Example usage for org.dom4j.io SAXReader read

List of usage examples for org.dom4j.io SAXReader read

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Introduction

In this page you can find the example usage for org.dom4j.io SAXReader read.

Prototype

public Document read(InputSource in) throws DocumentException

Source Link

Document

Reads a Document from the given InputSource using SAX

Usage

From source file:StreamFlusher.java

License:Apache License

private Document parseXMLPrefs(String filepath) throws Exception {
    SAXReader reader = new SAXReader();
    Document document = null;//from  ww  w  . j  av  a2 s  .  c om
    // Document document = reader.read(filepath) ;

    try {
        // the encoding should be UTF-8
        // then need to work around SUN's irresponsible decision not to
        //  handle the optional UTF-8 BOM correctly
        document = reader.read(
                new InputStreamReader(new UTF8BOMStripperInputStream(new FileInputStream(filepath)), "UTF-8"));
    } catch (Exception e) {
        e.printStackTrace();
        throw e;
    }

    return document;
}

From source file:SolrUpdate.java

License:Apache License

public void processUrl() throws Exception {

    String jv, jn, ji, jd, jm, jy, jsp, authorfull, doi, epday, epmonth, epyear, epubsum, epubsum2 = "";
    jv = jn = ji = jd = jm = jy = jsp = authorfull = doi = epday = epmonth = epyear = epubsum = epubsum2 = "";

    SAXReader reader = new SAXReader();
    SAXReader reader2 = new SAXReader();
    Document document = null;/*from  w w w. j a  va2 s.  c om*/

    String mytitle, myabstract, myyear, myfullname = "";
    Element journalname, journalyear, journalmonth, journalday, journalvolume, journalissue, journalpagestart,
            epubday, epubmonth, epubyear, pubdoi;
    int mypmid;

    List<String> mylauthors = new ArrayList<String>();
    List<String> myfauthors = new ArrayList<String>();
    List<String> myfnames = new ArrayList<String>();

    //PubMed

    String pubmedlist = "";
    Iterator iditer = publications.iterator();

    while (iditer.hasNext()) {
        int currpmid = ((Publication) iditer.next()).getPmid();
        if (pubmedlist.length() < 1) {
            pubmedlist += currpmid;

        } else {
            pubmedlist += "," + currpmid;
        }
    }

    String url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=" + pubmedlist
            + "&retmax=200&retmode=xml&rettype=abstract";
    Document pubdoc = reader2.read(url);

    @SuppressWarnings("unchecked")
    List<Node> thelist = pubdoc.selectNodes("//PubmedArticle| //PubmedBookArticle");

    Element abstractnode, titlenode, yearsnode, pmidnode;
    @SuppressWarnings("rawtypes")
    List firstnamenode;
    @SuppressWarnings("rawtypes")
    List lastnamenode;

    for (Node currnode : thelist) {
        mylauthors = new ArrayList<String>();
        myfauthors = new ArrayList<String>();
        myfnames = new ArrayList<String>();
        epubsum = epubsum2 = authorfull = "";

        titlenode = (Element) currnode.selectSingleNode(".//ArticleTitle | .//BookTitle");
        yearsnode = (Element) currnode
                .selectSingleNode(".//PubDate/Year | .//DateCompleted/Year | .//DateCreated/Year");
        journalname = (Element) currnode.selectSingleNode(".//Journal/Title");
        journalyear = (Element) currnode.selectSingleNode(".//PubDate/Year");
        journalmonth = (Element) currnode.selectSingleNode(".//PubDate/Month");

        journalday = (Element) currnode.selectSingleNode(".//PubDate/Day");
        journalvolume = (Element) currnode.selectSingleNode(".//JournalIssue/Volume");
        journalissue = (Element) currnode.selectSingleNode(".//JournalIssue/Issue");
        journalpagestart = (Element) currnode.selectSingleNode(".//Pagination/MedlinePgn");

        epubday = (Element) currnode.selectSingleNode(
                ".//PubMedPubDate[@PubStatus='aheadofprint']/Day  | .//PubMedPubDate[@PubStatus='epublish']/Day ");
        epubmonth = (Element) currnode.selectSingleNode(
                ".//PubMedPubDate[@PubStatus='aheadofprint']/Month | .//PubMedPubDate[@PubStatus='epublish']/Month");
        epubyear = (Element) currnode.selectSingleNode(
                ".//PubMedPubDate[@PubStatus='aheadofprint']/Year | .//PubMedPubDate[@PubStatus='epublish']/Year");

