Examples with XMLEvent javax.xml.stream.events.XMLEvent used on opensource projects

Example 81 with XMLEvent

use of javax.xml.stream.events.XMLEvent in project jvarkit by lindenb.

the class TreePackApp method parseNode.

private Node parseNode(XMLEventReader r, StartElement E, Node parent) throws XMLStreamException {
    Node node = new Node(parent);
    Attribute att = E.getAttributeByName(new QName("label"));
    node.label = (att != null ? att.getValue() : "");
    while (r.hasNext()) {
        XMLEvent evt = r.nextEvent();
        if (evt.isStartElement()) {
            QName qName = evt.asStartElement().getName();
            if (qName.getLocalPart().equals("node")) {
                Node child = parseNode(r, evt.asStartElement(), node);
                if (node.children == null)
                    node.children = new HashMap<String, Node>();
                node.children.put(node.label, child);
            } else {
                skip(r);
            }
        } else if (evt.isEndElement()) {
            if (node.children == null || node.children.isEmpty()) {
                att = E.getAttributeByName(new QName("weight"));
                if (att == null) {
                    node.weight = 1.0;
                } else {
                    node.weight = Double.parseDouble(att.getValue());
                    if (node.weight <= 0)
                        throw new XMLStreamException("bad @weight:" + node.weight, E.getLocation());
                }
            }
            return node;
        }
    }
    throw new IllegalStateException();
}

Example 82 with XMLEvent

use of javax.xml.stream.events.XMLEvent in project jvarkit by lindenb.

the class PubmedCodingLanguages method scanArticle.

private void scanArticle(PrintStream out, final String rootName, final XMLEventReader r) throws XMLStreamException, IOException {
    String article_pmid = null;
    String article_title = "";
    String article_year = null;
    String abstractText = "";
    boolean PubDate = false;
    while (r.hasNext()) {
        final XMLEvent evt = r.nextEvent();
        if (evt.isStartElement()) {
            final StartElement start = evt.asStartElement();
            final String eltName = start.getName().getLocalPart();
            if (article_pmid == null && eltName.equals("PMID")) {
                article_pmid = r.getElementText();
            } else if (article_title.isEmpty() && eltName.equals("ArticleTitle")) {
                article_title = textContent(r);
            } else if (eltName.equals("PubDate")) {
                PubDate = true;
            } else if (article_year == null && PubDate && eltName.equals("Year")) {
                article_year = r.getElementText();
            } else if (eltName.equals("Abstract")) {
                abstractText = textContent(r);
            }
        } else if (evt.isEndElement()) {
            final EndElement end = evt.asEndElement();
            final String eltName = end.getName().getLocalPart();
            if (eltName.equals("PubDate")) {
                PubDate = false;
            } else if (eltName.equals(rootName)) {
                break;
            }
        }
    }
    // end of xml read
    final String normalizedAbstract = (article_title + " " + abstractText).replace('\n', ' ').toLowerCase();
    boolean found_something = false;
    for (final ProgLanguage pg : this.languages) {
        if (this.common_only_false && !pg.isCommon())
            continue;
        final String context = pg.match(normalizedAbstract);
        if (context == null)
            continue;
        out.print(article_pmid);
        out.print('\t');
        out.print(pg.getName());
        out.print('\t');
        out.print(article_title);
        out.print('\t');
        out.print(article_year);
        out.print('\t');
        out.print(context);
        out.println();
        found_something = true;
    }
    if (!found_something && (normalizedAbstract.contains("programming language") || normalizedAbstract.contains("written in"))) {
        LOG.warning("Cannot get information in:\t" + normalizedAbstract);
    }
}

Example 83 with XMLEvent

use of javax.xml.stream.events.XMLEvent in project jvarkit by lindenb.

the class PubmedFilterJS method doWork.

