Example usage for org.w3c.dom Document getElementsByTagName

List of usage examples for org.w3c.dom Document getElementsByTagName

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Introduction

In this page you can find the example usage for org.w3c.dom Document getElementsByTagName.

Prototype

public NodeList getElementsByTagName(String tagname);

Source Link

Document

Returns a NodeList of all the Elements in document order with a given tag name and are contained in the document.

Usage

From source file:com.compomics.colims.core.service.impl.UniProtServiceImpl.java

@Override
public Map<String, String> getUniProtByAccession(String accession) throws RestClientException, IOException {
    Map<String, String> uniProt = new HashMap<>();

    try {// w  ww  .  ja  v a2s.c  om
        // Set XML content type explicitly to force response in XML (If not spring gets response in JSON)
        HttpHeaders headers = new HttpHeaders();
        headers.setAccept(Arrays.asList(MediaType.APPLICATION_XML));
        HttpEntity<String> entity = new HttpEntity<>("parameters", headers);

        ResponseEntity<String> response = restTemplate.exchange(UNIPROT_BASE_URL + "/" + accession + ".xml",
                HttpMethod.GET, entity, String.class);
        String responseBody = response.getBody();

        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        DocumentBuilder builder = factory.newDocumentBuilder();
        InputSource is = new InputSource(new StringReader(responseBody));

        Document document = (Document) builder.parse(is);
        document.getDocumentElement().normalize();
        NodeList recommendedName = document.getElementsByTagName("recommendedName");

        Node node = recommendedName.item(0);
        Element element = (Element) node;
        if (element.getElementsByTagName("fullName").item(0).getTextContent() != null
                && !element.getElementsByTagName("fullName").item(0).getTextContent().equals("")) {
            uniProt.put("description", element.getElementsByTagName("fullName").item(0).getTextContent());
        }

        NodeList organism = document.getElementsByTagName("organism");
        node = organism.item(0);
        element = (Element) node;
        if (element.getElementsByTagName("name").item(0).getTextContent() != null
                && !element.getElementsByTagName("name").item(0).getTextContent().equals("")) {
            uniProt.put("species", element.getElementsByTagName("name").item(0).getTextContent());
        }

        NodeList dbReference = document.getElementsByTagName("dbReference");
        node = dbReference.item(0);
        element = (Element) node;
        if (element.getAttribute("id") != null && !element.getAttribute("id").equals("")) {
            uniProt.put("taxid", element.getAttribute("id"));
        }

    } catch (HttpClientErrorException ex) {
        LOGGER.error(ex.getMessage(), ex);
        //ignore the exception if the namespace doesn't correspond to an ontology
        if (!ex.getStatusCode().equals(HttpStatus.NOT_FOUND)) {
            throw ex;
        }
    } catch (ParserConfigurationException | SAXException ex) {
        java.util.logging.Logger.getLogger(UniProtServiceImpl.class.getName()).log(Level.SEVERE, null, ex);
    }

