Add CompoundFeature serialization

api/common/data_handlers/compounds/download.py

@@ -64,7 +64,7 @@ def download_all(space_id: str, parcellation_id: str, region_id: str=None, featu
             try:
                 path_to_feature_export = Path(SIIBRA_API_SHARED_DIR, f"export-{feature_id}.zip")
                 if not path_to_feature_export.exists():
-                    feature = siibra.features.Feature.get_instance_by_id(feature_id)
+                    feature = siibra.features.Feature._get_instance_by_id(feature_id)
                     feature.export(path_to_feature_export)
                 zipfile.write(path_to_feature_export, f"export-{feature_id}.zip")
             except Exception as e:

api/common/data_handlers/features/types.py

@@ -40,7 +40,7 @@ def get_single_feature_from_id(feature_id: str, **kwargs):
     import siibra
     from api.serialization.util import instance_to_model
     try:
-        feature = siibra.features.Feature.get_instance_by_id(feature_id)
+        feature = siibra.features.Feature._get_instance_by_id(feature_id)
     except Exception as e:
         raise NotFound(str(e))
     else:
@@ -53,7 +53,7 @@ def get_single_feature_plot_from_id(feature_id: str, template="plotly", **kwargs
     import json
 
     try:
-        feature = siibra.features.Feature.get_instance_by_id(feature_id)
+        feature = siibra.features.Feature._get_instance_by_id(feature_id)
     except Exception as e:
         raise NotFound from e
 
@@ -79,7 +79,7 @@ def get_single_feature_download_zip_path(feature_id: str, **kwargs):
         return str(full_filename)
     import siibra
     try:
-        feat = siibra.features.Feature.get_instance_by_id(feature_id)
+        feat = siibra.features.Feature._get_instance_by_id(feature_id)
     except Exception as e:
         logger.error(f"Error finding single feature {feature_id=}, {str(e)}")
         raise NotFound from e

api/models/features/_basetypes/feature.py

@@ -20,3 +20,8 @@ class _FeatureModel(ConfigBaseModel, ABC, type="feature"):
 class FeatureModel(_FeatureModel):
     """FeatureModel"""
     pass
+
+
+class CompoundFeatureModel(_FeatureModel, type="compound_feature"):
+    """CompoundFeatureModel"""
+    subfeature_keys: List[str]

api/serialization/features/_basetypes/feature.py

@@ -1,6 +1,9 @@
 from api.serialization.util.siibra import Feature
 from api.serialization.util import serialize, instance_to_model
 from api.models.features._basetypes.feature import FeatureModel
+from api.serialization.util.siibra import CompoundFeature
+from api.models.features._basetypes.feature import CompoundFeatureModel
+
 
 @serialize(Feature)
 def feature_to_model(feat: Feature, detail: bool=False, **kwargs) -> FeatureModel:
@@ -22,3 +25,16 @@ def feature_to_model(feat: Feature, detail: bool=False, **kwargs) -> FeatureMode
         anchor=instance_to_model(feat.anchor, **kwargs) if detail else None,
         datasets=[instance_to_model(ds, **kwargs) for ds in feat.datasets]
     )
+
+
+@serialize(CompoundFeature, pass_super_model=True)
+def serialize_cf(
+    cf: CompoundFeature,
+    detail=False,
+    super_model_dict={},
+    **kwargs
+) -> CompoundFeatureModel:
+    return CompoundFeatureModel(
+        **super_model_dict,
+        indices=cf.indices
+    )

api/serialization/util/siibra.py

@@ -19,6 +19,7 @@
 from siibra.retrieval.datasets import EbrainsBaseDataset, GenericDataset
 
 from siibra.features.feature import Feature
+from siibra.features.feature import CompoundFeature
 from siibra.features.connectivity.regional_connectivity import RegionalConnectivity
 from siibra.features.tabular.cortical_profile import CorticalProfile
 from siibra.features.tabular.tabular import Tabular

docs/develop.md

@@ -21,6 +21,8 @@ uvicorn api.server:api --host 127.0.0.1 --port 5000 --reload
 ```
 
 ## With docker-compose
+0) Delete if there is a siibra-api docker image.
+1) Change the siibra requirement by chosing the new tag or install from a branch git+https://github.com/FZJ-INM1-BDA/siibra-python.git@BranchName
 ```sh
 docker-compose -f ./docker-compose-dev.yml up
 ```

requirements/siibra.txt

@@ -1,2 +1,2 @@
-siibra==0.4a74
+git+https://github.com/FZJ-INM1-BDA/siibra-python.git@feat_compoundFeat
 plotly