🐛 Source S3: Loading of files' metadata #8252

antixar · 2021-11-25T14:50:43Z

What

The code had following bottleneck: Loading of LastModified files' properties was implemented with multithreading. And it can have potential problems where a S3 storage have a lot of files.

How

Code refactoring:

All files' properties should be loaded while reading of bucket items. Certainly the "multithreading" must be replaced.
Add more informative log messages.

Add test suites for testing

Pre-merge Checklist

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Code reviews completed
Documentation updated
- Connector's README.md
- Connector's bootstrap.md. See description and examples
- Changelog updated in docs/integrations/<source or destination>/<name>.md including changelog. See changelog example
PR name follows PR naming conventions

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Create a non-forked branch based on this PR and test the below items on it
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Seed specs have been re-generated by building the platform and committing the changes to the seed spec files, as described here

antixar · 2021-11-25T14:57:38Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504229322
❌ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504229322
🐛 https://gradle.com/s/wrxbbaeqzi5yc

antixar · 2021-11-25T15:43:46Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504399931
❌ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504399931
🐛 https://gradle.com/s/fdypicnscjjz4

antixar · 2021-11-25T17:04:14Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504662348
❌ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504662348
🐛 https://gradle.com/s/mnfyvhhpbni7m

antixar · 2021-11-25T19:04:06Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504983223
✅ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1504983223
Python tests coverage:

	 ---------- coverage: platform linux, python 3.8.10-final-0 -----------
	 Name                                                 Stmts   Miss  Cover
	 ------------------------------------------------------------------------
	 source_acceptance_test/__init__.py                       2      0   100%
	 source_acceptance_test/base.py                          10      4    60%
	 source_acceptance_test/config.py                        75      8    89%
	 source_acceptance_test/conftest.py                     108    108     0%
	 source_acceptance_test/plugin.py                        47     47     0%
	 source_acceptance_test/tests/__init__.py                 4      0   100%
	 source_acceptance_test/tests/test_core.py              200     94    53%
	 source_acceptance_test/tests/test_full_refresh.py       38     27    29%
	 source_acceptance_test/tests/test_incremental.py        69     38    45%
	 source_acceptance_test/utils/__init__.py                 6      0   100%
	 source_acceptance_test/utils/asserts.py                 37      2    95%
	 source_acceptance_test/utils/common.py                  41     24    41%
	 source_acceptance_test/utils/compare.py                 62     25    60%
	 source_acceptance_test/utils/connector_runner.py        82     49    40%
	 source_acceptance_test/utils/json_schema_helper.py     115     14    88%
	 ------------------------------------------------------------------------
	 TOTAL                                                  896    440    51%
	 ---------- coverage: platform linux, python 3.8.10-final-0 -----------
	 Name                                                              Stmts   Miss  Cover
	 -------------------------------------------------------------------------------------
	 source_s3/__init__.py                                                 2      0   100%
	 source_s3/s3_utils.py                                                20      0   100%
	 source_s3/s3file.py                                                  37      2    95%
	 source_s3/source.py                                                  23      0   100%
	 source_s3/source_files_abstract/__init__.py                           0      0   100%
	 source_s3/source_files_abstract/file_info.py                         32     11    66%
	 source_s3/source_files_abstract/formats/abstract_file_parser.py      38      2    95%
	 source_s3/source_files_abstract/formats/csv_parser.py               126     23    82%
	 source_s3/source_files_abstract/formats/csv_spec.py                  15      0   100%
	 source_s3/source_files_abstract/formats/parquet_parser.py            62     44    29%
	 source_s3/source_files_abstract/formats/parquet_spec.py               9      0   100%
	 source_s3/source_files_abstract/source.py                            37     14    62%
	 source_s3/source_files_abstract/spec.py                              42     22    48%
	 source_s3/source_files_abstract/storagefile.py                       23      1    96%
	 source_s3/source_files_abstract/stream.py                           182     11    94%
	 source_s3/stream.py                                                  42      3    93%
	 -------------------------------------------------------------------------------------
	 TOTAL                                                               690    133    81%
	 ---------- coverage: platform linux, python 3.8.10-final-0 -----------
	 Name                                                              Stmts   Miss  Cover
	 -------------------------------------------------------------------------------------
	 source_s3/__init__.py                                                 2      0   100%
	 source_s3/s3_utils.py                                                20     13    35%
	 source_s3/s3file.py                                                  37     18    51%
	 source_s3/source.py                                                  23      0   100%
	 source_s3/source_files_abstract/__init__.py                           0      0   100%
	 source_s3/source_files_abstract/file_info.py                         32      5    84%
	 source_s3/source_files_abstract/formats/abstract_file_parser.py      38      0   100%
	 source_s3/source_files_abstract/formats/csv_parser.py               126     22    83%
	 source_s3/source_files_abstract/formats/csv_spec.py                  15      0   100%
	 source_s3/source_files_abstract/formats/parquet_parser.py            62      3    95%
	 source_s3/source_files_abstract/formats/parquet_spec.py               9      0   100%
	 source_s3/source_files_abstract/source.py                            37     15    59%
	 source_s3/source_files_abstract/spec.py                              42     22    48%
	 source_s3/source_files_abstract/storagefile.py                       23      5    78%
	 source_s3/source_files_abstract/stream.py                           182     91    50%
	 source_s3/stream.py                                                  42     30    29%
	 -------------------------------------------------------------------------------------
	 source_s3/stream.py                                                  42     30    29%/actions-runner/_work/airbyte/airbyte/airbyte-integrations/connectors/source-s3/.venv/lib/python3.8/site-packages/coverage/data.py:118: CoverageWarning: Data file '/actions-runner/_work/airbyte/airbyte/airbyte-integrations/connectors/source-s3/.coverage.ip-10-0-51-178.9125.575151' doesn't seem to be a coverage data file: Couldn't use data file '/actions-runner/_work/airbyte/airbyte/airbyte-integrations/connectors/source-s3/.coverage.ip-10-0-51-178.9125.575151': no such table: coverage_schema
	 TOTAL                                                               690    224    68%

Phlair

Some great stuff in here!

the file_info class and obtaining last_modified in stream are solid changes. We reduce network calls and potentially even use less memory (due to efficient class storage) 👍
adding a way to enforce memory cap during testing, awesome. This could be a great tool in cdk for developers to utilise in tests.

Would be great if you could update the docstrings and code comments where appropriate to indicate these logic changes, it will help any new developers to not get confused (e.g. at some point we'll be adding GCP/Azure Blob using this abstract framework).

Not sure on:

custom chunking in CSV. Can't/isn't PyArrow already doing this?
changes to stream slices, see my comment on that.

Let's discuss those on the comments I made and go from there 👍

(haven't done detailed review of all the new tests yet, will wait for any changes as this could alter those and then do so)

Phlair · 2021-12-08T11:47:52Z

airbyte-integrations/connectors/source-s3/source_s3/source_files_abstract/file_info.py

+        return self.__str__()
+
+    @classmethod
+    def create_by_local_file(cls, filepath: str) -> "FileInfo":


Looks like we're only using this method in testing... doesn't make sense as a method of the class imo, should rather be a separate private testing method to instantiate an instance of FileInfo if we need it.

moved to test folders

airbyte-integrations/connectors/source-s3/source_s3/source_files_abstract/formats/csv_parser.py

airbyte-integrations/connectors/source-s3/source_s3/source_files_abstract/stream.py

airbyte-integrations/connectors/source-s3/integration_tests/big_csv_file_test.py

airbyte-integrations/connectors/source-s3/source_s3/stream.py

airbyte-integrations/connectors/source-s3/source_s3/source_files_abstract/file_info.py

airbyte-integrations/connectors/source-s3/source_s3/source_files_abstract/stream.py

…es_abstract/file_info.py Co-authored-by: George Claireaux <[email protected]>

…-memory-leak

antixar · 2022-02-01T16:11:11Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779353901
✅ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779353901
No Python unittests run

antixar · 2022-02-01T17:21:19Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779708516
✅ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779708516
Python tests coverage:

