run test in ci

.github/workflows/workflow.yml

@@ -254,7 +254,7 @@ jobs:
           -e "NEUROVAULT_ACCESS_TOKEN=${NEUROVAULT_ACCESS_TOKEN}" \
           --rm -w /compose \
           compose \
-          bash -c "python -m pytest neurosynth_compose/tests && python -m pytest --celery neurosynth_compose/tests/api/celery_tests"
+          bash -c "python -m pytest neurosynth_compose/tests && python -m pytest --celery neurosynth_compose/tests/api/celery_tests && python -m pytest --auth neurosynth_compose/tests/api/test_auth.py"
 
   style_check:
     runs-on: ubuntu-latest

compose/neurosynth_compose/resources/analysis.py

@@ -44,6 +44,26 @@
 from .singular import singularize
 
 
+def create_user():
+    from auth0.v3.authentication.users import Users
+    auth = request.headers.get("Authorization", None)
+    if auth is None:
+        return None
+    token = auth.split()[1]
+    profile_info = Users(
+        current_app.config["AUTH0_BASE_URL"].removeprefix("https://")
+    ).userinfo(access_token=token)
+
+    # user signed up with auth0, but has not made any queries yet...
+    # should have endpoint to "create user" after sign on with auth0
+    current_user = User(
+        external_id=connexion.context["user"],
+        name=profile_info.get("name", "Unknown")
+    )
+
+    return current_user
+
+
 def get_current_user():
     user = connexion.context.get("user")
     if user:
@@ -81,9 +101,10 @@ def update_or_create(cls, data, id=None, commit=True):
         if not current_user:
             # user signed up with auth0, but has not made any queries yet...
             # should have endpoint to "create user" after sign on with auth0
-            current_user = User(external_id=connexion.context["user"])
-            db.session.add(current_user)
-            db.session.commit()
+            current_user = create_user()
+            if current_user:
+                db.session.add(current_user)
+                db.session.commit()
 
         id = id or data.get("id", None)  # want to handle case of {"id": "asdfasf"}
 

compose/neurosynth_compose/schemas/analysis.py

@@ -119,6 +119,9 @@ class BaseSchema(Schema):
     created_at = fields.DateTime()
     updated_at = fields.DateTime(allow_none=True)
     user_id = fields.String(data_key="user")
+    username = fields.String(
+        attribute="user.name", dump_only=True
+    )
 
 
 class EstimatorSchema(Schema):

compose/neurosynth_compose/tests/api/celery_tests/test_meta_analysis_result.py

@@ -14,7 +14,7 @@
 
 
 @celery_test
-def test_file_upload_neurovault(app, db, mock_pynv):
+def test_file_upload_neurovault(session, app, db, mock_pynv):
     import os
     from pathlib import Path
     import shutil
@@ -35,7 +35,7 @@ def test_file_upload_neurovault(app, db, mock_pynv):
 
 @celery_test
 def test_create_or_update_neurostore_analysis(
-    auth_client, app, db, mock_pynv, meta_analysis_cached_result_files
+    session, auth_client, app, db, mock_pynv, meta_analysis_cached_result_files
 ):
     cluster_tables = [
         f for f in meta_analysis_cached_result_files["tables"] if "clust.tsv" in f.name
@@ -78,7 +78,7 @@ def test_create_or_update_neurostore_analysis(
 
 
 @celery_test
-def test_result_upload(auth_client, app, db, meta_analysis_cached_result_files):
+def test_result_upload(session, auth_client, app, db, meta_analysis_cached_result_files):
     data = {}
     data["statistical_maps"] = [
         (open(m, "rb"), m.name) for m in meta_analysis_cached_result_files["maps"]

compose/neurosynth_compose/tests/api/test_annotation.py

@@ -1,4 +1,4 @@
-def test_get_annotations(auth_client, user_data):
+def test_get_annotations(session, auth_client, user_data):
     get_all = auth_client.get("/api/annotations")
     assert get_all.status_code == 200
     id_ = get_all.json["results"][0]["id"]

compose/neurosynth_compose/tests/api/test_crud.py

@@ -21,7 +21,7 @@
         ("projects", Project, ProjectSchema),
     ],
 )
-def test_create(auth_client, user_data, endpoint, model, schema):
+def test_create(session, auth_client, user_data, endpoint, model, schema):
     user = User.query.filter_by(name="user1").first()
     examples = model.query.filter_by(user=user).all()
     for example in examples:
@@ -42,6 +42,8 @@ def test_create(auth_client, user_data, endpoint, model, schema):
             del payload["neurostore_url"]
         if "neurostore_study" in payload:
             del payload["neurostore_study"]
+        if "username" in payload:
+            del payload["username"]
 
