nmdc-schema 11.11.0__tar.gz → 11.12.0rc1__tar.gz
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.
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/PKG-INFO +1 -1
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_10_0_to_11_11_0/migrator_from_11_10_0_to_11_11_0_part_1.py +2 -2
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc-pydantic.py +601 -224
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc.py +133 -39
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc.schema.json +37 -14
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc_materialized_patterns.json +1090 -57
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc_materialized_patterns.schema.json +37 -14
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc_materialized_patterns.yaml +845 -52
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/pyproject.toml +12 -1
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/LICENSE +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/README.md +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/README.md +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/anyuri_strings_to_iris.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/dump_single_modality.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/get_json_schema.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/get_nmdc_view.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/gold-to-mixs.sssom.tsv +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/id_helpers.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migration_recursion.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/.docker/.env.example +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/.docker/docker-compose.yaml +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/.docker/mongoKeyFile +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/.docker/mongo_init/initialize_replica_set.sh +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/.docker/wait-for-it.sh +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/README.md +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/adapters/adapter_base.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/adapters/dictionary_adapter.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/adapters/mongo_adapter.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/adapters/test_dictionary_adapter.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/adapters/test_mongo_adapter.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/assets/migrator_from_10_2_0_to_11_0_0_part_08/instrument_set.yaml +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/assets/migrator_from_11_7_to_11_8/data_category_map.yaml +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/assets/migrator_from_8_1_to_9_0/study_dois_changes.yaml +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/assets/migrator_from_9_1_to_9_2/websites_dois.yaml +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/cli/README.md +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/cli/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/cli/create_migrator.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/cli/migrator.py.template +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/cli/run_migrator.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/helpers.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migration_reporter.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_base.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_0_0_to_10_1_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_2_0_to_11_0_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_3_0_to_10_4_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_4_0_to_10_5_4.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_5_4_to_10_5_5.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_5_5_to_10_5_6.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_5_6_to_10_6_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_10_6_0_to_10_7_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_0_3_to_11_1_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_10_0_to_11_11_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_1_0_to_11_2_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_3_0_to_11_4_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_4_0_to_11_5_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_5_0_to_11_5_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_5_1_to_11_6_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_6_0_to_11_6_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_6_1_to_11_7_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_7_0_to_11_8_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_8_0_to_11_9_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_11_9_1_to_11_10_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_1_0_0_to_EXAMPLE.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_7_7_2_to_7_8_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_7_8_0_to_8_0_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_8_0_to_8_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_8_1_to_9_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_9_1_to_9_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/migrator_from_9_3_to_10_0.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/README.md +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_01.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_02.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_03.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_04.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_05.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_06.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_07.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_08.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_09.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_10.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_11.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_12.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_13.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_14.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_15.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/migrator_from_10_2_0_to_11_0_0_part_16.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_0_3_to_11_1_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_0_3_to_11_1_0/migrator_from_11_0_3_to_11_1_0_part_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_0_3_to_11_1_0/migrator_from_11_0_3_to_11_1_0_part_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_0_3_to_11_1_0/migrator_from_11_0_3_to_11_1_0_part_3.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_10_0_to_11_11_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_10_0_to_11_11_0/migrator_from_11_10_0_to_11_11_0_part_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_1_0_to_11_2_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_1_0_to_11_2_0/migrator_from_11_1_0_to_11_2_0_part_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_1_0_to_11_2_0/migrator_from_11_1_0_to_11_2_0_part_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_5_1_to_11_6_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_5_1_to_11_6_0/migrator_from_11_5_1_to_11_6_0_part_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_5_1_to_11_6_0/migrator_from_11_5_1_to_11_6_0_part_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_7_0_to_11_8_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_7_0_to_11_8_0/migrator_from_11_7_0_to_11_8_0_part_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_7_0_to_11_8_0/migrator_from_11_7_0_to_11_8_0_part_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_7_0_to_11_8_0/migrator_from_11_7_0_to_11_8_0_part_3.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_7_0_to_11_8_0/migrator_from_11_7_0_to_11_8_0_part_4.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_7_0_to_11_8_0/migrator_from_11_7_0_to_11_8_0_part_5.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_8_0_to_11_9_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_8_0_to_11_9_0/migrator_from_11_8_0_to_11_9_0_part_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_8_0_to_11_9_0/migrator_from_11_8_0_to_11_9_0_part_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_9_1_to_11_10_0/__init__.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_9_1_to_11_10_0/migrator_from_11_9_1_to_11_10_0_part_1.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_9_1_to_11_10_0/migrator_from_11_9_1_to_11_10_0_part_2.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/migrators/partials/migrator_from_11_9_1_to_11_10_0/migrator_from_11_9_1_to_11_10_0_part_3.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc_data.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/nmdc_version.py +0 -0
- {nmdc_schema-11.11.0 → nmdc_schema-11.12.0rc1}/nmdc_schema/validate_nmdc_json.py +0 -0
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def upgrade(self, commit_changes: bool = True) -> None:
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r"""Migrates the database from conforming to the original schema, to conforming to the new schema."""
|
|
12
12
|
self.adapter.do_for_each_document("biosample_set", self.check_for_fields)
|
|
13
13
|
|
|
14
|
-
def check_for_fields(self, biosample: dict) ->
|
|
14
|
+
def check_for_fields(self, biosample: dict) -> None:
|
|
15
15
|
r"""
|
|
16
16
|
Check each biosample record to ensure none of the removed slots are being used.
|
|
17
17
|
List of the slots that were removed:
|