Example usage for java.io File toString

List of usage examples for java.io File toString

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Introduction

In this page you can find the example usage for java.io File toString.

Prototype

public String toString()

Source Link

Document

Returns the pathname string of this abstract pathname.

Usage

From source file:edu.cornell.med.icb.goby.modes.TestCompactToFastaMode.java

/**
 * Test conversion of a compact file with no quality scores to Illumina/FASTQ format.
 * @throws IOException if the files cannot be read/written properly
 *///from   w w w .  j av a 2s. c o  m
@Test
public void toFastqIlluminaWithQuality() throws IOException {
    final String inputFilename = "test-data/compact-reads/five-with-quality.compact-reads";
    final File fastqFile = createTempFile("llumina", ".fastq");
    final String outputFilename = fastqFile.toString();
    final CompactToFastaMode compactToFastaMode = new CompactToFastaMode();
    compactToFastaMode.setInputFilename(inputFilename);
    compactToFastaMode.setOutputFilename(outputFilename);
    compactToFastaMode.setOutputFormat(CompactToFastaMode.OutputFormat.FASTQ);
    compactToFastaMode.setQualityEncoding(QualityEncoding.ILLUMINA);
    compactToFastaMode.execute();

    final FastXReader reader = new FastXReader(outputFilename);
    assertEquals("File should be in FASTQ format", "fq", reader.getFileType());

    int index = 0;
    for (final FastXEntry entry : reader) {
        assertEquals("Entry " + index + "symbol is not correct", '@', entry.getHeaderSymbol());
        assertEquals("Seqence for entry " + index + " is not correct", expectedSequence[index],
                entry.getSequence().toString());
        final MutableString quality = entry.getQuality();
        assertNotNull("Quality string should never be null", quality);
        assertEquals("There should be some quality values", 38, quality.length());
        // check quality scores
        for (int i = 0; i < 38; i++) {
            final char qualityCharacter = quality.charAt(i);
            assertEquals("Entry " + index + " has incorrect quality score at index " + i,
                    expectedQualityScores[index][i],
                    QualityEncoding.ILLUMINA.asciiEncodingToPhredQualityScore(qualityCharacter));
        }
        assertTrue("Entry " + index + " is not complete", entry.isEntryComplete());
        index++;
    }

    assertEquals(5, index);
    reader.close();
}

From source file:edu.cornell.med.icb.goby.modes.TestCompactToFastaMode.java

/**
 * Test conversion of a compact file with no quality scores to Sanger/FASTQ format.
 * @throws IOException if the files cannot be read/written properly
 *//*from w ww .  ja v  a  2s . c  om*/
@Test
public void toFastqSangerWithQuality() throws IOException {
    final String inputFilename = "test-data/compact-reads/five-with-quality.compact-reads";
    final File fastqFile = createTempFile("llumina", ".fastq");
    final String outputFilename = fastqFile.toString();
    final CompactToFastaMode compactToFastaMode = new CompactToFastaMode();
    compactToFastaMode.setInputFilename(inputFilename);
    compactToFastaMode.setOutputFilename(outputFilename);
    compactToFastaMode.setOutputFormat(CompactToFastaMode.OutputFormat.FASTQ);
    compactToFastaMode.setQualityEncoding(QualityEncoding.SANGER);
    compactToFastaMode.execute();

    final FastXReader reader = new FastXReader(outputFilename);
    assertEquals("File should be in FASTQ format", "fq", reader.getFileType());

    int index = 0;
    for (final FastXEntry entry : reader) {
        assertEquals("Entry " + index + "symbol is not correct", '@', entry.getHeaderSymbol());
        assertEquals("Seqence for entry " + index + " is not correct", expectedSequence[index],
                entry.getSequence().toString());
        final MutableString quality = entry.getQuality();
        assertNotNull("Quality string should never be null", quality);
        assertEquals("There should be some quality values", 38, quality.length());
        // check quality scores
        for (int i = 0; i < 38; i++) {
            final char qualityCharacter = quality.charAt(i);
            assertEquals("Entry " + index + " has incorrect quality score at index " + i,
                    expectedQualityScores[index][i],
                    QualityEncoding.SANGER.asciiEncodingToPhredQualityScore(qualityCharacter));
        }
        assertTrue("Entry " + index + " is not complete", entry.isEntryComplete());
        index++;
    }