    return uniProt;
}

From source file:org.shareok.data.plosdata.PlosApiDataImpl.java

private String getJsonApiResponseByQuery(String query) {
    String jsonData = null;/*  w  w  w  .jav  a  2s  .  co m*/
    try {
        if (null != query) {
            System.out.println(query);
            //                query = "http://api.plos.org/search?q=author_affiliate%3A%22University%20of%20Oklahoma%22%20AND%20publication_date:[2016-01-01T00:00:00Z+TO+2016-12-31T23:59:59Z]&rows=500&fl=affiliate,doi,author,volume,issue,title,journal,publication_date&api_key=mC8TEAzqwfvDWs4eamFh";
            ApplicationContext context = new ClassPathXmlApplicationContext("htmlRequestContext.xml");
            HttpRequestHandler req = (HttpRequestHandler) context.getBean("httpRequestHandler");
            String response = req.sendGet(query);
            String[] responseInfoArr = response.split("\\n");
            if (null != responseInfoArr[0] && responseInfoArr[0].equals("200")) {
                List<Map<String, String>> articleData = new ArrayList<>();
                String responseDocs = responseInfoArr[1];
                if (!DocumentProcessorUtil.isEmptyString(responseDocs)) {
                    Document doc = DocumentProcessorUtil.loadXMLFromStringContent(responseDocs);
                    NodeList docList = doc.getElementsByTagName("doc");
                    for (int i = 0; i < docList.getLength(); i++) {
                        Element item = (Element) docList.item(i);
                        Map<String, String> tmpMapData = getArticleMapData(item);
                        if (tmpMapData.containsKey("doi")) {
                            articleData.add(tmpMapData);
                        } else {
                            throw new NoDoiDataException(
                                    "Parseing the api response did not get DOI information!");
                        }
                    }
                }
                ObjectMapper mapper = new ObjectMapper();
                jsonData = mapper.writeValueAsString(articleData);
            } else {
                throw new ErrorPlosApiResponseException("Got the response code " + responseInfoArr[0]);
            }
        } else {
            throw new InvalidPlosApiQueryException("The plos api query is null");
        }
    } catch (Exception ex) {
        logger.error(ex);
    }
    return jsonData;
}

From source file:com.sparkred.mdex.metrics.publish.EndecaMDEXAgent.java

/**
 * sample XML : <throughput units="req/sec" five_minute_avg="0.02"
 * one_minute_avg="0.06" ten_second_avg="0.07" />
 * //  w  ww .ja  v a 2 s.  c o  m
 * 
 * @param pDoc
 */
private void reportThroughputMetrics(Document pDoc) {
    NodeList thorughPut_stats = pDoc.getElementsByTagName("throughput");
    Node node = thorughPut_stats.item(0);
    NamedNodeMap attr = node.getAttributes();
    Double fiveMinuteAvg = Double.valueOf(attr.getNamedItem("five_minute_avg").getNodeValue());
    Double oneMinuteAvg = Double.valueOf(attr.getNamedItem("one_minute_avg").getNodeValue());
    Double tenSecondAvg = Double.valueOf(attr.getNamedItem("ten_second_avg").getNodeValue());

    reportMetric(METRIC_THRPT_5_MIN_AVG, UNIT_REQ_SEC, fiveMinuteAvg);
    reportMetric(METRIC_THRPT_1_MIN_AVG, UNIT_REQ_SEC, oneMinuteAvg);
    reportMetric(METRIC_THRPT_10_SEC_AVG, UNIT_REQ_SEC, tenSecondAvg);
}

From source file:lv.coref.io.MmaxReaderWriter.java

public void readWords(Text text, String fileName) {
    try {//from   w w  w  . j  a v  a  2  s  . c  om
        File file = new File(fileName);
        DocumentBuilder dBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
        Document doc = dBuilder.parse(file);
        NodeList markables = doc.getElementsByTagName("word");
        words = new ArrayList<String>();
        for (int i = 0; i < markables.getLength(); i++) {
            Node markable = markables.item(i);
            String word = markable.getFirstChild().getNodeValue();
            word = StringEscapeUtils.unescapeXml(word);
            // String idString = markable.getAttributes().getNamedItem("id").getNodeValue();
            words.add(word);
        }
    } catch (Exception e) {
        log.log(Level.SEVERE, "Error reading " + fileName, e);
    }
}

