Example usage for javax.xml.xpath XPathConstants STRING

Introduction

In this page you can find the example usage for javax.xml.xpath XPathConstants STRING.

Prototype

QName STRING

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Document

The XPath 1.0 string data type.

Maps to Java String .

Usage

From source file:org.wso2.carbon.bpmn.core.types.datatypes.xml.api.XMLDocument.java

/**
 * Function to evaluate xPath query, and return specified return type
 *
 * @param xpathStr xpath expression to evaluate
 * @param returnType The desired return type of xpath evaluation. Supported retrun types : "NODESET", "NODE", "STRING", "NUMBER", "BOOLEAN"
 * @return result of xpath evaluation in specified return type
 * @throws BPMNXmlException//  w w w  . j  a v a2 s  .  com
 * @throws XPathExpressionException
 */
public Object xPath(String xpathStr, String returnType) throws BPMNXmlException, XPathExpressionException {

    if (returnType.equals(XPathConstants.NODESET.getLocalPart())) {
        Utils.evaluateXPath(doc, xpathStr, XPathConstants.NODESET);
    } else if (returnType.equals(XPathConstants.NODE.getLocalPart())) {
        Utils.evaluateXPath(doc, xpathStr, XPathConstants.NODE);
    } else if (returnType.equals(XPathConstants.STRING.getLocalPart())) {
        Utils.evaluateXPath(doc, xpathStr, XPathConstants.STRING);
    } else if (returnType.equals(XPathConstants.NUMBER.getLocalPart())) {
        Utils.evaluateXPath(doc, xpathStr, XPathConstants.NUMBER);
    } else if (returnType.equals(XPathConstants.BOOLEAN.getLocalPart())) {
        Utils.evaluateXPath(doc, xpathStr, XPathConstants.BOOLEAN);
    } else {
        //Unknown return type
        throw new BPMNXmlException("Unknown return type : " + returnType);
    }

    return null;
}

---

From source file:org.wso2.carbon.bpmn.core.types.datatypes.xml.Utils.java

/**
 * Function to evaluate xpath. This will resolve the NodeList to Node if the result contains only one node
 * @param doc/*from ww  w . j a v a2 s. c o  m*/
 * @param xpathStr
 * @return
 * @throws XPathExpressionException
 */
public static Object evaluateXPath(Document doc, String xpathStr) throws BPMNXmlException {

    Object result = null;
    NodeList outputObjList = null;
    try {
        outputObjList = (NodeList) evaluateXPath(doc, xpathStr, XPathConstants.NODESET);
        if (outputObjList.getLength() == 1) {
            //If there is only one node
            if (outputObjList.item(0) instanceof Text) {
                return ((Text) outputObjList.item(0)).getWholeText();
            }
            return outputObjList.item(0);
        }
        return outputObjList;

    } catch (XPathExpressionException eLevel1) {
        //provided xpath cannot be evaluated to NodeList, so it may be evaluated to string
        try {

            if (log.isDebugEnabled()) {
                log.debug("Since evaluating the xpath: " + xpathStr
                        + " to NodeList failed, retrying to evaluate it to a STRING");
            }
            return evaluateXPath(doc, xpathStr, XPathConstants.STRING);

        } catch (XPathExpressionException eLevel2) {
            if (log.isDebugEnabled()) {
                log.debug("Error occurred while evaluating xpath :" + xpathStr + " on xml: " + doc.toString());
            }
            throw new BPMNXmlException(
                    "Error occurred while evaluating xpath :" + xpathStr + " due to error in xpath", eLevel2);
        }
    }
}

---

From source file:org.wso2.carbon.humantask.core.engine.runtime.xpath.XPathExpressionRuntime.java

/**
 * Evaluate XPath expression//from  www. java  2s. c o  m
 *
 * @param exp     XPath expression string
 * @param evalCtx Evaluation context containing all the required context information
 * @return Return List of selected nodes or string
 */
@Override
public List evaluate(String exp, EvaluationContext evalCtx) {
    List result;
    Object someRes;
    try {
        someRes = evaluate(exp, evalCtx, XPathConstants.NODESET);
    } catch (Exception e) {
        someRes = evaluate(exp, evalCtx, XPathConstants.STRING);
    }
    if (someRes instanceof List) {
        result = (List) someRes;
        if (log.isDebugEnabled()) {
            log.debug("Returned list of size " + result.size());
        }

        if ((result.size() == 1) && !(result.get(0) instanceof Node)) {
            // Dealing with a Java class
            Object simpleType = result.get(0);
            // Dates get a separate treatment as we don't want to call toString on them
            String textVal;
            if (simpleType instanceof Date) {
                textVal = ISO8601DateParser.format((Date) simpleType);
            } else if (simpleType instanceof DurationValue) {
                textVal = ((DurationValue) simpleType).getStringValue();
            } else {
                textVal = simpleType.toString();
            }

            // Wrapping in a document
            Document document = DOMUtils.newDocument();
            // Giving our node a parent just in case it's an LValue expression
            Element wrapper = document.createElement("wrapper");
            Text text = document.createTextNode(textVal);
            wrapper.appendChild(text);
            document.appendChild(wrapper);
            result = Collections.singletonList(text);
        }
    } else if (someRes instanceof NodeList) {
        NodeList retVal = (NodeList) someRes;
        if (log.isDebugEnabled()) {
            log.debug("Returned node list of size " + retVal.getLength());
        }
        result = new ArrayList(retVal.getLength());
        for (int m = 0; m < retVal.getLength(); ++m) {
            Node val = retVal.item(m);
            if (val.getNodeType() == Node.DOCUMENT_NODE) {
                val = ((Document) val).getDocumentElement();
            }
            result.add(val);
        }
    } else if (someRes instanceof String) {
        // Wrapping in a document
        Document document = DOMUtils.newDocument();
        Element wrapper = document.createElement("wrapper");
        Text text = document.createTextNode((String) someRes);
        wrapper.appendChild(text);
        document.appendChild(wrapper);
        result = Collections.singletonList(text);
    } else {
        result = null;
    }

    return result;
}

---

From source file:org.wso2.carbon.humantask.core.engine.runtime.xpath.XPathExpressionRuntime.java

/**
 * Evaluate given XPath string and returns result as a string
 *
 * @param exp     XPath expression string
 * @param evalCtx Evaluation context containing all the required context information
 * @return String/*w w w  . j a v  a2s.  c  o m*/
 */
@Override
public String evaluateAsString(String exp, EvaluationContext evalCtx) {
    return (String) evaluate(exp, evalCtx, XPathConstants.STRING);
}

---

From source file:org.wso2.identity.scenarios.commons.SAML2SSOTestBase.java

/**
 * Return whether SAML Assertion has the canonicalization method
 * set to 'http://www.w3.org/2001/10/xml-exc-c14n#WithComments'.
 *
 * @param document/*www .j av  a2  s.c o  m*/
 * @return true if canonicalization method equals to 'http://www.w3.org/2001/10/xml-exc-c14n#WithComments'
 */
private boolean isSignedWithComments(Document document) {

    XPath xPath = XPathFactory.newInstance().newXPath();
    try {
        String assertionId = (String) xPath.compile("//*[local-name()='Assertion']/@ID").evaluate(document,
                XPathConstants.STRING);

        if (StringUtils.isBlank(assertionId)) {
            return false;
        }

        NodeList nodeList = ((NodeList) xPath
                .compile("//*[local-name()='Assertion']" + "/*[local-name()='Signature']"
                        + "/*[local-name()='SignedInfo']" + "/*[local-name()='Reference'][@URI='#" + assertionId
                        + "']" + "/*[local-name()='Transforms']" + "/*[local-name()='Transform']"
                        + "[@Algorithm='http://www.w3.org/2001/10/xml-exc-c14n#WithComments']")
                .evaluate(document, XPathConstants.NODESET));
        return nodeList != null && nodeList.getLength() > 0;
    } catch (XPathExpressionException e) {
        String message = "Failed to find the canonicalization algorithm of the assertion. Defaulting to: "
                + "http://www.w3.org/2001/10/xml-exc-c14n#";
        log.warn(message);
        return false;
    }
}

---

From source file:org.wso2.ppaas.configurator.tests.ConfiguratorTestManager.java

public String readXML(String resourcePath, String xpathExpression) {

    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    DocumentBuilder builder = null;
    try {/*from   w  w  w .  j  ava 2  s.c  o m*/
        String targetFile = ConfiguratorTestManager.class.getResource(PATH_SEP).getPath() + ".." + PATH_SEP
                + CONFIGURATOR_DIR_NAME + PATH_SEP + resourcePath;
        builder = factory.newDocumentBuilder();
        Document doc = builder.parse(targetFile);
        XPathFactory xPathfactory = XPathFactory.newInstance();
        XPath xpath = xPathfactory.newXPath();
        XPathExpression expr = xpath.compile(xpathExpression);
        String value = expr.evaluate(doc, XPathConstants.STRING).toString();
        log.info("Parsed value" + value);
        return value;

    } catch (ParserConfigurationException | SAXException | IOException | XPathExpressionException e) {
        log.error("Error in parsing xml " + e.getMessage());
    }
    return null;
}

---

From source file:org.xdi.service.XmlService.java

public String getNodeValue(Document xmlDocument, String xPathExpression, String attributeName)
        throws XPathExpressionException {
    XPath xPath = XPathFactory.newInstance().newXPath();
    XPathExpression formXPathExpression = xPath.compile(xPathExpression);

    if (StringHelper.isEmpty(attributeName)) {
        String nodeValue = (String) formXPathExpression.evaluate(xmlDocument, XPathConstants.STRING);

        return nodeValue;
    }/*  w ww  .  j a  v a2 s  .  com*/

    Node node = ((Node) formXPathExpression.evaluate(xmlDocument, XPathConstants.NODE));
    if (node == null) {
        return null;
    }

