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

Example 46 with Attribute

use of javax.xml.stream.events.Attribute 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 47 with Attribute

use of javax.xml.stream.events.Attribute 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;
}

Example 48 with Attribute

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

the class PubmedGraph method eSummary.

private void eSummary(final Article a) throws IOException, XMLStreamException {
    final QName attName = new QName("Name");
    final QName attType = new QName("Type");
    final String url = NcbiConstants.esummary() + "?retmode=xml&db=pubmed&" + "id=" + a.pmid + this.ncbiApiKey.getAmpParamValue();
    LOG.info(url);
    StreamSource src = new StreamSource(url);
    XMLEventReader reader = this.xmlInputFactory.createXMLEventReader(src);
    int in_title = 0;
    int in_date = 0;
    while (reader.hasNext() && !(a.title != null && a.year != null)) {
        XMLEvent evt = reader.nextEvent();
        if (evt.isStartElement()) {
            StartElement startE = evt.asStartElement();
            String localName = startE.getName().getLocalPart();
            if (localName.equals("Item")) {
                Attribute name = startE.getAttributeByName(attName);
                Attribute type = startE.getAttributeByName(attType);
                if (name.getValue().equals("Title") && type.getValue().equals("String")) {
                    in_title = 1;
                } else if (name.getValue().equals("PubDate") && type.getValue().equals("Date")) {
                    in_date = 1;
                }
            }
        } else if (evt.isCharacters()) {
            if (in_title == 1) {
                a.title = evt.asCharacters().getData();
            } else if (in_date == 1) {
                a.year = evt.asCharacters().getData();
            }
            in_title = 0;
            in_date = 0;
        }
    }
    reader.close();
}

Example 49 with Attribute

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

the class PubmedMap method doWork.

@Override
public int doWork(final List<String> args) {
    final String inputName = oneFileOrNull(args);
    OutputStream out = null;
    XMLEventReader r = null;
    InputStream in = null;
    XMLEventWriter w = null;
    try {
        final QName attDomainSuffix = new QName("domain");
        final QName attPlaceSuffix = new QName("place");
        final XMLEventFactory xmlEventFactory = XMLEventFactory.newFactory();
        final XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
        xmlInputFactory.setXMLResolver(new XMLResolver() {

            @Override
            public Object resolveEntity(String publicID, String systemID, String baseURI, String namespace) throws XMLStreamException {
                LOG.debug("Ignoring resolve Entity");
                return new ByteArrayInputStream(new byte[0]);
            }
        });
        in = (inputName == null ? stdin() : IOUtils.openURIForReading(inputName));
        r = xmlInputFactory.createXMLEventReader(in);
        out = super.openFileOrStdoutAsStream(this.outFile);
        final XMLOutputFactory xof = XMLOutputFactory.newFactory();
        w = xof.createXMLEventWriter(out, "UTF-8");
        while (r.hasNext()) {
            final XMLEvent evt = r.nextEvent();
            if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("Affiliation") && r.peek().isCharacters()) {
                final List<Attribute> attributes = new ArrayList<>();
                Iterator<?> t = evt.asStartElement().getAttributes();
                while (t.hasNext()) {
                    final Attribute att = (Attribute) t.next();
                    if (att.getName().equals(attDomainSuffix))
                        continue;
                    if (att.getName().equals(attPlaceSuffix))
                        continue;
                    attributes.add(att);
                }
                final XMLEvent textEvt = r.nextEvent();
                final String affiliation = textEvt.asCharacters().getData();
                final Country country = decodeAffiliation(affiliation);
                if (country != null) {
                    String suffix = country.suffix;
                    if (suffix.equals("gov"))
                        suffix = "us";
                    attributes.add(xmlEventFactory.createAttribute(attDomainSuffix, suffix));
                    attributes.add(xmlEventFactory.createAttribute(attPlaceSuffix, country.name));
                }
                w.add(xmlEventFactory.createStartElement(evt.asStartElement().getName(), attributes.iterator(), evt.asStartElement().getNamespaces()));
                w.add(textEvt);
                continue;
            }
            w.add(evt);
        }
        r.close();
        r = null;
        in.close();
        in = null;
        w.flush();
        w.close();
        w = null;
        out.flush();
        out.close();
        out = null;
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(r);
        CloserUtil.close(in);
        CloserUtil.close(w);
        CloserUtil.close(out);
    }
}

Example 50 with Attribute

use of javax.xml.stream.events.Attribute 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");
                }
            }
        }
    }
}