        pubdoi = (Element) currnode.selectSingleNode(".//ArticleId[@IdType='doi']");

        firstnamenode = currnode.selectNodes(".//ForeName");
        lastnamenode = currnode.selectNodes(".//LastName");
        abstractnode = (Element) currnode.selectSingleNode(".//Abstract/AbstractText[1]");
        pmidnode = (Element) currnode.selectSingleNode(".//PMID");

        myfnames = new ArrayList<String>();
        @SuppressWarnings("rawtypes")
        Iterator fiter = firstnamenode.iterator();
        @SuppressWarnings("rawtypes")
        Iterator liter = lastnamenode.iterator();

        if (journalname != null) {
            jn = journalname.getText();
        }
        if (journalvolume != null) {
            jv = journalvolume.getText();
        }
        if (journalissue != null) {
            ji = journalissue.getText();
        }
        if (journalmonth != null) {
            jm = journalmonth.getText();
        }
        if (journalyear != null) {
            jy = journalyear.getText();
        }
        if (journalpagestart != null) {
            jsp = journalpagestart.getText();
        }
        if (journalday != null) {
            jd = journalday.getText();
        }
        if (epubday != null) {
            epday = epubday.getText();
        }
        if (epubmonth != null) {
            epmonth = epubmonth.getText();
        }
        if (epubyear != null) {
            epyear = epubyear.getText();
        }
        if (pubdoi != null) {
            doi = "doi: " + pubdoi.getText();
        }
        if (jv.length() > 0) {
            epubsum2 += jv;
        }

        if (ji.length() > 0) {
            epubsum2 += "(" + ji + ")" + ":";
        }

        if (jsp.length() > 0) {
            epubsum2 += jsp + ".";
        }

        if (epmonth.length() < 1 && epyear.length() < 1 && epday.length() < 1) {
            epubsum = "[Epub ahead of print]";
        } else if (epyear.length() > 0) {
            epubsum = "Epub " + epyear + " " + epmonth + " " + epday;
        } else {
            epubsum = "";
        }

        mytitle = titlenode.getText();
        myyear = yearsnode.getText();
        mypmid = Integer.valueOf(pmidnode.getText());

        while (fiter.hasNext()) {
            Element fname = (Element) fiter.next();
            Element lname = (Element) liter.next();

            myfauthors.add(fname.getText());
            mylauthors.add(lname.getText());

            myfullname = fname.getText() + " " + lname.getText();
            myfnames.add(myfullname);

            if (fiter.hasNext()) {
                authorfull = authorfull + myfullname + ", ";
            } else {
                authorfull = authorfull + myfullname;
            }

        }

        if (abstractnode != null) {
            myabstract = abstractnode.getText();
        } else {
            myabstract = "NO ABSTRACT FOUND.";
        }

        publications.add(new Publication(mytitle, myabstract, myyear, myfauthors, mylauthors, myfnames, jv, jn,
                jy, jm, jd, jsp, ji, epday, epmonth, epyear, doi, epubsum, epubsum2, authorfull, mypmid));

    }

}

From source file:JenkinsHelper.java

License:Apache License

private String generateJobXML(String test, JSONObject repository) throws Exception {
    String templateJob = repository.getString("templateJob").toLowerCase();

    if (!jenkins.getJobs().containsKey(templateJob)) {
        throw new Exception("Template job not found in jenkins jobs, is the name right?");
    }/*from ww w.  j  av  a 2  s .  c  o  m*/

    String jobXML = client.get("/job/" + templateJob.replace(" ", "%20") + "/config.xml");
    SAXReader reader = new SAXReader();
    Document doc = reader.read(new StringReader(jobXML));
    Element root = doc.getRootElement();

    if (repository.has("mvnOptions") || repository.has("mvnCommand")) {
        root = insertMvnGoals(root, repository, test);
    } else if (repository.has("executeShells") || repository.has("executeShell")) {
        root = insertShellCommand(root, repository, test);
    } else {
        System.out.println("WARNING - Did not provide an executeShell or mvnOptions/mvnCommand in repo: "
                + repository.getString("repository"));
    }

    if (repository.has("description")) {
        root = setDescription(root, repository.getString("description"));
    } else {
        root = setDescription(root, "Automatically generated test job");
    }
    root = enableJob(root);

