Exemplo n.º 1
0
 public File getFile() {
   if (file == null) {
     file = new File(tmpDir, entry.getName());
     copyTo(file);
   }
   return file;
 }
Exemplo n.º 2
0
  @Override
  public void unarchive(InputStream source, File target) {
    try (TarArchiveInputStream tIn = new TarArchiveInputStream(source)) {

      TarArchiveEntry entry = tIn.getNextTarEntry();
      while (entry != null) {
        if (entry.isDirectory()) {
          entry = tIn.getNextTarEntry();
          continue;
        }
        File curfile = new File(target, entry.getName());
        File parent = curfile.getParentFile();
        if (!parent.exists()) {
          parent.mkdirs();
        }
        try (OutputStream out = new FileOutputStream(curfile)) {
          IOUtils.copy(tIn, out);

          entry = tIn.getNextTarEntry();
        }
      }
    } catch (IOException e) {
      throw new IllegalStateException(e);
    }
  }
Exemplo n.º 3
0
 /**
  * Move to the next tar entry.
  *
  * @param rootDir an entry path
  * @return true if a next tar entry can be read, or if this entry name is a sub-folder of rootDir
  */
 protected boolean hasNext(final String rootDir) {
   try {
     /*
      * if reader.available() is not equal to 0, then it means that this entry
      * has been loaded, but not read.
      */
     while (reader.available() == 0
         && (tarEntry = reader.getNextTarEntry()) == null) { // Next tar entry
       if (++inputPos >= input.length) {
         reader.close();
         return false;
       }
       // Next archive file
       reader.close();
       logger.info("Reading dump: {}", this.input[inputPos]);
       reader = getTarInputStream(input[inputPos]);
     }
   } catch (IOException e) {
     logger.error("Error while reading the input: {}\n{}", input[inputPos], e);
   }
   /*
    *  When returning from this method, the inputstream is positionned at a regular file,
    *  i.e., metadata, outgoing-triples.nt or incoming-triples.nt.
    */
   if (tarEntry.isDirectory()) {
     return hasNext(rootDir);
   }
   return rootDir == null || tarEntry.getName().startsWith(rootDir) ? true : false;
 }
Exemplo n.º 4
0
  public static List<File> untar(final File inputtar, final File outputDir)
      throws IOException, ArchiveException {
    final List<File> unpackedFiles = new ArrayList<File>();
    if (OMWPP.DEBUG) {
      Log.i("OMWPPtar", String.format("Unzipping tar file %s.", inputtar.getAbsoluteFile()));
    }

    final InputStream is = new FileInputStream(inputtar);
    final TarArchiveInputStream tarInputStream =
        (TarArchiveInputStream) new TarArchiveInputStream(is);
    TarArchiveEntry entry = null;
    while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
      if (OMWPP.DEBUG) Log.i("OMWPPtar", "Read entry: " + entry.getName());
      String filename = entry.getName().substring(entry.getName().lastIndexOf("/") + 1);
      if (filename.toLowerCase().endsWith(".png") || filename.toLowerCase().endsWith(".jpg")) {
        if (OMWPP.DEBUG) Log.i("OMWPPtar", "Is background, extracting.");
        final File outputFile = new File(outputDir, filename);
        final OutputStream outputFileStream = new FileOutputStream(outputFile);
        IOUtils.copy(tarInputStream, outputFileStream);
        outputFileStream.close();
        unpackedFiles.add(outputFile);

      } else if (filename.toLowerCase().endsWith(".gz")) {
        // RECURSIVE CALL
        final File outputFile = new File(outputDir, filename);
        final OutputStream outputFileStream = new FileOutputStream(outputFile);
        IOUtils.copy(tarInputStream, outputFileStream);
        outputFileStream.close();
        gunzip(outputFile, SDROOT);
        outputFile.delete();
      } else if (filename.toLowerCase().endsWith(".tar")) {
        // RECURSIVE CALL
        final File outputFile = new File(outputDir, filename);
        final OutputStream outputFileStream = new FileOutputStream(outputFile);
        IOUtils.copy(tarInputStream, outputFileStream);
        outputFileStream.close();
        untar(outputFile, SDROOT);
        outputFile.delete();
      } else {
        if (OMWPP.DEBUG) Log.i("OMWPPtar", "Is not background, skipping.");
      }
    }
    tarInputStream.close();
    return unpackedFiles;
  }
  @Test
  public void downloadDroplet() {
    this.applicationId
        .then(this::uploadAndStartApplication)
        .flatMap(
            applicationId ->
                this.cloudFoundryClient
                    .applicationsV2()
                    .downloadDroplet(
                        DownloadApplicationDropletRequest.builder()
                            .applicationId(applicationId)
                            .build()))
        .as(Stream::from)
        .reduceWith(ByteArrayOutputStream::new, ApplicationsTest::collectIntoByteArrayInputStream)
        .map(
            bytes -> {
              boolean staticFile = false;
              boolean indexFile = false;