    Node attributeNode = node.getAttributes().getNamedItem(attributeName);
    if (attributeNode == null) {
        return null;
    }

    return attributeNode.getNodeValue();
}

---

From source file:pl.edu.icm.cermine.pubmed.PubmedXMLGenerator.java

public BxDocument generateTrueViz(InputStream pdfStream, InputStream nlmStream)
        throws AnalysisException, ParserConfigurationException, SAXException, IOException,
        XPathExpressionException, TransformationException {
    XPath xpath = XPathFactory.newInstance().newXPath();
    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    dbf.setValidating(false);/*w ww  .j av  a  2s  . c  o  m*/
    dbf.setFeature("http://xml.org/sax/features/namespaces", false);
    dbf.setFeature("http://xml.org/sax/features/validation", false);
    dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
    dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);

    DocumentBuilder builder = dbf.newDocumentBuilder();
    Document domDoc = builder.parse(nlmStream);

    PdfBxStructureExtractor structureExtractor = new PdfBxStructureExtractor();
    BxDocument bxDoc = structureExtractor.extractStructure(pdfStream);
    Integer bxDocLen = bxDoc.asZones().size();

    SmartHashMap entries = new SmartHashMap();

    //abstract
    Node abstractNode = (Node) xpath.evaluate("/article/front/article-meta/abstract", domDoc,
            XPathConstants.NODE);
    String abstractString = XMLTools.extractTextFromNode(abstractNode);
    entries.putIf("Abstract " + abstractString, BxZoneLabel.MET_ABSTRACT);
    entries.putIf("Abstract", BxZoneLabel.MET_ABSTRACT);

    //title
    String titleString = (String) xpath.evaluate("/article/front/article-meta/title-group/article-title",
            domDoc, XPathConstants.STRING);
    entries.putIf(titleString, BxZoneLabel.MET_TITLE);
    String subtitleString = (String) xpath.evaluate("/article/front/article-meta/title-group/article-subtitle",
            domDoc, XPathConstants.STRING);
    entries.putIf(subtitleString, BxZoneLabel.MET_TITLE);
    //journal title
    String journalTitleString = (String) xpath.evaluate("/article/front/journal-meta/journal-title", domDoc,
            XPathConstants.STRING);
    if (journalTitleString == null || journalTitleString.isEmpty()) {
        journalTitleString = (String) xpath.evaluate(
                "/article/front/journal-meta/journal-title-group/journal-title", domDoc, XPathConstants.STRING);
    }
    entries.putIf(journalTitleString, BxZoneLabel.MET_BIB_INFO);

    //journal publisher
    String journalPublisherString = (String) xpath
            .evaluate("/article/front/journal-meta/publisher/publisher-name", domDoc, XPathConstants.STRING);
    entries.putIf(journalPublisherString, BxZoneLabel.MET_BIB_INFO);
    String journalPublisherIdString = (String) xpath.evaluate(
            "/article/front/journal-meta/journal-id[@journal-id-type='publisher-id']", domDoc,
            XPathConstants.STRING);
    entries.putIf(journalPublisherIdString, BxZoneLabel.MET_BIB_INFO);

    //journal issn
    String journalISSNString = (String) xpath.evaluate("/article/front/journal-meta/issn", domDoc,
            XPathConstants.STRING);
    entries.putIf(journalISSNString, BxZoneLabel.MET_BIB_INFO);

    //copyright/permissions
    String permissionsString = XMLTools.extractTextFromNode(
            (Node) xpath.evaluate("/article/front/article-meta/permissions", domDoc, XPathConstants.NODE));
    entries.putIf(permissionsString, BxZoneLabel.MET_COPYRIGHT);

    //license
    Node licenseNode = (Node) xpath.evaluate("/article/front/article-meta/license", domDoc,
            XPathConstants.NODE);
    String licenseString = (String) XMLTools.extractTextFromNode(licenseNode);
    entries.putIf(licenseString, BxZoneLabel.MET_COPYRIGHT);

    //article type
    NodeList articleTypeNodes = (NodeList) xpath.evaluate("/article/@article-type", domDoc,
            XPathConstants.NODESET);
    List<String> articleTypeStrings = XMLTools.extractTextAsList(articleTypeNodes);
    Node articleTypeNode = (Node) xpath.evaluate("/article/front/article-meta/article-categories/subj-group",
            domDoc, XPathConstants.NODE);
    articleTypeStrings.add(XMLTools.extractTextFromNode(articleTypeNode));

    entries.putIf(articleTypeStrings, BxZoneLabel.MET_TYPE);

    //received date
    List<String> receivedDate = XMLTools.extractChildrenAsTextList((Node) xpath.evaluate(
            "/article/front/article-meta/history/date[@date-type='received']", domDoc, XPathConstants.NODE));
    if (!receivedDate.isEmpty() && receivedDate.size() >= 3) {
        for (String date : StringTools.produceDates(receivedDate)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }

    //accepted date
    List<String> acceptedDate = XMLTools.extractChildrenAsTextList((Node) xpath.evaluate(
            "/article/front/article-meta/history/date[@date-type='accepted']", domDoc, XPathConstants.NODE));
    if (!acceptedDate.isEmpty() && acceptedDate.size() >= 3) {
        for (String date : StringTools.produceDates(acceptedDate)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }

    //publication date
    List<String> pubdateString;
    if (((NodeList) xpath.evaluate("/article/front/article-meta/pub-date", domDoc, XPathConstants.NODESET))
            .getLength() > 1) {
        Node pubdateNode = (Node) xpath.evaluate("/article/front/article-meta/pub-date[@pub-type='epub']",
                domDoc, XPathConstants.NODE);
        pubdateString = XMLTools.extractChildrenAsTextList(pubdateNode);
    } else {
        Node pubdateNode = (Node) xpath.evaluate("/article/front/article-meta/pub-date[@pub-type='collection']",
                domDoc, XPathConstants.NODE);
        pubdateString = XMLTools.extractChildrenAsTextList(pubdateNode);
    }
    if (pubdateString != null && pubdateString.size() >= 3) {
        for (String date : StringTools.produceDates(pubdateString)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }
    pubdateString.clear();
    if (((NodeList) xpath.evaluate("/article/front/article-meta/pub-date", domDoc, XPathConstants.NODESET))
            .getLength() > 1) {
        Node pubdateNode = (Node) xpath.evaluate("/article/front/article-meta/pub-date[@pub-type='ppub']",
                domDoc, XPathConstants.NODE);
        pubdateString = XMLTools.extractChildrenAsTextList(pubdateNode);
    }
    if (pubdateString != null && pubdateString.size() >= 3) {
        for (String date : StringTools.produceDates(pubdateString)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }

    String extLink = (String) xpath.evaluate(
            "/article/front/article-meta/ext-link[@ext-link-type='uri']/xlink:href", domDoc,
            XPathConstants.STRING);
    printlnVerbose(extLink);
    entries.putIf(extLink, BxZoneLabel.MET_ACCESS_DATA);
    //keywords
    Node keywordsNode = (Node) xpath.evaluate("/article/front/article-meta/kwd-group", domDoc,
            XPathConstants.NODE);
    String keywordsString = XMLTools.extractTextFromNode(keywordsNode);
    entries.putIf(keywordsString, BxZoneLabel.MET_KEYWORDS);

    //DOI
    String doiString = (String) xpath.evaluate("/article/front/article-meta/article-id[@pub-id-type='doi']",
            domDoc, XPathConstants.STRING);
    entries.putIf("DOI " + doiString, BxZoneLabel.MET_BIB_INFO);

    //volume
    String volumeString = (String) xpath.evaluate("/article/front/article-meta/volume", domDoc,
            XPathConstants.STRING);
    entries.putIf("volume " + volumeString, BxZoneLabel.MET_BIB_INFO);
    entries.putIf("vol " + volumeString, BxZoneLabel.MET_BIB_INFO);

    //issue
    String issueString = (String) xpath.evaluate("/article/front/article-meta/issue", domDoc,
            XPathConstants.STRING);
    entries.putIf("number " + issueString, BxZoneLabel.MET_BIB_INFO);

    entries.putIf("journal", BxZoneLabel.MET_BIB_INFO);
    entries.putIf("et al", BxZoneLabel.MET_BIB_INFO);

    List<String> authorNames = new ArrayList<String>();
    List<String> authorEmails = new ArrayList<String>();
    List<String> authorAffiliations = new ArrayList<String>();
    List<String> editors = new ArrayList<String>();

    //pages
    String fPage = (String) xpath.evaluate("/article/front/article-meta/fpage", domDoc, XPathConstants.STRING);
    String lPage = (String) xpath.evaluate("/article/front/article-meta/lpage", domDoc, XPathConstants.STRING);
    entries.putIf("pages " + fPage + " " + lPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf("pp " + fPage + " " + lPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf(fPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf(lPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf(lPage, BxZoneLabel.OTH_PAGE_NUMBER);
    entries.putIf(lPage, BxZoneLabel.OTH_PAGE_NUMBER);
    try {
        int f = Integer.valueOf(fPage);
        int l = Integer.valueOf(lPage);
        while (f < l) {
            f++;
            entries.putIf(String.valueOf(f), BxZoneLabel.OTH_PAGE_NUMBER);
        }
    } catch (NumberFormatException ex) {
    }

    entries.putIf("page of", BxZoneLabel.OTH_PAGE_NUMBER);

    //editors
    NodeList editorNodes = (NodeList) xpath.evaluate(
            "/article/front/article-meta/contrib-group/contrib[@contrib-type='editor']", domDoc,
            XPathConstants.NODESET);
    for (int nodeIdx = 0; nodeIdx < editorNodes.getLength(); ++nodeIdx) {
        String editorString = XMLTools.extractTextFromNode(editorNodes.item(nodeIdx));
        editors.add(editorString);
    }
    entries.putIf(StringTools.joinStrings(editors), BxZoneLabel.MET_EDITOR);

    NodeList authorsResult = (NodeList) xpath.evaluate(
            "/article/front/article-meta/contrib-group/contrib[@contrib-type='author']", domDoc,
            XPathConstants.NODESET);
    for (int nodeIdx = 0; nodeIdx < authorsResult.getLength(); ++nodeIdx) {
        Node curNode = authorsResult.item(nodeIdx);
        //author names
        String name = (String) xpath.evaluate("name/given-names", curNode, XPathConstants.STRING);
        String surname = (String) xpath.evaluate("name/surname", curNode, XPathConstants.STRING);
        //author affiliation
        List<String> aff = XMLTools.extractTextAsList((NodeList) xpath
                .evaluate("/article/front/article-meta/contrib-group/aff", domDoc, XPathConstants.NODESET));