	 Name                                                 Stmts   Miss  Cover
	 ------------------------------------------------------------------------
	 source_acceptance_test/__init__.py                       2      0   100%
	 source_acceptance_test/base.py                          10      4    60%
	 source_acceptance_test/config.py                        74      6    92%
	 source_acceptance_test/tests/__init__.py                 4      0   100%
	 source_acceptance_test/tests/test_core.py              275    106    61%
	 source_acceptance_test/tests/test_full_refresh.py       52      2    96%
	 source_acceptance_test/tests/test_incremental.py        69     38    45%
	 source_acceptance_test/utils/__init__.py                 6      0   100%
	 source_acceptance_test/utils/asserts.py                 37      2    95%
	 source_acceptance_test/utils/common.py                  70     17    76%
	 source_acceptance_test/utils/compare.py                 62     23    63%
	 source_acceptance_test/utils/connector_runner.py       110     48    56%
	 source_acceptance_test/utils/json_schema_helper.py     105     13    88%
	 ------------------------------------------------------------------------
	 TOTAL                                                  876    259    70%
	 Name                                                              Stmts   Miss  Cover
	 -------------------------------------------------------------------------------------
	 source_s3/__init__.py                                                 2      0   100%
	 source_s3/s3_utils.py                                                19      0   100%
	 source_s3/s3file.py                                                  37      2    95%
	 source_s3/source.py                                                  28      1    96%
	 source_s3/source_files_abstract/__init__.py                           0      0   100%
	 source_s3/source_files_abstract/file_info.py                         26      8    69%
	 source_s3/source_files_abstract/formats/abstract_file_parser.py      35      2    94%
	 source_s3/source_files_abstract/formats/csv_parser.py                74     18    76%
	 source_s3/source_files_abstract/formats/csv_spec.py                  16      0   100%
	 source_s3/source_files_abstract/formats/parquet_parser.py            61     44    28%
	 source_s3/source_files_abstract/formats/parquet_spec.py               9      0   100%
	 source_s3/source_files_abstract/source.py                            37     14    62%
	 source_s3/source_files_abstract/spec.py                              42     22    48%
	 source_s3/source_files_abstract/storagefile.py                       23      1    96%
	 source_s3/source_files_abstract/stream.py                           184     11    94%
	 source_s3/stream.py                                                  43      3    93%
	 source_s3/utils.py                                                   29     10    66%
	 -------------------------------------------------------------------------------------
	 TOTAL                                                               665    136    80%
	 Name                                                              Stmts   Miss  Cover
	 -------------------------------------------------------------------------------------
	 source_s3/__init__.py                                                 2      0   100%
	 source_s3/s3_utils.py                                                19     13    32%
	 source_s3/s3file.py                                                  37     18    51%
	 source_s3/source.py                                                  28      0   100%
	 source_s3/source_files_abstract/__init__.py                           0      0   100%
	 source_s3/source_files_abstract/file_info.py                         26     10    62%
	 source_s3/source_files_abstract/formats/abstract_file_parser.py      35      0   100%
	 source_s3/source_files_abstract/formats/csv_parser.py                74     18    76%
	 source_s3/source_files_abstract/formats/csv_spec.py                  16      0   100%
	 source_s3/source_files_abstract/formats/parquet_parser.py            61      3    95%
	 source_s3/source_files_abstract/formats/parquet_spec.py               9      0   100%
	 source_s3/source_files_abstract/source.py                            37     15    59%
	 source_s3/source_files_abstract/spec.py                              42     22    48%
	 source_s3/source_files_abstract/storagefile.py                       23      5    78%
	 source_s3/source_files_abstract/stream.py                           184     91    51%
	 source_s3/stream.py                                                  43     30    30%
	 source_s3/utils.py                                                   29      8    72%
	 -------------------------------------------------------------------------------------
	 TOTAL                                                               665    233    65%

antixar · 2022-02-01T17:43:56Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779814977
❌ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779814977
🐛 https://gradle.com/s/eqazn7stzdnwo

antixar · 2022-02-01T18:04:49Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779910305
❌ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1779910305
🐛 https://gradle.com/s/hm4nyrgi4zvc4

antixar · 2022-02-01T19:23:00Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1780270201
❌ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1780270201
🐛 https://gradle.com/s/7vle5cins4ylg

antixar · 2022-02-01T19:41:02Z

/test connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1780348324
✅ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1780348324
Python tests coverage:

