Example usage for org.dom4j Element elementIterator

Introduction

In this page you can find the example usage for org.dom4j Element elementIterator.

Prototype

Iterator<Element> elementIterator(QName qName);

Source Link

Document

Returns an iterator over the elements contained in this element which match the given fully qualified name.

Usage

From source file:com.flaptor.hounder.indexer.DocumentConverter.java

License:Apache License

/**
 * @todo refactor this method, is too long
 *///from w  w  w .j  a  va  2 s.c  o  m
private org.apache.lucene.document.Document processAdd(final Element e) throws IllegalDocumentException {
    // TODO: This method is too long, refactor.
    logger.debug("Processing Add");

    float documentBoost;
    Node node = e.selectSingleNode("boost");
    if (null == node) {
        documentBoost = 1.0F;
    } else {
        documentBoost = Float.parseFloat(node.getText());
        if (logger.isEnabledFor(Level.DEBUG)) {
            logger.debug("Using non-default document boost of " + documentBoost);
        }
    }
    if (Float.isNaN(documentBoost) || Float.isInfinite(documentBoost) || documentBoost <= 0) {
        throw new IllegalDocumentException("Document with invalid boost (" + documentBoost + ") received.");
    }

    org.apache.lucene.document.Document ldoc = new org.apache.lucene.document.Document();
    ldoc.setBoost(documentBoost);

    // For comparison with the required fields we keep track of the added
    // fields.
    HashSet<String> providedFields = new HashSet<String>();

    //First, we add the documentId as a field under the name provided in the configuration (docIdName)
    node = e.selectSingleNode("documentId");
    if (null == node) {
        throw new IllegalDocumentException("Add document missing documentId.");
    }
    String docIdText = node.getText();
    //now we add the documentId as another field, using the name provided in the configuration (docIdName)
    Field lfield = new Field(docIdName, docIdText, Field.Store.YES, Field.Index.NOT_ANALYZED);
    ldoc.add(lfield);
    providedFields.add(docIdName);
    if (logger.isEnabledFor(Level.DEBUG)) {
        logger.debug("Writer - adding documentId field:" + docIdName
                + ", index: true, store: true, token: false, text: " + docIdText);
    }
    // Now we add the regular fields
    for (Iterator iter = e.elementIterator("field"); iter.hasNext();) {
        Element field = (Element) iter.next();
        String fieldName, storedS, indexedS, tokenizedS, boostS, fieldText;
        boolean stored, tokenized, indexed;
        float boost = 1;

        fieldName = field.valueOf("@name");
        if (fieldName.equals("")) {
            throw new IllegalDocumentException("Field without name.");
        }

        //There cannot be a field with the name used to store the documentId (docIdName)
        //as it would collide with the documentId per se when saved to the lucene index.
        fieldText = field.getText();
        if (fieldName.equals(docIdName)) {
            throw new IllegalDocumentException(
                    "This document contains a field with the same name as the configured name "
                            + "to save the documentId( " + docIdName + ").");
        }

        storedS = field.valueOf("@stored");
        if (storedS.equals("")) {
            throw new IllegalDocumentException("Field without stored attribute.");
        }
        stored = Boolean.valueOf(storedS);

        indexedS = field.valueOf("@indexed");
        if (indexedS.equals("")) {
            throw new IllegalDocumentException("Field without indexed attribute.");
        }
        indexed = Boolean.valueOf(indexedS);
        //Lucene complains of an unindexed unstored field with a runtime exception
        //and it makes no sense anyway
        if (!(indexed || stored)) {
            throw new IllegalDocumentException("processAdd: unindexed unstored field \"" + fieldName + "\".");
        }

        tokenizedS = field.valueOf("@tokenized");
        if (tokenizedS.equals("")) {
            throw new IllegalDocumentException("Field without tokenized attribute.");
        }
        tokenized = Boolean.valueOf(tokenizedS);

        boostS = field.valueOf("@boost");
        if (!boostS.equals("")) {
            try {
                boost = new Float(boostS).floatValue();
            } catch (NumberFormatException exception) {
                throw new IllegalDocumentException(
                        "Unparsable boost value (" + boostS + ") for field  \"" + fieldName + "\".");
            }
        }

        // Now we add the fields. Depending on the parameter stored, indexed
        // and tokenized we call a different field constructor.
        lfield = null;
        Field.Index indexType = (indexed ? (tokenized ? Field.Index.ANALYZED : Field.Index.NOT_ANALYZED)
                : Field.Index.NO);
        Field.Store storeType;
        if (!stored) {
            storeType = Field.Store.NO;
        } else {
            if (compressedFields.contains(fieldName)) {
                storeType = Field.Store.COMPRESS;
            } else {
                storeType = Field.Store.YES;
            }
        }
        lfield = new Field(fieldName, fieldText, storeType, indexType);

        lfield.setBoost(boost);
        providedFields.add(fieldName); // for later comparison with the required fields

        ldoc.add(lfield);
        if (logger.isEnabledFor(Level.DEBUG)) {
            logger.debug("Writer - adding field:" + fieldName + ", index:" + indexed + ", store:" + stored
                    + ", token:" + tokenized + " ,boost: " + boost + ", text: " + fieldText);
        }
    } // for  (field iterator)

