nmdc-schema 11.15.1__tar.gz → 11.16.0__tar.gz

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc_schema
-Version: 11.15.1
+Version: 11.16.0
 Summary: Schema resources for the National Microbiome Data Collaborative (NMDC)
 License: MIT
 License-File: LICENSE

nmdc_schema-11.16.0/nmdc_schema/migrators/migrator_from_11_14_0_to_11_15_1.py

@@ -0,0 +1,12 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+
+class Migrator(MigratorBase):
+    r"""Migrates a database between two schemas."""
+
+    _from_version = "11.14.0"
+    _to_version = "11.15.1"
+
+    def upgrade(self, commit_changes: bool = False) -> None:
+        r"""No upgrade needed."""
+        pass

nmdc_schema-11.16.0/nmdc_schema/migrators/migrator_from_11_15_1_to_11_16_0.py

@@ -0,0 +1,28 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+
+class Migrator(MigratorBase):
+    r"""Migrates a database between two schemas."""
+
+    _from_version = "11.15.1"
+    _to_version = "11.16.0"
+
+    def upgrade(self, commit_changes: bool = False) -> None:
+        r"""Migrates the database from conforming to the original schema, to conforming to the new schema."""
+
+        self.adapter.process_each_document("workflow_execution_set", [self.make_uses_calibration_multivalued])
+
+    def make_uses_calibration_multivalued(self, workflow_execution: dict) -> dict:
+        r"""
+        If a WorkflowExecution record in the workflow_execution_set has a 'uses_calibration' field, convert it to a list containing the original value.
+
+        >>> m = Migrator()
+        >>> m.make_uses_calibration_multivalued({'id': 123})  # no `extraction_target` field
+        {'id': 123}
+        >>> m.make_uses_calibration_multivalued({'id': 123, 'uses_calibration': 'nmdc:calib-13-tester'})  # test: casts it as a list value
+        {'id': 123, 'uses_calibration': ['nmdc:calib-13-tester']}
+        """
+
+        if workflow_execution.get("uses_calibration") is not None:
+            workflow_execution["uses_calibration"] = [workflow_execution["uses_calibration"]]
+        return workflow_execution

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/nmdc_schema/nmdc.py

@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-21T19:39:27
+# Generation date: 2026-02-05T23:25:00
 # Schema: NMDC
 #
 # id: https://w3id.org/nmdc/nmdc
@@ -60,7 +60,7 @@ from linkml_runtime.linkml_model.types import Boolean, Decimal, Float, Integer,
 from linkml_runtime.utils.metamodelcore import Bool, Decimal, URIorCURIE
 
 metamodel_version = "1.7.0"
-version = "11.15.1"
+version = "11.16.0"
 
 # Namespaces
 BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_')
@@ -6231,7 +6231,7 @@ class MetabolomicsAnalysis(WorkflowExecution):
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
     metabolomics_analysis_category: Union[str, "MetabolomicsAnalysisCategoryEnum"] = None
     has_metabolite_identifications: Optional[Union[Union[dict, MetaboliteIdentification], list[Union[dict, MetaboliteIdentification]]]] = empty_list()
-    uses_calibration: Optional[Union[str, CalibrationInformationId]] = None
+    uses_calibration: Optional[Union[Union[str, CalibrationInformationId], list[Union[str, CalibrationInformationId]]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]] = empty_list()
     superseded_by: Optional[Union[str, MetabolomicsAnalysisId]] = None
 
@@ -6250,8 +6250,9 @@ class MetabolomicsAnalysis(WorkflowExecution):
             self.has_metabolite_identifications = [self.has_metabolite_identifications] if self.has_metabolite_identifications is not None else []
         self.has_metabolite_identifications = [v if isinstance(v, MetaboliteIdentification) else MetaboliteIdentification(**as_dict(v)) for v in self.has_metabolite_identifications]
 
