/**
* Unpack the markup in the document. This converts markup from the native format (e.g. XML, RTF)
* into annotations in GATE format. Uses the markupElementsMap to determine which elements to
* convert, and what annotation type names to use.
*/
public void unpackMarkup(Document doc) throws DocumentFormatException {
if (doc == null || doc.getContent() == null) return;
setNewLineProperty(doc);
// Create paragraph annotations in the specified annotation set
int endOffset = doc.getContent().toString().length();
int startOffset = 0;
annotateParagraphs(doc, startOffset, endOffset, GateConstants.ORIGINAL_MARKUPS_ANNOT_SET_NAME);
} // unpackMarkup
/**
* Constructs a XmlDocumentHandler object.
*
* @param aDocument the Gate document that will be processed.
* @param aMarkupElementsMap this map contains the elements name that we want to create.
* @param anElement2StringMap this map contains the strings that will be added to the text
* contained by the key element.
* @param anAnnotationSet is the annotation set that will be filled when the document was
* processed
*/
public XmlDocumentHandler(
gate.Document aDocument,
Map<String, String> aMarkupElementsMap,
Map<String, String> anElement2StringMap,
AnnotationSet anAnnotationSet) {
// init parent
super();
// init stack
stack = new Stack<CustomObject>();
// this string contains the plain text (the text without markup)
tmpDocContent = new StringBuffer(aDocument.getContent().size().intValue());
// colector is used later to transform all custom objects into annotation
// objects
colector = new LinkedList<CustomObject>();
// the Gate document
doc = aDocument;
// this map contains the elements name that we want to create
// if it's null all the elements from the XML documents will be transformed
// into Gate annotation objects
markupElementsMap = aMarkupElementsMap;
// this map contains the string that we want to insert iside the document
// content, when a certain element is found
// if the map is null then no string is added
element2StringMap = anElement2StringMap;
basicAS = anAnnotationSet;
customObjectsId = 0;
} // XmlDocumentHandler()/
/**
* Constructor initialises all the private memeber data
*
* @param aDocument The gate document that will be processed
* @param aMarkupElementsMap The map containing the elements that will transform into annotations
* @param anAnnotationSet The annotation set that will contain annotations resulted from the
* processing of the gate document
*/
public HtmlDocumentHandler(
gate.Document aDocument,
Map<String, String> aMarkupElementsMap,
gate.AnnotationSet anAnnotationSet) {
// init stack
stack = new Stack<CustomObject>();
// this string contains the plain text (the text without markup)
tmpDocContent = new StringBuffer(aDocument.getContent().size().intValue());
// colector is used later to transform all custom objects into
// annotation objects
colector = new LinkedList<CustomObject>();
// the Gate document
doc = aDocument;
// this map contains the elements name that we want to create
// if it's null all the elements from the XML documents will be transformed
// into Gate annotation objects
markupElementsMap = aMarkupElementsMap;
// init an annotation set for this gate document
basicAS = anAnnotationSet;
customObjectsId = 0;
} // HtmlDocumentHandler
/**
* Check the new line sequence and set document property. <br>
* Possible values are CRLF, LFCR, CR, LF
*/
protected void setNewLineProperty(Document doc) {
String content = doc.getContent().toString();
String newLineType = "";
char ch = ' ';
char lastch = ' ';
for (int i = 0; i < content.length(); ++i) {
ch = content.charAt(i);
if (lastch == '\r') {
if (ch == '\n') {
newLineType = "CRLF";
break;
} else {
newLineType = "CR";
break;
}
}
if (lastch == '\n') {
