FeatureEnVi: Visual Analytics for Feature Engineering Using Stepwise Selection and Semi-Automatic Extraction Approaches
https://doi.org/10.1109/TVCG.2022.3141040
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702 lines
27 KiB
702 lines
27 KiB
# Copyright 2014-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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"""The bulk write operations interface.
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.. versionadded:: 2.7
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"""
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import copy
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from itertools import islice
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from bson.objectid import ObjectId
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from bson.raw_bson import RawBSONDocument
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from bson.son import SON
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from pymongo.client_session import _validate_session_write_concern
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from pymongo.common import (validate_is_mapping,
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validate_is_document_type,
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validate_ok_for_replace,
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validate_ok_for_update)
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from pymongo.helpers import _RETRYABLE_ERROR_CODES
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from pymongo.collation import validate_collation_or_none
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from pymongo.errors import (BulkWriteError,
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ConfigurationError,
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InvalidOperation,
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OperationFailure)
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from pymongo.message import (_INSERT, _UPDATE, _DELETE,
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_do_batched_insert,
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_do_bulk_write_command,
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_randint,
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_BulkWriteContext)
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from pymongo.read_preferences import ReadPreference
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from pymongo.write_concern import WriteConcern
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_DELETE_ALL = 0
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_DELETE_ONE = 1
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# For backwards compatibility. See MongoDB src/mongo/base/error_codes.err
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_BAD_VALUE = 2
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_UNKNOWN_ERROR = 8
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_WRITE_CONCERN_ERROR = 64
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_COMMANDS = ('insert', 'update', 'delete')
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# These string literals are used when we create fake server return
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# documents client side. We use unicode literals in python 2.x to
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# match the actual return values from the server.
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_UOP = u"op"
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class _Run(object):
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"""Represents a batch of write operations.
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"""
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def __init__(self, op_type):
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"""Initialize a new Run object.
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"""
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self.op_type = op_type
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self.index_map = []
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self.ops = []
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self.idx_offset = 0
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def index(self, idx):
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"""Get the original index of an operation in this run.
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:Parameters:
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- `idx`: The Run index that maps to the original index.
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"""
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return self.index_map[idx]
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def add(self, original_index, operation):
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"""Add an operation to this Run instance.
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:Parameters:
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- `original_index`: The original index of this operation
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within a larger bulk operation.
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- `operation`: The operation document.
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"""
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self.index_map.append(original_index)
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self.ops.append(operation)
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def _merge_command(run, full_result, offset, result):
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"""Merge a write command result into the full bulk result.
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"""
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affected = result.get("n", 0)
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if run.op_type == _INSERT:
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full_result["nInserted"] += affected
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elif run.op_type == _DELETE:
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full_result["nRemoved"] += affected
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elif run.op_type == _UPDATE:
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upserted = result.get("upserted")
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if upserted:
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n_upserted = len(upserted)
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for doc in upserted:
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doc["index"] = run.index(doc["index"] + offset)
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full_result["upserted"].extend(upserted)
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full_result["nUpserted"] += n_upserted
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full_result["nMatched"] += (affected - n_upserted)
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else:
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full_result["nMatched"] += affected
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full_result["nModified"] += result["nModified"]
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write_errors = result.get("writeErrors")
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if write_errors:
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for doc in write_errors:
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# Leave the server response intact for APM.
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replacement = doc.copy()
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idx = doc["index"] + offset
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replacement["index"] = run.index(idx)
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# Add the failed operation to the error document.
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replacement[_UOP] = run.ops[idx]
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full_result["writeErrors"].append(replacement)
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wc_error = result.get("writeConcernError")
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if wc_error:
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full_result["writeConcernErrors"].append(wc_error)
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def _raise_bulk_write_error(full_result):
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"""Raise a BulkWriteError from the full bulk api result.
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"""
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if full_result["writeErrors"]:
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full_result["writeErrors"].sort(
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key=lambda error: error["index"])
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raise BulkWriteError(full_result)
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class _Bulk(object):
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"""The private guts of the bulk write API.
