Example usage 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:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetTissueTypeListener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setTissueTypeUI.getValues();
    Vector<String> samples = this.setTissueTypeUI.getSamples();
    File file = new File(this.dataType.getPath().toString() + File.separator
            + this.dataType.getStudy().toString() + ".subject_mapping.tmp");
    File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
    if (stsmf == null) {
        this.setTissueTypeUI.displayMessage("Error: no subject to sample mapping file");
    }/*from  w w w.  j  a  v  a 2  s.  c o  m*/
    try {
        FileWriter fw = new FileWriter(file);
        BufferedWriter out = new BufferedWriter(fw);
        out.write(
                "study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n");

        try {
            BufferedReader br = new BufferedReader(new FileReader(stsmf));
            String line = br.readLine();
            while ((line = br.readLine()) != null) {
                String[] fields = line.split("\t", -1);
                String sample = fields[3];
                String tissueType;
                if (samples.contains(sample)) {
                    tissueType = values.get(samples.indexOf(sample));
                } else {
                    br.close();
                    return;
                }
                out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + fields[4]
                        + "\t" + tissueType + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setTissueTypeUI.displayMessage("File error: " + e.getLocalizedMessage());
            out.close();
            e.printStackTrace();
        }
        out.close();
        try {
            File fileDest;
            if (stsmf != null) {
                String fileName = stsmf.getName();
                stsmf.delete();
                fileDest = new File(this.dataType.getPath() + File.separator + fileName);
            } else {
                fileDest = new File(this.dataType.getPath() + File.separator
                        + this.dataType.getStudy().toString() + ".subject_mapping");
            }
            FileUtils.moveFile(file, fileDest);
            ((GeneExpressionData) this.dataType).setSTSMF(fileDest);
        } catch (IOException ioe) {
            this.setTissueTypeUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setTissueTypeUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setTissueTypeUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

---

From source file:org.kitodo.sruimport.SRUImport.java

private SearchResult performQuery(String queryURL) {
    try {/*from  w  ww.  j av  a2s  .c o  m*/
        HttpResponse response = sruClient.execute(new HttpGet(queryURL));
        if (Objects.equals(response.getStatusLine().getStatusCode(), SC_OK)) {
            return ResponseHandler.getSearchResult(response);
        }
    } catch (IOException e) {
        logger.error(e.getLocalizedMessage());
    }
    return new SearchResult();
}

---

From source file:net.osten.watermap.convert.SanMateoWildernessReport.java

/**
 * Returns water reports from text file.
 * Text file format: name, description, state, last report, reported by, lat, lon.
 *
 * @return set of water reports/*from  w  ww  .j a va2s .c o  m*/
 */
public Set<WaterReport> convert() {
    Set<WaterReport> results = new HashSet<WaterReport>();

    int lineNumber = 1;

    try {
        log.info("opening filePath=" + filePath);
        ImmutableList<String> lines = filePath != null
                ? Files.asCharSource(new File(filePath), Charsets.UTF_8).readLines()
                : Resources.asCharSource(fileURL, Charsets.UTF_8).readLines();
        log.fine("found " + lines.size() + " lines");

        for (String line : lines) {

            // find start of data line section
            WaterReport wr = null;
            log.fine("parsing line[" + lineNumber + "]=" + line);
            wr = parseDataLine(line);

            if (wr != null && wr.getName() != null) {
                log.fine("adding wr=" + wr);
                boolean added = results.add(wr);
                if (!added) {
                    results.remove(wr);
                    results.add(wr);
                }
            } else {
                log.finer("did not add wr for line " + lineNumber);
            }

            lineNumber++;
        }
    } catch (IOException e) {
        log.severe(e.getLocalizedMessage());
    }

    return results;
}

---

From source file:org.sonews.daemon.sync.SynchronousNNTPDaemon.java

@Override
public void shutdownNow() {
    if (this.serverSocket != null) {
        try {//from   w  w w.j av  a2 s . c om
            this.serverSocket.close();
        } catch (IOException ex) {
            Log.get().log(Level.WARNING, ex.getLocalizedMessage(), ex);
        }
    }
}

---

From source file:com.ning.metrics.goodwill.access.GoodwillAccessor.java

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

---

From source file:com.kylinolap.job.flow.JobFlowNode.java

protected JobInstance updateJobStep(String jobInstanceUuid, int jobInstanceStepSeqId, KylinConfig config,
        JobStepStatusEnum newStatus, Long execStartTime, Long execEndTime, String output) throws IOException {
    // set step status to running
    JobInstance jobInstance = JobDAO.getInstance(config).getJob(jobInstanceUuid);
    JobStep currentStep = null;//  w ww  .  j  ava 2 s .  co  m

    try {
        currentStep = jobInstance.getSteps().get(jobInstanceStepSeqId);
        JobStepStatusEnum currentStatus = currentStep.getStatus();
        boolean hasChange = false;

        if (null != execStartTime) {
            hasChange = true;
            currentStep.setExecStartTime(execStartTime);
        }
        if (null != execEndTime) {
            hasChange = true;
            currentStep.setExecEndTime(execEndTime);
        }
        if (null != output) {
            hasChange = true;
            // currentStep.setCmdOutput(output);
            JobDAO.getInstance(config).saveJobOutput(currentStep, output);
        }
        if (JobStepStatusEnum.WAITING == currentStatus
                && (JobStepStatusEnum.RUNNING == newStatus || JobStepStatusEnum.FINISHED == newStatus)) {
            hasChange = true;
            currentStep.setExecWaitTime((System.currentTimeMillis() - currentStep.getExecStartTime()) / 1000);
        }
        if (null != newStatus) {
            hasChange = true;
            currentStep.setStatus(newStatus);
        }

        if (hasChange) {
            JobDAO.getInstance(config).updateJobInstance(jobInstance);
        }
    } catch (IOException e) {
        log.error(e.getLocalizedMessage(), e);
    }

    if (null != execEndTime) {
        JobEngine.JOB_DURATION.put(
                JobInstance.getStepIdentity(jobInstance, currentStep) + " - "
                        + String.valueOf(currentStep.getExecStartTime()),
                (double) (currentStep.getExecEndTime() - currentStep.getExecStartTime()) / 1000);
    }

    return jobInstance;
}

---

From source file:fr.sanofi.fcl4transmart.controllers.listeners.clinicalData.SelectOtherIdentifiersListener.java