@Override
public int doWork(List<String> args) {
    final String inputName = oneFileOrNull(args);
    CompiledScript compiledScript = null;
    Unmarshaller unmarshaller;
    Marshaller marshaller;
    try {
        compiledScript = this.compileJavascript(this.javascriptExpr, this.javascriptFile);
        JAXBContext jc = JAXBContext.newInstance("gov.nih.nlm.ncbi.pubmed");
        unmarshaller = jc.createUnmarshaller();
        marshaller = jc.createMarshaller();
        XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
        xmlInputFactory.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.FALSE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_REPLACING_ENTITY_REFERENCES, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, Boolean.FALSE);
        xmlInputFactory.setXMLResolver(new XMLResolver() {

            @Override
            public Object resolveEntity(String publicID, String systemID, String baseURI, String namespace) throws XMLStreamException {
                LOG.info("ignoring " + publicID + " " + baseURI + " " + namespace);
                return new ByteArrayInputStream(new byte[0]);
            }
        });
        marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
        marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
        PrintWriter pw = openFileOrStdoutAsPrintWriter(this.outFile);
        XMLOutputFactory xof = XMLOutputFactory.newFactory();
        XMLEventWriter w = xof.createXMLEventWriter(pw);
        StreamSource src = null;
        if (inputName == null) {
            LOG.info("Reading stdin");
            src = new StreamSource(System.in);
        } else {
            LOG.info("Reading file");
            src = new StreamSource(new File(inputName));
        }
        XMLEventReader r = xmlInputFactory.createXMLEventReader(src);
        XMLEventFactory eventFactory = XMLEventFactory.newFactory();
        SimpleBindings bindings = new SimpleBindings();
        long nArticles = 0L;
        while (r.hasNext()) {
            XMLEvent evt = r.peek();
            switch(evt.getEventType()) {
                case XMLEvent.START_ELEMENT:
                    {
                        String localName = evt.asStartElement().getName().getLocalPart();
                        Object article = null;
                        JAXBElement<?> jaxbElement = null;
                        if (localName.equals("PubmedArticle")) {
                            jaxbElement = unmarshaller.unmarshal(r, PubmedArticle.class);
                            article = jaxbElement.getValue();
                        } else /* no more in the latest dtd else if(localName.equals("PubmedBookArticle"))
							{
							jaxbElement= unmarshaller.unmarshal(r,PubmedBookArticle.class);
							article=jaxbElement.getValue();
							} */
                        {
                            w.add(r.nextEvent());
                            break;
                        }
                        if (article != null) {
                            bindings.put("article", article);
                            bindings.put("index", nArticles++);
                            if (!this.evalJavaScriptBoolean(compiledScript, bindings)) {
                                break;
                            }
                            marshaller.marshal(jaxbElement, w);
                            w.add(eventFactory.createCharacters("\n"));
                        }
                        break;
                    }
                default:
                    {
                        w.add(r.nextEvent());
                        break;
                    }
            }
            r.close();
        }
        w.flush();
        w.close();
        pw.flush();
        pw.close();
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
    }
}

Example 84 with XMLEvent

use of javax.xml.stream.events.XMLEvent in project jvarkit by lindenb.

the class SkipXmlElements method doWork.