    return doc.asXML();
}

From source file:Tools.java

public static void encryptApp(Object cert, String password, String sourceModelPath, String targetModelPath,
        String app, String isCompile) {
    if (null == password || "".equals(password))
        throw new RuntimeException("???");
    if (null == sourceModelPath || "".equals(sourceModelPath))
        throw new RuntimeException("");
    if (null == targetModelPath || "".equals(targetModelPath))
        throw new RuntimeException("?");
    if (null == app || "".equals(app))
        throw new RuntimeException("??");
    if (sourceModelPath.equalsIgnoreCase(targetModelPath))
        throw new RuntimeException(
                "?????");
    try {//from w w w  .ja  v  a 2  s . co  m
        password = java.net.URLDecoder.decode(password, "UTF8");
    } catch (UnsupportedEncodingException e1) {
        throw new RuntimeException("???", e1);
    }
    SAXReader reader = new SAXReader();
    Document doc = null;
    try {
        doc = reader.read((InputStream) cert);
    } catch (DocumentException e) {
        throw new RuntimeException("???", e);
    }
    byte[] bCert = loadCert(doc);
    EncryptModel eapp = new EncryptModel(bCert, sourceModelPath, targetModelPath);
    try {
        String[] appList = app.split(";");
        for (int i = 0; i < appList.length; i++)
            eapp.encrypt(appList[i], password, !"false".equalsIgnoreCase(isCompile));
    } catch (IOException e) {
        throw new RuntimeException("", e);
    }
}

From source file:Tools.java

public static Map<String, String> regAppLicense(String appLicense) {
    if (null == appLicense || "".equals(appLicense))
        throw new RuntimeException("License");
    BASE64Decoder decoder = new BASE64Decoder();
    try {/*w w w.j ava  2 s .com*/
        Map<String, String> ret = new HashMap<String, String>();
        SAXReader reader = new SAXReader();
        reader.setEncoding("UTF-8");
        Document doc = reader.read(new ByteArrayInputStream(decoder.decodeBuffer(appLicense)));
        Element root = doc.getRootElement();
        String app = root.elementTextTrim("models");
        ret.put("app", app);
        String content = root.elementTextTrim("content");
        String appPath = FileSystemWrapper.instance().getRealPath(app);
        File fApp = new File(appPath);
        if (!fApp.exists())
            throw new RuntimeException("?\"" + app + "\"?");
        File fAppLicenseDir = new File(appPath + "/license");
        fAppLicenseDir.mkdirs();
        FileOutputStream fo = null;
        try {
            fo = new FileOutputStream(appPath + "/license/license");
            fo.write(content.getBytes());
            fo.flush();
        } finally {
            if (null != fo)
                fo.close();
        }
        String developer = root.elementTextTrim("developer");
        ret.put("developer", developer);
        String validDate = root.elementTextTrim("valid-date");
        ret.put("valid-date", !"0".equals(validDate) ? validDate : "??");
        String userCount = root.elementTextTrim("user-count");
        ret.put("user-count", !"0".equals(userCount) ? userCount : "??");

        return ret;
    } catch (IOException e) {
        throw new RuntimeException("License", e);
    } catch (DocumentException e) {
        throw new RuntimeException("License", e);
    }
}

From source file:Addons.CepWebService.java

private static Document getDocumento(URL url) throws DocumentException {
    SAXReader reader = new SAXReader();
    Document document = reader.read(url);
    return document;
}

From source file:adr.main.AlcorAdrSettings.java

/**
 * ?  ?  .xml //from  w ww .  ja v  a 2 s  .  c  om
 * @return 
 * true  -   ?
 * false -   ? 
 */
public boolean LoadSettings() {
    boolean bResOk = true;
    try {
        SAXReader reader = new SAXReader();

        String strSettingsFilePathName = "alcor.adr.settings.xml";//System.getenv( "AMS_ROOT") + "/etc/settings.ams.xml";
        URL url = (new java.io.File(strSettingsFilePathName)).toURI().toURL();

        Document document = reader.read(url);

        Element root = document.getRootElement();

        // iterate through child elements of root
        for (Iterator i = root.elementIterator(); i.hasNext();) {
            Element element = (Element) i.next();
            String name = element.getName();
            String value = element.getText();

