Example usage for java.io IOException getLocalizedMessage

List of usage examples for java.io IOException getLocalizedMessage

Introduction

In this page you can find the example usage for java.io IOException getLocalizedMessage.

Prototype

public String getLocalizedMessage() 

Source Link

Document

Creates a localized description of this throwable.

Usage

From source file:ctd.services.getCleanData2.java

public String cleanData() {
    String message = "";
    String timestamp = new java.util.Date().getTime() + "";

    try {/*w  ww  .j  a v a  2 s.  co m*/
        CleanDataResult result = new CleanDataResult();
        String error_message = "";
        //get parameters.
        ResourceBundle res = ResourceBundle.getBundle("settings");
        ResourceBundle cdf_list = ResourceBundle.getBundle("cdf");
        //Base directory ftp folder: Here the temporary subfolders are found for each set of CEL-files, and the final assaytoken-based folder.
        String ftp_folder = res.getString("ws.upload_folder");
        String rscript_cleandata = res.getString("ws.rscript_cleandata");
        String rscript = res.getString("ws.rscript");
        //db
        String db_username = res.getString("db.username");
        String db_password = res.getString("db.password");
        String db_database = res.getString("db.database");

        //retrieve the information on the assignment from the database
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();
        Transaction tr = session.beginTransaction();
        Query q = session.createQuery(
                "from Ticket where password='" + getPassword() + "' AND ctd_REF='" + getCTD_REF() + "'");
        Ticket ticket = null;
        String closed = "";
        if (q.list().size() != 0) {
            ticket = (Ticket) q.list().get(0);
            closed = ticket.getClosed();
        }
        if (ticket == null) {
            error_message = "Ticket password and CTD_REF don't match.";
        }
        if (closed.equals("yes")) {
            error_message = "Ticket is already used for normalization of these CEL-files.";
            ticket = null;
        }

        if (ticket != null) {
            //get the folder
            String folder = ticket.getFolder();
            String zip_folder = ftp_folder + folder;
            //get contents
            File dir = new File(zip_folder);

            //find the zip file.
            File[] files = dir.listFiles(new FileFilter() {
                public boolean accept(File pathname) {
                    return pathname.isFile();
                }
            });
            String cel_zip_file = "";
            String zip_file = "";
            String gct_file = "";
            for (int i = 0; i < files.length; i++) {
                String file = files[i].getName();
                if (file.contains("zip")) {
                    // Add the timestamp to the zip
                    files[i].renameTo(new File(zip_folder + "/" + timestamp + "_zip.zip"));
                    file = timestamp + "_zip.zip";

                    cel_zip_file = file;
                    zip_file = zip_folder + "/" + cel_zip_file;
                    gct_file = zip_folder + "/" + timestamp + "_gctfile";
                }
            }
            Process p3 = Runtime.getRuntime().exec("chmod 777 " + zip_file);

            //////////////////////////////////////////////////////////////////
            //Do a system call to normalize. R. (zip_folder zip_file gct_file rscript)
            String args = rscript + " --verbose --vanilla " + rscript_cleandata + " -i" + zip_file + " -o"
                    + gct_file + " -w" + zip_folder;
            Logger.getLogger(getTicket.class.getName()).log(Level.INFO, timestamp + ": Running: " + args);
            Process p = Runtime.getRuntime().exec(args);
            // Check if CEL files are unzipped allready
            // This is done by checking every 5 seconds for the existence of a .chip file
            // This is a bad way of doing this, in future versions of CTD
            // the output of the R scripts should be parsed
            boolean do_loop = true;
            while (do_loop) {
                File dir2 = new File(zip_folder);
                String[] files2 = dir2.list();
                //Check if CEL files are allready there
                for (int i = 0; i < files2.length; i++) {
                    String file = files2[i];
                    if (file.endsWith("chip")) {
                        do_loop = false;
                        try {
                            Thread.sleep(5000);
                        } catch (InterruptedException ex) {
                            Logger.getLogger(getCleanData.class.getName()).log(Level.SEVERE, null,
                                    timestamp + ": " + ex);
                        }
                    }
                }
            }
            Logger.getLogger(getTicket.class.getName()).log(Level.INFO, timestamp + ": rscript has finished.");
            File dir2 = new File(zip_folder);
            String[] files2 = dir2.list();
            String chip_file = "";
            String chip_file_db = "";
            ArrayList<String> unziped_files = new ArrayList<String>();
            for (int i = 0; i < files2.length; i++) {
                String file = files2[i];
                if (file.endsWith("CEL")) {
                    unziped_files.add(file);
                }
                if (file.endsWith("chip")) {
                    chip_file = file;
                    chip_file_db = chip_file.split("_CDF_")[1];
                    File fileFile = new File(chip_file);
                    fileFile.renameTo(new File(zip_folder + "/" + chip_file_db)); //Making the file correspond to the database entry. Duplicates can be safely overwritten, and will be.
                }
            }

            //Check if all CEL files are derived from the same chip.
            //This is essential for normalization.
            //initiate check hashmap. This map contains all the unique chip definition file names. There should be only one per analysis.
            ArrayList<StudySampleAssay> map = new ArrayList<StudySampleAssay>();
            for (int i = 0; i < unziped_files.size(); i++) {
                String cel_file = unziped_files.get(i);

