java类com.mongodb.gridfs.GridFSInputFile的实例源码

/**
 * Inserts publication annex document.
 */
public void insertAnnexDocument(BinaryFile bf, String dateString) throws ParseException {
    try {
        GridFS gfs = new GridFS(db, MongoCollectionsInterface.PUB_ANNEXES);
        BasicDBObject whereQuery = new BasicDBObject();
        whereQuery.put("repositoryDocId", bf.getRepositoryDocId());
        whereQuery.put("filename", bf.getFileName());
        gfs.remove(whereQuery);
        //version ?
        GridFSInputFile gfsFile = gfs.createFile(bf.getStream(), true);
        gfsFile.put("uploadDate", Utilities.parseStringDate(dateString));
        gfsFile.setFilename(bf.getFileName());
        gfsFile.put("source", bf.getSource());
        gfsFile.put("version", bf.getRepositoryDocVersion());
        gfsFile.put("repositoryDocId", bf.getRepositoryDocId());
        gfsFile.put("anhalyticsId", bf.getAnhalyticsId());
        gfsFile.save();
    } catch (ParseException e) {
        logger.error(e.getMessage(), e.getCause());
    }
}

public DataAddress uploadData(String data, DataAddress dataAddress) throws UnknownHostException {
      ServerAddress server = new ServerAddress(dataAddress.hostname, dataAddress.port);
      GridFS database = connectToDatabase(server);

      logger.info("Database connected");

      GridFSInputFile file = database.createFile(data.getBytes());
      int newID = getNextId(database);
      logger.info("Got new id for uploaded file: " + newID);
file.setFilename(String.valueOf(newID));
      file.put("_id", newID);
      file.save();

      logger.info("after save");

      return new DataAddress(dataAddress.hostname, dataAddress.port, newID);
  }

@Override
public Boolean storeBlob(CallingContext context, String docPath, InputStream newContent, Boolean append) {
    GridFS gridFS = getGridFS();
    GridFSInputFile file;
    if (!append) {
        gridFS.remove(docPath);
        file = createNewFile(docPath, newContent);
    } else {
        GridFSDBFile existing = gridFS.findOne(docPath);
        if (existing != null) {
            try {
                file = updateExisting(context, docPath, newContent, gridFS, existing);
            } catch (IOException e) {
                file = null;
                log.error(String.format("Error while appending to docPath %s: %s", docPath, ExceptionToString.format(e)));
            }

        } else {
            file = createNewFile(docPath, newContent);
        }
    }
    return file != null;
}

@Override
public void process(CAS aCAS) throws AnalysisEngineProcessException {
  Type documentIdType = aCAS.getTypeSystem()
      .getType("edu.umn.biomedicus.uima.type1_5.DocumentId");
  Feature docIdFeat = documentIdType.getFeatureByBaseName("documentId");

  String documentId = aCAS.getIndexRepository()
      .getAllIndexedFS(documentIdType)
      .get()
      .getStringValue(docIdFeat);

  if (documentId == null) {
    documentId = UUID.randomUUID().toString();
  }

  GridFSInputFile file = gridFS.createFile(documentId + ".xmi");

  try (OutputStream outputStream = file.getOutputStream()) {
    XmiCasSerializer.serialize(aCAS, outputStream);
  } catch (IOException | SAXException e) {
    throw new AnalysisEngineProcessException(e);
  }
}

@Override
public void storeAttachment(AttachmentId attachmentId, InputStream data)
    throws IOException {
  GridFSInputFile file = getAttachmentGrid().createFile(data, attachmentId.serialise());

  try {
    file.save();
  } catch (MongoException e) {
    // Unfortunately, file.save() wraps any IOException thrown in a
    // 'MongoException'. Since the interface explicitly throws IOExceptions,
    // we unwrap any IOExceptions thrown.
    Throwable innerException = e.getCause();
    if (innerException instanceof IOException) {
      throw (IOException) innerException;
    } else {
      throw e;
    }
  }
}

public String saveFile(InputStream is, String contentType) throws IOException {
    GridFSInputFile file = getNewFile();    
    String id = file.getId().toString();
    OutputStream os = getFileOutputStream(id, contentType);
    if (os != null) {
        try {
            byte data[] = new byte[4096];
            int len = 0;
            while ((len = is.read(data, 0, data.length)) > 0) {
                os.write(data, 0, len);
            }
            return id;
        } finally {
            os.close();
        }
    }
    return null;
}