        //author correspondence
        String email;
        try {
            email = (String) xpath.evaluate("address/email", curNode, XPathConstants.STRING);
        } catch (XPathExpressionException e) {
            email = "";
        }
        if (email.isEmpty()) {
            try {
                email = (String) xpath.evaluate("email", curNode, XPathConstants.STRING);
            } catch (XPathExpressionException e) {
                //yaaay, probably there is no e-mail at all! => do nothing
            }
        }
        if (!email.isEmpty()) {
            authorEmails.add(email);
        }
        if (!aff.isEmpty()) {
            authorAffiliations.addAll(aff);
        }
        authorNames.add(name + " " + surname);
    }
    entries.putIf(StringTools.joinStrings(authorNames), BxZoneLabel.MET_AUTHOR);

    //authors' affiliations
    NodeList affNodes = (NodeList) xpath.evaluate("/article/front/article-meta/aff", domDoc,
            XPathConstants.NODESET);
    authorAffiliations.addAll(XMLTools.extractTextAsList(affNodes));
    entries.putIf(authorAffiliations, BxZoneLabel.MET_AFFILIATION);

    //correspondence again
    NodeList correspNodes = (NodeList) xpath.evaluate("/article/front/article-meta/author-notes/corresp",
            domDoc, XPathConstants.NODESET);
    authorEmails.add(XMLTools.extractTextFromNodes(correspNodes));
    entries.putIf(authorEmails, BxZoneLabel.MET_CORRESPONDENCE);

    //author notes
    Node notesNode = (Node) xpath.evaluate("/article/front/article-meta/author-notes/corresp/fn", domDoc,
            XPathConstants.NODE);
    String notesString = XMLTools.extractTextFromNode(notesNode);
    entries.putIf(notesString, BxZoneLabel.MET_CORRESPONDENCE);
    notesString = XMLTools
            .extractTextFromNode((Node) xpath.evaluate("/article/back/notes", domDoc, XPathConstants.NODE));

    //article body
    NodeList paragraphNodes = (NodeList) xpath.evaluate("/article/body//p", domDoc, XPathConstants.NODESET);
    List<String> paragraphStrings = XMLTools.extractTextAsList(paragraphNodes);
    entries.putIf(paragraphStrings, BxZoneLabel.BODY_CONTENT);

    NodeList appNodes = (NodeList) xpath.evaluate("/article/back/app-group//p", domDoc, XPathConstants.NODESET);
    String appStrings = XMLTools.extractTextFromNodes(appNodes);
    entries.putIf(appStrings, BxZoneLabel.BODY_CONTENT);

    //section titles
    NodeList sectionTitleNodes = (NodeList) xpath.evaluate("/article/body//title", domDoc,
            XPathConstants.NODESET);
    List<String> sectionTitles = XMLTools.extractTextAsList(sectionTitleNodes);
    entries.putIf(sectionTitles, BxZoneLabel.BODY_CONTENT);

    NodeList appTitleNodes = (NodeList) xpath.evaluate("/article/back/app-group//title", domDoc,
            XPathConstants.NODESET);
    List<String> appTitles = XMLTools.extractTextAsList(appTitleNodes);
    entries.putIf(appTitles, BxZoneLabel.BODY_CONTENT);

    //figures
    NodeList figureNodes = (NodeList) xpath.evaluate("/article/floats-wrap//fig", domDoc,
            XPathConstants.NODESET);
    List<String> figureStrings = XMLTools.extractTextAsList(figureNodes);

    figureNodes = (NodeList) xpath.evaluate("/article/floats-group//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    figureNodes = (NodeList) xpath.evaluate("/article/back//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    figureNodes = (NodeList) xpath.evaluate("/article/body//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    figureNodes = (NodeList) xpath.evaluate("/article/back/app-group//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    entries.putIf(figureStrings, BxZoneLabel.BODY_FIGURE);

    //tables
    List<String> tableCaptions = new ArrayList<String>();
    List<String> tableBodies = new ArrayList<String>();
    List<String> tableFootnotes = new ArrayList<String>();
    //tableNodes
    NodeList tableNodes = (NodeList) xpath.evaluate("/article//table-wrap", domDoc, XPathConstants.NODESET);

    for (Integer nodeIdx = 0; nodeIdx < tableNodes.getLength(); ++nodeIdx) {
        Node tableNode = tableNodes.item(nodeIdx);

        String caption = (String) xpath.evaluate("caption", tableNode, XPathConstants.STRING);
        tableCaptions.add(caption);

        String body = XMLTools
                .extractTextFromNode((Node) xpath.evaluate("table", tableNode, XPathConstants.NODE));
        tableBodies.add(body);

        List<String> footnotes = XMLTools.extractTextAsList(
                (NodeList) xpath.evaluate("table-wrap-foot/fn", tableNode, XPathConstants.NODESET));
        tableFootnotes.addAll(footnotes);

        entries.putIf(caption, BxZoneLabel.BODY_TABLE);
        entries.putIf(body, BxZoneLabel.BODY_TABLE);
        entries.putIf(footnotes, BxZoneLabel.BODY_TABLE);
    }

    //financial disclosure
    String financialDisclosure = XMLTools.extractTextFromNode((Node) xpath
            .evaluate("/article//fn[@fn-type='financial-disclosure']", domDoc, XPathConstants.NODE));
    entries.putIf(financialDisclosure, BxZoneLabel.BODY_ACKNOWLEDGMENT);

    //conflict
    String conflictString = XMLTools.extractTextFromNode(
            (Node) xpath.evaluate("/article//fn[@fn-type='conflict']", domDoc, XPathConstants.NODE));
    entries.putIf(conflictString, BxZoneLabel.BODY_CONFLICT_STMT);

    //copyright
    String copyrightString = XMLTools.extractTextFromNode((Node) xpath.evaluate(
            "/article/front/article-meta/permissions/copyright-statement", domDoc, XPathConstants.NODE));
    entries.putIf(copyrightString, BxZoneLabel.MET_COPYRIGHT);

    //acknowledgment
    String acknowledgement = XMLTools
            .extractTextFromNode((Node) xpath.evaluate("/article/back/ack", domDoc, XPathConstants.NODE));
    entries.putIf(acknowledgement, BxZoneLabel.BODY_ACKNOWLEDGMENT);

    acknowledgement = XMLTools.extractTextFromNode(
            (Node) xpath.evaluate("/article/back/fn-group/fn", domDoc, XPathConstants.NODE));
    entries.putIf(acknowledgement, BxZoneLabel.BODY_CONFLICT_STMT);

    //glossary
    String glossary = XMLTools
            .extractTextFromNode((Node) xpath.evaluate("/article/back/glossary", domDoc, XPathConstants.NODE));
    entries.putIf(glossary, BxZoneLabel.BODY_GLOSSARY);

    //formula
    NodeList formulaNodes = (NodeList) xpath.evaluate("/article/body//disp-formula", domDoc,
            XPathConstants.NODESET);
    for (int nodeIdx = 0; nodeIdx < formulaNodes.getLength(); ++nodeIdx) {
        Node curFormulaNode = formulaNodes.item(nodeIdx);
        String label = (String) xpath.evaluate("label", curFormulaNode);
        entries.putIf(label, BxZoneLabel.BODY_EQUATION);

        NodeList curNodeChildren = curFormulaNode.getChildNodes();
        List<String> formulaParts = new ArrayList<String>();
        for (int childIdx = 0; childIdx < curNodeChildren.getLength(); ++childIdx) {
            Node curChild = curNodeChildren.item(childIdx);
            if (curChild.getNodeName().equals("label")) {
                continue;
            }
            formulaParts.add(XMLTools.extractTextFromNode(curChild));
        }
        entries.putIf(StringTools.joinStrings(formulaParts), BxZoneLabel.BODY_EQUATION);
    }

    //references
    List<String> refStrings = new ArrayList<String>();
    Node refParentNode = (Node) xpath.evaluate("/article/back/ref-list", domDoc, XPathConstants.NODE);
    if (refParentNode != null) {
        for (Integer refIdx = 0; refIdx < refParentNode.getChildNodes().getLength(); ++refIdx) {
            refStrings.add(XMLTools.extractTextFromNode(refParentNode.getChildNodes().item(refIdx)));
        }
    }
    entries.putIf(StringTools.joinStrings(refStrings), BxZoneLabel.REFERENCES);
    entries.put("references", BxZoneLabel.REFERENCES);

    Set<String> allBibInfos = new HashSet<String>();
    for (Entry<String, BxZoneLabel> entry : entries.entrySet()) {
        if (BxZoneLabel.MET_BIB_INFO.equals(entry.getValue())) {
            allBibInfos.addAll(Arrays.asList(entry.getKey().split(" ")));
        }
    }
    entries.put(StringUtils.join(allBibInfos, " "), BxZoneLabel.MET_BIB_INFO);

    printlnVerbose("journalTitle: " + journalTitleString);
    printlnVerbose("journalPublisher: " + journalPublisherString);
    printlnVerbose("journalISSNPublisher: " + journalISSNString);

    printlnVerbose("articleType: " + articleTypeStrings);
    printlnVerbose("received: " + receivedDate);
    printlnVerbose("accepted: " + acceptedDate);
    printlnVerbose("pubdate: " + pubdateString);
    printlnVerbose("permissions: " + permissionsString);
    printlnVerbose("license: " + licenseString);

    printlnVerbose("title: " + titleString);
    printlnVerbose("abstract: " + abstractString);

    printlnVerbose("authorEmails: " + authorEmails);
    printlnVerbose("authorNames: " + authorNames);
    printlnVerbose("authorAff: " + authorAffiliations);
    printlnVerbose("authorNotes: " + notesString);
    printlnVerbose("editor: " + editors);

    printlnVerbose("keywords: " + keywordsString);
    printlnVerbose("DOI: " + doiString);
    printlnVerbose("volume: " + volumeString);
    printlnVerbose("issue: " + issueString);
    printlnVerbose("financial dis.: " + financialDisclosure);

    printlnVerbose("paragraphs: " + paragraphStrings);
    printlnVerbose("section titles: " + sectionTitles);

    printlnVerbose("tableBodies: " + tableBodies);
    printlnVerbose("tableCaptions: " + tableCaptions);
    printlnVerbose("tableFootnotes: " + tableFootnotes);

    printlnVerbose("figures: " + figureStrings);
    printlnVerbose("acknowledgement: " + acknowledgement);

    printlnVerbose("ref: " + refStrings.size() + " " + refStrings);