                StudySampleAssay ssa = new StudySampleAssay();
                // Open the file that is the first
                // command line parameter
                //String cel_file_path = zip_folder + "/" + cel_file;
                String name = cel_file;
                ssa.setNameRawfile(name);
                ssa.setXREF(getCTD_REF());
                map.add(ssa);
            }
            ticket.getStudySampleAssaies().addAll(map);
            session.saveOrUpdate(ticket);
            session.persist(ticket);
            tr.commit();
            session.close();

            //Storage chip definition file (CDF), creation gct file and database storage.
            SessionFactory sessionFactory1 = new Configuration().configure().buildSessionFactory();
            Session session1 = sessionFactory1.openSession();

            //check if cdf (chip definition file) is allready stored, if not, store it.
            List<ChipAnnotation> chip_annotation = null;
            Query q2 = session1.createQuery("from Chip Where Name='" + chip_file_db + "'");
            if (q2.uniqueResult() != null) {
                Chip chip = (Chip) q2.list().get(0);
                chip_annotation = chip.getChipAnnotation();
            }
            if (q2.uniqueResult() == null) {
                //Add this chip and its annotation
                Chip chip_new = new Chip();
                chip_new.setName(chip_file_db);

                //read chip file
                String chip_file_path = zip_folder + "/" + chip_file;
                chip_annotation = readChip(chip_file_path);

                //Store the whole
                chip_new.getChipAnnotation().addAll(chip_annotation);

                Transaction tr1 = session1.beginTransaction();
                session1.save(chip_new);
                session1.persist(chip_new);
                tr1.commit();
                session1.close();
            }

            //create the temp file for storage of the data_insert file.
            String data_file = zip_folder + "/expression.txt";
            FileOutputStream out = null;
            PrintStream pr = null;
            out = new FileOutputStream(data_file);
            pr = new PrintStream(out);

            //create array data input file for the database table, find correct foreign keys.
            //get the study_sample_assay id and the probeset ids.
            SessionFactory sessionFactory2 = new Configuration().configure().buildSessionFactory();
            Session session2 = sessionFactory2.openSession();

            //Get the cip_annotation_id
            Query q3 = session2.createQuery("from Chip Where Name='" + chip_file_db + "'");
            Chip chip = (Chip) q3.list().get(0);
            chip_annotation = chip.getChipAnnotation();
            Iterator it2 = chip_annotation.iterator();
            //for speed, put the chip annotation id in a hashmap
            HashMap<String, String> chip_annotation_ids = new HashMap<String, String>();
            while (it2.hasNext()) {
                ChipAnnotation ca = (ChipAnnotation) it2.next();
                String id = ca.getId().toString();
                String ps = ca.getProbeset();
                chip_annotation_ids.put(ps, id);
            }

            //Create the .gct-files
            try {

                Query qt = session2.createQuery("from Ticket where password='" + getPassword()
                        + "' AND ctd_REF='" + getCTD_REF() + "'");

                ticket = null;

                if (qt.list().size() != 0) {
                    ticket = (Ticket) qt.list().get(0);
                }

                Iterator it3 = ticket.getStudySampleAssaies().iterator();
                while (it3.hasNext()) {
                    StudySampleAssay ssa = (StudySampleAssay) it3.next();
                    String name_raw_file = ssa.getNameRawfile();
                    String sampleToken = getSampletokens().get(name_raw_file);
                    String ssa_id = ssa.getId().toString();
                    error_message = error_message + name_raw_file;

                    String gct_file_generated = gct_file + ".gct";
                    ArrayList<Double> values = writeFile(pr, chip_annotation_ids, ssa_id, gct_file_generated,
                            name_raw_file.replaceAll(".CEL", ""));

                    Statistics stat = new Statistics();
                    stat.setData(values);
                    Double average = stat.getAverage();
                    Double std = stat.getSTD();

                    ssa.setXREF(getCTD_REF());
                    ssa.setAverage(average);
                    ssa.setStudyToken(getStudytoken());
                    ssa.setSampleToken(sampleToken);
                    ssa.setStd(std);
                }

            } catch (IOException e) {
                Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, timestamp
                        + ": ERROR IN getCleanData2: " + e.getMessage() + "  " + e.getLocalizedMessage());
            }
            pr.close();
            out.close();

            //update ticket
            Transaction tr2 = session2.beginTransaction();
            session2.update(ticket);
            session2.persist(ticket);
            tr2.commit();
            session2.close();

            //import the data into the database
            String u = "--user=" + db_username;
            String passw = "--password=" + db_password;
            String[] commands = new String[] { "mysqlimport", u, passw, "--local", db_database, data_file };
            Process p4 = Runtime.getRuntime().exec(commands);
            message = message + " RMA and GRSN on the CEL-files is done, data is stored.";

            //close the ticket when finished, normalization can only be performed once by the client.
            CloseTicket();

            //Remove zip and data file (expression.txt)
            File fileFolderOld = new File(zip_folder);
            File fileFolderDest = new File(res.getString("ws.upload_folder") + getCTD_REF());
            File[] listOfFiles = fileFolderOld.listFiles();
            for (int i = 0; i < listOfFiles.length; i++) {
                if (listOfFiles[i].getPath().toLowerCase().endsWith(".zip")
                        || listOfFiles[i].getPath().toLowerCase().endsWith("expression.txt")) {
                    try {
                        listOfFiles[i].delete();
                    } catch (Exception e) {
                        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE,
                                timestamp + ": ERROR IN getCleanData2 (try to delete): " + e.toString());
                    }
                } else {
                    try {
                        FileUtils.copyFileToDirectory(listOfFiles[i], fileFolderDest, false);
                        listOfFiles[i].delete();
                    } catch (Exception e) {
                        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE,
                                timestamp + ": ERROR IN getCleanData2 (try to copy): " + e.toString());
                    }
                }
            }

