StackGenVis: Alignment of Data, Algorithms, and Models for Stacking Ensemble Learning Using Performance Metrics
https://doi.org/10.1109/TVCG.2020.3030352
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930 lines
36 KiB
930 lines
36 KiB
# Copyright 2009-present MongoDB, Inc.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""GridFS is a specification for storing large objects in Mongo.
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The :mod:`gridfs` package is an implementation of GridFS on top of
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:mod:`pymongo`, exposing a file-like interface.
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.. mongodoc:: gridfs
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"""
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from bson.py3compat import abc
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from gridfs.errors import NoFile
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from gridfs.grid_file import (GridIn,
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GridOut,
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GridOutCursor,
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DEFAULT_CHUNK_SIZE,
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_clear_entity_type_registry)
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from pymongo import (ASCENDING,
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DESCENDING)
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from pymongo.common import UNAUTHORIZED_CODES, validate_string
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from pymongo.database import Database
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from pymongo.errors import ConfigurationError, OperationFailure
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class GridFS(object):
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"""An instance of GridFS on top of a single Database.
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"""
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def __init__(self, database, collection="fs", disable_md5=False):
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"""Create a new instance of :class:`GridFS`.
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Raises :class:`TypeError` if `database` is not an instance of
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:class:`~pymongo.database.Database`.
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:Parameters:
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- `database`: database to use
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- `collection` (optional): root collection to use
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- `disable_md5` (optional): When True, MD5 checksums will not be
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computed for uploaded files. Useful in environments where MD5
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cannot be used for regulatory or other reasons. Defaults to False.
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.. versionchanged:: 3.1
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Indexes are only ensured on the first write to the DB.
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.. versionchanged:: 3.0
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`database` must use an acknowledged
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:attr:`~pymongo.database.Database.write_concern`
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.. mongodoc:: gridfs
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"""
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if not isinstance(database, Database):
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raise TypeError("database must be an instance of Database")
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database = _clear_entity_type_registry(database)
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if not database.write_concern.acknowledged:
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raise ConfigurationError('database must use '
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'acknowledged write_concern')
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self.__database = database
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self.__collection = database[collection]
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self.__files = self.__collection.files
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self.__chunks = self.__collection.chunks
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self.__disable_md5 = disable_md5
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def new_file(self, **kwargs):
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"""Create a new file in GridFS.
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Returns a new :class:`~gridfs.grid_file.GridIn` instance to
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which data can be written. Any keyword arguments will be
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passed through to :meth:`~gridfs.grid_file.GridIn`.
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If the ``"_id"`` of the file is manually specified, it must
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not already exist in GridFS. Otherwise
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:class:`~gridfs.errors.FileExists` is raised.
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:Parameters:
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- `**kwargs` (optional): keyword arguments for file creation
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"""
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# No need for __ensure_index_files_id() here; GridIn ensures
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# the (files_id, n) index when needed.
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return GridIn(
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self.__collection, disable_md5=self.__disable_md5, **kwargs)
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def put(self, data, **kwargs):
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"""Put data in GridFS as a new file.
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Equivalent to doing::
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try:
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f = new_file(**kwargs)
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f.write(data)
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finally:
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f.close()
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`data` can be either an instance of :class:`str` (:class:`bytes`
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in python 3) or a file-like object providing a :meth:`read` method.
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If an `encoding` keyword argument is passed, `data` can also be a
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:class:`unicode` (:class:`str` in python 3) instance, which will
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be encoded as `encoding` before being written. Any keyword arguments
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will be passed through to the created file - see
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:meth:`~gridfs.grid_file.GridIn` for possible arguments. Returns the
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``"_id"`` of the created file.
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If the ``"_id"`` of the file is manually specified, it must
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not already exist in GridFS. Otherwise
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:class:`~gridfs.errors.FileExists` is raised.
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:Parameters:
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- `data`: data to be written as a file.
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- `**kwargs` (optional): keyword arguments for file creation
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.. versionchanged:: 3.0
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w=0 writes to GridFS are now prohibited.
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"""
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grid_file = GridIn(
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self.__collection, disable_md5=self.__disable_md5, **kwargs)
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try:
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grid_file.write(data)
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finally:
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grid_file.close()
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return grid_file._id
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def get(self, file_id, session=None):
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"""Get a file from GridFS by ``"_id"``.