              try {
                TarArchiveInputStream tis =
                    new TarArchiveInputStream(
                        new GZIPInputStream(new ByteArrayInputStream(bytes.toByteArray())));
                for (TarArchiveEntry entry = tis.getNextTarEntry();
                    entry != null;
                    entry = tis.getNextTarEntry()) {
                  if (entry.getName().contains("Staticfile")) {
                    staticFile = true;
                  }
                  if (entry.getName().contains("index.html")) {
                    indexFile = true;
                  }
                }
              } catch (IOException e) {
                throw new RuntimeException(e);
              }
              return staticFile && indexFile;
            })
        .subscribe(testSubscriber().assertEquals(true));
  }
Exemplo n.º 6
0
 /**
  * Unpacks a workflow into specified directory. To be more precise: workflow package should
  * contain only a single directory with the workflow. This method will extract its contents into
  * target directory.
  *
  * @param target new workflow root directory
  */
 public void extract(File target) throws IOException {
   BufferedInputStream in = new BufferedInputStream(new FileInputStream(file));
   GzipCompressorInputStream gzIn = new GzipCompressorInputStream(in);
   TarArchiveInputStream tarIn = new TarArchiveInputStream(gzIn);
   TarArchiveEntry entry;
   while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
     // The archive should contain only a single directory: we want to unpack its content.
     final File outputFile =
         new File(target, entry.getName().substring(entry.getName().indexOf('/') + 1));
     if (entry.isDirectory()) {
       FileUtils.forceMkdir(outputFile);
     } else {
       OutputStream outputFileStream = null;
       try {
         outputFileStream = new FileOutputStream(outputFile);
         IOUtils.copy(tarIn, outputFileStream);
       } finally {
         IOUtils.closeQuietly(outputFileStream);
       }
     }
   }
 }
 public static String getVersionFromArtifact(ByteBuffer artifact) throws IOException {
   String versionNumber = null;
   try (CompressorInputStream uncompressedInput =
       new GzipCompressorInputStream(new ByteArrayInputStream(artifact.array()))) {
     ArchiveInputStream input = new TarArchiveInputStream(uncompressedInput);
     TarArchiveEntry entry;
     while ((entry = (TarArchiveEntry) input.getNextEntry()) != null) {
       if (!entry.isDirectory() && entry.getName().endsWith(VERSION_FILE)) {
         versionNumber = IOUtils.toString(input, Charsets.UTF_8).trim();
         break;
       }
     }
   }
   return versionNumber;
 }
Exemplo n.º 8
0
  public TarArchiveEntry map(final TarArchiveEntry entry) {
    final String name = entry.getName();

    final TarArchiveEntry newEntry =
        new TarArchiveEntry(prefix + '/' + Utils.stripPath(strip, name), true);

    // Set ownership
    if (uid > -1) {
      newEntry.setUserId(uid);
    } else {
      newEntry.setUserId(entry.getUserId());
    }
    if (gid > -1) {
      newEntry.setGroupId(gid);
    } else {
      newEntry.setGroupId(entry.getGroupId());
    }
    if (user != null) {
      newEntry.setUserName(user);
    } else {
      newEntry.setUserName(entry.getUserName());
    }
    if (group != null) {
      newEntry.setGroupName(group);
    } else {
      newEntry.setGroupName(entry.getGroupName());
    }

