Example usage for javax.xml.stream XMLStreamException printStackTrace

List of usage examples for javax.xml.stream XMLStreamException printStackTrace

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Introduction

In this page you can find the example usage for javax.xml.stream XMLStreamException printStackTrace.

Prototype

public void printStackTrace()

Source Link

Document

Prints this throwable and its backtrace to the standard error stream.

Usage

From source file:fr.openwide.talendalfresco.rest.client.RestAuthenticationTest.java

public void testRestLogin() {
    // create client and configure it
    HttpClient client = new HttpClient();
    client.getHttpConnectionManager().getParams().setConnectionTimeout(timeout);

    // instantiating a new method and configuring it
    GetMethod method = new GetMethod(restCommandUrlPrefix + "login");
    method.setFollowRedirects(true); // ?
    // Provide custom retry handler is necessary (?)
    method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
            new DefaultHttpMethodRetryHandler(3, false));
    NameValuePair[] params = new NameValuePair[] { new NameValuePair("username", "admin"),
            new NameValuePair("password", "admin") };
    method.setQueryString(params);//  www  . ja  va  2  s.c o m

    try {
        // Execute the method.
        int statusCode = client.executeMethod(method);

        if (statusCode != HttpStatus.SC_OK) {
            System.err.println("Method failed: " + method.getStatusLine());
        }

        // Read the response body.
        byte[] responseBody = method.getResponseBody();
        System.out.println(new String(responseBody)); // TODO rm

        HashSet<String> defaultElementSet = new HashSet<String>(
                Arrays.asList(new String[] { RestConstants.TAG_COMMAND, RestConstants.TAG_CODE,
                        RestConstants.TAG_CONTENT, RestConstants.TAG_ERROR, RestConstants.TAG_MESSAGE }));
        HashMap<String, String> elementValueMap = new HashMap<String, String>(6);

        try {
            XMLEventReader xmlReader = XmlHelper.getXMLInputFactory()
                    .createXMLEventReader(new ByteArrayInputStream(responseBody));
            StringBuffer singleLevelTextBuf = null;
            while (xmlReader.hasNext()) {
                XMLEvent event = xmlReader.nextEvent();
                switch (event.getEventType()) {
                case XMLEvent.CHARACTERS:
                case XMLEvent.CDATA:
                    if (singleLevelTextBuf != null) {
                        singleLevelTextBuf.append(event.asCharacters().getData());
                    } // else element not meaningful
                    break;
                case XMLEvent.START_ELEMENT:
                    StartElement startElement = event.asStartElement();
                    String elementName = startElement.getName().getLocalPart();
                    if (defaultElementSet.contains(elementName)
                            // TODO another command specific level
                            || "ticket".equals(elementName)) {
                        // reinit buffer at start of meaningful elements
                        singleLevelTextBuf = new StringBuffer();
                    } else {
                        singleLevelTextBuf = null; // not useful
                    }
                    break;
                case XMLEvent.END_ELEMENT:
                    if (singleLevelTextBuf == null) {
                        break; // element not meaningful
                    }

                    // TODO or merely put it in the map since the element has been tested at start
                    EndElement endElement = event.asEndElement();
                    elementName = endElement.getName().getLocalPart();
                    if (defaultElementSet.contains(elementName)) {
                        String value = singleLevelTextBuf.toString();
                        elementValueMap.put(elementName, value);
                        // TODO test if it is code and it is not OK, break to error handling
                    }
                    // TODO another command specific level
                    else if ("ticket".equals(elementName)) {
                        ticket = singleLevelTextBuf.toString();
                    }
                    // singleLevelTextBuf = new StringBuffer(); // no ! in start
                    break;
                }
            }
        } catch (XMLStreamException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (Throwable t) {
            // TODO Auto-generated catch block
            t.printStackTrace();
            //throw t;
        }

        String code = elementValueMap.get(RestConstants.TAG_CODE);
        assertTrue(RestConstants.CODE_OK.equals(code));
        System.out.println("got ticket " + ticket);

    } catch (HttpException e) {
        // TODO
        e.printStackTrace();
    } catch (IOException e) {
        // TODO
        e.printStackTrace();
    } finally {
        // Release the connection.
        method.releaseConnection();
    }
}

From source file:eu.interedition.collatex.tools.CollationServer.java

public void service(Request request, Response response) throws Exception {
    final Deque<String> path = path(request);
    if (path.isEmpty() || !"collate".equals(path.pop())) {
        response.sendError(404);//from w  ww . j  a va2s. c  om
        return;
    }

    final SimpleCollation collation = JsonProcessor.read(request.getInputStream());
    if (maxCollationSize > 0) {
        for (SimpleWitness witness : collation.getWitnesses()) {
            final int witnessLength = witness.getTokens().stream().filter(t -> t instanceof SimpleToken)
                    .map(t -> (SimpleToken) t).mapToInt(t -> t.getContent().length()).sum();
            if (witnessLength > maxCollationSize) {
                response.sendError(413, "Request Entity Too Large");
                return;
            }
        }
    }

    response.suspend(60, TimeUnit.SECONDS, new EmptyCompletionHandler<>());
    collationThreads.submit(() -> {
        try {
            final VariantGraph graph = new VariantGraph();
            collation.collate(graph);