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Returns an instance of :class:`~gridfs.grid_file.GridOut`,
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which provides a file-like interface for reading.
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:Parameters:
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- `file_id`: ``"_id"`` of the file to get
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- `session` (optional): a
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:class:`~pymongo.client_session.ClientSession`
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.. versionchanged:: 3.6
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Added ``session`` parameter.
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"""
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gout = GridOut(self.__collection, file_id, session=session)
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# Raise NoFile now, instead of on first attribute access.
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gout._ensure_file()
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return gout
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def get_version(self, filename=None, version=-1, session=None, **kwargs):
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"""Get a file from GridFS by ``"filename"`` or metadata fields.
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Returns a version of the file in GridFS whose filename matches
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`filename` and whose metadata fields match the supplied keyword
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arguments, as an instance of :class:`~gridfs.grid_file.GridOut`.
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Version numbering is a convenience atop the GridFS API provided
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by MongoDB. If more than one file matches the query (either by
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`filename` alone, by metadata fields, or by a combination of
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both), then version ``-1`` will be the most recently uploaded
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matching file, ``-2`` the second most recently
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uploaded, etc. Version ``0`` will be the first version
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uploaded, ``1`` the second version, etc. So if three versions
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have been uploaded, then version ``0`` is the same as version
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``-3``, version ``1`` is the same as version ``-2``, and
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version ``2`` is the same as version ``-1``.
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Raises :class:`~gridfs.errors.NoFile` if no such version of
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that file exists.
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:Parameters:
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- `filename`: ``"filename"`` of the file to get, or `None`
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- `version` (optional): version of the file to get (defaults
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to -1, the most recent version uploaded)
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- `session` (optional): a
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:class:`~pymongo.client_session.ClientSession`
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- `**kwargs` (optional): find files by custom metadata.
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.. versionchanged:: 3.6
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Added ``session`` parameter.
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.. versionchanged:: 3.1
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``get_version`` no longer ensures indexes.
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"""
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query = kwargs
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if filename is not None:
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query["filename"] = filename
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cursor = self.__files.find(query, session=session)
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if version < 0:
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skip = abs(version) - 1
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cursor.limit(-1).skip(skip).sort("uploadDate", DESCENDING)
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else:
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cursor.limit(-1).skip(version).sort("uploadDate", ASCENDING)
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try:
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doc = next(cursor)
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return GridOut(
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self.__collection, file_document=doc, session=session)
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except StopIteration:
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raise NoFile("no version %d for filename %r" % (version, filename))
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def get_last_version(self, filename=None, session=None, **kwargs):
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"""Get the most recent version of a file in GridFS by ``"filename"``
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or metadata fields.
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Equivalent to calling :meth:`get_version` with the default
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`version` (``-1``).
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:Parameters:
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- `filename`: ``"filename"`` of the file to get, or `None`
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- `session` (optional): a
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:class:`~pymongo.client_session.ClientSession`
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- `**kwargs` (optional): find files by custom metadata.
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.. versionchanged:: 3.6
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Added ``session`` parameter.
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"""
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return self.get_version(filename=filename, session=session, **kwargs)
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# TODO add optional safe mode for chunk removal?
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def delete(self, file_id, session=None):
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"""Delete a file from GridFS by ``"_id"``.
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Deletes all data belonging to the file with ``"_id"``:
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`file_id`.
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.. warning:: Any processes/threads reading from the file while
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this method is executing will likely see an invalid/corrupt
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file. Care should be taken to avoid concurrent reads to a file
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while it is being deleted.
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.. note:: Deletes of non-existent files are considered successful
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since the end result is the same: no file with that _id remains.
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:Parameters:
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- `file_id`: ``"_id"`` of the file to delete
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- `session` (optional): a
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:class:`~pymongo.client_session.ClientSession`
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.. versionchanged:: 3.6
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Added ``session`` parameter.
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.. versionchanged:: 3.1
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``delete`` no longer ensures indexes.
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"""
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self.__files.delete_one({"_id": file_id}, session=session)
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self.__chunks.delete_many({"files_id": file_id}, session=session)
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def list(self, session=None):
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"""List the names of all files stored in this instance of
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:class:`GridFS`.
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:Parameters:
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- `session` (optional): a
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:class:`~pymongo.client_session.ClientSession`
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.. versionchanged:: 3.6
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Added ``session`` parameter.
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.. versionchanged:: 3.1
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``list`` no longer ensures indexes.
