[REF] upgrade to using sqlalchemy 2.0 (neurosynth_compose) (#1126)

* upgrade to using sqlalchemy 2.0

* ignore selectin spelling

* remove leading db. where appropriate

* remove fallbacks for what should be failures

Author: jdkent

.codespellrc

@@ -2,4 +2,4 @@
 skip = .git,*.pdf,*.svg,*.ts,*.tsx,package-lock.json,data-*vocabulary.txt,sample_*.csv,CHANGELOG.rst,ingest_neurovault.yml,./compose/neurosynth-frontend/cypress/fixtures
 # regexes
 ignore-regex = r"\(\?i\).*\\\\1
-ignore-words-list = te,fwe,connexion,zoon,covert,rime
+ignore-words-list = te,fwe,connexion,zoon,covert,rime,selectin

compose/backend/neurosynth_compose/__init__.py

@@ -6,8 +6,6 @@
 import connexion
 from connexion.resolver import MethodViewResolver
 
-from .database import db
-
 
 def create_app():
     connexion_app = connexion.FlaskApp(
@@ -44,8 +42,10 @@ def create_app():
         },
     )
 
-    # initialize db
-    db.init_app(app)
+    # initialize db (ensure models register against the app-bound registry)
+    from .database import init_db
+
+    init_db(app)
 
     # setup authentication
     # jwt = JWTManager(app)

compose/backend/neurosynth_compose/database.py

@@ -1,17 +1,42 @@
-from sqlalchemy.ext.declarative import declarative_base
+import logging
+from sqlalchemy.orm import DeclarativeBase
 from flask_sqlalchemy import SQLAlchemy
 
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class Base(DeclarativeBase):
+    # Allow existing 1.4-style declarative mappings without
+    # requiring explicit typing with Mapped[] annotations.
+    __allow_unmapped__ = True
+
+
+# Defer assigning the model class so models are registered after app init
 db = SQLAlchemy()
 
-Base = declarative_base()
+
+def commit_session(session=None):
+    """Commit the provided session or the default db.session, rolling back on error."""
+    sess = session or db.session
+    try:
+        sess.commit()
+    except Exception:
+        sess.rollback()
+        logger.exception("Session commit failed, rolling back.")
 
 
 def init_db(app):
-    # Make Flask-Security, Flask-SQLAlchemy, and Graphene all play nice.
-    # See https://github.com/mattupstate/flask-security/issues/766#issuecomment-393567456
+    """Initialize Flask-SQLAlchemy with the Flask app and register models.
+
+    This sets the declarative base class on the SQLAlchemy object and imports
+    the models so they register against the same registry only once.
+    """
+    # Attach the DeclarativeBase as the model base
+    db.Model = Base
     with app.app_context():
-        db.app = app
         db.init_app(app)
-        Base.metadata.bind = db.engine
-        Base.query = db.session.query_property()
+        # Import models after db is initialized so mappings bind to this registry
+        # Importing here avoids duplicate mapper registration during test collection.
+        from . import models  # noqa: F401
     return db

compose/backend/neurosynth_compose/ingest/neurostore.py

@@ -12,7 +12,8 @@
     StudysetReference,
     AnnotationReference,
 )
-from ..database import db
+from ..database import db, commit_session
+from sqlalchemy import select
 
 
 def ingest_neurostore(
@@ -28,9 +29,9 @@ def ingest_neurostore(
     to_commit = []
     with db.session.no_autoflush:
         for studyset in studysets:
-            ss_ref = StudysetReference.query.filter_by(
-                id=studyset["id"]
-            ).one_or_none() or StudysetReference(id=studyset["id"])
+            ss_ref = db.session.execute(
+                select(StudysetReference).where(StudysetReference.id == studyset["id"])
+            ).scalar_one_or_none() or StudysetReference(id=studyset["id"])
             ss = Studyset(studyset_reference=ss_ref)
             to_commit.append(ss)
             # only ingest annotations for smaller studysets now.
@@ -39,9 +40,11 @@ def ingest_neurostore(
                     f"{url}/api/annotations/?studyset_id={studyset['id']}"
                 ).json()["results"]
                 for annot in annotations:
-                    annot_ref = AnnotationReference.query.filter_by(
-                        id=annot["id"]
-                    ).one_or_none() or AnnotationReference(id=annot["id"])
+                    annot_ref = db.session.execute(
+                        select(AnnotationReference).where(
+                            AnnotationReference.id == annot["id"]
+                        )
+                    ).scalar_one_or_none() or AnnotationReference(id=annot["id"])
                     to_commit.append(
                         Annotation(
                             studyset=ss,
@@ -50,12 +53,12 @@ def ingest_neurostore(
                     )
 
         db.session.add_all(to_commit)
-        db.session.commit()
+        commit_session()
 
 
 def create_meta_analyses(url="https://neurostore.org", n_studysets=None):
     ingest_neurostore(url, n_studysets)
-    stdsts = Studyset.query.all()
+    stdsts = db.session.execute(select(Studyset)).scalars().all()
     to_commit = []
     with db.session.no_autoflush:
         for ss in stdsts:
@@ -80,4 +83,4 @@ def create_meta_analyses(url="https://neurostore.org", n_studysets=None):
             )
 
         db.session.add_all(to_commit)
-        db.session.commit()
+        commit_session()