Example usage for java.nio.file Files createTempDirectory

List of usage examples for java.nio.file Files createTempDirectory

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Introduction

In this page you can find the example usage for java.nio.file Files createTempDirectory.

Prototype

public static Path createTempDirectory(String prefix, FileAttribute<?>... attrs) throws IOException

Source Link

Document

Creates a new directory in the default temporary-file directory, using the given prefix to generate its name.

Usage

From source file:org.corehunter.tests.data.simple.SimpleFrequencyGenotypeDataTest.java

@Test
public void toCsvFileWithAlleleNames() throws IOException {
    dataName = "out.csv";
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES;/* w  w  w.  jav a  2s .co  m*/
    expectedAlleleNames = ALLELE_NAMES;

    SimpleFrequencyGenotypeData genotypicData = new SimpleFrequencyGenotypeData(expectedHeaders,
            expectedMarkerNames, expectedAlleleNames, ALLELE_FREQUENCIES);

    Path path = Paths.get(TEST_OUTPUT);

    Files.createDirectories(path);

    path = Files.createTempDirectory(path, "GenoFreqs-CsvAlleleNames");

    path = Paths.get(path.toString(), dataName);

    System.out.println(" |- Write File " + dataName);
    genotypicData.writeData(path, FileType.CSV);

    System.out.println(" |- Read written File " + dataName);
    testData(SimpleFrequencyGenotypeData.readData(path, FileType.CSV));
}

From source file:org.corehunter.tests.data.simple.SimpleDefaultGenotypeDataTest.java

@Test
public void homozygousToCsvFileWithAllIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES_DEFAULT;
    expectedAlleleNames = ALLELE_NAMES_HOMOZYGOUS;

    SimpleDefaultGenotypeData genotypicData = new SimpleDefaultGenotypeData(NAME, HEADERS_UNIQUE_NAMES,
            MARKER_NAMES_DEFAULT, ALLELE_OBS_HOMOZYGOUS);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoHomozygous-AllIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);/*w ww  . j av  a  2s .  c  o  m*/
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (homozygous, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/homozygous_genotypes/out/all-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (homozygous, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, false);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/homozygous_genotypes/out/all-no-ids.csv").getPath()),
                    path.toFile()));

}

From source file:org.corehunter.tests.data.simple.SimpleBiAllelicGenotypeDataTest.java

@Test
public void toCsvFileWithAllIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES;//from   ww  w .  ja  v  a  2 s . co  m

    SimpleBiAllelicGenotypeData genotypicData = new SimpleBiAllelicGenotypeData(expectedHeaders,
            expectedMarkerNames, ALLELE_SCORES_BIALLELIC);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoBiallelic-AllIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);
    }

    Path path;

    // write allele score format with integer ids
    dataName = "bi-with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write biallelic genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, true);

    assertTrue("Output file is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/biallelic_genotypes/out/all-bi-with-ids.csv").getPath()),
                    path.toFile()));

    // write allele score format without integer ids
    dataName = "bi-no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write biallelic genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, false);

    assertTrue("Output file is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/biallelic_genotypes/out/all-bi-no-ids.csv").getPath()),
                    path.toFile()));

}

From source file:org.corehunter.tests.data.simple.SimpleFrequencyGenotypeDataTest.java

@Test
public void toCsvFileWithAllIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES;/*from   w  w  w . jav  a2s . c o  m*/
    expectedAlleleNames = ALLELE_NAMES;

    SimpleFrequencyGenotypeData genotypicData = new SimpleFrequencyGenotypeData(expectedHeaders,
            expectedMarkerNames, expectedAlleleNames, ALLELE_FREQUENCIES);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoFreqs-AllIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/frequency_genotypes/out/all-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, false);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/frequency_genotypes/out/all-no-ids.csv").getPath()),
                            path.toFile()));

}

From source file:org.corehunter.tests.data.simple.SimpleDistanceMatrixDataTest.java

@Test
public void toCsvFileWithUnselectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    SimpleDistanceMatrixData distanceData = new SimpleDistanceMatrixData(expectedHeaders, DISTANCES);

    Set<Integer> ids = distanceData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "DistanceMatrix-UnselectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);//from  w  w  w  .ja v  a 2s. c  o  m
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, true, false, true);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/distances/out/unsel-with-ids.csv").getPath()),
                            path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, false, false, true);

    assertTrue("Output is not correct!", FileUtils.contentEquals(new File(
            SimpleDistanceMatrixDataTest.class.getResource("/distances/out/unsel-no-ids.csv").getPath()),
            path.toFile()));