         if isinstance(example, MetaAnalysis):
             del payload["neurostore_analysis"]
@@ -75,7 +77,7 @@ def test_create(auth_client, user_data, endpoint, model, schema):
         ("projects", Project, ProjectSchema),
     ],
 )
-def test_read(auth_client, user_data, endpoint, model, schema):
+def test_read(session, auth_client, user_data, endpoint, model, schema):
     user = User.query.filter_by(name="user1").first()
     if hasattr(model, "public"):
         query = (model.user == user) | (model.public == True)  # noqa E712
@@ -107,7 +109,7 @@ def test_read(auth_client, user_data, endpoint, model, schema):
         ("projects", Project, ProjectSchema, {"name": "my project"}),
     ],
 )
-def test_update(auth_client, db, session, user_data, endpoint, model, schema, update):
+def test_update(session, auth_client, db, user_data, endpoint, model, schema, update):
     user = User.query.filter_by(name="user1").first()
     record = model.query.filter_by(user=user).first()
 

compose/neurosynth_compose/tests/api/test_meta_analysis.py

@@ -1,4 +1,4 @@
-def test_get_meta_analyses(app, auth_client, user_data):
+def test_get_meta_analyses(session, app, auth_client, user_data):
     get_all = auth_client.get("/api/meta-analyses")
     assert get_all.status_code == 200
 
@@ -15,5 +15,5 @@ def test_get_meta_analyses(app, auth_client, user_data):
         assert data[key] is None or isinstance(data[key], dict)
 
 
-def test_ingest_neurostore(neurostore_data):
+def test_ingest_neurostore(session, neurostore_data):
     pass

compose/neurosynth_compose/tests/api/test_meta_analysis_result.py

@@ -1,7 +1,7 @@
 from neurosynth_compose.models import MetaAnalysis
 
 
-def test_create_meta_analysis_result(app, auth_client, user_data):
+def test_create_meta_analysis_result(session, app, auth_client, user_data):
     meta_analysis = MetaAnalysis.query.first()
     headers = {"Compose-Upload-Key": meta_analysis.run_key}
     data = {
@@ -20,7 +20,7 @@ def test_create_meta_analysis_result(app, auth_client, user_data):
     assert meta_resp.status_code == 200
 
 
-def test_create_meta_analysis_result_no_snapshots(app, db, auth_client, user_data):
+def test_create_meta_analysis_result_no_snapshots(session, app, db, auth_client, user_data):
     meta_analysis = MetaAnalysis.query.first()
     meta_analysis.studyset.snapshot = None
     meta_analysis.annotation.snapshot = None

compose/neurosynth_compose/tests/api/test_specification.py

@@ -1,3 +1,3 @@
-def test_get_specification(app, auth_client, user_data):
+def test_get_specification(session, app, auth_client, user_data):
     get = auth_client.get("/api/specifications")
     assert get.status_code == 200

compose/neurosynth_compose/tests/api/test_studyset.py

@@ -2,17 +2,18 @@
 from ...schemas import StudysetSchema
 
 
-def test_get_studysets(auth_client, user_data):
+def test_get_studysets(session, auth_client, user_data):
     get = auth_client.get("/api/studysets")
     assert get.status_code == 200
 
 
-def test_post_studyset_with_new_neurostore_id(auth_client, user_data):
+def test_post_studyset_with_new_neurostore_id(session, auth_client, user_data):
     user = User.query.filter_by(name="user1").first()
     example = Studyset.query.filter_by(user=user).first()
     schema = StudysetSchema()
     payload = schema.dump(example)
     payload.pop("url")
+    payload.pop("username")
     # payload["neurostore_id"] = ""
 
     resp = auth_client.post("/api/studysets", data=payload)

compose/neurosynth_compose/tests/conftest.py

@@ -42,6 +42,12 @@ def pytest_addoption(parser):
         default=False,
         help="Run celery tests",
     )
+    parser.addoption(
+        "--auth",
+        action="store_true",
+        default=False,
+        help="Run authentication tests",
+    )
 
 
 celery_test = pytest.mark.skipif(
@@ -52,21 +58,56 @@ def pytest_addoption(parser):
     "not config.getoption('--schemathesis')",
     reason="Only run when --schemathesis is given",
 )
-
+auth_test = pytest.mark.skipif(
+    "not config.getoption('--auth')",
+    reason="Only run when --auth is given",
+)
 
 """
 Test fixtures for bypassing authentication
 """
 
 
-# https://github.com/pytest-dev/pytest/issues/363#issuecomment-406536200
 @pytest.fixture(scope="session")
-def monkeysession(request):
-    from _pytest.monkeypatch import MonkeyPatch
+def real_app():
+    """Session-wide test `Flask` application."""
+    from ..core import app as _app
 
-    mpatch = MonkeyPatch()
-    yield mpatch
-    mpatch.undo()
+    if "APP_SETTINGS" not in environ:
+        config = "neurostore.config.TestingConfig"
+    else:
+        config = environ["APP_SETTINGS"]
+    if not getattr(_app, "config", None):
+        _app = _app._app
+    _app.config.from_object(config)
+    # _app.config["SQLALCHEMY_ECHO"] = True
+
+    # Establish an application context before running the tests.
+    ctx = _app.app_context()
+    ctx.push()
+
+    yield _app
+
+    ctx.pop()
+
+
+@pytest.fixture(scope="session")
+def real_db(real_app):
+    """Session-wide test database."""
+    _db.create_all()
+
+    yield _db
+
+    _db.session.remove()
+    sa.orm.close_all_sessions()
+    _db.drop_all()
+
+
+# https://github.com/pytest-dev/pytest/issues/363#issuecomment-406536200
+@pytest.fixture(scope="session", autouse=False)
+def monkeysession(request):
+    with pytest.MonkeyPatch.context() as mp:
+        yield mp
 
 
 def mock_decode_token(token):
@@ -201,7 +242,7 @@ def celery_app(app, db):
     return make_celery(app)
 