            // CORS support
            response.setHeader("Access-Control-Allow-Origin",
                    Optional.ofNullable(request.getHeader("Origin")).orElse("*"));
            response.setHeader("Access-Control-Allow-Methods",
                    Optional.ofNullable(request.getHeader("Access-Control-Request-Method"))
                            .orElse("GET, POST, HEAD, OPTIONS"));
            response.setHeader("Access-Control-Allow-Headers",
                    Optional.ofNullable(request.getHeader("Access-Control-Request-Headers"))
                            .orElse("Content-Type, Accept, X-Requested-With"));
            response.setHeader("Access-Control-Max-Age", "86400");
            response.setHeader("Access-Control-Allow-Credentials", "true");

            final String clientAccepts = Optional.ofNullable(request.getHeader(Header.Accept)).orElse("");

            if (clientAccepts.contains("text/plain")) {
                response.setContentType("text/plain");
                response.setCharacterEncoding("utf-8");
                try (final Writer out = response.getWriter()) {
                    new SimpleVariantGraphSerializer(graph).toDot(out);
                }
                response.resume();

            } else if (clientAccepts.contains("application/tei+xml")) {
                XMLStreamWriter xml = null;
                try {
                    response.setContentType("application/tei+xml");
                    try (OutputStream responseStream = response.getOutputStream()) {
                        xml = XMLOutputFactory.newInstance().createXMLStreamWriter(responseStream);
                        xml.writeStartDocument();
                        new SimpleVariantGraphSerializer(graph).toTEI(xml);
                        xml.writeEndDocument();
                    } finally {
                        if (xml != null) {
                            xml.close();
                        }
                    }
                    response.resume();
                } catch (XMLStreamException e) {
                    e.printStackTrace();
                }
            } else if (clientAccepts.contains("application/graphml+xml")) {
                XMLStreamWriter xml = null;
                try {
                    response.setContentType("application/graphml+xml");
                    try (OutputStream responseStream = response.getOutputStream()) {
                        xml = XMLOutputFactory.newInstance().createXMLStreamWriter(responseStream);
                        xml.writeStartDocument();
                        new SimpleVariantGraphSerializer(graph).toGraphML(xml);
                        xml.writeEndDocument();
                    } finally {
                        if (xml != null) {
                            xml.close();
                        }
                    }
                    response.resume();
                } catch (XMLStreamException e) {
                    e.printStackTrace();
                }
            } else if (clientAccepts.contains("image/svg+xml")) {
                if (dotPath == null) {
                    response.sendError(204);
                    response.resume();
                } else {
                    final StringWriter dot = new StringWriter();
                    new SimpleVariantGraphSerializer(graph).toDot(dot);

                    final Process dotProc = new ProcessBuilder(dotPath, "-Grankdir=LR", "-Gid=VariantGraph",
                            "-Tsvg").start();
                    final StringWriter errors = new StringWriter();
                    CompletableFuture.allOf(CompletableFuture.runAsync(() -> {
                        final char[] buf = new char[8192];
                        try (final Reader errorStream = new InputStreamReader(dotProc.getErrorStream())) {
                            int len;
                            while ((len = errorStream.read(buf)) >= 0) {
                                errors.write(buf, 0, len);
                            }
                        } catch (IOException e) {
                            throw new CompletionException(e);
                        }
                    }, processThreads), CompletableFuture.runAsync(() -> {
                        try (final Writer dotProcStream = new OutputStreamWriter(dotProc.getOutputStream(),
                                "UTF-8")) {
                            dotProcStream.write(dot.toString());
                        } catch (IOException e) {
                            throw new CompletionException(e);
                        }
                    }, processThreads), CompletableFuture.runAsync(() -> {
                        response.setContentType("image/svg+xml");
                        final byte[] buf = new byte[8192];
                        try (final InputStream in = dotProc.getInputStream();
                                final OutputStream out = response.getOutputStream()) {
                            int len;
                            while ((len = in.read(buf)) >= 0) {
                                out.write(buf, 0, len);
                            }
                        } catch (IOException e) {
                            throw new CompletionException(e);
                        }
                    }, processThreads), CompletableFuture.runAsync(() -> {
                        try {
                            if (!dotProc.waitFor(60, TimeUnit.SECONDS)) {
                                throw new CompletionException(new RuntimeException(
                                        "dot processing took longer than 60 seconds, process was timed out."));
                            }
                            if (dotProc.exitValue() != 0) {
                                throw new CompletionException(new IllegalStateException(errors.toString()));
                            }
                        } catch (InterruptedException e) {
                            throw new CompletionException(e);
                        }
                    }, processThreads)).exceptionally(t -> {
                        t.printStackTrace();
                        return null;
                    }).thenRunAsync(response::resume, processThreads);
                }
            } else {
                response.setContentType("application/json");
                try (final OutputStream responseStream = response.getOutputStream()) {
                    JsonProcessor.write(graph, responseStream);
                }
                response.resume();
            }
        } catch (IOException e) {
            // FIXME: ignored
        }
    });
}

