nmdc-schema 11.14.0__py3-none-any.whl → 11.14.0rc1__py3-none-any.whl

{nmdc_schema-11.14.0.dist-info → nmdc_schema-11.14.0rc1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc_schema
-Version: 11.14.0
+Version: 11.14.0rc1
 Summary: Schema resources for the National Microbiome Data Collaborative (NMDC)
 License: MIT
 License-File: LICENSE
@@ -25,14 +25,13 @@ Requires-Dist: curies (>=0.9.0,<0.10.0)
 Requires-Dist: deprecated (>=1,<2)
 Requires-Dist: jsonasobj2 (>=1,<2)
 Requires-Dist: jsonschema (>=4,<5)
-Requires-Dist: linkml (>=1.9.6,<2.0.0)
-Requires-Dist: linkml-runtime (>=1.9.5,<2.0.0)
+Requires-Dist: linkml (>=1.9.1,<2.0.0)
+Requires-Dist: linkml-runtime (>=1.9.1,<2.0.0)
 Requires-Dist: pymongo (>=4.7.2,<5.0.0)
 Requires-Dist: python-dotenv
 Requires-Dist: pyyaml (>=6,<7)
 Requires-Dist: rdflib (>=6.2.0,<7.0.0)
 Requires-Dist: requests (>=2,<3)
-Requires-Dist: urllib3 (>=2.6.0)
 Project-URL: Documentation, https://microbiomedata.github.io/nmdc-schema/
 Project-URL: Homepage, https://microbiomedata.github.io/nmdc-schema/
 Project-URL: Repository, https://github.com/microbiomedata/nmdc-schema

