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

Example 71 with XMLEvent

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

the class EvsDumpXml method fetchEvsData.

private void fetchEvsData(String chrom, int start, int end) {
    SnpDataBinding dataBinding = new SnpDataBinding();
    double ratio = 100.0 * (this.genome_curr_size + start) / (double) this.genome_total_size;
    LOG.info(chrom + ":" + start + "-" + end + " N=" + count_records + " " + (int) ratio + "%");
    try {
        URL url = new URL("http://gvs-1.gs.washington.edu/wsEVS/EVSDataQueryService");
        // Send data
        URLConnection conn = null;
        for (int n_try = 0; n_try < MAX_TRY; ++n_try) {
            try {
                conn = url.openConnection();
            } catch (java.net.ConnectException err) {
                if (n_try + 1 == MAX_TRY)
                    throw err;
                LOG.warning("Error: trying " + (n_try) + "/" + MAX_TRY + " " + url);
            }
        }
        conn.setDoOutput(true);
        PrintStream wr = new PrintStream(conn.getOutputStream());
        wr.print("<?xml version='1.0' ?>" + "<S:Envelope xmlns:S='http://schemas.xmlsoap.org/soap/envelope/'>" + "<S:Body>" + "<ns2:getEvsData xmlns:ns2='http://webservice.evs.gs.washington.edu/'>" + "<arg0>");
        wr.print(chrom);
        wr.print(":");
        wr.print(String.valueOf(start));
        wr.print("-");
        wr.print(String.valueOf(end));
        wr.print("</arg0>" + "</ns2:getEvsData>" + "</S:Body>" + "</S:Envelope>");
        wr.flush();
        InputStream rd = conn.getInputStream();
        XMLEventReader xmlr = this.xmlInputFactory.createXMLEventReader(rd);
        while (xmlr.hasNext()) {
            XMLEvent evt = xmlr.peek();
            if (!evt.isStartElement() || !evt.asStartElement().getName().getLocalPart().equals("snpList")) {
                xmlr.nextEvent();
                continue;
            }
            SnpData snpData = dataBinding.unmarshaller.unmarshal(xmlr, SnpData.class).getValue();
            StringWriter sw = new StringWriter();
            dataBinding.marshaller.marshal(new JAXBElement<SnpData>(new QName("snpList"), SnpData.class, snpData), sw);
            if (this.sortingCollection != null) {
                this.sortingCollection.add(sw.toString());
            } else {
                this.outputstream.write(sw.toString().getBytes());
                this.outputstream.write('\n');
            }
            ++count_records;
            if (LIMIT > 0 && count_records >= LIMIT)
                break;
        }
        xmlr.close();
        wr.close();
        rd.close();
    } catch (Exception err) {
        err.printStackTrace();
    }
}

Example 72 with XMLEvent

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

the class MergeBlastXml method doWork.

@Override
public int doWork(List<String> args) {
    if (args.isEmpty()) {
        LOG.error("input xml missing");
        return -1;
    }
    XMLEventReader rx = null;
    XMLEventReader rx2 = null;
    XMLEventWriter wx = null;
    SortingCollection<Iteration> sortingCollection = null;
    try {
        JAXBContext jc = JAXBContext.newInstance("gov.nih.nlm.ncbi.blast");
        this.unmarshaller = jc.createUnmarshaller();
        this.marshaller = jc.createMarshaller();
        this.marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
        this.marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
        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 arg0, String arg1, String arg2, String arg3) throws XMLStreamException {
                LOG.info("resolveEntity:" + arg0 + "/" + arg1 + "/" + arg2);
                return null;
            }
        });
        final Comparator<Iteration> hitComparator = (A, B) -> {
            return A.getIterationQueryDef().compareTo(B.getIterationQueryDef());
        };
        sortingCollection = SortingCollection.newInstance(Iteration.class, new BlastIterationCodec(), hitComparator, this.maxRecordsInRam, this.tmpFile.toPath());
        rx = xmlInputFactory.createXMLEventReader(new FileReader(args.get(0)));
        XMLOutputFactory xof = XMLOutputFactory.newFactory();
        if (this.outputFile != null) {
            wx = xof.createXMLEventWriter(new StreamResult(this.outputFile));
        } else {
            wx = xof.createXMLEventWriter(new StreamResult(stdout()));
        }
        boolean in_iteration = false;
        while (rx.hasNext()) {
            final XMLEvent evt = rx.peek();
            if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("Iteration")) {
                final Iteration iteration = this.unmarshaller.unmarshal(rx, Iteration.class).getValue();
                sortingCollection.add(iteration);
            } else if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("BlastOutput_iterations")) {
                wx.add(rx.nextEvent());
                in_iteration = true;
            } else if (evt.isEndElement() && evt.asEndElement().getName().getLocalPart().equals("BlastOutput_iterations")) {
                for (int optind = 1; optind < args.size(); ++optind) {
                    LOG.info("opening " + args.get(optind));
                    rx2 = xmlInputFactory.createXMLEventReader(new FileReader(args.get(optind)));
                    while (rx2.hasNext()) {
                        XMLEvent evt2 = rx2.peek();
                        if (evt2.isStartElement() && evt2.asStartElement().getName().getLocalPart().equals("Iteration")) {
                            final Iteration iteration = this.unmarshaller.unmarshal(rx2, Iteration.class).getValue();
                            sortingCollection.add(iteration);
                        } else {
                            rx2.nextEvent();
                        }
                    }
                    rx2.close();
                    LOG.info("close");
                }
                sortingCollection.doneAdding();
                sortingCollection.setDestructiveIteration(true);
                final CloseableIterator<Iteration> coliter = sortingCollection.iterator();
                final EqualRangeIterator<Iteration> eq = new EqualRangeIterator<>(coliter, hitComparator);
                while (coliter.hasNext()) {
                    final List<Iteration> L = eq.next();
                    for (int i = 1; i < L.size(); ++i) {
                        L.get(0).getIterationHits().getHit().addAll(L.get(i).getIterationHits().getHit());
                    }
                    marshaller.marshal(L.get(0), wx);
                }
                eq.close();
                coliter.close();
                sortingCollection.cleanup();
                sortingCollection = null;
                wx.add(rx.nextEvent());
                in_iteration = false;
            } else if (in_iteration) {
                // consumme text
                rx.nextEvent();
            } else {
                wx.add(rx.nextEvent());
            }
        }
        wx.flush();
        wx.close();
        return 0;
    } catch (Exception e) {
        LOG.error(e);
        if (sortingCollection != null) {
            sortingCollection.cleanup();
        }
        return -1;
    } finally {
    }
}

