FeatureEnVi: Visual Analytics for Feature Engineering Using Stepwise Selection and Semi-Automatic Extraction Approaches
https://doi.org/10.1109/TVCG.2022.3141040
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
840 lines
30 KiB
840 lines
30 KiB
# Copyright 2009-present MongoDB, Inc.
|
|
#
|
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
|
# you may not use this file except in compliance with the License.
|
|
# You may obtain a copy of the License at
|
|
#
|
|
# http://www.apache.org/licenses/LICENSE-2.0
|
|
#
|
|
# Unless required by applicable law or agreed to in writing, software
|
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
# See the License for the specific language governing permissions and
|
|
# limitations under the License.
|
|
|
|
"""Tools for representing files stored in GridFS."""
|
|
import datetime
|
|
import hashlib
|
|
import io
|
|
import math
|
|
import os
|
|
|
|
from bson.son import SON
|
|
from bson.binary import Binary
|
|
from bson.objectid import ObjectId
|
|
from bson.py3compat import text_type, StringIO
|
|
from gridfs.errors import CorruptGridFile, FileExists, NoFile
|
|
from pymongo import ASCENDING
|
|
from pymongo.collection import Collection
|
|
from pymongo.cursor import Cursor
|
|
from pymongo.errors import (ConfigurationError,
|
|
CursorNotFound,
|
|
DuplicateKeyError,
|
|
OperationFailure)
|
|
from pymongo.read_preferences import ReadPreference
|
|
|
|
try:
|
|
_SEEK_SET = os.SEEK_SET
|
|
_SEEK_CUR = os.SEEK_CUR
|
|
_SEEK_END = os.SEEK_END
|
|
# before 2.5
|
|
except AttributeError:
|
|
_SEEK_SET = 0
|
|
_SEEK_CUR = 1
|
|
_SEEK_END = 2
|
|
|
|
EMPTY = b""
|
|
NEWLN = b"\n"
|
|
|
|
"""Default chunk size, in bytes."""
|
|
# Slightly under a power of 2, to work well with server's record allocations.
|
|
DEFAULT_CHUNK_SIZE = 255 * 1024
|
|
|
|
_C_INDEX = SON([("files_id", ASCENDING), ("n", ASCENDING)])
|
|
_F_INDEX = SON([("filename", ASCENDING), ("uploadDate", ASCENDING)])
|
|
|
|
|
|
def _grid_in_property(field_name, docstring, read_only=False,
|
|
closed_only=False):
|
|
"""Create a GridIn property."""
|
|
def getter(self):
|
|
if closed_only and not self._closed:
|
|
raise AttributeError("can only get %r on a closed file" %
|
|
field_name)
|
|
# Protect against PHP-237
|
|
if field_name == 'length':
|
|
return self._file.get(field_name, 0)
|
|
return self._file.get(field_name, None)
|
|
|
|
def setter(self, value):
|
|
if self._closed:
|
|
self._coll.files.update_one({"_id": self._file["_id"]},
|
|
{"$set": {field_name: value}})
|
|
self._file[field_name] = value
|
|
|
|
if read_only:
|
|
docstring += "\n\nThis attribute is read-only."
|
|
elif closed_only:
|
|
docstring = "%s\n\n%s" % (docstring, "This attribute is read-only and "
|
|
"can only be read after :meth:`close` "
|
|
"has been called.")
|
|
|
|
if not read_only and not closed_only:
|
|
return property(getter, setter, doc=docstring)
|
|
return property(getter, doc=docstring)
|
|
|
|
|
|
def _grid_out_property(field_name, docstring):
|
|
"""Create a GridOut property."""
|
|
def getter(self):
|
|
self._ensure_file()
|
|
|
|
# Protect against PHP-237
|
|
if field_name == 'length':
|
|
return self._file.get(field_name, 0)
|
|
return self._file.get(field_name, None)
|
|
|
|
docstring += "\n\nThis attribute is read-only."
|
|
return property(getter, doc=docstring)
|
|
|
|
|
|
def _clear_entity_type_registry(entity, **kwargs):
|
|
"""Clear the given database/collection object's type registry."""