    // Set permissions
    if (newEntry.isDirectory()) {
      if (dirMode > -1) {
        newEntry.setMode(dirMode);
      } else {
        newEntry.setMode(entry.getMode());
      }
    } else {
      if (fileMode > -1) {
        newEntry.setMode(fileMode);
      } else {
        newEntry.setMode(entry.getMode());
      }
    }

    newEntry.setSize(entry.getSize());

    return newEntry;
  }
  /*
   * Given a zip stream, unzips it and returns an input stream to the desired data file.
   *
   * @param importDataRecord ImportDataRecord
   * @param is InputStream
   * @return InputStream
   */
  private InputStream readContent(ImportDataRecord importDataRecord, InputStream is)
      throws Exception {

    InputStream toReturn = null;

    try {
      // decompress .gz file
      if (LOG.isInfoEnabled()) {
        LOG.info("readContent(), decompressing: " + importDataRecord.getCanonicalPathToData());
      }

      InputStream unzippedContent = new GzipCompressorInputStream(is);
      // if tarball, untar
      if (importDataRecord.getCanonicalPathToData().toLowerCase().endsWith("tar.gz")) {
        if (LOG.isInfoEnabled()) {
          LOG.info("readContent(), gzip file is a tarball, untarring");
        }
        TarArchiveInputStream tis = new TarArchiveInputStream(unzippedContent);
        TarArchiveEntry entry = null;
        while ((entry = tis.getNextTarEntry()) != null) {
          String entryName = entry.getName();
          String dataFile = importDataRecord.getDataFilename();
          if (dataFile.contains(DatatypeMetadata.TUMOR_TYPE_TAG)) {
            dataFile =
                dataFile.replaceAll(
                    DatatypeMetadata.TUMOR_TYPE_TAG, importDataRecord.getTumorType().toUpperCase());
          }
          if (entryName.contains(dataFile)) {
            if (LOG.isInfoEnabled()) {
              LOG.info("Processing tar-archive: " + importDataRecord.getDataFilename());
            }
            toReturn = tis;
            break;
          }
        }
      } else {
        toReturn = unzippedContent;
      }
    } catch (Exception e) {
      throw e;
    }

    // outta here
    return toReturn;
  }
Exemplo n.º 10
0
  /**
   * Unpack the content read from <i>source</i> into <i>targetFolder</i>. If the
   * <i>skipTopFolder</i> is set, then don't assume that the archive contains one single folder and
   * unpack the content of that folder, not including the folder itself.
   *
   * @param source The input source. Must be in <i>TAR</i> format.
   * @param targetFolder The destination folder for the unpack. Not used when a <tt>fileCatcher</tt>
   *     is provided
   * @param skipTopFolder Set to <code>true</code> to unpack beneath the top folder of the archive.
   *     The archive must consist of one single folder and nothing else in order for this to work.
   * @param fileCatcher Used when specific files should be picked from the archive without writing
   *     them to disk. Can be <tt>null</tt>.
   * @throws IOException
   */
  public static void unpack(
      InputStream source, File targetFolder, boolean skipTopFolder, FileCatcher fileCatcher)
      throws IOException {
    String topFolderName = null;
    Map<File, Map<Integer, List<String>>> chmodMap =
        new HashMap<File, Map<Integer, List<String>>>();
    TarArchiveInputStream in = new TarArchiveInputStream(source);
    try {
      TarArchiveEntry te = in.getNextTarEntry();
      if (te == null) {
        throw new IOException("No entry in the tar file");
      }
      do {
        if (te.isGlobalPaxHeader()) continue;

        String name = te.getName();
        if (name.startsWith("./._"))
          // MacOS specific extended attributes addition. Just skip it
          continue;

        if (skipTopFolder) {
          int firstSlash = name.indexOf('/');
          if (firstSlash < 0) throw new IOException("Archive doesn't contain one single folder");

          String tfName = name.substring(0, firstSlash);
          if (topFolderName == null) topFolderName = tfName;
          else if (!tfName.equals(topFolderName))
            throw new IOException("Archive doesn't contain one single folder");
          name = name.substring(firstSlash + 1);
        }
        if (name.length() == 0) continue;

        String linkName = te.getLinkName();
        if (linkName != null) {
          if (linkName.trim().equals("")) linkName = null;
        }

        if (fileCatcher != null) {
          if (linkName == null && !te.isDirectory() && fileCatcher.accept(name)) {
            if (fileCatcher.catchData(name, in))
              // We're done here
              return;
          }
          continue;
        }

