feat: extend models

siibra/core/datasets.py

@@ -31,7 +31,7 @@ class Url(ConfigBaseModel):
 
 class DatasetJsonModel(ConfigBaseModel):
     id: str = Field(..., alias="@id")
-    type: str = Field("siibra/base-dataset", const=True)
+    type: str = Field("siibra/core/dataset", const=True)
     metadata: DatasetVersionModel
     urls: List[Url]
 

siibra/core/parcellation.py

@@ -25,7 +25,7 @@
     Model as BrainAtlasVersionModel,
     HasTerminologyVersion,
 )
-from ..openminds.base import ConfigBaseModel
+from ..openminds.base import ConfigBaseModel, SiibraAtIdModel
 
 from datetime import date
 from typing import List, Optional, Set, Union
@@ -43,13 +43,21 @@ class AtlasType:
     PROBABILISTIC_ATLAS="https://openminds.ebrains.eu/instances/atlasType/probabilisticAtlas"
 
 
+class SiibraParcellationVersionModel(ConfigBaseModel):
+    name: str
+    deprecated: Optional[bool]
+    prev: Optional[SiibraAtIdModel]
+    next: Optional[SiibraAtIdModel]
+
+
 class SiibraParcellationModel(ConfigBaseModel):
     id: str = Field(..., alias="@id")
     type: str = Field(SIIBRA_PARCELLATION_MODEL_TYPE, const=True, alias="@type")
     name: str
     modality: Optional[str]
     datasets: List[DatasetJsonModel]
     brain_atlas_versions: List[BrainAtlasVersionModel] = Field(..., alias="brainAtlasVersions")
+    version: Optional[SiibraParcellationVersionModel]
 
 
 # NOTE : such code could be used to automatically resolve
@@ -62,7 +70,7 @@ class SiibraParcellationModel(ConfigBaseModel):
 #                    pass
 
 
-class ParcellationVersion:
+class ParcellationVersion(JSONSerializable):
     def __init__(
         self, name=None, collection=None, prev_id=None, next_id=None, deprecated=False
     ):
@@ -133,6 +141,24 @@ def _from_json(cls, obj):
             next_id=obj.get("@next", None),
             deprecated=obj.get("deprecated", False),
         )
+
+    @property
+    def model_id(self):
+        return self.name
+
+    def to_model(self, **kwargs) -> SiibraParcellationVersionModel:
+        assert self.prev is None or isinstance(self.prev, Parcellation), f"parcellationVersion to_model failed. expected .prev, if defined, to be instance of Parcellation, but is {self.prev.__class__} instead"
+        assert self.next is None or isinstance(self.next, Parcellation), f"parcellationVersion to_model failed. expected .next, if defined, to be instance of Parcellation, but is {self.next.__class__} instead"
+        return SiibraParcellationVersionModel(
+            name=self.name,
+            deprecated=self.deprecated,
+            prev=SiibraAtIdModel(
+                id=self.prev.model_id
+            ) if self.prev is not None else None,
+            next=SiibraAtIdModel(
+                id=self.next.model_id
+            ) if self.next is not None else None,
+        )
 
 
 @provide_registry
@@ -575,5 +601,6 @@ def to_model(self, **kwargs) -> SiibraParcellationModel:
                 short_name=self.name[:30],
                 version_identifier=f"{self.version} in {spc.to_model().full_name}",
                 version_innovation="",
-            ) for spc in self.supported_spaces]
+            ) for spc in self.supported_spaces],
+            version=self.version.to_model(**kwargs) if self.version is not None else None
         )

siibra/features/connectivity.py

@@ -31,7 +31,7 @@
 
 class ConnectivityMatrixDataModel(ConfigBaseModel):
     id: str = Field(..., alias="@id")
-    type: str = Field("siibra/connectivity", const=True)
+    type: str = Field("siibra/features/connectivity", const=True)
     name: str
     parcellations: List[Dict[str, str]]
     matrix: Optional[NpArrayDataModel]

siibra/features/ieeg.py

@@ -41,6 +41,7 @@ class IEEGElectrodeModel(ConfigBaseModel):
 
 class IEEGSessionModel(ConfigBaseModel):
     id: str = Field(..., alias="@id")
+    type: str = Field('siibra/features/ieegSession', const=True)
     dataset: DatasetJsonModel
     sub_id: str
     electrodes: Dict[str, IEEGElectrodeModel]

siibra/features/receptors.py

@@ -333,7 +333,7 @@ class ReceptorDataModel(ConfigBaseModel):
 
 class ReceptorDatasetModel(DatasetJsonModel):
     data: Optional[ReceptorDataModel]
-    type: str = Field("siibra/receptor", const=True)
+    type: str = Field("siibra/features/receptor", const=True)
 
 
 class DensityFingerprint:
@@ -464,7 +464,7 @@ def model_id(self):
 
     def to_model(self, detail=False, **kwargs) -> ReceptorDatasetModel:
         base_dict = dict(super().to_model(detail=detail, **kwargs).dict())
-        base_dict["type"] = "siibra/receptor"
+        base_dict["type"] = "siibra/features/receptor"
         if not detail:
             return ReceptorDatasetModel(
                 **base_dict,

siibra/features/voi.py

@@ -13,6 +13,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from pydantic import Field
 from .feature import SpatialFeature
 from .query import FeatureQuery
 
@@ -28,6 +29,7 @@
 
 
 class VOIDataModel(DatasetJsonModel):
+    type: str = Field('siibra/features/voi', const=True)
     volumes: List[VolumeModel]
     location: BoundingBoxModel
 
@@ -73,10 +75,12 @@ def model_id(self):
 
     def to_model(self, **kwargs) -> VOIDataModel:
         super_model = super().to_model(**kwargs)
+        super_model_dict = super_model.dict()
+        super_model_dict["type"] = "siibra/features/voi"
         return VOIDataModel(
             location=self.location.to_model(**kwargs),
             volumes=[vol.to_model(**kwargs) for vol in self.volumes],
-            **super_model.dict()
+            **super_model_dict,
         )