@Override
public void handleEvent(Event event) {
    //write in a new file
    File file = new File(this.dataType.getPath().toString() + File.separator
            + this.dataType.getStudy().toString() + ".columns.tmp");
    try {//from w  w w.ja va 2 s . co m
        FileWriter fw = new FileWriter(file);
        BufferedWriter out = new BufferedWriter(fw);
        out.write(
                "Filename\tCategory Code\tColumn Number\tData Label\tData Label Source\tControlled Vocab Code\n");

        //subject identifier
        Vector<File> rawFiles = ((ClinicalData) this.dataType).getRawFiles();
        Vector<String> siteIds = this.setOtherIdsUI.getSiteIds();
        Vector<String> visitNames = this.setOtherIdsUI.getVisitNames();
        for (int i = 0; i < rawFiles.size(); i++) {

            //site identifier
            if (siteIds.elementAt(i).compareTo("") != 0) {
                int columnNumber = FileHandler.getHeaderNumber(rawFiles.elementAt(i), siteIds.elementAt(i));
                if (columnNumber != -1) {
                    out.write(rawFiles.elementAt(i).getName() + "\t\t" + columnNumber + "\tSITE_ID\t\t\n");
                }
            }

            //visit name
            if (visitNames.elementAt(i).compareTo("") != 0) {
                int columnNumber = FileHandler.getHeaderNumber(rawFiles.elementAt(i), visitNames.elementAt(i));
                if (columnNumber != -1) {
                    out.write(rawFiles.elementAt(i).getName() + "\t\t" + columnNumber + "\tVISIT_NAME\t\t\n");
                }
            }
        }
        try {
            BufferedReader br = new BufferedReader(new FileReader(((ClinicalData) this.dataType).getCMF()));
            String line = br.readLine();
            while ((line = br.readLine()) != null) {
                String[] s = line.split("\t", -1);
                if (s[3].compareTo("SITE_ID") != 0 && s[3].compareTo("VISIT_NAME") != 0) {
                    out.write(line + "\n");
                }
            }
            br.close();
        } catch (Exception e) {
            this.setOtherIdsUI.displayMessage("Error: " + e.getLocalizedMessage());
            e.printStackTrace();
            out.close();
        }
        out.close();
        try {
            String fileName = ((ClinicalData) this.dataType).getCMF().getName();
            ((ClinicalData) this.dataType).getCMF().delete();
            File fileDest = new File(this.dataType.getPath() + File.separator + fileName);
            FileUtils.moveFile(file, fileDest);
            ((ClinicalData) this.dataType).setCMF(fileDest);
        } catch (IOException ioe) {
            this.setOtherIdsUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }

    } catch (Exception e) {
        this.setOtherIdsUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setOtherIdsUI.displayMessage("Column mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
    UsedFilesPart.sendFilesChanged(dataType);
}

---

From source file:org.openbaton.vnfm.generic.utils.LogDispatcher.java

@Override
public String sendLogs(String request) {
    String vnfrName = this.gson.fromJson(request, JsonObject.class).get("vnfrName").getAsString();
    String hostname = this.gson.fromJson(request, JsonObject.class).get("hostname").getAsString();

    Map<String, List<String>> logs = new HashMap<>();
    try {//  ww  w.j  ava2s . c om
        logs.put("output",
                readFile(this.logPath + vnfrName + '/' + hostname + ".log", Charset.defaultCharset()));
        logs.put("error",
                readFile(this.logPath + vnfrName + '/' + hostname + "-error.log", Charset.defaultCharset()));
    } catch (IOException exception) {
        exception.printStackTrace();
        this.log.error("Unable to retrieve logs: " + exception.getLocalizedMessage());
        return "{ \"answer\": \"" + "Unable to retrieve logs: " + exception.getLocalizedMessage() + "\"}";
    }

    return "{ \"answer\": " + this.gson.toJson(logs) + '}';
}

---

From source file:org.kitodo.sruimport.SRUImport.java

private Document performQueryToDocument(String queryURL) {
    try {/*from   www  . j a va 2 s .  co m*/
        HttpResponse response = sruClient.execute(new HttpGet(queryURL));
        if (Objects.equals(response.getStatusLine().getStatusCode(), SC_OK)) {
            return ResponseHandler.transformResponseToDocument(response);
        }
        throw new ConfigException("SRU Request Failed");
    } catch (IOException e) {
        throw new ConfigException(e.getLocalizedMessage());
    }
}

---

From source file:com.norconex.jefmon.instance.action.impl.LogViewerActionPanel.java

private Component createLogLines() {
    String text;/*from  w w  w.  j  a  v  a  2  s  . c o  m*/
    try {
        text = StringUtils.join(getLinesReader().readLines(), "\n");
    } catch (IOException e) {
        text = "Could not read log. Error is: " + e.getLocalizedMessage();
    }
    Label lines = new Label("logLines", text);
    return lines;
}

---

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