Example usage for java.nio.file Path toAbsolutePath

List of usage examples for java.nio.file Path toAbsolutePath

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Introduction

In this page you can find the example usage for java.nio.file Path toAbsolutePath.

Prototype

Path toAbsolutePath();

Source Link

Document

Returns a Path object representing the absolute path of this path.

Usage

From source file:org.codice.ddf.catalog.content.impl.FileSystemStorageProvider.java

@SuppressFBWarnings
public void setBaseContentDirectory(final String baseDirectory) throws IOException {

    Path directory;//ww w . j av  a2s.c o  m
    if (!baseDirectory.isEmpty()) {
        String path = FilenameUtils.normalize(baseDirectory);
        try {
            directory = Paths.get(path, DEFAULT_CONTENT_REPOSITORY, DEFAULT_CONTENT_STORE);
        } catch (InvalidPathException e) {
            path = System.getProperty(KARAF_HOME);
            directory = Paths.get(path, DEFAULT_CONTENT_REPOSITORY, DEFAULT_CONTENT_STORE);
        }
    } else {
        String path = System.getProperty("karaf.home");
        directory = Paths.get(path, DEFAULT_CONTENT_REPOSITORY, DEFAULT_CONTENT_STORE);
    }

    Path directories;
    if (!Files.exists(directory)) {
        directories = Files.createDirectories(directory);
        LOGGER.debug("Setting base content directory to: {}", directories.toAbsolutePath().toString());
    } else {
        directories = directory;
    }

    Path tmpDirectories;
    Path tmpDirectory = Paths.get(directories.toAbsolutePath().toString(), DEFAULT_TMP);
    if (!Files.exists(tmpDirectory)) {
        tmpDirectories = Files.createDirectories(tmpDirectory);
        LOGGER.debug("Setting base content directory to: {}", tmpDirectory.toAbsolutePath().toString());
    } else {
        tmpDirectories = tmpDirectory;
    }

    this.baseContentDirectory = directories;
    this.baseContentTmpDirectory = tmpDirectories;
}

From source file:at.ac.tuwien.ims.latex2mobiformulaconv.converter.Converter.java

/**
 * Converts a single input file from LaTeX to Mobi
 *
 * @return Path of the resulting File/*from   w w w. j a v a  2s  . com*/
 * @throws FileNotFoundException when there's no file at the inputPath location
 */
public Path convert() throws FileNotFoundException {
    // Currently only the first input path will be evaluated
    File inputFile = inputPaths.get(0).toFile();

    final String fullFilePath = inputFile.toPath().toAbsolutePath().toString();

    if (Files.exists(inputPaths.get(0))) {
        logger.debug("Input file found: " + fullFilePath);

    } else {
        throw new FileNotFoundException("Input file could not be found at: " + fullFilePath);
    }

    // set default title
    if (title == null) {
        title = inputFile.getName();
    }

    // Main Document conversion to HTML, without formulas
    logger.debug("Converting main document to HTML...");
    Document document = latexToHtmlConverter.convert(inputFile, title);

    logger.info("Parsing LaTeX formulas from resulting HTML...");

    Map<Integer, Formula> formulaMap = new HashMap<>();

    formulaConverter.setGenerateDebugMarkup(debugMarkupOutput);

    Map<Integer, String> latexFormulas = formulaConverter.extractFormulas(document);

    if (latexFormulas.isEmpty() == false) {
        Iterator<Integer> it = latexFormulas.keySet().iterator();
        while (it.hasNext()) {
            Integer id = it.next();
            String latexFormula = latexFormulas.get(id);

            Formula formula = formulaConverter.parse(id, latexFormula);

            if (formula != null) {
                formulaMap.put(id, formula);
            }
        }
        document = formulaConverter.replaceFormulas(document, formulaMap);
    }

    // Persisting markup
    File htmlFile = saveHtmlFile(document);

    Path markupDir = null;

    // markup is requested or implicit output
    if (exportMarkup || noMobiConversion) {
        markupDir = exportMarkup(htmlFile.toPath());
    }

    if (noMobiConversion) {
        // no mobi file will be generated in any way, just the markup
        return markupDir.toAbsolutePath();
    } else {
        // Convert to MOBI format
        logger.info("Converting completed HTML to MOBI format...");
        File mobiFile = htmlToMobiConverter.convertToMobi(htmlFile);