            // Remove temporary folder
            try {
                fileFolderOld.delete();
            } catch (Exception e) {
                Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE,
                        timestamp + ": ERROR IN getCleanData2: " + e.toString());
            }

            // --------------------------------------------
            // This piece of code is added in order to cleanup all the files
            // of aborted upload procedures. It checks for these old folders
            // (more than a day old and a temporaty name (which is just a number
            // from 1 upwards. It is assumed that a temporary folder has a
            // name shorter than 10 chars) and removes these files and folders
            File folderData = new File(res.getString("ws.upload_folder"));
            long lngTimestamp = new java.util.Date().getTime();
            listOfFiles = folderData.listFiles();
            for (int i = 0; i < listOfFiles.length; i++) {
                if (listOfFiles[i].lastModified() < (lngTimestamp - 10000)
                        && listOfFiles[i].getName().length() < 10) {
                    // This folder is more than a day old
                    // We know it is a temporary folder because the name is less than 10 chars long
                    File[] lstDelete = listOfFiles[i].listFiles();
                    for (int j = 0; j < lstDelete.length; j++) {
                        // Delete all content of the old folder
                        lstDelete[j].delete();
                    }
                    // Delete the old folder
                    if (!listOfFiles[i].delete()) {
                        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE,
                                "delSample(): Folder deletion failed: " + listOfFiles[i].getName());
                    }
                }
            }
            // --------------------------------------------
        }

        // set the messages of the response
        result.setErrorMessage(error_message);
        result.setMessage(message);

        // Use SKARINGA in order to create the JSON response
        ObjectTransformer trans = null;
        try {
            trans = ObjectTransformerFactory.getInstance().getImplementation();
            message = trans.serializeToString(result);
        } catch (NoImplementationException ex) {
            Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE,
                    "SKARINGA ERROR IN getCleanData2: " + ex.getLocalizedMessage());
        }

    } catch (Exception e) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE,
                timestamp + ": ERROR IN getCleanData2: " + e.toString());
    }
    return message;
}

From source file:com.adobe.phonegap.contentsync.Sync.java

private File backupExistingDirectory(String outputDirectory, String type, File dir) {
    File backup = new File(outputDirectory + ".bak");
    if (dir.exists()) {
        if (type.equals(TYPE_MERGE)) {
            try {
                copyFolder(dir, backup);
            } catch (IOException e) {
                Log.e(LOG_TAG, e.getLocalizedMessage(), e);
            }//from   w  w w . j  a  v  a 2 s . com
        } else {
            dir.renameTo(backup);
        }
    }
    return backup;
}

From source file:com.ning.billing.recurly.RecurlyClient.java

private void closeStream(final InputStream in) {
    if (in != null) {
        try {/*from  w w w.  j a v a 2  s.  co  m*/
            in.close();
        } catch (IOException e) {
            log.warn("Failed to close http-client - provided InputStream: {}", e.getLocalizedMessage());
        }
    }
}

From source file:ch.zhaw.iamp.rct.ui.GrammarWindow.java

private boolean writeFileOrShowError(String file, JTextComponent source) {
    try {/*ww  w  . j a  v a  2 s  .  c  om*/
        FileUtils.writeStringToFile(new File(file), source.getText());
        source.requestFocus();
        return true;
    } catch (IOException ex) {
        JOptionPane.showMessageDialog(this, "The file could not be written: " + ex.getLocalizedMessage(),
                "Error", JOptionPane.ERROR_MESSAGE);
    }

    return false;
}

From source file:nf.frex.android.FrexActivity.java

@Override
protected void onActivityResult(int requestCode, int resultCode, Intent data) {
    if (resultCode != Activity.RESULT_OK) {
        return;/* w  ww . j a  va  2s.  c  o  m*/
    }
    if (requestCode == R.id.manage_fractals && data.getAction().equals(Intent.ACTION_VIEW)) {
        final Uri imageUri = data.getData();
        if (imageUri != null) {
            File imageFile = new File(imageUri.getPath());
            String configName = FrexIO.getFilenameWithoutExt(imageFile);
            File paramFile = new File(imageFile.getParent(), configName + FrexIO.PARAM_FILE_EXT);
            try {
                FileInputStream fis = new FileInputStream(paramFile);
                try {
                    readFrexDoc(fis, configName);
                } finally {
                    fis.close();
                }
            } catch (IOException e) {
                Toast.makeText(FrexActivity.this, getString(R.string.error_msg, e.getLocalizedMessage()),
                        Toast.LENGTH_SHORT).show();
            }
        }
    } else if (requestCode == R.id.settings) {
        view.getGenerator().setNumTasks(SettingsActivity.getNumTasks(this));
    } else if (requestCode == SELECT_PICTURE_REQUEST_CODE) {
        final Uri imageUri = data.getData();
        final ColorQuantizer colorQuantizer = new ColorQuantizer();
        final ProgressDialog progressDialog = new ProgressDialog(FrexActivity.this);
        final DialogInterface.OnCancelListener cancelListener = new DialogInterface.OnCancelListener() {
            @Override
            public void onCancel(DialogInterface dialog) {
                if (progressDialog.isShowing()) {
                    progressDialog.dismiss();
                }
                colorQuantizer.cancel();
            }
        };
        final ColorQuantizer.ProgressListener progressListener = new ColorQuantizer.ProgressListener() {
            @Override
            public void progress(final String msg, final int iter, final int maxIter) {
                runOnUiThread(new Runnable() {
                    @Override
                    public void run() {
                        progressDialog.setMessage(msg);
                        progressDialog.setProgress(iter);
                    }
                });
            }
        };

