nmdc-schema 11.12.1__tar.gz → 11.13.0__tar.gz

{nmdc_schema-11.12.1 → nmdc_schema-11.13.0}/PKG-INFO

@@ -1,19 +1,18 @@
 Metadata-Version: 2.4
 Name: nmdc_schema
-Version: 11.12.1
+Version: 11.13.0
 Summary: Schema resources for the National Microbiome Data Collaborative (NMDC)
 License: MIT
 License-File: LICENSE
 Keywords: NMDC,schema,metadata,microbiome
 Author: Bill Duncan
 Author-email: wdduncan@gmail.com
-Requires-Python: >=3.9,<4.0
+Requires-Python: >=3.10,<4.0
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12

nmdc_schema-11.12.1/nmdc_schema/migrators/migrator_from_11_11_0_to_11_12_0.py → nmdc_schema-11.13.0/nmdc_schema/migrators/migrator_from_11_11_0_to_11_13_0.py

@@ -1,5 +1,5 @@
 from nmdc_schema.migrators.migrator_base import MigratorBase
-from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_12_0 import (
+from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_13_0 import (
     get_migrator_classes,
 )
 
@@ -10,7 +10,7 @@ class Migrator(MigratorBase):
     """
 
     _from_version = "11.11.0"
-    _to_version = "11.12.0"
+    _to_version = "11.13.0"
 
     def upgrade(self, commit_changes: bool = False) -> None:
         r"""
@@ -32,4 +32,4 @@ class Migrator(MigratorBase):
                 f"to {migrator_class.get_destination_version()}"
             )
             migrator = migrator_class(adapter=self.adapter, logger=self.logger)
-            migrator.upgrade(commit_changes=commit_changes)
+            migrator.upgrade(commit_changes=commit_changes)

{nmdc_schema-11.12.1/nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_12_0 → nmdc_schema-11.13.0/nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0}/__init__.py

@@ -1,9 +1,10 @@
 from typing import List, Type
 
 from nmdc_schema.migrators.migrator_base import MigratorBase
-from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_12_0 import (
-    migrator_from_11_11_0_to_11_12_0_part_1,
-    migrator_from_11_11_0_to_11_12_0_part_2,
+from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_13_0 import (
+    migrator_from_11_11_0_to_11_13_0_part_1,
+    migrator_from_11_11_0_to_11_13_0_part_2,
+    migrator_from_11_11_0_to_11_13_0_part_3
 )
 
 
@@ -23,6 +24,7 @@ def get_migrator_classes() -> List[Type[MigratorBase]]:
     """
 
     return [
-        migrator_from_11_11_0_to_11_12_0_part_1.Migrator,
-        migrator_from_11_11_0_to_11_12_0_part_2.Migrator,
+        migrator_from_11_11_0_to_11_13_0_part_1.Migrator,
+        migrator_from_11_11_0_to_11_13_0_part_2.Migrator,
+        migrator_from_11_11_0_to_11_13_0_part_3.Migrator
     ]

nmdc_schema-11.12.1/nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_12_0/migrator_from_11_11_0_to_11_12_0_part_1.py → nmdc_schema-11.13.0/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

@@ -13,7 +13,7 @@ class Migrator(MigratorBase):
     '''
 
     _from_version = '11.11.0'
-    _to_version = '11.12.0.part_1'
+    _to_version = '11.13.0.part_1'
 
     def upgrade(self, commit_changes: bool = False) -> None:
         r'''

nmdc_schema-11.12.1/nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_12_0/migrator_from_11_11_0_to_11_12_0_part_2.py → nmdc_schema-11.13.0/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

@@ -15,8 +15,8 @@ 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 = '11.11.0'
-    _to_version = '11.12.0.part_2'
+    _from_version = '11.13.0.part_1'
+    _to_version = '11.13.0.part_2'
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)

nmdc_schema-11.13.0/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

@@ -0,0 +1,47 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+
+class Migrator(MigratorBase):
+    r"""
+    Migrates a database between two schemas.
+    """
+
+    _from_version = "11.13.0.part_2"
+    _to_version = "11.13.0.part_3"
+
+    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("biosample_set", self.confirm_igsn_prefix)
+
+    def confirm_igsn_prefix(self, biosample: dict) -> None:
+        r"""
+        If a biosample  has a igsn_biosample_identifiers prefix of 'IGSN' raise an exception.
+
+        >>> m = Migrator()
+
+        # Test: igsn_biosample_identifiers matching "IGSN:"
+        >>> m.confirm_igsn_prefix({"id": 1, "type": "nmdc:Biosample", "igsn_biosample_identifiers": ["IGSN:AU124"]})
+        Traceback (most recent call last):
+            ...
+        ValueError: Biosample 1 'igsn_biosample_identifiers' list includes: IGSN:AU124
+
+        # Test: igsn_biosample_identifiers with another non-confirming prefix
+        >>> m.confirm_igsn_prefix({"id": 1, "type": "nmdc:Biosample", "igsn_biosample_identifiers": ["isng:AU124"]})
+        Traceback (most recent call last):
+            ...
+        ValueError: Biosample 1 'igsn_biosample_identifiers' list includes: isng:AU124
+
+        # Test: valid Biosample
+        >>> m.confirm_igsn_prefix({"id": 3, "type": "nmdc:Biosample", "igsn_biosample_identifiers": ["igsn:AU124"]}) is None
+        True
+        """
+        prefix = "igsn:"
+        igsn_values = biosample.get("igsn_biosample_identifiers", [])
+        biosample_id = biosample.get("id")
+        for record in igsn_values:
+            if not record.startswith(prefix):
+                raise ValueError(
+                    f"Biosample {biosample_id} 'igsn_biosample_identifiers' list includes: {record}"
+                )