Example usage for java.nio.file Path getFileName

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

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Introduction

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

Prototype

Path getFileName();

Source Link

Document

Returns the name of the file or directory denoted by this path as a Path object.

Usage

From source file:de.tudarmstadt.ukp.dkpro.core.api.datasets.internal.actions.Explode.java

private void extract(ActionDescription aAction, Path aArchive, ArchiveInputStream aAStream, Path aTarget)
        throws IOException {
    // We always extract archives into a subfolder. Figure out the name of the folder.
    String base = getBase(aArchive.getFileName().toString());

    Map<String, Object> cfg = aAction.getConfiguration();
    int strip = cfg.containsKey("strip") ? (int) cfg.get("strip") : 0;

    AntFileFilter filter = new AntFileFilter(coerceToList(cfg.get("includes")),
            coerceToList(cfg.get("excludes")));

    ArchiveEntry entry = null;//  ww  w  .j a v a2s .  c om
    while ((entry = aAStream.getNextEntry()) != null) {
        String name = stripLeadingFolders(entry.getName(), strip);

        if (name == null) {
            // Stripped to null - nothing left to extract - continue;
            continue;
        }

        if (filter.accept(name)) {
            Path out = aTarget.resolve(base).resolve(name);
            if (entry.isDirectory()) {
                Files.createDirectories(out);
            } else {
                Files.createDirectories(out.getParent());
                Files.copy(aAStream, out);
            }
        }
    }
}

From source file:ee.ria.xroad.common.conf.globalconf.ConfigurationDirectoryV2.java

private void loadSharedParameters(Path instanceDir, Map<String, SharedParametersV2> sharedParams)
        throws Exception {
    String instanceId = instanceDir.getFileName().toString();

    Path sharedParametersPath = Paths.get(instanceDir.toString(), SHARED_PARAMETERS_XML);
    if (Files.exists(sharedParametersPath)) {
        log.trace("Loading shared parameters from {}", sharedParametersPath);

        sharedParams.put(instanceId, loadParameters(sharedParametersPath, SharedParametersV2.class,
                this.sharedParameters.get(instanceId)));
    } else {//from   ww  w.  ja  va2 s.co  m
        log.trace("Not loading shared parameters from {}, " + "file does not exist", sharedParametersPath);
    }
}

From source file:org.alfresco.repo.bulkimport.impl.DirectoryAnalyserImpl.java

private boolean isVersionFile(Path file) {
    Matcher matcher = VERSION_SUFFIX_PATTERN.matcher(file.getFileName().toString());

    return matcher.matches();
}

From source file:ee.ria.xroad.common.conf.globalconf.ConfigurationDirectoryV1.java

private void loadSharedParameters(Path instanceDir, Map<String, SharedParametersV1> sharedParams)
        throws Exception {
    String instanceId = instanceDir.getFileName().toString();

    Path sharedParametersPath = Paths.get(instanceDir.toString(), SHARED_PARAMETERS_XML);
    if (Files.exists(sharedParametersPath)) {
        log.trace("Loading shared parameters from {}", sharedParametersPath);

        sharedParams.put(instanceId, loadParameters(sharedParametersPath, SharedParametersV1.class,
                this.sharedParameters.get(instanceId)));
    } else {/*  w w  w.  j a va 2 s  . c  o m*/
        log.trace("Not loading shared parameters from {}, " + "file does not exist", sharedParametersPath);
    }
}

From source file:ee.ria.xroad.common.conf.globalconf.ConfigurationDirectoryV2.java

private void loadPrivateParameters(Path instanceDir, Map<String, PrivateParametersV2> privateParams)
        throws Exception {
    String instanceId = instanceDir.getFileName().toString();

    Path privateParametersPath = Paths.get(instanceDir.toString(), PRIVATE_PARAMETERS_XML);

    if (Files.exists(privateParametersPath)) {
        log.trace("Loading private parameters from {}", privateParametersPath);

        privateParams.put(instanceId, loadParameters(privateParametersPath, PrivateParametersV2.class,
                this.privateParameters.get(instanceId)));
    } else {/*from   w ww  . j  a v  a  2 s  .co m*/
        log.trace("Not loading private parameters from {}, " + "file does not exist", privateParametersPath);
    }
}

