Example usage for javax.xml.parsers SAXParserFactory newSAXParser

List of usage examples for javax.xml.parsers SAXParserFactory newSAXParser

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Introduction

In this page you can find the example usage for javax.xml.parsers SAXParserFactory newSAXParser.

Prototype


public abstract SAXParser newSAXParser() throws ParserConfigurationException, SAXException;

Source Link

Document

Creates a new instance of a SAXParser using the currently configured factory parameters.

Usage

From source file:org.corpus_tools.pepper.core.PepperJobImpl.java

/**
 * {@inheritDoc PepperJob#load(URI)}//  ww  w.  j a  v  a  2 s.c o  m
 */
@Override
public void load(URI uri) {
    if (uri.isFile()) {
        File wdFile = new File(uri.toFileString());
        // set folder containing workflow description as base dir
        setBaseDir(uri.trimSegments(1));

        SAXParser parser;
        XMLReader xmlReader;
        SAXParserFactory factory = SAXParserFactory.newInstance();

        WorkflowDescriptionReader contentHandler = new WorkflowDescriptionReader();
        contentHandler.setPepperJob(this);
        contentHandler.setLocation(uri);

        // remove all existing steps
        clear();

        try {
            parser = factory.newSAXParser();
            xmlReader = parser.getXMLReader();
            xmlReader.setContentHandler(contentHandler);
        } catch (ParserConfigurationException e) {
            throw new PepperModuleXMLResourceException("Cannot load Pepper workflow description file '"
                    + wdFile.getAbsolutePath() + "': " + e.getMessage() + ". ", e);
        } catch (Exception e) {
            throw new PepperModuleXMLResourceException("Cannot load Pepper workflow description file '"
                    + wdFile.getAbsolutePath() + "': " + e.getMessage() + ". ", e);
        }
        try {
            InputStream inputStream = new FileInputStream(wdFile);
            Reader reader = new InputStreamReader(inputStream, "UTF-8");
            InputSource is = new InputSource(reader);
            is.setEncoding("UTF-8");
            xmlReader.parse(is);
        } catch (SAXException e) {
            try {
                parser = factory.newSAXParser();
                xmlReader = parser.getXMLReader();
                xmlReader.setContentHandler(contentHandler);
                xmlReader.parse(wdFile.getAbsolutePath());
            } catch (Exception e1) {
                throw new PepperModuleXMLResourceException("Cannot load Pepper workflow description file '"
                        + wdFile.getAbsolutePath() + "': " + e1.getMessage() + ". ", e1);
            }
        } catch (Exception e) {
            if (e instanceof PepperModuleException) {
                throw (PepperModuleException) e;
            } else {
                throw new PepperModuleXMLResourceException("Cannot load Pepper workflow description file'"
                        + wdFile + "', because of a nested exception: " + e.getMessage() + ". ", e);
            }
        }
    } else {
        throw new UnsupportedOperationException(
                "Currently Pepper can only load workflow description from local files.");
    }
}

From source file:org.corpus_tools.salt.util.SaltUtil.java

/**
 * Loads a list of root objects coming from a SaltXML (.{@link #FILE_ENDING_SALT_XML})
 * and returns it.// w  w  w  . ja  va2  s .c o  m
 * 
 * @param objectURI
 *            {@link URI} to SaltXML file containing the object
 * @return loaded objects
 */
public static List<Object> loadObjects(URI location) {
    if (location == null) {
        throw new SaltResourceException("Cannot load Salt object, because the given uri is null.");
    }
    File objectFile = new File(
            (location.toFileString() == null) ? location.toString() : location.toFileString());
    if (!objectFile.exists()) {
        throw new SaltResourceException("Cannot load Salt object, because the file '"
                + objectFile.getAbsolutePath() + "' does not exist.");
    }

    SAXParser parser;
    XMLReader xmlReader;
    SAXParserFactory factory = SAXParserFactory.newInstance();
    SaltXML10Handler contentHandler = new SaltXML10Handler();

