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

Example 86 with XMLEvent

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

the class XsltStream method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.targetQnames.isEmpty()) {
        LOG.error("No target name defined");
        return -1;
    }
    XMLEventReader xmlReader = null;
    OutputStream outputStream = null;
    try {
        final String inputSource = oneFileOrNull(args);
        final TransformerFactory transformerFactory = TransformerFactory.newInstance();
        final Templates template = transformerFactory.newTemplates(new StreamSource(this.templateFile));
        final Transformer transformer = template.newTransformer();
        outputStream = openFileOrStdoutAsStream(this.outputFile);
        final XMLInputFactory xif = XMLInputFactory.newFactory();
        xmlReader = (inputSource == null ? xif.createXMLEventReader(stdin()) : xif.createXMLEventReader(new StreamSource(new File(inputSource))));
        final Document dom = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
        while (xmlReader.hasNext()) {
            final XMLEvent evt = xmlReader.nextEvent();
            if (!evt.isStartElement()) {
                continue;
            }
            final StartElement SE = evt.asStartElement();
            if (!this.targetQnames.contains(SE.getName())) {
                continue;
            }
            dom.appendChild(parseDocument(dom, SE, xmlReader));
            transformer.transform(new DOMSource(dom), new StreamResult(outputStream));
            while (dom.hasChildNodes()) dom.removeChild(dom.getFirstChild());
        }
        outputStream.flush();
        outputStream.close();
        outputStream = null;
        xmlReader.close();
        xmlReader = null;
        return 0;
    } catch (final Exception e) {
        LOG.error(e);
        return -1;
    } finally {
        CloserUtil.close(xmlReader);
        CloserUtil.close(outputStream);
    }
}

Example 87 with XMLEvent

use of javax.xml.stream.events.XMLEvent 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 88 with XMLEvent

use of javax.xml.stream.events.XMLEvent 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 89 with XMLEvent

use of javax.xml.stream.events.XMLEvent 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 90 with XMLEvent

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

the class PubmedOrcidGraph method scanOrcid.

private void scanOrcid(final String orcid, int depth) throws IOException {
    if (orcid == null || orcid.trim().isEmpty()) {
        LOG.debug("empty orcid");
        return;
    }
    if (depth >= this.maxdepth)
        return;
    // author was already scanned
    Author au = getAuthorByOrcid(orcid);
    if (au != null) {
        if (au.depth > depth) {
            au.depth = depth;
            insertAuthor(au);
        }
        if (au.reviewed)
            return;
    }
    String WebEnv = null;
    String QueryKey = null;
    InputStream in = null;
    String urlstr = new StringBuilder(NcbiConstants.esearch()).append("?db=pubmed&usehistory=1&retmax=100000&term=").append(URLEncoder.encode("\"" + orcid + "\"[auid]", "UTF-8")).append(this.ncbiApiKey.getAmpParamValue()).toString();
    ;
    XMLEventReader r = null;
    /* first get NCBI WebEnv */
    try {
        LOG.debug(urlstr);
        in = new URL(urlstr).openStream();
        r = createXMLInputFactory().createXMLEventReader(in);
        while (r.hasNext()) {
            final XMLEvent evt = r.nextEvent();
            if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("WebEnv")) {
                WebEnv = r.getElementText();
            } else if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("QueryKey")) {
                QueryKey = r.getElementText();
            }
            if (QueryKey != null && WebEnv != null)
                break;
        }
    } catch (final Exception err) {
        LOG.error(err);
    } finally {
        CloserUtil.close(r);
        CloserUtil.close(in);
        r = null;
        in = null;
    }
    if (QueryKey == null || WebEnv == null) {
        LOG.debug("Cannot get QueryKey/WebEnv " + urlstr);
    } else {
        urlstr = new StringBuilder(NcbiConstants.efetch()).append("?db=pubmed&usehistory=1&retmode=xml").append(this.ncbiApiKey.getAmpParamValue()).append("&query_key=").append(QueryKey).append("&webenv=").append(WebEnv).toString();
        ;
        LOG.debug(urlstr);
        try {
            in = new URL(urlstr).openStream();
            scanArticles(in, depth);
        } catch (Exception err) {
            LOG.error(err);
        } finally {
            CloserUtil.close(in);
            r = null;
            in = null;
        }
    }
    /* we check we found an author with this orcid */
    au = getAuthorByOrcid(orcid);
    if (au == null) {
        au = new Author();
        au.orcid = orcid;
        au.reviewed = true;
        au.depth = depth;
        au.foreName = NAME_NOT_FOUND;
        au.lastName = NAME_NOT_FOUND;
    }
    au.reviewed = true;
    if (au.depth > depth)
        au.depth = depth;
    insertAuthor(au);
}