Remove aggregation of code metadata from default extraction ETL. #157

mmcdermott · 2024-08-14T01:13:05Z

Closes #110

Release candidate for 0.0.4

Release 0.0.5

coderabbitai · 2024-08-14T01:13:10Z

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codecov-commenter · 2024-08-14T01:14:38Z

Test Failures Detected: Due to failing tests, we cannot provide coverage reports at this time.

❌ Failed Test Results:

Completed 77 tests with 1 failed, 76 passed and 0 skipped.

View the full list of failed tests

pytest

Class name: tests.test_fit_vocabulary_indices
Test name: test_fit_vocabulary_indices_with_default_stage_config

want = shape: (12, 9)
┌───────────────────────┬────────────────────┬─────────────────┬──────────────────────┬─────────────┬──...───────────────────┴─────────────┴────────────────┴─────────────────────────────────┴──────────────┴──────────────────┘
got = shape: (12, 9)
┌───────────────────────┬────────────────────┬─────────────────┬──────────────────────┬─────────────┬──...───────────────┴─────────────┴────────────────┴─────────────────────────────────┴──────────────────┴──────────────────┘
msg = 'Expected the dataframe at .../output_cohort/metadata/codes.parquet to be equal to the target.\nScript st...it_vocabulary_indices\x1b[0m:\x1b[36mmain\x1b[0m:\x1b[36m237\x1b[0m - \x1b[1mDone with fit_vocabulary_indices\x1b[0m\n'
kwargs = {'check_column_order': False, 'check_row_order': True}

    def assert_df_equal(want: pl.DataFrame, got: pl.DataFrame, msg: str = None, **kwargs):
        try:
>           assert_frame_equal(want, got, **kwargs)

tests/utils.py:172: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

args = (shape: (12, 9)
┌───────────────────────┬────────────────────┬─────────────────┬──────────────────────┬─────────────┬─...──────────────┴─────────────┴────────────────┴─────────────────────────────────┴──────────────────┴──────────────────┘)
kwargs = {'check_column_order': False, 'check_row_order': True}

    @wraps(function)
    def wrapper(*args: P.args, **kwargs: P.kwargs) -> T:
        _rename_keyword_argument(
            old_name, new_name, kwargs, function.__qualname__, version
        )
>       return function(*args, **kwargs)
E       AssertionError: DataFrames are different (dtypes do not match)
E       [left]:  {'code': String, 'code/n_occurrences': UInt8, 'code/n_patients': UInt8, 'values/n_occurrences': UInt8, 'values/sum': Float32, 'values/sum_sqd': Float32, 'description': String, 'parent_codes': String, 'code/vocab_index': UInt8}
E       [right]: {'code': String, 'code/n_occurrences': UInt8, 'code/n_patients': UInt8, 'values/n_occurrences': UInt8, 'values/sum': Float32, 'values/sum_sqd': Float32, 'description': String, 'parent_codes': List(String), 'code/vocab_index': UInt8}

.../hostedtoolcache/Python/3.12.4.../x64/lib/python3.12.../polars/_utils/deprecation.py:91: AssertionError

The above exception was the direct cause of the following exception:

    def test_fit_vocabulary_indices_with_default_stage_config():
>       single_stage_transform_tester(
            transform_script=FIT_VOCABULARY_INDICES_SCRIPT,
            stage_name="fit_vocabulary_indices",
            transform_stage_kwargs=None,
            want_outputs=WANT_DF,
        )

tests/test_fit_vocabulary_indices.py:42: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/transform_tester_base.py:387: in single_stage_transform_tester
    check_df_output(cohort_metadata_dir / "codes.parquet", want_outputs, stderr, stdout)
tests/transform_tester_base.py:285: in check_df_output
    assert_df_equal(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

want = shape: (12, 9)
┌───────────────────────┬────────────────────┬─────────────────┬──────────────────────┬─────────────┬──...───────────────────┴─────────────┴────────────────┴─────────────────────────────────┴──────────────┴──────────────────┘
got = shape: (12, 9)
┌───────────────────────┬────────────────────┬─────────────────┬──────────────────────┬─────────────┬──...───────────────┴─────────────┴────────────────┴─────────────────────────────────┴──────────────────┴──────────────────┘
msg = 'Expected the dataframe at .../output_cohort/metadata/codes.parquet to be equal to the target.\nScript st...it_vocabulary_indices\x1b[0m:\x1b[36mmain\x1b[0m:\x1b[36m237\x1b[0m - \x1b[1mDone with fit_vocabulary_indices\x1b[0m\n'
kwargs = {'check_column_order': False, 'check_row_order': True}

    def assert_df_equal(want: pl.DataFrame, got: pl.DataFrame, msg: str = None, **kwargs):
        try:
            assert_frame_equal(want, got, **kwargs)
        except AssertionError as e:
            pl.Config.set_tbl_rows(-1)
            print(f"DFs are not equal: {msg}\nwant:")
            print(want)
            print("got:")
            print(got)
>           raise AssertionError(f"{msg}\n{e}") from e
E           AssertionError: Expected the dataframe at .../output_cohort/metadata/codes.parquet to be equal to the target.
E           Script stdout:
E           [2024-08-14 01:14:07,212][HYDRA] Hydra 1.3.2
E           [2024-08-14 01:14:07,212][HYDRA] ===========
E           [2024-08-14 01:14:07,212][HYDRA] Installed Hydra Plugins
E           [2024-08-14 01:14:07,212][HYDRA] ***********************
E           [2024-08-14 01:14:07,212][HYDRA] 	ConfigSource:
E           [2024-08-14 01:14:07,212][HYDRA] 	-------------
E           [2024-08-14 01:14:07,212][HYDRA] 		FileConfigSource
E           [2024-08-14 01:14:07,212][HYDRA] 		ImportlibResourcesConfigSource
E           [2024-08-14 01:14:07,212][HYDRA] 		StructuredConfigSource
E           [2024-08-14 01:14:07,212][HYDRA] 	CompletionPlugin:
E           [2024-08-14 01:14:07,212][HYDRA] 	-----------------
E           [2024-08-14 01:14:07,212][HYDRA] 		BashCompletion
E           [2024-08-14 01:14:07,212][HYDRA] 		FishCompletion
E           [2024-08-14 01:14:07,213][HYDRA] 		ZshCompletion
E           [2024-08-14 01:14:07,213][HYDRA] 	Launcher:
E           [2024-08-14 01:14:07,213][HYDRA] 	---------
E           [2024-08-14 01:14:07,213][HYDRA] 		BasicLauncher
E           [2024-08-14 01:14:07,213][HYDRA] 	Sweeper:
E           [2024-08-14 01:14:07,213][HYDRA] 	--------
E           [2024-08-14 01:14:07,213][HYDRA] 		BasicSweeper
E           [2024-08-14 01:14:07,213][HYDRA] 
E           [2024-08-14 01:14:07,213][HYDRA] Config search path
E           [2024-08-14 01:14:07,213][HYDRA] ******************
E           [2024-08-14 01:14:07,502][HYDRA] | Provider | Search path                                                                          |
E           [2024-08-14 01:14:07,502][HYDRA] ---------------------------------------------------------------------------------------------------
E           [2024-08-14 01:14:07,502][HYDRA] | hydra    | pkg://hydra.conf                                                                     |
E           [2024-08-14 01:14:07,502][HYDRA] | main     | file:.../src/MEDS_transforms/configs |
E           [2024-08-14 01:14:07,502][HYDRA] | schema   | structured://                                                                        |
E           [2024-08-14 01:14:07,502][HYDRA] ---------------------------------------------------------------------------------------------------
E           [2024-08-14 01:14:07,646][HYDRA] 
E           [2024-08-14 01:14:07,646][HYDRA] Defaults Tree
E           [2024-08-14 01:14:07,646][HYDRA] *************
E           [2024-08-14 01:14:07,646][HYDRA] <root>:
E           [2024-08-14 01:14:07,646][HYDRA]   hydra/config:
E           [2024-08-14 01:14:07,646][HYDRA]     hydra/output: default
E           [2024-08-14 01:14:07,646][HYDRA]     hydra/launcher: basic
E           [2024-08-14 01:14:07,646][HYDRA]     hydra/sweeper: basic
E           [2024-08-14 01:14:07,647][HYDRA]     hydra/help: default
E           [2024-08-14 01:14:07,647][HYDRA]     hydra/hydra_help: default
E           [2024-08-14 01:14:07,647][HYDRA]     hydra/hydra_logging: default
E           [2024-08-14 01:14:07,647][HYDRA]     hydra/job_logging: default
E           [2024-08-14 01:14:07,647][HYDRA]     hydra/callbacks: null
E           [2024-08-14 01:14:07,647][HYDRA]     hydra/env: default
E           [2024-08-14 01:14:07,647][HYDRA]     _self_
E           [2024-08-14 01:14:07,647][HYDRA]   preprocess:
E           [2024-08-14 01:14:07,647][HYDRA]     pipeline
E           [2024-08-14 01:14:07,647][HYDRA]     stage_configs/reshard_to_split
E           [2024-08-14 01:14:07,647][HYDRA]     stage_configs/filter_patients
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/add_time_derived_measurements
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/count_code_occurrences
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/filter_measurements
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/fit_outlier_detection
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/occlude_outliers
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/fit_normalization
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/fit_vocabulary_indices
E           [2024-08-14 01:14:07,648][HYDRA]     stage_configs/reorder_measurements
E           [2024-08-14 01:14:07,648][HYDRA]     _self_
E           [2024-08-14 01:14:07,791][HYDRA] 
E           [2024-08-14 01:14:07,791][HYDRA] Defaults List
E           [2024-08-14 01:14:07,791][HYDRA] *************
E           [2024-08-14 01:14:07,791][HYDRA] | Config path                                 | Package             | _self_ | Parent       | 