/**
 * Inserts grobid tei using GridFS.
 */
public void insertGrobidTei(String teiString, String repositoryDocId, String anhalyticsId, String version, String source, String type, String date) {
    try {
        GridFS gfs = new GridFS(db, MongoCollectionsInterface.GROBID_TEIS);
        gfs.remove(repositoryDocId + ".tei.xml");
        GridFSInputFile gfsFile = gfs.createFile(new ByteArrayInputStream(teiString.getBytes()), true);
        gfsFile.put("uploadDate", Utilities.parseStringDate(date));
        gfsFile.setFilename(repositoryDocId + ".tei.xml");
        gfsFile.put("repositoryDocId", repositoryDocId);
        gfsFile.put("anhalyticsId", anhalyticsId);
        gfsFile.put("source", source);
        gfsFile.put("version", version);
        gfsFile.put("documentType", type);
        gfsFile.save();
    } catch (ParseException e) {
        logger.error(e.getMessage(), e.getCause());
    }
}

/**
 * Inserts TEI metadata document in the GridFS.
 */
public void insertMetadataTei(String tei, String doi, String pdfUrl, String source, String repositoryDocId, String version, String type, String date) {
    try {
        GridFS gfs = new GridFS(db, MongoCollectionsInterface.METADATAS_TEIS);
        gfs.remove(repositoryDocId + ".tei.xml");
        GridFSInputFile gfsFile = gfs.createFile(new ByteArrayInputStream(tei.getBytes()), true);
        gfsFile.put("uploadDate", Utilities.parseStringDate(date));
        gfsFile.setFilename(repositoryDocId + ".tei.xml");
        gfsFile.put("repositoryDocId", repositoryDocId);
        gfsFile.put("anhalyticsId", generateAnhalyticsId(repositoryDocId, doi, pdfUrl));
        gfsFile.put("source", source);
        gfsFile.put("version", version);
        gfsFile.put("documentType", type);
        gfsFile.save();
    } catch (ParseException e) {
        logger.error(e.getMessage(), e.getCause());
    }
}

/**
 * Inserts PDF binary document in the GridFS.
 */
public void insertBinaryDocument(BinaryFile bf, String date) {
    try {
        GridFS gfs = new GridFS(db, MongoCollectionsInterface.BINARIES);
        gfs.remove(bf.getFileName());
        GridFSInputFile gfsFile = gfs.createFile(bf.getStream(), true);
        gfsFile.put("uploadDate", Utilities.parseStringDate(date));
        gfsFile.setFilename(bf.getFileName());
        gfsFile.put("repositoryDocId", bf.getRepositoryDocId());
        gfsFile.put("anhalyticsId", bf.getAnhalyticsId());
        gfsFile.put("source", bf.getSource());
        gfsFile.put("version", bf.getRepositoryDocVersion());
        gfsFile.put("documentType", bf.getDocumentType());
        gfsFile.setContentType(bf.getFileType());
        gfsFile.save();
    } catch (ParseException e) {
        logger.error(e.getMessage(), e.getCause());
    }

}

/**
 * Updates already existing tei with new (more enriched one, fulltext..).
 */
public void updateTei(String newTei, String repositoryDocId, String collection) {
    try {
        GridFS gfs = new GridFS(db, collection);
        GridFSDBFile gdf = gfs.findOne(repositoryDocId + ".tei.xml");
        GridFSInputFile gfsNew = gfs.createFile(new ByteArrayInputStream(newTei.getBytes()), true);
        gfsNew.put("uploadDate", gdf.getUploadDate());
        gfsNew.setFilename(gdf.get("repositoryDocId") + ".tei.xml");
        gfsNew.put("repositoryDocId", gdf.get("repositoryDocId"));
        gfsNew.put("documentType", gdf.get("documentType"));
        gfsNew.put("anhalyticsId", gdf.get("anhalyticsId"));
        gfsNew.put("source", gdf.get("source"));

        gfsNew.save();
        gfs.remove(gdf);
    } catch (Exception e) {
        logger.error(e.getMessage(), e.getCause());
    }
}

/**
 * inserts a Arxiv/istex TEI document in the GridFS.
 */
public void insertExternalTeiDocument(InputStream file, String identifier, String repository, String namespace, String dateString) {
    try {
        GridFS gfs = new GridFS(db, namespace);
        GridFSInputFile gfsFile = gfs.createFile(file, true);
        gfs.remove(identifier + ".pdf");
        gfsFile.put("uploadDate", Utilities.parseStringDate(dateString));
        gfsFile.setFilename(identifier + ".tei.xml");
        gfsFile.put("identifier", identifier);
        gfsFile.put("repository", repository);
        gfsFile.setContentType("application/tei+xml");
        gfsFile.save();
    } catch (ParseException e) {
        logger.error(e.getMessage(), e.getCause());
    }

