comments

Author: mgeplf

app/routers/brain_atlas.py

@@ -8,6 +8,8 @@
 )
 
 read_many = router.get("")(app.service.brain_atlas.read_many)
-read_one = router.get("/{id_}")(app.service.brain_atlas.read_one)
-read_many_region = router.get("/{id_}/regions")(app.service.brain_atlas.read_many_region)
-read_one_region = router.get("/{id_}/regions/{region_id}")(app.service.brain_atlas.read_one_region)
+read_one = router.get("/{atlas_id}")(app.service.brain_atlas.read_one)
+read_many_region = router.get("/{atlas_id}/regions")(app.service.brain_atlas.read_many_region)
+read_one_region = router.get("/{atlas_id}/regions/{atlas_region_id}")(
+    app.service.brain_atlas.read_one_region
+)

app/service/brain_atlas.py

@@ -1,7 +1,5 @@
 import uuid
 
-import sqlalchemy as sa
-
 import app.queries.common
 from app.db.model import BrainAtlas, BrainAtlasRegion
 from app.dependencies.auth import UserContextDep
@@ -35,9 +33,9 @@ def read_many(
     )
 
 
-def read_one(user_context: UserContextDep, id_: uuid.UUID, db: SessionDep) -> BrainAtlasRead:
+def read_one(user_context: UserContextDep, atlas_id: uuid.UUID, db: SessionDep) -> BrainAtlasRead:
     return app.queries.common.router_read_one(
-        id_=id_,
+        id_=atlas_id,
         db=db,
         db_model_class=BrainAtlas,
         authorized_project_id=user_context.project_id,
@@ -48,6 +46,7 @@ def read_one(user_context: UserContextDep, id_: uuid.UUID, db: SessionDep) -> Br
 
 def read_many_region(
     user_context: UserContextDep,
+    atlas_id: uuid.UUID,
     db: SessionDep,
     pagination_request: PaginationQuery,
     brain_atlas_region_filter: BrainAtlasRegionFilterDep,
@@ -60,7 +59,9 @@ def read_many_region(
         with_in_brain_region=None,
         facets=None,
         aliases=None,
-        apply_filter_query_operations=None,
+        apply_filter_query_operations=lambda q: q.filter(
+            BrainAtlasRegion.brain_atlas_id == atlas_id
+        ),
         apply_data_query_operations=None,
         pagination_request=pagination_request,
         response_schema_class=BrainAtlasRegionRead,
@@ -70,15 +71,13 @@ def read_many_region(
 
 
 def read_one_region(
-    user_context: UserContextDep, id_: uuid.UUID, region_id: uuid.UUID, db: SessionDep
+    user_context: UserContextDep, atlas_id: uuid.UUID, atlas_region_id: uuid.UUID, db: SessionDep
 ) -> BrainAtlasRegionRead:
     return app.queries.common.router_read_one(
-        id_=region_id,
+        id_=atlas_region_id,
         db=db,
         db_model_class=BrainAtlasRegion,
         authorized_project_id=user_context.project_id,
         response_schema_class=BrainAtlasRegionRead,
-        apply_operations=lambda q: q.filter(
-            sa.and_(BrainAtlasRegion.brain_atlas_id == id_, BrainAtlasRegion.id == region_id)
-        ),
+        apply_operations=lambda q: q.filter(BrainAtlasRegion.brain_atlas_id == atlas_id),
     )

tests/test_brain_atlas.py

@@ -1,3 +1,4 @@
+import itertools as it
 from unittest.mock import ANY
 
 import pytest
@@ -54,7 +55,7 @@ def test_brain_atlas(db, client, species_id):
     hierarchy_name = utils.create_hiearchy_name(db, "test_hierarchy")
     regions = utils.add_brain_region_hierarchy(db, HIERARCHY, hierarchy_name.id)
 