}

From source file:com.facebook.presto.hive.TestPrestoS3FileSystem.java

@Test
public void testCreateWithNonexistentStagingDirectory() throws Exception {
    java.nio.file.Path tmpdir = Paths.get(StandardSystemProperty.JAVA_IO_TMPDIR.value());
    java.nio.file.Path stagingParent = Files.createTempDirectory(tmpdir, "test");
    java.nio.file.Path staging = Paths.get(stagingParent.toString(), "staging");
    // stagingParent = /tmp/testXXX
    // staging = /tmp/testXXX/staging

    try (PrestoS3FileSystem fs = new PrestoS3FileSystem()) {
        MockAmazonS3 s3 = new MockAmazonS3();
        Configuration conf = new Configuration();
        conf.set(PrestoS3FileSystem.S3_STAGING_DIRECTORY, staging.toString());
        fs.initialize(new URI("s3n://test-bucket/"), conf);
        fs.setS3Client(s3);/*  w w w  . j a v  a2 s . c o m*/
        FSDataOutputStream stream = fs.create(new Path("s3n://test-bucket/test"));
        stream.close();
        assertTrue(Files.exists(staging));
    } finally {
        deleteRecursively(stagingParent.toFile());
    }
}

From source file:com.spectralogic.ds3client.metadata.MetadataReceivedListenerImpl_Test.java

@Test
public void testGettingMetadataFailureWindows() throws IOException, InterruptedException {
    Assume.assumeTrue(Platform.isWindows());

    try {/*  ww w  .ja  va2  s  .c om*/
        final String tempPathPrefix = null;
        final Path tempDirectory = Files.createTempDirectory(Paths.get("."), tempPathPrefix);

        final String fileName = "Gracie.txt";

        final Path filePath = Files.createFile(Paths.get(tempDirectory.toString(), fileName));

        try {
            // get permissions
            final ImmutableMap.Builder<String, Path> fileMapper = ImmutableMap.builder();
            fileMapper.put(filePath.toString(), filePath);
            final Map<String, String> metadataFromFile = new MetadataAccessImpl(fileMapper.build())
                    .getMetadataValue(filePath.toString());

            FileUtils.deleteDirectory(tempDirectory.toFile());

            // put old permissions back
            final Metadata metadata = new MetadataImpl(new MockedHeadersReturningKeys(metadataFromFile));

            new MetadataReceivedListenerImpl(tempDirectory.toString()).metadataReceived(fileName, metadata);
        } finally {
            FileUtils.deleteDirectory(tempDirectory.toFile());
        }
    } catch (final Throwable t) {
        fail("Throwing exceptions from metadata est verbotten");
    }
}

From source file:org.corehunter.tests.data.simple.SimpleDefaultGenotypeDataTest.java

@Test
public void homozygousToCsvFileWithSelectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES_DEFAULT;
    expectedAlleleNames = ALLELE_NAMES_HOMOZYGOUS;

    SimpleDefaultGenotypeData genotypicData = new SimpleDefaultGenotypeData(NAME, HEADERS_UNIQUE_NAMES,
            MARKER_NAMES_DEFAULT, ALLELE_OBS_HOMOZYGOUS);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoHomozygous-SelectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);// w  w w . j av  a  2s .c o  m
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (homozygous, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/homozygous_genotypes/out/sel-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (homozygous, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, false);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/homozygous_genotypes/out/sel-no-ids.csv").getPath()),
                    path.toFile()));

}

From source file:io.fabric8.maven.plugin.mojo.infra.AbstractInstallMojo.java

private File createDownloadFile(File downloadLocation, String fileName) throws MojoExecutionException {
    try {/*from  www .ja va2 s.co m*/
        File downloadDir = Files.createTempDirectory(downloadLocation.toPath(), "download").toFile();
        downloadDir.deleteOnExit();
        File ret = new File(downloadDir, fileName);
        ret.deleteOnExit();
        log.debug("Downloading %s to temporary file %s", fileName, ret);
        return ret;
    } catch (IOException e) {
        throw new MojoExecutionException("Failed to create a temporary file for the download");
    }
}

From source file:org.corehunter.tests.data.simple.SimpleBiAllelicGenotypeDataTest.java

@Test
public void toCsvFileWithSelectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES;//from   ww  w . j  a v a  2  s  .  c o m

    SimpleBiAllelicGenotypeData genotypicData = new SimpleBiAllelicGenotypeData(expectedHeaders,
            expectedMarkerNames, ALLELE_SCORES_BIALLELIC);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoBiallelic-SelectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);
    }

    Path path;

    // write allele score format with integer ids
    dataName = "bi-with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write biallelic genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, true);

    assertTrue("Output file is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/biallelic_genotypes/out/sel-bi-with-ids.csv").getPath()),
                    path.toFile()));

    // write allele score format without integer ids
    dataName = "bi-no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write biallelic genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, false);

    assertTrue("Output file is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/biallelic_genotypes/out/sel-bi-no-ids.csv").getPath()),
                    path.toFile()));

}