}

@Override
public void writeBlob(final String blobName, final InputStream is, final long sizeInBytes, final WriterListener listener) {
    blobStore.executor().execute(new Runnable() {
        @Override
        public void run() {
            try {
                blobStore.gridFS().remove(buildKey(blobName));  // need to remove old file if already exist
                GridFSInputFile file = blobStore.gridFS().createFile(is, buildKey(blobName));
                file.save();
                listener.onCompleted();
            } catch (Exception e) {
                listener.onFailure(e);
            }
        }
    });
}

@Override
public OutputStream createOutputStreamToWrite() {
  checkState(State.NEW);

  storingOutputStream = new FilterOutputStream(((GridFSInputFile) dbFile).getOutputStream()) {

    @Override
    public void close() throws IOException {
      putMetadataInGridFS(false);
      super.close();
      refreshAttributesOnClose();
    }
  };

  return storingOutputStream;
}

/**
 * 保存文件到Mongo中
 * @param file  文件对象
 * @param id    id_ 自定义序列
 * @param metaData  元数据类型 Key Value
 * @return
 */
public boolean concatGridFile(File file, Object id, DBObject metaData){
    GridFSInputFile gridFSInputFile;
    DBObject query  = new BasicDBObject("_id", id);
    GridFSDBFile gridFSDBFile = myFS.findOne(query);
    if(gridFSDBFile!= null)
        return false;
    try {
        gridFSInputFile = myFS.createFile(file);
        gridFSInputFile.put("_id",id);
        gridFSInputFile.setFilename(file.getName());
        gridFSInputFile.setMetaData(metaData);
        gridFSInputFile.setContentType(file.getName().substring(file.getName().lastIndexOf(".")));
        gridFSInputFile.save();
    } catch (Exception e) {
        e.printStackTrace();
        return false;
    }
    return true;
}

@Override
public void run() {
    try{
        File localPath = new File(localRoot, file.getFilename());
        log.info("Save to local file:" + localPath.getAbsolutePath());
        File dirName = localPath.getParentFile();
        if(!dirName.exists()){
            dirName.mkdirs();
        }
        file.writeTo(localPath);
        GridFSInputFile newFile = fs.createFile(new byte[]{0, 0,});
        newFile.setMetaData(file.getMetaData());
        newFile.setFilename(file.getFilename());
        newFile.put("localLength", file.getLength());
        newFile.save(10);
        //log.info("remove:%s" + file.getId() + ", fn:" + file.getFilename());
        fs.remove((ObjectId)file.getId());
    }catch(Throwable e){
        log.error("Failed to dump file to local fs, error:" + e.toString(), e);
    }
}

@Override
public void saveBlob(final MD5 md5, final InputStream data,
        final boolean sorted)
        throws BlobStoreCommunicationException {
    if(data == null || md5 == null) {
        throw new NullPointerException("Arguments cannot be null");
    }
    if (getFile(md5) != null) {
        return; //already exists
    }
    final GridFSInputFile gif = gfs.createFile(data, true);
    gif.setId(md5.getMD5());
    gif.setFilename(md5.getMD5());
    gif.put(Fields.GFS_SORTED, sorted);
    try {
        gif.save();
    } catch (DuplicateKeyException dk) {
        // already here, done
    } catch (MongoException me) {
        throw new BlobStoreCommunicationException(
                "Could not write to the mongo database", me);
    }
}

@Test
public void dataWithoutSortMarker() throws Exception {
    String s = "pootypoot";
    final GridFSInputFile gif = gfs.createFile(s.getBytes("UTF-8"));
    MD5 md5 = new MD5(a32);
    gif.setId(md5.getMD5());
    gif.setFilename(md5.getMD5());
    gif.save();

    ByteArrayFileCache d = gfsb.getBlob(md5, 
            new ByteArrayFileCacheManager(16000000, 2000000000L, tfm));
    assertThat("data returned marked as unsorted", d.isSorted(), is(false));
    String returned = IOUtils.toString(d.getJSON());
    assertThat("Didn't get same data back from store", returned, is(s));
    gfsb.removeBlob(md5);
}