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"""
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# With an index, distinct includes documents with no filename
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# as None.
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return [
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name for name in self.__files.distinct("filename", session=session)
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if name is not None]
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def find_one(self, filter=None, session=None, *args, **kwargs):
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"""Get a single file from gridfs.
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All arguments to :meth:`find` are also valid arguments for
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:meth:`find_one`, although any `limit` argument will be
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ignored. Returns a single :class:`~gridfs.grid_file.GridOut`,
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or ``None`` if no matching file is found. For example::
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file = fs.find_one({"filename": "lisa.txt"})
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:Parameters:
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- `filter` (optional): a dictionary specifying
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the query to be performing OR any other type to be used as
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the value for a query for ``"_id"`` in the file collection.
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- `*args` (optional): any additional positional arguments are
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the same as the arguments to :meth:`find`.
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- `session` (optional): a
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:class:`~pymongo.client_session.ClientSession`
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- `**kwargs` (optional): any additional keyword arguments
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are the same as the arguments to :meth:`find`.
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.. versionchanged:: 3.6
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Added ``session`` parameter.
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"""
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if filter is not None and not isinstance(filter, abc.Mapping):
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filter = {"_id": filter}
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for f in self.find(filter, *args, session=session, **kwargs):
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return f
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return None
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def find(self, *args, **kwargs):
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"""Query GridFS for files.
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Returns a cursor that iterates across files matching
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arbitrary queries on the files collection. Can be combined
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with other modifiers for additional control. For example::
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for grid_out in fs.find({"filename": "lisa.txt"},
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no_cursor_timeout=True):
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data = grid_out.read()
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would iterate through all versions of "lisa.txt" stored in GridFS.
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Note that setting no_cursor_timeout to True may be important to
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prevent the cursor from timing out during long multi-file processing
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work.
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As another example, the call::
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most_recent_three = fs.find().sort("uploadDate", -1).limit(3)
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would return a cursor to the three most recently uploaded files
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in GridFS.
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Follows a similar interface to
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:meth:`~pymongo.collection.Collection.find`
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in :class:`~pymongo.collection.Collection`.
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If a :class:`~pymongo.client_session.ClientSession` is passed to
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:meth:`find`, all returned :class:`~gridfs.grid_file.GridOut` instances
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are associated with that session.
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:Parameters:
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- `filter` (optional): a SON object specifying elements which
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must be present for a document to be included in the
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result set
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- `skip` (optional): the number of files to omit (from
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the start of the result set) when returning the results
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- `limit` (optional): the maximum number of results to
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return
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- `no_cursor_timeout` (optional): if False (the default), any
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returned cursor is closed by the server after 10 minutes of
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inactivity. If set to True, the returned cursor will never
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time out on the server. Care should be taken to ensure that
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cursors with no_cursor_timeout turned on are properly closed.
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- `sort` (optional): a list of (key, direction) pairs
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specifying the sort order for this query. See
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:meth:`~pymongo.cursor.Cursor.sort` for details.
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Raises :class:`TypeError` if any of the arguments are of
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improper type. Returns an instance of
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:class:`~gridfs.grid_file.GridOutCursor`
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corresponding to this query.
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.. versionchanged:: 3.0
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Removed the read_preference, tag_sets, and
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secondary_acceptable_latency_ms options.
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.. versionadded:: 2.7
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.. mongodoc:: find
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"""
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return GridOutCursor(self.__collection, *args, **kwargs)
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def exists(self, document_or_id=None, session=None, **kwargs):
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"""Check if a file exists in this instance of :class:`GridFS`.
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The file to check for can be specified by the value of its
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``_id`` key, or by passing in a query document. A query
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document can be passed in as dictionary, or by using keyword
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arguments. Thus, the following three calls are equivalent:
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>>> fs.exists(file_id)
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>>> fs.exists({"_id": file_id})
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>>> fs.exists(_id=file_id)
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As are the following two calls:
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>>> fs.exists({"filename": "mike.txt"})
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>>> fs.exists(filename="mike.txt")
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And the following two:
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>>> fs.exists({"foo": {"$gt": 12}})
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>>> fs.exists(foo={"$gt": 12})
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Returns ``True`` if a matching file exists, ``False``
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otherwise. Calls to :meth:`exists` will not automatically
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create appropriate indexes; application developers should be
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sure to create indexes if needed and as appropriate.