{nmdc_schema-11.14.0.dist-info → nmdc_schema-11.14.0rc1.dist-info}/RECORD

@@ -42,7 +42,7 @@ nmdc_schema/migrators/migrator_from_10_6_0_to_10_7_0.py,sha256=-FduiWWIioYFQ2eST
 nmdc_schema/migrators/migrator_from_11_0_3_to_11_1_0.py,sha256=3hHXGts_sfre4KuIpGCUNyRMgI92_lXm_U2UStU-fdw,1184
 nmdc_schema/migrators/migrator_from_11_10_0_to_11_11_0.py,sha256=R4nUrhxRznukwKgkMQy8uuPzn-fE9AaQYNLLNsVOfTk,1354
 nmdc_schema/migrators/migrator_from_11_11_0_to_11_13_0.py,sha256=p0giuWeWOvxLe22T0QXNWxjzWWqgzJ1ZetpdVCz86IY,1354
-nmdc_schema/migrators/migrator_from_11_13_0_to_11_14_0.py,sha256=Y6WY3QGn9fVPh_hzyyC0UXX1U0nQNB624v48sJV_Gzo,1354
+nmdc_schema/migrators/migrator_from_11_13_0_to_11_14_0.py,sha256=vUYKEMbfzBiNFlR7mEckwRcuM0cyUCfifom7Xn_kWMY,5002
 nmdc_schema/migrators/migrator_from_11_1_0_to_11_2_0.py,sha256=xGaG0oilg0Xvq-P6YOZea3EPQU8fyfcKo-KZl4BhgoM,1183
 nmdc_schema/migrators/migrator_from_11_3_0_to_11_4_0.py,sha256=XDRsT9KrKlZTOGHQekESZ2XSYD2UDydF1PWTRIeqOVE,1985
 nmdc_schema/migrators/migrator_from_11_4_0_to_11_5_0.py,sha256=uiFi5USF23lpuAbkDhVufnXxLsM-Aixrj4nw7GY-XO4,357
@@ -89,9 +89,6 @@ nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/__init__.py,sha2
 nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/migrator_from_11_11_0_to_11_13_0_part_1.py,sha256=ajPhHPDK1loTL7j_3hzBZo_EfT5gtoXlsNFmpDZCgPs,8668
 nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/migrator_from_11_11_0_to_11_13_0_part_2.py,sha256=sW5JhlO2DaGh9kvI9qWJQ85eYyUo9976sBurPdZ69Kk,4858
 nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/migrator_from_11_11_0_to_11_13_0_part_3.py,sha256=XKrq0jBLn6v4O96j045WkJsGubwP6ikLNyglEKH1_jE,1920
-nmdc_schema/migrators/partials/migrator_from_11_13_0_to_11_14_0/__init__.py,sha256=xXed_UcqkW7zWope_4ODapGf3xS_NKztCh6sK8GoUkc,999
-nmdc_schema/migrators/partials/migrator_from_11_13_0_to_11_14_0/migrator_from_11_13_0_to_11_14_0_part_1.py,sha256=7QuBZJlQE_emGgyQMfuiGBDDhdVVu57z6KQ8PStqyTs,5008
-nmdc_schema/migrators/partials/migrator_from_11_13_0_to_11_14_0/migrator_from_11_13_0_to_11_14_0_part_2.py,sha256=q5v3u6vFoIR12FbbI1Wji8guZ-D0RSxlOSTKzR0uNh0,1432
 nmdc_schema/migrators/partials/migrator_from_11_1_0_to_11_2_0/__init__.py,sha256=e-neqgmL6Zsy6h5PGmWPj9qIqrTm3yvNgo2l2i7Sduc,990
 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,sha256=4nN_2iZqML84R9EgznIcj7FjIlRHSSM8XqLerUgMYbI,13230
 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,sha256=HLGoX3KQZglHPODDO5FFHu2gjFjyBx8oGJ3D9PAkhNI,1628
@@ -111,18 +108,18 @@ nmdc_schema/migrators/partials/migrator_from_11_9_1_to_11_10_0/__init__.py,sha25
 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,sha256=6MYmrB9yfJ3XFb2QabTcJeycK2tyVO3MtSItns2s9Zg,35421
