[
https://issues.apache.org/jira/browse/BEAM-12119?focusedWorklogId=607234&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-607234
]
ASF GitHub Bot logged work on BEAM-12119:
-----------------------------------------
Author: ASF GitHub Bot
Created on: 04/Jun/21 18:24
Start Date: 04/Jun/21 18:24
Worklog Time Spent: 10m
Work Description: y1chi commented on a change in pull request #14460:
URL: https://github.com/apache/beam/pull/14460#discussion_r645769288
##########
File path: sdks/python/apache_beam/io/mongodbio.py
##########
@@ -136,30 +149,195 @@ def __init__(
Returns:
:class:`~apache_beam.transforms.ptransform.PTransform`
-
"""
if extra_client_params is None:
extra_client_params = {}
if not isinstance(db, str):
- raise ValueError('ReadFromMongDB db param must be specified as a string')
+ raise ValueError("ReadFromMongDB db param must be specified as a string")
if not isinstance(coll, str):
raise ValueError(
- 'ReadFromMongDB coll param must be specified as a '
- 'string')
+ "ReadFromMongDB coll param must be specified as a string")
self._mongo_source = _BoundedMongoSource(
uri=uri,
db=db,
coll=coll,
filter=filter,
projection=projection,
extra_client_params=extra_client_params,
- bucket_auto=bucket_auto)
+ bucket_auto=bucket_auto,
+ )
def expand(self, pcoll):
return pcoll | iobase.Read(self._mongo_source)
+class _ObjectIdRangeTracker(OrderedPositionRangeTracker):
+ """RangeTracker for tracking mongodb _id of bson ObjectId type."""
+ def position_to_fraction(
+ self,
+ pos: ObjectId,
+ start: ObjectId,
+ end: ObjectId,
+ ):
+ """Returns the fraction of keys in the range [start, end) that
+ are less than the given key.
+ """
+ pos_number = _ObjectIdHelper.id_to_int(pos)
+ start_number = _ObjectIdHelper.id_to_int(start)
+ end_number = _ObjectIdHelper.id_to_int(end)
+ return (pos_number - start_number) / (end_number - start_number)
+
+ def fraction_to_position(
+ self,
+ fraction: float,
+ start: ObjectId,
+ end: ObjectId,
+ ):
+ """Converts a fraction between 0 and 1
+ to a position between start and end.
+ """
+ start_number = _ObjectIdHelper.id_to_int(start)
+ end_number = _ObjectIdHelper.id_to_int(end)
+ total = end_number - start_number
+ pos = int(total * fraction + start_number)
+ # make sure split position is larger than start position and smaller than
+ # end position.
+ if pos <= start_number:
+ return _ObjectIdHelper.increment_id(start, 1)
+
+ if pos >= end_number:
+ return _ObjectIdHelper.increment_id(end, -1)
+
+ return _ObjectIdHelper.int_to_id(pos)
+
+
+class _StrRangeTracker(LexicographicKeyRangeTracker):
Review comment:
The amount of duplication makes me feel that either
LexicographicKeyRangeTracker should handle both bytes and str, or the common
logic should be extracted to helper functions.
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Issue Time Tracking
-------------------
Worklog Id: (was: 607234)
Time Spent: 13h 40m (was: 13.5h)
> Python IO MongoDB: integer and string `_id` keys are not supported
> ------------------------------------------------------------------
>
> Key: BEAM-12119
> URL: https://issues.apache.org/jira/browse/BEAM-12119
> Project: Beam
> Issue Type: Improvement
> Components: io-py-mongodb
> Affects Versions: 2.27.0, 2.28.0
> Reporter: Maksym Skorupskyi
> Priority: P2
> Labels: MongoDB, Python
> Time Spent: 13h 40m
> Remaining Estimate: 0h
>
> Python IO MongoDB: integer and string `_id` keys are not supported.
>
> Usually *ObjectId* is using for *`_id`* key, but sometimes you can deal with
> *int* and *str* keys. Reading from such MongoDB collection will raise errors.
