Propagate atlasRelease version along with id

src/blue_cwl/registering.py

@@ -16,7 +16,6 @@
 from entity_management.base import BrainLocation, Derivation, OntologyTerm
 from entity_management.core import DataDownload, Entity, Subject
 from entity_management.simulation import DetailedCircuit
-from entity_management.util import get_entity
 
 from blue_cwl.typing import StrOrPath
 from blue_cwl.utils import load_json, write_json
@@ -39,16 +38,19 @@ def _brain_location(brain_region_id: str) -> BrainLocation:
 
 
 def register_partial_circuit(
+    *,
     name: str,
     brain_region_id: str,
-    atlas_release_id: str,
+    atlas_release: AtlasRelease,
     sonata_config_path: StrOrPath,
     description: str = "",
     species_id: str | None = None,
+    base: str | None = None,
+    org: str | None = None,
+    proj: str | None = None,
+    token: str | None = None,
 ) -> DetailedCircuit:
     """Register a partial circuit."""
-    atlas_release = get_entity(resource_id=atlas_release_id, cls=AtlasRelease)
-
     circuit_config_path = DataDownload(url=f"file://{Path(sonata_config_path).resolve()}")
 
     return DetailedCircuit(
@@ -58,7 +60,7 @@ def register_partial_circuit(
         brainLocation=_brain_location(brain_region_id),
         atlasRelease=atlas_release,
         circuitConfigPath=circuit_config_path,
-    ).publish()
+    ).publish(include_rev=True, base=base, org=org, proj=proj, use_auth=token)
 
 
 def register_cell_composition_summary(

src/blue_cwl/wrappers/connectome_filtering_synapses.py

@@ -286,7 +286,7 @@ def register(
     partial_circuit = registering.register_partial_circuit(
         name="Partial circuit with functional connectivity",
         brain_region_id=utils.get_partial_circuit_region_id(partial_circuit),
-        atlas_release_id=partial_circuit.atlasRelease.get_id(),
+        atlas_release=partial_circuit.atlasRelease,
         description="Circuit with nodes and functionalized synapses.",
         sonata_config_path=output_config_file,
     )

src/blue_cwl/wrappers/connectome_generation_placeholder.py

@@ -246,7 +246,7 @@ def register(*, circuit_id: str, edges_file: StrOrPath, output_dir: StrOrPath):
     output_circuit = registering.register_partial_circuit(
         name="Partial circuit with connectivity",
         brain_region_id=utils.get_partial_circuit_region_id(input_circuit),
-        atlas_release_id=input_circuit.atlasRelease.get_id(),
+        atlas_release=input_circuit.atlasRelease,
         description="Partial circuit with cell properties, emodels, morphologies and connectivity.",
         sonata_config_path=sonata_config_file,
     )

src/blue_cwl/wrappers/memodel.py

@@ -237,7 +237,7 @@ def _register_circuit(partial_circuit, output_circuit_config_file):
     circuit = registering.register_partial_circuit(
         name="Partial circuit with biohysical emodel properties",
         brain_region_id=get_partial_circuit_region_id(partial_circuit),
-        atlas_release_id=partial_circuit.atlasRelease.get_id(),
+        atlas_release=partial_circuit.atlasRelease,
         description="Partial circuit with cell properties, morphologies, and biophysical models.",
         sonata_config_path=output_circuit_config_file,
     )

src/blue_cwl/wrappers/mmodel.py

@@ -454,7 +454,7 @@ def register(
     output_circuit = registering.register_partial_circuit(
         name="Partial circuit with morphologies",
         brain_region_id=get_partial_circuit_region_id(input_circuit),
-        atlas_release_id=input_circuit.atlasRelease.get_id(),
+        atlas_release=input_circuit.atlasRelease,
         description="Partial circuit built with cell properties, and morphologies.",
         sonata_config_path=sonata_config_file,
     )

src/blue_cwl/wrappers/neurons_cell_position.py

@@ -18,7 +18,10 @@
 from voxcell.nexus.voxelbrain import Atlas
 
 from blue_cwl import Variant, nexus, recipes, registering, staging, utils, validation
-from blue_cwl.statistics import mtype_etype_url_mapping, node_population_composition_summary
+from blue_cwl.statistics import (
+    mtype_etype_url_mapping,
+    node_population_composition_summary,
+)
 from blue_cwl.typing import StrOrPath
 
 SEED = 42
@@ -106,8 +109,12 @@ def _extract(
         output_file=me_type_densities_file,
     )
 
+    atlas_release = cell_composition.atlasRelease
+
+    full_atlas_id = utils.url_with_revision(url=atlas_release.get_id(), rev=atlas_release.get_rev())
+
     return {
-        "atlas-id": cell_composition.atlasRelease.get_id(),
+        "atlas-id": full_atlas_id,
         "region": region,
         "atlas-dir": atlas_dir,
         "me-type-densities-file": me_type_densities_file,
@@ -315,7 +322,12 @@ def _generate_circuit_config(
 
 
 def _generate_cell_composition_summary(
-    nodes_file, node_population_name, atlas_dir, mtype_urls, etype_urls, output_file: Path
+    nodes_file,
+    node_population_name,
+    atlas_dir,
+    mtype_urls,
+    etype_urls,
+    output_file: Path,
 ):
     atlas = Atlas.open(str(atlas_dir))
     population = libsonata.NodeStorage(nodes_file).open_population(node_population_name)
@@ -332,10 +344,12 @@ def _register(
     output_dir,
 ):
     """Register outputs to nexus."""
+    atlas_release = get_entity(generated_data["atlas-id"], cls=AtlasRelease)
+
     circuit_resource = registering.register_partial_circuit(
         name="Cell properties partial circuit",
         brain_region_id=region_id,
-        atlas_release_id=generated_data["atlas-id"],
+        atlas_release=atlas_release,
         description="Partial circuit built with cell positions and me properties.",
         sonata_config_path=generated_data["partial-circuit"],
     )
@@ -350,6 +364,6 @@ def _register(
         name="Cell Composition Summary",
         description="Cell Composition Summary of Node Population",
         distribution_file=generated_data["composition-summary-file"],
-        atlas_release=get_entity(generated_data["atlas-id"], cls=AtlasRelease),
+        atlas_release=atlas_release,
         derivation_entity=circuit_resource,
     )

tests/unit/test_registering.py

@@ -23,11 +23,18 @@ def atlas_release():
         "@type": "AtlasRelease",
         "label": "my-atlas",
         "name": "foo",
-        "brainTemplateDataLayer": {"@id": "template-id", "@type": "braintemplatedatalayer"},
+        "brainTemplateDataLayer": {
+            "@id": "template-id",
+            "@type": "braintemplatedatalayer",
+        },
         "parcellationOntology": {"@id": "ontology-id", "@type": "parcellationontology"},
         "parcellationVolume": {"@id": "volume-id", "@type": "parcellationvolume"},
         "subject": {"@type": "subject"},
-        "spatialReferenceSystem": {"@id": "ref-id", "@type": "spatialreferencesystem", "_rev": 1},
+        "spatialReferenceSystem": {
+            "@id": "ref-id",
+            "@type": "spatialreferencesystem",
+            "_rev": 1,
+        },
         "brainLocation": {"brainRegion": {"@id": "mba:997", "label": "root"}},
     }
 
@@ -51,7 +58,9 @@ def test_brain_location(monkeypatch):
     mock_region.get_id.return_value = "foo"
     mock_region.label = "bar"
 
-    monkeypatch.setattr(AtlasBrainRegion, "from_id", lambda *args, **kwargs: mock_region)
+    monkeypatch.setattr(
+        AtlasBrainRegion, "from_id", lambda *args, **kwargs: mock_region
+    )
 
     payload = {
         "@id": "foo",
@@ -70,7 +79,7 @@ def test_brain_location(monkeypatch):
     assert res.brainRegion.label == "bar"
 
 
-def test_register_partial_circuit():
+def test_register_partial_circuit(atlas_release):
     def load_by_url(url, *args, **kwargs):
         if "brain-region-id" in url:
             return {
@@ -87,11 +96,23 @@ def load_by_url(url, *args, **kwargs):
                 "@type": "AtlasRelease",
                 "label": "my-atlas",
                 "name": "foo",
-                "brainTemplateDataLayer": {"@id": "template-id", "@type": "braintemplatedatalayer"},
-                "parcellationOntology": {"@id": "ontology-id", "@type": "parcellationontology"},
-                "parcellationVolume": {"@id": "volume-id", "@type": "parcellationvolume"},
+                "brainTemplateDataLayer": {
+                    "@id": "template-id",
+                    "@type": "braintemplatedatalayer",
+                },
+                "parcellationOntology": {
+                    "@id": "ontology-id",
+                    "@type": "parcellationontology",
+                },
+                "parcellationVolume": {
+                    "@id": "volume-id",
+                    "@type": "parcellationvolume",
+                },
                 "subject": {"@type": "subject"},
-                "spatialReferenceSystem": {"@id": "ref-id", "@type": "spatialreferencesystem"},
+                "spatialReferenceSystem": {
+                    "@id": "ref-id",
+                    "@type": "spatialreferencesystem",
+                },
             }
         raise
 
@@ -105,7 +126,7 @@ def create(base_url, payload, *args, **kwargs):
         res = test_module.register_partial_circuit(
             name="my-circuit",
             brain_region_id="brain-region-id",
-            atlas_release_id="atlas-release-id",
+            atlas_release=atlas_release,
             sonata_config_path="my-sonata-path",
             description="my-description",
         )
@@ -403,13 +424,17 @@ def upload_file(name, data, *args, **kwargs):
                         "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/Foo",
                         "label": "Foo",
                         "about": ["https://neuroshapes.org/EType"],
-                        "hasPart": [{"@type": "METypeDensity", "@id": "foo-id", "_rev": 2}],
+                        "hasPart": [
+                            {"@type": "METypeDensity", "@id": "foo-id", "_rev": 2}
+                        ],
                     },
                     {
                         "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/Bar",
                         "label": "Bar",
                         "about": ["https://neuroshapes.org/EType"],
-                        "hasPart": [{"@id": "bar-id", "_rev": 1, "@type": "METypeDensity"}],
+                        "hasPart": [
+                            {"@id": "bar-id", "_rev": 1, "@type": "METypeDensity"}
+                        ],
                     },
                 ],
             }