E           [2024-08-14 01:14:07,791][HYDRA] ----------------------------------------------------------------------------------------------
E           [2024-08-14 01:14:07,791][HYDRA] | hydra/output/default                        | hydra               | False  | hydra/config |
E           [2024-08-14 01:14:07,791][HYDRA] | hydra/launcher/basic                        | hydra.launcher      | False  | hydra/config |
E           [2024-08-14 01:14:07,791][HYDRA] | hydra/sweeper/basic                         | hydra.sweeper       | False  | hydra/config |
E           [2024-08-14 01:14:07,791][HYDRA] | hydra/help/default                          | hydra.help          | False  | hydra/config |
E           [2024-08-14 01:14:07,791][HYDRA] | hydra/hydra_help/default                    | hydra.hydra_help    | False  | hydra/config |
E           [2024-08-14 01:14:07,791][HYDRA] | hydra/hydra_logging/default                 | hydra.hydra_logging | False  | hydra/config |
E           [2024-08-14 01:14:07,792][HYDRA] | hydra/job_logging/default                   | hydra.job_logging   | False  | hydra/config |
E           [2024-08-14 01:14:07,792][HYDRA] | hydra/env/default                           | hydra.env           | False  | hydra/config |
E           [2024-08-14 01:14:07,792][HYDRA] | hydra/config                                | hydra               | True   | <root>       |
E           [2024-08-14 01:14:07,792][HYDRA] | pipeline                                    |                     | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/reshard_to_split              | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/filter_patients               | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/add_time_derived_measurements | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/count_code_occurrences        | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/filter_measurements           | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/fit_outlier_detection         | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/occlude_outliers              | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/fit_normalization             | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/fit_vocabulary_indices        | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | stage_configs/reorder_measurements          | stage_configs       | False  | preprocess   |
E           [2024-08-14 01:14:07,792][HYDRA] | preprocess                                  |                     | True   | <root>       |
E           [2024-08-14 01:14:07,792][HYDRA] ----------------------------------------------------------------------------------------------
E           [2024-08-14 01:14:08,064][HYDRA] Config
E           [2024-08-14 01:14:08,064][HYDRA] ******
E           [2024-08-14 01:14:08,077][HYDRA] input_dir: ....../tmp/tmpewm0iuof/MEDS_cohort
E           cohort_dir: ........./tmp/tmpewm0iuof/output_cohort
E           _default_description: 'This is a MEDS pipeline ETL. Please set a more detailed description
E             at the top of your specific pipeline
E           
E             configuration file.'
E           log_dir: ${stage_cfg.output_dir}/.logs
E           do_overwrite: false
E           seed: 1
E           stages:
E           - fit_vocabulary_indices
E           stage_configs:
E             reshard_to_split:
E               n_patients_per_shard: 50000
E             filter_patients:
E               min_events_per_patient: null
E               min_measurements_per_patient: null
E             add_time_derived_measurements:
E               age:
E                 DOB_code: MEDS_BIRTH
E                 age_code: AGE
E                 age_unit: years
E               time_of_day:
E                 time_of_day_code: TIME_OF_DAY
E                 endpoints:
E                 - 6
E                 - 12
E                 - 18
E                 - 24
E             count_code_occurrences:
E               aggregations:
E               - code/n_occurrences
E               - code/n_patients
E               do_summarize_over_all_codes: true
E             filter_measurements:
E               min_patients_per_code: null
E               min_occurrences_per_code: null
E             fit_outlier_detection:
E               aggregations:
E               - values/n_occurrences
E               - values/sum
E               - values/sum_sqd
E             occlude_outliers:
E               stddev_cutoff: 4.5
E             fit_normalization:
E               aggregations:
E               - code/n_occurrences
E               - code/n_patients
E               - values/n_occurrences
E               - values/sum
E               - values/sum_sqd
E             fit_vocabulary_indices:
E               is_metadata: true
E               ordering_method: lexicographic
E               output_dir: ${cohort_dir}
E             reorder_measurements:
E               ordered_code_patterns: &&&
E           worker: 0
E           polling_time: 300
E           stage: ${current_script_name:}
E           stage_cfg: ${oc.create:${populate_stage:${stage}, ${input_dir}, ${cohort_dir}, ${stages},