        progressDialog.setTitle(getString(R.string.get_pal_from_img_title));
        progressDialog.setProgressStyle(ProgressDialog.STYLE_HORIZONTAL);
        progressDialog.setCancelable(true);
        progressDialog.setOnCancelListener(cancelListener);
        progressDialog.setMax(colorQuantizer.getMaxIterCount());
        progressDialog.show();

        Thread thread = new Thread(new Runnable() {
            @Override
            public void run() {
                Bitmap bitmap;
                try {
                    bitmap = FrexIO.readBitmap(getContentResolver(), imageUri, 256);
                } catch (IOException e) {
                    alert("I/O error: " + e.getLocalizedMessage());
                    return;
                }
                ColorScheme colorScheme = colorQuantizer.quantize(bitmap, progressListener);
                progressDialog.dismiss();
                if (colorScheme != null) {
                    Log.d(TAG, "SELECT_PICTURE_REQUEST_CODE: Got colorScheme");
                    String colorSchemeId = "$" + imageUri.toString();
                    colorSchemes.add(colorSchemeId, colorScheme);
                    view.setColorSchemeId(colorSchemeId);
                    view.setColorScheme(colorScheme);
                    view.recomputeColors();
                    runOnUiThread(new Runnable() {
                        @Override
                        public void run() {
                            Log.d(TAG, "SELECT_PICTURE_REQUEST_CODE: showDialog(R.id.colors)");
                            showDialog(R.id.colors);
                        }
                    });

                }
            }
        });
        thread.start();
    }
}

From source file:es.juntadeandalucia.panelGestion.presentacion.controlador.impl.NewGIController.java

/**
 * This method initializes the task which reads the file
 * and counts the number of lines//from w  w w  . ja  v a 2s .  c  o m
 */
public void initTask() {
    checkValidTable();

    if (validTable) {
        try {
            // if it is a new schema then creates a new one
            if (isNewSchema()) {
                schema = new Schema();
                schema.setDataBase(dataBase);
                schema.setName(schemaName);
            }

            // if it is a new table then creates a new one
            if (!taskvo.getTaskEntity().isUpdate()) {
                table = new Table();
                table.setSchema(schema);
                table.setName(tableName);
            }

            // assigns the table to the task entity
            taskvo.getTaskEntity().setTable(table);
            // initializes the task
            taskvo.init();

            // NEXT PHASE --> PROCESS FILE
            processFilePhase = true;
            uploadingFilePhase = false;
        } catch (IOException e) {
            String errorMsg = e.getLocalizedMessage();
            StatusMessages.instance().add(Severity.ERROR, errorMsg);
            log.error(errorMsg);
        } catch (Exception e) {
            String errorMsg = "Error al iniciar la tarea: " + e.getLocalizedMessage();
            StatusMessages.instance().add(Severity.ERROR, errorMsg);
            log.error(errorMsg);
        }
    }
}

From source file:ch.zhaw.iamp.rct.ui.GrammarWindow.java

private boolean readFileOrShowError(String file, JTextComponent target) {
    File source = new File(file);
    if (source.exists()) {
        try {//w w w  .ja  va2 s  .  com
            target.setText(FileUtils.readFileToString(source));
            target.setEnabled(true);
            target.requestFocus();
            return true;
        } catch (IOException ex) {
            JOptionPane.showMessageDialog(this, "The file could not be read: " + ex.getLocalizedMessage(),
                    "Error", JOptionPane.ERROR_MESSAGE);
            target.setEnabled(false);
        }
    } else {
        target.setText("");
        target.setEnabled(true);
        target.requestFocus();
    }

    return false;
}

From source file:com.evolveum.polygon.scim.ServiceAccessManager.java

/**
 * Used for login to the service. The data needed for this operation is
 * provided by the configuration./*  ww  w  . j  a  v a  2 s  .  c  o  m*/
 * 
 * @param configuration
 *            The instance of "ScimConnectorConfiguration" which holds all
 *            the provided configuration data.
 * 
 * @return a Map object carrying meta information about the login session.
 */
public void logIntoService(ScimConnectorConfiguration configuration) {

    HttpPost loginInstance = new HttpPost();

    Header authHeader = null;
    String loginAccessToken = null;
    String loginInstanceUrl = null;
    JSONObject jsonObject = null;
    String proxyUrl = configuration.getProxyUrl();
    LOGGER.ok("proxyUrl: {0}", proxyUrl);
    //   LOGGER.ok("Configuration: {0}", configuration);
    if (!"token".equalsIgnoreCase(configuration.getAuthentication())) {