From source file:fr.openwide.talendalfresco.rest.client.importer.RestImportFileTest.java

public void login() {
    // create client and configure it
    HttpClient client = new HttpClient();
    client.getHttpConnectionManager().getParams().setConnectionTimeout(timeout);

    // instantiating a new method and configuring it
    GetMethod method = new GetMethod(restCommandUrlPrefix + "login");
    method.setFollowRedirects(true); // ?
    // Provide custom retry handler is necessary (?)
    method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
            new DefaultHttpMethodRetryHandler(3, false));
    NameValuePair[] params = new NameValuePair[] { new NameValuePair("username", "admin"),
            new NameValuePair("password", "admin") };
    method.setQueryString(params);/*from w w  w.  j a v a 2s.  c  om*/

    try {
        // Execute the method.
        int statusCode = client.executeMethod(method);

        if (statusCode != HttpStatus.SC_OK) {
            System.err.println("Method failed: " + method.getStatusLine());
        }

        // Read the response body.
        byte[] responseBody = method.getResponseBody();
        System.out.println(new String(responseBody)); // TODO rm

        HashSet<String> defaultElementSet = new HashSet<String>(
                Arrays.asList(new String[] { RestConstants.TAG_COMMAND, RestConstants.TAG_CODE,
                        RestConstants.TAG_CONTENT, RestConstants.TAG_ERROR, RestConstants.TAG_MESSAGE }));
        HashMap<String, String> elementValueMap = new HashMap<String, String>(6);

        try {
            XMLEventReader xmlReader = XmlHelper.getXMLInputFactory()
                    .createXMLEventReader(new ByteArrayInputStream(responseBody));
            StringBuffer singleLevelTextBuf = null;
            while (xmlReader.hasNext()) {
                XMLEvent event = xmlReader.nextEvent();
                switch (event.getEventType()) {
                case XMLEvent.CHARACTERS:
                case XMLEvent.CDATA:
                    if (singleLevelTextBuf != null) {
                        singleLevelTextBuf.append(event.asCharacters().getData());
                    } // else element not meaningful
                    break;
                case XMLEvent.START_ELEMENT:
                    StartElement startElement = event.asStartElement();
                    String elementName = startElement.getName().getLocalPart();
                    if (defaultElementSet.contains(elementName)
                            // TODO another command specific level
                            || "ticket".equals(elementName)) {
                        // reinit buffer at start of meaningful elements
                        singleLevelTextBuf = new StringBuffer();
                    } else {
                        singleLevelTextBuf = null; // not useful
                    }
                    break;
                case XMLEvent.END_ELEMENT:
                    if (singleLevelTextBuf == null) {
                        break; // element not meaningful
                    }

                    // TODO or merely put it in the map since the element has been tested at start
                    EndElement endElement = event.asEndElement();
                    elementName = endElement.getName().getLocalPart();
                    if (defaultElementSet.contains(elementName)) {
                        String value = singleLevelTextBuf.toString();
                        elementValueMap.put(elementName, value);
                        // TODO test if it is code and it is not OK, break to error handling
                    }
                    // TODO another command specific level
                    else if ("ticket".equals(elementName)) {
                        ticket = singleLevelTextBuf.toString();
                    }
                    // singleLevelTextBuf = new StringBuffer(); // no ! in start
                    break;
                }
            }
        } catch (XMLStreamException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (Throwable t) {
            // TODO Auto-generated catch block
            t.printStackTrace();
            //throw t;
        }

        String code = elementValueMap.get(RestConstants.TAG_CODE);
        assertTrue(RestConstants.CODE_OK.equals(code));
        System.out.println("got ticket " + ticket);

    } catch (HttpException e) {
        // TODO
        e.printStackTrace();
    } catch (IOException e) {
        // TODO
        e.printStackTrace();
    } finally {
        // Release the connection.
        method.releaseConnection();
    }
}

From source file:edu.jhu.pha.vospace.node.Node.java

public String getXmlMetadata(Detail detail) {

    StringWriter jobWriter = new StringWriter();
    try {/*from w  ww . j ava  2 s. co m*/
        XMLStreamWriter xsw = XMLOutputFactory.newInstance().createXMLStreamWriter(jobWriter);
        xsw.writeStartDocument();

        xsw.setDefaultNamespace(VOS_NAMESPACE);

        xsw.writeStartElement("node");
        xsw.writeNamespace("xsi", XSI_NAMESPACE);
        xsw.writeNamespace(null, VOS_NAMESPACE);
        xsw.writeAttribute("xsi:type", this.getType().getTypeName());
        xsw.writeAttribute("uri", this.getUri().toString());

        if (detail == Detail.max) {
            xsw.writeStartElement("properties");
            Map<String, String> properties = this.getMetastore().getProperties(this.getUri());
            properties.put(LENGTH_PROPERTY, Long.toString(getNodeInfo().getSize()));
            properties.put(DATE_PROPERTY, dropboxDateFormat.format(getNodeInfo().getMtime()));
            if (this.getType() == NodeType.DATA_NODE || this.getType() == NodeType.STRUCTURED_DATA_NODE
                    || this.getType() == NodeType.UNSTRUCTURED_DATA_NODE) {
                properties.put(CONTENTTYPE_PROPERTY, getNodeInfo().getContentType());
            }

            for (String propUri : properties.keySet()) {
                xsw.writeStartElement("property");
                xsw.writeAttribute("uri", propUri);
                xsw.writeCharacters(properties.get(propUri));
                xsw.writeEndElement();
            }

            xsw.writeEndElement();

            xsw.writeStartElement("accepts");
            xsw.writeEndElement();

            xsw.writeStartElement("provides");
            xsw.writeEndElement();

            xsw.writeStartElement("capabilities");
            xsw.writeEndElement();

            if (this.getType() == NodeType.CONTAINER_NODE) {
                NodesList childrenList = ((ContainerNode) this).getDirectChildren(false, 0, -1);
                List<Node> children = childrenList.getNodesList();

                xsw.writeStartElement("nodes");
                for (Node childNode : children) {
                    xsw.writeStartElement("node");
                    xsw.writeAttribute("uri", childNode.getUri().getId().toString());
                    xsw.writeEndElement();
                }
                xsw.writeEndElement();

            }

        }

        xsw.writeEndElement();

        xsw.writeEndDocument();
        xsw.close();
    } catch (XMLStreamException e) {
        e.printStackTrace();
        throw new InternalServerErrorException(e);
    }
    return jobWriter.getBuffer().toString();
}

From source file:fr.openwide.talendalfresco.rest.client.importer.RestImportFileTest.java

public void testSingleFileImport() {
    // create client and configure it
    HttpClient client = new HttpClient();
    client.getHttpConnectionManager().getParams().setConnectionTimeout(timeout);

    // instantiating a new method and configuring it
    PostMethod method = new PostMethod(restCommandUrlPrefix + "import");
    // Provide custom retry handler is necessary (?)
    method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
            new DefaultHttpMethodRetryHandler(3, false));
    NameValuePair[] params = new NameValuePair[] { new NameValuePair("path", "/app:company_home"),
            new NameValuePair("ticket", ticket) };
    method.setQueryString(params);//from ww w. j  a v a  2 s. co  m

    try {
        //method.setRequestBody(new NameValuePair[] {
        //      new NameValuePair("path", "/app:company_home") });
        FileInputStream acpXmlIs = new FileInputStream(SAMPLE_SINGLE_FILE_PATH);
        InputStreamRequestEntity entity = new InputStreamRequestEntity(acpXmlIs);
        //InputStreamRequestEntity entity = new InputStreamRequestEntity(acpXmlIs, "text/xml; charset=ISO-8859-1");
        method.setRequestEntity(entity);
    } catch (IOException ioex) {
        fail("ACP XML file not found " + ioex.getMessage());
    }

    try {
        // Execute the method.
        int statusCode = client.executeMethod(method);

        if (statusCode != HttpStatus.SC_OK) {
            System.err.println("Method failed: " + method.getStatusLine());
        }

        // Read the response body.
        byte[] responseBody = method.getResponseBody();
        System.out.println(new String(responseBody)); // TODO rm

        HashSet<String> defaultElementSet = new HashSet<String>(
                Arrays.asList(new String[] { RestConstants.TAG_COMMAND, RestConstants.TAG_CODE,
                        RestConstants.TAG_CONTENT, RestConstants.TAG_ERROR, RestConstants.TAG_MESSAGE }));
        HashMap<String, String> elementValueMap = new HashMap<String, String>(6);

        try {
            XMLEventReader xmlReader = XmlHelper.getXMLInputFactory()
                    .createXMLEventReader(new ByteArrayInputStream(responseBody));
            StringBuffer singleLevelTextBuf = null;
            while (xmlReader.hasNext()) {
                XMLEvent event = xmlReader.nextEvent();
                switch (event.getEventType()) {
                case XMLEvent.CHARACTERS:
                case XMLEvent.CDATA:
                    if (singleLevelTextBuf != null) {
                        singleLevelTextBuf.append(event.asCharacters().getData());
                    } // else element not meaningful
                    break;
                case XMLEvent.START_ELEMENT:
                    StartElement startElement = event.asStartElement();
                    String elementName = startElement.getName().getLocalPart();
                    if (defaultElementSet.contains(elementName)
                            // TODO another command specific level
                            || "ticket".equals(elementName)) {
                        // reinit buffer at start of meaningful elements
                        singleLevelTextBuf = new StringBuffer();
                    } else {
                        singleLevelTextBuf = null; // not useful
                    }
                    break;
                case XMLEvent.END_ELEMENT:
                    if (singleLevelTextBuf == null) {
                        break; // element not meaningful
                    }