> h2. Integer `_id` key:
> {code:java}
> Traceback (most recent call last):
> File "apache_beam/runners/common.py", line 1239, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in
> apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1374, in
> apache_beam.runners.common._OutputProcessor.process_outputs
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 1426, in process
> element)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/iobase.py", line
> 1545, in initial_restriction
> range_tracker = element_source.get_range_tracker(None, None)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 243, in get_range_tracker
> start_position, stop_position)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 359, in _replace_none_positions
> stop_position = _ObjectIdHelper.increment_id(last_doc_id, 1)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 418, in increment_id
> id_number = _ObjectIdHelper.id_to_int(object_id)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 383, in id_to_int
> ints = struct.unpack('>III', id.binary)
> AttributeError: 'int' object has no attribute 'binary'
> During handling of the above exception, another exception occurred:
> Traceback (most recent call last):
> File "/data-pipelines/data_pipelines/mongo_to_bq_raw.py", line 325, in
> <module>
> sys.exit(run())
> File "/data-pipelines/data_pipelines/mongo_to_bq_raw.py", line 240, in run
> options=options, ingestion_ts=ingestion_ts, table_name=table_name
> File "/venv/lib/python3.7/site-packages/apache_beam/pipeline.py", line 582,
> in __exit__
> self.result = self.run()
> File "/venv/lib/python3.7/site-packages/apache_beam/pipeline.py", line 561,
> in run
> return self.runner.run_pipeline(self, self._options)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/direct/direct_runner.py",
> line 126, in run_pipeline
> return runner.run_pipeline(pipeline, options)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 183, in run_pipeline
> pipeline.to_runner_api(default_environment=self._default_environment))
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 193, in run_via_runner_api
> return self.run_stages(stage_context, stages)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 360, in run_stages
> bundle_context_manager,
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 556, in _run_stage
> bundle_manager)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 596, in _run_bundle
> data_input, data_output, input_timers, expected_timer_output)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 897, in process_bundle
> result_future = self._worker_handler.control_conn.push(process_bundle_req)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/worker_handlers.py",
> line 380, in push
> response = self.worker.do_instruction(request)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/sdk_worker.py",
> line 607, in do_instruction
> getattr(request, request_type), request.instruction_id)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/sdk_worker.py",
> line 644, in process_bundle
> bundle_processor.process_bundle(instruction_id))
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 1000, in process_bundle
> element.data)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 228, in process_encoded
> self.output(decoded_value)
> File "apache_beam/runners/worker/operations.py", line 357, in
> apache_beam.runners.worker.operations.Operation.output
> File "apache_beam/runners/worker/operations.py", line 359, in
> apache_beam.runners.worker.operations.Operation.output
> File "apache_beam/runners/worker/operations.py", line 221, in
> apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "apache_beam/runners/worker/operations.py", line 718, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/worker/operations.py", line 719, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/common.py", line 1241, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 1306, in
> apache_beam.runners.common.DoFnRunner._reraise_augmented
> File "apache_beam/runners/common.py", line 1239, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in
> apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1401, in
> apache_beam.runners.common._OutputProcessor.process_outputs
> File "apache_beam/runners/worker/operations.py", line 221, in
> apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "apache_beam/runners/worker/operations.py", line 718, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/worker/operations.py", line 719, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/common.py", line 1241, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 1321, in
> apache_beam.runners.common.DoFnRunner._reraise_augmented
> File "/venv/lib/python3.7/site-packages/future/utils/__init__.py", line
> 446, in raise_with_traceback
> raise exc.with_traceback(traceback)
> File "apache_beam/runners/common.py", line 1239, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in
> apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1374, in
> apache_beam.runners.common._OutputProcessor.process_outputs
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 1426, in process
> element)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/iobase.py", line
> 1545, in initial_restriction
> range_tracker = element_source.get_range_tracker(None, None)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 243, in get_range_tracker
> start_position, stop_position)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 359, in _replace_none_positions
> stop_position = _ObjectIdHelper.increment_id(last_doc_id, 1)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 418, in increment_id
> id_number = _ObjectIdHelper.id_to_int(object_id)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 383, in id_to_int
> ints = struct.unpack('>III', id.binary)
> AttributeError: 'int' object has no attribute 'binary' [while running
> 'sources/Read
> Collection/Read/SDFBoundedSourceReader/ParDo(SDFBoundedSourceDoFn)/PairWithRestriction']
> ERROR:root:mongo_to_bq_raw.py: 'int' object has no attribute 'binary' [while
> running 'sources/Read
> Collection/Read/SDFBoundedSourceReader/ParDo(SDFBoundedSourceDoFn)/PairWithRestriction']
> {code}
> h2. String `_id` key:
> {code:java}
> Traceback (most recent call last):