        // Save file
        Path resultFilepath = null;
        try {
            // Don't overwrite files
            Path outputFilepath;
            int i = 1;
            String replaceFilename = filename + FILE_EXTENSION;
            while (true) {
                outputFilepath = outputPath.resolve(replaceFilename);
                if (Files.exists(outputFilepath) == false) {
                    break;
                }
                replaceFilename = filename + " (" + i + ")" + FILE_EXTENSION;
                i++;
            }

            resultFilepath = Files.move(mobiFile.toPath(), outputFilepath);
            logger.debug("Mobi file moved to: " + resultFilepath.toAbsolutePath().toString());
            return resultFilepath.toAbsolutePath();

        } catch (IOException e) {
            logger.error("Error writing or moving output file");
            logger.error(e.getMessage(), e);
            return null;
        }
    }
}

From source file:org.holodeckb2b.deliverymethod.file.AbstractFileDeliverer.java

/**
 * Helper method to copy a the payload content to <i>delivery directory</i>.
 * //from ww w.j  a  v a  2  s . c  om
 * @param p         The payload for which the content must be copied
 * @param msgId     The message-id of the message that contains the payload, used for name the file
 * @return          The path where the payload content is now stored
 * @throws IOException  When the payload content could not be copied to the <i>delivery directory</i>
 */
private Path copyPayloadFile(IPayload p, String msgId) throws IOException {
    // If payload was external to message, it is not processed by Holodeck B2B, so no content to move
    if (IPayload.Containment.EXTERNAL == p.getContainment())
        return null;

    // Compose a file name for the payload file, based on msgId and href 
    String plRef = p.getPayloadURI();
    plRef = (plRef == null || plRef.isEmpty() ? "body" : plRef);
    // If this was a attachment the reference is a a MIME Content-id. As these are also quite lengthy we shorten 
    // it to the left part
    if (plRef.indexOf("@") > 0)
        plRef = plRef.substring(0, plRef.indexOf("@"));

    Path sourcePath = Paths.get(p.getContentLocation());
    // Try to set nice extension based on MIME Type of payload
    String mimeType = p.getMimeType();
    if (mimeType == null || mimeType.isEmpty()) {
        // No MIME type given in message, try to detect from content
        try {
            mimeType = Utils.detectMimeType(sourcePath.toFile());
        } catch (IOException ex) {
            mimeType = null;
        } // Unable to detect the MIME Type                        
    }
    String ext = Utils.getExtension(mimeType);

    Path targetPath = Paths.get(Utils.preventDuplicateFileName(directory + "pl-"
            + (msgId + "-" + plRef).replaceAll("[^a-zA-Z0-9.-]", "_") + (ext != null ? ext : "")));

    try {
        Files.copy(sourcePath, targetPath, StandardCopyOption.REPLACE_EXISTING);
    } catch (Exception ex) {
        // Can not move payload file -> delivery not possible
        throw new IOException("Unable to deliver message because payload file [" + p.getContentLocation()
                + "] can not be moved!", ex);
    }

    return targetPath.toAbsolutePath();
}

From source file:modules.NativeProcessIterativeDaemonModule.java

protected String extractNative(String command, String options, Path path) throws NativeExecutionException {
    if (command == null || command.equals("")) {
        System.err.println("command null at GeneralNativeCommandModule.extractNative()");
        return null;
    }/*from   w w w . ja  v  a 2 s.co m*/
    CommandLine commandLine = new CommandLine(command);

    if (options != null && !options.equals("")) {
        String[] args = options.split(" ");
        commandLine.addArguments(args);
    }

    if (path != null) {
        commandLine.addArgument(path.toAbsolutePath().toString(), false);
    }
    DefaultExecutor executor = new DefaultExecutor();
    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
    PumpStreamHandler streamHandler = new PumpStreamHandler(outputStream);
    executor.setStreamHandler(streamHandler);
    GeneralExecutableModuleConfig generalExecutableModuleConfig = getConfig();
    executor.setWatchdog(new ExecuteWatchdog(generalExecutableModuleConfig.timeout));
    if (getConfig().workingDirectory != null && getConfig().workingDirectory.exists()) {
        executor.setWorkingDirectory(getConfig().workingDirectory);
    }
    try {