                    // TODO or merely put it in the map since the element has been tested at start
                    EndElement endElement = event.asEndElement();
                    elementName = endElement.getName().getLocalPart();
                    if (defaultElementSet.contains(elementName)) {
                        String value = singleLevelTextBuf.toString();
                        elementValueMap.put(elementName, value);
                        // TODO test if it is code and it is not OK, break to error handling
                    }
                    // TODO another command specific level
                    else if ("ticket".equals(elementName)) {
                        ticket = singleLevelTextBuf.toString();
                    }
                    // singleLevelTextBuf = new StringBuffer(); // no ! in start
                    break;
                }
            }
        } catch (XMLStreamException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (Throwable t) {
            // TODO Auto-generated catch block
            t.printStackTrace();
            //throw t;
        }

        String code = elementValueMap.get(RestConstants.TAG_CODE);
        assertTrue(RestConstants.CODE_OK.equals(code));
        System.out.println("got ticket " + ticket);

    } catch (HttpException e) {
        // TODO
        e.printStackTrace();
    } catch (IOException e) {
        // TODO
        e.printStackTrace();
    } finally {
        // Release the connection.
        method.releaseConnection();
    }
}

From source file:com.biomeris.i2b2.export.ws.ExportService.java

public OMElement testSession(OMElement inputElement) throws I2B2Exception, JsonSyntaxException {
    Assert.notNull(inputElement, "Export Cell: Incoming request is null");

    MessageHeaderType messageHeaderType = MessageManager.extractReqMess(inputElement).getMessageHeader();
    String requestJsonStr = MessageManager.extractObsBlob(inputElement);

    Gson gson = new Gson();
    TestSessionRequest request = gson.fromJson(requestJsonStr, TestSessionRequest.class);

    TestSessionResponse response = new TestSessionResponse();

    WSession wSession = sessionManager.getSession(request.getSessionId());
    if (wSession != null) {
        response.setValid(true);//from   w  w w  .  j  a  va 2  s  .  co m
    } else {
        response.setValid(false);
    }
    response.setLifeSpan(sessionLifespan);

    String tsrString = new GsonBuilder().create().toJson(response);

    ObservationSet observationSet = new ObservationSet();
    ObservationType observationType = new ObservationType();
    BlobType blobType = new BlobType();
    blobType.getContent().add(tsrString);
    observationType.setObservationBlob(blobType);
    observationSet.getObservation().add(observationType);

    ResponseMessageType responseMessageType = MessageFactory.createBuildResponse(messageHeaderType,
            observationSet);
    String rmtString = MessageFactory.convertToXMLString(responseMessageType);

    OMElement out = null;
    try {
        out = MessageFactory.createResponseOMElementFromString(rmtString);
    } catch (XMLStreamException e) {
        e.printStackTrace();
    }

    log.debug(rmtString);

    return out;
}

From source file:com.biomeris.i2b2.export.ws.ExportService.java

public OMElement openNewSession(OMElement inputElement) throws I2B2Exception, JsonSyntaxException {
    Assert.notNull(inputElement, "Export Cell: Incoming request is null");

    MessageHeaderType messageHeaderType = MessageManager.extractReqMess(inputElement).getMessageHeader();
    String requestJsonStr = MessageManager.extractObsBlob(inputElement);

    Gson gson = new Gson();
    OpenNewSessionRequest request = gson.fromJson(requestJsonStr, OpenNewSessionRequest.class);

    boolean validUser = false;
    if (authStrategy > 0) {
        try {//ww w. ja  va 2s . c  o m
            validUser = validateUser(request.getNetwork());
        } catch (JAXBException | IOException | TransformerException e1) {
            // do nothing
        }
    } else {
        validUser = true;
    }

    OpenNewSessionResponse response = new OpenNewSessionResponse();
    if (!validUser) {
        String error = "You are not allowed to use export functions";
        response.setError(error);
    } else {
        WSession wSession = sessionManager.createNewSession();
        wSession.setNetwork(request.getNetwork());
        Session session = new Session();
        session.setId(wSession.getId());
        response.setSession(session);
    }

    String onsrString = new GsonBuilder().create().toJson(response);

