fix(migrations): move UPDATEs inside disable_sqlite_fkeys in migration 0097

[Lee-W]

Why

Migration 0097 failed on SQLite with FOREIGN KEY constraint failed when running DROP TABLE dag. PRAGMA foreign_keys=off (issued inside disable_sqlite_fkeys) is silently ignored when a transaction is already active — SQLite limitation. The two UPDATE statements before disable_sqlite_fkeys triggered SQLAlchemy's autobegin, starting a transaction before the PRAGMA ran.

How to reproduce

1. Bring up a 3.1.8 instance

breeze start-airflow  --backend sqlite --load-example-dags --use-airflow-version 3.1.8

2. