fix cors issue (#611)

* fix cors issue

* style change with black

* do not test options in compose

store/manage.py

@@ -10,7 +10,7 @@
 from neurostore import ingest
 from neurostore import models
 
-if not getattr(app, 'config', None):
+if not getattr(app, "config", None):
     app = app._app
 
 app.config.from_object(os.environ["APP_SETTINGS"])

store/neurostore/core.py

@@ -2,21 +2,21 @@
 from pathlib import Path
 from werkzeug.middleware.profiler import ProfilerMiddleware
 
+from connexion.middleware import MiddlewarePosition
+from starlette.middleware.cors import CORSMiddleware
 from authlib.integrations.flask_client import OAuth
 import connexion
+
 # from connexion.json_schema import default_handlers as json_schema_handlers
 from connexion.resolver import MethodResolver
 from flask_caching import Cache
-from flask_cors import CORS
 import sqltap.wsgi
 
 from .or_json import ORJSONDecoder, ORJSONEncoder
 from .database import init_db
 
 
-connexion_app = connexion.FlaskApp(
-    __name__, specification_dir="openapi/"
-)
+connexion_app = connexion.FlaskApp(__name__, specification_dir="openapi/")
 
 app = connexion_app.app
 
@@ -35,6 +35,16 @@
 
 openapi_file = Path(os.path.dirname(__file__) + "/openapi/neurostore-openapi.yml")
 
+# Enable CORS
+connexion_app.add_middleware(
+    CORSMiddleware,
+    position=MiddlewarePosition.BEFORE_ROUTING,
+    allow_origins=["*"],
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
 connexion_app.add_api(
     openapi_file,
     base_path="/api",
@@ -45,8 +55,6 @@
     validate_responses=os.getenv("DEBUG", False) == "True",
 )
 
-# Enable CORS
-cors = CORS(app)
 
 auth0 = oauth.register(
     "auth0",

store/neurostore/requirements.txt

@@ -1,12 +1,11 @@
 aniso8601~=8.1
 auth0-python~=3.16
 authlib~=0.15
-connexion[swagger-ui,uvicorn,flask]==3.0.0a7
+connexion[swagger-ui,uvicorn,flask]==3.0.0
 email-validator~=1.1
 flake8~=3.8
 flask~=2.0
 flask-caching~=2.0
-flask-cors~=3.0
 flask-dance~=3.2
 flask-shell-ipython~=0.4
 flask-migrate~=2.5

store/neurostore/resources/base.py

@@ -304,9 +304,13 @@ def get(self, id):
             snapshot = StudysetSnapshot()
             return snapshot.dump(record), 200, {"Content-Type": "application/json"}
         else:
-            return self._schema(
-                context=dict(args),
-            ).dump(record), 200, {"Content-Type": "application/json"}
+            return (
+                self._schema(
+                    context=dict(args),
+                ).dump(record),
+                200,
+                {"Content-Type": "application/json"},
+            )
 
     def put(self, id):
         request_data = self.insert_data(id, request.json)

store/neurostore/resources/data.py

@@ -218,9 +218,7 @@ def post(self):
         to_commit = []
         for study_data in data:
             filter_params = {
-                k: study_data.get(k)
-                for k in search_keys
-                if study_data.get(k)
+                k: study_data.get(k) for k in search_keys if study_data.get(k)
             }
             if "name" in filter_params and (set(filter_params) - {"name"}) != set():
                 del filter_params["name"]
@@ -408,7 +406,7 @@ def pre_nested_record_update(record):
             has_pmid = True
         if record.name and not record.doi and not record.pmid:
             name_search = func.regexp_replace(
-                record.name, r'[' + string.punctuation + ']', '', 'g'
+                record.name, r"[" + string.punctuation + "]", "", "g"
             )
             query = query.filter(BaseStudy.name.ilike(f"%{name_search}%"))
             has_name = True

store/neurostore/resources/utils.py

@@ -18,9 +18,7 @@ def camel_case_split(str):
 def get_current_user():
     user = context.get("user")
     if user:
-        return models.User.query.filter_by(
-            external_id=user
-        ).first()
+        return models.User.query.filter_by(external_id=user).first()
     return None
 
 

store/neurostore/schemas/auth.py

@@ -8,7 +8,9 @@
 
 class UserSchema(BaseSchema):
     name = fields.Str(metadata={"description": "User full name"})
-    external_id = fields.Str(metadata={"description": "External authentication service user ID"})
+    external_id = fields.Str(
+        metadata={"description": "External authentication service user ID"}
+    )
 
     class Meta:
         unknown = EXCLUDE

store/neurostore/schemas/data.py

@@ -330,7 +330,9 @@ class StudySchema(BaseDataSchema):
         dump_only=True, metadata={"db_only": True}, allow_none=True
     )
     studysets = fields.Pluck("StudysetSchema", "_id", many=True, dump_only=True)
-    base_study = fields.Pluck("BaseStudySchema", "_id", dump_only=True, metadata={"db_only": True})
+    base_study = fields.Pluck(
+        "BaseStudySchema", "_id", dump_only=True, metadata={"db_only": True}
+    )
     has_coordinates = fields.Bool(dump_only=True)
     has_images = fields.Bool(dump_only=True)
     # studysets = fields.Nested(
@@ -569,10 +571,7 @@ def dump(self, p):
             "space": p.space,
             "image": p.image,
             "label_id": p.label_id,
-            "values": [
-                v_schema.dump(v)
-                for v in p.values
-            ],
+            "values": [v_schema.dump(v) for v in p.values],
         }
 