    ObservationSet observationSet = new ObservationSet();
    ObservationType observationType = new ObservationType();
    BlobType blobType = new BlobType();
    blobType.getContent().add(onsrString);
    observationType.setObservationBlob(blobType);
    observationSet.getObservation().add(observationType);

    ResponseMessageType responseMessageType = MessageFactory.createBuildResponse(messageHeaderType,
            observationSet);
    String rmtString = MessageFactory.convertToXMLString(responseMessageType);

    OMElement out = null;
    try {
        out = MessageFactory.createResponseOMElementFromString(rmtString);
    } catch (XMLStreamException e) {
        e.printStackTrace();
    }

    log.debug(rmtString);

    return out;
}

From source file:net.cloudkit.toolkit.DownloadTest.java

@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_EACH_TEST_METHOD)
@Transactional/*from  w  ww.j  a v  a 2  s  .  com*/
@Test
public void test() throws Exception {

    Map<String, Object> cdl = new HashMap<>();
    Map<String, String> cdlBillHead = null;
    Map<String, String> cdlBillList = null;
    List<Map<String, String>> cdlBillLists = new ArrayList<>();
    Map<String, String> cdlBillDoc = null;
    List<Map<String, String>> cdlBillDocs = new ArrayList<>();

    // MESSAGE_CONFIG
    // InputStream
    InputStream in = null;
    try {

        // StAX?
        XMLInputFactory xif = XMLInputFactory.newInstance();
        // ?
        XMLStreamReader reader = xif
                .createXMLStreamReader(new FileInputStream(new File("D:\\temp\\bill\\CDL100000006531646.xml")));

        // 
        while (reader.hasNext()) {
            // ?
            int event = reader.next();

            // 
            // if (reader.getEventType() == XMLStreamConstants.START_ELEMENT) {
            if (event == XMLStreamReader.START_ELEMENT) {
                // CdlBill/CdlBillHead
                if ("CdlBillHead".equals(reader.getLocalName())) {
                    cdlBillHead = new LinkedHashMap<>();
                }
                {
                    // BillSeq
                    if ("BillSeq".equals(reader.getLocalName())) {
                        cdlBillHead.put("BillSeq", reader.getElementText());
                    }
                    // ListNo
                    if ("ListNo".equals(reader.getLocalName())) {
                        cdlBillHead.put("ListNo", reader.getElementText());
                    }
                    // IEFlag
                    if ("IEFlag".equals(reader.getLocalName())) {
                        cdlBillHead.put("IEFlag", reader.getElementText());
                    }
                    // IEPort
                    if ("IEPort".equals(reader.getLocalName())) {
                        cdlBillHead.put("IEPort", reader.getElementText());
                    }
                    // IEDate
                    if ("IEDate".equals(reader.getLocalName())) {
                        cdlBillHead.put("IEDate", reader.getElementText());
                    }
                    // RecordsNo
                    if ("RecordsNo".equals(reader.getLocalName())) {
                        cdlBillHead.put("RecordsNo", reader.getElementText());
                    }
                    // TradeCode
                    if ("TradeCode".equals(reader.getLocalName())) {
                        cdlBillHead.put("TradeCode", reader.getElementText());
                    }
                    // TradeName
                    if ("TradeName".equals(reader.getLocalName())) {
                        cdlBillHead.put("TradeName", reader.getElementText());
                    }
                    // OwnerCode
                    if ("OwnerCode".equals(reader.getLocalName())) {
                        cdlBillHead.put("OwnerCode", reader.getElementText());
                    }
                    // OwnerName
                    if ("OwnerName".equals(reader.getLocalName())) {
                        cdlBillHead.put("OwnerName", reader.getElementText());
                    }
                    // TrafMode
                    if ("TrafMode".equals(reader.getLocalName())) {
                        cdlBillHead.put("TrafMode", reader.getElementText());
                    }
                    // ShipName
                    if ("ShipName".equals(reader.getLocalName())) {
                        cdlBillHead.put("ShipName", reader.getElementText());
                    }
                    // VoyageNo
                    if ("VoyageNo".equals(reader.getLocalName())) {
                        cdlBillHead.put("VoyageNo", reader.getElementText());
                    }
                    // BillNo
                    if ("BillNo".equals(reader.getLocalName())) {
                        cdlBillHead.put("BillNo", reader.getElementText());
                    }
                    // TradeMode
                    if ("TradeMode".equals(reader.getLocalName())) {
                        cdlBillHead.put("TradeMode", reader.getElementText());
                    }
                    // TradeCountry
                    if ("TradeCountry".equals(reader.getLocalName())) {
                        cdlBillHead.put("TradeCountry", reader.getElementText());
                    }
                    // DestinationPort
                    if ("DestinationPort".equals(reader.getLocalName())) {
                        cdlBillHead.put("DestinationPort", reader.getElementText());
                    }
                    // DistrictCode
                    if ("DistrictCode".equals(reader.getLocalName())) {
                        cdlBillHead.put("DistrictCode", reader.getElementText());
                    }
                    // PackNum
                    if ("PackNum".equals(reader.getLocalName())) {
                        cdlBillHead.put("PackNum", reader.getElementText());
                    }
                    // WrapType
                    if ("WrapType".equals(reader.getLocalName())) {
                        cdlBillHead.put("WrapType", reader.getElementText());
                    }
                    // GrossWt
                    if ("GrossWt".equals(reader.getLocalName())) {
                        cdlBillHead.put("GrossWt", reader.getElementText());
                    }
                    // NetWt
                    if ("NetWt".equals(reader.getLocalName())) {
                        cdlBillHead.put("NetWt", reader.getElementText());
                    }
                    // ListType
                    if ("ListType".equals(reader.getLocalName())) {
                        cdlBillHead.put("ListType", reader.getElementText());
                    }
                    // ListStat
                    if ("ListStat".equals(reader.getLocalName())) {
                        cdlBillHead.put("ListStat", reader.getElementText());
                    }
                    // DocuCodeCom
                    if ("DocuCodeCom".equals(reader.getLocalName())) {
                        cdlBillHead.put("DocuCodeCom", reader.getElementText());
                    }
                    // AgentCode
                    if ("AgentCode".equals(reader.getLocalName())) {
                        cdlBillHead.put("AgentCode", reader.getElementText());
                    }
                    // AgentName
                    if ("AgentName".equals(reader.getLocalName())) {
                        cdlBillHead.put("AgentName", reader.getElementText());
                    }
                    // DeclCustom
                    if ("DeclCustom".equals(reader.getLocalName())) {
                        cdlBillHead.put("DeclCustom", reader.getElementText());
                    }
                    // DeclDate
                    if ("DeclDate".equals(reader.getLocalName())) {
                        cdlBillHead.put("DeclDate", reader.getElementText());
                    }
                    // GType
                    if ("GType".equals(reader.getLocalName())) {
                        cdlBillHead.put("GType", reader.getElementText());
                    }