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:Parameters:
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- `document_or_id` (optional): query document, or _id of the
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document to check for
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- `session` (optional): a
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:class:`~pymongo.client_session.ClientSession`
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- `**kwargs` (optional): keyword arguments are used as a
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query document, if they're present.
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.. versionchanged:: 3.6
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Added ``session`` parameter.
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"""
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if kwargs:
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f = self.__files.find_one(kwargs, ["_id"], session=session)
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else:
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f = self.__files.find_one(document_or_id, ["_id"], session=session)
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return f is not None
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class GridFSBucket(object):
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"""An instance of GridFS on top of a single Database."""
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def __init__(self, db, bucket_name="fs",
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chunk_size_bytes=DEFAULT_CHUNK_SIZE, write_concern=None,
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read_preference=None, disable_md5=False):
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"""Create a new instance of :class:`GridFSBucket`.
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Raises :exc:`TypeError` if `database` is not an instance of
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:class:`~pymongo.database.Database`.
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Raises :exc:`~pymongo.errors.ConfigurationError` if `write_concern`
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is not acknowledged.
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:Parameters:
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- `database`: database to use.
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- `bucket_name` (optional): The name of the bucket. Defaults to 'fs'.
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- `chunk_size_bytes` (optional): The chunk size in bytes. Defaults
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to 255KB.
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- `write_concern` (optional): The
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:class:`~pymongo.write_concern.WriteConcern` to use. If ``None``
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(the default) db.write_concern is used.
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- `read_preference` (optional): The read preference to use. If
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``None`` (the default) db.read_preference is used.
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- `disable_md5` (optional): When True, MD5 checksums will not be
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computed for uploaded files. Useful in environments where MD5
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cannot be used for regulatory or other reasons. Defaults to False.
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.. versionadded:: 3.1
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.. mongodoc:: gridfs
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"""
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if not isinstance(db, Database):
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raise TypeError("database must be an instance of Database")
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db = _clear_entity_type_registry(db)
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wtc = write_concern if write_concern is not None else db.write_concern
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if not wtc.acknowledged:
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raise ConfigurationError('write concern must be acknowledged')
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self._db = db
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self._bucket_name = bucket_name
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self._collection = db[bucket_name]
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self._disable_md5 = disable_md5
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self._chunks = self._collection.chunks.with_options(
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write_concern=write_concern,
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read_preference=read_preference)
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self._files = self._collection.files.with_options(
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write_concern=write_concern,
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read_preference=read_preference)
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self._chunk_size_bytes = chunk_size_bytes
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def open_upload_stream(self, filename, chunk_size_bytes=None,
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metadata=None, session=None):
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"""Opens a Stream that the application can write the contents of the
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file to.
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The user must specify the filename, and can choose to add any
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additional information in the metadata field of the file document or
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modify the chunk size.
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For example::
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my_db = MongoClient().test
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fs = GridFSBucket(my_db)
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grid_in = fs.open_upload_stream(
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"test_file", chunk_size_bytes=4,
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metadata={"contentType": "text/plain"})
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grid_in.write("data I want to store!")
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grid_in.close() # uploaded on close
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Returns an instance of :class:`~gridfs.grid_file.GridIn`.
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Raises :exc:`~gridfs.errors.NoFile` if no such version of
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that file exists.
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Raises :exc:`~ValueError` if `filename` is not a string.
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:Parameters:
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- `filename`: The name of the file to upload.
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- `chunk_size_bytes` (options): The number of bytes per chunk of this
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file. Defaults to the chunk_size_bytes in :class:`GridFSBucket`.
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- `metadata` (optional): User data for the 'metadata' field of the
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files collection document. If not provided the metadata field will
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be omitted from the files collection document.
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- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
validate_string("filename", filename)
|
|
|
|
opts = {"filename": filename,
|
|
"chunk_size": (chunk_size_bytes if chunk_size_bytes
|
|
is not None else self._chunk_size_bytes)}
|
|
if metadata is not None:
|
|
opts["metadata"] = metadata
|
|
|
|
return GridIn(
|
|
self._collection,
|
|
session=session,
|
|
disable_md5=self._disable_md5,
|
|
**opts)
|
|
|
|
def open_upload_stream_with_id(
|
|
self, file_id, filename, chunk_size_bytes=None, metadata=None,
|
|
session=None):
|
|
"""Opens a Stream that the application can write the contents of the
|
|
file to.
|
|
|
|
The user must specify the file id and filename, and can choose to add
|
|
any additional information in the metadata field of the file document
|
|
or modify the chunk size.