|
|
codecopts = entity.codec_options.with_options(type_registry=None)
|
|
return entity.with_options(codec_options=codecopts, **kwargs)
|
|
|
|
|
|
class GridIn(object):
|
|
"""Class to write data to GridFS.
|
|
"""
|
|
def __init__(
|
|
self, root_collection, session=None, disable_md5=False, **kwargs):
|
|
"""Write a file to GridFS
|
|
|
|
Application developers should generally not need to
|
|
instantiate this class directly - instead see the methods
|
|
provided by :class:`~gridfs.GridFS`.
|
|
|
|
Raises :class:`TypeError` if `root_collection` is not an
|
|
instance of :class:`~pymongo.collection.Collection`.
|
|
|
|
Any of the file level options specified in the `GridFS Spec
|
|
<http://dochub.mongodb.org/core/gridfsspec>`_ may be passed as
|
|
keyword arguments. Any additional keyword arguments will be
|
|
set as additional fields on the file document. Valid keyword
|
|
arguments include:
|
|
|
|
- ``"_id"``: unique ID for this file (default:
|
|
:class:`~bson.objectid.ObjectId`) - this ``"_id"`` must
|
|
not have already been used for another file
|
|
|
|
- ``"filename"``: human name for the file
|
|
|
|
- ``"contentType"`` or ``"content_type"``: valid mime-type
|
|
for the file
|
|
|
|
- ``"chunkSize"`` or ``"chunk_size"``: size of each of the
|
|
chunks, in bytes (default: 255 kb)
|
|
|
|
- ``"encoding"``: encoding used for this file. In Python 2,
|
|
any :class:`unicode` that is written to the file will be
|
|
converted to a :class:`str`. In Python 3, any :class:`str`
|
|
that is written to the file will be converted to
|
|
:class:`bytes`.
|
|
|
|
:Parameters:
|
|
- `root_collection`: root collection to write to
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession` to use for all
|
|
commands
|
|
- `disable_md5` (optional): When True, an MD5 checksum will not be
|
|
computed for the uploaded file. Useful in environments where
|
|
MD5 cannot be used for regulatory or other reasons. Defaults to
|
|
False.
|
|
- `**kwargs` (optional): file level options (see above)
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
|
|
.. versionchanged:: 3.0
|
|
`root_collection` must use an acknowledged
|
|
:attr:`~pymongo.collection.Collection.write_concern`
|
|
"""
|
|
if not isinstance(root_collection, Collection):
|
|
raise TypeError("root_collection must be an "
|
|
"instance of Collection")
|
|
|
|
if not root_collection.write_concern.acknowledged:
|
|
raise ConfigurationError('root_collection must use '
|
|
'acknowledged write_concern')
|
|
|
|
# Handle alternative naming
|
|
if "content_type" in kwargs:
|
|
kwargs["contentType"] = kwargs.pop("content_type")
|
|
if "chunk_size" in kwargs:
|
|
kwargs["chunkSize"] = kwargs.pop("chunk_size")
|
|
|
|
coll = _clear_entity_type_registry(
|
|
root_collection, read_preference=ReadPreference.PRIMARY)
|
|
|
|
if not disable_md5:
|
|
kwargs["md5"] = hashlib.md5()
|
|
# Defaults
|
|
kwargs["_id"] = kwargs.get("_id", ObjectId())
|
|
kwargs["chunkSize"] = kwargs.get("chunkSize", DEFAULT_CHUNK_SIZE)
|
|
object.__setattr__(self, "_session", session)
|
|
object.__setattr__(self, "_coll", coll)
|
|
object.__setattr__(self, "_chunks", coll.chunks)
|
|
object.__setattr__(self, "_file", kwargs)
|
|
object.__setattr__(self, "_buffer", StringIO())
|
|
object.__setattr__(self, "_position", 0)
|
|
object.__setattr__(self, "_chunk_number", 0)
|
|
object.__setattr__(self, "_closed", False)
|
|
object.__setattr__(self, "_ensured_index", False)
|
|
|
|
def __create_index(self, collection, index_key, unique):
|
|
doc = collection.find_one(projection={"_id": 1}, session=self._session)
|
|
if doc is None:
|
|
try:
|
|
index_keys = [index_spec['key'] for index_spec in
|
|
collection.list_indexes(session=self._session)]
|
|
except OperationFailure:
|
|
index_keys = []
|
|
if index_key not in index_keys:
|
|
collection.create_index(
|
|
index_key.items(), unique=unique, session=self._session)
|
|
|
|
def __ensure_indexes(self):
|
|
if not object.__getattribute__(self, "_ensured_index"):
|
|
self.__create_index(self._coll.files, _F_INDEX, False)
|
|
self.__create_index(self._coll.chunks, _C_INDEX, True)
|
|
object.__setattr__(self, "_ensured_index", True)
|
|
|
|
def abort(self):
|
|
"""Remove all chunks/files that may have been uploaded and close.
