Why is SQLAlchemy only loading one instance from my many-to-many relationship?

Question

I'm trying to add attributes to a many-to-many relationship in my model, and now when I load an object I'm only getting one related object from my query.

Specifically I'm trying to get all the Apps associated with a given Backup, and also the BackupApp.status column.

Sorry for the info-dump:

The code is here:

I know I have hundreds of relationships to load:

$ sqlite3 dev.db "select count(*) from backups_apps where backup_id = 3 and app_id is not null;"
415

but I'm only getting one:

{
  "children": [
    {
      "children": [
        {
          "bundle_id": "com.iojoe.10", 
          "compressed": 13151750, 
          "name": "10", 
          "size": 14458882
        }
      ], 
      "name": "Games"
    }
  ], 
  "name": "root"
}

The models:

# -*- coding: utf-8 -*-
from app_sizer.database import db, CRUDMixin, TimestampMixin, jsonify_plist

from sqlalchemy.ext.associationproxy import association_proxy

class App(db.Model, CRUDMixin, TimestampMixin):
    __tablename__ = 'apps'
    bundle_id = db.Column(db.String, unique=True, index=True)
    app_id = db.Column(db.Integer, unique=True, index=True)
    path = db.Column(db.String, unique=True, index=True)
    name = db.Column(db.String, index=True)
    main_genre = db.Column(db.String, index=True)
    compressed_size = db.Column(db.Integer)
    full_size = db.Column(db.Integer)
    plist = db.Column(db.PickleType)
    plist_json = db.Column(db.Text, default=jsonify_plist, onupdate=jsonify_plist)
    subgenre_1 = db.Column(db.String, index=True)
    subgenre_2 = db.Column(db.String, index=True)

    @classmethod
    def get_by_bundle_id(cls, bundle_id):
        return db.session.query(cls).filter(App.bundle_id == bundle_id).first()


    @classmethod
    def get_by_path(cls, path):
        return db.session.query(cls).filter(App.path == path).first()

    @classmethod
    def get_all(cls):
        return db.session.query(cls).all()

"""
class AppTag(CRUDMixin):
    app_id = db.Column(db.Integer, foreign_key='app.id')
    user_id = db.Column(db.Integer, foreign_key='user.id')
    tag = db.Column(db.String)
"""

# db.Index('idx_tag_user', 'app_tag.user_id', 'app_tag.tag')

class Backup(db.Model, CRUDMixin, TimestampMixin):
    __tablename__ = 'backups'
    path = db.Column(db.String, unique=True)
    name = db.Column(db.String)
    notes = db.Column(db.Text)
    # Springboard plist
    plist = db.Column(db.PickleType)
    plist_json = db.Column(db.Text, default=jsonify_plist, onupdate=jsonify_plist)
    @classmethod
    def get_by_path(cls, path):
        return db.session.query(Backup).filter(Backup.path == path).first()

    @classmethod
    def get_all(cls):
        return db.session.query(Backup).all()

# Why does this work but a declarative class doesn't?  No idea.
# http://xsnippet.org/359350/
# http://stackoverflow.com/q/5756559/25625
class BackupApp(db.Model, CRUDMixin):
    __tablename__ = 'backups_apps'
    backup_id = db.Column(db.Integer, db.ForeignKey('backups.id'), nullable=False, default=1)
    app_id = db.Column(db.Integer, db.ForeignKey('apps.id'), nullable=False, default=1)
    status = db.Column(db.String)

    app = db.relationship(App, backref="installed_apps")
    backup = db.relationship(Backup, backref="installed_apps")

    def __init__(self, app=None, backup=None, status=None):
        self.app = app
        self.backup = backup
        self.status = status

Backup.apps = association_proxy("installed_apps", "app")
App.backups = association_proxy("installed_apps", "backup")

The action:

@blueprint.route("/backup/<int:backup_id>/apps.json")
def apps_json_for_backup(backup_id):
    print "in apps_json_for_backup({})".format(backup_id)
    backup = Backup.get_by_id(backup_id)
    root = to_treemap(backup.apps)
    return jsonify(root)


def to_treemap(apps):
    root = {"name": "root", "children": list()}
    genres = dict()
    for app in apps:
        if app.main_genre not in genres:
            genres[app.main_genre] = list()
        leaf = dict(name=app.name, size=app.full_size, compressed=app.compressed_size, bundle_id=app.bundle_id)
        genres[app.main_genre].append(leaf)
    for genre, leaves in genres.items():
        root['children'].append(dict(name=genre, children=leaves))
    return root

Answer 1

Ok, so here's what happened:

When I first made the backups_apps table, I wasn't using CRUDMixin so it didn't have an id column. When I migrated the ID column in, all the values initialized at 0. SQLAlchemy quietly ignored all those multiple rows with the same id.