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
grid_in = fs.open_upload_stream_with_id(
|
|
ObjectId(),
|
|
"test_file",
|
|
chunk_size_bytes=4,
|
|
metadata={"contentType": "text/plain"})
|
|
grid_in.write("data I want to store!")
|
|
grid_in.close() # uploaded on close
|
|
|
|
Returns an instance of :class:`~gridfs.grid_file.GridIn`.
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no such version of
|
|
that file exists.
|
|
Raises :exc:`~ValueError` if `filename` is not a string.
|
|
|
|
:Parameters:
|
|
- `file_id`: The id to use for this file. The id must not have
|
|
already been used for another file.
|
|
- `filename`: The name of the file to upload.
|
|
- `chunk_size_bytes` (options): The number of bytes per chunk of this
|
|
file. Defaults to the chunk_size_bytes in :class:`GridFSBucket`.
|
|
- `metadata` (optional): User data for the 'metadata' field of the
|
|
files collection document. If not provided the metadata field will
|
|
be omitted from the files collection document.
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
validate_string("filename", filename)
|
|
|
|
opts = {"_id": file_id,
|
|
"filename": filename,
|
|
"chunk_size": (chunk_size_bytes if chunk_size_bytes
|
|
is not None else self._chunk_size_bytes)}
|
|
if metadata is not None:
|
|
opts["metadata"] = metadata
|
|
|
|
return GridIn(
|
|
self._collection,
|
|
session=session,
|
|
disable_md5=self._disable_md5,
|
|
**opts)
|
|
|
|
def upload_from_stream(self, filename, source, chunk_size_bytes=None,
|
|
metadata=None, session=None):
|
|
"""Uploads a user file to a GridFS bucket.
|
|
|
|
Reads the contents of the user file from `source` and uploads
|
|
it to the file `filename`. Source can be a string or file-like object.
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
file_id = fs.upload_from_stream(
|
|
"test_file",
|
|
"data I want to store!",
|
|
chunk_size_bytes=4,
|
|
metadata={"contentType": "text/plain"})
|
|
|
|
Returns the _id of the uploaded file.
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no such version of
|
|
that file exists.
|
|
Raises :exc:`~ValueError` if `filename` is not a string.
|
|
|
|
:Parameters:
|
|
- `filename`: The name of the file to upload.
|
|
- `source`: The source stream of the content to be uploaded. Must be
|
|
a file-like object that implements :meth:`read` or a string.
|
|
- `chunk_size_bytes` (options): The number of bytes per chunk of this
|
|
file. Defaults to the chunk_size_bytes of :class:`GridFSBucket`.
|
|
- `metadata` (optional): User data for the 'metadata' field of the
|
|
files collection document. If not provided the metadata field will
|
|
be omitted from the files collection document.
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
with self.open_upload_stream(
|
|
filename, chunk_size_bytes, metadata, session=session) as gin:
|
|
gin.write(source)
|
|
|
|
return gin._id
|
|
|
|
def upload_from_stream_with_id(self, file_id, filename, source,
|
|
chunk_size_bytes=None, metadata=None,
|
|
session=None):
|
|
"""Uploads a user file to a GridFS bucket with a custom file id.
|
|
|
|
Reads the contents of the user file from `source` and uploads
|
|
it to the file `filename`. Source can be a string or file-like object.
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
file_id = fs.upload_from_stream(
|
|
ObjectId(),
|
|
"test_file",
|
|
"data I want to store!",
|
|
chunk_size_bytes=4,
|
|
metadata={"contentType": "text/plain"})
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no such version of
|
|
that file exists.
|
|
Raises :exc:`~ValueError` if `filename` is not a string.
|
|
|
|
:Parameters:
|
|
- `file_id`: The id to use for this file. The id must not have
|
|
already been used for another file.
|
|
- `filename`: The name of the file to upload.
|
|
- `source`: The source stream of the content to be uploaded. Must be
|
|
a file-like object that implements :meth:`read` or a string.
|
|
- `chunk_size_bytes` (options): The number of bytes per chunk of this
|
|
file. Defaults to the chunk_size_bytes of :class:`GridFSBucket`.
|
|
- `metadata` (optional): User data for the 'metadata' field of the
|
|
files collection document. If not provided the metadata field will
|
|
be omitted from the files collection document.
