nmdc-schema 11.13.0__py3-none-any.whl → 11.14.0rc1__py3-none-any.whl

nmdc_schema/migrators/migrator_from_11_13_0_to_11_14_0.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'
+
+    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/nmdc-pydantic.py

@@ -27,7 +27,7 @@ from pydantic import (
 
 
 metamodel_version = "None"
-version = "11.13.0"
+version = "11.14.0rc1"
 
 
 class ConfiguredBaseModel(BaseModel):
@@ -3422,25 +3422,17 @@ class SubmissionStatusEnum(str, Enum):
     """
     Submission is ready for NMDC review, the submitter cannot edit.
     """
-    Resubmitted___Pending_review = "ResubmittedPendingReview"
-    """
-    Submission has been resubmitted after updates. It is now ready for NMDC review. The submitter cannot edit.
-    """
     Approved___Held = "ApprovedHeld"
     """
     Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. The submitter cannot edit.
     """
-    Pending___Sent_to_User_Facility = "PendingUserFacility"
+    Approved___Sent_to_User_Facility = "ApprovedPendingUserFacility"
     """
-    Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. Sample information shared with designated user facility and pending approvals. The submitter cannot edit.
+    Submission has been reviewed and approved by NMDC. Sample information has been shared with designated user facility and is ready for their review. The submitter cannot edit.
     """
     Updates_Required = "UpdatesRequired"
     """
-    Submission has been reviewed and submitter edits are required for approval. The submitter can reopen and edit the submission.
-    """
-    In_Progress___UpdateSOLIDUSAddition = "InProgressUpdate"
-    """
-    NMDC reviewer has reopened submission on behalf of submitter. The submitter is currently editing the submission.
+    Submission has been reviewed and submitter edits are required for approval. The submitter can edit the submission.
     """
     Denied = "Denied"
     """
@@ -10196,8 +10188,7 @@ class Biosample(Sample):
                          'occurrence': {'tag': 'occurrence', 'value': '1'},
                          'preferred_unit': {'tag': 'preferred_unit',
                                             'value': 'gram of air, kilogram of air'},
-                         'units_alignment_excuse': {'tag': 'units_alignment_excuse',
-                                                    'value': 'mixs_inconsistent'}},
+                         'storage_units': {'tag': 'storage_units', 'value': 'g/kg'}},
          'domain_of': ['Biosample'],
          'examples': [{'value': '15 per kilogram of air'}],
          'is_a': 'core field',
@@ -10686,8 +10677,7 @@ class Biosample(Sample):
                                             'value': 'measurement value'},
                          'occurrence': {'tag': 'occurrence', 'value': '1'},
                          'preferred_unit': {'tag': 'preferred_unit', 'value': 'meter'},
-                         'units_alignment_excuse': {'tag': 'units_alignment_excuse',
-                                                    'value': 'complex_unit'}},
+                         'storage_units': {'tag': 'storage_units', 'value': 'm'}},
          'domain_of': ['Biosample'],
          'examples': [{'value': ''}],
          'is_a': 'core field',
@@ -11455,8 +11445,7 @@ class Biosample(Sample):
          'slot_group': 'Sample ID',
          'string_serialization': '{text}:{text}'} })
     bulk_elect_conductivity: Optional[QuantityValue] = Field(default=None, title="bulk electrical conductivity", description="""Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.""", json_schema_extra = { "linkml_meta": {'alias': 'bulk_elect_conductivity',
-         'annotations': {'units_alignment_excuse': {'tag': 'units_alignment_excuse',
-                                                    'value': 'pending_analysis'}},
+         'annotations': {'storage_units': {'tag': 'storage_units', 'value': 'mS/cm'}},
          'comments': ['Provide the value output of the field instrument.'],
          'domain_of': ['Biosample'],
          'examples': [{'description': 'The conductivity measurement was 0.017 '
@@ -13575,8 +13564,7 @@ class SubSamplingProcess(MaterialProcessing):
                                    'name': 'volume'}}})
 
