Example usage for org.apache.commons.io FileUtils moveFile

List of usage examples for org.apache.commons.io FileUtils moveFile

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Introduction

In this page you can find the example usage for org.apache.commons.io FileUtils moveFile.

Prototype

public static void moveFile(File srcFile, File destFile) throws IOException

Source Link

Document

Moves a file.

Usage

From source file:edu.ucsd.crbs.cws.cluster.SyncWorkspaceFileToFileSystemImpl.java

@Override
public void sync(WorkspaceFile wsf) throws Exception {

    if (wsf == null) {
        throw new IllegalArgumentException("WorkspaceFile cannot be null");
    }/*from w w w.  j a v  a2  s  .c om*/

    if (doesWorkspaceFileExistOnFileSystem(wsf) == true) {
        return;
    }

    File wFile = _fileDownloader.downloadFile(_getURL + "/workspacefile", Constants.WSFID_PARAM,
            wsf.getId().toString(), _userLogin, _token);

    if (wFile == null) {
        throw new Exception("No file obtained from web request to base url: " + _getURL);
    }

    //make the directory for the workflow
    File wfDir = new File(getWorkspaceDirectory(wsf));
    if (wfDir.isDirectory() == false) {
        _log.log(Level.INFO, "Creating directories: {0}", wfDir.getAbsolutePath());
        if (wfDir.mkdirs() == false) {
            throw new Exception("Unable to create directory: " + wfDir.getAbsolutePath());
        }
    }

    FileUtils.moveFile(wFile, getWorkspaceFile(wsf));

    if (doesWorkspaceFileExistOnFileSystem(wsf) == false) {
        throw new Exception("Unable to put workspace file on file system");
    }

    // need to update WorkspaceFile on GAE with path

}

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

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setSiteIdUI.getValues();
    Vector<String> samples = this.setSiteIdUI.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.setSiteIdUI.displayMessage("Error: no subject to sample mapping file");
    }/*from www  .jav a  2s . co  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 site;
                if (samples.contains(sample)) {
                    site = values.get(samples.indexOf(sample));
                } else {
                    br.close();
                    return;
                }
                out.write(fields[0] + "\t" + site + "\t" + fields[2] + "\t" + sample + "\t" + fields[4] + "\t"
                        + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setSiteIdUI.displayMessage("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.setSiteIdUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setSiteIdUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setSiteIdUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

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

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setPlatformsUI.getValues();
    Vector<String> samples = this.setPlatformsUI.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.setPlatformsUI.displayMessage("Error: no subject to sample mapping file");
    }/*  w ww  .  j  a  va 2s.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 platform;
                if (samples.contains(sample)) {
                    platform = values.get(samples.indexOf(sample));
                } else {
                    br.close();
                    return;
                }
                out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + platform
                        + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setPlatformsUI.displayMessage("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.setPlatformsUI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setPlatformsUI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetAttribute1Listener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setAttribute1UI.getValues();
    Vector<String> samples = this.setAttribute1UI.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.setAttribute1UI.displayMessage("Error: no subject to sample mapping file");
    }//from   w  ww.ja  v a2  s. com
    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 attribute;
                if (samples.contains(sample)) {
                    attribute = 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" + fields[5] + "\t" + attribute + "\t" + fields[7] + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            setAttribute1UI.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.setAttribute1UI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setAttribute1UI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setAttribute1UI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetAttribute2Listener.java

@Override
public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Vector<String> values = this.setAttribute2UI.getValues();
    Vector<String> samples = this.setAttribute2UI.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.setAttribute2UI.displayMessage("Error: no subject to sample mapping file");
    }//from   w  w  w. j av  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 attribute;
                if (samples.contains(sample)) {
                    attribute = 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" + fields[5] + "\t" + fields[6] + "\t" + attribute + "\t" + fields[8] + "\n");
            }
            br.close();
        } catch (Exception e) {
            this.setAttribute2UI.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.setAttribute2UI.displayMessage("File error: " + ioe.getLocalizedMessage());
            return;
        }
    } catch (Exception e) {
        this.setAttribute2UI.displayMessage("Error: " + e.getLocalizedMessage());
        e.printStackTrace();
    }
    this.setAttribute2UI.displayMessage("Subject to sample mapping file updated");
    WorkPart.updateSteps();
    WorkPart.updateFiles();
}