        // System.out.println("Now execute " + commandLine);
        executor.execute(commandLine);
    } catch (ExecuteException xs) {
        NativeExecutionException n = new NativeExecutionException();
        n.initCause(xs);
        if (path != null) {
            n.path = path.toAbsolutePath().toString();
        }
        n.executionResult = outputStream.toString();
        n.exitCode = xs.getExitValue();
        throw n;
    } catch (IOException xs) {
        NativeExecutionException n = new NativeExecutionException();
        n.initCause(xs);
        if (path != null) {
            n.path = path.toAbsolutePath().toString();
        }
        n.executionResult = outputStream.toString();
        throw n;
    }
    return outputStream.toString().trim();
}

From source file:org.ng200.openolympus.cerberus.compilers.GNUCompiler.java

@Override
public void compile(final List<Path> inputFiles, final Path outputFile,
        final Map<String, Object> additionalParameters) throws CompilationException {
    GNUCompiler.logger.debug("Compiling {} to {} using GCC", inputFiles, outputFile);

    final CommandLine commandLine = new CommandLine("g++");
    commandLine.setSubstitutionMap(additionalParameters);

    this.arguments.forEach((arg) -> commandLine.addArgument(arg));

    commandLine.addArgument("-w"); // Prohibit warnings because they screw
    // up error detection

    commandLine.addArgument("-o");
    commandLine.addArgument(MessageFormat.format("\"{0}\"", outputFile.toAbsolutePath().toString())); // Set outuput file

    inputFiles.forEach((file) -> commandLine
            .addArguments(MessageFormat.format("\"{0}\"", file.toAbsolutePath().toString()))); // Add
    // input//from  ww  w  .  j a v  a  2s. c  o  m
    // files

    GNUCompiler.logger.debug("Running GCC with arguments: {}", Arrays.asList(commandLine.getArguments()));

    final DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValues(new int[] { 0, 1 });

    final ByteArrayOutputStream errorStream = new ByteArrayOutputStream();
    executor.setStreamHandler(new PumpStreamHandler(null, errorStream, null));

    executor.setWatchdog(new ExecuteWatchdog(20000));// 20 seconds to
    // compile
    int result;
    try {
        result = executor.execute(commandLine);
    } catch (final IOException e) {
        GNUCompiler.logger.error("Could not execute GCC: {}", e);
        throw new CompilationException("Could not execute GCC", e);
    }

    switch (result) {
    case 0:
        return;
    case 1:
        try {
            String errorString = errorStream.toString(StandardCharsets.UTF_8.name());

            final Pattern pattern = Pattern.compile(
                    "^(" + inputFiles.stream().map(file -> Pattern.quote(file.toAbsolutePath().toString()))
                            .collect(Collectors.joining("|")) + "):",
                    Pattern.MULTILINE);
            errorString = pattern.matcher(errorString).replaceAll("");

            GNUCompiler.logger.debug("Compilation error: {}", errorString);
            throw new CompilerError("gcc.wrote.stderr", errorString);
        } catch (final UnsupportedEncodingException e) {
            throw new CompilationException("Unsupported encoding! The compiler should output UTF-8!", e);
        }
    }
}

From source file:io.undertow.server.handlers.file.FileHandlerSymlinksTestCase.java

@Test
public void testExplicitAccessSymlinkDeniedUsingSpecificFilters() throws IOException, URISyntaxException {
    TestHttpClient client = new TestHttpClient();
    Path rootPath = Paths.get(getClass().getResource("page.html").toURI()).getParent();
    Path newSymlink = rootPath.resolve("newSymlink");

    try {/*from w w w .ja va2 s .co m*/
        DefaultServer.setRootHandler(new CanonicalPathHandler().setNext(new PathHandler().addPrefixPath("/path",
                new ResourceHandler(new PathResourceManager(newSymlink, 10485760, true,
                        rootPath.toAbsolutePath().toString().concat("/otherDir")))
                                .setDirectoryListingEnabled(false).addWelcomeFiles("page.html"))));
        /**
         * This request should return a 404 code as rootPath + "/otherDir" doesnt match in rootPath + "/path/innerSymlink/page.html"
         */
        HttpGet get = new HttpGet(DefaultServer.getDefaultServerURL() + "/path/innerSymlink/page.html");
        HttpResponse result = client.execute(get);
        Assert.assertEquals(StatusCodes.NOT_FOUND, result.getStatusLine().getStatusCode());
    } finally {
        client.getConnectionManager().shutdown();
    }
}

From source file:io.undertow.server.handlers.file.FileHandlerSymlinksTestCase.java

@Test
public void testExplicitAccessSymlinkDeniedUsingSameSymlinkName() throws IOException, URISyntaxException {
    TestHttpClient client = new TestHttpClient();
    Path rootPath = Paths.get(getClass().getResource("page.html").toURI()).getParent();
    Path newSymlink = rootPath.resolve("newSymlink");

    try {/*  w w w  . j a va2  s  .  c  om*/
        DefaultServer.setRootHandler(new CanonicalPathHandler().setNext(new PathHandler().addPrefixPath("/path",
                new ResourceHandler(new PathResourceManager(newSymlink, 10485760, true,
                        rootPath.toAbsolutePath().toString().concat("/innerSymlink")))
                                .setDirectoryListingEnabled(false).addWelcomeFiles("page.html"))));
        /**
         * This request should return a 404 code as rootPath + "/innerSymlink" in safePaths will not match with canonical "/innerSymlink"
         */
        HttpGet get = new HttpGet(DefaultServer.getDefaultServerURL() + "/path/innerSymlink/page.html");
        HttpResponse result = client.execute(get);
        Assert.assertEquals(StatusCodes.NOT_FOUND, result.getStatusLine().getStatusCode());
    } finally {
        client.getConnectionManager().shutdown();
    }
}

From source file:org.opennms.test.FileAnticipator.java

/**
 * Delete expected files, throwing an AssertionFailedError if any of
 * the expected files don't exist./*  w w w. j ava  2s .  c o  m*/
 *
 * @param ignoreNonExistantFiles if true, non-existant files will be
 *      ignored and will not throw an AssertionFailedError
 * @throws AssertionFailedError if ignoreNonExistantFiles is false
 *      and an expected file does not exist, or if a file cannot be deleted
 */
public void deleteExpected(boolean ignoreNonExistantFiles) {
    assertInitialized();

    Collections.sort(m_expecting, new Comparator<File>() {
        @Override
        public int compare(File a, File b) {
            return a.getAbsolutePath().compareTo(b.getAbsolutePath());
        }
    });

    List<String> errors = new ArrayList<String>();

    for (ListIterator<File> i = m_expectingPrefixes.listIterator(m_expectingPrefixes.size()); i
            .hasPrevious();) {
        File f = i.previous();
        List<Path> matches = getMatches(f);
        if (matches.size() < 1 && !ignoreNonExistantFiles) {
            errors.add("Expected prefix that needs to be deleted does not exist: " + f.getAbsolutePath());
        }
        for (Path match : matches) {
            if (!match.toFile().delete())
                errors.add("Could not delete expected file: " + match.toAbsolutePath());
        }
        i.remove();
    }

    for (ListIterator<File> i = m_expecting.listIterator(m_expecting.size()); i.hasPrevious();) {
        File f = i.previous();
        if (!f.exists()) {
            if (!ignoreNonExistantFiles) {
                errors.add("Expected file that needs to be deleted does not exist: " + f.getAbsolutePath());
            }
        } else {
            if (f.isDirectory()) {
                String[] files = f.list();
                if (files.length > 0) {
                    StringBuffer fileList = new StringBuffer("{ ");
                    fileList.append(files[0]);
                    for (int j = 1; j < files.length; j++) {
                        fileList.append(", ").append(files[j]);
                    }
                    fileList.append(" }");
                    errors.add("Directory was not empty: " + f.getAbsolutePath() + ": " + fileList.toString());
                } else {
                    if (!f.delete())
                        errors.add("Could not delete directory: " + f.getAbsolutePath());
                }
            } else {
                if (!f.delete())
                    errors.add("Could not delete expected file: " + f.getAbsolutePath());
            }
        }
        i.remove();
    }
    assertEquals("No expected files left over", m_expecting.size(), 0);
    if (errors.size() > 0) {
        StringBuffer errorString = new StringBuffer();
        for (String error : errors) {
            errorString.append(error).append("\n");
        }
        fail("Errors occurred inside FileAnticipator:\n" + errorString.toString().trim());
    }
}

From source file:io.undertow.server.handlers.file.FileHandlerSymlinksTestCase.java

@Test
public void testExplicitAccessSymlinkGrantedUsingSpecificFilters() throws IOException, URISyntaxException {
    TestHttpClient client = new TestHttpClient();
    Path rootPath = Paths.get(getClass().getResource("page.html").toURI()).getParent();
    Path newSymlink = rootPath.resolve("newSymlink");

    try {/*  w  ww.j a  va 2s.c  om*/
        DefaultServer.setRootHandler(new CanonicalPathHandler().setNext(new PathHandler().addPrefixPath("/path",
                new ResourceHandler(new PathResourceManager(newSymlink, 10485760, true,
                        rootPath.toAbsolutePath().toString().concat("/newDir")))
                                .setDirectoryListingEnabled(false).addWelcomeFiles("page.html"))));
        /**
         * This request should return a 200 code as rootPath + "/newDir" is used in the safePaths
         */
        HttpGet get = new HttpGet(DefaultServer.getDefaultServerURL() + "/path/innerSymlink/page.html");
        HttpResponse result = client.execute(get);
        Assert.assertEquals(StatusCodes.OK, result.getStatusLine().getStatusCode());
        final String response = HttpClientUtils.readResponse(result);
        Header[] headers = result.getHeaders("Content-Type");
        Assert.assertEquals("text/html", headers[0].getValue());
        Assert.assertTrue(response, response.contains("A web page"));
    } finally {
        client.getConnectionManager().shutdown();
    }
}

From source file:org.opencb.hpg.bigdata.app.cli.local.VariantCommandExecutor.java

private void convertToProtoBuf(Path inputPath, OutputStream outputStream) throws Exception {
    // Creating reader
    VcfBlockIterator iterator = (StringUtils.equals("-", inputPath.toAbsolutePath().toString()))
            ? new VcfBlockIterator(new BufferedInputStream(System.in), new FullVcfCodec())
            : new VcfBlockIterator(inputPath.toFile(), new FullVcfCodec());

    LocalCliOptionsParser.ConvertVariantCommandOptions cliOptions = variantCommandOptions.convertVariantCommandOptions;
    int numTasks = Math.max(cliOptions.numThreads, 1);
    int batchSize = Integer.parseInt(cliOptions.options.getOrDefault("batch.size", "50"));
    int bufferSize = Integer.parseInt(cliOptions.options.getOrDefault("buffer.size", "100000"));
    int capacity = numTasks + 1;
    ParallelTaskRunner.Config config = new ParallelTaskRunner.Config(numTasks, batchSize, capacity, true,
            false);/*from   w  ww  .  ja  v a2  s .c  om*/

    ParallelTaskRunner<CharSequence, ByteBuffer> runner = new ParallelTaskRunner<>(iterator.toLineDataReader(),
            () -> { //Task supplier. Will supply a task instance for each thread.

                //VCFCodec is not thread safe. MUST exist one instance per thread
                VCFCodec codec = new FullVcfCodec(iterator.getHeader(), iterator.getVersion());
                VariantContextBlockIterator blockIterator = new VariantContextBlockIterator(codec);
                Converter<VariantContext, VariantProto.Variant> converter = new VariantContextToVariantProtoConverter();
                return new ProtoEncoderTask<>(
                        charBuffer -> converter.convert(blockIterator.convert(charBuffer)), bufferSize);
            }, batch -> {
                batch.forEach(byteBuffer -> {
                    try {
                        outputStream.write(byteBuffer.array(), byteBuffer.arrayOffset(), byteBuffer.limit());
                    } catch (IOException e) {
                        throw new RuntimeException(e);
                    }
                });
                return true;
            }, config);
    runner.run();
    outputStream.close();

    //        InputStream inputStream = new FileInputStream(variantCommandOptions.convertVariantCommandOptions.output);
    //        if (outputStream instanceof GZIPOutputStream) {
    //            inputStream = new GZIPInputStream(inputStream);
    //        }
    //        VariantProto.Variant variant;
    //        int i = 0;
    //        try {
    //            while ((variant = VariantProto.Variant.parseDelimitedFrom(inputStream)) != null) {
    //                i++;
    //            System.out.println(variant.getChromosome() + ":" + variant.getStart()
    //                    + ":" + variant.getReference() + ":" + variant.getAlternate());
    ////            System.out.println("variant = " + variant.toString());
    //            }
    //        } finally {
    //            System.out.println("Num variants = " + i);
    //            inputStream.close();
    //        }
}