|
|
"""
|
|
self._coll.chunks.delete_many(
|
|
{"files_id": self._file['_id']}, session=self._session)
|
|
self._coll.files.delete_one(
|
|
{"_id": self._file['_id']}, session=self._session)
|
|
object.__setattr__(self, "_closed", True)
|
|
|
|
@property
|
|
def closed(self):
|
|
"""Is this file closed?
|
|
"""
|
|
return self._closed
|
|
|
|
_id = _grid_in_property("_id", "The ``'_id'`` value for this file.",
|
|
read_only=True)
|
|
filename = _grid_in_property("filename", "Name of this file.")
|
|
name = _grid_in_property("filename", "Alias for `filename`.")
|
|
content_type = _grid_in_property("contentType", "Mime-type for this file.")
|
|
length = _grid_in_property("length", "Length (in bytes) of this file.",
|
|
closed_only=True)
|
|
chunk_size = _grid_in_property("chunkSize", "Chunk size for this file.",
|
|
read_only=True)
|
|
upload_date = _grid_in_property("uploadDate",
|
|
"Date that this file was uploaded.",
|
|
closed_only=True)
|
|
md5 = _grid_in_property("md5", "MD5 of the contents of this file "
|
|
"if an md5 sum was created.",
|
|
closed_only=True)
|
|
|
|
def __getattr__(self, name):
|
|
if name in self._file:
|
|
return self._file[name]
|
|
raise AttributeError("GridIn object has no attribute '%s'" % name)
|
|
|
|
def __setattr__(self, name, value):
|
|
# For properties of this instance like _buffer, or descriptors set on
|
|
# the class like filename, use regular __setattr__
|
|
if name in self.__dict__ or name in self.__class__.__dict__:
|
|
object.__setattr__(self, name, value)
|
|
else:
|
|
# All other attributes are part of the document in db.fs.files.
|
|
# Store them to be sent to server on close() or if closed, send
|
|
# them now.
|
|
self._file[name] = value
|
|
if self._closed:
|
|
self._coll.files.update_one({"_id": self._file["_id"]},
|
|
{"$set": {name: value}})
|
|
|
|
def __flush_data(self, data):
|
|
"""Flush `data` to a chunk.
|
|
"""
|
|
self.__ensure_indexes()
|
|
if 'md5' in self._file:
|
|
self._file['md5'].update(data)
|
|
|
|
if not data:
|
|
return
|
|
assert(len(data) <= self.chunk_size)
|
|
|
|
chunk = {"files_id": self._file["_id"],
|
|
"n": self._chunk_number,
|
|
"data": Binary(data)}
|
|
|
|
try:
|
|
self._chunks.insert_one(chunk, session=self._session)
|
|
except DuplicateKeyError:
|
|
self._raise_file_exists(self._file['_id'])
|
|
self._chunk_number += 1
|
|
self._position += len(data)
|
|
|
|
def __flush_buffer(self):
|
|
"""Flush the buffer contents out to a chunk.
|
|
"""
|
|
self.__flush_data(self._buffer.getvalue())
|
|
self._buffer.close()
|
|
self._buffer = StringIO()
|
|
|
|
def __flush(self):
|
|
"""Flush the file to the database.
