Fairscape version

CHANGELOG.md

@@ -0,0 +1,6 @@
+# Changelog
+
+## [1.0.24] - 2026-02-16
+
+Added a property `fairscapeVersion` to all classes which is set to the version of this models package.
+Added a bound method `generateFileElem` to `fairscape_models.rocrate.ROCrateMetadataElem` to generate the `fairscape_models.rocrate.ROCrateFileElem` required in an ROCrate.

fairscape_models/_version.py

@@ -0,0 +1 @@
+__version__ = "1.0.24"

fairscape_models/activity.py

@@ -2,6 +2,7 @@
 from typing import Optional, List, Union
 
 from fairscape_models.fairscape_base import IdentifierValue
+from fairscape_models._version import __version__
 
 class Activity(BaseModel):
     """Base class for Activity types (Computation, Annotation, Experiment)"""
@@ -16,5 +17,6 @@ class Activity(BaseModel):
     # PROV-O fields (auto-populated)
     used: Optional[List[Union[str, IdentifierValue]]] = Field(default=[], alias="prov:used")
     wasAssociatedWith: Optional[List[Union[str, IdentifierValue]]] = Field(default=[], alias="prov:wasAssociatedWith")
+    fairscapeVersion: str = __version__
 
     model_config = ConfigDict(extra="allow", populate_by_name=True)

fairscape_models/biochem_entity.py

@@ -2,6 +2,7 @@
 from typing import Optional, List, Union
 
 from fairscape_models.fairscape_base import IdentifierValue, IdentifierPropertyValue
+from fairscape_models._version import __version__
 
 class BioChemEntity(BaseModel):
     """ Pydantic model for the Schema.org BioChemEntity datatype
@@ -16,5 +17,6 @@ class BioChemEntity(BaseModel):
     usedBy: Optional[List[IdentifierValue]] = Field(default=[])
     description: Optional[str] = Field(default=None)
     isPartOf: Optional[List[IdentifierValue]] = Field(default=[])
+    fairscapeVersion: str = __version__
 
     model_config = ConfigDict(extra="allow")

fairscape_models/digital_object.py

@@ -2,6 +2,7 @@
 from typing import Optional, List, Union
 
 from fairscape_models.fairscape_base import IdentifierValue
+from fairscape_models._version import __version__
 
 class DigitalObject(BaseModel):
     """Base class for DigitalObject types (Dataset, Software, MLModel)"""
@@ -16,6 +17,7 @@ class DigitalObject(BaseModel):
     contentUrl: Optional[Union[str, List[str]]] = Field(default=None)
     isPartOf: Optional[List[IdentifierValue]] = Field(default=[])
     usedByComputation: Optional[List[IdentifierValue]] = Field(default=[])
+    fairscapeVersion: str = __version__
 
     # PROV-O fields (auto-populated)
     wasGeneratedBy: Optional[List[Union[str, IdentifierValue]]] = Field(default=[], alias="prov:wasGeneratedBy")

fairscape_models/instrument.py

@@ -1,6 +1,7 @@
 from pydantic import BaseModel, Field, ConfigDict
 from typing import Optional, List, Union
 from fairscape_models.fairscape_base import IdentifierValue
+from fairscape_models._version import __version__
 
 class Instrument(BaseModel):
     guid: str = Field(alias="@id")
@@ -14,4 +15,5 @@ class Instrument(BaseModel):
     usedByExperiment: Optional[List[IdentifierValue]] = Field(default=[])  # changed from usedByComputation
     contentUrl: Optional[str] = Field(default=None)
     isPartOf: Optional[List[IdentifierValue]] = Field(default=[])
-    model_config = ConfigDict(extra="allow")
+    model_config = ConfigDict(extra="allow")
+    fairscapeVersion: str = __version__

fairscape_models/medical_condition.py

@@ -2,6 +2,7 @@
 from typing import Optional, List
 
 from fairscape_models.fairscape_base import IdentifierValue, IdentifierPropertyValue
+from fairscape_models._version import __version__
 
 class MedicalCondition(BaseModel):
     """ Pydantic model for the Schema.org MedicalCondition datatype
@@ -15,4 +16,5 @@ class MedicalCondition(BaseModel):
     drug: Optional[List[IdentifierValue]] = Field(default=[])
     usedBy: Optional[List[IdentifierValue]] = Field(default=[])
     isPartOf: Optional[List[IdentifierValue]] = Field(default=[])
-    description: str
+    description: str 
+    fairscapeVersion: str = __version__

fairscape_models/patient.py

@@ -10,6 +10,7 @@
   Union
 )
 from fairscape_models.fairscape_base import IdentifierValue
+from fairscape_models._version import __version__
 