            //logger.debug( "Pairs: [" + name + " : " + value + "]");

            if ("COM_Port".equals(name))
                m_pCOMPortSettings.SetPort(value);

            if ("COM_Baudrate".equals(name))
                m_pCOMPortSettings.SetBaudRate(Integer.parseInt(value));

            if ("COM_DataBits".equals(name)) {
                switch (value) {
                case "5":
                    m_pCOMPortSettings.SetDataBits(SerialPort.DATABITS_5);
                    break;
                case "6":
                    m_pCOMPortSettings.SetDataBits(SerialPort.DATABITS_6);
                    break;
                case "7":
                    m_pCOMPortSettings.SetDataBits(SerialPort.DATABITS_7);
                    break;
                case "8":
                    m_pCOMPortSettings.SetDataBits(SerialPort.DATABITS_8);
                    break;
                default:
                    logger.warn("Unknown COM_DataBits value '" + value + "' in settings.xml! Using default!");
                    bResOk = false;
                    break;
                }
            }

            if ("COM_Parity".equals(name)) {
                switch (value) {
                case "None":
                    m_pCOMPortSettings.SetParity(SerialPort.PARITY_NONE);
                    break;
                case "Odd":
                    m_pCOMPortSettings.SetParity(SerialPort.PARITY_ODD);
                    break;
                case "Even":
                    m_pCOMPortSettings.SetParity(SerialPort.PARITY_EVEN);
                    break;
                case "Mark":
                    m_pCOMPortSettings.SetParity(SerialPort.PARITY_MARK);
                    break;
                case "Space":
                    m_pCOMPortSettings.SetParity(SerialPort.PARITY_SPACE);
                    break;
                default:
                    logger.warn("Unknown COM_Parity value '" + value + "' in settings.xml! Using default!");
                    bResOk = false;
                    break;
                }
            }

            if ("COM_StopBits".equals(name)) {
                switch (value) {
                case "1":
                    m_pCOMPortSettings.SetStopBits(SerialPort.STOPBITS_1);
                    break;
                case "2":
                    m_pCOMPortSettings.SetParity(SerialPort.STOPBITS_2);
                    break;
                default:
                    logger.warn("Unknown COM_StopBits value '" + value + "' in settings.xml! Using default!");
                    bResOk = false;
                    break;
                }
            }
        }

    } catch (MalformedURLException ex) {
        logger.error("MalformedURLException caught while loading settings!", ex);
        bResOk = false;
    } catch (DocumentException ex) {
        logger.error("DocumentException caught while loading settings!", ex);
        bResOk = false;
    }

    return bResOk;
}

From source file:aml.match.Alignment.java

License:Apache License

private void loadMappingsRDF(String file) throws DocumentException {
    AML aml = AML.getInstance();//from  w  w  w. ja  v a2  s .c om
    URIMap uris = aml.getURIMap();

    //Open the alignment file using SAXReader
    SAXReader reader = new SAXReader();
    File f = new File(file);

    Document doc = reader.read(f);
    //Read the root, then go to the "Alignment" element
    Element root = doc.getRootElement();
    Element align = root.element("Alignment");
    //Get an iterator over the mappings
    Iterator<?> map = align.elementIterator("map");
    while (map.hasNext()) {
        //Get the "Cell" in each mapping
        Element e = ((Element) map.next()).element("Cell");

        if (e == null)
            continue;
        //Get the source class
        String sourceURI = e.element("entity1").attributeValue("resource");

        //Get the target class
        String targetURI = e.element("entity2").attributeValue("resource");

        //Get the similarity measure
        String measure = e.elementText("measure");
        //Parse it, assuming 1 if a valid measure is not found
        double similarity = 1;
        if (measure != null) {
            try {
                similarity = Double.parseDouble(measure);
                if (similarity < 0 || similarity > 1)
                    similarity = 1;
            } catch (Exception ex) {
                /*Do nothing - use the default value*/}
            ;
        }
        //Get the relation
        String r = e.elementText("relation");
        if (r == null)
            r = "?";
        MappingRelation rel = MappingRelation.parseRelation(StringEscapeUtils.unescapeXml(r));
        //Check if the URIs are listed in the URI map 
        int sourceIndex = uris.getIndex(sourceURI);
        int targetIndex = uris.getIndex(targetURI);
        //If they are, add the mapping to the maps and proceed to next mapping
        if (sourceIndex > -1 && targetIndex > -1) {
            if (sourceIndex < targetIndex)
                add(sourceIndex, targetIndex, similarity, rel);
            else
                add(targetIndex, sourceIndex, similarity, rel);
        }
    }
}