|
|
"""
|
|
try:
|
|
self.__flush_buffer()
|
|
|
|
if "md5" in self._file:
|
|
self._file["md5"] = self._file["md5"].hexdigest()
|
|
self._file["length"] = self._position
|
|
self._file["uploadDate"] = datetime.datetime.utcnow()
|
|
|
|
return self._coll.files.insert_one(
|
|
self._file, session=self._session)
|
|
except DuplicateKeyError:
|
|
self._raise_file_exists(self._id)
|
|
|
|
def _raise_file_exists(self, file_id):
|
|
"""Raise a FileExists exception for the given file_id."""
|
|
raise FileExists("file with _id %r already exists" % file_id)
|
|
|
|
def close(self):
|
|
"""Flush the file and close it.
|
|
|
|
A closed file cannot be written any more. Calling
|
|
:meth:`close` more than once is allowed.
|
|
"""
|
|
if not self._closed:
|
|
self.__flush()
|
|
object.__setattr__(self, "_closed", True)
|
|
|
|
def read(self, size=-1):
|
|
raise io.UnsupportedOperation('read')
|
|
|
|
def readable(self):
|
|
return False
|
|
|
|
def seekable(self):
|
|
return False
|
|
|
|
def write(self, data):
|
|
"""Write data to the file. There is no return value.
|
|
|
|
`data` can be either a string of bytes or a file-like object
|
|
(implementing :meth:`read`). If the file has an
|
|
:attr:`encoding` attribute, `data` can also be a
|
|
:class:`unicode` (:class:`str` in python 3) instance, which
|
|
will be encoded as :attr:`encoding` before being written.
|
|
|
|
Due to buffering, the data may not actually be written to the
|
|
database until the :meth:`close` method is called. Raises
|
|
:class:`ValueError` if this file is already closed. Raises
|
|
:class:`TypeError` if `data` is not an instance of
|
|
:class:`str` (:class:`bytes` in python 3), a file-like object,
|
|
or an instance of :class:`unicode` (:class:`str` in python 3).
|
|
Unicode data is only allowed if the file has an :attr:`encoding`
|
|
attribute.
|
|
|
|
:Parameters:
|
|
- `data`: string of bytes or file-like object to be written
|
|
to the file
|
|
"""
|
|
if self._closed:
|
|
raise ValueError("cannot write to a closed file")
|
|
|
|
try:
|
|
# file-like
|
|
read = data.read
|
|
except AttributeError:
|
|
# string
|
|
if not isinstance(data, (text_type, bytes)):
|
|
raise TypeError("can only write strings or file-like objects")
|
|
if isinstance(data, text_type):
|
|
try:
|
|
data = data.encode(self.encoding)
|
|
except AttributeError:
|
|
raise TypeError("must specify an encoding for file in "
|
|
"order to write %s" % (text_type.__name__,))
|
|
read = StringIO(data).read
|
|
|
|
if self._buffer.tell() > 0:
|
|
# Make sure to flush only when _buffer is complete
|
|
space = self.chunk_size - self._buffer.tell()
|
|
if space:
|
|
try:
|
|
to_write = read(space)
|
|
except:
|
|
self.abort()
|
|
raise
|
|
self._buffer.write(to_write)
|
|
if len(to_write) < space:
|
|
return # EOF or incomplete
|
|
self.__flush_buffer()
|
|
to_write = read(self.chunk_size)
|
|
while to_write and len(to_write) == self.chunk_size:
|
|
self.__flush_data(to_write)
|
|
to_write = read(self.chunk_size)
|
|
self._buffer.write(to_write)
|
|
|
|
def writelines(self, sequence):
|
|
"""Write a sequence of strings to the file.
|
|
|
|
Does not add seperators.
|
|
"""
|
|
for line in sequence:
|
|
self.write(line)
|
|
|
|
def writeable(self):
|
|
return True
|
|
|
|
def __enter__(self):
|
|
"""Support for the context manager protocol.
|
|
"""
|
|
return self
|
|
|
|
def __exit__(self, exc_type, exc_val, exc_tb):
|
|
"""Support for the context manager protocol.
