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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# Copyright 2014-present MongoDB, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""The bulk write operations interface.
.. versionadded:: 2.7
"""
import copy
from itertools import islice
from bson.objectid import ObjectId
from bson.raw_bson import RawBSONDocument
from bson.son import SON
from pymongo.client_session import _validate_session_write_concern
from pymongo.common import (validate_is_mapping,
validate_is_document_type,
validate_ok_for_replace,
validate_ok_for_update)
from pymongo.helpers import _RETRYABLE_ERROR_CODES
from pymongo.collation import validate_collation_or_none
from pymongo.errors import (BulkWriteError,
ConfigurationError,
InvalidOperation,
OperationFailure)
from pymongo.message import (_INSERT, _UPDATE, _DELETE,
_do_batched_insert,
_do_bulk_write_command,
_randint,
_BulkWriteContext)
from pymongo.read_preferences import ReadPreference
from pymongo.write_concern import WriteConcern
_DELETE_ALL = 0
_DELETE_ONE = 1
# For backwards compatibility. See MongoDB src/mongo/base/error_codes.err
_BAD_VALUE = 2
_UNKNOWN_ERROR = 8
_WRITE_CONCERN_ERROR = 64
_COMMANDS = ('insert', 'update', 'delete')
# These string literals are used when we create fake server return
# documents client side. We use unicode literals in python 2.x to
# match the actual return values from the server.
_UOP = u"op"
class _Run(object):
"""Represents a batch of write operations.
"""
def __init__(self, op_type):
"""Initialize a new Run object.
"""
self.op_type = op_type
self.index_map = []
self.ops = []
self.idx_offset = 0
def index(self, idx):
"""Get the original index of an operation in this run.
:Parameters:
- `idx`: The Run index that maps to the original index.
"""
return self.index_map[idx]
def add(self, original_index, operation):
"""Add an operation to this Run instance.
:Parameters:
- `original_index`: The original index of this operation
within a larger bulk operation.
- `operation`: The operation document.
"""
self.index_map.append(original_index)
self.ops.append(operation)
def _merge_command(run, full_result, offset, result):
"""Merge a write command result into the full bulk result.
"""
affected = result.get("n", 0)
if run.op_type == _INSERT:
full_result["nInserted"] += affected
elif run.op_type == _DELETE:
full_result["nRemoved"] += affected
elif run.op_type == _UPDATE:
upserted = result.get("upserted")
if upserted:
n_upserted = len(upserted)
for doc in upserted:
doc["index"] = run.index(doc["index"] + offset)
full_result["upserted"].extend(upserted)
full_result["nUpserted"] += n_upserted
full_result["nMatched"] += (affected - n_upserted)
else:
full_result["nMatched"] += affected
full_result["nModified"] += result["nModified"]
write_errors = result.get("writeErrors")
if write_errors:
for doc in write_errors:
# Leave the server response intact for APM.
replacement = doc.copy()
idx = doc["index"] + offset
replacement["index"] = run.index(idx)
# Add the failed operation to the error document.
replacement[_UOP] = run.ops[idx]
full_result["writeErrors"].append(replacement)
wc_error = result.get("writeConcernError")
if wc_error:
full_result["writeConcernErrors"].append(wc_error)
def _raise_bulk_write_error(full_result):
"""Raise a BulkWriteError from the full bulk api result.
"""
if full_result["writeErrors"]:
full_result["writeErrors"].sort(
key=lambda error: error["index"])
raise BulkWriteError(full_result)
class _Bulk(object):
"""The private guts of the bulk write API.
"""
def __init__(self, collection, ordered, bypass_document_validation):
"""Initialize a _Bulk instance.
"""
self.collection = collection.with_options(
codec_options=collection.codec_options._replace(
unicode_decode_error_handler='replace',
document_class=dict))
self.ordered = ordered
self.ops = []
self.name = "%s.%s" % (collection.database.name, collection.name)
self.namespace = collection.database.name + '.$cmd'
self.executed = False
self.bypass_doc_val = bypass_document_validation
self.uses_collation = False
self.uses_array_filters = False
self.is_retryable = True
self.retrying = False
self.started_retryable_write = False
# Extra state so that we know where to pick up on a retry attempt.
self.current_run = None
def add_insert(self, document):
"""Add an insert document to the list of ops.
"""
validate_is_document_type("document", document)
# Generate ObjectId client side.
if not (isinstance(document, RawBSONDocument) or '_id' in document):
document['_id'] = ObjectId()
self.ops.append((_INSERT, document))
def add_update(self, selector, update, multi=False, upsert=False,
collation=None, array_filters=None):
"""Create an update document and add it to the list of ops.
"""
validate_ok_for_update(update)
cmd = SON([('q', selector), ('u', update),
('multi', multi), ('upsert', upsert)])
collation = validate_collation_or_none(collation)
if collation is not None:
self.uses_collation = True
cmd['collation'] = collation
if array_filters is not None:
self.uses_array_filters = True
cmd['arrayFilters'] = array_filters
if multi:
# A bulk_write containing an update_many is not retryable.
self.is_retryable = False
self.ops.append((_UPDATE, cmd))
def add_replace(self, selector, replacement, upsert=False,
collation=None):
"""Create a replace document and add it to the list of ops.
"""
validate_ok_for_replace(replacement)
cmd = SON([('q', selector), ('u', replacement),
('multi', False), ('upsert', upsert)])
collation = validate_collation_or_none(collation)
if collation is not None:
self.uses_collation = True
cmd['collation'] = collation
self.ops.append((_UPDATE, cmd))
def add_delete(self, selector, limit, collation=None):
"""Create a delete document and add it to the list of ops.
"""
cmd = SON([('q', selector), ('limit', limit)])
collation = validate_collation_or_none(collation)
if collation is not None:
self.uses_collation = True
cmd['collation'] = collation
if limit == _DELETE_ALL:
# A bulk_write containing a delete_many is not retryable.
self.is_retryable = False
self.ops.append((_DELETE, cmd))
def gen_ordered(self):
"""Generate batches of operations, batched by type of
operation, in the order **provided**.
"""
run = None
for idx, (op_type, operation) in enumerate(self.ops):
if run is None:
run = _Run(op_type)
elif run.op_type != op_type:
yield run
run = _Run(op_type)
run.add(idx, operation)
yield run
def gen_unordered(self):
"""Generate batches of operations, batched by type of
operation, in arbitrary order.
"""
operations = [_Run(_INSERT), _Run(_UPDATE), _Run(_DELETE)]
for idx, (op_type, operation) in enumerate(self.ops):
operations[op_type].add(idx, operation)
for run in operations:
if run.ops:
yield run
def _execute_command(self, generator, write_concern, session,
sock_info, op_id, retryable, full_result):
if sock_info.max_wire_version < 5 and self.uses_collation:
raise ConfigurationError(
'Must be connected to MongoDB 3.4+ to use a collation.')
if sock_info.max_wire_version < 6 and self.uses_array_filters:
raise ConfigurationError(
'Must be connected to MongoDB 3.6+ to use arrayFilters.')
db_name = self.collection.database.name
client = self.collection.database.client
listeners = client._event_listeners
if not self.current_run:
self.current_run = next(generator)
run = self.current_run
# sock_info.command validates the session, but we use
# sock_info.write_command.
sock_info.validate_session(client, session)
while run:
cmd = SON([(_COMMANDS[run.op_type], self.collection.name),
('ordered', self.ordered)])
if not write_concern.is_server_default:
cmd['writeConcern'] = write_concern.document
if self.bypass_doc_val and sock_info.max_wire_version >= 4:
cmd['bypassDocumentValidation'] = True
bwc = _BulkWriteContext(db_name, cmd, sock_info, op_id,
listeners, session)
while run.idx_offset < len(run.ops):
if session:
# Start a new retryable write unless one was already
# started for this command.
if retryable and not self.started_retryable_write:
session._start_retryable_write()
self.started_retryable_write = True
session._apply_to(cmd, retryable, ReadPreference.PRIMARY,
sock_info)
sock_info.send_cluster_time(cmd, session, client)
check_keys = run.op_type == _INSERT
ops = islice(run.ops, run.idx_offset, None)
# Run as many ops as possible.
request_id, msg, to_send = _do_bulk_write_command(
self.namespace, run.op_type, cmd, ops, check_keys,
self.collection.codec_options, bwc)
if not to_send:
raise InvalidOperation("cannot do an empty bulk write")
result = bwc.write_command(request_id, msg, to_send)
client._receive_cluster_time(result, session)
# Retryable writeConcernErrors halt the execution of this run.
wce = result.get('writeConcernError', {})
if wce.get('code', 0) in _RETRYABLE_ERROR_CODES:
# Synthesize the full bulk result without modifying the
# current one because this write operation may be retried.
full = copy.deepcopy(full_result)
_merge_command(run, full, run.idx_offset, result)
_raise_bulk_write_error(full)
_merge_command(run, full_result, run.idx_offset, result)
# We're no longer in a retry once a command succeeds.
self.retrying = False
self.started_retryable_write = False
if self.ordered and "writeErrors" in result:
break
run.idx_offset += len(to_send)
# We're supposed to continue if errors are
# at the write concern level (e.g. wtimeout)
if self.ordered and full_result['writeErrors']:
break
# Reset our state
self.current_run = run = next(generator, None)
def execute_command(self, generator, write_concern, session):
"""Execute using write commands.