        File outFile = new File(targetFolder, name);
        if (linkName != null) {
          if (!OsUtil.link(targetFolder, name, te.getLinkName()))
            throw new IOException(
                "Archive contains links but they are not supported on this platform");
        } else {
          if (te.isDirectory()) {
            outFile.mkdirs();
          } else {
            outFile.getParentFile().mkdirs();
            OutputStream target = new FileOutputStream(outFile);
            StreamUtil.copy(in, target);
            target.close();
            outFile.setLastModified(te.getModTime().getTime());
          }
          registerChmodFile(chmodMap, targetFolder, Integer.valueOf(te.getMode()), name);
        }
      } while ((te = in.getNextTarEntry()) != null);
    } finally {
      StreamUtil.close(in);
    }
    chmod(chmodMap);
  }
Exemplo n.º 11
0
 public void execute() {
   if (repoDir == null) {
     log("repoDir attribute is empty !", LogLevel.ERR.getLevel());
     throw new RuntimeException("Bad attributes for apt-repo task");
   }
   log("repo dir: " + repoDir);
   File repoFolder = new File(repoDir);
   if (!repoFolder.exists()) {
     repoFolder.mkdirs();
   }
   File[] files =
       repoFolder.listFiles(
           new FileFilter() {
             public boolean accept(File pathname) {
               if (pathname.getName().endsWith(FILE_DEB_EXT)) {
                 return true;
               }
               return false;
             }
           });
   Packages packages = new Packages();
   for (int i = 0; i < files.length; i++) {
     File file = files[i];
     PackageEntry packageEntry = new PackageEntry();
     packageEntry.setSize(file.length());
     packageEntry.setSha1(Utils.getDigest("SHA-1", file));
     packageEntry.setSha256(Utils.getDigest("SHA-256", file));
     packageEntry.setMd5sum(Utils.getDigest("MD5", file));
     String fileName = file.getName();
     packageEntry.setFilename(fileName);
     log("found deb: " + fileName);
     try {
       ArchiveInputStream control_tgz;
       ArArchiveEntry entry;
       TarArchiveEntry control_entry;
       ArchiveInputStream debStream =
           new ArchiveStreamFactory().createArchiveInputStream("ar", new FileInputStream(file));
       while ((entry = (ArArchiveEntry) debStream.getNextEntry()) != null) {
         if (entry.getName().equals("control.tar.gz")) {
           ControlHandler controlHandler = new ControlHandler();
           GZIPInputStream gzipInputStream = new GZIPInputStream(debStream);
           control_tgz =
               new ArchiveStreamFactory().createArchiveInputStream("tar", gzipInputStream);
           while ((control_entry = (TarArchiveEntry) control_tgz.getNextEntry()) != null) {
             log("control entry: " + control_entry.getName(), LogLevel.DEBUG.getLevel());
             if (control_entry.getName().trim().equals(CONTROL_FILE_NAME)) {
               ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
               IOUtils.copy(control_tgz, outputStream);
               String content_string = outputStream.toString("UTF-8");
               outputStream.close();
               controlHandler.setControlContent(content_string);
               log("control cont: " + outputStream.toString("utf-8"), LogLevel.DEBUG.getLevel());
               break;
             }
           }
           control_tgz.close();
           if (controlHandler.hasControlContent()) {
             controlHandler.handle(packageEntry);
           } else {
             throw new RuntimeException("no control content found for: " + file.getName());
           }
           break;
         }
       }
       debStream.close();
       packages.addPackageEntry(packageEntry);
     } catch (Exception e) {
       String msg = FAILED_TO_CREATE_APT_REPO + " " + file.getName();
       log(msg, e, LogLevel.ERR.getLevel());
       throw new RuntimeException(msg, e);
     }
   }
   try {
     File packagesFile = new File(repoDir, PACKAGES_GZ);
     packagesWriter =
         new BufferedWriter(
             new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(packagesFile))));
     packagesWriter.write(packages.toString());
     DefaultHashes hashes = Utils.getDefaultDigests(packagesFile);
     ReleaseInfo pinfo = new ReleaseInfo(PACKAGES_GZ, packagesFile.length(), hashes);
     Release release = new Release();
     release.addInfo(pinfo);
     final File releaseFile = new File(repoDir, RELEASE);
     FileUtils.fileWrite(releaseFile, release.toString());
   } catch (IOException e) {
     throw new RuntimeException("writing files failed", e);
   } finally {
     if (packagesWriter != null) {
       try {
         packagesWriter.close();
       } catch (IOException e) {
         throw new RuntimeException("writing files failed", e);
       }
     }
   }
 }
Exemplo n.º 12
0
  /**
   * Untar an input file into an output file.
   *
   * <p>The output file is created in the output folder, having the same name as the input file,
   * minus the '.tar' extension.
   *
   * @param archiveFile input TAR file
   * @param lastModified when collection has been last modified
   * @throws FileNotFoundException
   * @throws ArchiveException
   */
  private static List<FileWithMeta> performUnTar(
      File archiveFile,
      IonConfig config,
      Collection collection,
      String lastModified,
      Context context)
      throws FileNotFoundException, IOException, ArchiveException {
    File collectionFolder = FilePaths.getCollectionFolderPath(config, context);
    File collectionFolderTemp = FilePaths.getTempFilePath(collectionFolder);