From source file:com.amazonaws.mturk.cmd.GetResults.java

/**
 * Gets the HIT and assignment headers and adds additional rows
 * for each question identifier in a HIT in case the ARG_KVP
 * flag is not set/*from   w  w  w  . j a v a2 s.com*/
 */
private String[] getHeaderRow(HITResults r) {
    if (headerFields == null) {
        headerFields = new ArrayList<String>();

        for (HITProperties.HITField field : HITProperties.HIT_FIELDS) {
            headerFields.add(field.getFieldName());
        }

        for (HITProperties.AssignmentField field : HITProperties.ASSIGNMENT_FIELDS) {
            headerFields.add(field.getFieldName());
        }
    }

    if (!outputAsNameValuePair) {
        headerFields.remove(HITProperties.AssignmentField.Answers.getFieldName());
        // parse question for first hit to write out the header based on the question IDs
        try {
            DOMParser p = new DOMParser();
            p.parse(new InputSource(new StringReader(r.getHIT().getQuestion())));
            Document doc = p.getDocument();
            NodeList nodes = doc.getElementsByTagName("QuestionIdentifier");
            for (int i = 0; i < nodes.getLength(); i++) {
                headerFields
                        .add(resultProcessor.getAnswerPrefix() + nodes.item(i).getFirstChild().getNodeValue());
            }
        } catch (Exception e) {
            log.error("Failed to parse HIT question to produce proper header information: "
                    + e.getLocalizedMessage(), e);
        }
    }

    return headerFields.toArray(new String[] {});
}

From source file:com.sun.socialsite.web.rest.opensocial.ConsumerContextValidator.java

private void initRules(InputStream resourceStream) {

    try {/*from ww  w.  ja  v  a  2s.co m*/
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        DocumentBuilder builder = factory.newDocumentBuilder();
        Document doc = builder.parse(resourceStream);
        NodeList nl = doc.getElementsByTagName("rule");
        for (int i = 0; i < nl.getLength(); i++) {
            Rule rule = new Rule((Element) (nl.item(i)));
            rules.add(rule);
        }
    } catch (Exception e) {
        String msg = "Failed to load validator rules";
        log.error(msg, e);
        throw new RuntimeException(msg, e);
    }

}

From source file:com.runwaysdk.request.ClientRequestManager.java

/**
 * Parses an XML document to extract connection information, ultimately creating Connection objects.
 * /*  ww w .j  a va 2  s  . c  o  m*/
 * @param document
 */
private void parseDocument(Document document) {
    NodeList connectionsList = document.getElementsByTagName(CONNECTION_ELEMENT);

    // go through each connection
    for (int i = 0; i < connectionsList.getLength(); i++) {
        Node connection = connectionsList.item(i);
        NodeList connectionData = connection.getChildNodes();

        // get the data for each connection
        String label = null;
        ConnectionLabel.Type type = null;
        String address = null;

        // we have to loop through all child nodes since whitespace
        // counts as a text node
        for (int j = 0; j < connectionData.getLength(); j++) {
            Node data = connectionData.item(j);

            // ignore all \n\t text nodes
            if (data.getNodeType() == Node.TEXT_NODE) {
                continue;
            }

            if (data.getNodeName().equals(LABEL_ELEMENT)) {
                label = data.getTextContent();
            } else if (data.getNodeName().equals(TYPE_ELEMENT)) {
                String typeValue = data.getTextContent();
                type = ConnectionLabel.Type.dereference(typeValue);
            } else if (data.getNodeName().equals(ADDRESS_ELEMENT)) {
                address = data.getTextContent();
            }
        }

        connections.put(label, new ConnectionLabel(label, type, address));
    }
}

From source file:cz.incad.kramerius.k5indexer.IndexDocs.java

private void getDocs(int start) throws Exception {

    _init = true;/*  w ww . jav a  2  s  .  com*/
    docs.clear();

    String urlStr = host + "/select?wt=" + wt + "&q=" + URLEncoder.encode(query, "UTF-8") + "&rows=" + rows
            + "&start=" + (start + initStart);
    if (fl != null) {
        urlStr += "&fl=" + fl;
    }
    logger.log(Level.INFO, "urlStr: {0}", urlStr);

    java.net.URL url = new java.net.URL(urlStr);
    InputStream is;
    StringWriter resp = new StringWriter();
    try {
        is = url.openStream();
    } catch (Exception ex) {
        logger.log(Level.WARNING, "", ex);
        is = url.openStream();
    }

    if (wt.equals("json")) {
        org.apache.commons.io.IOUtils.copy(is, resp, "UTF-8");
        JSONObject json = new JSONObject(resp.toString());
        JSONObject response = json.getJSONObject("response");
        numFound = response.getInt("numFound");
        JSONArray jdocs = response.getJSONArray("docs");
        numDocs = jdocs.length();
        for (int i = 0; i < jdocs.length(); i++) {
            docs.add(jdocs.getJSONObject(i));
        }
    } else {