    SmithWatermanDistance smith = new SmithWatermanDistance(.1, 0.1);
    CosineDistance cos = new CosineDistance();

    //index: (zone,entry)
    List<List<LabelTrio>> swLabelSim = new ArrayList<List<LabelTrio>>(bxDocLen);
    List<List<LabelTrio>> cosLabProb = new ArrayList<List<LabelTrio>>(bxDocLen);
    for (Integer i = 0; i < bxDocLen; ++i) {
        swLabelSim.add(new ArrayList<LabelTrio>());
        cosLabProb.add(new ArrayList<LabelTrio>());
    }

    //iterate over entries
    for (Entry<String, BxZoneLabel> entry : entries.entrySet()) {
        List<String> entryTokens = StringTools.tokenize(entry.getKey());
        printlnVerbose("--------------------");
        printlnVerbose(entry.getValue() + " " + entry.getKey() + "\n");
        //iterate over zones
        for (Integer zoneIdx = 0; zoneIdx < bxDocLen; ++zoneIdx) {
            BxZone curZone = bxDoc.asZones().get(zoneIdx);
            List<String> zoneTokens = StringTools.tokenize(StringTools
                    .removeOrphantSpaces(StringTools.cleanLigatures(curZone.toText().toLowerCase())));

            Double smithSim;
            Double cosSim;
            if (curZone.toText().contains("www.biomedcentral.com")) {
                //ignore
                smithSim = 0.;
                cosSim = 0.;
            } else {
                smithSim = smith.compare(entryTokens, zoneTokens);
                cosSim = cos.compare(entryTokens, zoneTokens);
            }
            printlnVerbose(smithSim + " " + bxDoc.asZones().get(zoneIdx).toText() + "\n\n");
            swLabelSim.get(zoneIdx).add(new LabelTrio(entry.getValue(), entryTokens, smithSim));
            cosLabProb.get(zoneIdx).add(new LabelTrio(entry.getValue(), entryTokens, cosSim));
        }
    }

    printlnVerbose("===========================");
    for (BxPage page : bxDoc.getPages()) {
        for (BxZone zone : page.getZones()) {
            Integer zoneIdx = bxDoc.asZones().indexOf(zone);
            BxZone curZone = bxDoc.asZones().get(zoneIdx);
            String zoneText = StringTools.removeOrphantSpaces(curZone.toText().toLowerCase());
            List<String> zoneTokens = StringTools.tokenize(zoneText);
            Boolean valueSet = false;

            Collections.sort(swLabelSim.get(zoneIdx), new Comparator<LabelTrio>() {

                @Override
                public int compare(LabelTrio t1, LabelTrio t2) {
                    Double simDif = t1.alignment / t1.entryTokens.size() - t2.alignment / t2.entryTokens.size();
                    if (Math.abs(simDif) < 0.0001) {
                        return t2.entryTokens.size() - t1.entryTokens.size();
                    }
                    if (simDif > 0) {
                        return 1;
                    } else {
                        return -1;
                    }
                }
            });
            Collections.reverse(swLabelSim.get(zoneIdx));

            List<String> entryTokens = swLabelSim.get(zoneIdx).get(0).entryTokens;
            if (Math.max(zoneTokens.size(), entryTokens.size()) > 0
                    && Math.min(zoneTokens.size(), entryTokens.size())
                            / Math.max(zoneTokens.size(), (double) entryTokens.size()) > 0.7
                    && swLabelSim.get(zoneIdx).get(0).alignment / entryTokens.size() > 0.7) {
                curZone.setLabel(swLabelSim.get(zoneIdx).get(0).label);
                valueSet = true;
                printVerbose("0 ");
            }

            if (!valueSet) {
                Collections.sort(swLabelSim.get(zoneIdx), new Comparator<LabelTrio>() {

                    @Override
                    public int compare(LabelTrio t1, LabelTrio t2) {
                        Double simDif = t1.alignment - t2.alignment;
                        if (Math.abs(simDif) < 0.0001) {
                            return t2.entryTokens.size() - t1.entryTokens.size();
                        }
                        if (simDif > 0) {
                            return 1;
                        } else {
                            return -1;
                        }
                    }
                });
                Collections.reverse(swLabelSim.get(zoneIdx));
                printlnVerbose("-->" + swLabelSim.get(zoneIdx).get(0).alignment / zoneTokens.size());
                if (swLabelSim.get(zoneIdx).get(0).alignment / zoneTokens.size() > 0.5) {
                    curZone.setLabel(swLabelSim.get(zoneIdx).get(0).label);
                    valueSet = true;
                    printVerbose("1 ");
                }
            }

            if (!valueSet) {
                Map<BxZoneLabel, Double> cumulated = new EnumMap<BxZoneLabel, Double>(BxZoneLabel.class);
                for (LabelTrio trio : swLabelSim.get(zoneIdx)) {
                    if (cumulated.containsKey(trio.label)) {
                        cumulated.put(trio.label, cumulated.get(trio.label)
                                + trio.alignment / Math.max(zoneTokens.size(), trio.entryTokens.size()));
                    } else {
                        cumulated.put(trio.label,
                                trio.alignment / Math.max(zoneTokens.size(), trio.entryTokens.size()));
                    }
                }
                Double max = Double.NEGATIVE_INFINITY;
                BxZoneLabel bestLabel = null;
                for (Entry<BxZoneLabel, Double> entry : cumulated.entrySet()) {
                    if (entry.getValue() > max) {
                        max = entry.getValue();
                        bestLabel = entry.getKey();
                    }
                }
                if (max >= 0.5) {
                    curZone.setLabel(bestLabel);
                    printVerbose("2 ");
                    valueSet = true;
                }
            }

            if (!valueSet) {
                Collections.sort(swLabelSim.get(zoneIdx), new Comparator<LabelTrio>() {

                    @Override
                    public int compare(LabelTrio t1, LabelTrio t2) {
                        Double simDif = t1.alignment / t1.entryTokens.size()
                                - t2.alignment / t2.entryTokens.size();
                        if (Math.abs(simDif) < 0.001) {
                            return t2.entryTokens.size() - t1.entryTokens.size();
                        }
                        if (simDif > 0) {
                            return 1;
                        } else {
                            return -1;
                        }
                    }
                });
                Collections.reverse(swLabelSim.get(zoneIdx));
                List<LabelTrio> l = swLabelSim.get(zoneIdx);

                BxZoneLabel best = null;
                int bestScore = 0;
                for (LabelTrio lt : l) {
                    int i = 0;
                    for (String zt : zoneTokens) {
                        if (lt.entryTokens.contains(zt)) {
                            i++;
                        }
                    }
                    if (i > bestScore && i > 1) {
                        best = lt.label;
                        bestScore = i;
                    }
                }
                if (best != null) {
                    curZone.setLabel(best);
                    valueSet = true;
                } else {
                    for (LabelTrio lt : l) {
                        int i = 0;
                        for (String zt : zoneTokens) {
                            for (String j : lt.entryTokens) {
                                if (zt.replaceAll("[^0-9a-zA-Z,;\\.!\\?]", "")
                                        .equals(j.replaceAll("[^0-9a-zA-Z,;\\.!\\?]", ""))) {
                                    i++;
                                    break;
                                }
                            }
                        }
                        if (i > bestScore && i > 1) {
                            best = lt.label;
                            bestScore = i;
                        }
                    }
                }

                if (best != null) {
                    curZone.setLabel(best);
                    valueSet = true;
                }
            }
            if (!valueSet) {
                curZone.setLabel(null);
            }
            printlnVerbose(zone.getLabel() + " " + zone.toText() + "\n");
        }
        Map<BxZone, ZoneLocaliser> zoneLocMap = new HashMap<BxZone, ZoneLocaliser>();
        Set<BxZone> unlabeledZones = new HashSet<BxZone>();
        for (BxZone zone : page.getZones()) {
            if (zone.getLabel() == null) {
                unlabeledZones.add(zone);
                zoneLocMap.put(zone, new ZoneLocaliser(zone));
            }
        }
        Integer lastNumberOfUnlabeledZones;
        do {
            lastNumberOfUnlabeledZones = unlabeledZones.size();
            infereLabels(unlabeledZones, zoneLocMap);
            infereLabels(unlabeledZones, zoneLocMap);
        } while (lastNumberOfUnlabeledZones != unlabeledZones.size());
    }
    printlnVerbose("=>=>=>=>=>=>=>=>=>=>=>=>=>=");

    return bxDoc;
}

---

From source file:pl.edu.icm.cermine.pubmed.RuleBasedPubmedXMLGenerator.java

public BxDocument generateTrueViz(InputStream pdfStream, InputStream nlmStream)
        throws AnalysisException, ParserConfigurationException, SAXException, IOException,
        XPathExpressionException, TransformationException {
    XPath xpath = XPathFactory.newInstance().newXPath();
    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    dbf.setValidating(false);//w  w  w. j a  va  2 s. c  om
    dbf.setFeature("http://xml.org/sax/features/namespaces", false);
    dbf.setFeature("http://xml.org/sax/features/validation", false);
    dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
    dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);

    DocumentBuilder builder = dbf.newDocumentBuilder();
    Document domDoc = builder.parse(nlmStream);

    TrueVizToBxDocumentReader reader = new TrueVizToBxDocumentReader();
    Reader r = new InputStreamReader(pdfStream);
    BxDocument bxDoc = new BxDocument().setPages(reader.read(r));