    assertEquals(5, index);
    reader.close();
}

From source file:gool.generator.android.AndroidCodePrinter.java

/**
 * Returns a list of all the classes containing main methods
 * //from  w  w w.j  a v  a2s .com
 * @param mainFolder
 * @param mainClassFiles
 * @return
 */
private void populateMainMethodClasses(File mainFolder, List<File> mainClassFiles) {
    File[] tempFileList = mainFolder.listFiles();
    for (File tempFile : tempFileList) {
        if (tempFile.isDirectory()) {
            populateMainMethodClasses(tempFile, mainClassFiles);
        } else {
            if (tempFile.toString().endsWith("Activity.java")) {
                mainClassFiles.add(tempFile);
            }
        }
    }

}

From source file:jobhunter.persistence.Persistence.java

private void updateLastMod(final File file) {
    this.lastModification = file.lastModified();
    try (InputStream in = new FileInputStream(file)) {
        this.md5sum = DigestUtils.md5(in);
    } catch (IOException e) {
        l.error("Failed to read MD5 checksum from {}", file.toString(), e);
    }/*from   ww  w .  j  av  a2 s .co m*/
    l.debug("File was last modified on {} with MD5 {}", lastModification, this.md5sum.toString());
}

From source file:com.cloudera.sqoop.hive.HiveImport.java

/**
 * Perform the import of data from an HDFS path to a Hive table.
 *
 * @param inputTableName the name of the table as loaded into HDFS
 * @param outputTableName the name of the table to create in Hive.
 * @param createOnly if true, run the CREATE TABLE statement but not
 * LOAD DATA./*from  w w w.  jav  a  2  s  .  co m*/
 */
public void importTable(String inputTableName, String outputTableName, boolean createOnly) throws IOException {

    if (!isGenerateOnly()) {
        removeTempLogs(inputTableName);
        LOG.info("Loading uploaded data into Hive");
    }

    if (null == outputTableName) {
        outputTableName = inputTableName;
    }
    LOG.debug("Hive.inputTable: " + inputTableName);
    LOG.debug("Hive.outputTable: " + outputTableName);

    // For testing purposes against our mock hive implementation,
    // if the sysproperty "expected.script" is set, we set the EXPECTED_SCRIPT
    // environment variable for the child hive process. We also disable
    // timestamp comments so that we have deterministic table creation scripts.
    String expectedScript = System.getProperty("expected.script");
    List<String> env = Executor.getCurEnvpStrings();
    boolean debugMode = expectedScript != null;
    if (debugMode) {
        env.add("EXPECTED_SCRIPT=" + expectedScript);
        env.add("TMPDIR=" + options.getTempDir());
    }

    // generate the HQL statements to run.
    TableDefWriter tableWriter = new TableDefWriter(options, connManager, inputTableName, outputTableName,
            configuration, !debugMode);
    String createTableStr = tableWriter.getCreateTableStmt() + ";\n";
    String loadDataStmtStr = tableWriter.getLoadDataStmt() + ";\n";

    // write them to a script file.
    File scriptFile = getScriptFile(outputTableName);
    try {
        String filename = scriptFile.toString();
        BufferedWriter w = null;
        try {
            FileOutputStream fos = new FileOutputStream(scriptFile);
            w = new BufferedWriter(new OutputStreamWriter(fos));
            w.write(createTableStr, 0, createTableStr.length());
            if (!createOnly) {
                w.write(loadDataStmtStr, 0, loadDataStmtStr.length());
            }
        } catch (IOException ioe) {
            LOG.error("Error writing Hive load-in script: " + ioe.toString());
            ioe.printStackTrace();
            throw ioe;
        } finally {
            if (null != w) {
                try {
                    w.close();
                } catch (IOException ioe) {
                    LOG.warn("IOException closing stream to Hive script: " + ioe.toString());
                }
            }
        }

        if (!isGenerateOnly()) {
            executeScript(filename, env);

