[
https://issues.apache.org/jira/browse/BEAM-12119?focusedWorklogId=618190&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-618190
]
ASF GitHub Bot logged work on BEAM-12119:
-----------------------------------------
Author: ASF GitHub Bot
Created on: 02/Jul/21 17:34
Start Date: 02/Jul/21 17:34
Worklog Time Spent: 10m
Work Description: tvalentyn commented on pull request #14460:
URL: https://github.com/apache/beam/pull/14460#issuecomment-873155030
@MaksymSkorupskyi FYI this PR might have started causing test flakiness that
we cannot yet explain. The flakiness is likely unrelated to the PR, but seems
to go away if we try to revert it. if you have time/interest you could take a
look as well at https://issues.apache.org/jira/browse/BEAM-12515
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Issue Time Tracking
-------------------
Worklog Id: (was: 618190)
Time Spent: 15h 40m (was: 15.5h)
> 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
> Fix For: 2.31.0
>
> Time Spent: 15h 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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