                }

                // CdlBill/CdlBillLists/CdlBillList
                if ("CdlBillList".equals(reader.getLocalName())) {
                    cdlBillList = new LinkedHashMap<>();
                }
                {
                    // GNo
                    if ("GNo".equals(reader.getLocalName())) {
                        cdlBillList.put("GNo", reader.getElementText());
                    }
                    // ItemNo
                    if ("ItemNo".equals(reader.getLocalName())) {
                        cdlBillList.put("ItemNo", reader.getElementText());
                    }
                    // CodeTs
                    if ("CodeTs".equals(reader.getLocalName())) {
                        cdlBillList.put("CodeTs", reader.getElementText());
                    }
                    // GName
                    if ("GName".equals(reader.getLocalName())) {
                        cdlBillList.put("GName", reader.getElementText());
                    }
                    // GModel
                    if ("GModel".equals(reader.getLocalName())) {
                        cdlBillList.put("GModel", reader.getElementText());
                    }
                    // GQty
                    if ("GQty".equals(reader.getLocalName())) {
                        cdlBillList.put("GQty", reader.getElementText());
                    }
                    // GUnit
                    if ("GUnit".equals(reader.getLocalName())) {
                        cdlBillList.put("GUnit", reader.getElementText());
                    }
                    // DeclPrice
                    if ("DeclPrice".equals(reader.getLocalName())) {
                        cdlBillList.put("DeclPrice", reader.getElementText());
                    }
                    // DeclTotal
                    if ("DeclTotal".equals(reader.getLocalName())) {
                        cdlBillList.put("DeclTotal", reader.getElementText());
                    }
                    // TradeCurr
                    if ("TradeCurr".equals(reader.getLocalName())) {
                        cdlBillList.put("TradeCurr", reader.getElementText());
                    }
                    // OriginalalCountry
                    if ("OriginalalCountry".equals(reader.getLocalName())) {
                        cdlBillList.put("OriginalalCountry", reader.getElementText());
                    }
                    // DutyMode
                    if ("DutyMode".equals(reader.getLocalName())) {
                        cdlBillList.put("DutyMode", reader.getElementText());
                    }
                    // Unit1
                    if ("Unit1".equals(reader.getLocalName())) {
                        cdlBillList.put("Unit1", reader.getElementText());
                    }
                    // Unit2
                    if ("Unit2".equals(reader.getLocalName())) {
                        cdlBillList.put("Unit2", reader.getElementText());
                    }
                }