From source file:com.htmlhifive.visualeditor.persister.LocalFileContentsPersister.java

/**
 * ????./*from  ww  w  .ja v a2  s .c  o  m*/
 * 
 * @param metadata ?urlTree
 * @param ctx urlTree
 */
@Override
public void rmdir(UrlTreeMetaData<InputStream> metadata, UrlTreeContext ctx)
        throws BadContentException, FileNotFoundException {
    Path f = generateFileObj(metadata.getAbsolutePath());
    logger.debug("called rmdir: " + f.getFileName());
    if (!Files.exists(f)) {
        throw new FileNotFoundException("file not exists");
    }

    try {
        Files.delete(f);
    } catch (IOException e) {
        logger.error("rmdir failure", e);
        throw new RuntimeException(e);
    }
}

From source file:com.bekwam.resignator.commands.UnsignCommand.java

private void registerCleanup() {
    Runtime.getRuntime().addShutdownHook(new Thread() {
        @Override//  ww  w  . j  a va 2s  .  com
        public void run() {
            if (logger.isDebugEnabled()) {
                logger.debug("[UNSIGN] shutting down unsign jar command");
            }
            if (tempDir != null) {
                if (logger.isDebugEnabled()) {
                    logger.debug("[UNSIGN] tempDir is not null");
                }
                try {
                    Files.walkFileTree(tempDir, new SimpleFileVisitor<Path>() {
                        @Override
                        public FileVisitResult visitFile(Path file, BasicFileAttributes attrs)
                                throws IOException {
                            if (logger.isDebugEnabled()) {
                                logger.debug("[UNSIGN] deleting file={}", file.getFileName());
                            }
                            Files.delete(file);
                            return FileVisitResult.CONTINUE;
                        }

                        @Override
                        public FileVisitResult postVisitDirectory(Path dir, IOException exc)
                                throws IOException {
                            if (exc == null) {
                                if (logger.isDebugEnabled()) {
                                    logger.debug("[UNSIGN] deleting dir={}", dir.getFileName());
                                }
                                Files.delete(dir);
                                return FileVisitResult.CONTINUE;
                            } else {
                                // directory iteration failed
                                throw exc;
                            }
                        }
                    });
                } catch (Exception exc) {
                    logger.error("error removing tempDir=" + tempDir, exc);
                }
            }
        }
    });
}

From source file:ee.ria.xroad.common.conf.globalconf.ConfigurationDirectoryV1.java

private void loadPrivateParameters(Path instanceDir, Map<String, PrivateParametersV1> privateParams)
        throws Exception {
    String instanceId = instanceDir.getFileName().toString();

    Path privateParametersPath = Paths.get(instanceDir.toString(), PRIVATE_PARAMETERS_XML);

    if (Files.exists(privateParametersPath)) {
        log.trace("Loading private parameters from {}", privateParametersPath);

        privateParams.put(instanceId, loadParameters(privateParametersPath, PrivateParametersV1.class,
                this.privateParameters.get(instanceId)));
    } else {/*from  w  w w. j  av  a2s  . co  m*/
        log.trace("Not loading private parameters from {}, " + "file does not exist", privateParametersPath);
    }
}

From source file:com.ejisto.util.visitor.ConditionMatchingCopyFileVisitor.java

private void copy(Path srcFile) throws IOException {
    Path relative = options.srcRoot.relativize(srcFile);
    int count = relative.getNameCount();
    StringBuilder newFileName = new StringBuilder();
    if (count > 1) {
        newFileName.append(relative.getParent().toString());
        newFileName.append(File.separator);
    }/*from ww w .  ja v  a  2 s  . c o  m*/
    newFileName.append(defaultString(options.filesPrefix)).append(srcFile.getFileName().toString());
    Files.copy(srcFile, options.targetRoot.resolve(newFileName.toString()),
            StandardCopyOption.REPLACE_EXISTING);
}