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
with self.open_upload_stream_with_id(
|
|
file_id, filename, chunk_size_bytes, metadata,
|
|
session=session) as gin:
|
|
gin.write(source)
|
|
|
|
def open_download_stream(self, file_id, session=None):
|
|
"""Opens a Stream from which the application can read the contents of
|
|
the stored file specified by file_id.
|
|
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
# get _id of file to read.
|
|
file_id = fs.upload_from_stream("test_file", "data I want to store!")
|
|
grid_out = fs.open_download_stream(file_id)
|
|
contents = grid_out.read()
|
|
|
|
Returns an instance of :class:`~gridfs.grid_file.GridOut`.
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no file with file_id exists.
|
|
|
|
:Parameters:
|
|
- `file_id`: The _id of the file to be downloaded.
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
gout = GridOut(self._collection, file_id, session=session)
|
|
|
|
# Raise NoFile now, instead of on first attribute access.
|
|
gout._ensure_file()
|
|
return gout
|
|
|
|
def download_to_stream(self, file_id, destination, session=None):
|
|
"""Downloads the contents of the stored file specified by file_id and
|
|
writes the contents to `destination`.
|
|
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
# Get _id of file to read
|
|
file_id = fs.upload_from_stream("test_file", "data I want to store!")
|
|
# Get file to write to
|
|
file = open('myfile','wb+')
|
|
fs.download_to_stream(file_id, file)
|
|
file.seek(0)
|
|
contents = file.read()
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no file with file_id exists.
|
|
|
|
:Parameters:
|
|
- `file_id`: The _id of the file to be downloaded.
|
|
- `destination`: a file-like object implementing :meth:`write`.
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
with self.open_download_stream(file_id, session=session) as gout:
|
|
for chunk in gout:
|
|
destination.write(chunk)
|
|
|
|
def delete(self, file_id, session=None):
|
|
"""Given an file_id, delete this stored file's files collection document
|
|
and associated chunks from a GridFS bucket.
|
|
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
# Get _id of file to delete
|
|
file_id = fs.upload_from_stream("test_file", "data I want to store!")
|
|
fs.delete(file_id)
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no file with file_id exists.
|
|
|
|
:Parameters:
|
|
- `file_id`: The _id of the file to be deleted.
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
res = self._files.delete_one({"_id": file_id}, session=session)
|
|
self._chunks.delete_many({"files_id": file_id}, session=session)
|
|
if not res.deleted_count:
|
|
raise NoFile(
|
|
"no file could be deleted because none matched %s" % file_id)
|
|
|
|
def find(self, *args, **kwargs):
|
|
"""Find and return the files collection documents that match ``filter``
|
|
|
|
Returns a cursor that iterates across files matching
|
|
arbitrary queries on the files collection. Can be combined
|
|
with other modifiers for additional control.
|
|
|
|
For example::
|
|
|
|
for grid_data in fs.find({"filename": "lisa.txt"},
|
|
no_cursor_timeout=True):
|
|
data = grid_data.read()
|
|
|
|
would iterate through all versions of "lisa.txt" stored in GridFS.
|
|
Note that setting no_cursor_timeout to True may be important to
|
|
prevent the cursor from timing out during long multi-file processing
|
|
work.
|
|
|
|
As another example, the call::
|
|
|
|
most_recent_three = fs.find().sort("uploadDate", -1).limit(3)
|
|
|
|
would return a cursor to the three most recently uploaded files
|
|
in GridFS.
|
|
|
|
Follows a similar interface to
|
|
:meth:`~pymongo.collection.Collection.find`
|
|
in :class:`~pymongo.collection.Collection`.
|
|
|
|
If a :class:`~pymongo.client_session.ClientSession` is passed to
|
|
:meth:`find`, all returned :class:`~gridfs.grid_file.GridOut` instances
|
|
are associated with that session.
|
|
|
|
:Parameters:
|
|
- `filter`: Search query.
|
|
- `batch_size` (optional): The number of documents to return per
|
|
batch.
|
|
- `limit` (optional): The maximum number of documents to return.
|
|
- `no_cursor_timeout` (optional): The server normally times out idle
|
|
cursors after an inactivity period (10 minutes) to prevent excess
|
|
memory use. Set this option to True prevent that.
|
|
- `skip` (optional): The number of documents to skip before
|
|
returning.
|
|
- `sort` (optional): The order by which to sort results. Defaults to
|
|
None.
|
|
"""
|
|
return GridOutCursor(self._collection, *args, **kwargs)
|
|
|
|
def open_download_stream_by_name(self, filename, revision=-1, session=None):
|
|
"""Opens a Stream from which the application can read the contents of
|
|
`filename` and optional `revision`.
|
|
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
grid_out = fs.open_download_stream_by_name("test_file")
|
|
contents = grid_out.read()
|
|
|
|
Returns an instance of :class:`~gridfs.grid_file.GridOut`.