    try {
        parser = factory.newSAXParser();
        xmlReader = parser.getXMLReader();
        xmlReader.setContentHandler(contentHandler);
    } catch (ParserConfigurationException e) {
        throw new SaltResourceException(
                "Cannot load Salt object from file '" + objectFile.getAbsolutePath() + "'.", e);
    } catch (Exception e) {
        throw new SaltResourceException(
                "Cannot load Salt object from file '" + objectFile.getAbsolutePath() + "'.", e);
    }
    try {
        InputStream inputStream = new FileInputStream(objectFile);
        Reader reader = new InputStreamReader(inputStream, "UTF-8");
        InputSource is = new InputSource(reader);
        is.setEncoding("UTF-8");
        xmlReader.parse(is);
    } catch (SAXException e) {
        try {
            parser = factory.newSAXParser();
            xmlReader = parser.getXMLReader();
            xmlReader.setContentHandler(contentHandler);
            xmlReader.parse(objectFile.getAbsolutePath());
        } catch (Exception e1) {
            throw new SaltResourceException(
                    "Cannot load Salt object from file '" + objectFile.getAbsolutePath() + "'.", e1);
        }
    } catch (Exception e) {
        if (e instanceof SaltException) {
            throw (SaltException) e;
        } else {
            throw new SaltResourceException(
                    "Cannot load Salt object from file'" + objectFile + "', because of a nested exception. ",
                    e);
        }
    }
    return contentHandler.getRootObjects();
}

From source file:org.dcm4che.tool.dcm2xml.Dcm2Xml.java

private static Attributes parseXML(String fname) throws Exception {
    Attributes attrs = new Attributes();
    ContentHandlerAdapter ch = new ContentHandlerAdapter(attrs);
    SAXParserFactory f = SAXParserFactory.newInstance();
    SAXParser p = f.newSAXParser();
    p.parse(new File(fname), ch);
    return attrs;
}

From source file:org.dcm4che.tool.xml2dcm.Xml2Dcm.java

private static void parseXML(String fname, ContentHandlerAdapter ch) throws Exception {
    SAXParserFactory f = SAXParserFactory.newInstance();
    SAXParser p = f.newSAXParser();
    if (fname.equals("-")) {
        p.parse(System.in, ch);/*from  w w w .  ja  v a 2s. c  om*/
    } else {
        p.parse(new File(fname), ch);
    }
}

From source file:org.dcm4che2.tool.chess3d.Chess3D.java

public void extrude(File xmlFile, int slices) throws IOException, ParserConfigurationException, SAXException {
    DicomObject obj = new BasicDicomObject();
    String fn;/*from   w  ww .  ja v a2  s  . c om*/
    File parent;
    if (xmlFile != null) {
        SAXParserFactory f = SAXParserFactory.newInstance();
        SAXParser p = f.newSAXParser();
        ContentHandlerAdapter ch = new ContentHandlerAdapter(obj);
        p.parse(xmlFile, ch);
        fn = obj.getString(Tag.PatientID);
        if (fn == null)
            fn = xmlFile.getName();
        parent = destDir == null ? xmlFile.getParentFile() : destDir;
    } else {
        fn = "test";
        parent = destDir == null ? null : destDir;
    }
    File oFile;
    String ext;
    int pos = fn.lastIndexOf('.');
    if (pos != -1) {
        ext = fn.substring(pos);//we want '.' too
        fn = fn.substring(0, pos);
    } else {
        ext = "";
    }
    fn += "_";
    obj = prepare(obj);
    prepareLineBuffer();
    int imageSize = lineLength * yRect * rectHeight;
    for (int z = 0; z < zRect; z++) {
        for (int i = 0; i < slices; i++) {
            System.out.print("*");
            chgAttributes(obj, i);
            oFile = new File(parent, fn + z + "_" + (i) + ext);
            DicomOutputStream dos = new DicomOutputStream(oFile);
            dos.writeDicomFile(obj);
            dos.writeHeader(Tag.PixelData, VR.OB, (imageSize + 1) & ~1);
            writePixelData(dos, z);
            if ((imageSize & 1) != 0)
                dos.write(0);
            dos.close();
        }
    }
}

From source file:org.dcm4che2.tool.xml2dcm.Xml2Dcm.java

private static void parseXML(String xmlFile, DicomObject dcmobj, String baseDir)
        throws FactoryConfigurationError, ParserConfigurationException, SAXException, IOException {
    SAXParserFactory f = SAXParserFactory.newInstance();
    SAXParser p = f.newSAXParser();
    ContentHandlerAdapter ch = new ContentHandlerAdapter(dcmobj);
    if (xmlFile != null) {
        p.parse(new File(xmlFile), ch);
    } else if (baseDir != null) {
        String uri = "file:" + new File(baseDir, "STDIN").getAbsolutePath();
        if (File.separatorChar == '\\') {
            uri = uri.replace('\\', '/');
        }/*from  ww w. j  a  v a 2s.co  m*/
        p.parse(System.in, ch, uri);
    } else {
        p.parse(System.in, ch);
    }
}

