/**
* This will invoke the <code>startElement</code> callback in the <code>ContentHandler</code>.
*
* @param element <code>Element</code> used in callbacks.
* @param nsAtts <code>List</code> of namespaces to declare with the element or <code>null</code>.
*/
private void startElement(Element element, Attributes nsAtts) throws JDOMException {
String namespaceURI = element.getNamespaceURI();
String localName = element.getName();
String rawName = element.getQualifiedName();
// Allocate attribute list.
AttributesImpl atts = (nsAtts != null) ? new AttributesImpl(nsAtts) : new AttributesImpl();
List attributes = element.getAttributes();
Iterator i = attributes.iterator();
while (i.hasNext()) {
Attribute a = (Attribute) i.next();
atts.addAttribute(
a.getNamespaceURI(),
a.getName(),
a.getQualifiedName(),
getAttributeTypeName(a.getAttributeType()),
a.getValue());
}
try {
contentHandler.startElement(namespaceURI, localName, rawName, atts);
} catch (SAXException se) {
throw new JDOMException("Exception in startElement", se);
}
}
/**
* This will take the supplied <code>{@link Element}</code> and transfer its namespaces to the
* global namespace storage.
*
* @param element <code>Element</code> to read namespaces from.
*/
private void transferNamespaces(Element element) {
Iterator i = declaredNamespaces.iterator();
while (i.hasNext()) {
Namespace ns = (Namespace) i.next();
if (ns != element.getNamespace()) {
element.addNamespaceDeclaration(ns);
}
}
declaredNamespaces.clear();
}
/**
* This will add the prefix mapping to the JDOM <code>Document</code> object.
*
* @param prefix <code>String</code> namespace prefix.
* @param uri <code>String</code> namespace URI.
*/
public void startPrefixMapping(String prefix, String uri) throws SAXException {
if (suppress) return;
Namespace ns = Namespace.getNamespace(prefix, uri);
declaredNamespaces.add(ns);
}
/**
* This will output a list of JDOM nodes as a fragment of an XML document, firing off the SAX
* events that have been registered.
*
* <p><strong>Warning</strong>: This method does not call the {@link
* ContentHandler#setDocumentLocator}, {@link ContentHandler#startDocument} and {@link
* ContentHandler#endDocument} callbacks on the {@link #setContentHandler ContentHandler}. The
* user shall invoke these methods directly prior/after outputting the document fragments.
*
* @param nodes <code>List</code> of JDOM nodes to output.
* @throws JDOMException if any error occurred.
* @see #outputFragment(org.jdom2.Content)
*/
public void outputFragment(List<? extends Content> nodes) throws JDOMException {
if ((nodes == null) || (nodes.size() == 0)) {
return;
}
// Output node list as a document fragment.
elementContent(nodes, new NamespaceStack());
}
/**
* This will invoke the <code>ContentHandler.startPrefixMapping</code> callback when a new
* namespace is encountered in the <code>Document</code>.
*
* @param element <code>Element</code> used in callbacks.
* @param namespaces <code>List</code> stack of Namespaces in scope.
* @return <code>Attributes</code> declaring the namespaces local to <code>element</code> or
* <code>null</code>.
*/
private Attributes startPrefixMapping(Element element, NamespaceStack namespaces)
throws JDOMException {
AttributesImpl nsAtts = null; // The namespaces as xmlns attributes
Namespace ns = element.getNamespace();
if (ns != Namespace.XML_NAMESPACE) {
String prefix = ns.getPrefix();
String uri = namespaces.getURI(prefix);
if (!ns.getURI().equals(uri)) {
namespaces.push(ns);
nsAtts = this.addNsAttribute(nsAtts, ns);
try {
contentHandler.startPrefixMapping(prefix, ns.getURI());
} catch (SAXException se) {
throw new JDOMException("Exception in startPrefixMapping", se);
}
}
}
// Fire additional namespace declarations
List additionalNamespaces = element.getAdditionalNamespaces();
if (additionalNamespaces != null) {
Iterator itr = additionalNamespaces.iterator();
while (itr.hasNext()) {
ns = (Namespace) itr.next();
String prefix = ns.getPrefix();
String uri = namespaces.getURI(prefix);
if (!ns.getURI().equals(uri)) {
namespaces.push(ns);
nsAtts = this.addNsAttribute(nsAtts, ns);
try {
contentHandler.startPrefixMapping(prefix, ns.getURI());
} catch (SAXException se) {
throw new JDOMException("Exception in startPrefixMapping", se);
}
}
}
}
return nsAtts;
}
/**
* This will invoke the callbacks for the content of an element.
*
* @param content element content as a <code>List</code> of nodes.
* @param namespaces <code>List</code> stack of Namespaces in scope.
*/
private void elementContent(List content, NamespaceStack namespaces) throws JDOMException {
for (Iterator i = content.iterator(); i.hasNext(); ) {
Object obj = i.next();
if (obj instanceof Content) {
this.elementContent((Content) obj, namespaces);
} else {
// Not a valid element child. This could happen with
// application-provided lists which may contain non
// JDOM objects.
handleError(new JDOMException("Invalid element content: " + obj));
}
}
}
/**
* Returns the content of a JDOM Element detached from it.
*
* @param elt the element to get the content from.
* @return a (possibly empty) list of JDOM nodes, detached from their parent.
*/
private List getDetachedContent(Element elt) {
List content = elt.getContent();
List nodes = new ArrayList(content.size());
while (content.size() != 0) {
Object o = content.remove(0);
nodes.add(o);
}
return (nodes);
}
/**
* This will output a list of JDOM nodes as a document, firing off the SAX events that have been
* registered.
*
* <p><strong>Warning</strong>: This method may output ill-formed XML documents if the list
* contains top-level objects that are not legal at the document level (e.g. Text or CDATA nodes,
* multiple Element nodes, etc.). Thus, it should only be used to output document portions towards
* ContentHandlers capable of accepting such ill-formed documents (such as XSLT processors).
*
* @param nodes <code>List</code> of JDOM nodes to output.
* @throws JDOMException if any error occurred.
* @see #output(org.jdom2.Document)
*/
public void output(List<? extends Content> nodes) throws JDOMException {
if ((nodes == null) || (nodes.size() == 0)) {
return;
}
// contentHandler.setDocumentLocator()
documentLocator(null);
// contentHandler.startDocument()
startDocument();
// Process node list.
elementContent(nodes, new NamespaceStack());
// contentHandler.endDocument()
endDocument();
}
/**
* Returns the result of an XSL Transformation as a list of JDOM nodes.
*
* <p>If the result of the transformation is a JDOM document, this method converts it into a list
* of JDOM nodes; any subsequent call to {@link #getDocument} will return <code>null</code>.
*
* @return the transformation result as a (possibly empty) list of JDOM nodes (Elements, Texts,
* Comments, PIs...).
*/
public List getResult() {
List nodes = Collections.EMPTY_LIST;
// Retrieve result from the document builder if not set.
this.retrieveResult();
if (result instanceof List) {
nodes = (List) result;
} else {
if ((result instanceof Document) && (queried == false)) {
List content = ((Document) result).getContent();
nodes = new ArrayList(content.size());
while (content.size() != 0) {
Object o = content.remove(0);
nodes.add(o);
}
result = nodes;
}
}
queried = true;
return (nodes);
}
/**
* This reports the occurrence of an actual element. It will include the element's attributes,
* with the exception of XML vocabulary specific attributes, such as <code>
* xmlns:[namespace prefix]</code> and <code>xsi:schemaLocation</code>.