     container_size: Optional[QuantityValue] = Field(default=None, description="""The volume of the container an analyte is stored in or an activity takes place in""", json_schema_extra = { "linkml_meta": {'alias': 'container_size',
-         'annotations': {'units_alignment_excuse': {'tag': 'units_alignment_excuse',
-                                                    'value': 'pending_analysis'}},
+         'annotations': {'storage_units': {'tag': 'storage_units', 'value': 'mL'}},
          'contributors': ['ORCID:0009-0001-1555-1601', 'ORCID:0000-0002-8683-0050'],
          'domain_of': ['SubSamplingProcess', 'FiltrationProcess']} })
     contained_in: Optional[ContainerCategoryEnum] = Field(default=None, description="""A type of container.""", json_schema_extra = { "linkml_meta": {'alias': 'contained_in',
@@ -13985,8 +13973,7 @@ class FiltrationProcess(MaterialProcessing):
          'domain_of': ['FiltrationProcess'],
          'list_elements_ordered': True} })
     container_size: Optional[QuantityValue] = Field(default=None, description="""The volume of the container an analyte is stored in or an activity takes place in""", json_schema_extra = { "linkml_meta": {'alias': 'container_size',
-         'annotations': {'units_alignment_excuse': {'tag': 'units_alignment_excuse',
-                                                    'value': 'pending_analysis'}},
+         'annotations': {'storage_units': {'tag': 'storage_units', 'value': 'mL'}},
          'contributors': ['ORCID:0009-0001-1555-1601', 'ORCID:0000-0002-8683-0050'],
          'domain_of': ['SubSamplingProcess', 'FiltrationProcess']} })
     filter_material: Optional[str] = Field(default=None, description="""A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained.""", json_schema_extra = { "linkml_meta": {'alias': 'filter_material',
@@ -14002,8 +13989,7 @@ class FiltrationProcess(MaterialProcessing):
                       '(0.45−0.8 μm are commonly employed).'],
          'domain_of': ['FiltrationProcess']} })
     filter_pore_size: Optional[QuantityValue] = Field(default=None, description="""A quantitative or qualitative measurement of the physical dimensions of the pores in a material.""", json_schema_extra = { "linkml_meta": {'alias': 'filter_pore_size',
-         'annotations': {'units_alignment_excuse': {'tag': 'units_alignment_excuse',
-                                                    'value': 'pending_analysis'}},
+         'annotations': {'storage_units': {'tag': 'storage_units', 'value': 'um'}},
          'domain_of': ['FiltrationProcess']} })
     filtration_category: Optional[str] = Field(default=None, description="""The type of conditioning applied to a filter, device, etc.""", json_schema_extra = { "linkml_meta": {'alias': 'filtration_category', 'domain_of': ['FiltrationProcess']} })
     is_pressurized: Optional[bool] = Field(default=None, description="""Whether or not pressure was applied to a thing or process.""", json_schema_extra = { "linkml_meta": {'alias': 'is_pressurized', 'domain_of': ['FiltrationProcess']} })
@@ -14599,8 +14585,7 @@ class ChemicalConversionProcess(MaterialProcessing):
                        'ChemicalConversionProcess',
                        'MobilePhaseSegment']} })
     substances_volume: Optional[QuantityValue] = Field(default=None, description="""The volume of the combined substances that was included in a ChemicalConversionProcess.""", json_schema_extra = { "linkml_meta": {'alias': 'substances_volume',
-         'annotations': {'units_alignment_excuse': {'tag': 'units_alignment_excuse',
-                                                    'value': 'pending_analysis'}},
+         'annotations': {'storage_units': {'tag': 'storage_units', 'value': 'mL'}},
          'domain_of': ['ChemicalConversionProcess']} })
     instrument_used: Optional[list[str]] = Field(default=None, description="""What instrument was used during DataGeneration or MaterialProcessing.""", json_schema_extra = { "linkml_meta": {'alias': 'instrument_used',
          'domain_of': ['MaterialProcessing', 'DataGeneration'],

