[REF] update connexion to 3.0.0 (#606)

* update connexion to 3.0.0

* fix requirements

* add flask extension to connexion

* use uvicorn workers

* switch openapi to main

store/docker-compose.dev.yml

@@ -7,7 +7,7 @@ services:
   neurostore:
     expose:
       - "8000"
-    command: /usr/local/bin/gunicorn -w 1 -b :8000 neurostore.core:app --log-level debug --timeout 300 --reload
+    command: /usr/local/bin/gunicorn -w 1 -b :8000 neurostore.core:connexion_app --worker-class uvicorn.workers.UvicornWorker --log-level debug --timeout 300 --reload
     restart: "no"
     stdin_open: true # docker run -i
     tty: true        # docker run -t

store/docker-compose.yml

@@ -14,7 +14,7 @@ services:
       - ./:/neurostore
       - ${FILE_DIR}:/file-data
       - ${ACE_DIR}:/ace
-    command: /usr/local/bin/gunicorn -w 8 -b :8000 neurostore.core:app --log-level debug --timeout 120
+    command: /usr/local/bin/gunicorn -w 8 -b :8000 neurostore.core:connexion_app --worker-class uvicorn.workers.UvicornWorker --log-level debug --timeout 120
     env_file:
       - .env
     container_name: neurostore

store/neurostore/core.py

@@ -4,19 +4,18 @@
 
 from authlib.integrations.flask_client import OAuth
 import connexion
-from connexion.json_schema import default_handlers as json_schema_handlers
-from connexion.resolver import MethodViewResolver
+# 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 prance
 import sqltap.wsgi
 
 from .or_json import ORJSONDecoder, ORJSONEncoder
 from .database import init_db
 
 
 connexion_app = connexion.FlaskApp(
-    __name__, specification_dir="openapi/", debug=os.getenv("DEBUG", False) == "True"
+    __name__, specification_dir="openapi/"
 )
 
 app = connexion_app.app
@@ -34,29 +33,14 @@
 
 options = {"swagger_ui": True}
 
-# https://github.com/spec-first/connexion/issues/254#issuecomment-1133843523
-json_schema_handlers[""] = lambda uri: (
-    json_schema_handlers["file"](str(connexion_app.specification_dir / uri))
-)
-
-
-# https://github.com/spec-first/connexion/issues/254#issuecomment-504699959
-def get_bundled_specs(main_file):
-    parser = prance.ResolvingParser(
-        str(main_file.absolute()), lazy=True, backend="openapi-spec-validator"
-    )
-    parser.parse()
-    return parser.specification
-
-
 openapi_file = Path(os.path.dirname(__file__) + "/openapi/neurostore-openapi.yml")
 
 connexion_app.add_api(
-    get_bundled_specs(openapi_file),
+    openapi_file,
     base_path="/api",
     options=options,
     arguments={"title": "NeuroStore API"},
-    resolver=MethodViewResolver("neurostore.resources"),
+    resolver=MethodResolver("neurostore.resources"),
     strict_validation=os.getenv("DEBUG", False) == "True",
     validate_responses=os.getenv("DEBUG", False) == "True",
 )

store/neurostore/models/auth.py

@@ -1,4 +1,4 @@
-from flask_security import UserMixin, RoleMixin, SQLAlchemyUserDatastore
+# from flask_security import UserMixin, RoleMixin, SQLAlchemyUserDatastore
 
 
 from ..database import db
@@ -13,14 +13,14 @@
 )
 
 
-class Role(BaseMixin, db.Model, RoleMixin):
+class Role(BaseMixin, db.Model):
     __tablename__ = "roles"
 
     name = db.Column(db.Text, unique=True)
     description = db.Column(db.Text)
 
 
-class User(BaseMixin, db.Model, UserMixin):
+class User(BaseMixin, db.Model):
     __tablename__ = "users"
     active = db.Column(db.Boolean())
     name = db.Column(db.Text, index=True)
@@ -30,4 +30,4 @@ class User(BaseMixin, db.Model, UserMixin):
     )
 
 
-user_datastore = SQLAlchemyUserDatastore(db, User, Role)
+# user_datastore = SQLAlchemyUserDatastore(db, User, Role)

store/neurostore/requirements.txt

@@ -1,7 +1,7 @@
 aniso8601~=8.1
 auth0-python~=3.16
 authlib~=0.15
-connexion[swagger-ui]~=2.7
+connexion[swagger-ui,uvicorn,flask]==3.0.0a7
 email-validator~=1.1
 flake8~=3.8
 flask~=2.0
@@ -10,7 +10,6 @@ flask-cors~=3.0
 flask-dance~=3.2
 flask-shell-ipython~=0.4
 flask-migrate~=2.5
-flask-security~=3.0
 flask-sqlalchemy==3.0.2 # fix multiple instance error: https://flask-sqlalchemy.palletsprojects.com/en/3.0.x/changes/#version-3-0-3
 gunicorn~=20.0
 ipython~=7.19
@@ -31,4 +30,3 @@ openapi-spec-validator~=0.3
 scipy~=1.9
 pytest~=7.1
 orjson~=3.8
-prance

store/neurostore/resources/base.py

@@ -3,7 +3,7 @@
 """
 import re
 
-import connexion
+from connexion.context import context
 from flask import abort, request, current_app  # jsonify
 from flask.views import MethodView
 