|
|
|
|
Close the file and allow exceptions to propagate.
|
|
"""
|
|
self.close()
|
|
|
|
# propagate exceptions
|
|
return False
|
|
|
|
|
|
class GridOut(object):
|
|
"""Class to read data out of GridFS.
|
|
"""
|
|
def __init__(self, root_collection, file_id=None, file_document=None,
|
|
session=None):
|
|
"""Read a file from GridFS
|
|
|
|
Application developers should generally not need to
|
|
instantiate this class directly - instead see the methods
|
|
provided by :class:`~gridfs.GridFS`.
|
|
|
|
Either `file_id` or `file_document` must be specified,
|
|
`file_document` will be given priority if present. Raises
|
|
:class:`TypeError` if `root_collection` is not an instance of
|
|
:class:`~pymongo.collection.Collection`.
|
|
|
|
:Parameters:
|
|
- `root_collection`: root collection to read from
|
|
- `file_id` (optional): value of ``"_id"`` for the file to read
|
|
- `file_document` (optional): file document from
|
|
`root_collection.files`
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession` to use for all
|
|
commands
|
|
|
|
.. versionchanged:: 3.8
|
|
For better performance and to better follow the GridFS spec,
|
|
:class:`GridOut` now uses a single cursor to read all the chunks in
|
|
the file.
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
|
|
.. versionchanged:: 3.0
|
|
Creating a GridOut does not immediately retrieve the file metadata
|
|
from the server. Metadata is fetched when first needed.
|
|
"""
|
|
if not isinstance(root_collection, Collection):
|
|
raise TypeError("root_collection must be an "
|
|
"instance of Collection")
|
|
|
|
root_collection = _clear_entity_type_registry(root_collection)
|
|
|
|
self.__chunks = root_collection.chunks
|
|
self.__files = root_collection.files
|
|
self.__file_id = file_id
|
|
self.__buffer = EMPTY
|
|
self.__chunk_iter = None
|
|
self.__position = 0
|
|
self._file = file_document
|
|
self._session = session
|
|
|
|
_id = _grid_out_property("_id", "The ``'_id'`` value for this file.")
|
|
filename = _grid_out_property("filename", "Name of this file.")
|
|
name = _grid_out_property("filename", "Alias for `filename`.")
|
|
content_type = _grid_out_property("contentType", "Mime-type for this file.")
|
|
length = _grid_out_property("length", "Length (in bytes) of this file.")
|
|
chunk_size = _grid_out_property("chunkSize", "Chunk size for this file.")
|
|
upload_date = _grid_out_property("uploadDate",
|
|
"Date that this file was first uploaded.")
|
|
aliases = _grid_out_property("aliases", "List of aliases for this file.")
|
|
metadata = _grid_out_property("metadata", "Metadata attached to this file.")
|
|
md5 = _grid_out_property("md5", "MD5 of the contents of this file "
|
|
"if an md5 sum was created.")
|
|
|
|
def _ensure_file(self):
|
|
if not self._file:
|
|
self._file = self.__files.find_one({"_id": self.__file_id},
|
|
session=self._session)
|
|
if not self._file:
|
|
raise NoFile("no file in gridfs collection %r with _id %r" %
|
|
(self.__files, self.__file_id))
|
|
|
|
def __getattr__(self, name):
|
|
self._ensure_file()
|
|
if name in self._file:
|
|
return self._file[name]
|
|
raise AttributeError("GridOut object has no attribute '%s'" % name)
|
|
|
|
def readable(self):
|
|
return True
|
|
|
|
def readchunk(self):
|
|
"""Reads a chunk at a time. If the current position is within a
|
|
chunk the remainder of the chunk is returned.
|
|
"""
|
|
received = len(self.__buffer)
|
|
chunk_data = EMPTY
|
|
chunk_size = int(self.chunk_size)
|
|
|
|
if received > 0:
|
|
chunk_data = self.__buffer
|
|
elif self.__position < int(self.length):
|
|
chunk_number = int((received + self.__position) / chunk_size)
|
|
if self.__chunk_iter is None:
|
|
self.__chunk_iter = _GridOutChunkIterator(
|
|
self, self.__chunks, self._session, chunk_number)
|
|
|
|
chunk = self.__chunk_iter.next()
|
|
chunk_data = chunk["data"][self.__position % chunk_size:]
|
|
|
|
if not chunk_data:
|
|
raise CorruptGridFile("truncated chunk")
|
|
|
|
self.__position += len(chunk_data)
|
|
self.__buffer = EMPTY
|
|
return chunk_data
|
|
|
|
def read(self, size=-1):
|
|
"""Read at most `size` bytes from the file (less if there
|
|
isn't enough data).
|
|
|
|
The bytes are returned as an instance of :class:`str` (:class:`bytes`
|
|
in python 3). If `size` is negative or omitted all data is read.
|
|
|
|
:Parameters:
|
|
- `size` (optional): the number of bytes to read
|
|
|
|
.. versionchanged:: 3.8
|
|
This method now only checks for extra chunks after reading the
|
|
entire file. Previously, this method would check for extra chunks
|
|
on every call.
|
|
"""
|
|
self._ensure_file()
|
|
|
|
remainder = int(self.length) - self.__position
|
|
if size < 0 or size > remainder:
|
|
size = remainder
|
|
|
|
if size == 0:
|
|
return EMPTY
|
|
|
|
received = 0
|
|
data = StringIO()
|
|
while received < size:
|
|
chunk_data = self.readchunk()
|
|
received += len(chunk_data)
|
|
data.write(chunk_data)
|
|
|
|
# Detect extra chunks after reading the entire file.
|
|
if size == remainder and self.__chunk_iter:
|
|
try:
|
|
self.__chunk_iter.next()
|
|
except StopIteration:
|
|
pass
|
|
|
|
self.__position -= received - size
|
|
|
|
# Return 'size' bytes and store the rest.
|
|
data.seek(size)
|
|
self.__buffer = data.read()
|
|
data.seek(0)
|
|
return data.read(size)
|
|
|
|
def readline(self, size=-1):
|
|
"""Read one line or up to `size` bytes from the file.
|
|
|
|
:Parameters:
|
|
- `size` (optional): the maximum number of bytes to read
|
|
"""
|
|
remainder = int(self.length) - self.__position
|
|
if size < 0 or size > remainder:
|
|
size = remainder
|
|
|
|
if size == 0:
|
|
return EMPTY
|
|
|
|
received = 0
|
|
data = StringIO()
|
|
while received < size:
|
|
chunk_data = self.readchunk()
|
|
pos = chunk_data.find(NEWLN, 0, size)
|
|
if pos != -1:
|
|
size = received + pos + 1
|
|
|
|
received += len(chunk_data)
|
|
data.write(chunk_data)
|
|
if pos != -1:
|
|
break
|
|
|
|
self.__position -= received - size
|
|
|
|
# Return 'size' bytes and store the rest.
|
|
data.seek(size)
|
|
self.__buffer = data.read()
|
|
data.seek(0)
|
|
return data.read(size)
|
|
|
|
def tell(self):
|
|
"""Return the current position of this file.
|
|
"""
|
|
return self.__position
|
|
|
|
def seek(self, pos, whence=_SEEK_SET):
|
|
"""Set the current position of this file.
|
|
|
|
:Parameters:
|
|
- `pos`: the position (or offset if using relative
|
|
positioning) to seek to
|
|
- `whence` (optional): where to seek
|
|
from. :attr:`os.SEEK_SET` (``0``) for absolute file
|
|
positioning, :attr:`os.SEEK_CUR` (``1``) to seek relative
|
|
to the current position, :attr:`os.SEEK_END` (``2``) to
|
|
seek relative to the file's end.