nmdc_schema/nmdc.py

@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-10-29T21:55:59
+# Generation date: 2025-11-19T00:25:31
 # Schema: NMDC
 #
 # id: https://w3id.org/nmdc/nmdc
@@ -60,7 +60,7 @@ from linkml_runtime.linkml_model.types import Boolean, Decimal, Double, Float, I
 from linkml_runtime.utils.metamodelcore import Bool, Decimal, URIorCURIE
 
 metamodel_version = "1.7.0"
-version = "11.13.0"
+version = "11.14.0rc1"
 
 # Namespaces
 BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_')
@@ -10473,21 +10473,15 @@ class SubmissionStatusEnum(EnumDefinitionImpl):
     SubmittedPendingReview = PermissibleValue(
         text="SubmittedPendingReview",
         description="Submission is ready for NMDC review, the submitter cannot edit.")
-    ResubmittedPendingReview = PermissibleValue(
-        text="ResubmittedPendingReview",
-        description="""Submission has been resubmitted after updates. It is now ready for NMDC review. The submitter cannot edit.""")
     ApprovedHeld = PermissibleValue(
         text="ApprovedHeld",
         description="""Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. The submitter cannot edit.""")
-    PendingUserFacility = PermissibleValue(
-        text="PendingUserFacility",
-        description="""Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. Sample information shared with designated user facility and pending approvals. The submitter cannot edit.""")
+    ApprovedPendingUserFacility = PermissibleValue(
+        text="ApprovedPendingUserFacility",
+        description="""Submission has been reviewed and approved by NMDC. Sample information has been shared with designated user facility and is ready for their review. The submitter cannot edit.""")
     UpdatesRequired = PermissibleValue(
         text="UpdatesRequired",
-        description="""Submission has been reviewed and submitter edits are required for approval. The submitter can reopen and edit the submission.""")
-    InProgressUpdate = PermissibleValue(
-        text="InProgressUpdate",
-        description="""NMDC reviewer has reopened submission on behalf of submitter. The submitter is currently editing the submission.""")
+        description="""Submission has been reviewed and submitter edits are required for approval. The submitter can edit the submission.""")
     Denied = PermissibleValue(
         text="Denied",
         description="Submission has been reviewed and denied. The submitter cannot edit.")

nmdc_schema/nmdc.schema.json

@@ -14917,11 +14917,9 @@
             "enum": [
                 "InProgress",
                 "SubmittedPendingReview",
-                "ResubmittedPendingReview",
                 "ApprovedHeld",
-                "PendingUserFacility",
+                "ApprovedPendingUserFacility",
                 "UpdatesRequired",
-                "InProgressUpdate",
                 "Denied",
                 "Released"
             ],
@@ -15715,5 +15713,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.13.0"
+    "version": "11.14.0rc1"
 }