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"""
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def __init__(self, collection, ordered, bypass_document_validation):
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"""Initialize a _Bulk instance.
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"""
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self.collection = collection.with_options(
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codec_options=collection.codec_options._replace(
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unicode_decode_error_handler='replace',
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document_class=dict))
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self.ordered = ordered
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self.ops = []
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self.name = "%s.%s" % (collection.database.name, collection.name)
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self.namespace = collection.database.name + '.$cmd'
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self.executed = False
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self.bypass_doc_val = bypass_document_validation
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self.uses_collation = False
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self.uses_array_filters = False
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self.is_retryable = True
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self.retrying = False
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self.started_retryable_write = False
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# Extra state so that we know where to pick up on a retry attempt.
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self.current_run = None
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def add_insert(self, document):
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"""Add an insert document to the list of ops.
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"""
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validate_is_document_type("document", document)
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# Generate ObjectId client side.
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if not (isinstance(document, RawBSONDocument) or '_id' in document):
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document['_id'] = ObjectId()
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self.ops.append((_INSERT, document))
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def add_update(self, selector, update, multi=False, upsert=False,
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collation=None, array_filters=None):
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"""Create an update document and add it to the list of ops.
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"""
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validate_ok_for_update(update)
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cmd = SON([('q', selector), ('u', update),
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('multi', multi), ('upsert', upsert)])
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collation = validate_collation_or_none(collation)
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if collation is not None:
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self.uses_collation = True
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cmd['collation'] = collation
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if array_filters is not None:
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self.uses_array_filters = True
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cmd['arrayFilters'] = array_filters
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if multi:
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# A bulk_write containing an update_many is not retryable.
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self.is_retryable = False
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self.ops.append((_UPDATE, cmd))
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def add_replace(self, selector, replacement, upsert=False,
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collation=None):
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"""Create a replace document and add it to the list of ops.
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"""
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validate_ok_for_replace(replacement)
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cmd = SON([('q', selector), ('u', replacement),
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('multi', False), ('upsert', upsert)])
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collation = validate_collation_or_none(collation)
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if collation is not None:
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self.uses_collation = True
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cmd['collation'] = collation
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self.ops.append((_UPDATE, cmd))
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def add_delete(self, selector, limit, collation=None):
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"""Create a delete document and add it to the list of ops.
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"""
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cmd = SON([('q', selector), ('limit', limit)])
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collation = validate_collation_or_none(collation)
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if collation is not None:
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self.uses_collation = True
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cmd['collation'] = collation
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if limit == _DELETE_ALL:
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# A bulk_write containing a delete_many is not retryable.
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self.is_retryable = False
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self.ops.append((_DELETE, cmd))
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def gen_ordered(self):
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"""Generate batches of operations, batched by type of
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operation, in the order **provided**.
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"""
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run = None
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for idx, (op_type, operation) in enumerate(self.ops):
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if run is None:
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run = _Run(op_type)
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elif run.op_type != op_type:
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yield run
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run = _Run(op_type)
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run.add(idx, operation)
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yield run
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def gen_unordered(self):
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"""Generate batches of operations, batched by type of
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operation, in arbitrary order.
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"""
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operations = [_Run(_INSERT), _Run(_UPDATE), _Run(_DELETE)]
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for idx, (op_type, operation) in enumerate(self.ops):
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operations[op_type].add(idx, operation)
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for run in operations:
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if run.ops:
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yield run
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def _execute_command(self, generator, write_concern, session,
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sock_info, op_id, retryable, full_result):
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if sock_info.max_wire_version < 5 and self.uses_collation:
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raise ConfigurationError(
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'Must be connected to MongoDB 3.4+ to use a collation.')
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if sock_info.max_wire_version < 6 and self.uses_array_filters:
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raise ConfigurationError(
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'Must be connected to MongoDB 3.6+ to use arrayFilters.')