 
@@ -596,19 +595,10 @@ def dump(self, a):
             "user": a.user_id,
             "name": a.name,
             "description": a.description,
-            "conditions": [
-                ac_schema.dump(ac)
-                for ac in a.analysis_conditions
-            ],
+            "conditions": [ac_schema.dump(ac) for ac in a.analysis_conditions],
             "weights": list(a.weights),
-            "points": [
-                p_schema.dump(p)
-                for p in a.points
-            ],
-            "images": [
-                i_schema.dump(i)
-                for i in a.images
-            ],
+            "points": [p_schema.dump(p) for p in a.points],
+            "images": [i_schema.dump(i) for i in a.images],
         }
 
 
@@ -648,8 +638,5 @@ def dump(self, studyset):
             "pmid": studyset.pmid,
             "created_at": self._serialize_dt(studyset.created_at),
             "updated_at": self._serialize_dt(studyset.updated_at),
-            "studies": [
-                s_schema.dump(s)
-                for s in studyset.studies
-            ],
+            "studies": [s_schema.dump(s) for s in studyset.studies],
         }

store/neurostore/tests/api/test_annotations.py

@@ -303,7 +303,9 @@ def test_correct_note_overwrite(auth_client, ingest_neurosynth, session):
     new_value = "something new"
     data[0]["note"]["doo"] = new_value
     doo_payload = {"notes": data}
-    put_resp = auth_client.put(f"/api/annotations/{annot.json()['id']}", data=doo_payload)
+    put_resp = auth_client.put(
+        f"/api/annotations/{annot.json()['id']}", data=doo_payload
+    )
 
     get_resp = auth_client.get(f"/api/annotations/{annot.json()['id']}")
 

store/neurostore/tests/api/test_crud.py

@@ -87,6 +87,14 @@ def test_read(auth_client, user_data, endpoint, model, schema, session):
 
     expected_results = model.query.filter(query).all()
 
+    pre = auth_client.client.options(
+        f"/api/{endpoint}",
+        headers={
+            "Origin": "http://example.com",
+            "Access-Control-Request-Method": "GET",
+        },
+    )
+    assert pre.status_code == 200
     resp = auth_client.get(f"/api/{endpoint}/")
 
     assert resp.status_code == 200

store/neurostore/tests/api/test_studies.py

@@ -72,7 +72,9 @@ def test_put_studies(auth_client, ingest_neurosynth, data, session):
         if payload["analyses"][0].get("conditions"):
             conditions = []
             for cond in payload["analyses"][0]["conditions"]:
-                conditions.append(auth_client.post("/api/conditions/", data=cond).json())
+                conditions.append(
+                    auth_client.post("/api/conditions/", data=cond).json()
+                )
             payload["analyses"][0]["conditions"] = [
                 {"id": cond["id"]} for cond in conditions
             ]

store/neurostore/tests/request_utils.py

@@ -54,7 +54,7 @@ def _make_request(
 
             if data is not None and json_dump is True:
                 data = json.dumps(data)
-                kwargs['data'] = data
+                kwargs["data"] = data
 
             return request_function(
                 route,

store/scripts/ace_ingestion.py

@@ -4,6 +4,8 @@
 metadata_file = "/ace/no-pubmed-central-july-11-2023/metadata.csv"
 text_file = "/ace/no-pubmed-central-july-11-2023/text.csv"
 
-coordinates_df, metadata_df, text_df = load_ace_files(coordinates_file, metadata_file, text_file)
+coordinates_df, metadata_df, text_df = load_ace_files(
+    coordinates_file, metadata_file, text_file
+)
 
 ace_ingestion_logic(coordinates_df, metadata_df, text_df)

store/scripts/create_neurostore_studyset.py

@@ -2,9 +2,11 @@
 from sqlalchemy.orm import joinedload
 
 
-base_studies = BaseStudy.query.options(
-    joinedload("versions")
-).filter_by(has_coordinates=True).all()
+base_studies = (
+    BaseStudy.query.options(joinedload("versions"))
+    .filter_by(has_coordinates=True)
+    .all()
+)
 
 neurostore_studyset = []
 for bs in base_studies:
@@ -20,12 +22,14 @@
             if selected_study.user is None:
                 selected_study = v
             else:
-                if (
-                    selected_study.updated_at or selected_study.created_at
-                ) <= (v.updated_at or v.created_at):
+                if (selected_study.updated_at or selected_study.created_at) <= (
+                    v.updated_at or v.created_at
+                ):
                     selected_study = v
     neurostore_studyset.append(selected_study)
 
-ss = Studyset(name="Neurostore Studyset", description="aggregation of studies on the neurostore database. Ran periodically, may not represent the latest state of the database.", studies=neurostore_studyset)
-
-
+ss = Studyset(
+    name="Neurostore Studyset",
+    description="aggregation of studies on the neurostore database. Ran periodically, may not represent the latest state of the database.",
+    studies=neurostore_studyset,
+)

store/scripts/load_testing/locustfile.py

@@ -6,7 +6,7 @@
 with open("concepts.json", "r") as c_j:
     concepts = json.load(c_j)
 
-CONCEPT_NAMES = [c['name'] for c in concepts]
+CONCEPT_NAMES = [c["name"] for c in concepts]
 
 
 class QuickstartUser(HttpUser):
@@ -24,12 +24,12 @@ def view_studyset_and_studies(self):
         result = self.client.get("/studysets/?page_size=100")
         if result.status_code != 200:
             return
-        studyset_ids = [ss['id'] for ss in result.json()['results']]
+        studyset_ids = [ss["id"] for ss in result.json()["results"]]
         studyset_id = random.choice(studyset_ids)
         studyset = self.client.get(f"/studysets/{studyset_id}")
         if studyset.status_code != 200:
             return
-        study_ids = [s for s in studyset.json()['studies']]
+        study_ids = [s for s in studyset.json()["studies"]]
         for study_id in study_ids:
             self.client.get(f"/studies/{study_id}?nested=true")