Merge pull request #198 from FZJ-INM1-BDA/bugfix_parcsEbrainDoi

bugfix: parcellation ebrains doi

Author: xgui3783

siibra/core/parcellation.py

@@ -570,6 +570,13 @@ def model_id(self):
         return self.id
 
     def to_model(self, **kwargs) -> SiibraParcellationModel:
+
+        dois = [url.get("doi") if url.get("doi").startswith("http") else f"https://doi.org/{url.get('doi')}"
+            for info in self.infos
+            if hasattr(info, 'urls')
+            for url in info.urls
+            if url.get("doi")]
+        ebrains_doi = dois[0] if len(dois) > 0 else None
         return SiibraParcellationModel(
             id=self.model_id,
             type=SIIBRA_PARCELLATION_MODEL_TYPE,
@@ -608,7 +615,11 @@ def to_model(self, **kwargs) -> SiibraParcellationModel:
                 release_date=date(1970,1,1),
                 short_name=self.name[:30],
                 version_identifier=f"{self.version} in {spc.to_model().full_name}",
-                version_innovation="",
+                version_innovation=self.description,
+                digital_identifier={
+                    "@id": ebrains_doi,
+                    "@type": "https://openminds.ebrains.eu/core/DOI"
+                } if ebrains_doi is not None else None
             ) for spc in self.supported_spaces],
             version=self.version.to_model(**kwargs) if self.version is not None else None
         )

test/core/test_parcellation.py

@@ -95,6 +95,22 @@ def test_should_be_able_to_fetch_map(atlas_id,space_id,parc_id,map_type):
 
     parc.get_map(space, map_type)
 
+parc_has_ebrains_doi = [
+    ("human", "julich brain 2.9")
+]
+
+@pytest.mark.parametrize('atlas_id,parc_id', parc_has_ebrains_doi)
+def test_should_have_ebrains_doi(atlas_id,parc_id):
+    
+    atlas = siibra.atlases[atlas_id]
+    parc = atlas.parcellations[parc_id]
+    model = parc.to_model()
+    all(
+        ver.digital_identifier is not None
+        and ver.digital_identifier.get("@type") == "https://openminds.ebrains.eu/core/DOI"
+        and ver.digital_identifier.get("@id").startswith("https://doi.org")
+        for ver in model.brain_atlas_versions
+    )
 
 if __name__ == "__main__":
     unittest.main()