@Override
public String putBlob(String container, Blob blob, PutOptions options) {
    if (options != null && !options.isMultipart()) {
        throw new IllegalArgumentException("only multipart is supported by this provider");
    }
    Payload payload = checkNotNull(blob.getPayload());
    BlobMetadata metadata = blob.getMetadata();
    ContentMetadata contentMetadata = metadata.getContentMetadata();
    GridFS gridFS = parseGridFSIdentifier(container).connect(mongo);
    GridFSInputFile inputFile = gridFS.createFile(payload.getInput(), metadata.getName(), true);
    inputFile.setContentType(contentMetadata.getContentType());
    DBObject fileMetadata = new BasicDBObject();
    fileMetadata.putAll(metadata.getUserMetadata());
    inputFile.setMetaData(fileMetadata);
    inputFile.save();
    return inputFile.getMD5();
}

public Optional<FileEntry> save(final String name, final String mime,
                                final String creator, final boolean privateFile, final String description,
                                InputStream in) {
    GridFS gf = gridFS;
    GridFSInputFile f = gf.createFile(in);
    f.setFilename(name);
    f.setContentType(mime);
    //
    DBObject metadata = f.getMetaData();
    if (metadata == null) {
        metadata = new BasicDBObject();
        f.setMetaData(metadata);
    }
    metadata.put("creator", creator);
    metadata.put("private", privateFile);
    metadata.put("description", description);
    //
    f.save();
    //
    return this.loadFileEntry((ObjectId) f.getId());
}

@Override
synchronized public OutputStream openOutputStream(final byte[] key) {
    return new ByteArrayOutputStream(256) {
        @Override
        public void close() throws IOException {
            super.close();
            byte[] keyString = adoptKey(key);
            byte[] byteArray = toByteArray();
            if (byteArray.length < MAX_BSON_SIZE) {
                collection.update(new BasicDBObject(KEY, keyString), new BasicDBObject(KEY, keyString).append(TYPE, TYPE_BSON).append(VALUE, byteArray), true, false);
            } else {
                // do grid fs
                GridFSInputFile gridFsFile = gridFs.createFile(byteArray);
                String fileName = URIUtils.encode(key);
                gridFsFile.setFilename(fileName);
                gridFsFile.save();
                collection.update(new BasicDBObject(KEY, keyString), new BasicDBObject(KEY, keyString).append(TYPE, TYPE_GRID_FS).append(FILE_NAME, fileName), true, false);
            }
        }
    };
}

@Override
public void execute() throws Exception {
    MongoClient mdb = MongoFactory.getInst().getMongo( sName );

    if ( mdb == null )
        throw new Exception("no server selected");

    if ( sDb == null )
        throw new Exception("no database selected");

    MongoFactory.getInst().setActiveDB(sDb);
    DB db   = mdb.getDB(sDb);

    GridFS  gfs = new GridFS( db, sColl.substring(0,sColl.lastIndexOf(".")) );

    GridFSInputFile gridFSInputFile = gfs.createFile(getFile);
    gridFSInputFile.setContentType( MimetypesFileTypeMap.getDefaultFileTypeMap().getContentType(getFile) );
    gridFSInputFile.save();

    setMessage( "fileLoaded=" + getFile + "; size=" + getFile.length() );
}

public DataAddress prefetchData(DataAddress givenAddress, ServerAddress destAddress) throws IOException {
    logger.info("yo2");
    ServerAddress givenServer = new ServerAddress(givenAddress.hostname, givenAddress.port);
    GridFS givenDatabase = connectToDatabase(givenServer);

    logger.info("yo");

       GridFSDBFile givenPackage = givenDatabase.findOne(new BasicDBObject("_id", givenAddress.ID));
       ByteArrayOutputStream baos = new ByteArrayOutputStream((int)givenPackage.getLength());
       givenPackage.writeTo(baos);

       logger.info("Prefetched");

       GridFS destDatabase = connectToDatabase(destAddress);
       GridFSInputFile destPackage = destDatabase.createFile(baos.toByteArray());
       int newID = getNextId(destDatabase);
       logger.info("Got new id for prefetched package: " + newID);
       destPackage.put("_id", newID);
       destPackage.save();

       logger.info("after save");

       DataAddress ret = new DataAddress();
       ret.hostname = destAddress.getHost();
       ret.port = destAddress.getPort();
       ret.ID = newID;            
       return ret;        
}

/**
 *
 * @param inputStream 文件流
 * @param format 文件格式，“pdf”，“png”等，不包含后缀符号“.”
 * @return
 */
public String saveFile(InputStream inputStream,String format,String uid) {
    try {
        GridFS gridFS = getInstance();