nmdc_schema/nmdc_materialized_patterns.json

@@ -6,7 +6,7 @@
     "not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1"
   ],
   "id": "https://w3id.org/nmdc/nmdc",
-  "version": "11.13.0",
+  "version": "11.14.0rc1",
   "license": "https://creativecommons.org/publicdomain/zero/1.0/",
   "prefixes": {
     "BFO": {
@@ -7708,31 +7708,21 @@
           "description": "Submission is ready for NMDC review, the submitter cannot edit.",
           "title": "Submitted - Pending Review"
         },
-        "ResubmittedPendingReview": {
-          "text": "ResubmittedPendingReview",
-          "description": "Submission has been resubmitted after updates. It is now ready for NMDC review. The submitter cannot edit.",
-          "title": "Resubmitted - Pending review"
-        },
         "ApprovedHeld": {
           "text": "ApprovedHeld",
           "description": "Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. The submitter cannot edit.",
           "title": "Approved - Held"
         },
-        "PendingUserFacility": {
-          "text": "PendingUserFacility",
-          "description": "Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. Sample information shared with designated user facility and pending approvals. The submitter cannot edit.",
-          "title": "Pending - Sent to User Facility"
+        "ApprovedPendingUserFacility": {
+          "text": "ApprovedPendingUserFacility",
+          "description": "Submission has been reviewed and approved by NMDC. Sample information has been shared with designated user facility and is ready for their review. The submitter cannot edit.",
+          "title": "Approved - Sent to User Facility"
         },
         "UpdatesRequired": {
           "text": "UpdatesRequired",
-          "description": "Submission has been reviewed and submitter edits are required for approval. The submitter can reopen and edit the submission.",
+          "description": "Submission has been reviewed and submitter edits are required for approval. The submitter can edit the submission.",
           "title": "Updates Required"
         },
-        "InProgressUpdate": {
-          "text": "InProgressUpdate",
-          "description": "NMDC reviewer has reopened submission on behalf of submitter. The submitter is currently editing the submission.",
-          "title": "In Progress - Update/Addition"
-        },
         "Denied": {
           "text": "Denied",
           "description": "Submission has been reviewed and denied. The submitter cannot edit.",
@@ -8290,9 +8280,9 @@
     "container_size": {
       "name": "container_size",
       "annotations": {
-        "units_alignment_excuse": {
-          "tag": "units_alignment_excuse",
-          "value": "pending_analysis"
+        "storage_units": {
+          "tag": "storage_units",
+          "value": "mL"
         }
       },
       "description": "The volume of the container an analyte is stored in or an activity takes place in",
@@ -8315,9 +8305,9 @@
     "filter_pore_size": {
       "name": "filter_pore_size",
       "annotations": {
-        "units_alignment_excuse": {
-          "tag": "units_alignment_excuse",
-          "value": "pending_analysis"
+        "storage_units": {
+          "tag": "storage_units",
+          "value": "um"
         }
       },
       "description": "A quantitative or qualitative measurement of the physical dimensions of the pores in a material.",
@@ -8393,9 +8383,9 @@
     "input_volume": {
       "name": "input_volume",
       "annotations": {
-        "units_alignment_excuse": {
-          "tag": "units_alignment_excuse",
-          "value": "pending_analysis"
+        "storage_units": {
+          "tag": "storage_units",
+          "value": "mL"
         }
       },
       "description": "The volume of the input sample.",
@@ -8439,9 +8429,9 @@
     "substances_volume": {
       "name": "substances_volume",
       "annotations": {
-        "units_alignment_excuse": {
-          "tag": "units_alignment_excuse",
-          "value": "pending_analysis"
+        "storage_units": {
+          "tag": "storage_units",
+          "value": "mL"
         }
       },
       "description": "The volume of the combined substances that was included in a ChemicalConversionProcess.",
@@ -8470,9 +8460,9 @@
     "bulk_elect_conductivity": {
       "name": "bulk_elect_conductivity",
       "annotations": {
-        "units_alignment_excuse": {
-          "tag": "units_alignment_excuse",
-          "value": "pending_analysis"
+        "storage_units": {
+          "tag": "storage_units",
+          "value": "mS/cm"
         }
       },
       "description": "Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.",
@@ -21849,9 +21839,9 @@
           "tag": "occurrence",
           "value": "1"
         },
-        "units_alignment_excuse": {
-          "tag": "units_alignment_excuse",
-          "value": "mixs_inconsistent"
+        "storage_units": {
+          "tag": "storage_units",
+          "value": "g/kg"
         }
       },
       "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.",
@@ -23260,9 +23250,9 @@
           "tag": "occurrence",
           "value": "1"
         },
-        "units_alignment_excuse": {
-          "tag": "units_alignment_excuse",
-          "value": "complex_unit"
+        "storage_units": {
+          "tag": "storage_units",
+          "value": "m"
         }
       },
       "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).",