*
* @param namespaceURI <code>String</code> namespace URI this element is associated with, or an
* empty <code>String</code>
* @param localName <code>String</code> name of element (with no namespace prefix, if one is
* present)
* @param qName <code>String</code> XML 1.0 version of element name: [namespace
* prefix]:[localName]
* @param atts <code>Attributes</code> list for this element
* @throws SAXException when things go wrong
*/
public void startElement(String namespaceURI, String localName, String qName, Attributes atts)
throws SAXException {
if (suppress) return;
Element element = null;
if ((namespaceURI != null) && (!namespaceURI.equals(""))) {
String prefix = "";
// Determine any prefix on the Element
if (!qName.equals(localName)) {
int split = qName.indexOf(":");
prefix = qName.substring(0, split);
}
Namespace elementNamespace = Namespace.getNamespace(prefix, namespaceURI);
element = factory.element(localName, elementNamespace);
} else {
element = factory.element(localName);
}
// Take leftover declared namespaces and add them to this element's
// map of namespaces
if (declaredNamespaces.size() > 0) {
transferNamespaces(element);
}
// Handle attributes
for (int i = 0, len = atts.getLength(); i < len; i++) {
Attribute attribute = null;
String attLocalName = atts.getLocalName(i);
String attQName = atts.getQName(i);
int attType = getAttributeType(atts.getType(i));
// Bypass any xmlns attributes which might appear, as we got
// them already in startPrefixMapping().
// This is sometimes necessary when SAXHandler is used with
// another source than SAXBuilder, as with JDOMResult.
if (attQName.startsWith("xmlns:") || attQName.equals("xmlns")) {
continue;
}
// First clause per http://markmail.org/message/2p245ggcjst27xe6
// patch from Mattias Jiderhamn
if ("".equals(attLocalName) && attQName.indexOf(":") == -1) {
attribute = factory.attribute(attQName, atts.getValue(i), attType);
} else if (!attQName.equals(attLocalName)) {
String attPrefix = attQName.substring(0, attQName.indexOf(":"));
Namespace attNs = Namespace.getNamespace(attPrefix, atts.getURI(i));
attribute = factory.attribute(attLocalName, atts.getValue(i), attType, attNs);
} else {
attribute = factory.attribute(attLocalName, atts.getValue(i), attType);
}
factory.setAttribute(element, attribute);
}
flushCharacters();
if (atRoot) {
document.setRootElement(element); // XXX should we use a factory call?
atRoot = false;
} else {
factory.addContent(getCurrentElement(), element);
}
currentElement = element;
}
public void startElement(String namespaceURI, String localName, String qName, Attributes atts)
throws SAXException {
if (qName.equals("patent-document") || qName.equals("fulltext-document")) {
nbNPLRef = 0;
nbPatentRef = 0;
nbAllRef = 0;
int length = atts.getLength();
// Process each attribute
for (int i = 0; i < length; i++) {
// Get names and values for each attribute
String name = atts.getQName(i);
String value = atts.getValue(i);
if (name != null) {
if (name.equals("lang")) {
// Global_Language_Code = value.toLowerCase();
}
if (name.equals("doc-number")) {
PatentNumber = "EP" + value;
}
if (name.equals("kind")) {
CodeType = value;
}
if (name.equals("date")) {
PublicDate = value;
}
}
}
CitedPatentNumber = new ArrayList<String>();
accumulatedText = new StringBuffer();
allContent = new StringBuffer();
accumulator.setLength(0);
} else if (qName.equals("description")) {
accumulator.setLength(0);
} else if (qName.equals("ref") || qName.equals("bibl")) {
int length = atts.getLength();
nbAllRef++;
// Process each attribute
for (int i = 0; i < length; i++) {
// Get names and values for each attribute
String name = atts.getQName(i);
String value = atts.getValue(i);
if (name != null) {
if (name.equals("type") || name.equals("typ")) {
if (value.equals("npl") || value.equals("book") || value.equals("journal")) {
String content = getText();