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");
    }//w  w w .  jav a2  s  . co  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:com.github.cbismuth.fdupes.io.PathOrganizer.java

private void onNoTimestampPath(final Path destination, final PathElement pathElement,
        final AtomicInteger counter) {
    final Path path = pathElement.getPath();

    final String baseName = FilenameUtils.getBaseName(path.toString());
    final int count = counter.getAndIncrement();
    final String extension = FilenameUtils.getExtension(path.toString());

    final String newName = String.format("%s-%d.%s", baseName, count, extension);

    final Path sibling = path.resolveSibling(newName);

    try {// w ww.j a v  a 2s . c  o m
        FileUtils.moveFile(path.toFile(), sibling.toFile());

        FileUtils.moveFileToDirectory(sibling.toFile(), Paths.get(destination.toString(), "misc").toFile(),
                true);
    } catch (final IOException e) {
        LOGGER.error(e.getMessage());
    }
}

From source file:de.uzk.hki.da.cb.ShortenFileNamesAction.java

@Override
public void rollback() throws Exception {

    for (Event e : o.getLatestPackage().getEvents()) {
        if (!"CONVERT".equals(e.getType()))
            continue;

        DAFile daFile = e.getTarget_file();
        File file = wa.toFile(daFile);
        String filePath = daFile.getRelative_path();
        if (!map.containsKey(filePath))
            continue;
        String oldFilePath = map.get(filePath);
        File oldFile = new File(file.getAbsolutePath().replaceAll(filePath + "$", oldFilePath));

        daFile.setRelative_path(oldFilePath);
        FileUtils.forceMkdir(oldFile.getParentFile());
        FileUtils.moveFile(file, oldFile);

    }/*w w  w.j  a va 2 s. c  o  m*/

    logger.info("@Admin: You can safely roll back this job to status " + this.getStartStatus() + " now.");
}

From source file:com.springer.omelet.driver.DriverUtility.java

/***
 * Take Screen Shot/*w  w  w  .  ja v a2 s  .  c  om*/
 * 
 * @param driver
 * @param path
 *            :File path to store screen Shot
 * @author kapilA
 */
public static File takeScreenShot(WebDriver driver, String path) {
    File saved = new File(path);
    File scrFile;
    try {
        if (driver != null) {
            if (Driver.getBrowserConf().isRemoteFlag()) {
                Augmenter augumenter = new Augmenter();
                scrFile = ((TakesScreenshot) augumenter.augment(driver)).getScreenshotAs(OutputType.FILE);
            } else {
                scrFile = ((TakesScreenshot) driver).getScreenshotAs(OutputType.FILE);
            }
            FileUtils.moveFile(scrFile, saved);
        } else {
            LOGGER.info("As the driver is null no point in taking screen shot");
        }
    } catch (Exception e) {
        LOGGER.info("Not able to take Screen Shot", e);
    }
    return saved;
}

From source file:com.xebialabs.overcast.OvercastPropertiesTest.java

@Test
public void testPropertyHasPrecedenceOverClasspath() throws IOException {

    System.setProperty("user.home", new File("src/test/resources/dir-without-conf").getAbsolutePath());
    System.clearProperty("precedenceTestValue");
    System.setProperty("overcast.conf.file", "src/test/resources/property-path/overcast.conf");

    File cfg = new File("overcast.conf");
    File bkp = new File("backup.conf");

    try {/*from  w ww.  jav a 2 s .  c  o m*/
        FileUtils.moveFile(cfg, bkp);
        OvercastProperties.reloadOvercastProperties();
        assertThat(OvercastProperties.getOvercastProperty("precedenceTestValue"), is("valueFromProperty"));
    } finally {
        FileUtils.moveFile(bkp, cfg);
    }
}