        Document respDoc = builder.parse(is);
        numFound = Integer.parseInt(respDoc.getElementsByTagName("result").item(0).getAttributes()
                .getNamedItem("numFound").getNodeValue());
        numDocs = respDoc.getElementsByTagName("doc").getLength();
        docs.add(respDoc);
    }

}

From source file:net.frontlinesms.plugins.forms.FormsPluginController.java

/**
 * Fabaris_a.zanchi Static utility method to extract tag contents from a xml
 *
 * @param xmlContent The xml conent//from   w  w  w.  java  2 s .  c om
 * @param tag the specified xml tag we want to fetch contents from
 * @return a List of Strings with the tags' content
 */
public static List<String> getTagContentFromXml(String xmlContent, String tag) throws Exception {
    List<String> ret = new ArrayList<String>();
    DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
    DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
    InputSource inStream = new InputSource();
    inStream.setCharacterStream(new StringReader(xmlContent));
    org.w3c.dom.Document xmlDoc = docBuilder.parse(inStream);
    xmlDoc.getDocumentElement().normalize();
    if (!tag.equals("client_version")) {
        NodeList nodeList = xmlDoc.getElementsByTagName(tag);
        for (int i = 0; i < nodeList.getLength(); i++) {
            Node dataNode = nodeList.item(i);
            Element elem = (Element) dataNode;
            ret.add(elem.getFirstChild().getNodeValue());
        }
    } else {
        // Search for client version not knowing its index
        NodeList dataNode = xmlDoc.getElementsByTagName("data");
        Element dataElem = (Element) dataNode.item(0);
        NodeList allNodes = dataElem.getChildNodes();
        for (int i = 0; i < allNodes.getLength(); i++) {
            if (allNodes.item(i).getNodeName().contains("client_version")) {
                ret.add(allNodes.item(i).getTextContent());
            }
        }
    }
    return ret;
}

From source file:canreg.client.dataentry.Import.java

/**
 *
 * @param doc// w  w  w.  j a va 2 s  .  c  om
 * @param lineElements
 * @return
 */
public static List<Relation> constructRelations(Document doc, String[] lineElements) {
    LinkedList<Relation> list = new LinkedList();
    NodeList nl = doc.getElementsByTagName(namespace + "variable");
    String[] variableNames = canreg.common.Tools.getVariableNames(doc, namespace);
    for (int i = 0; i < lineElements.length; i++) {
        boolean found = false;
        int j = 0;
        while (!found && j < variableNames.length) {
            found = lineElements[i].equalsIgnoreCase(variableNames[j++]);
        }
        //build relation
        Relation rel = new Relation();
        rel.setFileVariableName(lineElements[i]);
        rel.setFileColumnNumber(i);
        if (found) {
            //backtrack
            j--;
            Element e = (Element) nl.item(j);
            rel.setDatabaseTableName(e.getElementsByTagName(namespace + "table").item(0).getTextContent());
            rel.setDatabaseTableVariableID(Integer
                    .parseInt(e.getElementsByTagName(namespace + "variable_id").item(0).getTextContent()));
            rel.setVariableType(e.getElementsByTagName(namespace + "variable_type").item(0).getTextContent());
            rel.setDatabaseVariableName(variableNames[j]);
        } else {
            rel.setDatabaseTableName("");
            rel.setDatabaseTableVariableID(-1);
            rel.setVariableType("");
            rel.setDatabaseVariableName("");
        }
        list.add(rel);
    }
    return list;
}