// we output what has been read so far in the description
// we tokenize the text
// ArrayList<String> tokens =
// StringTokenizer st = new StringTokenizer(content, delimiters, true);
List<String> tokenizations = new ArrayList<String>();
try {
// TBD: pass a language object to the tokenize method call
tokenizations = analyzer.tokenize(content);
} catch (Exception e) {
LOGGER.debug("Tokenization for XML patent document has failed.");
}
// int nbTokens = st.countTokens();
int nbTokens = tokenizations.size();
int j = 0;
// while (st.hasMoreTokens()) {
for (String token : tokenizations) {
// String token = st.nextToken().trim();
if ((token.trim().length() == 0)
|| (token.equals(" "))
|| (token.equals("\t"))
|| (token.equals("\n"))
|| (token.equals("\r"))) {
continue;
}
if ((j > (nbTokens - N) && (N != -1)) || (refFound && (j < N) && (N != -1))) {
try {
accumulatedText.append(token + "\t" + "<other>\n");
allContent.append(token + " ");
} catch (Exception e) {
// e.printStackTrace();
throw new GrobidException("An exception occured while running Grobid.", e);
}
} else {
try {
accumulatedText.append(token + "\t" + "<ignore>\n");
allContent.append(token + " ");
} catch (Exception e) {
// e.printStackTrace();
throw new GrobidException("An exception occured while running Grobid.", e);
}
}
j++;
}
accumulator.setLength(0);
npl = true;
ref = true;
} else if (value.equals("patent") || value.equals("pl")) {
String content = getText();
// we output what has been read so far in the description
// we tokenize the text
// ArrayList<String> tokens =
// TextUtilities.segment(content,"[("+TextUtilities.punctuations);
// StringTokenizer st = new StringTokenizer(content, delimiters, true);
List<String> tokenizations = new ArrayList<String>();
try {
// TBD: pass a language object to the tokenize method call
tokenizations = analyzer.tokenize(content);
} catch (Exception e) {
LOGGER.debug("Tokenization for XML patent document has failed.");
}
// int nbTokens = st.countTokens();
int nbTokens = tokenizations.size();
int j = 0;
for (String token : tokenizations) {
// while (st.hasMoreTokens()) {
// String token = st.nextToken().trim();
if ((token.trim().length() == 0)
|| (token.equals(" "))
|| (token.equals("\t"))
|| (token.equals("\n"))
|| (token.equals("\r"))) {
continue;
}
if ((j > (nbTokens - N)) | (refFound & (j < N))) {
try {
accumulatedText.append(token + "\t" + "<other>\n");
allContent.append(token + " ");
} catch (Exception e) {
// e.printStackTrace();
throw new GrobidException("An exception occured while running Grobid.", e);
}
} else {
try {
accumulatedText.append(token + "\t" + "<ignore>\n");
allContent.append(token + " ");
} catch (Exception e) {
// e.printStackTrace();
throw new GrobidException("An exception occured while running Grobid.", e);
}
}
j++;
}
accumulator.setLength(0);
npl = false;
ref = true;
} else {
System.out.println("Warning: unknown attribute value for ref or bibl: " + value);
ref = false;
npl = false;
}
}
}
}
accumulatorRef.setLength(0);
} else if (qName.equals("claim")) {
accumulator.setLength(0);
} else if (qName.equals("invention-title")) {
accumulator.setLength(0);
} else if (qName.equals("patcit")) {
int length = atts.getLength();
// Process each attribute
for (int i = 0; i < length; i++) {
// Get names and values for each attribute
String name = atts.getQName(i);
String value = atts.getValue(i);
if (name != null) {
if (name.equals("ucid")) {
cited_number = value;
// we normally need to normalize a little bit this patent nummer
}
}
}
}
}
public void endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
throws SAXException {
if (qName.equals("date")) {
accumulator.setLength(0);
} else if (qName.equals("ref") || qName.equals("bibl")) {
String refString = getRefText();
refString = refString.replace("\n", " ");
refString = refString.replace("\t", " ");
refString = refString.replace(" ", " ");
if (npl && ref) {
