Example usage for java.io File getCanonicalFile

Introduction

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

Prototype

public File getCanonicalFile() throws IOException 

Source Link

Document

Returns the canonical form of this abstract pathname.

Usage

From source file:uk.ac.tgac.rampart.stage.analyse.asm.analysers.QuastAsmAnalyser.java

@Override
public List<ExecutionResult> execute(List<File> assemblies, File outputDir, String jobPrefix,
        ConanExecutorService ces)/*from  ww w  . j av a 2  s .  c om*/
        throws InterruptedException, ProcessExecutionException, ConanParameterException, IOException {

    if (outputDir.exists()) {
        FileUtils.deleteDirectory(outputDir);
    }

    outputDir.mkdirs();

    // Create mapping between quast assembly name and actual file path
    this.assemblies = new HashMap<>();

    for (File assembly : assemblies) {
        this.assemblies.put(assembly.getName().substring(0, assembly.getName().length() - 3),
                assembly.getCanonicalFile());
    }

    // Add quast job id to list
    List<ExecutionResult> jobResults = new ArrayList<>();

    File reference = args.getOrganism().getReference() != null ? args.getOrganism().getReference().getPath()
            : null;

    long estGenomeSize = reference != null ? 0 : args.getOrganism().getGenomeSize();

    QuastV23 quastProcess = this.makeQuast(assemblies, outputDir, estGenomeSize,
            args.getOrganism().getPloidy() > 1, reference, args.getThreads(), false // Assume all sequences are not scaffolds... I don't like this options much in Quast.
    );

    ExecutionResult result = ces.executeProcess(quastProcess, outputDir, jobPrefix, args.getThreads(),
            args.getMemory(), false);

    jobResults.add(result);

    return jobResults;
}

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From source file:android.databinding.compilationTest.SimpleCompilationTest.java

private ScopedException singleFileErrorTest(String resource, String targetFile, String expectedExtract,
        String errorMessage) throws IOException, URISyntaxException, InterruptedException {
    prepareProject();//from  w  w  w  .  j  a  va  2  s  . c  om
    copyResourceTo(resource, targetFile);
    CompilationResult result = runGradle("assembleDebug");
    assertNotEquals(0, result.resultCode);
    ScopedException scopedException = result.getBindingException();
    assertNotNull(result.error, scopedException);
    ScopedErrorReport report = scopedException.getScopedErrorReport();
    assertNotNull(report);
    assertEquals(1, report.getLocations().size());
    Location loc = report.getLocations().get(0);
    if (expectedExtract != null) {
        String extract = extract(targetFile, loc);
        assertEquals(expectedExtract, extract);
    }
    final File errorFile = new File(report.getFilePath());
    assertTrue(errorFile.exists());
    assertEquals(new File(testFolder, targetFile).getCanonicalFile(), errorFile.getCanonicalFile());
    if (errorMessage != null) {
        assertEquals(errorMessage, scopedException.getBareMessage());
    }
    return scopedException;
}

---

From source file:org.red5.server.war.MainServlet.java

/**
 * Main entry point for the Red5 Server as a war
 *//*from w ww .j  a  v a 2 s  . co m*/
// Notification that the web application is ready to process requests
public void contextInitialized(ServletContextEvent sce) {
    System.setProperty("red5.deployment.type", "war");

    if (null != servletContext) {
        return;
    }
    servletContext = sce.getServletContext();
    String prefix = servletContext.getRealPath("/");

    long time = System.currentTimeMillis();

    logger.info("RED5 Server (http://www.osflash.org/red5)");
    logger.info("Loading red5 global context from: " + red5Config);
    logger.info("Path: " + prefix);

    try {
        // Detect root of Red5 configuration and set as system property
        String root;
        String classpath = System.getProperty("java.class.path");
        File fp = new File(prefix + red5Config);
        fp = fp.getCanonicalFile();
        if (!fp.isFile()) {
            // Given file does not exist, search it on the classpath
            String[] paths = classpath.split(System.getProperty("path.separator"));
            for (String element : paths) {
                fp = new File(element + "/" + red5Config);
                fp = fp.getCanonicalFile();
                if (fp.isFile()) {
                    break;
                }
            }
        }
        if (!fp.isFile()) {
            throw new Exception(
                    "could not find configuration file " + red5Config + " on your classpath " + classpath);
        }

        root = fp.getAbsolutePath();
        root = root.replace('\\', '/');
        int idx = root.lastIndexOf('/');
        root = root.substring(0, idx);
        // update classpath
        System.setProperty("java.class.path",
                classpath + File.pathSeparatorChar + root + File.pathSeparatorChar + root + "/classes");
        logger.debug("New classpath: " + System.getProperty("java.class.path"));
        // set configuration root
        System.setProperty("red5.config_root", root);
        logger.info("Setting configuation root to " + root);

        // Setup system properties so they can be evaluated
        Properties props = new Properties();
        props.load(new FileInputStream(root + "/red5.properties"));
        for (Object o : props.keySet()) {
            String key = (String) o;
            if (StringUtils.isNotBlank(key)) {
                System.setProperty(key, props.getProperty(key));
            }
        }

        // Store root directory of Red5
        idx = root.lastIndexOf('/');
        root = root.substring(0, idx);
        if (System.getProperty("file.separator").equals("/")) {
            // Workaround for linux systems
            root = "/" + root;
        }
        System.setProperty("red5.root", root);
        logger.info("Setting Red5 root to " + root);

        Class contextClass = org.springframework.web.context.support.XmlWebApplicationContext.class;
        ConfigurableWebApplicationContext applicationContext = (ConfigurableWebApplicationContext) BeanUtils
                .instantiateClass(contextClass);

        String[] strArray = servletContext.getInitParameter(ContextLoader.CONFIG_LOCATION_PARAM)
                .split("[,\\s]");
        logger.info("Config location files: " + strArray.length);
        applicationContext.setConfigLocations(strArray);
        applicationContext.setServletContext(servletContext);
        applicationContext.refresh();

        // set web application context as an attribute of the servlet
        // context so that it may be located via Springs
        // WebApplicationContextUtils
        servletContext.setAttribute(WebApplicationContext.ROOT_WEB_APPLICATION_CONTEXT_ATTRIBUTE,
                applicationContext);

        ConfigurableBeanFactory factory = applicationContext.getBeanFactory();
        // register default
        // add the context to the parent
        factory.registerSingleton("default.context", applicationContext);

    } catch (Throwable e) {
        logger.error("", e);
    }

    long startupIn = System.currentTimeMillis() - time;
    logger.info("Startup done in: " + startupIn + " ms");

}

---

From source file:io.wcm.maven.plugins.i18n.TransformMojo.java

/**
 * Get the JSON file for source file.//from w ww. j  a  v a  2s .  c om
 * @param sourceFile the source file
 * @param selectedOutputFormat Output format
 * @return File with name and path based on file parameter
 * @throws IOException
 */
private File getTargetFile(File sourceFile, OutputFormat selectedOutputFormat) throws IOException {

    File sourceDirectory = getSourceDirectory();
    String relativePath = StringUtils.substringAfter(sourceFile.getAbsolutePath(),
            sourceDirectory.getAbsolutePath());
    String relativeTargetPath = FileUtils.removeExtension(relativePath) + "."
            + selectedOutputFormat.getFileExtension();

    File jsonFile = new File(getGeneratedResourcesFolder().getPath() + relativeTargetPath);

    jsonFile = jsonFile.getCanonicalFile();

    File parentDirectory = jsonFile.getParentFile();
    if (!parentDirectory.exists()) {
        parentDirectory.mkdirs();
    }

    return jsonFile;
}

---

From source file:org.apache.servicemix.jbi.deployer.impl.SharedLibraryInstaller.java

protected ClassLoader createClassLoader() {
    SharedLibraryDesc library = descriptor.getSharedLibrary();
    // Make the current ClassLoader the parent
    ClassLoader parent = BundleDelegatingClassLoader.createBundleClassLoaderFor(bundle,
            getClass().getClassLoader());
    boolean parentFirst = library.isParentFirstClassLoaderDelegation();
    ClassPath cp = library.getSharedLibraryClassPath();
    String[] classPathNames = cp.getPathElements();
    List<URL> urls = new ArrayList<URL>();
    for (String classPathName : classPathNames) {
        File f = new File(installRoot, classPathName);
        if (!f.exists()) {
            LOGGER.warn("Shared library classpath entry not found: '" + classPathName + "'");
        }//from  ww  w .jav a  2 s.  co m
        try {
            urls.add(f.getCanonicalFile().toURL());
        } catch (IOException e) {
            throw new IllegalArgumentException(
                    "Shared library classpath entry not found: '" + classPathName + "'");
        }
    }
    return new MultiParentClassLoader(library.getIdentification().getName(), urls.toArray(new URL[urls.size()]),
            parent, !parentFirst, new String[0], new String[] { "java.", "javax." });
}

---

From source file:org.sonatype.nexus.proxy.storage.local.fs.DefaultFSLocalRepositoryStorageTest.java

@Test
public void getFileFromBaseRelative() throws Exception {
    {/*from   ww  w. j  a va  2  s. c  om*/
        final File fileFromBase = subject.getFileFromBase(repository,
                new ResourceStoreRequest("/foo/bar/../baz"));
        assertThat(fileFromBase.getCanonicalFile(), equalTo(new File(baseDir, "foo/baz")));
    }
    {
        final File fileFromBase = subject.getFileFromBase(repository,
                new ResourceStoreRequest("/foo/bar/../bar/../../baz"));
        assertThat(fileFromBase.getCanonicalFile(), equalTo(new File(baseDir, "baz")));
    }
}

---

From source file:org.apache.torque.generator.configuration.DirectoryConfigurationProvider.java

private File getFile(String name, String directory, String description) throws ConfigurationException {
    File file = null;
    try {/*from ww w  .j  av  a 2s . c  o m*/
        File configDir = new File(projectPaths.getConfigurationPath(), directory);

        file = new File(configDir, name);
        // use canonical file to resolve . and .. directories
        file = file.getCanonicalFile();
    } catch (IOException e) {
        throw new ConfigurationException(
                "Canonical name for " + description + file + " could not be calculated", e);
    }
    return file;
}

---

From source file:org.apache.catalina.startup.SetDocBaseRule.java

/**
 * Handle the beginning of an XML element.
 *
 * @param attributes The attributes of this element
 *
 * @exception Exception if a processing error occurs
 *///w ww. j  av  a 2  s . c  om
public void begin(Attributes attributes) throws Exception {

    Context child = (Context) digester.peek(0);
    Deployer parent = (Deployer) digester.peek(1);
    Host host = null;
    if (!(parent instanceof StandardHost)) {
        Method method = parent.getClass().getMethod("getHost", null);
        host = (Host) method.invoke(parent, null);
    } else {
        host = (Host) parent;
    }
    String appBase = host.getAppBase();

    boolean unpackWARs = true;
    if (host instanceof StandardHost) {
        unpackWARs = ((StandardHost) host).isUnpackWARs();
    }
    if (!unpackWARs && !("true".equals(attributes.getValue("unpackWAR")))) {
        return;
    }
    if ("false".equals(attributes.getValue("unpackWAR"))) {
        return;
    }

    File canonicalAppBase = new File(appBase);
    if (canonicalAppBase.isAbsolute()) {
        canonicalAppBase = canonicalAppBase.getCanonicalFile();
    } else {
        canonicalAppBase = new File(System.getProperty("catalina.base"), appBase).getCanonicalFile();
    }

    String docBase = child.getDocBase();
    if (docBase == null) {
        // Trying to guess the docBase according to the path
        String path = child.getPath();
        if (path == null) {
            return;
        }
        if (path.equals("")) {
            docBase = "ROOT";
        } else {
            if (path.startsWith("/")) {
                docBase = path.substring(1);
            } else {
                docBase = path;
            }
        }
    }

    File file = new File(docBase);
    if (!file.isAbsolute()) {
        docBase = (new File(canonicalAppBase, docBase)).getPath();
    } else {
        docBase = file.getCanonicalPath();
    }

    if (docBase.toLowerCase().endsWith(".war")) {
        URL war = new URL("jar:" + (new File(docBase)).toURL() + "!/");
        String contextPath = child.getPath();
        if (contextPath.equals("")) {
            contextPath = "ROOT";
        }
        docBase = ExpandWar.expand(host, war, contextPath);
        file = new File(docBase);
        docBase = file.getCanonicalPath();
    } else {
        File docDir = new File(docBase);
        if (!docDir.exists()) {
            File warFile = new File(docBase + ".war");
            if (warFile.exists()) {
                URL war = new URL("jar:" + warFile.toURL() + "!/");
                docBase = ExpandWar.expand(host, war, child.getPath());
                file = new File(docBase);
                docBase = file.getCanonicalPath();
            }
        }
    }

    if (docBase.startsWith(canonicalAppBase.getPath())) {
        docBase = docBase.substring(canonicalAppBase.getPath().length());
        docBase = docBase.replace(File.separatorChar, '/');
        if (docBase.startsWith("/")) {
            docBase = docBase.substring(1);
        }
    } else {
        docBase = docBase.replace(File.separatorChar, '/');
    }

    child.setDocBase(docBase);

}

---

From source file:org.rhq.plugins.jbossas.script.ScriptFileFinder.java

protected void findScriptFiles(File scanDir, List<File> excludeDirs, List<File> scriptFiles) {
    if (!scanDir.isDirectory()) {
        return;/*from  w w w . ja v  a 2 s  .co m*/
    }

    File canonicalScanDir = null;

    try {
        canonicalScanDir = scanDir.getCanonicalFile();
    } catch (IOException e) {
        // if we aren't allowed to reach the canonical path, skip this directory
        return;
    }

    // if we've seen this directory before (or it's explicitly excluded by the caller) skip this directory. 
    // this protects against following cyclic symbolic links.
    if (excludeDirs.contains(canonicalScanDir)) {
        return;
    }

    // add to the directories we've seen
    excludeDirs.add(canonicalScanDir);

    scriptFiles.addAll(Arrays.asList(scanDir.listFiles(new ScriptFileFilter())));

    File[] subDirs = scanDir.listFiles(new DirectoryFilter());
    for (File subDir : subDirs) {
        findScriptFiles(subDir, excludeDirs, scriptFiles); // recurse
    }
}

---

From source file:org.rhq.plugins.jbossas5.script.ScriptFileFinder.java

protected void findScriptFiles(File scanDir, List<File> excludeDirs, List<File> scriptFiles) {
    if (!scanDir.isDirectory()) {
        return;//from  ww w  . ja  v a  2  s. c  o  m
    }

    File canonicalScanDir = null;

    try {
        canonicalScanDir = scanDir.getCanonicalFile();
    } catch (IOException e) {
        // if we aren't allowed to reach the canonical path, skip this
        // directory
        return;
    }

    // if we've seen this directory before (or it's explicitly excluded by
    // the caller) skip this directory.
    // this protects against following cyclic symbolic links.
    if (excludeDirs.contains(canonicalScanDir)) {
        return;
    }

    // add to the directories we've seen
    excludeDirs.add(canonicalScanDir);

    scriptFiles.addAll(Arrays.asList(scanDir.listFiles(getScriptFileFilter(systemInfo))));

    File[] subDirs = scanDir.listFiles(new DirectoryFilter());
    for (File subDir : subDirs) {
        findScriptFiles(subDir, excludeDirs, scriptFiles); // recurse
    }
}

---

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