From source file:org.dspace.content.authority.LCNameAuthority.java

/**
 * Guts of the implementation, returns a complete Choices result, or
 * null for a failure./* w w w . java 2s  .com*/
 */
private Choices queryPerson(String text, int start, int limit) {
    // punt if there is no query text
    if (text == null || text.trim().length() == 0) {
        return new Choices(true);
    }

    // 1. build CQL query
    DCPersonName pn = new DCPersonName(text);
    StringBuilder query = new StringBuilder();
    query.append("local.FirstName = \"").append(pn.getFirstNames()).append("\" and local.FamilyName = \"")
            .append(pn.getLastName()).append("\"");

    // XXX arbitrary default limit - should be configurable?
    if (limit == 0) {
        limit = 50;
    }

    NameValuePair args[] = new NameValuePair[6];
    args[0] = new NameValuePair("operation", "searchRetrieve");
    args[1] = new NameValuePair("version", "1.1");
    args[2] = new NameValuePair("recordSchema", "info:srw/schema/1/marcxml-v1.1");
    args[3] = new NameValuePair("query", query.toString());
    args[4] = new NameValuePair("maximumRecords", String.valueOf(limit));
    args[5] = new NameValuePair("startRecord", String.valueOf(start + 1));
    HttpClient hc = new HttpClient();
    String srUrl = url + "?" + EncodingUtil.formUrlEncode(args, "UTF8");
    GetMethod get = new GetMethod(srUrl);

    log.debug("Trying SRU query, URL=" + srUrl);

    // 2. web request
    try {
        int status = hc.executeMethod(get);
        if (status == 200) {
            SAXParserFactory spf = SAXParserFactory.newInstance();
            SAXParser sp = spf.newSAXParser();
            XMLReader xr = sp.getXMLReader();
            SRUHandler handler = new SRUHandler();

            // XXX FIXME: should turn off validation here explicitly, but
            //  it seems to be off by default.
            xr.setFeature("http://xml.org/sax/features/namespaces", true);
            xr.setContentHandler(handler);
            xr.setErrorHandler(handler);
            xr.parse(new InputSource(get.getResponseBodyAsStream()));

            // this probably just means more results available..
            if (handler.hits != handler.result.size()) {
                log.warn("Discrepency in results, result.length=" + handler.result.size()
                        + ", yet expected results=" + handler.hits);
            }
            boolean more = handler.hits > (start + handler.result.size());

            // XXX add non-auth option; perhaps the UI should do this?
            // XXX it's really a policy matter if they allow unauth result.
            // XXX good, stop it.
            // handler.result.add(new Choice("", text, "Non-Authority: \""+text+"\""));

            int confidence;
            if (handler.hits == 0) {
                confidence = Choices.CF_NOTFOUND;
            } else if (handler.hits == 1) {
                confidence = Choices.CF_UNCERTAIN;
            } else {
                confidence = Choices.CF_AMBIGUOUS;
            }
            return new Choices(handler.result.toArray(new Choice[handler.result.size()]), start, handler.hits,
                    confidence, more);
        }
    } catch (HttpException e) {
        log.error("SRU query failed: ", e);
        return new Choices(true);
    } catch (IOException e) {
        log.error("SRU query failed: ", e);
        return new Choices(true);
    } catch (ParserConfigurationException e) {
        log.warn("Failed parsing SRU result: ", e);
        return new Choices(true);
    } catch (SAXException e) {
        log.warn("Failed parsing SRU result: ", e);
        return new Choices(true);
    } finally {
        get.releaseConnection();
    }
    return new Choices(true);
}

From source file:org.dspace.content.authority.SHERPARoMEOProtocol.java

protected Choices query(String result, String label, String authority, NameValuePair[] args, int start,
        int limit) {
    HttpClient hc = new HttpClient();
    String srUrl = url + "?" + EncodingUtil.formUrlEncode(args, "UTF8");
    GetMethod get = new GetMethod(srUrl);

    log.debug("Trying SHERPA/RoMEO Query, URL=" + srUrl);

    try {//from   w  w  w. jav a 2  s  . c o m
        int status = hc.executeMethod(get);
        if (status == 200) {
            SAXParserFactory spf = SAXParserFactory.newInstance();
            SAXParser sp = spf.newSAXParser();
            XMLReader xr = sp.getXMLReader();
            SRHandler handler = new SRHandler(result, label, authority);