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db_name = self.collection.database.name
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client = self.collection.database.client
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listeners = client._event_listeners
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if not self.current_run:
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self.current_run = next(generator)
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run = self.current_run
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# sock_info.command validates the session, but we use
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# sock_info.write_command.
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sock_info.validate_session(client, session)
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while run:
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cmd = SON([(_COMMANDS[run.op_type], self.collection.name),
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('ordered', self.ordered)])
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if not write_concern.is_server_default:
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cmd['writeConcern'] = write_concern.document
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if self.bypass_doc_val and sock_info.max_wire_version >= 4:
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cmd['bypassDocumentValidation'] = True
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bwc = _BulkWriteContext(db_name, cmd, sock_info, op_id,
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listeners, session)
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while run.idx_offset < len(run.ops):
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if session:
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# Start a new retryable write unless one was already
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# started for this command.
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if retryable and not self.started_retryable_write:
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session._start_retryable_write()
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self.started_retryable_write = True
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session._apply_to(cmd, retryable, ReadPreference.PRIMARY,
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sock_info)
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sock_info.send_cluster_time(cmd, session, client)
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check_keys = run.op_type == _INSERT
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ops = islice(run.ops, run.idx_offset, None)
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# Run as many ops as possible.
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request_id, msg, to_send = _do_bulk_write_command(
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self.namespace, run.op_type, cmd, ops, check_keys,
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self.collection.codec_options, bwc)
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if not to_send:
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raise InvalidOperation("cannot do an empty bulk write")
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result = bwc.write_command(request_id, msg, to_send)
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client._receive_cluster_time(result, session)
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# Retryable writeConcernErrors halt the execution of this run.
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wce = result.get('writeConcernError', {})
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if wce.get('code', 0) in _RETRYABLE_ERROR_CODES:
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# Synthesize the full bulk result without modifying the
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# current one because this write operation may be retried.
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full = copy.deepcopy(full_result)
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_merge_command(run, full, run.idx_offset, result)
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_raise_bulk_write_error(full)
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_merge_command(run, full_result, run.idx_offset, result)
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# We're no longer in a retry once a command succeeds.
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self.retrying = False
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self.started_retryable_write = False
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if self.ordered and "writeErrors" in result:
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break
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run.idx_offset += len(to_send)
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# We're supposed to continue if errors are
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# at the write concern level (e.g. wtimeout)
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if self.ordered and full_result['writeErrors']:
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break
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# Reset our state
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self.current_run = run = next(generator, None)
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def execute_command(self, generator, write_concern, session):
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"""Execute using write commands.
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"""
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# nModified is only reported for write commands, not legacy ops.
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full_result = {
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"writeErrors": [],
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"writeConcernErrors": [],
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"nInserted": 0,
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"nUpserted": 0,
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"nMatched": 0,
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"nModified": 0,
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"nRemoved": 0,
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"upserted": [],
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}
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op_id = _randint()
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def retryable_bulk(session, sock_info, retryable):
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self._execute_command(
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generator, write_concern, session, sock_info, op_id,
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retryable, full_result)
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client = self.collection.database.client
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with client._tmp_session(session) as s:
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client._retry_with_session(
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self.is_retryable, retryable_bulk, s, self)
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if full_result["writeErrors"] or full_result["writeConcernErrors"]:
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_raise_bulk_write_error(full_result)
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return full_result
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def execute_insert_no_results(self, sock_info, run, op_id, acknowledged):
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"""Execute insert, returning no results.
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"""
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command = SON([('insert', self.collection.name),
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('ordered', self.ordered)])
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concern = {'w': int(self.ordered)}
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command['writeConcern'] = concern
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if self.bypass_doc_val and sock_info.max_wire_version >= 4:
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command['bypassDocumentValidation'] = True
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db = self.collection.database
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bwc = _BulkWriteContext(
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db.name, command, sock_info, op_id, db.client._event_listeners,
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session=None)
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# Legacy batched OP_INSERT.