if (ch == '\r') {
newLineType = "LFCR";
break;
} else {
newLineType = "LF";
break;
}
}
lastch = ch;
} // for
doc.getFeatures().put(GateConstants.DOCUMENT_NEW_LINE_TYPE, newLineType);
} // setNewLineProperty()
/**
* Generation of a GATE document from a Behemoth one
*
* @param key URL of the input doc
* @param inputDoc
* @return
* @throws ResourceInstantiationException
* @throws InvalidOffsetException
* @throws IOException
*/
public gate.Document generateGATEDoc(BehemothDocument inputDoc)
throws ResourceInstantiationException, InvalidOffsetException, IOException {
gate.Document gatedocument = null;
// if no text is available (e.g. Tika has not extracted it)
// let GATE do the parsing itself from the binary content
if (inputDoc.getText() == null) {
try {
gatedocument = generateGATEDocFromLocalDump(inputDoc);
// transfer the text from GATE to Behemoth
String textContent = gatedocument.getContent().toString();
inputDoc.setText(textContent);
return gatedocument;
} catch (Exception e) {
LOG.error("Can't generate GATE doc from byte dump", e);
}
}
// if the input document does not have any text -> create a doc with an
// empty text
String text = inputDoc.getText();
if (inputDoc.getText() == null) text = "";
else text = inputDoc.getText();
gatedocument = Factory.newDocument(text);
// then the metadata as document features
FeatureMap docFeatures = gatedocument.getFeatures();
String docUrl = inputDoc.getUrl();
if (docUrl != null) docFeatures.put("gate.SourceURL", docUrl);
if (inputDoc.getMetadata() != null) {
Iterator<Entry<Writable, Writable>> iter = inputDoc.getMetadata().entrySet().iterator();
while (iter.hasNext()) {
Entry<Writable, Writable> entry = iter.next();
String skey = entry.getKey().toString().trim();
String svalue = null;
if (entry.getValue() != null) svalue = entry.getValue().toString().trim();
docFeatures.put(skey, svalue);
}
}
// finally the annotations as original markups
// TODO change the name of the annotation set via config
AnnotationSet outputAS = gatedocument.getAnnotations("Original markups");
for (Annotation annot : inputDoc.getAnnotations()) {
// add to outputAS as a GATE annotation
FeatureMap features = Factory.newFeatureMap();
features.putAll(annot.getFeatures());
outputAS.add(annot.getStart(), annot.getEnd(), annot.getType(), features);
}
return gatedocument;
}
/**
* This is a test to see if the GATE document has a valid URL or a valid content.
*
* @param doc
* @throws DocumentFormatException
*/
protected static boolean hasContentButNoValidUrl(Document doc) throws DocumentFormatException {
try {
if (doc.getSourceUrl() == null && doc.getContent() != null) {
// The doc's url is null but there is a content.
return true;
} else {
doc.getSourceUrl().openConnection();
}
} catch (IOException ex1) {
// The URL is not null but is not valid.
if (doc.getContent() == null)
// The document content is also null. There is nothing we can do.
throw new DocumentFormatException(
"The document doesn't have a" + " valid URL and also no content");
return true;
} // End try
return false;
}
/** Delete '\r' in combination CRLF or LFCR in document content */
private void removeExtraNewLine(Document doc) {
String content = doc.getContent().toString();
StringBuffer buff = new StringBuffer(content);
char ch = ' ';
char lastch = ' ';
for (int i = content.length() - 1; i > -1; --i) {
ch = content.charAt(i);
if (ch == '\n' && lastch == '\r') {
buff.deleteCharAt(i + 1);
}
if (ch == '\r' && lastch == '\n') {
buff.deleteCharAt(i);
ch = lastch;
}
lastch = ch;
} // for
doc.setContent(new DocumentContentImpl(buff.toString()));
} // removeExtraNewLine(Document doc)
/**
* Checks two documents for equality.
*
* @param doc1 a document
* @param doc2 another document
* @return a boolean.
