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

Example 16 with EndElement

use of javax.xml.stream.events.EndElement 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 17 with EndElement

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

the class PubmedOrcidGraph method scanArticle.

private void scanArticle(final String rootName, final XMLEventReader r, int depth) throws XMLStreamException, IOException {
    final Article article = new Article();
    boolean PubDate = false;
    final List<Author> authors = new ArrayList<>();
    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.ISOAbbreviation == null && eltName.equals("ISOAbbreviation")) {
                article.ISOAbbreviation = r.getElementText();
            } else if (article.ArticleTitle == null && eltName.equals("ArticleTitle")) {
                article.ArticleTitle = this.textContent(r);
            } else if (eltName.equals("PubDate")) {
                PubDate = true;
            } else if (article.doi == null && eltName.equals("ArticleId")) {
                final Attribute idType = start.getAttributeByName(new QName("IdType"));
                if (idType != null && idType.getValue().equalsIgnoreCase("doi")) {
                    article.doi = r.getElementText().trim();
                }
            } else if (article.Year == null && PubDate && eltName.equals("Year")) {
                article.Year = r.getElementText();
            } else if (eltName.equals("Author")) {
                final Author author = parseAuthor(r, article.pmid, depth + 1);
                if (author != null && author.orcid != null) {
                    authors.add(author);
                }
            }
        } else if (evt.isEndElement()) {
            final EndElement end = evt.asEndElement();
            final String eltName = end.getName().getLocalPart();
            if (eltName.equals("PubDate")) {
                PubDate = false;
            }
            if (eltName.equals(rootName))
                break;
        }
    }
    if (authors.isEmpty()) {
        // do nothing
        return;
    }
    DatabaseEntry key = new DatabaseEntry();
    DatabaseEntry data = new DatabaseEntry();
    Collections.sort(authors);
    for (int x = 0; x + 1 < authors.size(); ++x) {
        for (int y = x + 1; y < authors.size(); ++y) {
            Link L = null;
            final String orcid1 = authors.get(x).orcid;
            final String orcid2 = authors.get(y).orcid;
            if (this.all_links_between_authors) {
                LongBinding.longToEntry(++ID_GENERATOR, key);
            } else {
                StringBinding.stringToEntry(orcid1 + "~" + orcid2, key);
                if (this.linkDatabase.get(txn, key, data, LockMode.DEFAULT) != OperationStatus.NOTFOUND) {
                    L = this.linkBinding.entryToObject(data);
                }
            }
            if (L == null) {
                L = new Link();
                L.orcid1 = orcid1;
                L.orcid2 = orcid2;
            }
            L.pmids.add(article.pmid);
            this.linkBinding.objectToEntry(L, data);
            if (this.linkDatabase.put(txn, key, data) != OperationStatus.SUCCESS) {
                throw new JvarkitException.BerkeleyDbError("Cannot put in article db");
            }
        }
    }
    // for comparing names
    final Collator collator = Collator.getInstance(Locale.US);
    collator.setStrength(Collator.PRIMARY);
    StringBinding.stringToEntry(article.pmid, key);
    if (this.articleDatabase.get(txn, key, data, LockMode.DEFAULT) != OperationStatus.NOTFOUND) {
        LOG.debug("Article already in database : " + article.pmid);
    } else {
        LOG.debug("inserting article " + article.pmid);
        this.articleBinding.objectToEntry(article, data);
        if (this.articleDatabase.put(txn, key, data) != OperationStatus.SUCCESS) {
            throw new JvarkitException.BerkeleyDbError("Cannot put in article db");
        }
        for (final Author au : authors) {
            StringBinding.stringToEntry(au.orcid, key);
            if (this.authorDatabase.get(txn, key, data, LockMode.DEFAULT) != OperationStatus.NOTFOUND) {
                LOG.debug("Author already in database : " + au.orcid);
                final Author other = this.authorBinding.entryToObject(data);
                if (!StringUtil.isBlank(other.lastName) && !StringUtil.isBlank(au.lastName) && collator.compare(au.lastName, other.lastName) != 0) {
                    this.errPrintWriter.println("Conflict\t" + au.orcid + "\t" + au.foreName + "\t" + other.foreName);
                }
            } else {
                this.authorBinding.objectToEntry(au, data);
                if (this.authorDatabase.put(txn, key, data) != OperationStatus.SUCCESS) {
                    throw new JvarkitException.BerkeleyDbError("Cannot put in author db");
                }
            }
        }
    }
}