    final List<FileWithMeta> untaredFiles = new LinkedList<>();

    InputStream is = null;
    TarArchiveInputStream debInputStream = null;
    try {
      IonLog.d(
          TAG,
          String.format(
              "Untaring %s to dir %s.", archiveFile.getPath(), collectionFolder.getPath()));

      is = new FileInputStream(archiveFile);
      debInputStream =
          (TarArchiveInputStream) new ArchiveStreamFactory().createArchiveInputStream("tar", is);

      TarArchiveEntry entry;
      List<ArchiveIndex> index = null;
      boolean indexHasBeenRead = false;
      while ((entry = (TarArchiveEntry) debInputStream.getNextEntry()) != null) {
        if (!indexHasBeenRead) {
          // get index.json
          InputStreamReader inputStreamReader = new InputStreamReader(debInputStream, "UTF-8");
          index =
              Arrays.asList(
                  GsonHolder.getInstance().fromJson(inputStreamReader, ArchiveIndex[].class));
          indexHasBeenRead = true;
          continue;
        }

        // write the "content" files
        if (!entry.isDirectory()) {
          String archiveFileName = entry.getName();
          ArchiveIndex fileInfo = ArchiveIndex.getByName(archiveFileName, index);
          if (fileInfo == null) {
            IonLog.w(
                TAG, "Skipping " + entry.getName() + " because it was not found in index.json.");
            continue;
          }

          IonLog.i(TAG, fileInfo.url);
          FileWithMeta fileWithMeta = getFilePath(fileInfo, collectionFolderTemp, config, context);
          File targetFile = fileWithMeta.file;
          FileUtils.createDir(targetFile.getParentFile());

          targetFile = FileUtils.writeToFile(debInputStream, targetFile);

          if (targetFile != null) {
            untaredFiles.add(fileWithMeta);
          }
        }
      }
    } finally {
      // finished reading TAR archive
      if (is != null) {
        is.close();
      }
      if (debInputStream != null) {
        debInputStream.close();
      }
      if (archiveFile != null && archiveFile.exists()) {
        archiveFile.delete();
      }
    }

    // if lastModified date was not passed, look if cache index entry exists for collection and
    // retrieve it from there
    if (collection != null && lastModified == null) {
      CollectionCacheIndex collectionCacheIndex = CollectionCacheIndex.retrieve(config, context);
      lastModified = collectionCacheIndex == null ? null : collectionCacheIndex.getLastModified();
      IonLog.d(TAG, "Restoring last_modified from cache index: " + lastModified);
    }

    // delete old cache index entries of the collection in shared preferences and in memory cache
    CacheIndexStore.clearCollection(config, context);
    MemoryCache.clear();

    // replace collection folder (containing json files) - deletes old file cache
    boolean jsonWriteSuccess = FileUtils.move(collectionFolderTemp, collectionFolder, true);
    if (!jsonWriteSuccess) {
      throw new IOException("JSON files could not be moved to final path.");
    }