 
-@pytest.fixture(scope="function", autouse=True)
+@pytest.fixture(scope="function", autouse=False)
 def session(db):
     """Creates a new db session for a test.
     Changes in session are rolled back"""
@@ -295,11 +336,11 @@ def mock_add_users(app, db, mock_auth):
 
 
 @pytest.fixture(scope="function")
-def add_users(app, db):
+def add_users(real_app, real_db):
     """Adds a test user to db"""
     from neurosynth_compose.resources.auth import decode_token
 
-    domain = app.config["AUTH0_BASE_URL"].split("://")[1]
+    domain = real_app.config["AUTH0_BASE_URL"].split("://")[1]
     token = GetToken(domain)
 
     users = [
@@ -318,26 +359,28 @@ def add_users(app, db):
         name = u["name"]
         passw = u["password"]
         payload = token.login(
-            client_id=app.config["AUTH0_CLIENT_ID"],
-            client_secret=app.config["AUTH0_CLIENT_SECRET"],
+            client_id=real_app.config["AUTH0_CLIENT_ID"],
+            client_secret=real_app.config["AUTH0_CLIENT_SECRET"],
             username=name + "@email.com",
             password=passw,
             realm="Username-Password-Authentication",
-            audience=app.config["AUTH0_API_AUDIENCE"],
-            scope="openid",
+            audience=real_app.config["AUTH0_API_AUDIENCE"],
+            scope="openid profile email",
         )
         token_info = decode_token(payload["access_token"])
-        user = User(
-            name=name,
-            external_id=token_info["sub"],
-        )
-        if User.query.filter_by(name=token_info["sub"]).first() is None:
-            db.session.add(user)
-            db.session.commit()
+        # do not add user1 into database
+        if name != "user1":
+            user = User(
+                name=name,
+                external_id=token_info["sub"],
+            )
+            if User.query.filter_by(external_id=token_info["sub"]).first() is None:
+                real_db.session.add(user)
+                real_db.session.commit()
 
         tokens[name] = {
             "token": payload["access_token"],
-            "id": User.query.filter_by(external_id=token_info["sub"]).first().id,
+            "external_id": token_info["sub"],
         }
 
     yield tokens

compose/neurosynth_compose/tests/schemathesis_api/test_annotation.py

@@ -7,6 +7,6 @@
 
 @schemathesis_test
 @schema.parametrize(endpoint="^/api/annotations")
-def test_annotation_endpoint(case, auth_client):
+def test_annotation_endpoint(case, auth_client, session):
     response = case.call_wsgi(headers=auth_client._get_headers())
     case.validate_response(response)

compose/neurosynth_compose/tests/schemathesis_api/test_meta_analysis.py

@@ -7,7 +7,7 @@
 
 @schemathesis_test
 @schema.parametrize(endpoint="^/api/meta-analyses")
-def test_meta_analysis_endpoint(case, auth_client):
+def test_meta_analysis_endpoint(case, auth_client, session):
     # The `session` argument must be supplied.
     response = case.call_wsgi(headers=auth_client._get_headers())
     case.validate_response(response)

compose/neurosynth_compose/tests/schemathesis_api/test_specification.py

@@ -7,7 +7,7 @@
 
 @schemathesis_test
 @schema.parametrize(endpoint="^/api/specifications")
-def test_specification_endpoint(case, auth_client):
+def test_specification_endpoint(case, auth_client, session):
     # The `session` argument must be supplied.
     response = case.call_wsgi(headers=auth_client._get_headers())
     case.validate_response(response)

compose/neurosynth_compose/tests/schemathesis_api/test_studyset.py

@@ -7,7 +7,7 @@
 
 @schemathesis_test
 @schema.parametrize(endpoint="^/api/studysets")
-def test_studyset_endpoint(case, auth_client):
+def test_studyset_endpoint(case, auth_client, session):
     # The `session` argument must be supplied.
     response = case.call_wsgi(headers=auth_client._get_headers())
     case.validate_response(response)

store/neurostore/tests/test_auth.py

@@ -2,7 +2,7 @@
 import pytest
 
 
-@auth_test
+#@auth_test
 def test_decode_token(add_users):
     from ..resources.auth import decode_token, AuthError
 
@@ -13,7 +13,7 @@ def test_decode_token(add_users):
         decode_token(user["token"])
 
 
-@auth_test
+#@auth_test
 def test_creating_new_user_on_db(add_users):
     from .request_utils import Client