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_do_batched_insert(
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self.collection.full_name, run.ops, True, acknowledged, concern,
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not self.ordered, self.collection.codec_options, bwc)
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def execute_op_msg_no_results(self, sock_info, generator):
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"""Execute write commands with OP_MSG and w=0 writeConcern, unordered.
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"""
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db_name = self.collection.database.name
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client = self.collection.database.client
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listeners = client._event_listeners
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op_id = _randint()
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if not self.current_run:
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self.current_run = next(generator)
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run = self.current_run
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while run:
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cmd = SON([(_COMMANDS[run.op_type], self.collection.name),
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('ordered', False),
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('writeConcern', {'w': 0})])
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bwc = _BulkWriteContext(db_name, cmd, sock_info, op_id,
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listeners, None)
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while run.idx_offset < len(run.ops):
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check_keys = run.op_type == _INSERT
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ops = islice(run.ops, run.idx_offset, None)
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# Run as many ops as possible.
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request_id, msg, to_send = _do_bulk_write_command(
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self.namespace, run.op_type, cmd, ops, check_keys,
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self.collection.codec_options, bwc)
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if not to_send:
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raise InvalidOperation("cannot do an empty bulk write")
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run.idx_offset += len(to_send)
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# Though this isn't strictly a "legacy" write, the helper
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# handles publishing commands and sending our message
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# without receiving a result. Send 0 for max_doc_size
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# to disable size checking. Size checking is handled while
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# the documents are encoded to BSON.
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bwc.legacy_write(request_id, msg, 0, False, to_send)
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self.current_run = run = next(generator, None)
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def execute_command_no_results(self, sock_info, generator):
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"""Execute write commands with OP_MSG and w=0 WriteConcern, ordered.
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"""
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full_result = {
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"writeErrors": [],
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"writeConcernErrors": [],
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"nInserted": 0,
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"nUpserted": 0,
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"nMatched": 0,
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"nModified": 0,
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"nRemoved": 0,
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"upserted": [],
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}
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# Ordered bulk writes have to be acknowledged so that we stop
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# processing at the first error, even when the application
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# specified unacknowledged writeConcern.
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write_concern = WriteConcern()
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op_id = _randint()
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try:
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self._execute_command(
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generator, write_concern, None,
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sock_info, op_id, False, full_result)
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except OperationFailure:
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pass
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def execute_no_results(self, sock_info, generator):
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"""Execute all operations, returning no results (w=0).
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"""
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if self.uses_collation:
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raise ConfigurationError(
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'Collation is unsupported for unacknowledged writes.')
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if self.uses_array_filters:
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raise ConfigurationError(
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'arrayFilters is unsupported for unacknowledged writes.')
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# Cannot have both unacknowledged writes and bypass document validation.
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if self.bypass_doc_val and sock_info.max_wire_version >= 4:
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raise OperationFailure("Cannot set bypass_document_validation with"
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" unacknowledged write concern")
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# OP_MSG
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if sock_info.max_wire_version > 5:
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if self.ordered:
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return self.execute_command_no_results(sock_info, generator)
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return self.execute_op_msg_no_results(sock_info, generator)
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coll = self.collection
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# If ordered is True we have to send GLE or use write
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# commands so we can abort on the first error.
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write_concern = WriteConcern(w=int(self.ordered))
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op_id = _randint()
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next_run = next(generator)
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while next_run:
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# An ordered bulk write needs to send acknowledged writes to short
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# circuit the next run. However, the final message on the final
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# run can be unacknowledged.