|
|
"""
|
|
if whence == _SEEK_SET:
|
|
new_pos = pos
|
|
elif whence == _SEEK_CUR:
|
|
new_pos = self.__position + pos
|
|
elif whence == _SEEK_END:
|
|
new_pos = int(self.length) + pos
|
|
else:
|
|
raise IOError(22, "Invalid value for `whence`")
|
|
|
|
if new_pos < 0:
|
|
raise IOError(22, "Invalid value for `pos` - must be positive")
|
|
|
|
# Optimization, continue using the same buffer and chunk iterator.
|
|
if new_pos == self.__position:
|
|
return
|
|
|
|
self.__position = new_pos
|
|
self.__buffer = EMPTY
|
|
if self.__chunk_iter:
|
|
self.__chunk_iter.close()
|
|
self.__chunk_iter = None
|
|
|
|
def seekable(self):
|
|
return True
|
|
|
|
def __iter__(self):
|
|
"""Return an iterator over all of this file's data.
|
|
|
|
The iterator will return chunk-sized instances of
|
|
:class:`str` (:class:`bytes` in python 3). This can be
|
|
useful when serving files using a webserver that handles
|
|
such an iterator efficiently.
|
|
|
|
.. note::
|
|
This is different from :py:class:`io.IOBase` which iterates over
|
|
*lines* in the file. Use :meth:`GridOut.readline` to read line by
|
|
line instead of chunk by chunk.
|
|
|
|
.. versionchanged:: 3.8
|
|
The iterator now raises :class:`CorruptGridFile` when encountering
|
|
any truncated, missing, or extra chunk in a file. The previous
|
|
behavior was to only raise :class:`CorruptGridFile` on a missing
|
|
chunk.
|
|
"""
|
|
return GridOutIterator(self, self.__chunks, self._session)
|
|
|
|
def close(self):
|
|
"""Make GridOut more generically file-like."""
|
|
if self.__chunk_iter:
|
|
self.__chunk_iter.close()
|
|
self.__chunk_iter = None
|
|
|
|
def write(self, value):
|
|
raise io.UnsupportedOperation('write')
|
|
|
|
def __enter__(self):
|
|
"""Makes it possible to use :class:`GridOut` files
|
|
with the context manager protocol.
|
|
"""
|
|
return self
|
|
|
|
def __exit__(self, exc_type, exc_val, exc_tb):
|
|
"""Makes it possible to use :class:`GridOut` files
|
|
with the context manager protocol.
|
|
"""
|
|
self.close()
|
|
return False
|
|
|
|
|
|
class _GridOutChunkIterator(object):
|
|
"""Iterates over a file's chunks using a single cursor.
|
|
|
|
Raises CorruptGridFile when encountering any truncated, missing, or extra
|
|
chunk in a file.
|
|
"""
|
|
def __init__(self, grid_out, chunks, session, next_chunk):
|
|
self._id = grid_out._id
|
|
self._chunk_size = int(grid_out.chunk_size)
|
|
self._length = int(grid_out.length)
|
|
self._chunks = chunks
|
|
self._session = session
|
|
self._next_chunk = next_chunk
|
|
self._num_chunks = math.ceil(float(self._length) / self._chunk_size)
|
|
self._cursor = None
|
|
|
|
def expected_chunk_length(self, chunk_n):
|
|
if chunk_n < self._num_chunks - 1:
|
|
return self._chunk_size
|
|
return self._length - (self._chunk_size * (self._num_chunks - 1))
|
|
|
|
def __iter__(self):
|
|
return self
|
|
|
|
def _create_cursor(self):
|
|
filter = {"files_id": self._id}
|
|
if self._next_chunk > 0:
|
|
filter["n"] = {"$gte": self._next_chunk}
|
|
self._cursor = self._chunks.find(filter, sort=[("n", 1)],
|
|
session=self._session)
|
|
|
|
def _next_with_retry(self):
|
|
"""Return the next chunk and retry once on CursorNotFound.
|
|
|
|
We retry on CursorNotFound to maintain backwards compatibility in
|
|
cases where two calls to read occur more than 10 minutes apart (the
|
|
server's default cursor timeout).
