Example usage for java.io IOException getLocalizedMessage

List of usage examples for java.io IOException getLocalizedMessage

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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:org.eclipse.cdt.arduino.core.internal.board.ArduinoBoardManager.java

public ArduinoBoardManager() {
    new Job(Messages.ArduinoBoardManager_0) {
        protected IStatus run(IProgressMonitor monitor) {
            try (CloseableHttpClient client = HttpClients.createDefault()) {
                HttpGet get = new HttpGet("http://downloads.arduino.cc/packages/package_index.json"); //$NON-NLS-1$
                try (CloseableHttpResponse response = client.execute(get)) {
                    if (response.getStatusLine().getStatusCode() >= 400) {
                        return new Status(IStatus.ERROR, Activator.getId(),
                                response.getStatusLine().getReasonPhrase());
                    } else {
                        HttpEntity entity = response.getEntity();
                        if (entity == null) {
                            return new Status(IStatus.ERROR, Activator.getId(), Messages.ArduinoBoardManager_1);
                        }/* ww  w  . j  av  a2  s .  co m*/
                        Files.createDirectories(packageIndexPath.getParent());
                        Files.copy(entity.getContent(), packageIndexPath, StandardCopyOption.REPLACE_EXISTING);
                    }
                }
            } catch (IOException e) {
                return new Status(IStatus.ERROR, Activator.getId(), e.getLocalizedMessage(), e);
            }
            return Status.OK_STATUS;
        }
    }.schedule();
}

From source file:org.lobid.lodmill.JsonDecoder.java

@Override
public void process(final Reader reader) {
    STARTED = false;/*from w  w  w.ja v  a  2 s  .  c o m*/
    LOG.debug("############################ New");
    try {
        JsonToken currentToken = parseJson(reader);
        if (currentToken == null)
            return;
        processTokens(currentToken);
    } catch (final IOException e) {
        try {
            LOG.warn(e.getLocalizedMessage() + "while computing " + this.jsonParser.getText());
        } catch (JsonParseException e1) {
            e1.printStackTrace();
        } catch (IOException e1) {
            e1.printStackTrace();
        }
    }
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetStudyTreeListener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    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.setStudyTreeUI.displayMessage("Error: no subject to sample mapping file");
    }/*from w  w w  .j a  v  a2  s.co m*/
    String category = "";
    TreeNode node = this.setStudyTreeUI.getRoot();
    if (!node.hasChildren()) {
        this.setStudyTreeUI.displayMessage("You have to set a category code");
        return;
    }
    node = node.getChildren().get(0);
    while (node != null) {
        if (category.compareTo("") == 0) {
            category += node.toString().replace(' ', '_');
        } else {
            category += "+" + node.toString().replace(' ', '_');
        }
        if (node.hasChildren()) {
            node = node.getChildren().get(0);
        } else {
            node = null;
        }
    }
    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);
                out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + fields[3] + "\t" + fields[4]
                        + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + category + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setStudyTreeUI.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.setStudyTreeUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setStudyTreeUI.displayMessage("Eerror: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setStudyTreeUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

From source file:fr.fastconnect.factory.tibco.bw.maven.run.LaunchDesignerMojo.java

public void execute() throws MojoExecutionException {
    enableTestScope();/*  w w w  .j a  va  2  s. co  m*/

    super.execute();

    if (adaptAliases) {
        try {
            updateAliasesFile();
        } catch (IOException e) {
            throw new MojoExecutionException(e.getLocalizedMessage(), e);
        }
    }

    try {
        launchDesigner();
    } catch (IOException e) {
        throw new MojoExecutionException(LAUNCH_DESIGNER_FAILED, e);
    }
}

From source file:com.amazonaws.mturk.cmd.EvaluateQualificationRequests.java

protected void runCommand(CommandLine cmdLine) throws Exception {
    if (!cmdLine.hasOption(QUAL_TYPE) && !cmdLine.hasOption(INPUT_FILE)) {

        log.error("Either -" + QUAL_TYPE + " or -" + INPUT_FILE + " should be passed");

        System.exit(-1);/*from w  w w.  j a v a  2s. c o  m*/

    } else {
        String qualIds[] = null;
        if (cmdLine.hasOption(QUAL_TYPE)) {
            qualIds = new String[1];
            qualIds[0] = cmdLine.getOptionValue(QUAL_TYPE);
        } else {
            try {
                qualIds = super.getFieldValuesFromFile(cmdLine.getOptionValue(INPUT_FILE), QUAL_TYPE);
            } catch (IOException e) {
                log.error("error occured reading file: " + e.getLocalizedMessage(), e);
                System.exit(-1);
            }
            if (qualIds.length == 0) {
                log.error("qualtypeid must be present in the -" + INPUT_FILE + " file");
                System.exit(-1);
            }
        }

        for (String qualId : qualIds) {
            evaluateQualificationRequests(qualId, cmdLine.getOptionValue("answers"),
                    cmdLine.hasOption("preview"));
        }
    }
}