    List<BxZone> zones = Lists.newArrayList(bxDoc.asZones());

    Integer bxDocLen = zones.size();

    SmartHashMap entries = new SmartHashMap();

    //abstract
    Node abstractNode = (Node) xpath.evaluate("/article/front/article-meta/abstract", domDoc,
            XPathConstants.NODE);
    String abstractString = XMLTools.extractTextFromNode(abstractNode);
    entries.putIf("Abstract " + abstractString, BxZoneLabel.MET_ABSTRACT);
    entries.putIf("Abstract", BxZoneLabel.MET_ABSTRACT);

    //title
    String titleString = (String) xpath.evaluate("/article/front/article-meta/title-group/article-title",
            domDoc, XPathConstants.STRING);
    entries.putIf(titleString, BxZoneLabel.MET_TITLE);
    String subtitleString = (String) xpath.evaluate("/article/front/article-meta/title-group/article-subtitle",
            domDoc, XPathConstants.STRING);
    entries.putIf(subtitleString, BxZoneLabel.MET_TITLE);
    //journal title
    String journalTitleString = (String) xpath.evaluate("/article/front/journal-meta/journal-title", domDoc,
            XPathConstants.STRING);
    if (journalTitleString == null || journalTitleString.isEmpty()) {
        journalTitleString = (String) xpath.evaluate(
                "/article/front/journal-meta/journal-title-group/journal-title", domDoc, XPathConstants.STRING);
    }
    entries.putIf(journalTitleString, BxZoneLabel.MET_BIB_INFO);

    //journal publisher
    String journalPublisherString = (String) xpath
            .evaluate("/article/front/journal-meta/publisher/publisher-name", domDoc, XPathConstants.STRING);
    entries.putIf(journalPublisherString, BxZoneLabel.MET_BIB_INFO);
    String journalPublisherIdString = (String) xpath.evaluate(
            "/article/front/journal-meta/journal-id[@journal-id-type='publisher-id']", domDoc,
            XPathConstants.STRING);
    entries.putIf(journalPublisherIdString, BxZoneLabel.MET_BIB_INFO);

    //journal issn
    String journalISSNString = (String) xpath.evaluate("/article/front/journal-meta/issn", domDoc,
            XPathConstants.STRING);
    entries.putIf(journalISSNString, BxZoneLabel.MET_BIB_INFO);

    //copyright/permissions
    String permissionsString = XMLTools.extractTextFromNode(
            (Node) xpath.evaluate("/article/front/article-meta/permissions", domDoc, XPathConstants.NODE));
    entries.putIf(permissionsString, BxZoneLabel.MET_COPYRIGHT);

    //license
    Node licenseNode = (Node) xpath.evaluate("/article/front/article-meta/license", domDoc,
            XPathConstants.NODE);
    String licenseString = (String) XMLTools.extractTextFromNode(licenseNode);
    entries.putIf(licenseString, BxZoneLabel.MET_COPYRIGHT);

    //article type
    NodeList articleTypeNodes = (NodeList) xpath.evaluate("/article/@article-type", domDoc,
            XPathConstants.NODESET);
    List<String> articleTypeStrings = XMLTools.extractTextAsList(articleTypeNodes);
    Node articleTypeNode = (Node) xpath.evaluate("/article/front/article-meta/article-categories/subj-group",
            domDoc, XPathConstants.NODE);
    articleTypeStrings.add(XMLTools.extractTextFromNode(articleTypeNode));

    entries.putIf(articleTypeStrings, BxZoneLabel.MET_TYPE);

    //received date
    List<String> receivedDate = XMLTools.extractChildrenAsTextList((Node) xpath.evaluate(
            "/article/front/article-meta/history/date[@date-type='received']", domDoc, XPathConstants.NODE));
    if (!receivedDate.isEmpty() && receivedDate.size() >= 3) {
        for (String date : TextUtils.produceDates(receivedDate)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }

    //accepted date
    List<String> acceptedDate = XMLTools.extractChildrenAsTextList((Node) xpath.evaluate(
            "/article/front/article-meta/history/date[@date-type='accepted']", domDoc, XPathConstants.NODE));
    if (!acceptedDate.isEmpty() && acceptedDate.size() >= 3) {
        for (String date : TextUtils.produceDates(acceptedDate)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }

    //publication date
    List<String> pubdateString;
    if (((NodeList) xpath.evaluate("/article/front/article-meta/pub-date", domDoc, XPathConstants.NODESET))
            .getLength() > 1) {
        Node pubdateNode = (Node) xpath.evaluate("/article/front/article-meta/pub-date[@pub-type='epub']",
                domDoc, XPathConstants.NODE);
        pubdateString = XMLTools.extractChildrenAsTextList(pubdateNode);
    } else {
        Node pubdateNode = (Node) xpath.evaluate("/article/front/article-meta/pub-date[@pub-type='collection']",
                domDoc, XPathConstants.NODE);
        pubdateString = XMLTools.extractChildrenAsTextList(pubdateNode);
    }
    if (pubdateString != null && pubdateString.size() >= 3) {
        for (String date : TextUtils.produceDates(pubdateString)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }
    pubdateString.clear();
    if (((NodeList) xpath.evaluate("/article/front/article-meta/pub-date", domDoc, XPathConstants.NODESET))
            .getLength() > 1) {
        Node pubdateNode = (Node) xpath.evaluate("/article/front/article-meta/pub-date[@pub-type='ppub']",
                domDoc, XPathConstants.NODE);
        pubdateString = XMLTools.extractChildrenAsTextList(pubdateNode);
    }
    if (pubdateString != null && pubdateString.size() >= 3) {
        for (String date : TextUtils.produceDates(pubdateString)) {
            entries.putIf(date, BxZoneLabel.MET_DATES);
        }
    }

    String extLink = (String) xpath.evaluate(
            "/article/front/article-meta/ext-link[@ext-link-type='uri']/xlink:href", domDoc,
            XPathConstants.STRING);
    printlnVerbose(extLink);
    entries.putIf(extLink, BxZoneLabel.MET_ACCESS_DATA);
    //keywords
    Node keywordsNode = (Node) xpath.evaluate("/article/front/article-meta/kwd-group", domDoc,
            XPathConstants.NODE);
    String keywordsString = XMLTools.extractTextFromNode(keywordsNode);
    entries.putIf(keywordsString, BxZoneLabel.MET_KEYWORDS);

    //DOI
    String doiString = (String) xpath.evaluate("/article/front/article-meta/article-id[@pub-id-type='doi']",
            domDoc, XPathConstants.STRING);
    entries.putIf("DOI " + doiString, BxZoneLabel.MET_BIB_INFO);

    //volume
    String volumeString = (String) xpath.evaluate("/article/front/article-meta/volume", domDoc,
            XPathConstants.STRING);
    entries.putIf("volume " + volumeString, BxZoneLabel.MET_BIB_INFO);
    entries.putIf("vol " + volumeString, BxZoneLabel.MET_BIB_INFO);

    //issue
    String issueString = (String) xpath.evaluate("/article/front/article-meta/issue", domDoc,
            XPathConstants.STRING);
    entries.putIf("number " + issueString, BxZoneLabel.MET_BIB_INFO);

    entries.putIf("journal", BxZoneLabel.MET_BIB_INFO);
    entries.putIf("et al", BxZoneLabel.MET_BIB_INFO);

    List<String> authorNames = new ArrayList<String>();
    List<String> authorEmails = new ArrayList<String>();
    List<String> authorAffiliations = new ArrayList<String>();
    List<String> editors = new ArrayList<String>();

    //pages
    String fPage = (String) xpath.evaluate("/article/front/article-meta/fpage", domDoc, XPathConstants.STRING);
    String lPage = (String) xpath.evaluate("/article/front/article-meta/lpage", domDoc, XPathConstants.STRING);
    entries.putIf("pages " + fPage + " " + lPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf("pp " + fPage + " " + lPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf(fPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf(lPage, BxZoneLabel.MET_BIB_INFO);
    entries.putIf(lPage, BxZoneLabel.OTH_PAGE_NUMBER);
    entries.putIf(lPage, BxZoneLabel.OTH_PAGE_NUMBER);
    try {
        int f = Integer.valueOf(fPage);
        int l = Integer.valueOf(lPage);
        while (f < l) {
            f++;
            entries.putIf(String.valueOf(f), BxZoneLabel.OTH_PAGE_NUMBER);
        }
    } catch (NumberFormatException ex) {
    }

    entries.putIf("page of", BxZoneLabel.OTH_PAGE_NUMBER);

    //editors
    NodeList editorNodes = (NodeList) xpath.evaluate(
            "/article/front/article-meta/contrib-group/contrib[@contrib-type='editor']", domDoc,
            XPathConstants.NODESET);
    for (int nodeIdx = 0; nodeIdx < editorNodes.getLength(); ++nodeIdx) {
        String editorString = XMLTools.extractTextFromNode(editorNodes.item(nodeIdx));
        editors.add(editorString);
    }
    entries.putIf(TextUtils.joinStrings(editors), BxZoneLabel.MET_EDITOR);

    NodeList authorsResult = (NodeList) xpath.evaluate(
            "/article/front/article-meta/contrib-group/contrib[@contrib-type='author']", domDoc,
            XPathConstants.NODESET);
    for (int nodeIdx = 0; nodeIdx < authorsResult.getLength(); ++nodeIdx) {
        Node curNode = authorsResult.item(nodeIdx);
        //author names
        String name = (String) xpath.evaluate("name/given-names", curNode, XPathConstants.STRING);
        String surname = (String) xpath.evaluate("name/surname", curNode, XPathConstants.STRING);
        //author affiliation
        List<String> aff = XMLTools.extractTextAsList((NodeList) xpath
                .evaluate("/article/front/article-meta/contrib-group/aff", domDoc, XPathConstants.NODESET));