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run = next_run
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next_run = next(generator, None)
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needs_ack = self.ordered and next_run is not None
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try:
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if run.op_type == _INSERT:
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self.execute_insert_no_results(
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sock_info, run, op_id, needs_ack)
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elif run.op_type == _UPDATE:
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for operation in run.ops:
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doc = operation['u']
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check_keys = True
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if doc and next(iter(doc)).startswith('$'):
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check_keys = False
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coll._update(
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sock_info,
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operation['q'],
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doc,
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operation['upsert'],
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check_keys,
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operation['multi'],
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write_concern=write_concern,
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op_id=op_id,
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ordered=self.ordered,
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bypass_doc_val=self.bypass_doc_val)
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else:
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for operation in run.ops:
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|
coll._delete(sock_info,
|
|
operation['q'],
|
|
not operation['limit'],
|
|
write_concern,
|
|
op_id,
|
|
self.ordered)
|
|
except OperationFailure:
|
|
if self.ordered:
|
|
break
|
|
|
|
def execute(self, write_concern, session):
|
|
"""Execute operations.
|
|
"""
|
|
if not self.ops:
|
|
raise InvalidOperation('No operations to execute')
|
|
if self.executed:
|
|
raise InvalidOperation('Bulk operations can '
|
|
'only be executed once.')
|
|
self.executed = True
|
|
write_concern = write_concern or self.collection.write_concern
|
|
session = _validate_session_write_concern(session, write_concern)
|
|
|
|
if self.ordered:
|
|
generator = self.gen_ordered()
|
|
else:
|
|
generator = self.gen_unordered()
|
|
|
|
client = self.collection.database.client
|
|
if not write_concern.acknowledged:
|
|
with client._socket_for_writes() as sock_info:
|
|
self.execute_no_results(sock_info, generator)
|
|
else:
|
|
return self.execute_command(generator, write_concern, session)
|
|
|
|
|
|
class BulkUpsertOperation(object):
|
|
"""An interface for adding upsert operations.
|
|
"""
|
|
|
|
__slots__ = ('__selector', '__bulk', '__collation')
|
|
|
|
def __init__(self, selector, bulk, collation):
|
|
self.__selector = selector
|
|
self.__bulk = bulk
|
|
self.__collation = collation
|
|
|
|
def update_one(self, update):
|
|
"""Update one document matching the selector.
|
|
|
|
:Parameters:
|
|
- `update` (dict): the update operations to apply
|
|
"""
|
|
self.__bulk.add_update(self.__selector,
|
|
update, multi=False, upsert=True,
|
|
collation=self.__collation)
|
|
|
|
def update(self, update):
|
|
"""Update all documents matching the selector.
|
|
|
|
:Parameters:
|
|
- `update` (dict): the update operations to apply
|
|
"""
|
|
self.__bulk.add_update(self.__selector,
|
|
update, multi=True, upsert=True,
|
|
collation=self.__collation)
|
|
|
|
def replace_one(self, replacement):
|
|
"""Replace one entire document matching the selector criteria.
|
|
|
|
:Parameters:
|
|
- `replacement` (dict): the replacement document
|
|
"""
|
|
self.__bulk.add_replace(self.__selector, replacement, upsert=True,
|
|
collation=self.__collation)
|
|
|
|
|
|
class BulkWriteOperation(object):
|
|
"""An interface for adding update or remove operations.
|
|
"""
|
|
|
|
__slots__ = ('__selector', '__bulk', '__collation')
|
|
|
|
def __init__(self, selector, bulk, collation):
|
|
self.__selector = selector
|
|
self.__bulk = bulk
|
|
self.__collation = collation
|
|
|
|
def update_one(self, update):
|
|
"""Update one document matching the selector criteria.
|
|
|
|
:Parameters:
|
|
- `update` (dict): the update operations to apply
|
|
"""
|
|
self.__bulk.add_update(self.__selector, update, multi=False,
|
|
collation=self.__collation)
|
|
|
|
def update(self, update):
|
|
"""Update all documents matching the selector criteria.
|
|
|
|
:Parameters:
|
|
- `update` (dict): the update operations to apply
|
|
"""
|
|
self.__bulk.add_update(self.__selector, update, multi=True,
|
|
collation=self.__collation)
|
|
|
|
def replace_one(self, replacement):
|
|
"""Replace one entire document matching the selector criteria.