        HttpClient httpClient;

        if (proxyUrl != null && !proxyUrl.isEmpty()) {

            HttpHost proxy = new HttpHost(proxyUrl, configuration.getProxyPortNumber());

            DefaultProxyRoutePlanner routePlanner = new DefaultProxyRoutePlanner(proxy);

            httpClient = HttpClientBuilder.create().setRoutePlanner(routePlanner).build();

            LOGGER.ok("Proxy enabled: {0}:{1}", proxyUrl, configuration.getProxyPortNumber());
        } else {

            httpClient = HttpClientBuilder.create().build();

        }
        String loginURL = new StringBuilder(configuration.getLoginURL()).append(configuration.getService())
                .toString();

        GuardedString guardedPassword = configuration.getPassword();
        GuardedStringAccessor accessor = new GuardedStringAccessor();
        guardedPassword.access(accessor);

        String contentUri = new StringBuilder("&client_id=").append(configuration.getClientID())
                .append("&client_secret=").append(configuration.getClientSecret()).append("&username=")
                .append(configuration.getUserName()).append("&password=").append(accessor.getClearString())
                .toString();

        loginInstance = new HttpPost(loginURL);
        CloseableHttpResponse response = null;

        StringEntity bodyContent;
        String getResult = null;
        Integer statusCode = null;
        try {
            bodyContent = new StringEntity(contentUri);
            bodyContent.setContentType("application/x-www-form-urlencoded");
            loginInstance.setEntity(bodyContent);

            response = (CloseableHttpResponse) httpClient.execute(loginInstance);

            getResult = EntityUtils.toString(response.getEntity());

            statusCode = response.getStatusLine().getStatusCode();

            if (statusCode == 200) {

                LOGGER.info("Login Successful");

            } else {

                String[] loginUrlParts;
                String providerName = "";

                if (configuration.getLoginURL() != null && !configuration.getLoginURL().isEmpty()) {

                    loginUrlParts = configuration.getLoginURL().split("\\."); // e.g.
                    // https://login.salesforce.com

                } else {

                    loginUrlParts = configuration.getBaseUrl().split("\\."); // e.g.
                }
                // https://login.salesforce.com
                if (loginUrlParts.length >= 2) {
                    providerName = loginUrlParts[1];
                }

                if (!providerName.isEmpty()) {

                    StrategyFetcher fetcher = new StrategyFetcher();
                    HandlingStrategy strategy = fetcher.fetchStrategy(providerName);
                    strategy.handleInvalidStatus(" while loging into service", getResult, "loging into service",
                            statusCode);
                }

            }

            jsonObject = (JSONObject) new JSONTokener(getResult).nextValue();

            loginAccessToken = jsonObject.getString("access_token");
            loginInstanceUrl = jsonObject.getString("instance_url");

        } catch (UnsupportedEncodingException e) {
            LOGGER.error("Unsupported encoding: {0}. Occurrence in the process of login into the service",
                    e.getLocalizedMessage());
            LOGGER.info("Unsupported encoding: {0}. Occurrence in the process of login into the service", e);

            throw new ConnectorException(
                    "Unsupported encoding. Occurrence in the process of login into the service", e);
        }

        catch (ClientProtocolException e) {

            LOGGER.error(
                    "An protocol exception has occurred while processing the http response to the login request. Possible mismatch in interpretation of the HTTP specification: {0}",
                    e.getLocalizedMessage());
            LOGGER.info(
                    "An protocol exception has occurred while processing the http response to the login request. Possible mismatch in interpretation of the HTTP specification: {0}",
                    e);

            throw new ConnectionFailedException(
                    "An protocol exception has occurred while processing the http response to the login request. Possible mismatch in interpretation of the HTTP specification",
                    e);

        } catch (IOException ioException) {

            StringBuilder errorBuilder = new StringBuilder(
                    "An error occurred while processing the query http response to the login request. ");

            if ((ioException instanceof SocketTimeoutException
                    || ioException instanceof NoRouteToHostException)) {

                errorBuilder.insert(0, "The connection timed out. ");

                throw new OperationTimeoutException(errorBuilder.toString(), ioException);
            } else {

                LOGGER.error(
                        "An error occurred while processing the query http response to the login request : {0}",
                        ioException.getLocalizedMessage());
                LOGGER.info(
                        "An error occurred while processing the query http response to the login request : {0}",
                        ioException);
                throw new ConnectorIOException(errorBuilder.toString(), ioException);
            }
        } catch (JSONException jsonException) {

            LOGGER.error(
                    "An exception has occurred while setting the \"jsonObject\". Occurrence while processing the http response to the login request: {0}",
                    jsonException.getLocalizedMessage());
            LOGGER.info(
                    "An exception has occurred while setting the \"jsonObject\". Occurrence while processing the http response to the login request: {0}",
                    jsonException);
            throw new ConnectorException("An exception has occurred while setting the \"jsonObject\".",
                    jsonException);
        } finally {
            try {
                response.close();
            } catch (IOException e) {

                if ((e instanceof SocketTimeoutException || e instanceof NoRouteToHostException)) {

                    throw new OperationTimeoutException(
                            "The connection timed out while closing the http connection. Occurrence in the process of logging into the service",
                            e);
                } else {