 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,sha256=wzard2sUTeRS7voVTfPt3_OtafTffnv0o0OyE1OBzA0,2987
 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,sha256=crm2NEmn0xepEMKWHvCSkfX3G6hRn377f38rq24XlO8,3710
-nmdc_schema/nmdc-pydantic.py,sha256=-KFRbsDhJgamDFB25YrE-MDyJIYotUfumfyCtsVp16o,1407574
-nmdc_schema/nmdc.py,sha256=ekyLtGlyT7dMcZ-dwui7P_ZRc5NfM99xiZ3Attlk0rw,744344
-nmdc_schema/nmdc.schema.json,sha256=rwNxfZfGmJIP_uLwslNvX_xh64_sMpUWlsYGnVbisQ0,632806
+nmdc_schema/nmdc-pydantic.py,sha256=KsCmfMksl-cw4Z117-q3cHhEc8Oo4xzGJXnKaUVoDfI,1449828
+nmdc_schema/nmdc.py,sha256=ZqLvE_GJFJXJHvRlEW_XX716RCW5Yy6BRps-RQErro4,737461
+nmdc_schema/nmdc.schema.json,sha256=JsUcoZvBYBU94OqjRp9tIgNsfFblEEy5-VAoUki65Ho,630048
 nmdc_schema/nmdc_data.py,sha256=_wNKi5NDxuvvRsJEim2ialX7VJkDBJLRpiTOPpFHBm8,9608
-nmdc_schema/nmdc_materialized_patterns.json,sha256=4BxPDYqUiYMKvJfTMIXeM8fkcnv5KDEX75qlRFe518g,915842
-nmdc_schema/nmdc_materialized_patterns.schema.json,sha256=UYOWffYZaiUfVdCV0GXRnN2o2EIeYFVe8aZ2IdPv46A,642131
-nmdc_schema/nmdc_materialized_patterns.yaml,sha256=rMUjokG3a2WfhGS4YWonbIc4Rv1r9szX9_7D2KxINcc,711525
+nmdc_schema/nmdc_materialized_patterns.json,sha256=zmYoq8BL4PdUCVn4dQdN7pM11gdFFNIvBw2Ih5RKkpY,912372
+nmdc_schema/nmdc_materialized_patterns.schema.json,sha256=1SxFfOBnB9fuyfcihHikDbs2pd3X7Oa3bROai1ZmHUg,639373
+nmdc_schema/nmdc_materialized_patterns.yaml,sha256=tIyM9hg9PLfTe2O3XFWL3V8f6su0wLT_8eKN8H0QNJ4,708950
 nmdc_schema/nmdc_schema_validation_plugin.py,sha256=rjtn1tYhngGyc1AV8vcT8BJ9a_MmHbcK3hRUf9dzPtA,4799
 nmdc_schema/nmdc_version.py,sha256=DsfEKnmN3LHR831WWELxyfZY6rnP9U8tfygamkrsaHY,2305
 nmdc_schema/validate_nmdc_json.py,sha256=PVJV2O1qQXMi206HaUKqRNLiLc164OpNYKPURSKN8_E,3148
-nmdc_schema-11.14.0.dist-info/METADATA,sha256=Qqe_PIlPIQt1vy2rup3JD0DixWGnpe7iMVqsgwyCHns,5883
-nmdc_schema-11.14.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-nmdc_schema-11.14.0.dist-info/entry_points.txt,sha256=ioyD5P6op5Zy68bqg5MafLAryb73rfzyx8YXKItroC8,1531
-nmdc_schema-11.14.0.dist-info/licenses/LICENSE,sha256=ogEPNDSH0_dhiv_lT3ifVIdgIzHAqNA_SemnxUfPBJk,7048
-nmdc_schema-11.14.0.dist-info/RECORD,,
+nmdc_schema-11.14.0rc1.dist-info/METADATA,sha256=t4DH8Zj0l7cEMHXQikzWicxyNiyhEL3wSPI2JlSdeW0,5853
+nmdc_schema-11.14.0rc1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+nmdc_schema-11.14.0rc1.dist-info/entry_points.txt,sha256=-UOl7vTEjS6eaJreIu_UenULpuKAYz8JiLeuKbEqPB8,2079
+nmdc_schema-11.14.0rc1.dist-info/licenses/LICENSE,sha256=ogEPNDSH0_dhiv_lT3ifVIdgIzHAqNA_SemnxUfPBJk,7048
+nmdc_schema-11.14.0rc1.dist-info/RECORD,,