            LOG.info("Hive import complete.");
        }
    } finally {
        if (!isGenerateOnly()) {
            // User isn't interested in saving the DDL. Remove the file.
            if (!scriptFile.delete()) {
                LOG.warn("Could not remove temporary file: " + scriptFile.toString());
                // try to delete the file later.
                scriptFile.deleteOnExit();
            }
        }
    }
}

From source file:net.sf.eclipsecs.core.config.configtypes.ConfigurationType.java

/**
 * Gets the property resolver for this configuration type used to expand
 * property values within the checkstyle configuration.
 * /*from  w ww. ja  v a 2  s.c  o  m*/
 * @param checkConfiguration
 *            the actual check configuration
 * @return the property resolver
 * @throws IOException
 *             error creating the property resolver
 */
protected PropertyResolver getPropertyResolver(ICheckConfiguration config,
        CheckstyleConfigurationFile configFile) throws IOException {

    MultiPropertyResolver multiResolver = new MultiPropertyResolver();
    multiResolver.addPropertyResolver(new ResolvablePropertyResolver(config));

    File f = FileUtils.toFile(configFile.getResolvedConfigFileURL());
    if (f != null) {
        multiResolver.addPropertyResolver(new StandardPropertyResolver(f.toString()));
    } else {
        multiResolver.addPropertyResolver(
                new StandardPropertyResolver(configFile.getResolvedConfigFileURL().toString()));
    }

    multiResolver.addPropertyResolver(new ClasspathVariableResolver());
    multiResolver.addPropertyResolver(new SystemPropertyResolver());

    if (configFile.getAdditionalPropertiesBundleStream() != null) {
        ResourceBundle bundle = new PropertyResourceBundle(configFile.getAdditionalPropertiesBundleStream());
        multiResolver.addPropertyResolver(new ResourceBundlePropertyResolver(bundle));
    }

    return multiResolver;
}

From source file:org.encog.workbench.util.graph.EncogChartPanel.java

/**
 * Opens a file chooser and gives the user an opportunity to save the chart
 * in PNG format./*from  w  w  w . java 2 s .c o m*/
 *
 * @throws IOException if there is an I/O error.
 */
public void doSaveAs() throws IOException {

    SaveImageDialog dialog = new SaveImageDialog(EncogWorkBench.getInstance().getMainWindow());

    dialog.getImageWidth().setValue(640);
    dialog.getImageHeight().setValue(480);

    if (dialog.process()) {

        File filename = new File(dialog.getTargetFile().getValue());
        int width = dialog.getImageWidth().getValue();
        int height = dialog.getImageHeight().getValue();

        switch (dialog.getFileType().getSelectedIndex()) {
        case 0:
            filename = new File(FileUtil.forceExtension(filename.toString(), "png"));
            ChartUtilities.saveChartAsPNG(filename, this.getChart(), width, height);
            break;
        case 1:
            filename = new File(FileUtil.forceExtension(filename.toString(), "jpg"));
            ChartUtilities.saveChartAsPNG(filename, this.getChart(), width, height);
            break;
        case 2:
            filename = new File(FileUtil.forceExtension(filename.toString(), "pdf"));
            DocumentPDF.savePDF(filename, getChart(), width, height);
            break;
        case 3:
            filename = new File(FileUtil.forceExtension(filename.toString(), "svg"));
            DocumentSVG.saveSVG(filename, getChart(), width, height);
            break;

        }
    }

}

From source file:com.linkedin.pinot.core.segment.index.converter.SegmentV1V2ToV3FormatConverter.java

@Override
public void convert(File v2SegmentDirectory) throws Exception {
    Preconditions.checkNotNull(v2SegmentDirectory, "Segment directory should not be null");

    Preconditions.checkState(v2SegmentDirectory.exists() && v2SegmentDirectory.isDirectory(),
            "Segment directory: " + v2SegmentDirectory.toString() + " must exist and should be a directory");

