metameq 2026.1.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- metameq/__init__.py +42 -0
- metameq/_version.py +21 -0
- metameq/config/__init__.py +0 -0
- metameq/config/config.yml +3 -0
- metameq/config/standards.yml +1648 -0
- metameq/src/__init__.py +0 -0
- metameq/src/__main__.py +34 -0
- metameq/src/metadata_configurator.py +512 -0
- metameq/src/metadata_extender.py +1168 -0
- metameq/src/metadata_merger.py +362 -0
- metameq/src/metadata_transformers.py +335 -0
- metameq/src/metadata_validator.py +387 -0
- metameq/src/util.py +299 -0
- metameq/tests/__init__.py +0 -0
- metameq/tests/data/invalid.yml +1 -0
- metameq/tests/data/test_config.yml +9 -0
- metameq/tests/test_metadata_configurator.py +2334 -0
- metameq/tests/test_metadata_extender.py +2610 -0
- metameq/tests/test_metadata_merger.py +657 -0
- metameq/tests/test_metadata_transformers.py +277 -0
- metameq/tests/test_metadata_validator.py +1191 -0
- metameq/tests/test_util.py +436 -0
- metameq-2026.1.1.dist-info/METADATA +21 -0
- metameq-2026.1.1.dist-info/RECORD +27 -0
- metameq-2026.1.1.dist-info/WHEEL +5 -0
- metameq-2026.1.1.dist-info/entry_points.txt +2 -0
- metameq-2026.1.1.dist-info/top_level.txt +1 -0
metameq/__init__.py
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from metameq.src.util import HOSTTYPE_SHORTHAND_KEY, SAMPLETYPE_SHORTHAND_KEY, \
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SAMPLE_TYPE_KEY, QC_NOTE_KEY, LEAVE_BLANK_VAL, DO_NOT_USE_VAL, \
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NOT_PROVIDED_VAL, HOST_SUBJECT_ID_KEY, SAMPLE_NAME_KEY, \
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COLLECTION_TIMESTAMP_KEY, METADATA_TRANSFORMERS_KEY, SOURCES_KEY, \
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FUNCTION_KEY, PRE_TRANSFORMERS_KEY, POST_TRANSFORMERS_KEY, \
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extract_config_dict, deepcopy_dict, load_df_with_best_fit_encoding
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from metameq.src.metadata_configurator import build_full_flat_config_dict
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from metameq.src.metadata_extender import \
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write_extended_metadata, write_extended_metadata_from_df, \
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get_reserved_cols, get_extended_metadata_from_df_and_yaml, \
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write_metadata_results, id_missing_cols, find_standard_cols, \
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find_nonstandard_cols, get_qc_failures
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from metameq.src.metadata_merger import merge_sample_and_subject_metadata, \
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merge_many_to_one_metadata, merge_one_to_one_metadata, \
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find_common_col_names, find_common_df_cols
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from metameq.src.metadata_transformers import \
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format_a_datetime, standardize_input_sex, set_life_stage_from_age_yrs, \
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transform_input_sex_to_std_sex, transform_age_to_life_stage, \
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transform_date_to_formatted_date
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__all__ = ["HOSTTYPE_SHORTHAND_KEY", "SAMPLETYPE_SHORTHAND_KEY",
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"SAMPLE_TYPE_KEY", "QC_NOTE_KEY", "LEAVE_BLANK_VAL",
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"DO_NOT_USE_VAL", "NOT_PROVIDED_VAL",
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"HOST_SUBJECT_ID_KEY", "SAMPLE_NAME_KEY",
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"COLLECTION_TIMESTAMP_KEY", "METADATA_TRANSFORMERS_KEY",
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"SOURCES_KEY", "FUNCTION_KEY", "PRE_TRANSFORMERS_KEY",
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"POST_TRANSFORMERS_KEY",
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"extract_config_dict", "build_full_flat_config_dict",
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"deepcopy_dict", "load_df_with_best_fit_encoding",
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"merge_sample_and_subject_metadata", "merge_many_to_one_metadata",
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"merge_one_to_one_metadata", "find_common_col_names",
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"find_common_df_cols",
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"write_extended_metadata", "get_extended_metadata_from_df_and_yaml",
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"write_extended_metadata_from_df", "write_metadata_results",
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"get_reserved_cols", "id_missing_cols", "find_standard_cols",
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"find_nonstandard_cols", "get_qc_failures",
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"format_a_datetime", "standardize_input_sex",
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"set_life_stage_from_age_yrs", "transform_input_sex_to_std_sex",
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"transform_age_to_life_stage", "transform_date_to_formatted_date"]
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from . import _version
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__version__ = _version.get_versions()['version']
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metameq/_version.py
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# This file was generated by 'versioneer.py' (0.29) from
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# revision-control system data, or from the parent directory name of an
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# unpacked source archive. Distribution tarballs contain a pre-generated copy
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# of this file.
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import json
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version_json = '''
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{
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"date": "2026-01-28T14:30:42-0800",
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"dirty": false,
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"error": null,
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"full-revisionid": "b60757af0c4b7b16d71119971565d9991779f6d2",
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"version": "2026.01.1"
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}
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''' # END VERSION_JSON
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def get_versions():
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return json.loads(version_json)
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File without changes
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