From source file:aml.match.Alignment.java

License:Apache License

private void loadMappingsRDF2(String file) throws DocumentException {
    AML aml = AML.getInstance();/*from w ww  .j a  va 2s .  c om*/
    URIMap uris = aml.getURIMap();

    //Open the alignment file using SAXReader
    SAXReader reader = new SAXReader();
    File f = new File(file);

    Document doc = reader.read(f);
    //Read the root, then go to the "Alignment" element
    Element root = doc.getRootElement();
    Element align = root.element("Alignment");
    //Get an iterator over the mappings
    Iterator<?> map = align.elementIterator("map");
    while (map.hasNext()) {
        //Get the "Cell" in each mapping
        Element e = ((Element) map.next()).element("Cell");

        if (e == null)
            continue;

        //Get the source class
        String sourceURI = e.element("entity1").element("Class").attributeValue("about");

        //Get the target class
        String targetURI = e.element("entity2").element("Class").element("and").element("Class")
                .attributeValue("about");

        //Get the similarity measure
        String measure = e.elementText("measure");
        //Parse it, assuming 1 if a valid measure is not found
        double similarity = 1;
        if (measure != null) {
            try {
                similarity = Double.parseDouble(measure);
                if (similarity < 0 || similarity > 1)
                    similarity = 1;
            } catch (Exception ex) {
                /*Do nothing - use the default value*/}
            ;
        }

        //Get the relation
        String r = e.elementText("relation");
        if (r == null)
            r = "?";

        MappingRelation rel = MappingRelation.parseRelation(StringEscapeUtils.unescapeXml(r));
        //Check if the URIs are listed in the URI map 

        int sourceIndex = uris.getIndex(sourceURI);

        int targetIndex = uris.getIndex(targetURI);

        //If they are, add the mapping to the maps and proceed to next mapping

        if (sourceIndex > -1 && targetIndex > -1) {
            if (sourceIndex < targetIndex)
                add(sourceIndex, targetIndex, similarity, rel);
            else
                add(targetIndex, sourceIndex, similarity, rel);
        }

    }
}

From source file:aml.match.CompoundAlignment.java

License:Apache License

private void loadMappingsRDF(String file) throws DocumentException {
    AML aml = AML.getInstance();/*from w ww. j a v a2s  .c  om*/
    URIMap uris = aml.getURIMap();

    //Open the alignment file using SAXReader
    SAXReader reader = new SAXReader();

    File f = new File(file);

    Document doc = reader.read(f);
    //Read the root, then go to the "Alignment" element
    Element root = doc.getRootElement();

    Element align = root.element("Alignment");
    //Get an iterator over the mappings
    Iterator<?> map = align.elementIterator("map");

    while (map.hasNext()) {

        //Get the "Cell" in each mapping
        Element e = ((Element) map.next()).element("Cell");
        if (e == null) {
            continue;
        }
        //Get the source class
        String sourceURI = e.element("entity1").element("Class").attributeValue("about");
        uris.addURI(sourceURI);
        //Get the target class

        //Get the both target classes
        List<Element> elements = e.element("entity2").element("Class").element("and").elements("Class");

        //Get the target 1
        String targetURI = elements.get(0).attributeValue("about");
        uris.addURI(targetURI);
        //Get the target 2
        String target2URI = elements.get(1).attributeValue("about");

        uris.addURI(target2URI);
        //Get the similarity measure
        String measure = e.elementText("measure");

        //Parse it, assuming 1 if a valid measure is not found
        double similarity = 1;
        if (measure != null) {
            try {
                similarity = Double.parseDouble(measure);
                if (similarity < 0 || similarity > 1)
                    similarity = 1;
            } catch (Exception ex) {
                /*Do nothing - use the default value*/}
            ;
        }

        //Get the relation
        String r = e.elementText("relation");
        if (r == null)
            r = "?";
        MappingRelation rel = MappingRelation.parseRelation(StringEscapeUtils.unescapeXml(r));
        //Check if the URIs are listed in the URI map 
        int sourceIndex = uris.getIndex(sourceURI);
        int targetIndex = uris.getIndex(targetURI);
        int targetIndex2 = uris.getIndex(target2URI);
        //If they are, add the mapping to the maps and proceed to next mapping

        if (sourceIndex > -1 && targetIndex > -1 && targetIndex2 > -1) {
            if (sourceIndex < targetIndex)
                add(sourceIndex, targetIndex, targetIndex2, similarity, rel);
            else
                add(targetIndex, sourceIndex, targetIndex2, similarity, rel);
        }

    }
}