                    LOGGER.error(
                            "An error has occurred while processing the http response and closing the http connection. Occurrence in the process of logging into the service: {0}",
                            e.getLocalizedMessage());

                    throw new ConnectorIOException(
                            "An error has occurred while processing the http response and closing the http connection. Occurrence in the process of logging into the service",
                            e);
                }

            }

        }
        authHeader = new BasicHeader("Authorization", "OAuth " + loginAccessToken);
    } else {
        loginInstanceUrl = configuration.getBaseUrl();

        GuardedString guardedToken = configuration.getToken();

        GuardedStringAccessor accessor = new GuardedStringAccessor();
        guardedToken.access(accessor);

        loginAccessToken = accessor.getClearString();

        authHeader = new BasicHeader("Authorization", "Bearer " + loginAccessToken);
    }
    String scimBaseUri = new StringBuilder(loginInstanceUrl).append(configuration.getEndpoint())
            .append(configuration.getVersion()).toString();

    this.baseUri = scimBaseUri;
    this.aHeader = authHeader;
    if (jsonObject != null) {
        this.loginJson = jsonObject;
    }

}

From source file:de.dfki.iui.mmds.application.ScxmlDebugGui.java

/**
 * Create contents of the window./*  w  w w. j  a va  2s  . c  om*/
 */
protected void createContents(final Display display) {
    shlSiamDpDebug = new Shell(display);
    shlSiamDpDebug.setMinimumSize(new Point(680, 480));
    shlSiamDpDebug
            .setImage(ResourceManager.getPluginImage("de.dfki.iui.mmds.dialogue", "resources/siamIcon.png"));
    shlSiamDpDebug.setSize(1166, 750);
    shlSiamDpDebug.setText("SiAM-dp Debug GUI");
    shlSiamDpDebug.setLayout(new FormLayout());

    topBox = new Composite(shlSiamDpDebug, SWT.NONE);
    topBox.setLayout(new FormLayout());
    FormData fd_topBox = new FormData();
    fd_topBox.top = new FormAttachment(0, 10);
    fd_topBox.bottom = new FormAttachment(0, 160);
    fd_topBox.right = new FormAttachment(100, -10);
    fd_topBox.left = new FormAttachment(0, 10);
    topBox.setLayoutData(fd_topBox);

    sashForm = new SashForm(shlSiamDpDebug, SWT.NONE);
    FormData fd_sashForm = new FormData();
    fd_sashForm.top = new FormAttachment(topBox, 10, SWT.BOTTOM);

    composite = new Composite(topBox, SWT.BORDER);
    FormData fd_composite = new FormData();
    fd_composite.right = new FormAttachment(0, 200);
    fd_composite.bottom = new FormAttachment(100, -60);
    fd_composite.top = new FormAttachment(0, 5);
    fd_composite.left = new FormAttachment(0, 5);
    composite.setLayoutData(fd_composite);

    deviceComboBox = new Combo(composite, SWT.BORDER);
    deviceComboBox.setLocation(10, 23);
    deviceComboBox.setSize(175, 21);

    Button btnOpenMicrophone = new Button(composite, SWT.NONE);
    btnOpenMicrophone.setLocation(10, 50);
    btnOpenMicrophone.setSize(121, 25);
    btnOpenMicrophone.addSelectionListener(new SelectionAdapter() {
        @Override
        public void widgetSelected(SelectionEvent e) {
            openMicrophonePushed();
        }
    });
    btnOpenMicrophone.setText("Open Microphone");

    Label lblDeviceId = new Label(composite, SWT.NONE);
    lblDeviceId.setBounds(10, 7, 55, 15);
    lblDeviceId.setText("Device Id:");

    composite_1 = new Composite(topBox, SWT.BORDER);
    composite_1.setLayout(new FormLayout());
    FormData fd_composite_1 = new FormData();
    fd_composite_1.top = new FormAttachment(0, 5);
    fd_composite_1.left = new FormAttachment(composite, 5);
    fd_composite_1.right = new FormAttachment(100, -146);
    fd_composite_1.bottom = new FormAttachment(100, -5);
    composite_1.setLayoutData(fd_composite_1);

    eventComboBox = new Combo(composite_1, SWT.NONE);
    FormData fd_eventComboBox = new FormData();
    fd_eventComboBox.right = new FormAttachment(0, 150);
    fd_eventComboBox.top = new FormAttachment(0, 3);
    fd_eventComboBox.left = new FormAttachment(0, 3);
    eventComboBox.setLayoutData(fd_eventComboBox);

    Button btnFireEvent = new Button(composite_1, SWT.NONE);
    FormData fd_btnFireEvent = new FormData();
    fd_btnFireEvent.top = new FormAttachment(eventComboBox, 3);
    fd_btnFireEvent.right = new FormAttachment(eventComboBox, 0, SWT.RIGHT);
    fd_btnFireEvent.left = new FormAttachment(eventComboBox, 0, SWT.LEFT);
    btnFireEvent.setLayoutData(fd_btnFireEvent);
    btnFireEvent.addSelectionListener(new SelectionAdapter() {
        @Override
        public void widgetSelected(SelectionEvent e) {
            try {
                Message message = (Message) EmfPersistence.readFromString(messageTextBox.getText())
                        .getContents().get(0);
                if (message instanceof InputMessage)
                    eventService.postInputEvent((InputMessage) message, this);
                else if (message instanceof OutputMessage)
                    eventService.postOutputEvent((OutputMessage) message, this);
                else if (message instanceof CustomMessage)
                    eventService.postCustomEvent((CustomMessage) message, this);
            } catch (IOException e1) {
                MessageBox m = new MessageBox(display.getActiveShell(), SWT.OK | SWT.ERROR);
                m.setText("Parsing Error");
                m.setMessage(e1.getLocalizedMessage());
                m.open();
            }
        }
    });
    btnFireEvent.setText("Fire Event");