Example 18 with EndElement

use of javax.xml.stream.events.EndElement in project rpki-validator-3 by RIPE-NCC.

the class RrdpParser method delta.

public Delta delta(final InputStream inputStream) {
    final Map<String, DeltaElement> objects = new HashMap<>();
    try {
        final XMLInputFactory factory = XMLInputFactory.newInstance();
        final XMLEventReader eventReader = factory.createXMLEventReader(inputStream);
        String sessionId = null;
        BigInteger serial = null;
        String uri = null;
        String hash = null;
        StringBuilder base64 = new StringBuilder();
        boolean inPublishElement = false;
        final Base64.Decoder decoder = Base64.getDecoder();
        while (eventReader.hasNext()) {
            final XMLEvent event = eventReader.nextEvent();
            switch(event.getEventType()) {
                case XMLStreamConstants.START_ELEMENT:
                    final StartElement startElement = event.asStartElement();
                    final String qName = startElement.getName().getLocalPart();
                    switch(qName) {
                        case "publish":
                            uri = getAttr(startElement, "uri", "Uri is not present in 'publish' element");
                            hash = getAttr(startElement, "hash");
                            inPublishElement = true;
                            break;
                        case "withdraw":
                            uri = getAttr(startElement, "uri", "Uri is not present in 'publish' element");
                            hash = getAttr(startElement, "hash", "Hash is not present in 'withdraw' element");
                            break;
                        case "delta":
                            serial = new BigInteger(getAttr(startElement, "serial", "Notification serial is not present"));
                            sessionId = getAttr(startElement, "session_id", "Session id is not present");
                            break;
                    }
                    break;
                case XMLStreamConstants.CHARACTERS:
                    final Characters characters = event.asCharacters();
                    if (inPublishElement) {
                        final String thisBase64 = characters.getData();
                        base64.append(thisBase64.replaceAll("\\s", ""));
                    }
                    break;
                case XMLStreamConstants.END_ELEMENT:
                    final EndElement endElement = event.asEndElement();
                    final String qqName = endElement.getName().getLocalPart();
                    switch(qqName) {
                        case "publish":
                            final byte[] decoded = decoder.decode(base64.toString());
                            objects.put(uri, new DeltaPublish(decoded, uri, Hex.parse(hash)));
                            base64 = new StringBuilder();
                            break;
                        case "withdraw":
                            objects.put(uri, new DeltaWithdraw(uri, Hex.parse(hash)));
                            break;
                    }
                    break;
            }
        }
        return new Delta(objects, sessionId, serial);
    } catch (XMLStreamException e) {
        throw new RrdpException("Couldn't parse snapshot: ", e);
    }
}

Example 19 with EndElement

use of javax.xml.stream.events.EndElement in project spring-framework by spring-projects.

the class XMLEventStreamWriter method writeEndElement.

@Override
public void writeEndElement() throws XMLStreamException {
    closeEmptyElementIfNecessary();
    int last = this.endElements.size() - 1;
    EndElement lastEndElement = this.endElements.remove(last);
    this.eventWriter.add(lastEndElement);
}

Example 20 with EndElement

use of javax.xml.stream.events.EndElement in project spring-framework by spring-projects.

the class XMLEventStreamWriter method doWriteNamespace.

@SuppressWarnings("rawtypes")
private void doWriteNamespace(Namespace namespace) throws XMLStreamException {
    int last = this.endElements.size() - 1;
    EndElement oldEndElement = this.endElements.get(last);
    Iterator oldNamespaces = oldEndElement.getNamespaces();
    List<Namespace> newNamespaces = new ArrayList<>();
    while (oldNamespaces.hasNext()) {
        Namespace oldNamespace = (Namespace) oldNamespaces.next();
        newNamespaces.add(oldNamespace);
    }
    newNamespaces.add(namespace);
    EndElement newEndElement = this.eventFactory.createEndElement(oldEndElement.getName(), newNamespaces.iterator());
    this.eventWriter.add(namespace);
    this.endElements.set(last, newEndElement);
}