nmdc_schema/nmdc_materialized_patterns.schema.json

@@ -15013,11 +15013,9 @@
             "enum": [
                 "InProgress",
                 "SubmittedPendingReview",
-                "ResubmittedPendingReview",
                 "ApprovedHeld",
-                "PendingUserFacility",
+                "ApprovedPendingUserFacility",
                 "UpdatesRequired",
-                "InProgressUpdate",
                 "Denied",
                 "Released"
             ],
@@ -15811,5 +15809,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.13.0"
+    "version": "11.14.0rc1"
 }

nmdc_schema/nmdc_materialized_patterns.yaml

@@ -13,7 +13,7 @@ notes:
 - not importing any MIxS terms where the relationship between the name (SCN) and the
   id isn't 1:1
 id: https://w3id.org/nmdc/nmdc
-version: 11.13.0
+version: 11.14.0rc1
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   BFO:
@@ -5693,32 +5693,22 @@ enums:
         text: SubmittedPendingReview
         description: Submission is ready for NMDC review, the submitter cannot edit.
         title: Submitted - Pending Review
-      ResubmittedPendingReview:
-        text: ResubmittedPendingReview
-        description: Submission has been resubmitted after updates. It is now ready
-          for NMDC review. The submitter cannot edit.
-        title: Resubmitted - Pending review
       ApprovedHeld:
         text: ApprovedHeld
         description: Submission has been reviewed and approved. Information is complete,
           but not yet shared on the data portal. The submitter cannot edit.
         title: Approved - Held
-      PendingUserFacility:
-        text: PendingUserFacility
-        description: Submission has been reviewed and approved. Information is complete,
-          but not yet shared on the data portal. Sample information shared with designated
-          user facility and pending approvals. The submitter cannot edit.
-        title: Pending - Sent to User Facility
+      ApprovedPendingUserFacility:
+        text: ApprovedPendingUserFacility
+        description: Submission has been reviewed and approved by NMDC. Sample information
+          has been shared with designated user facility and is ready for their review.
+          The submitter cannot edit.
+        title: Approved - Sent to User Facility
       UpdatesRequired:
         text: UpdatesRequired
         description: Submission has been reviewed and submitter edits are required
-          for approval. The submitter can reopen and edit the submission.
+          for approval. The submitter can edit the submission.
         title: Updates Required
-      InProgressUpdate:
-        text: InProgressUpdate
-        description: NMDC reviewer has reopened submission on behalf of submitter.
-          The submitter is currently editing the submission.
-        title: In Progress - Update/Addition
       Denied:
         text: Denied
         description: Submission has been reviewed and denied. The submitter cannot
@@ -6178,9 +6168,9 @@ slots:
   container_size:
     name: container_size
     annotations:
-      units_alignment_excuse:
-        tag: units_alignment_excuse
-        value: pending_analysis
+      storage_units:
+        tag: storage_units
+        value: mL
     description: The volume of the container an analyte is stored in or an activity
       takes place in
     from_schema: https://w3id.org/nmdc/nmdc
@@ -6205,9 +6195,9 @@ slots:
   filter_pore_size:
     name: filter_pore_size
     annotations:
-      units_alignment_excuse:
-        tag: units_alignment_excuse
-        value: pending_analysis
+      storage_units:
+        tag: storage_units
+        value: um
     description: A quantitative or qualitative measurement of the physical dimensions
       of the pores in a material.
     from_schema: https://w3id.org/nmdc/nmdc
@@ -6269,9 +6259,9 @@ slots:
   input_volume:
     name: input_volume
     annotations:
-      units_alignment_excuse:
-        tag: units_alignment_excuse
-        value: pending_analysis
+      storage_units:
+        tag: storage_units
+        value: mL
     description: The volume of the input sample.
     from_schema: https://w3id.org/nmdc/nmdc
     range: QuantityValue
@@ -6307,9 +6297,9 @@ slots:
   substances_volume:
     name: substances_volume
     annotations:
-      units_alignment_excuse:
-        tag: units_alignment_excuse
-        value: pending_analysis
+      storage_units:
+        tag: storage_units
+        value: mL
     description: The volume of the combined substances that was included in a ChemicalConversionProcess.
     from_schema: https://w3id.org/nmdc/nmdc
     range: QuantityValue
@@ -6331,9 +6321,9 @@ slots:
   bulk_elect_conductivity:
     name: bulk_elect_conductivity
     annotations:
-      units_alignment_excuse:
-        tag: units_alignment_excuse
-        value: pending_analysis
+      storage_units:
+        tag: storage_units
+        value: mS/cm
     description: Electrical conductivity is a measure of the ability to carry electric
       current, which is mostly dictated by the chemistry of and amount of water.
     title: bulk electrical conductivity
@@ -16676,9 +16666,9 @@ slots:
       occurrence:
         tag: occurrence
         value: '1'
-      units_alignment_excuse:
-        tag: units_alignment_excuse
-        value: mixs_inconsistent
+      storage_units:
+        tag: storage_units
+        value: g/kg
     description: The mass of water vapour in a unit mass of moist air, usually expressed
       as grams of vapour per kilogram of air, or, in air conditioning, as grains per
       pound.
@@ -17729,9 +17719,9 @@ slots:
       occurrence:
         tag: occurrence
         value: '1'
-      units_alignment_excuse:
-        tag: units_alignment_excuse
-        value: complex_unit
+      storage_units:
+        tag: storage_units
+        value: m
     description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where
       the original temperature was measured (e.g. 1345 m).
     title: depth (TVDSS) of hydrocarbon resource temperature