{nmdc_schema-11.14.0.dist-info → nmdc_schema-11.14.0rc1.dist-info}/entry_points.txt

@@ -22,4 +22,12 @@ schema-pattern-linting=src.scripts.schema_pattern_linting:main
 schema-view-relation-graph=src.scripts.schema_view_relation_graph:cli
 scrutinize-elements=src.scripts.scrutinize_elements:process_schema_elements
 slot-range-type-reporter=src.scripts.slot_range_type_reporter:cli
+units-mongodb-analyze=units.scripts.mongodb_analyze_units:main
+units-schema-convert=units.scripts.schema_convert_to_ucum:main
+units-schema-extract=units.scripts.schema_extract_preferred_units:main
+units-schema-extract-slot-unit-pairs=units.scripts.schema_expand_storage_units:main
+units-schema-generate=units.scripts.schema_generate_yq_commands:main
+units-testdata-check=units.scripts.testdata_check_has_unit:main
+units-testdata-extract=units.scripts.testdata_extract_quantity_values:main
+units-ucum-validate=units.scripts.ucum_validate_units:main
 

nmdc_schema/migrators/partials/migrator_from_11_13_0_to_11_14_0/__init__.py

@@ -1,28 +0,0 @@
-from typing import List, Type
-
-from nmdc_schema.migrators.migrator_base import MigratorBase
-from nmdc_schema.migrators.partials.migrator_from_11_13_0_to_11_14_0 import (
-    migrator_from_11_13_0_to_11_14_0_part_1,
-    migrator_from_11_13_0_to_11_14_0_part_2
-)
-
-
-def get_migrator_classes() -> List[Type[MigratorBase]]:
-    r"""
-    Returns a list of migrator classes in the order in which they (i.e. their `upgrade` methods)
-    were designed to be run.
-
-    >>> migrator_classes = get_migrator_classes()
-    >>> type(migrator_classes) is list and len(migrator_classes) > 0  # the function returns a list
-    True
-    >>> from inspect import isclass
-    >>> all(isclass(c) for c in migrator_classes)  # each list item is a class
-    True
-    >>> all(callable(getattr(c, "upgrade")) for c in migrator_classes)  # each class has an `upgrade` method
-    True
-    """
-
-    return [
-        migrator_from_11_13_0_to_11_14_0_part_1.Migrator,
-        migrator_from_11_13_0_to_11_14_0_part_2.Migrator
-    ]

nmdc_schema/migrators/partials/migrator_from_11_13_0_to_11_14_0/migrator_from_11_13_0_to_11_14_0_part_1.py

@@ -1,113 +0,0 @@
-from linkml.validator import Validator
-
-from nmdc_schema.migrators.migrator_base import MigratorBase
-import sys
-from pathlib import Path
-from nmdc_schema.migrators.helpers import create_schema_view, get_classes_with_slots_by_range, \
-    get_database_collections_for_class
-from nmdc_schema import NmdcSchemaValidationPlugin
-
-project_root = Path(__file__).parent.parent.parent
-sys.path.insert(0, str(project_root))
-
-
-class Migrator(MigratorBase):
-    r"""A check-only migrator that raises an exception if any QuantityValue's has_unit slot
-    is not valid against the slot's storage_unit or UnitEnum constraints."""
-
-    _from_version = '11.13.0'
-    _to_version = '11.14.0_part_1'
-
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-
-        self.schema_view = create_schema_view()
-        self.validator = Validator(
-            self.schema_view.schema,
-            # This is intentionally *only* using the NMDC plugin, because this migrator is *only*
-            # concerned with validating the QuantityValue-related constraints that the plugin
-            # implements.
-            validation_plugins=[
-                NmdcSchemaValidationPlugin()
-            ]
-        )
-
-    def upgrade(self, commit_changes: bool = False) -> None:
-        r'''
-        Migrates the database from conforming to the original schema, to conforming to the new schema.
-        '''
-
-        # Get the schema classes which have slots with range QuantityValue
-        classes_with_qv_slots = get_classes_with_slots_by_range(self.schema_view, 'QuantityValue')
-
-        # Get the Database collection names that can hold these classes
-        eligible_collection_names = set()
-        for class_name in classes_with_qv_slots.keys():
-            collection_names = get_database_collections_for_class(self.schema_view, class_name)
-            eligible_collection_names.update(collection_names)
-
-        # Apply migrator through collections
-        self.logger.info("Checking QuantityValue units against UnitEnum and storage_units constraints")
-        for collection_name in eligible_collection_names:
-            self.logger.info(f"  Checking collection '{collection_name}'")
-            self.adapter.do_for_each_document(collection_name, self.confirm_units_fit_unitenum_and_storage_units)
-
-    def confirm_units_fit_unitenum_and_storage_units(self, document: dict) -> None:
-        r'''
-        Raise an exception if the QuantityValue's has_unit slot is not valid against slot's storage_unit or UnitEnum constraints.
-
-        >>> m = Migrator()
-
-        # Test: valid QuantityValue with proper units in biosample
-        >>> valid_biosample = {
-        ...     "id": "test1",
-        ...     "type": "nmdc:Biosample",
-        ...     "bulk_elect_conductivity": {
-        ...         "type": "nmdc:QuantityValue",
-        ...         "has_unit": "mS/cm",
-        ...         "has_numeric_value": 25.0
-        ...     }
-        ... }
-        >>> m.confirm_units_fit_unitenum_and_storage_units(valid_biosample)  # Should not raise
-
-        # Test: unit not allowed for bulk_elect_conductivity's storage_units
-        >>> invalid_biosample_storage = {
-        ...     "id": "test2",
-        ...     "type": "nmdc:Biosample",
-        ...     "bulk_elect_conductivity": {
-        ...         "type": "nmdc:QuantityValue",
-        ...         "has_unit": "Cel",
-        ...         "has_numeric_value": 25.0
-        ...     }
-        ... }
-        >>> m.confirm_units_fit_unitenum_and_storage_units(invalid_biosample_storage)
-        Traceback (most recent call last):
-            ...
-        ValueError: In test2:
-          QuantityValue at /bulk_elect_conductivity has unit 'Cel' which is not allowed for slot 'bulk_elect_conductivity' (allowed: mS/cm)
-
-        # Test: unit not allowed for substances_volume's storage_units
-        >>> invalid_chem_storage = {
-        ...     "id": "test3",
-        ...     "type": "nmdc:ChemicalConversionProcess",
-        ...     "substances_volume": {
-        ...         "type": "nmdc:QuantityValue",
-        ...         "has_unit": "J/K",  # Wrong unit type for substances_volume
-        ...         "has_numeric_value": 25.0
-        ...     }
-        ... }
-        >>> m.confirm_units_fit_unitenum_and_storage_units(invalid_chem_storage)
-        Traceback (most recent call last):
-            ...
-        ValueError: In test3:
-          QuantityValue at /substances_volume has unit 'J/K' which is not allowed for slot 'substances_volume' (allowed: mL)
-        '''
-
-        document_id = document.get('id', '<unknown id>')
-        document_type = document.get('type')
-        if not document_type:
-            raise ValueError(f"Unable to infer target_class for document with id '{document_id}'")
-        target_class = document_type.replace('nmdc:', '')
-        report = self.validator.validate(document, target_class)
-        if report.results:
-            raise ValueError(f"In {document_id}:\n" + "\n".join("  " + result.message for result in report.results))