    HashSet<String> providedPayloads = new HashSet<String>();
    // Now we add the payloads
    for (Iterator iter = e.elementIterator("payload"); iter.hasNext();) {
        Element payload = (Element) iter.next();

        String payloadName = payload.valueOf("@name");
        if (payloadName.equals("")) {
            throw new IllegalDocumentException("Payload without name.");
        }
        providedPayloads.add(payloadName);
        try {
            Long payloadValue = Long.parseLong(payload.getText());
            ldoc.add(new Field(payloadName, new FixedValueTokenStream(payloadName, payloadValue)));
            logger.debug("Adding payload \"" + payloadName + "\" to document \"" + docIdText + "\" with value "
                    + payloadValue);
        } catch (NumberFormatException nfe) {
            throw new IllegalDocumentException(
                    "Writer - while parsing Long payload \"" + payloadName + "\": " + nfe.getMessage());
        }
    }

    // no we test for the presence of the required fields
    if (!providedFields.containsAll(requiredFields) || !providedPayloads.containsAll(requiredPayloads)) {
        StringBuffer sb = new StringBuffer();
        sb.append("Document with missing required fields or payloads. Ignoring addition.\n");
        sb.append("Provided fields are: \n");
        for (String field : providedFields) {
            sb.append(field + "\n");
        }
        sb.append("The fields required are: \n");
        for (String field : requiredFields) {
            sb.append(field + "\n");
        }

        sb.append("Provided payloads are: \n");
        for (String payload : providedPayloads) {
            sb.append(payload + "\n");
        }
        sb.append("Required payloads are: \n");
        for (String payload : requiredPayloads) {
            sb.append(payload + "\n");
        }
        throw new IllegalDocumentException(sb.toString());
    }
    return ldoc;
}

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From source file:com.flaptor.util.DomUtil.java

License:Apache License

/**
 * Returns the first attribute's value of the first ocurrence of an element.
 * @param root the root element of the dom
 * @param elementName the name of the element
 * @param attribName the name of the attribute
 * @return the value of the first element, or null if not found.
 * The first matching element is considered only.
 */// www .j a va2s  . c o m
public static String getAttributeValue(final Element root, final String elementName, final String attribName) {
    String value = null;
    Element element;
    Iterator elementIterator = root.elementIterator(elementName);
    while (elementIterator.hasNext()) {
        element = (Element) elementIterator.next();
        value = element.attributeValue(attribName);
    }
    return value;
}

---

From source file:com.flaptor.util.DomUtil.java

License:Apache License

/**
 * Returns the text of the first ocurrence of an element.
 * @param root the root element of the dom
 * @param elementName the name of the element
 * @return the value of the text of the first element, or null if not found.
 * The first matching element is considered only.
 *///from w w  w  . j a v  a  2s  .  c  o  m
public static String getElementText(final Element root, final String elementName) {
    String value = null;
    Element element;
    Iterator elementIterator = root.elementIterator(elementName);
    while (elementIterator.hasNext()) {
        element = (Element) elementIterator.next();
        value = element.getText();
        if (value != null)
            break;
    }
    return value;
}

---

From source file:com.flaptor.util.DomUtil.java

License:Apache License

/**
 * Returns the first attribute's value of the first ocurrence of an element.
 * @param root the root element of the dom
 * @param elementName the name of the element
 * @param attribName the name of the attribute
 * @return the value of the first element, or null if not found.
 * The first matching element is considered only.
 *///from ww w . ja  v a  2s  . c o m
public static void replaceElementValueByName(final Element root, final String elementName, final String name,
        final String value) {
    Element element;
    Iterator elementIterator = root.elementIterator(elementName);
    while (elementIterator.hasNext()) {
        element = (Element) elementIterator.next();
        if (name.equals(element.attributeValue("name"))) {
            element.setText(DomUtil.filterXml(value));
            break;
        }
    }
}

---

From source file:com.github.autoprimer3.AutoPrimer3Config.java

License:Open Source License

public LinkedHashSet<String> readTableFile(Document dasXml) throws DocumentException {
    LinkedHashSet<String> tables = new LinkedHashSet<>();
    Element root = dasXml.getRootElement();
    Element gff = root.element("GFF");
    Element segment = gff.element("SEGMENT");
    for (Iterator i = segment.elementIterator("TYPE"); i.hasNext();) {
        Element type = (Element) i.next();
        Attribute id = type.attribute("id");
        tables.add(id.getValue());//from  w  w  w.  j a  v a2s . c om
    }
    return tables;
}