        //author correspondence
        String email;
        try {
            email = (String) xpath.evaluate("address/email", curNode, XPathConstants.STRING);
        } catch (XPathExpressionException e) {
            email = "";
        }
        if (email.isEmpty()) {
            try {
                email = (String) xpath.evaluate("email", curNode, XPathConstants.STRING);
            } catch (XPathExpressionException e) {
                //yaaay, probably there is no e-mail at all! => do nothing
            }
        }
        if (!email.isEmpty()) {
            authorEmails.add(email);
        }
        if (!aff.isEmpty()) {
            authorAffiliations.addAll(aff);
        }
        authorNames.add(name + " " + surname);
    }
    entries.putIf(TextUtils.joinStrings(authorNames), BxZoneLabel.MET_AUTHOR);

    //authors' affiliations
    NodeList affNodes = (NodeList) xpath.evaluate("/article/front/article-meta/aff", domDoc,
            XPathConstants.NODESET);
    authorAffiliations.addAll(XMLTools.extractTextAsList(affNodes));
    entries.putIf(authorAffiliations, BxZoneLabel.MET_AFFILIATION);

    //correspondence again
    NodeList correspNodes = (NodeList) xpath.evaluate("/article/front/article-meta/author-notes/corresp",
            domDoc, XPathConstants.NODESET);
    authorEmails.add(XMLTools.extractTextFromNodes(correspNodes));
    entries.putIf(authorEmails, BxZoneLabel.MET_CORRESPONDENCE);

    //author notes
    Node notesNode = (Node) xpath.evaluate("/article/front/article-meta/author-notes/corresp/fn", domDoc,
            XPathConstants.NODE);
    String notesString = XMLTools.extractTextFromNode(notesNode);
    entries.putIf(notesString, BxZoneLabel.MET_CORRESPONDENCE);
    notesString = XMLTools
            .extractTextFromNode((Node) xpath.evaluate("/article/back/notes", domDoc, XPathConstants.NODE));

    //article body
    NodeList paragraphNodes = (NodeList) xpath.evaluate("/article/body//p", domDoc, XPathConstants.NODESET);
    List<String> paragraphStrings = XMLTools.extractTextAsList(paragraphNodes);
    entries.putIf(paragraphStrings, BxZoneLabel.BODY_CONTENT);

    NodeList appNodes = (NodeList) xpath.evaluate("/article/back/app-group//p", domDoc, XPathConstants.NODESET);
    String appStrings = XMLTools.extractTextFromNodes(appNodes);
    entries.putIf(appStrings, BxZoneLabel.BODY_CONTENT);

    //section titles
    NodeList sectionTitleNodes = (NodeList) xpath.evaluate("/article/body//title", domDoc,
            XPathConstants.NODESET);
    List<String> sectionTitles = XMLTools.extractTextAsList(sectionTitleNodes);
    entries.putIf(sectionTitles, BxZoneLabel.BODY_CONTENT);

    NodeList appTitleNodes = (NodeList) xpath.evaluate("/article/back/app-group//title", domDoc,
            XPathConstants.NODESET);
    List<String> appTitles = XMLTools.extractTextAsList(appTitleNodes);
    entries.putIf(appTitles, BxZoneLabel.BODY_CONTENT);

    //figures
    NodeList figureNodes = (NodeList) xpath.evaluate("/article/floats-wrap//fig", domDoc,
            XPathConstants.NODESET);
    List<String> figureStrings = XMLTools.extractTextAsList(figureNodes);

    figureNodes = (NodeList) xpath.evaluate("/article/floats-group//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    figureNodes = (NodeList) xpath.evaluate("/article/back//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    figureNodes = (NodeList) xpath.evaluate("/article/body//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    figureNodes = (NodeList) xpath.evaluate("/article/back/app-group//fig", domDoc, XPathConstants.NODESET);
    figureStrings.addAll(XMLTools.extractTextAsList(figureNodes));

    entries.putIf(figureStrings, BxZoneLabel.BODY_FIGURE);

    //tables
    List<String> tableCaptions = new ArrayList<String>();
    List<String> tableBodies = new ArrayList<String>();
    List<String> tableFootnotes = new ArrayList<String>();
    //tableNodes
    NodeList tableNodes = (NodeList) xpath.evaluate("/article//table-wrap", domDoc, XPathConstants.NODESET);

    for (Integer nodeIdx = 0; nodeIdx < tableNodes.getLength(); ++nodeIdx) {
        Node tableNode = tableNodes.item(nodeIdx);

        String caption = (String) xpath.evaluate("caption", tableNode, XPathConstants.STRING);
        tableCaptions.add(caption);

        String body = XMLTools
                .extractTextFromNode((Node) xpath.evaluate("table", tableNode, XPathConstants.NODE));
        tableBodies.add(body);

        List<String> footnotes = XMLTools.extractTextAsList(
                (NodeList) xpath.evaluate("table-wrap-foot/fn", tableNode, XPathConstants.NODESET));
        tableFootnotes.addAll(footnotes);

        entries.putIf(caption, BxZoneLabel.BODY_TABLE);
        entries.putIf(body, BxZoneLabel.BODY_TABLE);
        entries.putIf(footnotes, BxZoneLabel.BODY_TABLE);
    }

    //financial disclosure
    String financialDisclosure = XMLTools.extractTextFromNode((Node) xpath
            .evaluate("/article//fn[@fn-type='financial-disclosure']", domDoc, XPathConstants.NODE));
    entries.putIf(financialDisclosure, BxZoneLabel.BODY_ACKNOWLEDGMENT);

    //conflict
    String conflictString = XMLTools.extractTextFromNode(
            (Node) xpath.evaluate("/article//fn[@fn-type='conflict']", domDoc, XPathConstants.NODE));
    entries.putIf(conflictString, BxZoneLabel.BODY_CONFLICT_STMT);

    //copyright
    String copyrightString = XMLTools.extractTextFromNode((Node) xpath.evaluate(
            "/article/front/article-meta/permissions/copyright-statement", domDoc, XPathConstants.NODE));
    entries.putIf(copyrightString, BxZoneLabel.MET_COPYRIGHT);

    //acknowledgment
    String acknowledgement = XMLTools
            .extractTextFromNode((Node) xpath.evaluate("/article/back/ack", domDoc, XPathConstants.NODE));
    entries.putIf(acknowledgement, BxZoneLabel.BODY_ACKNOWLEDGMENT);

    acknowledgement = XMLTools.extractTextFromNode(
            (Node) xpath.evaluate("/article/back/fn-group/fn", domDoc, XPathConstants.NODE));
    entries.putIf(acknowledgement, BxZoneLabel.BODY_CONFLICT_STMT);

    //glossary
    String glossary = XMLTools
            .extractTextFromNode((Node) xpath.evaluate("/article/back/glossary", domDoc, XPathConstants.NODE));
    entries.putIf(glossary, BxZoneLabel.BODY_GLOSSARY);

    //formula
    NodeList formulaNodes = (NodeList) xpath.evaluate("/article/body//disp-formula", domDoc,
            XPathConstants.NODESET);
    for (int nodeIdx = 0; nodeIdx < formulaNodes.getLength(); ++nodeIdx) {
        Node curFormulaNode = formulaNodes.item(nodeIdx);
        String label = (String) xpath.evaluate("label", curFormulaNode);
        entries.putIf(label, BxZoneLabel.BODY_EQUATION);

        NodeList curNodeChildren = curFormulaNode.getChildNodes();
        List<String> formulaParts = new ArrayList<String>();
        for (int childIdx = 0; childIdx < curNodeChildren.getLength(); ++childIdx) {
            Node curChild = curNodeChildren.item(childIdx);
            if (curChild.getNodeName().equals("label")) {
                continue;
            }
            formulaParts.add(XMLTools.extractTextFromNode(curChild));
        }
        entries.putIf(TextUtils.joinStrings(formulaParts), BxZoneLabel.BODY_EQUATION);
    }

    //references
    List<String> refStrings = new ArrayList<String>();
    Node refParentNode = (Node) xpath.evaluate("/article/back/ref-list", domDoc, XPathConstants.NODE);
    if (refParentNode != null) {
        for (Integer refIdx = 0; refIdx < refParentNode.getChildNodes().getLength(); ++refIdx) {
            refStrings.add(XMLTools.extractTextFromNode(refParentNode.getChildNodes().item(refIdx)));
        }
    }
    entries.putIf(TextUtils.joinStrings(refStrings), BxZoneLabel.REFERENCES);
    entries.put("references", BxZoneLabel.REFERENCES);

    Set<String> allBibInfos = new HashSet<String>();
    for (Entry<String, BxZoneLabel> entry : entries.entrySet()) {
        if (BxZoneLabel.MET_BIB_INFO.equals(entry.getValue())) {
            allBibInfos.addAll(Arrays.asList(entry.getKey().split(" ")));
        }
    }
    entries.put(StringUtils.join(allBibInfos, " "), BxZoneLabel.MET_BIB_INFO);

    printlnVerbose("journalTitle: " + journalTitleString);
    printlnVerbose("journalPublisher: " + journalPublisherString);
    printlnVerbose("journalISSNPublisher: " + journalISSNString);

    printlnVerbose("articleType: " + articleTypeStrings);
    printlnVerbose("received: " + receivedDate);
    printlnVerbose("accepted: " + acceptedDate);
    printlnVerbose("pubdate: " + pubdateString);
    printlnVerbose("permissions: " + permissionsString);
    printlnVerbose("license: " + licenseString);

    printlnVerbose("title: " + titleString);
    printlnVerbose("abstract: " + abstractString);

    printlnVerbose("authorEmails: " + authorEmails);
    printlnVerbose("authorNames: " + authorNames);
    printlnVerbose("authorAff: " + authorAffiliations);
    printlnVerbose("authorNotes: " + notesString);
    printlnVerbose("editor: " + editors);

    printlnVerbose("keywords: " + keywordsString);
    printlnVerbose("DOI: " + doiString);
    printlnVerbose("volume: " + volumeString);
    printlnVerbose("issue: " + issueString);
    printlnVerbose("financial dis.: " + financialDisclosure);

    printlnVerbose("paragraphs: " + paragraphStrings);
    printlnVerbose("section titles: " + sectionTitles);

    printlnVerbose("tableBodies: " + tableBodies);
    printlnVerbose("tableCaptions: " + tableCaptions);
    printlnVerbose("tableFootnotes: " + tableFootnotes);

    printlnVerbose("figures: " + figureStrings);
    printlnVerbose("acknowledgement: " + acknowledgement);

    printlnVerbose("ref: " + refStrings.size() + " " + refStrings);

