatomy_space_region_junction", options);
addWordPattern("anatomy_part_adjective", options);
addWordPattern("anatomy_latin_noun", options);
addWordPattern("anatomy_muscle", options);
addWordPluralPattern("anatomy_part", options);
addWordPluralPattern("anatomy_fluid", options);
} catch (NullPointerException ne) {
gracefulExit = true;
gate.util.Err.println(
"Missing or unset configuration options. Please check configuration file.");
}
return this;
} // end init()
/**
* Run from the command-line, with a list of URLs as argument.
*
* <p><B>NOTE:</B><br>
* This code will run with all the documents in memory - if you want to unload each from memory
* after use, add code to store the corpus in a DataStore.
*/
public static void main(String args[]) throws GateException, IOException {
// initialise the GATE library
Out.prln("Initialising GATE...");
Gate.init();
Out.prln("...GATE initialised");
// initialise ANNIE (this may take several minutes)
StandAloneAnnie annie = new StandAloneAnnie();
annie.initAnnie();
// create a GATE corpus and add a document for each command-line
// argument
Corpus corpus = Factory.newCorpus("StandAloneAnnie corpus");
for (int i = 0; i < args.length; i++) {
URL u = new URL(args[i]);
FeatureMap params = Factory.newFeatureMap();
params.put("sourceUrl", u);
params.put("preserveOriginalContent", new Boolean(true));
params.put("collectRepositioningInfo", new Boolean(true));
Out.prln("Creating doc for " + u);
Document doc = (Document) Factory.createResource("gate.corpora.DocumentImpl", params);
corpus.add(doc);
} // for each of args
// tell the pipeline about the corpus and run it
annie.setCorpus(corpus);
annie.execute();
// for each document, get an XML document with the
// person and location names added
Iterator iter = corpus.iterator();
int count = 0;
String startTagPart_1 = "<span GateID=\"";
String startTagPart_2 = "\" title=\"";
String startTagPart_3 = "\" style=\"background:Red;\">";
String endTag = "</span>";
while (iter.hasNext()) {
Document doc = (Document) iter.next();
AnnotationSet defaultAnnotSet = doc.getAnnotations();
Set annotTypesRequired = new HashSet();
annotTypesRequired.add("Person");
annotTypesRequired.add("Location");
Set<Annotation> peopleAndPlaces =
new HashSet<Annotation>(defaultAnnotSet.get(annotTypesRequired));
FeatureMap features = doc.getFeatures();
String originalContent =
(String) features.get(GateConstants.ORIGINAL_DOCUMENT_CONTENT_FEATURE_NAME);
RepositioningInfo info =
(RepositioningInfo) features.get(GateConstants.DOCUMENT_REPOSITIONING_INFO_FEATURE_NAME);
++count;
File file = new File("StANNIE_" + count + ".HTML");
Out.prln("File name: '" + file.getAbsolutePath() + "'");
if (originalContent != null && info != null) {
Out.prln("OrigContent and reposInfo existing. Generate file...");
Iterator it = peopleAndPlaces.iterator();
Annotation currAnnot;
SortedAnnotationList sortedAnnotations = new SortedAnnotationList();
while (it.hasNext()) {
currAnnot = (Annotation) it.next();
sortedAnnotations.addSortedExclusive(currAnnot);
} // while
StringBuffer editableContent = new StringBuffer(originalContent);
long insertPositionEnd;
long insertPositionStart;
// insert anotation tags backward
Out.prln("Unsorted annotations count: " + peopleAndPlaces.size());
Out.prln("Sorted annotations count: " + sortedAnnotations.size());
for (int i = sortedAnnotations.size() - 1; i >= 0; --i) {
currAnnot = (Annotation) sortedAnnotations.get(i);
insertPositionStart = currAnnot.getStartNode().getOffset().longValue();
insertPositionStart = info.getOriginalPos(insertPositionStart);
insertPositionEnd = currAnnot.getEndNode().getOffset().longValue();
insertPositionEnd = info.getOriginalPos(insertPositionEnd, true);
if (insertPositionEnd != -1 && insertPositionStart != -1) {
editableContent.insert((int) insertPositionEnd, endTag);
editableContent.insert((int) insertPositionStart, startTagPart_3);
editableContent.insert((int) insertPositionStart, currAnnot.getType());
editableContent.insert((int) insertPositionStart, startTagPart_2);
editableContent.insert((int) insertPositionStart, currAnnot.getId().toString());
editableContent.insert((int) insertPositionStart, startTagPart_1);
} // if
} // for
FileWriter writer = new FileWriter(file);
writer.write(editableContent.toString());
writer.close();
} // if - should generate
else if (originalContent != null) {
Out.prln("OrigContent existing. Generate file...");
Iterator it = peopleAndPlaces.iterator();
Annotation currAnnot;
SortedAnnotationList sortedAnnotations = new SortedAnnotationList();
while (it.hasNext()) {
currAnnot = (Annotation) it.next();
sortedAnnotations.addSortedExclusive(currAnnot);
} // while
StringBuffer editableContent = new StringBuffer(originalContent);
long insertPositionEnd;
long insertPositionStart;
// insert anotation tags backward
Out.prln("Unsorted annotations count: " + peopleAndPlaces.size());
Out.prln("Sorted annotations count: " + sortedAnnotations.size());
for (int i = sortedAnnotations.size() - 1; i >= 0; --i) {
currAnnot = (Annotation) sortedAnnotations.get(i);
insertPositionStart = currAnnot.getStartNode().getOffset().longValue();
insertPositionEnd = currAnnot.getEndNode().getOffset().longValue();
if (insertPositionEnd != -1 && insertPositionStart != -1) {
editableContent.insert((int) insertPositionEnd, endTag);
editableContent.insert((int) insertPositionStart, startTagPart_3);
editableContent.insert((int) insertPositionStart, currAnnot.getType());
editableContent.insert((int) insertPositionStart, startTagPart_2);
editableContent.insert((int) insertPositionStart, currAnnot.getId().toString());
editableContent.insert((int) insertPositionStart, startTagPart_1);
} // if
} // for
FileWriter writer = new FileWriter(file);
writer.write(editableContent.toString());
writer.close();
} else {
Out.prln("Content : " + originalContent);
Out.prln("Repositioning: " + info);
}
String xmlDocument = doc.toXml(peopleAndPlaces, false);
String fileName = new String("StANNIE_toXML_" + count + ".HTML");
FileWriter writer = new FileWriter(fileName);
writer.write(xmlDocument);
writer.close();
} // for each doc
} // main