---

From source file:com.github.autoprimer3.AutoPrimer3Config.java

License:Open Source License

public LinkedHashSet<String> readTableFile(Document dasXml, String category) throws DocumentException {
    LinkedHashSet<String> tables = new LinkedHashSet<>();
    Element root = dasXml.getRootElement();
    Element gff = root.element("GFF");
    Element segment = gff.element("SEGMENT");
    for (Iterator i = segment.elementIterator("TYPE"); i.hasNext();) {
        Element type = (Element) i.next();
        Attribute id = type.attribute("id");
        Attribute cat = type.attribute("category");
        if (cat.getValue().equals(category)) {
            tables.add(id.getValue());//from   ww  w .ja  v a 2s .c o m
        }
    }
    return tables;
}

---

From source file:com.github.autoprimer3.GetUcscBuildsAndTables.java

License:Open Source License

public void readDasGenomeXmlDocument() {
    if (dasGenomeXml == null) {
        return;// www  . j  av a 2  s .co m
    }
    Element root = dasGenomeXml.getRootElement();
    for (Iterator i = root.elementIterator("DSN"); i.hasNext();) {
        Element dsn = (Element) i.next();
        Element source = dsn.element("SOURCE");
        Attribute build = source.attribute("id");
        Element mapmaster = dsn.element("MAPMASTER");
        Element desc = dsn.element("DESCRIPTION");
        buildToMapMaster.put(build.getValue(), mapmaster.getText());
        buildToDescription.put(build.getValue(), desc.getText());
    }
}

---

From source file:com.github.autoprimer3.GetUcscBuildsAndTables.java

License:Open Source License

public String retrieveSequence(String build, String chrom, Integer start, Integer end)
        throws DocumentException, MalformedURLException {
    if (buildToDescription.isEmpty()) {
        this.connectToUcsc();
    }/*  w ww .j a  v  a2s  .c  om*/
    if (!buildToMapMaster.containsKey(build)) {
        return null;
    } else {
        StringBuilder dna = new StringBuilder();
        URL genomeUrl = new URL(
                buildToMapMaster.get(build) + "/dna?segment=" + chrom + ":" + (start + 1) + "," + end);
        SAXReader reader = new SAXReader();
        Document dasXml;
        dasXml = reader.read(genomeUrl);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("SEQUENCE"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element seq = dsn.element("DNA");
            String text = seq.getText().replaceAll("\n", "");
            dna.append(text);
            //dna.append(seq.getText());
        }
        return dna.toString();

    }

}

---

From source file:com.github.autoprimer3.SequenceFromDasUcsc.java

License:Open Source License

SequenceFromDasUcsc() {//get build names and DAS urls
    try {/*from  w  ww.java 2s  .  c  o m*/
        SAXReader reader = new SAXReader();
        URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/dsn");//usa    
        //URL url = new URL("http://genome-euro.ucsc.edu/cgi-bin/das/dsn");    
        Document dasXml;
        dasXml = reader.read(url);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("DSN"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element source = dsn.element("SOURCE");
            Attribute build = source.attribute("id");
            Element mapmaster = dsn.element("MAPMASTER");
            buildToMapMaster.put(build.getValue(), mapmaster.getText());
        }
    } catch (DocumentException | MalformedURLException ex) {
        //TO DO - handle (throw) this error properly
        ex.printStackTrace();
    }
}

---

From source file:com.github.autoprimer3.SequenceFromDasUcsc.java

License:Open Source License

public String retrieveSequence(String build, String chrom, Integer start, Integer end)
        throws DocumentException, MalformedURLException {
    if (!buildToMapMaster.containsKey(build)) {
        return null;
    } else {//from   www . ja  v a  2 s  .  co m
        String chromNumber = chrom.replaceFirst("chr", "");
        int length = 0;
        URL entryPointUrl = new URL(buildToMapMaster.get(build) + "/entry_points");
        Document dasXml;
        SAXReader reader = new SAXReader();
        dasXml = reader.read(entryPointUrl);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("ENTRY_POINTS"); i.hasNext();) {
            Element dsn = (Element) i.next();
            for (Iterator j = dsn.elementIterator("SEGMENT"); j.hasNext();) {
                Element seg = (Element) j.next();
                String id = seg.attributeValue("id");
                if (id != null && id.equals(chromNumber)) {
                    String stop = seg.attributeValue("stop");
                    length = Integer.valueOf(stop);
                    break;
                }
            }
        }
        if (length > 0) {
            end = end <= length ? end : length;
        }
        StringBuilder dna = new StringBuilder();
        URL genomeUrl = new URL(
                buildToMapMaster.get(build) + "/dna?segment=" + chrom + ":" + (start + 1) + "," + end);
        dasXml = reader.read(genomeUrl);
        root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("SEQUENCE"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element seq = dsn.element("DNA");
            String text = seq.getText().replaceAll("\n", "");
            dna.append(text);
            //dna.append(seq.getText());
        }
        return dna.toString();

    }

}

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