nmdc_schema/migrators/partials/migrator_from_11_13_0_to_11_14_0/migrator_from_11_13_0_to_11_14_0_part_2.py

@@ -1,40 +0,0 @@
-from nmdc_schema.migrators.migrator_base import MigratorBase
-
-
-class Migrator(MigratorBase):
-    r"""
-    Migrates a database between two schemas.
-    """
-
-    _from_version = "11.14.0_part_1"
-    _to_version = "11.14.0_part_2"
-
-    def upgrade(self, commit_changes: bool = False) -> None:
-        r"""
-        Migrates the database from conforming to the original schema, to conforming to the new schema.
-        """
-        self.adapter.do_for_each_document("processed_sample_set", self.confirm_empty)
-
-    def confirm_empty(self, processedsample: dict) -> None:
-        r"""
-        If a processedsample has a value for 'biomaterial_purity' raise an exception.
-
-        >>> m = Migrator()
-
-        # Test: processed sample has biomaterial_purity value
-        >>> m.confirm_empty({"id": 1, "type": "nmdc:ProcessedSample", "biomaterial_purity": ["Test_Value"]})
-        Traceback (most recent call last):
-            ...
-        ValueError: Biosample 1 'biomaterial_purity' values include: ['Test_Value']
-
-        # Test: valid processedsample
-        >>> m.confirm_empty({"id": 3, "type": "nmdc:ProcessedSample"}) is None
-        True
-        """
-        bp_values = processedsample.get("biomaterial_purity", [])
-        biosample_id = processedsample.get("id")
-
-        if len(bp_values)>0:
-            raise ValueError(
-                f"Biosample {biosample_id} 'biomaterial_purity' values include: {bp_values}"
-            )