|
|
"""
|
|
if self._cursor is None:
|
|
self._create_cursor()
|
|
|
|
try:
|
|
return self._cursor.next()
|
|
except CursorNotFound:
|
|
self._cursor.close()
|
|
self._create_cursor()
|
|
return self._cursor.next()
|
|
|
|
def next(self):
|
|
try:
|
|
chunk = self._next_with_retry()
|
|
except StopIteration:
|
|
if self._next_chunk >= self._num_chunks:
|
|
raise
|
|
raise CorruptGridFile("no chunk #%d" % self._next_chunk)
|
|
|
|
if chunk["n"] != self._next_chunk:
|
|
self.close()
|
|
raise CorruptGridFile(
|
|
"Missing chunk: expected chunk #%d but found "
|
|
"chunk with n=%d" % (self._next_chunk, chunk["n"]))
|
|
|
|
if chunk["n"] >= self._num_chunks:
|
|
# According to spec, ignore extra chunks if they are empty.
|
|
if len(chunk["data"]):
|
|
self.close()
|
|
raise CorruptGridFile(
|
|
"Extra chunk found: expected %d chunks but found "
|
|
"chunk with n=%d" % (self._num_chunks, chunk["n"]))
|
|
|
|
expected_length = self.expected_chunk_length(chunk["n"])
|
|
if len(chunk["data"]) != expected_length:
|
|
self.close()
|
|
raise CorruptGridFile(
|
|
"truncated chunk #%d: expected chunk length to be %d but "
|
|
"found chunk with length %d" % (
|
|
chunk["n"], expected_length, len(chunk["data"])))
|
|
|
|
self._next_chunk += 1
|
|
return chunk
|
|
|
|
__next__ = next
|
|
|
|
def close(self):
|
|
if self._cursor:
|
|
self._cursor.close()
|
|
self._cursor = None
|
|
|
|
|
|
class GridOutIterator(object):
|
|
def __init__(self, grid_out, chunks, session):
|
|
self.__chunk_iter = _GridOutChunkIterator(grid_out, chunks, session, 0)
|
|
|
|
def __iter__(self):
|
|
return self
|
|
|
|
def next(self):
|
|
chunk = self.__chunk_iter.next()
|
|
return bytes(chunk["data"])
|
|
|
|
__next__ = next
|
|
|
|
|
|
class GridOutCursor(Cursor):
|
|
"""A cursor / iterator for returning GridOut objects as the result
|
|
of an arbitrary query against the GridFS files collection.
|
|
"""
|
|
def __init__(self, collection, filter=None, skip=0, limit=0,
|
|
no_cursor_timeout=False, sort=None, batch_size=0,
|
|
session=None):
|
|
"""Create a new cursor, similar to the normal
|
|
:class:`~pymongo.cursor.Cursor`.
|
|
|
|
Should not be called directly by application developers - see
|
|
the :class:`~gridfs.GridFS` method :meth:`~gridfs.GridFS.find` instead.
|
|
|
|
.. versionadded 2.7
|
|
|
|
.. mongodoc:: cursors
|
|
"""
|
|
collection = _clear_entity_type_registry(collection)
|
|
|
|
# Hold on to the base "fs" collection to create GridOut objects later.
|
|
self.__root_collection = collection
|
|
|
|
super(GridOutCursor, self).__init__(
|
|
collection.files, filter, skip=skip, limit=limit,
|
|
no_cursor_timeout=no_cursor_timeout, sort=sort,
|
|
batch_size=batch_size, session=session)
|
|
|
|
def next(self):
|
|
"""Get next GridOut object from cursor.
|
|
"""
|
|
# Work around "super is not iterable" issue in Python 3.x
|
|
next_file = super(GridOutCursor, self).next()
|
|
return GridOut(self.__root_collection, file_document=next_file,
|
|
session=self.session)
|
|
|
|
__next__ = next
|
|
|
|
def add_option(self, *args, **kwargs):
|
|
raise NotImplementedError("Method does not exist for GridOutCursor")
|
|
|
|
def remove_option(self, *args, **kwargs):
|
|
raise NotImplementedError("Method does not exist for GridOutCursor")
|
|
|
|
def _clone_base(self, session):
|
|
"""Creates an empty GridOutCursor for information to be copied into.
|
|
"""
|
|
return GridOutCursor(self.__root_collection, session=session)
|
|
|