*/
public static boolean documentsEqual(Document doc1, Document doc2) {
message = "";
if (doc1 == null ^ doc2 == null) {
message = "Documents not equal: null<>non-null!";
return false;
}
if (doc1 == null) return true;
if (!check(doc1.getContent(), doc2.getContent())) {
message = "Document contents different!";
return false;
}
if (!check(doc1.getAnnotations(), doc2.getAnnotations())) {
message = "Documents default AS not equal!";
return false;
}
if (doc1 instanceof TextualDocument) {
if (doc2 instanceof TextualDocument) {
if (!check(
((TextualDocument) doc1).getEncoding(), ((TextualDocument) doc2).getEncoding())) {
message = "Textual documents with different encodings!";
return false;
}
} else {
message = "Documents not equal: textual<>non-textual!";
return false;
}
}
if (!check(doc1.getFeatures(), doc2.getFeatures())) {
message = "Documents features not equal!";
return false;
}
// needs friend declaration :(
// if(!markupAware.equals(doc.markupAware)) return false;
if (!check(doc1.getNamedAnnotationSets(), doc2.getNamedAnnotationSets())) {
message = "Documents named annots not equal!";
return false;
}
// if(doc1 instanceof DocumentImpl){
// if(doc2 instanceof DocumentImpl){
// if(! check(((DocumentImpl)doc1).getNextNodeId(),
// ((DocumentImpl)doc2).getNextNodeId())){
// message = "Documents next nodeID not equal!";
// return false;
// }
// if(! check(((DocumentImpl)doc1).getNextAnnotationId(),
// ((DocumentImpl)doc2).getNextAnnotationId())){
// message = "Documents next annotationIDs not equal!";
// return false;
// }
// }else{
// message = "Documents not equal: DocumentImpl<>non-DocumentImpl!";
// return false;
// }
// }
if (!check(doc1.getSourceUrl(), doc2.getSourceUrl())) {
message = "Documents sourceURLs not equal!";
return false;
}
if (!(check(doc1.getSourceUrlStartOffset(), doc2.getSourceUrlStartOffset())
&& check(doc1.getSourceUrlEndOffset(), doc2.getSourceUrlEndOffset()))) {
message = "Documents sourceURLOffsets not equal!";
return false;
}
return true;
}
// carry out the actual annotations on the given span of text in the
// document.
protected void annotateText(Document doc, AnnotationSet outputAS, long from, long to) {
String text = "";
try {
text = doc.getContent().getContent(from, to).toString();
} catch (InvalidOffsetException ex) {
throw new GateRuntimeException("Unexpected offset exception, offsets are " + from + "/" + to);
}
// send the text to the service and get back the response
// System.out.println("Annotating text: "+text);
// System.out.println("Starting offset is "+from);
// NOTE: there is a bug in the TagMe service which causes offset errors
// if we use the tweet mode and there are certain patterns in the tweet.
// The approach recommended by Francesco Piccinno is to replace those
// patterns by spaces.
if (getIsTweet()) {
logger.debug("Text before cleaning: >>" + text + "<<");
// replace
text = text.replaceAll(patternStringRT3, " ");
text = text.replaceAll(patternStringRT2, " ");
text = text.replaceAll(patternHashTag, " $1");
// now replace the remaining patterns by spaces
StringBuilder sb = new StringBuilder(text);
Matcher m = patternUrl.matcher(text);
while (m.find()) {
int start = m.start();
int end = m.end();
sb.replace(start, end, nSpaces(end - start));
}
m = patternUser.matcher(text);
while (m.find()) {
int start = m.start();
int end = m.end();
sb.replace(start, end, nSpaces(end - start));
}
text = sb.toString();
logger.debug("Text after cleaning: >>" + text + "<<");
}
TagMeAnnotation[] tagmeAnnotations = getTagMeAnnotations(text);
for (TagMeAnnotation tagmeAnn : tagmeAnnotations) {
if (tagmeAnn.rho >= minrho) {
FeatureMap fm = Factory.newFeatureMap();
fm.put("tagMeId", tagmeAnn.id);
fm.put("title", tagmeAnn.title);
fm.put("rho", tagmeAnn.rho);
fm.put("spot", tagmeAnn.spot);
fm.put("link_probability", tagmeAnn.link_probability);
if (tagmeAnn.title == null) {
throw new GateRuntimeException("Odd: got a null title from the TagMe service" + tagmeAnn);
} else {
fm.put("inst", "http://dbpedia.org/resource/" + recodeForDbp38(tagmeAnn.title));
}
try {
gate.Utils.addAnn(
outputAS, from + tagmeAnn.start, from + tagmeAnn.end, getOutputAnnotationType(), fm);
} catch (Exception ex) {
System.err.println(
"Got an exception in document " + doc.getName() + ": " + ex.getLocalizedMessage());
ex.printStackTrace(System.err);
System.err.println("from=" + from + ", to=" + to + " TagMeAnn=" + tagmeAnn);
}
}
}
}
/**
* This method annotates paragraphs in a GATE document. The investigated text spans beetween start
* and end offsets and the paragraph annotations are created in the annotSetName. If annotSetName
* is null then they are creted in the default annotation set.
*
* @param aDoc is the gate document on which the paragraph detection would be performed.If it is
* null or its content it's null then the method woul simply return doing nothing.
* @param startOffset is the index form the document content from which the paragraph detection
* will start
* @param endOffset is the offset where the detection will end.
* @param annotSetName is the name of the set in which paragraph annotation would be created.The
* annotation type created will be "paragraph"
*/
public void annotateParagraphs(Document aDoc, int startOffset, int endOffset, String annotSetName)
throws DocumentFormatException {
// Simply return if the document is null or its content
if (aDoc == null || aDoc.getContent() == null) return;
// Simply return if the start is > than the end
if (startOffset > endOffset) return;
// Decide where to put the newly detected annotations
AnnotationSet annotSet = null;
if (annotSetName == null) annotSet = aDoc.getAnnotations();
else annotSet = aDoc.getAnnotations(annotSetName);
// Extract the document content
String content = aDoc.getContent().toString();
// This is the offset marking the start of a para
int startOffsetPara = startOffset;
// This marks the ned of a para
int endOffsetPara = endOffset;
// The initial sate of the FSA
int state = 1;
// This field marks that a BR entity was read
// A BR entity can be NL or NL CR, depending on the operating system (UNIX
// or DOS)
boolean readBR = false;
int index = startOffset;
while (index < endOffset) {
// Read the current char
char ch = content.charAt(index);
// Test if a BR entity was read
if (ch == '\n') {
readBR = true;
// If \n is followed by a \r then advance the index in order to read a
// BR entity
while ((index + 1 < endOffset) && (content.charAt(index + 1) == '\r')) index++;
} // End if
switch (state) {
// It is the initial and also a final state
// Stay in state 1 while it reads whitespaces
case 1:
{
// If reads a non whitespace char then move to state 2 and record
// the beggining of a paragraph
if (!Character.isWhitespace(ch)) {
state = 2;
startOffsetPara = index;
} // End if
}
break;
// It can be also a final state.
case 2:
{
// Stay in state 2 while reading chars != BR entities
if (readBR) {
// If you find a BR char go to state 3. The possible end of the para
// can be index. This will be confirmed by state 3. So, this is why
// the end of a para is recorded here.
readBR = false;
endOffsetPara = index;
state = 3;
} // End if
}
break;
// It can be also a final state
// From state 3 there are only 2 possible ways: (state 2 or state1)
// In state 1 it needs to read a BR
// For state 2 it nead to read something different then a BR
case 3:
{
if (readBR) {
// A BR was read. Go to state 1
readBR = false;
state = 1;
// Create an annotation type paragraph
try {
annotSet.add(
new Long(startOffsetPara),
new Long(endOffsetPara),
"paragraph",
Factory.newFeatureMap());
} catch (gate.util.InvalidOffsetException ioe) {
throw new DocumentFormatException(
"Coudn't create a paragraph" + " annotation", ioe);
} // End try
} else {
// Go to state 2 an keep reading chars
state = 2;
} // End if
}
break;
} // End switch
// Prepare to read the next char.
index++;
} // End while
endOffsetPara = index;
// Investigate where the finite automata has stoped
if (state == 2 || state == 3) {
// Create an annotation type paragraph
try {
annotSet.add(
new Long(startOffsetPara),
// Create the final annotation using the endOffset
new Long(endOffsetPara),
"paragraph",
Factory.newFeatureMap());
} catch (gate.util.InvalidOffsetException ioe) {
throw new DocumentFormatException("Coudn't create a paragraph" + " annotation", ioe);
} // End try
} // End if
} // End annotateParagraphs();