Example 73 with XMLEvent

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

the class Biostar3654 method fetchAnnotations.

/**
 * fetches the annotation for a given entry if the name starts with gi|....
 */
private List<INSDFeature> fetchAnnotations(final String database, final String acn, int start, int end) throws Exception {
    InputStream in = null;
    XMLEventReader r = null;
    final List<INSDFeature> L = new ArrayList<INSDFeature>();
    if (start > end)
        return fetchAnnotations(database, acn, end, start);
    try {
        if (acn != null && !acn.isEmpty() && !acn.startsWith("Query")) {
            String uri = NcbiConstants.efetch() + "?db=" + database + "&id=" + URLEncoder.encode(acn, "UTF-8") + "&rettype=gbc&retmode=xml&seq_start=" + start + "&seq_stop=" + end + this.ncbiApiKey.getAmpParamValue();
            LOG.info(uri);
            in = new URL(uri).openStream();
            r = this.xif.createXMLEventReader(in);
            while (r.hasNext()) {
                XMLEvent evt = r.peek();
                if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("INSDFeature")) {
                    INSDFeature feature = this.unmarshaller.unmarshal(r, INSDFeature.class).getValue();
                    INSDFeatureIntervals its = feature.getINSDFeatureIntervals();
                    if (its == null || its.getINSDInterval().isEmpty())
                        continue;
                    for (INSDInterval interval : its.getINSDInterval()) {
                        // when using seq_start and seq_stop , the NCBI shifts the data...
                        if (interval.getINSDIntervalFrom() != null && interval.getINSDIntervalTo() != null) {
                            interval.setINSDIntervalFrom(String.valueOf(Integer.parseInt(interval.getINSDIntervalFrom()) + start - 1));
                            interval.setINSDIntervalTo(String.valueOf(Integer.parseInt(interval.getINSDIntervalTo()) + start - 1));
                        } else if (interval.getINSDIntervalPoint() != null) {
                            interval.setINSDIntervalPoint(String.valueOf(Integer.parseInt(interval.getINSDIntervalPoint()) + start - 1));
                        }
                    }
                    L.add(feature);
                } else {
                    // consumme
                    r.next();
                }
            }
        }
    } catch (Exception err) {
        LOG.error(err);
    } finally {
        CloserUtil.close(r);
        CloserUtil.close(in);
    }
    LOG.info("N(INSDFeature)=" + L.size());
    // not found, return empty table
    return L;
}

Example 74 with XMLEvent

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

the class Biostar3654 method parseBlast.

/**
 * parses BLAST output
 */
private void parseBlast(XMLEventReader r) throws Exception {
    String database = "nucleotide";
    while (r.hasNext()) {
        XMLEvent evt = r.peek();
        if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("BlastOutput_program")) {
            r.next();
            String BlastOutput_program = r.getElementText();
            if ("blastn".equals(BlastOutput_program)) {
                database = "nucleotide";
            } else if ("blastp".equals(BlastOutput_program)) {
                database = "protein";
            } else {
                throw new IOException("only blastn && blastn are supported: " + database);
            }
        } else if (evt.isStartElement() && evt.asStartElement().getName().getLocalPart().equals("Iteration")) {
            Iteration iteration = this.unmarshaller.unmarshal(r, Iteration.class).getValue();
            parseIteration(database, iteration);
        } else {
            // consumme
            r.next();
        }
    }
}

Example 75 with XMLEvent

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

the class GenbankToGff3 method parseGenBank.

private void parseGenBank(final XMLEventReader r) throws JAXBException, XMLStreamException, IOException {
    while (r.hasNext()) {
        final XMLEvent evt = r.peek();
        if (evt.isStartElement()) {
            final String name = evt.asStartElement().getName().getLocalPart();
            if (name.equals("GBFeature")) {
                final GBFeature feature = this.unmarshaller.unmarshal(r, GBFeature.class).getValue();
                final MyFeature my = new MyFeature(feature);
                if (!my.getIntervals().isEmpty()) {
                    // we can print things like SNP right now...
                    if (StringUtil.isBlank(my.findQualifier("locus_tag"))) {
                        my.print();
                    } else {
                        this.buffer.add(my);
                    }
                }
                continue;
            } else if (name.equals("GBSeq")) {
                r.nextEvent();
                dump();
                continue;
            }
        }
        // consumme event
        r.nextEvent();
    }
    dump();
}