Added collection unit tests.

Author: jstone-dev

src/mavedb/lib/validation/urn_re.py

@@ -24,6 +24,10 @@
 MAVEDB_VARIANT_URN_PATTERN = rf"{MAVEDB_SCORE_SET_URN_PATTERN}#[1-9]\d*"
 MAVEDB_VARIANT_URN_RE = re.compile(MAVEDB_VARIANT_URN_PATTERN)
 
+# Collection URN
+MAVEDB_COLLECTION_URN_PATTERN = r"urn:mavedb:collection-[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}"
+MAVEDB_COLLECTION_URN_RE = re.compile(MAVEDB_COLLECTION_URN_PATTERN)
+
 # Any URN
 MAVEDB_ANY_URN_PATTERN = "|".join(
     [

src/mavedb/view_models/collection.py

@@ -64,7 +64,6 @@ class AddUserToCollectionRoleRequest(BaseModel):
 
 # Properties shared by models stored in DB
 class SavedCollection(CollectionBase):
-    id: int
     urn: str
     created_by: Optional[SavedUser]
     modified_by: Optional[SavedUser]

tests/conftest.py

@@ -31,7 +31,7 @@
 
 sys.path.append(".")
 
-from tests.helpers.constants import ADMIN_USER, TEST_USER
+from tests.helpers.constants import ADMIN_USER, EXTRA_USER, TEST_USER
 
 # needs the pytest_postgresql plugin installed
 assert pytest_postgresql.factories
@@ -242,6 +242,39 @@ def override_hgvs_data_provider():
     yield anonymous_overrides
 
 
+@pytest.fixture()
+def extra_user_app_overrides(session, data_provider, arq_redis):
+    def override_get_db():
+        try:
+            yield session
+        finally:
+            session.close()
+
+    async def override_get_worker():
+        yield arq_redis
+
+    def override_current_user():
+        default_user = session.query(User).filter(User.username == EXTRA_USER["username"]).one_or_none()
+        yield UserData(default_user, default_user.roles)
+
+    def override_require_user():
+        default_user = session.query(User).filter(User.username == EXTRA_USER["username"]).one_or_none()
+        yield UserData(default_user, default_user.roles)
+
+    def override_hgvs_data_provider():
+        yield data_provider
+
+    anonymous_overrides = {
+        get_db: override_get_db,
+        get_worker: override_get_worker,
+        get_current_user: override_current_user,
+        require_current_user: require_current_user,
+        hgvs_data_provider: override_hgvs_data_provider,
+    }
+
+    yield anonymous_overrides
+
+
 @pytest.fixture()
 def admin_app_overrides(session, data_provider, arq_redis):
     def override_get_db():

tests/helpers/constants.py

@@ -696,3 +696,36 @@
     "positiveLikelihoodRatios": [100, 10, 1, 0.1],
     "priorProbabilityPathogenicity": 0.20,
 }
+
+
+TEST_COLLECTION = {"name": "Test collection", "description": None, "private": True}
+
+
+TEST_COLLECTION_RESPONSE = {
+    "name": "Test collection",
+    # "description": None,
+    "private": True,
+    "createdBy": {
+        "firstName": TEST_USER["first_name"],
+        "lastName": TEST_USER["last_name"],
+        "orcidId": TEST_USER["username"],
+    },
+    "modifiedBy": {
+        "firstName": TEST_USER["first_name"],
+        "lastName": TEST_USER["last_name"],
+        "orcidId": TEST_USER["username"],
+    },
+    "creationDate": date.today().isoformat(),
+    "modificationDate": date.today().isoformat(),
+    "experimentUrns": [],
+    "scoreSetUrns": [],
+    "admins": [
+        {
+            "firstName": TEST_USER["first_name"],
+            "lastName": TEST_USER["last_name"],
+            "orcidId": TEST_USER["username"],
+        }
+    ],
+    "editors": [],
+    "viewers": [],
+}

tests/helpers/util.py

@@ -14,11 +14,13 @@
 from mavedb.models.score_set import ScoreSet as ScoreSetDbModel
 from mavedb.models.license import License
 from mavedb.models.user import User
+from mavedb.view_models.collection import Collection
 from mavedb.view_models.experiment import Experiment, ExperimentCreate
 from mavedb.view_models.score_set import ScoreSet, ScoreSetCreate
 from tests.helpers.constants import (
     EXTRA_USER,
     TEST_CDOT_TRANSCRIPT,
+    TEST_COLLECTION,
     TEST_MINIMAL_ACC_SCORESET,
     TEST_MINIMAL_EXPERIMENT,
     TEST_MINIMAL_SEQ_SCORESET,
@@ -64,6 +66,19 @@ def change_to_inactive_license(db, urn):
     db.commit()
 
 
+def create_collection(client, update=None):
+    collection_payload = deepcopy(TEST_COLLECTION)
+    if update is not None:
+        collection_payload.update(update)
+
+    response = client.post("/api/v1/collections/", json=collection_payload)
+    assert response.status_code == 200, "Could not create collection."
+
+    response_data = response.json()
+    jsonschema.validate(instance=response_data, schema=Collection.schema())
+    return response_data
+
+
 def create_experiment(client, update=None):
     experiment_payload = deepcopy(TEST_MINIMAL_EXPERIMENT)
     if update is not None: