Examples with Files java.nio.file.Files used on opensource projects

Example 21 with Files

use of java.nio.file.Files in project hmftools by hartwigmedical.

the class FilteredSVWriter method processVcfFiles.

public void processVcfFiles() {
    final List<File> vcfFiles;
    final Path root = Paths.get(mVcfFileLocation);
    try (final Stream<Path> stream = Files.walk(root, 5, FileVisitOption.FOLLOW_LINKS)) {
        vcfFiles = stream.map(p -> p.toFile()).filter(p -> !p.isDirectory()).filter(p_ -> p_.getName().endsWith("somaticSV_bpi.vcf")).collect(Collectors.toList());
        LOGGER.debug("found {} BPI VCF files", vcfFiles.size());
        // add the filtered and passed SV entries for each file
        for (final File vcfFile : vcfFiles) {
            if (vcfFile.isDirectory())
                continue;
            if (!vcfFile.getPath().contains("structuralVariants/bpi/"))
                continue;
            if (!vcfFile.getName().endsWith("somaticSV_bpi.vcf"))
                continue;
            LOGGER.debug("BPI VCF path({}) file({})", vcfFile.getPath(), vcfFile.getName());
            // extract sampleId from the directory or file name
            String[] itemsStr = vcfFile.getName().split("_");
            if (itemsStr.length != 4)
                continue;
            String sampleId = itemsStr[1];
            LOGGER.debug("sampleId({})", sampleId);
            List<StructuralVariant> variants = readFromVcf(vcfFile.getPath());
            generateFilteredSVFile(variants, sampleId);
        }
        if (mFileWriter != null)
            mFileWriter.close();
    } catch (Exception e) {
    }
}

Example 22 with Files

use of java.nio.file.Files in project hmftools by hartwigmedical.

the class SvVCFAnnotator method processVcfFiles.

public void processVcfFiles() {
    final List<File> vcfFiles;
    final Path root = Paths.get(mVcfFileLocation);
    try (final Stream<Path> stream = Files.walk(root, 5, FileVisitOption.FOLLOW_LINKS)) {
        vcfFiles = stream.map(p -> p.toFile()).filter(p -> !p.isDirectory()).filter(p_ -> p_.getName().endsWith("somaticSV_bpi.vcf")).collect(Collectors.toList());
        LOGGER.debug("found {} BPI VCF files", vcfFiles.size());
        // add the filtered and passed SV entries for each file
        for (final File vcfFile : vcfFiles) {
            if (vcfFile.isDirectory())
                continue;
            if (!vcfFile.getPath().contains("structuralVariants/bpi/"))
                continue;
            if (!vcfFile.getName().endsWith("somaticSV_bpi.vcf"))
                continue;
            LOGGER.debug("BPI VCF path({}) file({})", vcfFile.getPath(), vcfFile.getName());
            // extract sampleId from the directory or file name
            String[] itemsStr = vcfFile.getName().split("_");
            if (itemsStr.length != 4)
                continue;
            String sampleId = itemsStr[1];
            LOGGER.debug("sampleId({})", sampleId);
            List<VariantContext> variants = readFromVcf(vcfFile.getPath());
            for (final VariantContext variant : variants) {
                if (variant.hasAttribute("IMPRECISE")) {
                    LOGGER.debug("var({}) has imprecise call", variant.getID());
                }
            }
        // generateFilteredSVFile(variants, sampleId);
        }
        if (mFileWriter != null)
            mFileWriter.close();
    } catch (Exception e) {
    }
}

Example 23 with Files

use of java.nio.file.Files in project support-core-plugin by jenkinsci.

the class OtherConfigFilesComponentTest method missingFile.

@Test
public void missingFile() throws Exception {
    File file = new File(j.jenkins.root, "x.xml");
    FileUtils.writeStringToFile(file, xml);
    Map<String, Content> contents = new HashMap<>();
    new OtherConfigFilesComponent().addContents(new Container() {

        @Override
        public void add(Content content) {
            contents.put(MessageFormat.format(content.getName(), (Object[]) content.getFilterableParameters()), content);
        }
    });
    Files.delete(file.toPath());
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    Content content = contents.get("jenkins-root-configuration-files/x.xml");
    assertNotNull(content);
    content.writeTo(baos);
    assertThat("routine build should not issue warnings", logging.getRecords().stream().filter(// TODO .record(…, WARNING) does not accomplish this
    lr -> lr.getLevel().intValue() >= Level.WARNING.intValue()).map(lr -> lr.getSourceClassName() + "." + lr.getSourceMethodName() + ": " + lr.getMessage()).collect(// LogRecord does not override toString
    Collectors.toList()), emptyIterable());
    assertThat(baos.toString(), allOf(containsString("FileNotFoundException"), containsString(file.getAbsolutePath())));
}

Example 24 with Files

use of java.nio.file.Files in project keycloak by keycloak.

the class CopyDependencies method main.

public static void main(String[] args) throws IOException {
    String version = args[2];
    Path repository = new File(args[0]).toPath().resolve("org").resolve("keycloak");
    Path targetRoot = new File(args[1]).toPath().resolve(version);
    BufferedReader br = new BufferedReader(new InputStreamReader(CopyDependencies.class.getResourceAsStream("files")));
    Path target = targetRoot;
    for (String l = br.readLine(); l != null; l = br.readLine()) {
        if (l.startsWith("./")) {
            target = targetRoot.resolve(l.replace("./", "").replace('/', File.separatorChar));
            if (!target.toFile().isDirectory()) {
                target.toFile().mkdirs();
            }
        } else if (l.trim().length() > 0) {
            String[] t = l.trim().split(":");
            String artifactName = t[0];
            String destName = t.length == 1 ? artifactName : t[1];
            File artifactDir = repository.resolve(artifactName).resolve(version).toFile();
            for (File f : artifactDir.listFiles((file, name) -> name.contains(".tar.gz") || name.contains(".zip"))) {
                Files.copy(f.toPath(), target.resolve(f.getName().replace(artifactName, destName)), StandardCopyOption.REPLACE_EXISTING);
            }
            System.out.println(artifactName);
        }
    }
    br.close();
}

Example 25 with Files

use of java.nio.file.Files in project keycloak by keycloak.

the class TomcatDeploymentArchiveProcessorUtils method copyWarClasspathFilesToCommonTomcatClasspath.

/**
 * Tomcat doesn't load files (e. g. secure-portal keystore) from webarchive classpath
 * we need to copy it to common classpath /catalina_home/lib
 * @param archive
 */
public static void copyWarClasspathFilesToCommonTomcatClasspath(Archive<?> archive) {
    Stream<Node> contentOfArchiveClasspath = archive.getContent(archivePath -> archivePath.get().startsWith(WAR_CLASSPATH)).values().stream().filter(node -> StringUtils.countMatches(node.toString(), "/") == // get only files not directories
    StringUtils.countMatches(WAR_CLASSPATH, "/") && node.toString().contains("."));
    String catalinaHome = System.getProperty("app.server.home");
    contentOfArchiveClasspath.forEach((Node node) -> {
        Path p = Paths.get(node.toString());
        File outputFile = new File(catalinaHome + "/lib/" + p.getFileName().toString());
        if (!outputFile.exists()) {
            try {
                Files.copy(node.getAsset().openStream(), outputFile.toPath());
            } catch (IOException e) {
                throw new RuntimeException("Couldn't copy classpath files from deployed war to common classpath of tomcat", e);
            }
        }
    });
}