@@ -45,7 +45,7 @@ def create_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"], name=profile_info.get("name", "Unknown")
+        external_id=context["user"], name=profile_info.get("name", "Unknown")
     )
 
     return current_user
@@ -302,11 +302,11 @@ def get(self, id):
         record = q.filter_by(id=id).first_or_404()
         if self._model is Studyset and args["nested"]:
             snapshot = StudysetSnapshot()
-            return snapshot.dump(record)
+            return snapshot.dump(record), 200, {"Content-Type": "application/json"}
         else:
             return self._schema(
                 context=dict(args),
-            ).dump(record)
+            ).dump(record), 200, {"Content-Type": "application/json"}
 
     def put(self, id):
         request_data = self.insert_data(id, request.json)
@@ -343,12 +343,12 @@ def post_delete(self, record):
 
 
 LIST_USER_ARGS = {
-    "search": fields.String(missing=None),
-    "sort": fields.String(missing="created_at"),
-    "page": fields.Int(missing=1),
-    "desc": fields.Boolean(missing=True),
-    "page_size": fields.Int(missing=20, validate=lambda val: val < 30000),
-    "user_id": fields.String(missing=None),
+    "search": fields.String(load_default=None),
+    "sort": fields.String(load_default="created_at"),
+    "page": fields.Int(load_default=1),
+    "desc": fields.Boolean(load_default=True),
+    "page_size": fields.Int(load_default=20, validate=lambda val: val < 30000),
+    "user_id": fields.String(load_default=None),
 }
 
 

store/neurostore/resources/data.py

@@ -44,13 +44,13 @@
 ]
 
 LIST_CLONE_ARGS = {
-    "source_id": fields.String(missing=None),
-    "source": fields.String(missing=None),
-    "unique": BooleanOrString(missing=False),
+    "source_id": fields.String(load_default=None),
+    "source": fields.String(load_default=None),
+    "unique": BooleanOrString(load_default=False),
 }
 
 LIST_NESTED_ARGS = {
-    "nested": fields.Boolean(load_default=False, missing=False),
+    "nested": fields.Boolean(load_default=False),
 }
 
 
@@ -91,7 +91,7 @@ def serialize_records(self, records, args):
 
 @view_maker
 class AnnotationsView(ObjectView, ListView):
-    _view_fields = {**LIST_CLONE_ARGS, "studyset_id": fields.String(missing=None)}
+    _view_fields = {**LIST_CLONE_ARGS, "studyset_id": fields.String(load_default=None)}
     _nested = {"annotation_analyses": "AnnotationAnalysesResource"}
     _linked = {
         "studyset": "StudysetsView",
@@ -154,10 +154,10 @@ class BaseStudiesView(ObjectView, ListView):
     _nested = {"versions": "StudiesView"}
 
     _view_fields = {
-        "level": fields.String(default="group", missing="group"),
-        "flat": fields.Boolean(load_default=False, missing=False),
-        "info": fields.Boolean(load_default=False, missing=False),
-        "data_type": fields.String(missing=None),
+        "level": fields.String(dump_default="group", load_default="group"),
+        "flat": fields.Boolean(load_default=False),
+        "info": fields.Boolean(load_default=False),
+        "data_type": fields.String(load_default=None),
     }
 
     _multi_search = ("name", "description")
@@ -272,11 +272,11 @@ def post(self):
 class StudiesView(ObjectView, ListView):
     _view_fields = {
         **{
-            "data_type": fields.String(missing=None),
-            "studyset_owner": fields.String(missing=None),
-            "level": fields.String(default="group", missing="group"),
-            "flat": fields.Boolean(load_default=False, missing=False),
-            "info": fields.Boolean(load_default=False, missing=False),
+            "data_type": fields.String(load_default=None),
+            "studyset_owner": fields.String(load_default=None),
+            "level": fields.String(dump_default="group", load_default="group"),
+            "flat": fields.Boolean(load_default=False),
+            "info": fields.Boolean(load_default=False),
         },
         **LIST_NESTED_ARGS,
         **LIST_CLONE_ARGS,

store/neurostore/resources/utils.py

@@ -3,7 +3,7 @@
 """
 import re
 
-import connexion
+from connexion.context import context
 
 from .. import models
 from .. import schemas
@@ -16,10 +16,10 @@ def camel_case_split(str):
 
 
 def get_current_user():
-    user = connexion.context.get("user")
+    user = context.get("user")
     if user:
         return models.User.query.filter_by(
-            external_id=connexion.context["user"]
+            external_id=user
         ).first()
     return None
 

store/neurostore/schemas/auth.py

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