            // XXX FIXME: should turn off validation here explicitly, but
            //  it seems to be off by default.
            xr.setFeature("http://xml.org/sax/features/namespaces", true);
            xr.setContentHandler(handler);
            xr.setErrorHandler(handler);
            xr.parse(new InputSource(get.getResponseBodyAsStream()));
            int confidence;
            if (handler.total == 0) {
                confidence = Choices.CF_NOTFOUND;
            } else if (handler.total == 1) {
                confidence = Choices.CF_UNCERTAIN;
            } else {
                confidence = Choices.CF_AMBIGUOUS;
            }
            return new Choices(handler.result, start, handler.total, confidence, false);
        }
    } catch (HttpException e) {
        log.error("SHERPA/RoMEO query failed: ", e);
        return null;
    } catch (IOException e) {
        log.error("SHERPA/RoMEO query failed: ", e);
        return null;
    } catch (ParserConfigurationException e) {
        log.warn("Failed parsing SHERPA/RoMEO result: ", e);
        return null;
    } catch (SAXException e) {
        log.warn("Failed parsing SHERPA/RoMEO result: ", e);
        return null;
    } finally {
        get.releaseConnection();
    }
    return null;
}

From source file:org.dspace.content.authority.SkylightAPIProtocol.java

protected Choices query(String result, String label, String authority, String args, int start, int limit)
        throws UnsupportedEncodingException {
    String encodedArgs = new String(args.getBytes("UTF-8"), "UTF-8");
    HttpClient hc = new HttpClient();
    String srUrl = url + "/search/" + encodedArgs + ".xml?field=" + label;
    GetMethod get = new GetMethod(srUrl);

    log.info("Trying Skylight Query, URL=" + srUrl);

    try {/*from  www . ja  v  a  2s  . co m*/
        int status = hc.executeMethod(get);
        log.info("Status" + status);
        if (status == 200) {
            SAXParserFactory spf = SAXParserFactory.newInstance();
            SAXParser sp = spf.newSAXParser();
            XMLReader xr = sp.getXMLReader();
            SRHandler handler = new SRHandler(result, label, authority);

            // XXX FIXME: should turn off validation here explicitly, but
            //  it seems to be off by default.
            xr.setFeature("http://xml.org/sax/features/namespaces", true);
            xr.setContentHandler(handler);
            xr.setErrorHandler(handler);
            InputSource src = new InputSource(get.getResponseBodyAsStream());
            log.info("Source from sklightui :: " + src.toString());
            xr.parse(src);

            int confidence;
            if (handler.total == 0) {
                confidence = Choices.CF_NOTFOUND;
            } else if (handler.total == 1) {
                confidence = Choices.CF_UNCERTAIN;
            } else {
                confidence = Choices.CF_AMBIGUOUS;
            }
            return new Choices(handler.result, start, handler.total, confidence, false);
        }
    } catch (HttpException e) {
        log.error("Skylight query failed: ", e);
        return null;
    } catch (IOException e) {
        log.error("Skylight query failed: ", e);
        return null;
    } catch (ParserConfigurationException e) {
        log.warn("Failed parsing SHERPA/RoMEO result: ", e);
        return null;
    } catch (SAXException e) {
        log.warn("Failed parsing Skylight result: ", e);
        return null;
    } finally {
        get.releaseConnection();
    }
    return null;
}

From source file:org.dspace.testing.PubMedToImport.java

public static void main(String args[]) {
    Options options = new Options();

    options.addOption(new Option("s", "source", true, "Source xml"));
    options.addOption(new Option("o", "output", true, "Output directory"));

    try {/*w  w  w .ja va 2  s. co  m*/
        CommandLine cli = new PosixParser().parse(options, args);

        String source = cli.getOptionValue("s");
        String output = cli.getOptionValue("o");

        if (!new File(source).exists()) {
            throw new IllegalArgumentException("Source file does not exist");
        }

        outputDir = new File(output);
        if (outputDir.exists()) {
            if (outputDir.list().length > 0) {
                throw new IllegalStateException("Output directory must be empty");
            }
        } else {
            if (!outputDir.mkdirs()) {
                throw new IllegalStateException("Unable to create output directory");
            }
        }

        SAXParserFactory factory = SAXParserFactory.newInstance();
        SAXParser saxParser = factory.newSAXParser();

        saxParser.parse(source, new PubMedHandler());

    } catch (Exception e) {

    }
}