 class Patient(BaseModel):
   guid: str = Field(alias="@id")
@@ -26,3 +27,4 @@ class Patient(BaseModel):
   gender: Optional[str]
   birthDate: Optional[str] = Field(default=None)
   deathDate: Optional[str] = Field(default=None)
+  fairscapeVersion: str = __version__

fairscape_models/rocrate.py

@@ -18,6 +18,7 @@
 from fairscape_models.sample import Sample
 from fairscape_models.activity import Activity
 from fairscape_models.digital_object import DigitalObject
+from fairscape_models._version import __version__
 
 class GenericMetadataElem(BaseModel):
     """Generic Metadata Element of an ROCrate"""
@@ -27,6 +28,7 @@ class GenericMetadataElem(BaseModel):
 
     model_config = ConfigDict(extra="allow")
 
+
 class ROCrateMetadataFileElem(BaseModel):
     """Metadata Element of an ROCrate cooresponding to the `ro-crate-metadata.json` file itself
 
@@ -49,6 +51,7 @@ class ROCrateMetadataFileElem(BaseModel):
     metadataType: Literal["CreativeWork"] = Field(alias="@type")
     conformsTo: IdentifierValue
     about: IdentifierValue
+    fairscapeVersion: str = __version__
 
 
 class ROCrateMetadataElem(BaseModel):
@@ -96,6 +99,7 @@ class ROCrateMetadataElem(BaseModel):
     associatedPublication: Optional[Union[str, List[str]]] = Field(default=None)
     conditionsOfAccess: Optional[str] = Field(default=None)
     copyrightNotice: Optional[str] = Field(default=None)
+    fairscapeVersion: str = __version__
 
     rai_data_limitations: Optional[str] = Field(alias="rai:dataLimitations", default=None)
     rai_data_biases: Optional[str] = Field(alias="rai:dataBiases", default=None)
@@ -129,7 +133,17 @@ class ROCrateMetadataElem(BaseModel):
     evi_total_entities: Optional[int] = Field(alias="evi:totalEntities", default=None)
     evi_formats: Optional[List[str]] = Field(alias="evi:formats", default=None)
 
-
+    def generateFileElem(self)->ROCrateMetadataFileElem:
+        return ROCrateMetadataFileElem.validate({
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": self.guid,
+                "@type": ["EVI:Dataset", "EVI:ROCrate"],
+                "name": self.name
+            },
+            "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"}
+        })
 
 
 class ROCrateDistribution(BaseModel):
@@ -138,7 +152,6 @@ class ROCrateDistribution(BaseModel):
     extractedObjectPath: Optional[List[str]] = Field(default=[])
     archivedObjectPath: Optional[str] = Field(default=None)
 
-
 
 class ROCrateV1_2(BaseModel):
     context: Optional[Dict] = Field(alias="@context")

fairscape_models/sample.py

@@ -1,6 +1,7 @@
 from pydantic import BaseModel, Field, ConfigDict
 from typing import Optional, List, Union, Dict
 from fairscape_models.fairscape_base import IdentifierValue
+from fairscape_models._version import __version__
 
 class Sample(BaseModel):
     guid: str = Field(alias="@id")
@@ -12,5 +13,6 @@ class Sample(BaseModel):
     contentUrl: Optional[Union[str, List[str]]] = Field(default=None)
     cellLineReference: Optional[IdentifierValue] = Field(default=None) 
     isPartOf: Optional[List[IdentifierValue]] = Field(default=[])
+    fairscapeVersion: str = __version__
 
     model_config = ConfigDict(extra='allow')

fairscape_models/schema.py

@@ -13,6 +13,7 @@
 import re
 from enum import Enum 
 from fairscape_models.fairscape_base import IdentifierValue, FairscapeEVIBaseModel
+from fairscape_models._version import __version__
 
 # TODO switch to ENUM for better clarification
 class ItemTypeEnum(Enum):
@@ -76,5 +77,7 @@ class Schema(FairscapeEVIBaseModel):
     header: Optional[bool] = Field(default=True)
     examples: Optional[List[Dict]] = []
     isPartOf: Optional[List[IdentifierValue]] = Field(default=[])
+    fairscapeVersion: str = __version__
+
 
     model_config = ConfigDict(extra='allow')

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fairscape-models"
-version = "1.0.22"
+version = "1.0.24"
 description = "Fairscape pydantic models"
 readme = "README.md"
 authors = [
@@ -40,3 +40,9 @@ exclude_lines = [
     "raise NotImplementedError",
     "if __name__ == .__main__.:",
 ]
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.5",
+    "pytest-cov>=5.0.0",
+]