> File "apache_beam/runners/common.py", line 1239, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in
> apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1374, in
> apache_beam.runners.common._OutputProcessor.process_outputs
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 1426, in process
> element)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/iobase.py", line
> 1545, in initial_restriction
> range_tracker = element_source.get_range_tracker(None, None)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 243, in get_range_tracker
> start_position, stop_position)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 359, in _replace_none_positions
> stop_position = _ObjectIdHelper.increment_id(last_doc_id, 1)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 418, in increment_id
> id_number = _ObjectIdHelper.id_to_int(object_id)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 383, in id_to_int
> ints = struct.unpack('>III', id.binary)
> AttributeError: 'str' object has no attribute 'binary'During handling of the
> above exception, another exception occurred:Traceback (most recent call last):
> File "/data-pipelines/data_pipelines/mongo_to_bq_raw.py", line 325, in
> <module>
> sys.exit(run())
> File "/data-pipelines/data_pipelines/mongo_to_bq_raw.py", line 240, in run
> options=options, ingestion_ts=ingestion_ts, table_name=table_name
> File "/venv/lib/python3.7/site-packages/apache_beam/pipeline.py", line 582,
> in __exit__
> self.result = self.run()
> File "/venv/lib/python3.7/site-packages/apache_beam/pipeline.py", line 561,
> in run
> return self.runner.run_pipeline(self, self._options)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/direct/direct_runner.py",
> line 126, in run_pipeline
> return runner.run_pipeline(pipeline, options)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 183, in run_pipeline
> pipeline.to_runner_api(default_environment=self._default_environment))
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 193, in run_via_runner_api
> return self.run_stages(stage_context, stages)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 360, in run_stages
> bundle_context_manager,
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 556, in _run_stage
> bundle_manager)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 596, in _run_bundle
> data_input, data_output, input_timers, expected_timer_output)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/fn_runner.py",
> line 897, in process_bundle
> result_future = self._worker_handler.control_conn.push(process_bundle_req)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/portability/fn_api_runner/worker_handlers.py",
> line 380, in push
> response = self.worker.do_instruction(request)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/sdk_worker.py",
> line 607, in do_instruction
> getattr(request, request_type), request.instruction_id)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/sdk_worker.py",
> line 644, in process_bundle
> bundle_processor.process_bundle(instruction_id))
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 1000, in process_bundle
> element.data)
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 228, in process_encoded
> self.output(decoded_value)
> File "apache_beam/runners/worker/operations.py", line 357, in
> apache_beam.runners.worker.operations.Operation.output
> File "apache_beam/runners/worker/operations.py", line 359, in
> apache_beam.runners.worker.operations.Operation.output
> File "apache_beam/runners/worker/operations.py", line 221, in
> apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "apache_beam/runners/worker/operations.py", line 718, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/worker/operations.py", line 719, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/common.py", line 1241, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 1306, in
> apache_beam.runners.common.DoFnRunner._reraise_augmented
> File "apache_beam/runners/common.py", line 1239, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in
> apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1401, in
> apache_beam.runners.common._OutputProcessor.process_outputs
> File "apache_beam/runners/worker/operations.py", line 221, in
> apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "apache_beam/runners/worker/operations.py", line 718, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/worker/operations.py", line 719, in
> apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/common.py", line 1241, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 1321, in
> apache_beam.runners.common.DoFnRunner._reraise_augmented
> File "/venv/lib/python3.7/site-packages/future/utils/__init__.py", line
> 446, in raise_with_traceback
> raise exc.with_traceback(traceback)
> File "apache_beam/runners/common.py", line 1239, in
> apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in
> apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1374, in
> apache_beam.runners.common._OutputProcessor.process_outputs
> File
> "/venv/lib/python3.7/site-packages/apache_beam/runners/worker/bundle_processor.py",
> line 1426, in process
> element)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/iobase.py", line
> 1545, in initial_restriction
> range_tracker = element_source.get_range_tracker(None, None)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 243, in get_range_tracker
> start_position, stop_position)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 359, in _replace_none_positions
> stop_position = _ObjectIdHelper.increment_id(last_doc_id, 1)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 418, in increment_id
> id_number = _ObjectIdHelper.id_to_int(object_id)
> File "/venv/lib/python3.7/site-packages/apache_beam/io/mongodbio.py", line
> 383, in id_to_int
> ints = struct.unpack('>III', id.binary)
> AttributeError: 'str' object has no attribute 'binary' [while running
> 'tagged_objects/Read
> Collection/Read/SDFBoundedSourceReader/ParDo(SDFBoundedSourceDoFn)/PairWithRestriction']
> ERROR:root:mongo_to_bq_raw.py: 'str' object has no attribute 'binary' [while
> running 'tagged_objects/Read
> Collection/Read/SDFBoundedSourceReader/ParDo(SDFBoundedSourceDoFn)/PairWithRestriction']
> {code}
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