{nmdc_schema-11.13.0.dist-info → nmdc_schema-11.14.0rc1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc_schema
-Version: 11.13.0
+Version: 11.14.0rc1
 Summary: Schema resources for the National Microbiome Data Collaborative (NMDC)
 License: MIT
 License-File: LICENSE

{nmdc_schema-11.13.0.dist-info → nmdc_schema-11.14.0rc1.dist-info}/RECORD

@@ -42,6 +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=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
@@ -107,18 +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=dQoo1bJBuS5Ty3XzQtY3R2ncdAXw5oG2R5hNsUlD65k,1450830
-nmdc_schema/nmdc.py,sha256=2TJmzEsPmqlCmu5nDeuNp3V2CeylaoPlCPSyU1MssEc,737930
-nmdc_schema/nmdc.schema.json,sha256=16LurO8g4cN9XlbNmj4gGxN3b0xoAgIA1_ZZ2ISiUhQ,630117
+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=isiIXZdo0gq6mPmUY12DNL-TqkwPxPuzfHwgimPKbr4,913170
-nmdc_schema/nmdc_materialized_patterns.schema.json,sha256=1eVg49IoSY3ejgEehY0KXPSA2zr_diGz2b-SdvrPPbI,639442
-nmdc_schema/nmdc_materialized_patterns.yaml,sha256=c5C03aM1Vqbt5BdXe105YONT5ghe679AhVo3NDow2B8,709694
+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-11.13.0.dist-info/METADATA,sha256=zR2pMlG9SDIDlHH3i4ptpC6QYbC2JyK3hApj3rEOaRc,5850
-nmdc_schema-11.13.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-nmdc_schema-11.13.0.dist-info/entry_points.txt,sha256=-UOl7vTEjS6eaJreIu_UenULpuKAYz8JiLeuKbEqPB8,2079
-nmdc_schema-11.13.0.dist-info/licenses/LICENSE,sha256=ogEPNDSH0_dhiv_lT3ifVIdgIzHAqNA_SemnxUfPBJk,7048
-nmdc_schema-11.13.0.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
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+nmdc_schema-11.14.0rc1.dist-info/licenses/LICENSE,sha256=ogEPNDSH0_dhiv_lT3ifVIdgIzHAqNA_SemnxUfPBJk,7048
+nmdc_schema-11.14.0rc1.dist-info/RECORD,,