-        if self.uses_calibration is not None and not isinstance(self.uses_calibration, CalibrationInformationId):
-            self.uses_calibration = CalibrationInformationId(self.uses_calibration)
+        if not isinstance(self.uses_calibration, list):
+            self.uses_calibration = [self.uses_calibration] if self.uses_calibration is not None else []
+        self.uses_calibration = [v if isinstance(v, CalibrationInformationId) else CalibrationInformationId(v) for v in self.uses_calibration]
 
         if not isinstance(self.was_informed_by, list):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
@@ -6281,7 +6282,7 @@ class NomAnalysis(WorkflowExecution):
     started_at_time: str = None
     has_input: Union[Union[str, DataObjectId], list[Union[str, DataObjectId]]] = None
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
-    uses_calibration: Optional[Union[str, CalibrationInformationId]] = None
+    uses_calibration: Optional[Union[Union[str, CalibrationInformationId], list[Union[str, CalibrationInformationId]]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]] = empty_list()
     superseded_by: Optional[Union[str, NomAnalysisId]] = None
 
@@ -6291,8 +6292,9 @@ class NomAnalysis(WorkflowExecution):
         if not isinstance(self.id, NomAnalysisId):
             self.id = NomAnalysisId(self.id)
 
-        if self.uses_calibration is not None and not isinstance(self.uses_calibration, CalibrationInformationId):
-            self.uses_calibration = CalibrationInformationId(self.uses_calibration)
+        if not isinstance(self.uses_calibration, list):
+            self.uses_calibration = [self.uses_calibration] if self.uses_calibration is not None else []
+        self.uses_calibration = [v if isinstance(v, CalibrationInformationId) else CalibrationInformationId(v) for v in self.uses_calibration]
 
         if not isinstance(self.was_informed_by, list):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
@@ -6531,6 +6533,7 @@ class CalibrationStandardEnum(EnumDefinitionImpl):
 
     fames = PermissibleValue(text="fames")
     alkanes = PermissibleValue(text="alkanes")
+    srfa = PermissibleValue(text="srfa")
 
     _defn = EnumDefinition(
         name="CalibrationStandardEnum",
@@ -10450,7 +10453,7 @@ slots.generates_calibration = Slot(uri=NMDC.generates_calibration, name="generat
                    model_uri=NMDC.generates_calibration, domain=None, range=Optional[Union[str, CalibrationInformationId]])
 
 slots.uses_calibration = Slot(uri=NMDC.uses_calibration, name="uses_calibration", curie=NMDC.curie('uses_calibration'),
-                   model_uri=NMDC.uses_calibration, domain=None, range=Optional[Union[str, CalibrationInformationId]])
+                   model_uri=NMDC.uses_calibration, domain=None, range=Optional[Union[Union[str, CalibrationInformationId], list[Union[str, CalibrationInformationId]]]])
 
 slots.calibration_object = Slot(uri=NMDC.calibration_object, name="calibration_object", curie=NMDC.curie('calibration_object'),
                    model_uri=NMDC.calibration_object, domain=None, range=Optional[Union[str, DataObjectId]])

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/nmdc_schema/nmdc.schema.json

@@ -5222,7 +5222,8 @@
             "description": "",
             "enum": [
                 "fames",
-                "alkanes"
+                "alkanes",
+                "srfa"
             ],
             "title": "CalibrationStandardEnum",
             "type": "string"
@@ -9787,8 +9788,11 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
+                    "items": {
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -11928,8 +11932,11 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
+                    "items": {
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -15466,5 +15473,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.15.1"
+    "version": "11.16.0"
 }

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/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": "11.15.1",
+  "version": "11.16.0",
   "license": "https://creativecommons.org/publicdomain/zero/1.0/",
   "prefixes": {
     "BFO": {
@@ -752,6 +752,18 @@
           "aliases": [
             "Alkanes"
           ]
+        },
+        "srfa": {
+          "text": "srfa",
+          "comments": [
+            "Reference standard Suwannee River Fulvic Acid Standard II (2S101F) from International Humic Substances Society"
+          ],
+          "see_also": [
+            "https://humic-substances.org/source-materials-for-ihss-samples/"
+          ],
+          "aliases": [
+            "Suwannee River fulvic acid"
+          ]
         }
       }
     },
@@ -7539,6 +7551,7 @@
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "range": "CalibrationInformation",
+      "multivalued": true,
       "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
       "structured_pattern": {
         "syntax": "{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$",