        //随机生成文件名称，多次重试
        String filename = this.randomFileName();
        //如果有文件重复，则重新生成filename
        while (true) {
            GridFSDBFile _current = gridFS.findOne(filename);
            //如果文件不存在，则保存操作
            if (_current == null) {
                break;
            }
            filename = this.randomFileName();
        }

        GridFSInputFile file = gridFS.createFile(inputStream, filename);
        if(format != null) {
            file.put("format", format);
        }
        if(uid != null) {
            file.put("uid",uid);
        }
        file.put("content-type","application/octet-stream");
        file.save();
        return concat(filename,format);
    }catch (Exception e) {

        throw new RuntimeException(e);
    } finally {
        try{
            inputStream.close();
        }catch (Exception ex) {
            //
        }
    }
}

@Override
public boolean create(String filename, byte[] data) {
    this.delete(filename);
    GridFSInputFile file = getGridFS().createFile(data);
    file.setFilename(filename);
    file.save();
    return true;
}

@Override
public void put(String keyText, T obj) throws IOException {
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    ObjectOutputStream objectOutput = new ObjectOutputStream(baos);
    objectOutput.writeObject(obj);
    objectOutput.close();
    byte[] binaryObject = baos.toByteArray();

    GridFSInputFile objFile = gridfs.createFile(binaryObject);
    objFile.setFilename(DigestUtils.sha256Hex(keyText));
    //it will not update content of existing file
    objFile.save();
}

protected GridFSInputFile createNewFile(String docPath, InputStream content) {
    GridFSInputFile file = getGridFS().createFile(content, docPath);
    if (file != null) {
        file.save();
    }
    return file;
}

public long createGridFsFile(Id id, InputStream inputStream, String filename, String mimeType) {
    DB db = (DB) connections.getConnection("mongodb.dma");
    GridFS fs = new GridFS(db);
    GridFSInputFile gridFile = fs.createFile(inputStream, filename);
    gridFile.setId(id);
    gridFile.setContentType(mimeType);
    gridFile.save();
    return gridFile.getLength();
}

private long createGridFsFile(Id id, InputStream inputStream, String filename, String mimeType) {
    DB db = (DB) connections.getConnection("mongodb.dma");
    GridFS fs = new GridFS(db);
    GridFSInputFile gridFile = fs.createFile(inputStream, filename);
    gridFile.setId(id);
    gridFile.setContentType(mimeType);
    gridFile.save();
    return gridFile.getLength();
}

@SuppressWarnings("serial")
@POST
@Consumes(MediaType.APPLICATION_JSON)
public Response insertImageInDb(String jsonRequest, @Context Request request) throws IOException {
    EndpointUtil.printClientInfo(request);

    DBObject json = ((DBObject) JSON.parse(jsonRequest));
    String imageData = (String) json.get("imageData");
    byte[] screenshotBytes = Base64Utils.decode(imageData);

    String testName = json.get(BaseScreenshotModel.TEST_NAME).toString();
    String testBrowser = json.get(BaseScreenshotModel.TEST_BROWSER).toString();
    String description = json.get(BaseScreenshotModel.DESCRIPTION).toString();

    Type type = new TypeToken<List<Rectangle>>() {
    }.getType();

    String ignoreZonesString = ((Object) json.get(BaseScreenshotModel.IGNORE_ZONES)).toString();
    List<Rectangle> ignoreZones = new ArrayList<>();

    if (ignoreZonesString != null) {
        ignoreZones = GsonUtil.gson.fromJson(ignoreZonesString, type);
    }

    File tmpFile = new File("tmpFile");
    FileUtils.writeByteArrayToFile(tmpFile, screenshotBytes);
    GridFSInputFile gfsFile = GFS_PHOTO.createFile(tmpFile);

    gfsFile.setFilename(String.format("%s|%s|%s", testName, testBrowser, description));
    gfsFile.save();
    // after the file has been saved, get the id and add it into the table of base_images
    BaseScreenshotModel up = new BaseScreenshotModel(testName, testBrowser, description,
        new ObjectId(gfsFile.getId().toString()), ignoreZones);

    TMP_IMAGES.save(up);
    tmpFile.delete();
    return Response.ok().entity(JSON.serialize(up)).build();
}

@Override
public String saveArtifact(DBKey dbKey, InputStream data, String contentType) {
  String resultObjectId = null;
  GridFS gfs = getGridFS(dbKey);
  GridFSInputFile file = gfs.createFile(data);
  if (file != null) {
    file.setContentType(contentType);
    file.save();
    resultObjectId = file.getId().toString();
  }
  return resultObjectId;
}