    LOGGER.info("Converting segment: {} to v3 format", v2SegmentDirectory);

    // check existing segment version
    SegmentMetadataImpl v2Metadata = new SegmentMetadataImpl(v2SegmentDirectory);
    SegmentVersion oldVersion = SegmentVersion.valueOf(v2Metadata.getVersion());
    Preconditions.checkState(oldVersion != SegmentVersion.v3,
            "Segment {} is already in v3 format but at wrong path", v2Metadata.getName());

    Preconditions.checkArgument(oldVersion == SegmentVersion.v1 || oldVersion == SegmentVersion.v2,
            "Can not convert segment version: {} at path: {} ", oldVersion, v2SegmentDirectory);

    deleteStaleConversionDirectories(v2SegmentDirectory);

    File v3TempDirectory = v3ConversionTempDirectory(v2SegmentDirectory);
    setDirectoryPermissions(v3TempDirectory);

    createMetadataFile(v2SegmentDirectory, v3TempDirectory);
    copyCreationMetadata(v2SegmentDirectory, v3TempDirectory);
    copyIndexData(v2SegmentDirectory, v2Metadata, v3TempDirectory);

    File newLocation = SegmentDirectoryPaths.segmentDirectoryFor(v2SegmentDirectory, SegmentVersion.v3);
    LOGGER.info("v3 segment location for segment: {} is {}", v2Metadata.getName(), newLocation);
    v3TempDirectory.renameTo(newLocation);
}

From source file:io.druid.segment.IndexMaker.java

public static File append(final List<IndexableAdapter> adapters, final File outDir, final IndexSpec indexSpec)
        throws IOException {
    return append(adapters, outDir, new LoggingProgressIndicator(outDir.toString()), indexSpec);
}

From source file:com.dmsl.anyplace.tasks.UploadRSSLogTask.java

@Override
protected String doInBackground(Void... params) {
    try {//from  w ww  .j  av  a 2s .co m
        JSONObject j;
        j = new JSONObject();
        j.put("username", username);
        j.put("password", password);
        String json = j.toString();

        File rsslog = new File(this.file);
        if (rsslog.exists() == false) {
            exceptionOccured = true;
            return "File not found";
        }
        Log.d("radio upload", rsslog.toString());
        String response;

        HttpClient httpclient = new DefaultHttpClient();
        httppost = new HttpPost(AnyplaceAPI.getRadioUploadUrl());

        MultipartEntity entity = new MultipartEntity();
        entity.addPart("radiomap", new FileBody(rsslog));
        entity.addPart("json", new StringBody(json));

        ProgressCallback progressCallback = new ProgressCallback() {

            @Override
            public void progress(float progress) {
                if (currentProgress != (int) (progress)) {
                    currentProgress = (int) progress;
                    publishProgress(currentProgress);
                }
            }

        };

        httppost.setEntity(new ProgressHttpEntityWrapper(entity, progressCallback));
        HttpResponse httpresponse = httpclient.execute(httppost);
        HttpEntity resEntity = httpresponse.getEntity();

        response = EntityUtils.toString(resEntity);

        Log.d("radio upload", "response: " + response);

        j = new JSONObject(response);
        if (j.getString("status").equalsIgnoreCase("error")) {
            exceptionOccured = true;
            return "Error: " + j.getString("message");
        }

    } catch (JSONException e) {
        exceptionOccured = true;
        Log.d("upload rss log", e.getMessage());
        return "Cannot upload RSS log. JSONException occurred[ " + e.getMessage() + " ]";
    } catch (ParseException e) {
        exceptionOccured = true;
        Log.d("upload rss log", e.getMessage());
        return "Cannot upload RSS log. ParseException occurred[ " + e.getMessage() + " ]";
    } catch (IOException e) {
        exceptionOccured = true;
        Log.d("upload rss log", e.getMessage());

        if (httppost != null && httppost.isAborted()) {
            return "Uploading cancelled!";
        } else {
            return "Cannot upload RSS log. IOException occurred[ " + e.getMessage() + " ]";
        }

    }
    return "Successfully uploaded RSS log!";
}