CELE-17 chore: Merge with develop

applications/visualizer/backend/README.md

@@ -18,6 +18,7 @@ backend
 ├── openapi
 │   └── openapi.json         # The openapi.json generated from the routes defined in "api.py"
 ├── populate-db.bash         # the script to populate the DB
+├── tests/**            # The directory that contains the tests
 └── visualizer
     ├── asgi.py
     ├── models.py
@@ -45,4 +46,19 @@ If you also want to see the SQL commands that are sent to the DB, you can start
 ```bash
 # from inside the "backend" folder
 python manage.py shell_plus --print-sql
-```
+```
+
+## Run tests
+
+The tests are written with `pytest` and `pytest-django`.
+To run the test, simply execute in the `backend` folder one of the following command:
+
+```bash
+python -m pytest
+# or simply
+pytest
+```
+
+The data in the test are paritally generated.
+Some of the fields are manually set and the ones that we don't want to write and/or test are generated (e.g: the field is marked `not null` in the django model, so it has to be here).
+The value generation is done with [`model-bakery`](https://model-bakery.readthedocs.io/), which offers a nice level of flexibility and customization.

applications/visualizer/backend/api/api.py

@@ -1,6 +1,7 @@
 from ninja import NinjaAPI, Router, Schema
 from ninja.pagination import paginate, PageNumberPagination
 from django.shortcuts import aget_object_or_404
+from django.db.models import Q
 
 
 from .schemas import Dataset, FullDataset, Neuron, Connection, ConnectionRequest
@@ -74,6 +75,29 @@ async def get_dataset(request, dataset: str):
     return await aget_object_or_404(DatasetModel, id=dataset)
 
 
+@api.get(
+    "/datasets/{dataset}/neurons",
+    response={200: list[Neuron], 404: ErrorMessage},
+    tags=["datasets"],
+)
+async def get_dataset_neurons(request, dataset: str):
+    """Returns all the neurons of a dedicated dataset"""
+    return await to_list(
+        NeuronModel.objects.filter(
+            Q(
+                name__in=ConnectionModel.objects.filter(
+                    dataset__id=dataset
+                ).values_list("pre", flat=True)
+            )
+            | Q(
+                name__in=ConnectionModel.objects.filter(
+                    dataset__id=dataset
+                ).values_list("post", flat=True)
+            )
+        )
+    )
+
+
 @api.get("/cells", response=list[Neuron], tags=["neurons"])
 @paginate(PageNumberPagination, page_size=50)
 def get_all_cells(request):

applications/visualizer/backend/pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+DJANGO_SETTINGS_MODULE = visualizer.settings
+django_debug_mode = keep

applications/visualizer/backend/requirements-dev.txt

@@ -3,4 +3,6 @@ django_extensions
 ipdb
 pytest
 pytest-django
+pytest-asyncio
+model-bakery
 black

applications/visualizer/backend/tests/test_connections.py

@@ -0,0 +1,25 @@
+import pytest
+
+from api.models import Connection
+from .utils import generate_instance
+
+
+# Some test data
+connections = [
+    {"id": "1", "dataset": {"id": "ds3", "name": "Dr. Seuss"}},
+]
+
+
+@pytest.fixture(scope="module")
+def django_db_setup(django_db_setup, django_db_blocker):
+    with django_db_blocker.unblock():
+        generate_instance(Connection, connections)
+
+
+@pytest.mark.django_db
+def test__fk_creation():
+    o = Connection.objects.get(id=1)
+
+    assert o.dataset
+    assert o.dataset.id == "ds3"
+    assert o.dataset.name == "Dr. Seuss"

applications/visualizer/backend/tests/test_datasets.py

@@ -0,0 +1,75 @@
+from ninja.testing import TestAsyncClient
+import pytest
+
+
+from api.api import api as celegans_api
+from api.models import Dataset
+from .utils import generate_instance
+
+
+# Some test data
+datasets = [
+    {
+        "id": "ds1",
+        "name": "Dataset 1",
+    },
+    {
+        "id": "gg",
+        "name": "Gamma Goblin",
+    },
+    {
+        "id": "ds3",
+        "name": "Dr. Seuss",
+    },
+]
+
+
+# Setup the db for this module with some data
+# Data are baked with "baker", it allows to create dummy values automatically
+# and also to specify some fields. It is used here to "fill" the fields which are
+# marked as "non-null" in the model which we don't want to manually fill.
+@pytest.fixture(scope="module")
+def django_db_setup(django_db_setup, django_db_blocker):
+    with django_db_blocker.unblock():
+        generate_instance(Dataset, datasets)
+
+
+# Fixture to access the test client in all test functions
+@pytest.fixture
+def api_client():
+    client = TestAsyncClient(celegans_api.default_router)
+    return client
+
+
+# Test function
+@pytest.mark.django_db  # required to access the DB
+@pytest.mark.asyncio  # required as we access a async function
+async def test__get_nonexisting_dataset(api_client):
+    response = await api_client.get("/datasets/nonexisting")
+    assert response.status_code == 404
+
+
+@pytest.mark.django_db
+@pytest.mark.asyncio
+async def test__get_existing_dataset(api_client):
+    response = await api_client.get("/datasets/ds3")
+    assert response.status_code == 200
+
+    dataset = response.json()
+    assert dataset["id"] == "ds3"
+    assert dataset["name"] == "Dr. Seuss"
+
+
+@pytest.mark.django_db
+@pytest.mark.asyncio
+async def test__get_all_datasets(api_client):
+    response = await api_client.get("/datasets")
+    assert response.status_code == 200
+
+    datasets = response.json()
+    assert len(datasets) == 3
+
+    datasets_id = [dataset["id"] for dataset in datasets]
+    assert "ds1" in datasets_id
+    assert "ds3" in datasets_id
+    assert "gg" in datasets_id

applications/visualizer/backend/tests/utils.py

@@ -0,0 +1,18 @@
+from model_bakery import baker
+
+
+def flat_dict(d):
+    res = {}
+    for key, value in d.items():
+        if isinstance(value, dict):
+            subdict = flat_dict(value)
+            for subk, subv in subdict.items():
+                res[f"{key}__{subk}"] = subv
+        else:
+            res[key] = value
+    return res
+
+
+def generate_instance(cls, instance_list):
+    for instance in instance_list:
+        baker.make(cls, **flat_dict(instance))

applications/visualizer/backend/visualizer/settings/development.py

@@ -12,5 +12,6 @@
     "default": {
         "ENGINE": "django.db.backends.sqlite3",
         "NAME": BASE_DIR / "db.sqlite3",
+        "TEST": {"NAME": BASE_DIR / "tests" / "testdb.sqlite3"},
     }
 }