E             ${stage_configs}}}
E           etl_metadata:
E             pipeline_name: &&&
E             dataset_name: &&&
E             dataset_version: &&&
E             package_name: ${get_package_name:}
E             package_version: ${get_package_version:}
E           etl_metadata.pipeline_name: preprocess
E           code_modifiers: &&&
E           
E           
E           Script stderr:
E           #x1B[32m2024-08-14 01:14:08.218#x1B[0m | #x1B[1mINFO    #x1B[0m | #x1B[36mMEDS_transforms.fit_vocabulary_indices#x1B[0m:#x1B[36mmain#x1B[0m:#x1B[36m203#x1B[0m - #x1B[1mRunning with config:
E           input_dir: ....../tmp/tmpewm0iuof/MEDS_cohort
E           cohort_dir: ........./tmp/tmpewm0iuof/output_cohort
E           _default_description: 'This is a MEDS pipeline ETL. Please set a more detailed description
E             at the top of your specific pipeline
E           
E             configuration file.'
E           log_dir: ${stage_cfg.output_dir}/.logs
E           do_overwrite: false
E           seed: 1
E           stages:
E           - fit_vocabulary_indices
E           stage_configs:
E             reshard_to_split:
E               n_patients_per_shard: 50000
E             filter_patients:
E               min_events_per_patient: null
E               min_measurements_per_patient: null
E             add_time_derived_measurements:
E               age:
E                 DOB_code: MEDS_BIRTH
E                 age_code: AGE
E                 age_unit: years
E               time_of_day:
E                 time_of_day_code: TIME_OF_DAY
E                 endpoints:
E                 - 6
E                 - 12
E                 - 18
E                 - 24
E             count_code_occurrences:
E               aggregations:
E               - code/n_occurrences
E               - code/n_patients
E               do_summarize_over_all_codes: true
E             filter_measurements:
E               min_patients_per_code: null
E               min_occurrences_per_code: null
E             fit_outlier_detection:
E               aggregations:
E               - values/n_occurrences
E               - values/sum
E               - values/sum_sqd
E             occlude_outliers:
E               stddev_cutoff: 4.5
E             fit_normalization:
E               aggregations:
E               - code/n_occurrences
E               - code/n_patients
E               - values/n_occurrences
E               - values/sum
E               - values/sum_sqd
E             fit_vocabulary_indices:
E               is_metadata: true
E               ordering_method: lexicographic
E               output_dir: ${cohort_dir}
E             reorder_measurements:
E               ordered_code_patterns: &&&
E           worker: 0
E           polling_time: 300
E           stage: ${current_script_name:}
E           stage_cfg: ${oc.create:${populate_stage:${stage}, ${input_dir}, ${cohort_dir}, ${stages},
E             ${stage_configs}}}
E           etl_metadata:
E             pipeline_name: &&&
E             dataset_name: &&&
E             dataset_version: &&&
E             package_name: ${get_package_name:}
E             package_version: ${get_package_version:}
E           etl_metadata.pipeline_name: preprocess
E           code_modifiers: &&&
E           
E           Stage: fit_vocabulary_indices
E           
E           Stage config:
E           is_metadata: true
E           ordering_method: lexicographic
E           output_dir: ........./tmp/tmpewm0iuof/output_cohort
E           data_input_dir: ........./tmpewm0iuof/MEDS_cohort/data
E           metadata_input_dir: ........./tmpewm0iuof/MEDS_cohort/metadata
E           reducer_output_dir: ............/tmpewm0iuof/output_cohort/metadata
E           train_only: true
E           #x1B[0m
E           #x1B[32m2024-08-14 01:14:08.473#x1B[0m | #x1B[1mINFO    #x1B[0m | #x1B[36mMEDS_transforms.fit_vocabulary_indices#x1B[0m:#x1B[36mmain#x1B[0m:#x1B[36m222#x1B[0m - #x1B[1mAssigning code vocabulary indices via a lexicographic order.#x1B[0m
E           #x1B[32m2024-08-14 01:14:08.477#x1B[0m | #x1B[1mINFO    #x1B[0m | #x1B[36mMEDS_transforms.fit_vocabulary_indices#x1B[0m:#x1B[36mmain#x1B[0m:#x1B[36m233#x1B[0m - #x1B[1mIndices assigned. Writing to .../output_cohort/metadata/codes.parquet#x1B[0m
E           #x1B[32m2024-08-14 01:14:08.479#x1B[0m | #x1B[1mINFO    #x1B[0m | #x1B[36mMEDS_transforms.fit_vocabulary_indices#x1B[0m:#x1B[36mmain#x1B[0m:#x1B[36m237#x1B[0m - #x1B[1mDone with fit_vocabulary_indices#x1B[0m
E           
E           DataFrames are different (dtypes do not match)
E           [left]:  {'code': String, 'code/n_occurrences': UInt8, 'code/n_patients': UInt8, 'values/n_occurrences': UInt8, 'values/sum': Float32, 'values/sum_sqd': Float32, 'description': String, 'parent_codes': String, 'code/vocab_index': UInt8}
E           [right]: {'code': String, 'code/n_occurrences': UInt8, 'code/n_patients': UInt8, 'values/n_occurrences': UInt8, 'values/sum': Float32, 'values/sum_sqd': Float32, 'description': String, 'parent_codes': List(String), 'code/vocab_index': UInt8}