From source file:diffhunter.Indexer.java

public void Make_Index(Database hashdb, String file_name, String read_gene_location)
        throws FileNotFoundException, IOException {
    Set_Parameters();//from  w  w  w .j  ava2 s.  co m
    //System.out.print("Sasa");
    ConcurrentHashMap<String, Map<Integer, Integer>> dic_gene_loc_count = new ConcurrentHashMap<>();
    ArrayList<String> lines_from_bed_file = new ArrayList<>();
    BufferedReader br = new BufferedReader(new FileReader(file_name));

    String line = br.readLine();
    List<String> toks = Arrays.asList(line.split("\t"));
    lines_from_bed_file.add(line);
    String last_Seen_chromosome = toks.get(0).replace("chr", "");
    line = br.readLine();
    lines_from_bed_file.add(line);
    toks = Arrays.asList(line.split("\t"));
    String new_chromosome = toks.get(0).replace("chr", "");

    while (((line = br.readLine()) != null) || lines_from_bed_file.size() > 0) {
        if (line != null) {
            toks = Arrays.asList(line.split("\t"));
            new_chromosome = toks.get(0).replace("chr", "");
        }
        // process the line.
        if (line == null || !new_chromosome.equals(last_Seen_chromosome)) {
            System.out.println("Processing chromosome" + "\t" + last_Seen_chromosome);
            last_Seen_chromosome = new_chromosome;
            lines_from_bed_file.parallelStream().forEach(content -> {

                List<String> inner_toks = Arrays.asList(content.split("\t"));
                //WARNINNG WARNING WARNING WARNINNG WARNING WARNING WARNINNG WARNING WARNING WARNINNG WARNING WARNING WARNINNG WARNING WARNING WARNINNG WARNING WARNING WARNINNG WARNING WARNING WARNINNG WARNING WARNING 
                //STRAND column count should be changed. 
                String strand = inner_toks.get(5);
                String chromosome_ = inner_toks.get(0).replace("chr", "");
                if (!dic_Loc_gene.get(strand).containsKey(chromosome_)) {
                    return;
                }
                Integer start_loc = Integer.parseInt(inner_toks.get(1));
                Integer end_loc = Integer.parseInt(inner_toks.get(2));
                List<Interval<String>> res__ = dic_Loc_gene.get(strand).get(chromosome_).getIntervals(start_loc,
                        end_loc);
                //IntervalTree<String> pot_gene_name=new IntervalTree<>(res__);
                //                        for (int z = 0; z < pot_gene_name.Intervals.Count; z++)
                //{
                for (int z = 0; z < res__.size(); z++) {

                    dic_gene_loc_count.putIfAbsent(res__.get(z).getData(), new HashMap<>());
                    String gene_symbol = res__.get(z).getData();
                    Integer temp_gene_start_loc = dic_genes.get(gene_symbol).start_loc;
                    Integer temp_gene_end_loc = dic_genes.get(gene_symbol).end_loc;
                    if (start_loc < temp_gene_start_loc) {
                        start_loc = temp_gene_start_loc;
                    }
                    if (end_loc > temp_gene_end_loc) {
                        end_loc = temp_gene_end_loc;
                    }
                    synchronized (dic_synchrinzer_genes.get(gene_symbol)) {
                        for (int k = start_loc; k <= end_loc; k++) {
                            Integer value_inside = 0;
                            value_inside = dic_gene_loc_count.get(gene_symbol).get(k);
                            dic_gene_loc_count.get(gene_symbol).put(k,
                                    value_inside == null ? 1 : (value_inside + 1));
                        }
                    }
                }
            });
            /*                    List<string> keys_ = dic_gene_loc_count.Keys.ToList();
             List<string> alt_keys = new List<string>();// dic_gene_loc_count.Keys.ToList();
             for (int i = 0; i < keys_.Count; i++)
             {
             Dictionary<int, int> dicccc_ = new Dictionary<int, int>();
             dic_gene_loc_count[keys_[i]] = new Dictionary<int, int>(dic_gene_loc_count[keys_[i]].Where(x => x.Value >= 2).ToDictionary(x => x.Key, x => x.Value));
             if (dic_gene_loc_count[keys_[i]].Count == 0)
             {
                    