    // replace media files in collection
    File mediaFolderTemp = FilePaths.getMediaFolderPath(config, context, true);
    File mediaFolder = FilePaths.getMediaFolderPath(config, context, false);
    if (mediaFolderTemp.exists()) {
      boolean mediaWriteSuccess = FileUtils.move(mediaFolderTemp, mediaFolder, true);
      if (!mediaWriteSuccess) {
        throw new IOException("Media files could not be moved to final path.");
      }
    } else {
      IonLog.w(TAG, "No media files were contained in archive.");
    }

    // add collection to file cache again
    if (collection != null) {
      MemoryCache.saveCollection(collection, config, context);
      try {
        saveCollectionToFileCache(config, collection, context);
        CollectionCacheIndex.save(config, context, lastModified);
      } catch (IOException e) {
        IonLog.e("ION Archive", "Collection could not be saved.");
        IonLog.ex(e);
      }
    }

    // cache index entries are not written yet at this point
    return untaredFiles;
  }
Exemplo n.º 13
0
 public RelativePath getRelativePath() {
   return new RelativePath(true, entry.getName().split("/"));
 }
Exemplo n.º 14
0
 public String getDisplayName() {
   return String.format("tar entry %s!%s", tarFile, entry.getName());
 }
  /**
   * Extracts files to the specified destination
   *
   * @param file the file to extract to
   * @param dest the destination directory
   * @throws IOException
   */
  public static void unzipFileTo(String file, String dest) throws IOException {
    File target = new File(file);
    if (!target.exists()) throw new IllegalArgumentException("Archive doesnt exist");
    FileInputStream fin = new FileInputStream(target);
    int BUFFER = 2048;
    byte data[] = new byte[BUFFER];

    if (file.endsWith(".zip")) {
      // get the zip file content
      ZipInputStream zis = new ZipInputStream(fin);
      // get the zipped file list entry
      ZipEntry ze = zis.getNextEntry();

      while (ze != null) {

        String fileName = ze.getName();
        File newFile = new File(dest + File.separator + fileName);

        log.info("file unzip : " + newFile.getAbsoluteFile());

        // create all non exists folders
        // else you will hit FileNotFoundException for compressed folder
        new File(newFile.getParent()).mkdirs();

        FileOutputStream fos = new FileOutputStream(newFile);

        int len;
        while ((len = zis.read(data)) > 0) {
          fos.write(data, 0, len);
        }

        fos.close();
        ze = zis.getNextEntry();
      }

      zis.closeEntry();
      zis.close();

    } else if (file.endsWith(".tar.gz") || file.endsWith(".tgz")) {

      BufferedInputStream in = new BufferedInputStream(fin);
      GzipCompressorInputStream gzIn = new GzipCompressorInputStream(in);
      TarArchiveInputStream tarIn = new TarArchiveInputStream(gzIn);

      TarArchiveEntry entry = null;

      /** Read the tar entries using the getNextEntry method * */
      while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {

        log.info("Extracting: " + entry.getName());

        /** If the entry is a directory, create the directory. * */
        if (entry.isDirectory()) {

          File f = new File(dest + File.separator + entry.getName());
          f.mkdirs();
        }
        /**
         * If the entry is a file,write the decompressed file to the disk and close destination
         * stream.
         */
        else {
          int count;

          FileOutputStream fos = new FileOutputStream(dest + File.separator + entry.getName());
          BufferedOutputStream destStream = new BufferedOutputStream(fos, BUFFER);
          while ((count = tarIn.read(data, 0, BUFFER)) != -1) {
            destStream.write(data, 0, count);
          }

          destStream.flush();
          ;

          IOUtils.closeQuietly(destStream);
        }
      }

      /** Close the input stream * */
      tarIn.close();
    } else if (file.endsWith(".gz")) {
      GZIPInputStream is2 = new GZIPInputStream(fin);
      File extracted = new File(target.getParent(), target.getName().replace(".gz", ""));
      if (extracted.exists()) extracted.delete();
      extracted.createNewFile();
      OutputStream fos = FileUtils.openOutputStream(extracted);
      IOUtils.copyLarge(is2, fos);
      is2.close();
      fos.flush();
      fos.close();
    }

    target.delete();
  }