|
|
|
|
:Parameters:
|
|
- `replacement` (dict): the replacement document
|
|
"""
|
|
self.__bulk.add_replace(self.__selector, replacement,
|
|
collation=self.__collation)
|
|
|
|
def remove_one(self):
|
|
"""Remove a single document matching the selector criteria.
|
|
"""
|
|
self.__bulk.add_delete(self.__selector, _DELETE_ONE,
|
|
collation=self.__collation)
|
|
|
|
def remove(self):
|
|
"""Remove all documents matching the selector criteria.
|
|
"""
|
|
self.__bulk.add_delete(self.__selector, _DELETE_ALL,
|
|
collation=self.__collation)
|
|
|
|
def upsert(self):
|
|
"""Specify that all chained update operations should be
|
|
upserts.
|
|
|
|
:Returns:
|
|
- A :class:`BulkUpsertOperation` instance, used to add
|
|
update operations to this bulk operation.
|
|
"""
|
|
return BulkUpsertOperation(self.__selector, self.__bulk,
|
|
self.__collation)
|
|
|
|
|
|
class BulkOperationBuilder(object):
|
|
"""**DEPRECATED**: An interface for executing a batch of write operations.
|
|
"""
|
|
|
|
__slots__ = '__bulk'
|
|
|
|
def __init__(self, collection, ordered=True,
|
|
bypass_document_validation=False):
|
|
"""**DEPRECATED**: Initialize a new BulkOperationBuilder instance.
|
|
|
|
:Parameters:
|
|
- `collection`: A :class:`~pymongo.collection.Collection` instance.
|
|
- `ordered` (optional): If ``True`` all operations will be executed
|
|
serially, in the order provided, and the entire execution will
|
|
abort on the first error. If ``False`` operations will be executed
|
|
in arbitrary order (possibly in parallel on the server), reporting
|
|
any errors that occurred after attempting all operations. Defaults
|
|
to ``True``.
|
|
- `bypass_document_validation`: (optional) If ``True``, allows the
|
|
write to opt-out of document level validation. Default is
|
|
``False``.
|
|
|
|
.. note:: `bypass_document_validation` requires server version
|
|
**>= 3.2**
|
|
|
|
.. versionchanged:: 3.5
|
|
Deprecated. Use :meth:`~pymongo.collection.Collection.bulk_write`
|
|
instead.
|
|
|
|
.. versionchanged:: 3.2
|
|
Added bypass_document_validation support
|
|
"""
|
|
self.__bulk = _Bulk(collection, ordered, bypass_document_validation)
|
|
|
|
def find(self, selector, collation=None):
|
|
"""Specify selection criteria for bulk operations.
|
|
|
|
:Parameters:
|
|
- `selector` (dict): the selection criteria for update
|
|
and remove operations.
|
|
- `collation` (optional): An instance of
|
|
:class:`~pymongo.collation.Collation`. This option is only
|
|
supported on MongoDB 3.4 and above.
|
|
|
|
:Returns:
|
|
- A :class:`BulkWriteOperation` instance, used to add
|
|
update and remove operations to this bulk operation.
|
|
|
|
.. versionchanged:: 3.4
|
|
Added the `collation` option.
|
|
|
|
"""
|
|
validate_is_mapping("selector", selector)
|
|
return BulkWriteOperation(selector, self.__bulk, collation)
|
|
|
|
def insert(self, document):
|
|
"""Insert a single document.
|
|
|
|
:Parameters:
|
|
- `document` (dict): the document to insert
|
|
|
|
.. seealso:: :ref:`writes-and-ids`
|
|
"""
|
|
self.__bulk.add_insert(document)
|
|
|
|
def execute(self, write_concern=None):
|
|
"""Execute all provided operations.
|
|
|
|
:Parameters:
|
|
- write_concern (optional): the write concern for this bulk
|
|
execution.
|
|
"""
|
|
if write_concern is not None:
|
|
write_concern = WriteConcern(**write_concern)
|
|
return self.__bulk.execute(write_concern, session=None)
|
|
|