                // CdlBill/CdlBillDocs/CdlBillDoc
                if ("CdlBillDoc".equals(reader.getLocalName())) {
                    cdlBillDoc = new LinkedHashMap<>();
                }
                {
                    // DocCode
                    if ("DocCode".equals(reader.getLocalName())) {
                        cdlBillDoc.put("DocCode", reader.getElementText());
                    }
                    // CertNo
                    if ("CertNo".equals(reader.getLocalName())) {
                        cdlBillDoc.put("CertNo", reader.getElementText());
                    }
                }
            }

            if (event == XMLStreamReader.END_ELEMENT) {
                // CdlBill/CdlBillHead
                if ("CdlBillHead".equals(reader.getLocalName())) {

                }

                // CdlBill/CdlBillLists/CdlBillList
                if ("CdlBillList".equals(reader.getLocalName())) {
                    cdlBillLists.add(cdlBillList);
                }

                // CdlBill/CdlBillDocs/CdlBillDoc
                if ("CdlBillDoc".equals(reader.getLocalName())) {
                    cdlBillDocs.add(cdlBillDoc);
                }
            }
        }
    } catch (XMLStreamException e) {
        e.printStackTrace();
    } finally {
        if (in != null) {
            try {
                in.close();
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }

    cdl.put("CdlBillHead", cdlBillHead);
    cdl.put("CdlBillLists", cdlBillLists);
    cdl.put("CdlBillDocs", cdlBillDocs);
    System.out.println(cdlBillLists.size() + " " + cdlBillDocs.size());
    persistentRepositoryService.save(cdl);

}

From source file:cysbml.SBMLGraphReader.java

/** Reading the SBML and creating cytoscape network. */
@Override/*from  www.ja  v  a2 s  .  co m*/
public void read() throws IOException {
    InputStream instream;
    if ((fileURL == null) && (fileName != null))
        instream = new FileInputStream(fileName);
    else if ((fileURL != null) && (fileName == null))
        instream = fileURL.openStream();
    else if ((fileURL == null) && (fileName == null) && (sbmlStream != null))
        instream = sbmlStream;
    else
        throw new IOException("No file to open!");

    // Read SBML document if valid SBML      
    SBMLReader reader = new SBMLReader();
    try {
        document = reader.readSBMLFromStream(instream);
        createCytoscapeGraphFromSBMLDocument();
    } catch (XMLStreamException e) {
        e.printStackTrace();
        document = null;
    }
}

From source file:com.biomeris.i2b2.export.ws.ExportService.java

public OMElement export(OMElement inputElement) throws I2B2Exception, JsonSyntaxException, ExportCellException {
    Assert.notNull(inputElement, "Export Cell: Incoming request is null");

    OMElement returnElement = null;//from w ww.j  av a2  s.  com
    MessageHeaderType messageHeaderType = MessageManager.extractReqMess(inputElement).getMessageHeader();
    String requestJsonStr = MessageManager.extractObsBlob(inputElement);

    Gson gson = new Gson();
    ExportRequest request = gson.fromJson(requestJsonStr, ExportRequest.class);

    String sessionId = request.getSessionId();
    WSession wSession = sessionManager.getSession(sessionId);

    if (wSession == null) {
        throw new ExportCellException("Session does not exist");
    }

    if (request.getNewPassword() != null) {
        wSession.getNetwork().setPassword(request.getNewPassword());
    } else {
        if (authStrategy > 1) {
            throw new ExportCellException("Password not provided.");
        }
    }

    boolean validUser = false;
    if (authStrategy > 1) {
        try {
            validUser = validateUser(wSession.getNetwork());
        } catch (JAXBException | IOException | TransformerException e1) {
            // do nothing
        }
    } else {
        validUser = true;
    }

    ExportResponse response = new ExportResponse();

    if (validUser) {
        response.setSessionId(sessionId);

        WExport wExport = null;
        wExport = wSession.addNewExport(request.getName());
        wExport.setExportParams(request.getExportParams());
        wExport.setConcepts(request.getConcepts());
        wExport.setPatSetId(request.getPatientSetId());
        wExport.setPatSetName(request.getPatientSetName());

        response.setExportId(wExport.getId());

        ExportRunnable erun = new ExportRunnable(wSession, wExport);
        Thread t = new Thread(erun);
        t.start();
    } else {
        String error = "You're not allowed to use export functions";
        response.setError(error);
    }

    String jsonRespStr = new GsonBuilder().create().toJson(response);

    ObservationSet observationSet = new ObservationSet();
    ObservationType observationType = new ObservationType();
    BlobType blobType = new BlobType();
    blobType.getContent().add(jsonRespStr);
    observationType.setObservationBlob(blobType);
    observationSet.getObservation().add(observationType);
    ResponseMessageType responseMessageType = MessageFactory.createBuildResponse(messageHeaderType,
            observationSet);
    String rmtStr = MessageFactory.convertToXMLString(responseMessageType);

    try {
        returnElement = MessageFactory.createResponseOMElementFromString(rmtStr);
    } catch (XMLStreamException e) {
        e.printStackTrace();
    }

    log.debug(rmtStr);

    return returnElement;
}