tests/utils.py:179: AssertionError

mmcdermott added 3 commits August 11, 2024 14:35

Merge pull request #146 from mmcdermott/dev

b5f0277

Release candidate for 0.0.4

Merge pull request #151 from mmcdermott/dev

e7ed727

Release 0.0.5

Removed aggregate from default ETL and added dedicated test.

1969ea1

mmcdermott linked an issue Aug 14, 2024 that may be closed by this pull request

The default extraction ETL should likely not include an aggregate_code_metadata.py stage, unless anyone thinks it would be almost universally useful. #110

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Fixed a parent_codes schema error in vocabulary index

fc17317

mmcdermott merged commit a751f72 into dev Aug 14, 2024
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mmcdermott deleted the 110_remove_agg_from_default_extract branch August 14, 2024 01:19

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Remove aggregation of code metadata from default extraction ETL. #157

Remove aggregation of code metadata from default extraction ETL. #157

mmcdermott commented Aug 14, 2024 •

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codecov-commenter commented Aug 14, 2024

pytest

Remove aggregation of code metadata from default extraction ETL. #157

Remove aggregation of code metadata from default extraction ETL. #157

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codecov-commenter commented Aug 14, 2024

❌ Failed Test Results:

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mmcdermott commented Aug 14, 2024 •

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