    messageTextBox = new Text(composite_1, SWT.BORDER | SWT.H_SCROLL | SWT.V_SCROLL | SWT.CANCEL | SWT.MULTI);
    FormData fd_messageTextBox = new FormData();
    fd_messageTextBox.top = new FormAttachment(0, 3);
    fd_messageTextBox.left = new FormAttachment(eventComboBox, 3);
    fd_messageTextBox.bottom = new FormAttachment(100, -3);
    fd_messageTextBox.right = new FormAttachment(100, -10);
    messageTextBox.setLayoutData(fd_messageTextBox);

    composite_2 = new Composite(topBox, SWT.BORDER);
    FormData fd_composite_2 = new FormData();
    fd_composite_2.top = new FormAttachment(composite, 6);
    fd_composite_2.bottom = new FormAttachment(100, -5);
    fd_composite_2.left = new FormAttachment(0, 5);
    fd_composite_2.right = new FormAttachment(0, 200);
    composite_2.setLayoutData(fd_composite_2);

    btnStepwise = new Button(composite_2, SWT.CHECK);
    btnStepwise.setBounds(10, 15, 67, 16);
    btnStepwise.setEnabled(true);
    btnStepwise.addSelectionListener(new SelectionAdapter() {
        @Override
        public void widgetSelected(SelectionEvent e) {
            getEngine().setSuperStep(!btnStepwise.getSelection());
        }
    });
    btnStepwise.setText("Stepwise");

    btnNext = new Button(composite_2, SWT.NONE);
    btnNext.setBounds(96, 10, 89, 25);
    btnNext.setEnabled(false);
    btnNext.addSelectionListener(new SelectionAdapter() {
        @Override
        public void widgetSelected(SelectionEvent e) {
            getEngine().step();
        }
    });
    btnNext.setText("Next Step ==>");

    Composite composite_3 = new Composite(topBox, SWT.BORDER);
    FormData fd_composite_3 = new FormData();
    fd_composite_3.bottom = new FormAttachment(composite_1, 0, SWT.BOTTOM);
    fd_composite_3.right = new FormAttachment(composite_1, 146, SWT.RIGHT);
    fd_composite_3.top = new FormAttachment(0, 5);
    fd_composite_3.left = new FormAttachment(composite_1, 6);
    composite_3.setLayoutData(fd_composite_3);

    Button discourseContextButton = new Button(composite_3, SWT.TOGGLE);
    discourseContextButton.addSelectionListener(new SelectionAdapter() {

        @Override
        public void widgetSelected(SelectionEvent e) {
            if (discourseContextGui == null) {
                discourseContextGui = new DiscourseContextGui(
                        fadeService.getWorkingMemory().getDiscourseContext());

            }
            if (!discourseContextGuiOpen) {
                discourseContextGui.open();
                DisposeListener dl = new DisposeListener() {
                    @Override
                    public void widgetDisposed(DisposeEvent e) {
                        discourseContextGuiOpen = false;
                        discourseContextGui = null;
                        discourseContextButton.setSelection(false);
                    }
                };
                discourseContextGui.getShell().addDisposeListener(dl);
                discourseContextGuiOpen = true;
                discourseContextButton.setSelection(true);
            } else {
                discourseContextGui.close();
                discourseContextGuiOpen = false;
                discourseContextButton.setSelection(false);
            }
        }
    });
    discourseContextButton.setBounds(3, 2, 130, 25);
    discourseContextButton.setText("Discourse Context");

    Button discourseHistoryButton = new Button(composite_3, SWT.TOGGLE);
    discourseHistoryButton.addSelectionListener(new SelectionAdapter() {

        @Override
        public void widgetSelected(SelectionEvent e) {
            if (discourseHistoryGui == null) {
                discourseHistoryGui = new DiscourseHistoryGui(
                        fadeService.getWorkingMemory().getDiscourseHistory());
            }
            if (!discourseHistoryGuiOpen) {
                discourseHistoryGui.open();
                DisposeListener dl = new DisposeListener() {
                    @Override
                    public void widgetDisposed(DisposeEvent e) {
                        discourseHistoryGuiOpen = false;
                        discourseHistoryButton.setSelection(false);
                    }
                };
                discourseHistoryGui.getShell().addDisposeListener(dl);
                discourseHistoryGuiOpen = true;
                discourseHistoryButton.setSelection(true);
            } else {
                discourseHistoryGui.close();
                discourseHistoryGuiOpen = false;
                discourseHistoryButton.setSelection(false);
            }
        }

    });
    discourseHistoryButton.setBounds(3, 32, 130, 25);
    discourseHistoryButton.setText("Discourse History");

