nmdc-schema 11.13.0__tar.gz → 11.14.0__tar.gz

{nmdc_schema-11.13.0 → nmdc_schema-11.14.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc_schema
-Version: 11.13.0
+Version: 11.14.0
 Summary: Schema resources for the National Microbiome Data Collaborative (NMDC)
 License: MIT
 License-File: LICENSE
@@ -25,13 +25,14 @@ 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 (>=1.9.1,<2.0.0)
-Requires-Dist: linkml-runtime (>=1.9.1,<2.0.0)
+Requires-Dist: linkml (>=1.9.6,<2.0.0)
+Requires-Dist: linkml-runtime (>=1.9.5,<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/nmdc_schema/migrators/migrator_from_11_13_0_to_11_14_0.py

@@ -0,0 +1,35 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+from nmdc_schema.migrators.partials.migrator_from_11_13_0_to_11_14_0 import (
+    get_migrator_classes,
+)
+
+
+class Migrator(MigratorBase):
+    r"""
+    Migrates a database between two schemas.
+    """
+
+    _from_version = "11.13.0"
+    _to_version = "11.14.0"
+
+    def upgrade(self, commit_changes: bool = False) -> None:
+        r"""
+        Migrates the database from conforming to the original schema, to conforming to the new schema.
+
+        This migrator uses partial migrators. It runs them in the order in which they are returned by
+        the `get_migrator_classes` function.
+        
+        Args:
+            commit_changes: If True, commits the changes. If False (default), performs a dry run or rollback.
+        """
+
+        migrator_classes = get_migrator_classes()
+        num_migrators = len(migrator_classes)
+        for idx, migrator_class in enumerate(migrator_classes):
+            self.logger.info(f"Running migrator {idx + 1} of {num_migrators}")
+            self.logger.debug(
+                f"Migrating from {migrator_class.get_origin_version()} "
+                f"to {migrator_class.get_destination_version()}"
+            )
+            migrator = migrator_class(adapter=self.adapter, logger=self.logger)
+            migrator.upgrade(commit_changes=commit_changes)

nmdc_schema-11.14.0/nmdc_schema/migrators/partials/migrator_from_11_13_0_to_11_14_0/__init__.py

@@ -0,0 +1,28 @@
+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-11.14.0/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

@@ -0,0 +1,113 @@
+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-11.14.0/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

@@ -0,0 +1,40 @@
+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}"
+            )