if (referencesNPL == null) referencesNPL = new ArrayList<String>();
referencesNPL.add(refString);
refFound = true;
if (nplReferences) nbNPLRef++;
} else if (ref) {
if (referencesPatent == null) {
referencesPatent = new HashMap<String, ArrayList<String>>();
}
ArrayList<String> refss = referencesPatent.get(currentFileName);
if (refss == null) {
refss = new ArrayList<String>();
}
refss.add(refString);
referencesPatent.put(currentFileName, refss);
refFound = true;
if (patentReferences) {
nbPatentRef++;
}
}
if (refFound) {
// we tokenize the text
// ArrayList<String> tokens = TextUtilities.segment(refString,
// "[("+TextUtilities.punctuations);
// StringTokenizer st = new StringTokenizer(refString, delimiters, true);
List<String> tokenizations = new ArrayList<String>();
try {
// TBD: pass a language object to the tokenize method call
tokenizations = analyzer.tokenize(refString);
} catch (Exception e) {
LOGGER.debug("Tokenization for XML patent document has failed.");
}
int i = 0;
// String token = null;
// for(String token : tokens) {
// while (st.hasMoreTokens()) {
for (String token : tokenizations) {
// token = st.nextToken().trim();
if ((token.trim().length() == 0)
|| (token.equals(" "))
|| (token.equals("\t"))
|| (token.equals("\n"))
|| (token.equals("\r"))) {
continue;
}
try {
accumulatedText.append(token + "\t");
allContent.append(token + " ");
if (npl) {
if (nplReferences) {
if (i == 0) {
// accumulatedText.append("refNPLBegin\n");
accumulatedText.append("I-<refNPL>\n");
} else if (token == null) {
// accumulatedText.append("refNPLEnd\n");
accumulatedText.append("E-<refNPL>\n");
} else {
accumulatedText.append("<refNPL>\n");
}
} else accumulatedText.append("<other>\n");
} else {
if (patentReferences) {
if (i == 0) accumulatedText.append("I-<refPatent>\n");
else if (token == null) accumulatedText.append("E-<refPatent>\n");
else accumulatedText.append("<refPatent>\n");
} else accumulatedText.append("<other>\n");
}
} catch (Exception e) {
// e.printStackTrace();
throw new GrobidException("An exception occured while running Grobid.", e);
}
i++;
}
}
ref = false;
} else if (qName.equals("classification-ipcr")) {
accumulator.setLength(0);
} else if (qName.equals("classification-symbol")) {
accumulator.setLength(0);
} else if (qName.equals("abstract")) {
accumulator.setLength(0);
} else if (qName.equals("heading")) {
accumulator.append(" ");
} else if (qName.equals("description")) {
if (refFound) {
String content = getText();
// we tokenize the text
// ArrayList<String> tokens = TextUtilities.segment(content,
// "[("+TextUtilities.punctuations);
// StringTokenizer st = new StringTokenizer(content, delimiters, true);
List<String> tokenizations = new ArrayList<String>();
try {
// TBD: pass a language object to the tokenize method call
tokenizations = analyzer.tokenize(content);
} catch (Exception e) {
LOGGER.debug("Tokenization for XML patent document has failed.");
}
int i = 0;
// String token = null;
// for(String token : tokens) {
// while (st.hasMoreTokens()) {
for (String token : tokenizations) {
// token = st.nextToken().trim();
if ((token.trim().length() == 0)
|| (token.equals(" "))
|| (token.equals("\t"))
|| (token.equals("\n"))
|| (token.equals("\r"))) {
continue;
}
// we print only a window of N words
if ((i > N) && (N != -1)) {
// break;
token = token.trim();
if (token.length() > 0) {
accumulatedText.append(token + "\t" + "<ignore>\n");
allContent.append(token + " ");
}
} else {
try {
token = token.trim();
if (token.length() > 0) {
accumulatedText.append(token + "\t" + "<other>\n");
allContent.append(token + " ");
}
} catch (Exception e) {
throw new GrobidException("An exception occured while running Grobid.", e);
}
}
i++;
}
accumulator.setLength(0);
refFound = false;
}
} else if (qName.equals("patcit")) {
// we register the citation, the citation context will be marked in a later stage
if (citations == null) citations = new ArrayList<String>();