From source file:org.angrycamel.ivydav.DavResource.java

/**
 * Get a list of direct descendents of the given resource. Note that attempts to get a list of
 * children does <emphasize>not</emphasize> result in an error. Instead an error message is
 * logged and an empty ArrayList returned.
 *//*ww w  .  j  ava  2 s . c o  m*/
public List<String> getChildren() {
    init();
    Existence type = existence();
    if (Existence.ABSENT.equals(type)) {
        Message.error(uri + " does not exist; cannot enumerate children!");
        return Collections.emptyList();
    } else if (Existence.FILE.equals(type)) {
        Message.error(uri + " exists but is not a directory; cannot enumerate children");
        return Collections.emptyList();
    }
    List<String> list = null;
    try {
        list = repository.getDirectoryResources(uri);
    } catch (IOException e) {
        Message.verbose(e.getLocalizedMessage());
    }
    return list;
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetSubjectsIdListener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setSubjectsIdUI.getValues();
    Vector<String> samples = this.setSubjectsIdUI.getSamples();
    for (String v : values) {
        if (v.compareTo("") == 0) {
            this.setSubjectsIdUI.displayMessage("All identifiers have to be set");
            return;
        }//from ww w.j  a  va  2 s. c  om
    }

    File file = new File(this.dataType.getPath().toString() + File.separator
            + this.dataType.getStudy().toString() + ".subject_mapping.tmp");
    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");

        File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
        if (stsmf == null) {
            for (int i = 0; i < samples.size(); i++) {
                out.write(this.dataType.getStudy().toString() + "\t" + "\t" + values.elementAt(i) + "\t"
                        + samples.elementAt(i) + "\t" + "\t" + "\t" + "\t" + "\t" + "\n");
            }
        } else {
            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 subject;
                    if (samples.contains(sample)) {
                        subject = values.get(samples.indexOf(sample));
                    } else {
                        br.close();
                        return;
                    }
                    out.write(fields[0] + "\t" + fields[1] + "\t" + subject + "\t" + sample + "\t" + fields[4]
                            + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n");
                }
                br.close();
            } catch (Exception e) {
                this.setSubjectsIdUI.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.setSubjectsIdUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setSubjectsIdUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setSubjectsIdUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
    UsedFilesPart.sendFilesChanged(dataType);
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.clinicalData.SelectIdentifiersListener.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 {/*  w  w w .ja va 2s . c  o m*/
        Vector<String> subjectIds = this.setSubjectsIdUI.getSubjectIds();
        for (String s : subjectIds) {
            if (s.compareTo("") == 0) {
                this.setSubjectsIdUI.displayMessage("Subjects identifier columns have to be choosen");
                return;
            }
        }

        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();
        for (int i = 0; i < rawFiles.size(); i++) {
            int columnNumber = FileHandler.getHeaderNumber(rawFiles.elementAt(i), subjectIds.elementAt(i));
            if (columnNumber != -1) {
                out.write(rawFiles.elementAt(i).getName() + "\t\t" + columnNumber + "\tSUBJ_ID\t\t\n");
            }
        }
        if (((ClinicalData) this.dataType).getCMF() == null) {
            out.close();
            File fileDest = new File(this.dataType.getPath().toString() + File.separator
                    + this.dataType.getStudy().toString() + ".columns");
            FileUtils.moveFile(file, fileDest);
            ((ClinicalData) this.dataType).setCMF(fileDest);
            WorkPart.updateSteps();
        } else {
            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("SUBJ_ID") != 0) {
                        out.write(line + "\n");
                    }
                }
                br.close();
            } catch (Exception e) {
                this.setSubjectsIdUI.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.setSubjectsIdUI.displayMessage("File errorrror: " + ioe.getLocalizedMessage());
                return;
            }

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

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.RemoveRawFileListener.java

@Override
public void handleEvent(Event event) {
    Vector<File> files = this.selectRawFilesUI.getSelectedRemovedFile();
    if (files.size() < 1) {
        this.selectRawFilesUI.displayMessage("No file selected");
        return;//from  www.  j  a va 2 s.c om
    }
    File mapping = ((GeneExpressionData) this.dataType).getStsmf();
    boolean confirm = this.selectRawFilesUI.confirm(
            "The column mapping file and the word mapping file will be removed consequently.\nAre you sure to remove these files?");
    for (File file : files) {
        if (file == null) {
            return;
        }
        if (((GeneExpressionData) this.dataType).getRawFiles().size() == files.size()) {
            if (mapping != null) {
                if (confirm) {
                    ((GeneExpressionData) this.dataType).setSTSMF(null);
                    try {
                        FileUtils.forceDelete(mapping);
                    } catch (IOException e) {
                        // TODO Auto-generated catch block
                        this.selectRawFilesUI.displayMessage("File error: " + e.getLocalizedMessage());
                        e.printStackTrace();
                    }

                    ((GeneExpressionData) this.dataType).getRawFiles().remove(file);
                    FileUtils.deleteQuietly(file);
                    UsedFilesPart.sendFilesChanged(dataType);
                }
            } else {
                if (confirm) {
                    ((GeneExpressionData) this.dataType).getRawFiles().remove(file);
                    FileUtils.deleteQuietly(file);
                    UsedFilesPart.sendFilesChanged(dataType);
                }
            }
        }
    }
    this.selectRawFilesUI.updateViewer();
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

From source file:ru.codemine.ccms.service.DataFileService.java

@Transactional
public void delete(DataFile file) {
    File f = new File(file.getFilename());
    try {/*from w  ww .j ava2s  .c  o  m*/
        Files.deleteIfExists(f.toPath());
    } catch (IOException ex) {
        log.warn("    ? ?: " + file.getViewName() + "("
                + file.getFilename() + "), : " + ex.getLocalizedMessage());
    }
    dataFileDAO.delete(file);
}