"""
# nModified is only reported for write commands, not legacy ops.
full_result = {
"writeErrors": [],
"writeConcernErrors": [],
"nInserted": 0,
"nUpserted": 0,
"nMatched": 0,
"nModified": 0,
"nRemoved": 0,
"upserted": [],
}
op_id = _randint()
def retryable_bulk(session, sock_info, retryable):
self._execute_command(
generator, write_concern, session, sock_info, op_id,
retryable, full_result)
client = self.collection.database.client
with client._tmp_session(session) as s:
client._retry_with_session(
self.is_retryable, retryable_bulk, s, self)
if full_result["writeErrors"] or full_result["writeConcernErrors"]:
_raise_bulk_write_error(full_result)
return full_result
def execute_insert_no_results(self, sock_info, run, op_id, acknowledged):
"""Execute insert, returning no results.
"""
command = SON([('insert', self.collection.name),
('ordered', self.ordered)])
concern = {'w': int(self.ordered)}
command['writeConcern'] = concern
if self.bypass_doc_val and sock_info.max_wire_version >= 4:
command['bypassDocumentValidation'] = True
db = self.collection.database
bwc = _BulkWriteContext(
db.name, command, sock_info, op_id, db.client._event_listeners,
session=None)
# Legacy batched OP_INSERT.
_do_batched_insert(
self.collection.full_name, run.ops, True, acknowledged, concern,
not self.ordered, self.collection.codec_options, bwc)
def execute_op_msg_no_results(self, sock_info, generator):
"""Execute write commands with OP_MSG and w=0 writeConcern, unordered.
"""
db_name = self.collection.database.name
client = self.collection.database.client
listeners = client._event_listeners
op_id = _randint()
if not self.current_run:
self.current_run = next(generator)
run = self.current_run
while run:
cmd = SON([(_COMMANDS[run.op_type], self.collection.name),
('ordered', False),
('writeConcern', {'w': 0})])
bwc = _BulkWriteContext(db_name, cmd, sock_info, op_id,
listeners, None)
while run.idx_offset < len(run.ops):
check_keys = run.op_type == _INSERT
ops = islice(run.ops, run.idx_offset, None)
# Run as many ops as possible.
request_id, msg, to_send = _do_bulk_write_command(
self.namespace, run.op_type, cmd, ops, check_keys,
self.collection.codec_options, bwc)
if not to_send:
raise InvalidOperation("cannot do an empty bulk write")
run.idx_offset += len(to_send)
# Though this isn't strictly a "legacy" write, the helper
# handles publishing commands and sending our message
# without receiving a result. Send 0 for max_doc_size
# to disable size checking. Size checking is handled while
# the documents are encoded to BSON.
bwc.legacy_write(request_id, msg, 0, False, to_send)
self.current_run = run = next(generator, None)
def execute_command_no_results(self, sock_info, generator):
"""Execute write commands with OP_MSG and w=0 WriteConcern, ordered.
"""
full_result = {
"writeErrors": [],
"writeConcernErrors": [],
"nInserted": 0,
"nUpserted": 0,
"nMatched": 0,
"nModified": 0,
"nRemoved": 0,
"upserted": [],
}
# Ordered bulk writes have to be acknowledged so that we stop
# processing at the first error, even when the application
# specified unacknowledged writeConcern.
write_concern = WriteConcern()
op_id = _randint()
try:
self._execute_command(
generator, write_concern, None,
sock_info, op_id, False, full_result)
except OperationFailure:
pass
def execute_no_results(self, sock_info, generator):
"""Execute all operations, returning no results (w=0).
"""
if self.uses_collation:
raise ConfigurationError(
'Collation is unsupported for unacknowledged writes.')
if self.uses_array_filters:
raise ConfigurationError(
'arrayFilters is unsupported for unacknowledged writes.')
# Cannot have both unacknowledged writes and bypass document validation.
if self.bypass_doc_val and sock_info.max_wire_version >= 4:
raise OperationFailure("Cannot set bypass_document_validation with"
" unacknowledged write concern")
# OP_MSG
if sock_info.max_wire_version > 5:
if self.ordered:
return self.execute_command_no_results(sock_info, generator)
return self.execute_op_msg_no_results(sock_info, generator)
coll = self.collection
# If ordered is True we have to send GLE or use write
# commands so we can abort on the first error.
write_concern = WriteConcern(w=int(self.ordered))
op_id = _randint()
next_run = next(generator)
while next_run:
# An ordered bulk write needs to send acknowledged writes to short
# circuit the next run. However, the final message on the final
# run can be unacknowledged.
run = next_run
next_run = next(generator, None)
needs_ack = self.ordered and next_run is not None
try:
if run.op_type == _INSERT:
self.execute_insert_no_results(
sock_info, run, op_id, needs_ack)
elif run.op_type == _UPDATE:
for operation in run.ops:
doc = operation['u']
check_keys = True
if doc and next(iter(doc)).startswith('$'):
check_keys = False
coll._update(
sock_info,
operation['q'],
doc,
operation['upsert'],
check_keys,
operation['multi'],
write_concern=write_concern,
op_id=op_id,
ordered=self.ordered,
bypass_doc_val=self.bypass_doc_val)
else:
for operation in run.ops:
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)