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no such version of
|
|
that file exists.
|
|
|
|
Raises :exc:`~ValueError` filename is not a string.
|
|
|
|
:Parameters:
|
|
- `filename`: The name of the file to read from.
|
|
- `revision` (optional): Which revision (documents with the same
|
|
filename and different uploadDate) of the file to retrieve.
|
|
Defaults to -1 (the most recent revision).
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
:Note: Revision numbers are defined as follows:
|
|
|
|
- 0 = the original stored file
|
|
- 1 = the first revision
|
|
- 2 = the second revision
|
|
- etc...
|
|
- -2 = the second most recent revision
|
|
- -1 = the most recent revision
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
validate_string("filename", filename)
|
|
|
|
query = {"filename": filename}
|
|
|
|
cursor = self._files.find(query, session=session)
|
|
if revision < 0:
|
|
skip = abs(revision) - 1
|
|
cursor.limit(-1).skip(skip).sort("uploadDate", DESCENDING)
|
|
else:
|
|
cursor.limit(-1).skip(revision).sort("uploadDate", ASCENDING)
|
|
try:
|
|
grid_file = next(cursor)
|
|
return GridOut(
|
|
self._collection, file_document=grid_file, session=session)
|
|
except StopIteration:
|
|
raise NoFile(
|
|
"no version %d for filename %r" % (revision, filename))
|
|
|
|
def download_to_stream_by_name(self, filename, destination, revision=-1,
|
|
session=None):
|
|
"""Write the contents of `filename` (with optional `revision`) to
|
|
`destination`.
|
|
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
# Get file to write to
|
|
file = open('myfile','wb')
|
|
fs.download_to_stream_by_name("test_file", file)
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no such version of
|
|
that file exists.
|
|
|
|
Raises :exc:`~ValueError` if `filename` is not a string.
|
|
|
|
:Parameters:
|
|
- `filename`: The name of the file to read from.
|
|
- `destination`: A file-like object that implements :meth:`write`.
|
|
- `revision` (optional): Which revision (documents with the same
|
|
filename and different uploadDate) of the file to retrieve.
|
|
Defaults to -1 (the most recent revision).
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
:Note: Revision numbers are defined as follows:
|
|
|
|
- 0 = the original stored file
|
|
- 1 = the first revision
|
|
- 2 = the second revision
|
|
- etc...
|
|
- -2 = the second most recent revision
|
|
- -1 = the most recent revision
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
with self.open_download_stream_by_name(
|
|
filename, revision, session=session) as gout:
|
|
for chunk in gout:
|
|
destination.write(chunk)
|
|
|
|
def rename(self, file_id, new_filename, session=None):
|
|
"""Renames the stored file with the specified file_id.
|
|
|
|
For example::
|
|
|
|
my_db = MongoClient().test
|
|
fs = GridFSBucket(my_db)
|
|
# Get _id of file to rename
|
|
file_id = fs.upload_from_stream("test_file", "data I want to store!")
|
|
fs.rename(file_id, "new_test_name")
|
|
|
|
Raises :exc:`~gridfs.errors.NoFile` if no file with file_id exists.
|
|
|
|
:Parameters:
|
|
- `file_id`: The _id of the file to be renamed.
|
|
- `new_filename`: The new name of the file.
|
|
- `session` (optional): a
|
|
:class:`~pymongo.client_session.ClientSession`
|
|
|
|
.. versionchanged:: 3.6
|
|
Added ``session`` parameter.
|
|
"""
|
|
result = self._files.update_one({"_id": file_id},
|
|
{"$set": {"filename": new_filename}},
|
|
session=session)
|
|
if not result.matched_count:
|
|
raise NoFile("no files could be renamed %r because none "
|
|
"matched file_id %i" % (new_filename, file_id))
|
|
|