-    brain_atlas = utils.add_db(
+    brain_atlas0 = utils.add_db(
         db,
         BrainAtlas(
             name="test brain atlas",
@@ -65,10 +66,21 @@ def test_brain_atlas(db, client, species_id):
             authorized_public=True,
         ),
     )
+    brain_atlas1 = utils.add_db(
+        db,
+        BrainAtlas(
+            name="test brain atlas 1",
+            description="test brain atlas description 1",
+            species_id=species_id,
+            hierarchy_id=hierarchy_name.id,
+            authorized_project_id=utils.PROJECT_ID,
+            authorized_public=True,
+        ),
+    )
     expected = {
         "creation_date": ANY,
         "hierarchy_id": str(hierarchy_name.id),
-        "id": str(brain_atlas.id),
+        "id": str(brain_atlas0.id),
         "name": "test brain atlas",
         "species": {
             "creation_date": ANY,
@@ -83,19 +95,23 @@ def test_brain_atlas(db, client, species_id):
     response = client.get(ROUTE)
     assert response.status_code == 200
     response = response.json()
-    assert len(response["data"]) == 1
-    assert response["data"] == [
-        expected,
-    ]
+    assert len(response["data"]) == 2
+    assert response["data"][0] == expected
 
-    response = client.get(f"{ROUTE}/{brain_atlas.id}")
+    response = client.get(f"{ROUTE}/{brain_atlas0.id}")
     assert response.status_code == 200
     response = response.json()
     assert response == expected
 
     data = (("root", False, -1), ("blue", False, -1), ("red", True, 15), ("grey", True, 10))
     ids = {}
-    for name, leaf, volume in data:
+    for brain_atlas, (name, leaf, volume) in it.product(
+        (
+            brain_atlas0,
+            brain_atlas1,
+        ),
+        data,
+    ):
         row = BrainAtlasRegion(
             volume=volume,
             leaf_region=leaf,
@@ -104,58 +120,58 @@ def test_brain_atlas(db, client, species_id):
             authorized_project_id=utils.PROJECT_ID,
             authorized_public=True,
         )
-        ids[name] = utils.add_db(db, row)
+        ids[brain_atlas.name, name] = utils.add_db(db, row)
 
     response = client.get(
-        f"{ROUTE}/{brain_atlas.id}/regions", params={"order_by": "+creation_date"}
+        f"{ROUTE}/{brain_atlas0.id}/regions", params={"order_by": "+creation_date"}
     )
     assert response.status_code == 200
     assert response.json()["data"] == [
         {
-            "brain_atlas_id": str(brain_atlas.id),
+            "brain_atlas_id": str(brain_atlas0.id),
             "brain_region_id": str(regions["root"].id),
             "creation_date": ANY,
-            "id": str(ids["root"].id),
+            "id": str(ids[brain_atlas0.name, "root"].id),
             "leaf_region": False,
             "update_date": ANY,
             "volume": -1.0,
         },
         {
-            "brain_atlas_id": str(brain_atlas.id),
+            "brain_atlas_id": str(brain_atlas0.id),
             "brain_region_id": str(regions["blue"].id),
             "creation_date": ANY,
-            "id": str(ids["blue"].id),
+            "id": str(ids[brain_atlas0.name, "blue"].id),
             "leaf_region": False,
             "update_date": ANY,
             "volume": -1.0,
         },
         {
-            "brain_atlas_id": str(brain_atlas.id),
+            "brain_atlas_id": str(brain_atlas0.id),
             "brain_region_id": str(regions["red"].id),
             "creation_date": ANY,
-            "id": str(ids["red"].id),
+            "id": str(ids[brain_atlas0.name, "red"].id),
             "leaf_region": True,
             "update_date": ANY,
             "volume": 15.0,
         },
         {
-            "brain_atlas_id": str(brain_atlas.id),
+            "brain_atlas_id": str(brain_atlas0.id),
             "brain_region_id": str(regions["grey"].id),
             "creation_date": ANY,
-            "id": str(ids["grey"].id),
+            "id": str(ids[brain_atlas0.name, "grey"].id),
             "leaf_region": True,
             "update_date": ANY,
             "volume": 10.0,
         },
     ]
 
-    response = client.get(f"{ROUTE}/{brain_atlas.id}/regions/{ids['root'].id}")
+    response = client.get(f"{ROUTE}/{brain_atlas0.id}/regions/{ids[brain_atlas0.name, 'root'].id}")
     assert response.status_code == 200
     assert response.json() == {
-        "brain_atlas_id": str(brain_atlas.id),
+        "brain_atlas_id": str(brain_atlas0.id),
         "brain_region_id": str(regions["root"].id),
         "creation_date": ANY,
-        "id": str(ids["root"].id),
+        "id": str(ids[brain_atlas0.name, "root"].id),
         "leaf_region": False,
         "update_date": ANY,
         "volume": -1.0,