    SmithWatermanDistance smith = new SmithWatermanDistance(.1, 0.1);
    CosineDistance cos = new CosineDistance();

    //index: (zone,entry)
    List<List<LabelTrio>> swLabelSim = new ArrayList<List<LabelTrio>>(bxDocLen);
    List<List<LabelTrio>> cosLabProb = new ArrayList<List<LabelTrio>>(bxDocLen);
    for (Integer i = 0; i < bxDocLen; ++i) {
        swLabelSim.add(new ArrayList<LabelTrio>());
        cosLabProb.add(new ArrayList<LabelTrio>());
    }

    //iterate over entries
    for (Entry<String, BxZoneLabel> entry : entries.entrySet()) {
        List<String> entryTokens = TextUtils.tokenize(entry.getKey());
        printlnVerbose("--------------------");
        printlnVerbose(entry.getValue() + " " + entry.getKey() + "\n");
        //iterate over zones
        for (Integer zoneIdx = 0; zoneIdx < bxDocLen; ++zoneIdx) {
            BxZone curZone = zones.get(zoneIdx);
            List<String> zoneTokens = TextUtils.tokenize(
                    TextUtils.removeOrphantSpaces(TextUtils.cleanLigatures(curZone.toText().toLowerCase())));

            Double smithSim;
            Double cosSim;
            if (curZone.toText().contains("www.biomedcentral.com")) {
                //ignore
                smithSim = 0.;
                cosSim = 0.;
            } else {
                smithSim = smith.compare(entryTokens, zoneTokens);
                cosSim = cos.compare(entryTokens, zoneTokens);
            }
            printlnVerbose(smithSim + " " + zones.get(zoneIdx).toText() + "\n\n");
            swLabelSim.get(zoneIdx).add(new LabelTrio(entry.getValue(), entryTokens, smithSim));
            cosLabProb.get(zoneIdx).add(new LabelTrio(entry.getValue(), entryTokens, cosSim));
        }
    }

    for (BxPage pp : bxDoc) {

        boolean changed = true;
        while (changed) {

            changed = false;
            boolean wasIntro = false;

            for (BxZone z : pp) {
                BxZoneLabel orig = z.getLabel();
                int i = zones.indexOf(z);

                double titleAl = 0;
                double authorAl = 0;
                List<LabelTrio> sims = swLabelSim.get(i);
                for (LabelTrio t : sims) {
                    if (t.label.equals(BxZoneLabel.MET_TITLE)) {
                        titleAl = t.alignment / t.entryTokens.size();
                    }
                    if (t.label.equals(BxZoneLabel.MET_AUTHOR)) {
                        authorAl = t.alignment / t.entryTokens.size();
                    }
                }

                String text = ContentCleaner.cleanAllAndBreaks(z.toText()).toLowerCase();
                int linesCount = z.childrenCount();
                int pageIdx = Lists.newArrayList(bxDoc).indexOf(z.getParent());
                BxLine firstLine = z.getFirstChild();

                if (pageIdx == 0
                        && (z.getLabel().equals(BxZoneLabel.MET_TITLE)
                                || z.getLabel().equals(BxZoneLabel.BODY_CONTENT))
                        && titleAl >= 0.7 && authorAl >= 0.4) {
                    z.setLabel(BxZoneLabel.MET_TITLE_AUTHOR);
                }
                if (linesCount == 2 && text.contains("page") && text.contains("of")
                        && text.contains("page number not for")) {
                    z.setLabel(BxZoneLabel.OTH_PAGE_NUMBER);
                }
                if (linesCount == 1 && (text.contains("page number not for")
                        || (text.contains("page") && text.contains("of")))) {
                    z.setLabel(BxZoneLabel.OTH_PAGE_NUMBER);
                }

                if (pageIdx == 0 && !z.getLabel().isOfCategory(BxZoneLabelCategory.CAT_METADATA)
                        && linesCount < 11 && (text.contains("department") || text.contains("university"))) {
                    z.setLabel(BxZoneLabel.MET_AFFILIATION);
                }
                if (pageIdx > 0 && z.getLabel().equals(BxZoneLabel.MET_COPYRIGHT)) {
                    z.setLabel(BxZoneLabel.MET_BIB_INFO);
                }
                if (linesCount < 5 && firstLine.toText().length() < 11
                        && firstLine.toText().startsWith("Figure")
                        && z.getLabel().equals(BxZoneLabel.BODY_CONTENT)) {
                    z.setLabel(BxZoneLabel.BODY_FIGURE);
                }
                if (pageIdx > 0 && z.getLabel().equals(BxZoneLabel.MET_TITLE)) {
                    z.setLabel(BxZoneLabel.BODY_CONTENT);
                }
                if (pageIdx > 0 && z.hasPrev() && z.hasNext()
                        && (z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                                || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN)
                                || z.getLabel().equals(BxZoneLabel.MET_DATES)
                                || z.getLabel().equals(BxZoneLabel.BODY_ACKNOWLEDGMENT))
                        && (z.getPrev().getLabel().equals(BxZoneLabel.BODY_TABLE)
                                || z.getNext().getLabel().equals(BxZoneLabel.BODY_TABLE))
                        && z.getWidth() < 100) {
                    if (z.getPrev().getLabel().equals(BxZoneLabel.BODY_TABLE)
                            && z.getNext().getLabel().equals(BxZoneLabel.BODY_TABLE)) {
                        z.setLabel(BxZoneLabel.BODY_TABLE);
                    }
                    if (z.getPrev().getLabel().equals(BxZoneLabel.BODY_TABLE)) {
                        double prevMX = z.getPrev().getX() + z.getPrev().getWidth() / 2;
                        double prevMY = z.getPrev().getY() + z.getPrev().getHeight() / 2;
                        double zMX = z.getX() + z.getWidth() / 2;
                        double zMY = z.getY() + z.getHeight() / 2;
                        if (Math.abs(prevMX - zMX) < 200 && Math.abs(prevMY - zMY) < 200) {
                            z.setLabel(BxZoneLabel.BODY_TABLE);
                        }
                    }
                    if (z.getNext().getLabel().equals(BxZoneLabel.BODY_TABLE)) {
                        double prevMX = z.getNext().getX() + z.getNext().getWidth() / 2;
                        double prevMY = z.getNext().getY() + z.getNext().getHeight() / 2;
                        double zMX = z.getX() + z.getWidth() / 2;
                        double zMY = z.getY() + z.getHeight() / 2;
                        if (Math.abs(prevMX - zMX) < 200 && Math.abs(prevMY - zMY) < 200) {
                            z.setLabel(BxZoneLabel.BODY_TABLE);
                        }
                    }
                }
                if (pageIdx > 1 && (z.getLabel().equals(BxZoneLabel.MET_AFFILIATION)
                        || z.getLabel().equals(BxZoneLabel.MET_ABSTRACT))) {
                    z.setLabel(BxZoneLabel.BODY_CONTENT);
                }
                if (pageIdx == 0 && linesCount < 10 && (text.startsWith("citation:")
                        || text.contains(" volume ") || text.contains("vol\\. ") || text.contains("doi"))) {
                    z.setLabel(BxZoneLabel.MET_BIB_INFO);
                }
                if (pageIdx == 0 && (text.startsWith("editor:") || text.startsWith("academic editor:"))) {
                    z.setLabel(BxZoneLabel.MET_EDITOR);
                }
                if (pageIdx == 0 && text.startsWith("copyright:")) {
                    z.setLabel(BxZoneLabel.MET_COPYRIGHT);
                }
                if (z.getLabel().equals(BxZoneLabel.MET_DATES) && text.contains("volume")
                        && text.contains("issue")) {
                    z.setLabel(BxZoneLabel.MET_BIB_INFO);
                }
                if ((z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        || z.getLabel().equals(BxZoneLabel.MET_AUTHOR)
                        || z.getLabel().equals(BxZoneLabel.REFERENCES)
                        || z.getLabel().equals(BxZoneLabel.MET_DATES)) && linesCount < 6
                        && (z.getY() < 100 || z.getParent().getHeight() - z.getY() < 100)) {
                    BxPage p = z.getParent();
                    if (pageIdx > 0) {
                        BxPage prevPage = p.getPrev();
                        for (BxZone z1 : prevPage) {
                            if (z1.toText().replaceAll("[^a-zA-Z]", "")
                                    .equals(z.toText().replaceAll("[^a-zA-Z]", ""))
                                    && Math.abs(z1.getY() - z.getY()) < 10) {
                                z.setLabel(BxZoneLabel.MET_BIB_INFO);
                            }
                        }
                    }
                    if (pageIdx < bxDoc.childrenCount() - 1) {
                        BxPage nextPage = p.getNext();
                        for (BxZone z1 : nextPage) {
                            if (z1.toText().replaceAll("[^a-zA-Z]", "")
                                    .equals(z.toText().replaceAll("[^a-zA-Z]", ""))
                                    && Math.abs(z1.getY() - z.getY()) < 10) {
                                z.setLabel(BxZoneLabel.MET_BIB_INFO);
                            }
                        }
                    }
                    if (pageIdx > 1) {
                        BxPage prevPage = p.getPrev().getPrev();
                        for (BxZone z1 : prevPage) {
                            if (z1.toText().replaceAll("[^a-zA-Z]", "")
                                    .equals(z.toText().replaceAll("[^a-zA-Z]", ""))
                                    && Math.abs(z1.getY() - z.getY()) < 10) {
                                z.setLabel(BxZoneLabel.MET_BIB_INFO);
                            }
                        }
                    }
                    if (pageIdx < bxDoc.childrenCount() - 2) {
                        BxPage nextPage = p.getNext().getNext();
                        for (BxZone z1 : nextPage) {
                            if (z1.toText().replaceAll("[^a-zA-Z]", "")
                                    .equals(z.toText().replaceAll("[^a-zA-Z]", ""))
                                    && Math.abs(z1.getY() - z.getY()) < 10) {
                                z.setLabel(BxZoneLabel.MET_BIB_INFO);
                            }
                        }
                    }
                }
                if ((z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN)
                        || z.getLabel().equals(BxZoneLabel.MET_BIB_INFO)
                        || z.getLabel().equals(BxZoneLabel.REFERENCES)) && text.matches("d?[0-9]+")
                        && text.length() <= 4
                        && (z.getY() < 100 || z.getParent().getHeight() - z.getY() < 100)) {
                    z.setLabel(BxZoneLabel.OTH_PAGE_NUMBER);
                }
                if (text.equals("acknowledgments")) {
                    z.setLabel(BxZoneLabel.BODY_ACKNOWLEDGMENT);
                }
                if (text.startsWith("introduction") && z.hasPrev()
                        && !z.getPrev().toText().toLowerCase().equals("abstract")) {
                    wasIntro = true;
                }
                if (wasIntro && z.getLabel().equals(BxZoneLabel.MET_ABSTRACT)) {
                    z.setLabel(BxZoneLabel.BODY_CONTENT);
                }