             dic_gene_loc_count.TryRemove(keys_[i], out dicccc_);
             continue;
             }
             hashdb.Put(Get_BDB(keys_[i]), Get_BDB_Dictionary(dic_gene_loc_count[keys_[i]]));
             alt_keys.Add(keys_[i]);
             dic_gene_loc_count.TryRemove(keys_[i], out dicccc_);
             }*/
            ArrayList<String> keys_ = new ArrayList<>(dic_gene_loc_count.keySet());
            ArrayList<String> alt_keys = new ArrayList<>();
            for (int i = 0; i < keys_.size(); i++) {

                //LinkedHashMap<Integer, Integer> tmep_map = new LinkedHashMap<>(dic_gene_loc_count.get(keys_.get(i)));
                LinkedHashMap<Integer, Integer> tmep_map = new LinkedHashMap<>();
                /*tmep_map = */
                dic_gene_loc_count.get(keys_.get(i)).entrySet().stream().filter(p -> p.getValue() >= 2)
                        .sorted(Comparator.comparing(E -> E.getKey()))
                        .forEach((entry) -> tmep_map.put(entry.getKey(), entry.getValue()));//.collect(Collectors.toMap(p -> p.getKey(), p -> p.getValue()));
                if (tmep_map.isEmpty()) {
                    dic_gene_loc_count.remove(keys_.get(i));
                    continue;
                }

                //Map<Integer, Integer> tmep_map1 = new LinkedHashMap<>();
                //tmep_map1=sortByKey(tmep_map);
                //tmep_map.entrySet().stream().sorted(Comparator.comparing(E -> E.getKey())).forEach((entry) -> tmep_map1.put(entry.getKey(), entry.getValue()));
                //BerkeleyDB_Box box=new BerkeleyDB_Box();
                hashdb.put(null, BerkeleyDB_Box.Get_BDB(keys_.get(i)),
                        BerkeleyDB_Box.Get_BDB_Dictionary(tmep_map));
                alt_keys.add(keys_.get(i));
                dic_gene_loc_count.remove(keys_.get(i));
                //dic_gene_loc_count.put(keys_.get(i),tmep_map);
            }

            hashdb.sync();
            int a = 1111;
            /*                    hashdb.Sync();
             File.AppendAllLines("InputDB\\" + Path.GetFileNameWithoutExtension(file_name) + "_genes.txt", alt_keys);
             //total_lines_processed_till_now += lines_from_bed_file.Count;
             //worker.ReportProgress(total_lines_processed_till_now / count_);
             lines_from_bed_file.Clear();
             if (!reader.EndOfStream)
             {
             lines_from_bed_file.Add(_line_);
             }
             last_Seen_chromosome = new_choromosome;*/
            lines_from_bed_file.clear();
            if (line != null) {
                lines_from_bed_file.add(line);
            }
            Path p = Paths.get(file_name);
            file_name = p.getFileName().toString();

            BufferedWriter output = new BufferedWriter(new FileWriter((Paths
                    .get(read_gene_location, FilenameUtils.removeExtension(file_name) + ".txt").toString()),
                    true));
            for (String alt_key : alt_keys) {
                output.append(alt_key);
                output.newLine();
            }
            output.close();
            /*if (((line = br.readLine()) != null))
            {
            lines_from_bed_file.add(line);
            toks=Arrays.asList(line.split("\t"));
            new_chromosome=toks.get(0).replace("chr", "");
            }*/
            //last_Seen_chromosome=new_chromosome;
        } else if (new_chromosome.equals(last_Seen_chromosome)) {
            lines_from_bed_file.add(line);
        }

    }
    br.close();
    hashdb.sync();
    hashdb.close();

}