@Override
public int doWork(List<String> args) {
    String scriptExpr = null;
    File scriptFile = null;
    CompiledScript compiledScript = null;
    try {
        compiledScript = super.compileJavascript(scriptExpr, scriptFile);
        XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
        xmlInputFactory.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_REPLACING_ENTITY_REFERENCES, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, Boolean.FALSE);
        PrintWriter pw = super.openFileOrStdoutAsPrintWriter(outputFile);
        XMLOutputFactory xof = XMLOutputFactory.newFactory();
        XMLEventWriter w = xof.createXMLEventWriter(pw);
        StreamSource src = null;
        if (args.isEmpty()) {
            src = new StreamSource(stdin());
        } else if (args.size() == 1) {
            src = new StreamSource(new File(args.get(0)));
        } else {
            LOG.error("illegal.number.of.arguments");
            return -1;
        }
        XMLEventReader r = xmlInputFactory.createXMLEventReader(src);
        SimpleBindings bindings = new SimpleBindings();
        TagImpl curr = null;
        while (r.hasNext()) {
            XMLEvent evt = r.peek();
            switch(evt.getEventType()) {
                case XMLEvent.START_ELEMENT:
                    {
                        if (curr == null) {
                            curr = new TagImpl(evt.asStartElement());
                        } else {
                            TagImpl node = new TagImpl(evt.asStartElement());
                            node.parent = curr;
                            curr = node;
                        }
                        int keep = 1;
                        bindings.put("element", curr);
                        Object result = compiledScript.eval(bindings);
                        if (result == null) {
                            throw new RuntimeException("User's Script returned null");
                        } else if ((result instanceof Boolean)) {
                            keep = (Boolean.class.cast(result).booleanValue() ? 1 : 0);
                        } else if (!(result instanceof Number)) {
                            throw new RuntimeException("User's Script didn't return a number.");
                        } else // if(result instanceof Number)
                        {
                            keep = ((Number) result).intValue();
                        }
                        if (keep == KEEP_ELEMENT) {
                            w.add(r.nextEvent());
                        } else /* skip this element or keep and descendant */
                        {
                            curr = curr.parent;
                            int depth = 0;
                            while (r.hasNext()) {
                                evt = r.nextEvent();
                                switch(evt.getEventType()) {
                                    case XMLEvent.START_ELEMENT:
                                        {
                                            depth++;
                                            break;
                                        }
                                    case XMLEvent.END_ELEMENT:
                                        {
                                            depth--;
                                            break;
                                        }
                                    default:
                                        break;
                                }
                                if (keep == KEEP_ELEMENT_AND_DESCENDANTS) {
                                    w.add(evt);
                                }
                                if (depth == 0)
                                    break;
                            }
                        }
                        break;
                    }
                case XMLEvent.COMMENT:
                    {
                        // just consumme
                        r.nextEvent();
                        break;
                    }
                case XMLEvent.END_ELEMENT:
                    {
                        curr = curr.parent;
                        w.add(r.nextEvent());
                        break;
                    }
                default:
                    {
                        w.add(r.nextEvent());
                        break;
                    }
            }
            r.close();
        }
        w.flush();
        w.close();
        pw.flush();
        pw.close();
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
    }
}

Example 85 with XMLEvent

use of javax.xml.stream.events.XMLEvent in project jvarkit by lindenb.

the class XsltStream method parseDocument.

private Node parseDocument(final Document owner, final StartElement startE, final XMLEventReader r) throws XMLStreamException {
    final QName qname = startE.getName();
    final Element root;
    if (qname.getNamespaceURI() == null || qname.getNamespaceURI().isEmpty()) {
        root = owner.createElement(toQNAME(qname));
    } else {
        root = owner.createElementNS(qname.getNamespaceURI(), toQNAME(qname));
    }
    Iterator<?> it = startE.getNamespaces();
    while (it.hasNext()) {
        final Namespace att = Namespace.class.cast(it.next());
        root.setAttribute("xmlns:" + att.getPrefix(), att.getNamespaceURI());
    }
    it = startE.getAttributes();
    while (it.hasNext()) {
        final Attribute att = Attribute.class.cast(it.next());
        final QName attName = att.getName();
        if (attName.getNamespaceURI() == null || attName.getNamespaceURI().isEmpty()) {
            root.setAttribute(toQNAME(attName), att.getValue());
        } else {
            root.setAttributeNS(attName.getNamespaceURI(), toQNAME(attName), att.getValue());
        }
    }
    while (r.hasNext()) {
        final XMLEvent evt = r.nextEvent();
        if (evt.isCharacters()) {
            root.appendChild(owner.createTextNode(evt.asCharacters().getData()));
        } else if (evt.isProcessingInstruction()) {
        } else if (evt.isEndElement()) {
            break;
        } else if (evt.isStartElement()) {
            if (this.skipQNames.contains(evt.asStartElement().getName())) {
                skip(evt.asStartElement(), r);
            } else {
                root.appendChild(parseDocument(owner, evt.asStartElement(), r));
            }
        } else {
            LOG.warn("Cannot handle " + evt);
        }
    }
    return root;
}