    Button physicalContextButton = new Button(composite_3, SWT.TOGGLE);

    physicalContextButton.addSelectionListener(new SelectionAdapter() {
        @Override
        public void widgetSelected(SelectionEvent e) {
            if (physicalContextGui == null) {
                physicalContextGui = new KnowledgeBaseGui(knowledgeManager.getWorld().getEntries(),
                        entityResources);
            }
            if (!physicalContextGuiOpen) {
                physicalContextGui.open();
                DisposeListener dl = new DisposeListener() {
                    @Override
                    public void widgetDisposed(DisposeEvent e) {
                        physicalContextGuiOpen = false;
                        physicalContextGui = null;
                        physicalContextButton.setSelection(false);
                    }
                };
                physicalContextGui.getShell().addDisposeListener(dl);
                physicalContextGuiOpen = true;
                physicalContextButton.setSelection(true);
            } else {
                physicalContextGui.close();
                physicalContextGuiOpen = false;
                physicalContextButton.setSelection(false);
            }
        }
    });
    physicalContextButton.setBounds(3, 62, 130, 25);
    physicalContextButton.setText("Knowledge Base");

    eventComboBox.addSelectionListener(new SelectionAdapter() {
        @Override
        public void widgetSelected(SelectionEvent e) {
            Message message = testMessages.get(eventComboBox.getText());
            if (message != null) {
                messageTextBox.setText(EmfPersistence.writeToString(message));
            }
        }
    });
    fd_sashForm.right = new FormAttachment(100, -10);
    fd_sashForm.left = new FormAttachment(0, 10);

    sashForm.setLayoutData(fd_sashForm);

    logGroup = new Group(sashForm, SWT.NONE);
    logGroup.setText("Logs");
    logGroup.setLayout(new FillLayout(SWT.VERTICAL));

    logTable = new Table(logGroup, SWT.BORDER | SWT.FULL_SELECTION);
    logTable.setHeaderVisible(true);
    logTable.setLinesVisible(true);

    eventColumn = new TableColumn(logTable, SWT.NONE);
    eventColumn.setWidth(120);
    eventColumn.setText("Event");

    stateIdColumn = new TableColumn(logTable, SWT.NONE);
    stateIdColumn.setWidth(380);
    stateIdColumn.setText("StateID");

    dialogueNodeIdColumn = new TableColumn(logTable, SWT.NONE);
    dialogueNodeIdColumn.setWidth(131);
    dialogueNodeIdColumn.setText("DialogueNodeID");

    variableGroup = new Group(sashForm, SWT.NONE);
    variableGroup.setText("Variables");
    variableGroup.setLayout(new FillLayout(SWT.HORIZONTAL));

    variableTable = new Table(variableGroup, SWT.BORDER | SWT.FULL_SELECTION);
    variableTable.addMouseListener(new MouseAdapter() {
        @Override
        public void mouseDoubleClick(MouseEvent event) {
            TableItem item = variableTable.getItem(new Point(event.x, event.y));
            Object content = null;
            final String key = item.getText(0);
            if (!item.getText(0).equals("null")) {
                content = ProjectManager.dialogueManager.getCurrentScxmlContext().get(key);
            }

            if (content instanceof EObject) {
                try {
                    DebugGuiVariableInfo window = new DebugGuiVariableInfo((EObject) content);
                    if (varInfos.get(key) == null) {
                        window.open();
                        varInfos.put(key, window);
                        DisposeListener dl = new DisposeListener() {

                            @Override
                            public void widgetDisposed(DisposeEvent e) {
                                varInfos.put(key, null);

                            }

                        };
                        window.getShell().addDisposeListener(dl);
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }

        }
    });
    variableTable.setHeaderVisible(true);
    variableTable.setLinesVisible(true);

    variableTableColumn1 = new TableColumn(variableTable, SWT.NONE);
    variableTableColumn1.setWidth(212);
    variableTableColumn1.setText("Name");

    variableTableColumn2 = new TableColumn(variableTable, SWT.NONE);
    variableTableColumn2.setWidth(240);
    variableTableColumn2.setText("Content");

    picturesComposite = new Composite(shlSiamDpDebug, SWT.NONE);
    fd_sashForm.bottom = new FormAttachment(picturesComposite, -10, SWT.TOP);

    FormData fd_picturesComposite = new FormData();
    fd_picturesComposite.top = new FormAttachment(100, -120);
    fd_picturesComposite.bottom = new FormAttachment(100, -10);
    fd_picturesComposite.right = new FormAttachment(100, -10);
    fd_picturesComposite.left = new FormAttachment(0, 10);
    sashForm.setWeights(new int[] { 654, 473 });
    picturesComposite.setLayout(null);

    picturesComposite.setLayoutData(fd_picturesComposite);

    Label siamLogo = new Label(picturesComposite, SWT.NONE);
    siamLogo.setImage(ResourceManager.getPluginImage("de.dfki.iui.mmds.dialogue", "resources/siam.png"));
    siamLogo.setBounds(285, 25, 228, 70);

    lblNewLabel = new Label(picturesComposite, SWT.NONE);
    lblNewLabel
            .setImage(ResourceManager.getPluginImage("de.dfki.iui.mmds.dialogue", "resources/bmbf_klein.png"));
    lblNewLabel.setBounds(519, 10, 116, 100);

    lblDfkiimage = new Label(picturesComposite, SWT.NONE);
    lblDfkiimage.setImage(ResourceManager.getPluginImage("de.dfki.iui.mmds.dialogue", "resources/dfki.png"));
    lblDfkiimage.setBounds(15, 15, 253, 90);

}