                if (pageIdx == 0 && z.getLabel().equals(BxZoneLabel.REFERENCES) && !text.equals("references")
                        && !(z.hasPrev() && z.getPrev().toText().toLowerCase().equals("references"))) {
                    z.setLabel(BxZoneLabel.MET_BIB_INFO);
                }
                if (z.getLabel().equals(BxZoneLabel.REFERENCES) && linesCount < 10
                        && !text.matches(".*[1-2][09][0-9][0-9].*") && z.hasNext() && z.hasPrev()
                        && z.getPrev().getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        && z.getNext().getLabel().equals(BxZoneLabel.BODY_CONTENT)) {
                    z.setLabel(BxZoneLabel.BODY_CONTENT);
                }
                if (z.getLabel().equals(BxZoneLabel.MET_ABSTRACT) && z.hasPrev()
                        && z.getPrev().getLabel().equals(BxZoneLabel.MET_ABSTRACT)
                        && z.getX() + 10 < z.getPrev().getX() && z.getWidth() * 2 < pp.getWidth()) {
                    z.setLabel(BxZoneLabel.BODY_CONTENT);
                }
                if (z.getLabel().equals(BxZoneLabel.MET_ABSTRACT) && z.hasPrev()
                        && z.getPrev().getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        && !text.startsWith("abstract") && z.getWidth() * 2 < pp.getWidth()) {
                    z.setLabel(BxZoneLabel.BODY_CONTENT);
                }
                if ((z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN)) && z.hasPrev()
                        && z.getPrev().getLabel().equals(BxZoneLabel.REFERENCES)
                        && (text.matches("[1-9][0-9]?[0-9]?\\.?")
                                || text.matches(".*[1-2][0-9][0-9][0-9].*"))) {
                    z.setLabel(BxZoneLabel.REFERENCES);
                }
                if ((z.getLabel().equals(BxZoneLabel.REFERENCES)
                        || z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN))
                        && (text.startsWith("doi") || text.startsWith("cite this article"))) {
                    z.setLabel(BxZoneLabel.MET_BIB_INFO);
                }
                if ((z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN))
                        && firstLine.toText().toLowerCase().equals("author details")) {
                    z.setLabel(BxZoneLabel.MET_AFFILIATION);
                }
                if ((z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN))
                        && (firstLine.toText().toLowerCase().equals("acknowledgments")
                                || firstLine.toText().toLowerCase().equals("acknowledgements"))) {
                    z.setLabel(BxZoneLabel.BODY_ACKNOWLEDGMENT);
                }
                if (z.getLabel().equals(BxZoneLabel.MET_TITLE) && z.getY() * 2 > pp.getHeight()) {
                    z.setLabel(BxZoneLabel.BODY_CONTENT);
                }
                if ((z.getY() < 100 || z.getParent().getHeight() - z.getY() < 100)
                        && text.matches("sup-[0-9][0-9]?")) {
                    z.setLabel(BxZoneLabel.OTH_PAGE_NUMBER);
                }
                if ((z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                        || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN))
                        && firstLine.toText().toLowerCase().equals("references")) {
                    z.setLabel(BxZoneLabel.REFERENCES);
                }
                if (z.getLabel().equals(BxZoneLabel.BODY_CONTENT) && (firstLine.toText()
                        .matches("F[iI][gG][uU][rR][eE] [0-9IV][0-9IV]?[0-9IV]?[\\.:] [A-Z].*")
                        || firstLine.toText().matches("F[iI][gG]\\. [0-9IV][0-9IV]?[0-9IV]?[\\.:] [A-Z].*")
                        || firstLine.toText().matches("F[iI][gG][uU][rR][eE] [0-9IV][0-9IV]?[0-9IV]?\\.")
                        || firstLine.toText().matches("F[iI][gG]\\. [0-9IV][0-9IV]?[0-9IV]?\\.")
                        || firstLine.toText().matches("F[iI][gG][uU][rR][eE] [0-9IV][0-9IV]?[0-9IV]?")
                        || firstLine.toText().matches("F[iI][gG]\\. [0-9IV][0-9IV]?[0-9IV]?"))) {
                    z.setLabel(BxZoneLabel.BODY_FIGURE);
                }
                if (z.getLabel().equals(BxZoneLabel.BODY_CONTENT) && (firstLine.toText()
                        .matches("T[aA][bB][lL][eE] [0-9IV][0-9IV]?[0-9IV]?[\\.:] [A-Z].*")
                        || firstLine.toText().matches("T[aA][bB][lL][eE] [0-9IV][0-9IV]?[0-9IV]?\\.?"))) {
                    z.setLabel(BxZoneLabel.BODY_TABLE);
                }
                if (z.getLabel().equals(BxZoneLabel.BODY_ACKNOWLEDGMENT)
                        && text.contains("this article is distributed")) {
                    z.setLabel(BxZoneLabel.MET_COPYRIGHT);
                }

                if (pageIdx == 0 && !z.getLabel().isOfCategory(BxZoneLabelCategory.CAT_METADATA)
                        && text.contains("journal")) {
                    z.setLabel(BxZoneLabel.MET_BIB_INFO);
                }

                if (pageIdx == 0 && !z.getLabel().isOfCategory(BxZoneLabelCategory.CAT_METADATA)
                        && text.contains("correspondence")) {
                    z.setLabel(BxZoneLabel.MET_CORRESPONDENCE);
                }
                if (pageIdx == 0
                        && (z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                                || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN))
                        && text.contains("accepted") && text.contains("published")) {
                    z.setLabel(BxZoneLabel.MET_DATES);
                }

                if (pageIdx == 0 && linesCount < 10
                        && (z.getLabel().equals(BxZoneLabel.BODY_CONTENT)
                                || z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN))
                        && z.hasPrev() && z.getY() - z.getHeight() - z.getPrev().getY() < 4
                        && Math.abs(firstLine.getHeight() - z.getPrev().getFirstChild().getHeight()) < 0.5) {
                    if (!z.getPrev().getLabel().equals(BxZoneLabel.MET_KEYWORDS)) {
                        z.setLabel(z.getPrev().getLabel());
                    }
                }
                if (pageIdx == bxDoc.childrenCount() - 1 && (text.startsWith("publish with")
                        || text.contains("will be the most significant development")
                        || text.contains("disseminating the results of biomedical")
                        || text.contains("sir paul nurse") || text.contains("your research papers")
                        || text.contains("available free of charge")
                        || text.contains("peer reviewed and published")
                        || text.contains("cited in pubmed and archived")
                        || text.contains("you keep the copyright") || text.contains("submit your manuscript")
                        || text.contains("submit your next manuscript") || text.contains("online submission")
                        || text.contains("peer review") || text.contains("space constraints")
                        || text.contains("publication on acceptance") || text.contains("inclusion in pubmed")
                        || text.contains("freely available") || text.contains("publication history"))) {
                    z.setLabel(BxZoneLabel.OTH_UNKNOWN);
                }
                if (text.startsWith("funding:") || firstLine.toText().equals("Funding")) {
                    z.setLabel(BxZoneLabel.BODY_ACKNOWLEDGMENT);
                }

                if (text.startsWith("conflicts of interest") || text.startsWith("conflict of interest")
                        || text.startsWith("competing interests")
                        || (z.hasPrev() && (z.getPrev().toText().toLowerCase().equals("conflicts of interest")
                                || z.getPrev().toText().toLowerCase().equals("conflict of interest")
                                || z.getPrev().toText().toLowerCase().equals("competing interests")))) {
                    z.setLabel(BxZoneLabel.BODY_CONFLICT_STMT);
                }

                changed = changed || !orig.equals(z.getLabel());
            }

            boolean wasAuthor = false;
            for (BxZone z : pp) {
                BxZoneLabel orig = z.getLabel();

                String text = ContentCleaner.cleanAllAndBreaks(z.toText()).toLowerCase();
                if (BxZoneLabel.MET_AUTHOR.equals(z.getLabel()) && wasAuthor
                        && ((text.contains("email") && text.contains("@"))
                                || text.startsWith("correspondence"))) {
                    z.setLabel(BxZoneLabel.MET_CORRESPONDENCE);
                }

                if (BxZoneLabel.MET_AUTHOR.equals(z.getLabel())
                        || BxZoneLabel.MET_TITLE_AUTHOR.equals(z.getLabel())) {
                    wasAuthor = true;
                }
                changed = changed || !orig.equals(z.getLabel());
            }

        }
    }

    return bxDoc;
}

---

From source file:sf.net.experimaestro.connectors.OARLauncher.java

/**
 * Evaluate an XPath to a string//from  w ww.ja  v a 2s .c o  m
 */
static private String evaluateXPathToString(String expression, Document document) {
    String value;
    XPath xpath = XPathFactory.newInstance().newXPath();
    try {
        value = (String) xpath.evaluate(expression, document, XPathConstants.STRING);
    } catch (XPathExpressionException e) {
        throw new XPMRuntimeException(e, "Cannot evaluted XPath expression [%s]", xpath);
    }
    return value;
}

---

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