	 Name                                                 Stmts   Miss  Cover
	 ------------------------------------------------------------------------
	 source_acceptance_test/__init__.py                       2      0   100%
	 source_acceptance_test/base.py                          10      4    60%
	 source_acceptance_test/config.py                        74      6    92%
	 source_acceptance_test/tests/__init__.py                 4      0   100%
	 source_acceptance_test/tests/test_core.py              275    106    61%
	 source_acceptance_test/tests/test_full_refresh.py       52      2    96%
	 source_acceptance_test/tests/test_incremental.py        69     38    45%
	 source_acceptance_test/utils/__init__.py                 6      0   100%
	 source_acceptance_test/utils/asserts.py                 37      2    95%
	 source_acceptance_test/utils/common.py                  70     17    76%
	 source_acceptance_test/utils/compare.py                 62     23    63%
	 source_acceptance_test/utils/connector_runner.py       110     48    56%
	 source_acceptance_test/utils/json_schema_helper.py     105     13    88%
	 ------------------------------------------------------------------------
	 TOTAL                                                  876    259    70%
	 Name                                                              Stmts   Miss  Cover
	 -------------------------------------------------------------------------------------
	 source_s3/__init__.py                                                 2      0   100%
	 source_s3/s3_utils.py                                                19      0   100%
	 source_s3/s3file.py                                                  37      2    95%
	 source_s3/source.py                                                  28      1    96%
	 source_s3/source_files_abstract/__init__.py                           0      0   100%
	 source_s3/source_files_abstract/file_info.py                         26      8    69%
	 source_s3/source_files_abstract/formats/abstract_file_parser.py      35      2    94%
	 source_s3/source_files_abstract/formats/csv_parser.py                74     18    76%
	 source_s3/source_files_abstract/formats/csv_spec.py                  16      0   100%
	 source_s3/source_files_abstract/formats/parquet_parser.py            61     44    28%
	 source_s3/source_files_abstract/formats/parquet_spec.py               9      0   100%
	 source_s3/source_files_abstract/source.py                            37     14    62%
	 source_s3/source_files_abstract/spec.py                              42     22    48%
	 source_s3/source_files_abstract/storagefile.py                       23      1    96%
	 source_s3/source_files_abstract/stream.py                           184     11    94%
	 source_s3/stream.py                                                  43      3    93%
	 source_s3/utils.py                                                   29     10    66%
	 -------------------------------------------------------------------------------------
	 TOTAL                                                               665    136    80%
	 Name                                                              Stmts   Miss  Cover
	 -------------------------------------------------------------------------------------
	 source_s3/__init__.py                                                 2      0   100%
	 source_s3/s3_utils.py                                                19     13    32%
	 source_s3/s3file.py                                                  37     18    51%
	 source_s3/source.py                                                  28      0   100%
	 source_s3/source_files_abstract/__init__.py                           0      0   100%
	 source_s3/source_files_abstract/file_info.py                         26     10    62%
	 source_s3/source_files_abstract/formats/abstract_file_parser.py      35      0   100%
	 source_s3/source_files_abstract/formats/csv_parser.py                74     18    76%
	 source_s3/source_files_abstract/formats/csv_spec.py                  16      0   100%
	 source_s3/source_files_abstract/formats/parquet_parser.py            61      3    95%
	 source_s3/source_files_abstract/formats/parquet_spec.py               9      0   100%
	 source_s3/source_files_abstract/source.py                            37     15    59%
	 source_s3/source_files_abstract/spec.py                              42     22    48%
	 source_s3/source_files_abstract/storagefile.py                       23      5    78%
	 source_s3/source_files_abstract/stream.py                           184     91    51%
	 source_s3/stream.py                                                  43     30    30%
	 source_s3/utils.py                                                   29      8    72%
	 -------------------------------------------------------------------------------------
	 TOTAL                                                               665    233    65%

antixar · 2022-02-01T22:21:20Z

/publish connector=connectors/source-s3

🕑 connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1781019772
✅ connectors/source-s3 https://github.com/airbytehq/airbyte/actions/runs/1781019772

antixar added 2 commits November 23, 2021 09:56

update unit tests

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update tests

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github-actions bot added the area/connectors Connector related issues label Nov 25, 2021

antixar self-assigned this Nov 25, 2021

antixar linked an issue Nov 25, 2021 that may be closed by this pull request

Memory leak in source-s3 while reading big CSV file #6870

Closed

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fix conftest

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antixar requested review from midavadim and annalvova05 November 25, 2021 17:07

correction connection_setup

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antixar requested a review from Phlair November 26, 2021 08:03

Phlair previously requested changes Dec 8, 2021

View reviewed changes

Update airbyte-integrations/connectors/source-s3/source_s3/source_fil…

a84d5bb

…es_abstract/file_info.py Co-authored-by: George Claireaux <[email protected]>

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antixar added 3 commits December 16, 2021 01:38

merge with master

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restore slice logic

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Merge remote-tracking branch 'origin' into antixar/6870-source-s3-csv…

fb5daa0

…-memory-leak

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test failed unittests

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test failed integration tests

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antixar merged commit 91eff1d into master Feb 1, 2022

antixar deleted the antixar/6870-source-s3-csv-memory-leak branch February 1, 2022 22:49

octavia-squidington-iii mentioned this pull request Feb 3, 2022

Bump Airbyte version from 0.35.15-alpha to 0.35.16-alpha #10048

Merged

🐛 Source S3: Loading of files' metadata #8252

🐛 Source S3: Loading of files' metadata #8252

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antixar commented Nov 25, 2021 •

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