citations.add(cited_number);
accumulator.setLength(0);
} else if (qName.equals("invention-title")) {
accumulator.setLength(0);
} else if (qName.equals("applicants")) {
accumulator.setLength(0);
} else if (qName.equals("inventors")) {
accumulator.setLength(0);
} else if (qName.equals("document-id")) {
accumulator.setLength(0);
} else if (qName.equals("legal-status")) {
accumulator.setLength(0);
} else if (qName.equals("bibliographic-data")) {
accumulator.setLength(0);
} else if (qName.equals("doc-number")) {
accumulator.setLength(0);
} else if (qName.equals("country")) {
accumulator.setLength(0);
} else if (qName.equals("kind")) {
accumulator.setLength(0);
} else if (qName.equals("classification-symbol")) {
accumulator.setLength(0);
} else if (qName.equals("classification-ecla")) {
accumulator.setLength(0);
} else if (qName.equals("patent-document") || qName.equals("fulltext-document")) {
String allString = allContent.toString();
journalsPositions = lexicon.inJournalNames(allString);
abbrevJournalsPositions = lexicon.inAbbrevJournalNames(allString);
conferencesPositions = lexicon.inConferenceNames(allString);
publishersPositions = lexicon.inPublisherNames(allString);
allContent = null;
allString = null;
} else if (qName.equals("row")) {
accumulator.append(" ");
} else if (qName.equals("p")) {
accumulator.append("\n");
}
}
public String getText() {
String text = accumulator.toString();
if (text.trim().length() == 0) {
return "";
}
/*text = text.replace("\n", " ");
text = text.replace(" ", " ");*/
if (counting) {
/*
StringTokenizer st = new StringTokenizer(text, delimiters, true);
int count = 0;
while(st.hasMoreTokens()) {
String token = st.nextToken().trim();
if (token.length() == 0) {
continue;
}
count++;
}
*/
int i = currentPatentIndex;
int count = text.length();
while (i < patents.size()) {
PatentItem currentPatent = patents.get(i);
if (currentPatent != null) {
int startOffset = currentPatent.getOffsetBegin();
int endOffset = currentPatent.getOffsetEnd();
if ((startOffset >= offset) && (endOffset <= offset + count)) {
String context = currentPatent.getContext();
/*System.out.println("OFFSET: " + offset);
System.out.println("count: " + count);
System.out.println("startOffset: " + startOffset);
System.out.println("endOffset: " + endOffset);
System.out.println("context: " + context);
System.out.println("text: " + text);*/
String target = "";
if (context.charAt(0) == ' ') {
target = " <ref type=\"patent\">" + context.substring(1, context.length()) + "</ref>";
} else {
target = "<ref type=\"patent\">" + context + "</ref>";
}
text = text.replace(context, target);
currentPatentIndex = i;
}
}
i++;
}
// i = currentArticleIndex;
i = 0;
while (i < articles.size()) {
BibDataSet currentArticle = articles.get(i);
if (currentArticle != null) {
List<Integer> offsets = currentArticle.getOffsets();
int startOffset = -1;
int endOffset = -1;
String context = currentArticle.getRawBib().trim();
if (offsets.size() > 0) {
if (offsets.get(0) != null) {
startOffset = offsets.get(0).intValue();
/*StringTokenizer stt = new StringTokenizer(context, delimiters, true);
int count2 = 0;
while(stt.hasMoreTokens()) {
String token2 = stt.nextToken().trim();
if (token2.length() == 0) {
continue;
}
count2++;
}*/
// endOffset = offsets.get(1).intValue();
endOffset = startOffset + context.length();
}
}
// if ( (startOffset >= offset) && (endOffset <= offset+count) ) {
if ((startOffset >= offset)) {
/*System.out.println("OFFSET: " + offset);
System.out.println("count: " + count);
System.out.println("startOffset: " + startOffset);
System.out.println("endOffset: " + endOffset);
System.out.println("context: " + context);
System.out.println("text: " + text);*/
String target = " <ref type=\"npl\">" + context + "</ref> ";
text = text.replace(context, target);
currentArticleIndex = i;
}
}
i++;
}
offset += count;
}
return text;
}