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/nmdc_schema/nmdc_materialized_patterns.schema.json

@@ -5430,7 +5430,8 @@
             "description": "",
             "enum": [
                 "fames",
-                "alkanes"
+                "alkanes",
+                "srfa"
             ],
             "title": "CalibrationStandardEnum",
             "type": "string"
@@ -10039,9 +10040,12 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
-                    "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                    "items": {
+                        "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -12211,9 +12215,12 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
-                    "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                    "items": {
+                        "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -15772,6 +15779,6 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.15.1"
+    "version": "11.16.0"
 }
 

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/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: 11.15.1
+version: 11.16.0
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   BFO:
@@ -619,6 +619,15 @@ enums:
         text: alkanes
         aliases:
         - Alkanes
+      srfa:
+        text: srfa
+        comments:
+        - Reference standard Suwannee River Fulvic Acid Standard II (2S101F) from
+          International Humic Substances Society
+        see_also:
+        - https://humic-substances.org/source-materials-for-ihss-samples/
+        aliases:
+        - Suwannee River fulvic acid
   StrandedOrientationEnum:
     name: StrandedOrientationEnum
     description: This enumeration specifies information about stranded RNA library
@@ -5636,6 +5645,7 @@ slots:
       run is used when analyzing metabolomics data
     from_schema: https://w3id.org/nmdc/nmdc
     range: CalibrationInformation
+    multivalued: true
     pattern: ^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$
     structured_pattern:
       syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/nmdc_schema/nmdc_pydantic.py

@@ -30,7 +30,7 @@ from pydantic import (
 
 
 metamodel_version = "None"
-version = "11.15.1"
+version = "11.16.0"
 
 
 class ConfiguredBaseModel(BaseModel):
@@ -650,6 +650,7 @@ class CalibrationTargetEnum(str, Enum):
 class CalibrationStandardEnum(str, Enum):
     fames = "fames"
     alkanes = "alkanes"
+    srfa = "srfa"
 
 
 class StrandedOrientationEnum(str, Enum):
@@ -20909,7 +20910,7 @@ class MetabolomicsAnalysis(WorkflowExecution):
                                                                    'syntax': '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'}}}})
 
     has_metabolite_identifications: Optional[list[MetaboliteIdentification]] = Field(default=[], json_schema_extra = { "linkml_meta": {'domain_of': ['MetabolomicsAnalysis']} })
-    uses_calibration: Optional[str] = Field(default=None, description="""calibration information is used by a process""", json_schema_extra = { "linkml_meta": {'comments': ['Retenion index calibration data generated by a gas '
+    uses_calibration: Optional[list[str]] = Field(default=[], description="""calibration information is used by a process""", json_schema_extra = { "linkml_meta": {'comments': ['Retenion index calibration data generated by a gas '
                       'chromatography mass spectromery run is used when analyzing '
                       'metabolomics data'],
          'domain_of': ['MetabolomicsAnalysis', 'NomAnalysis'],
@@ -21396,7 +21397,7 @@ class NomAnalysis(WorkflowExecution):
                                             'structured_pattern': {'interpolated': True,
                                                                    'syntax': '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'}}}})
 
-    uses_calibration: Optional[str] = Field(default=None, description="""calibration information is used by a process""", json_schema_extra = { "linkml_meta": {'comments': ['Retenion index calibration data generated by a gas '
+    uses_calibration: Optional[list[str]] = Field(default=[], description="""calibration information is used by a process""", json_schema_extra = { "linkml_meta": {'comments': ['Retenion index calibration data generated by a gas '
                       'chromatography mass spectromery run is used when analyzing '
                       'metabolomics data'],
          'domain_of': ['MetabolomicsAnalysis', 'NomAnalysis'],

{nmdc_schema-11.15.1 → nmdc_schema-11.16.0}/pyproject.toml

@@ -8,7 +8,7 @@ license = "MIT"
 name = "nmdc_schema"
 readme = "README.md"
 repository = "https://github.com/microbiomedata/nmdc-schema"
-version = "11.15.1"
+version = "11.16.0"
 authors = [
     "Bill Duncan <wdduncan@gmail.com>",
     "Chris Mungall <cjmungall@lbl.gov>",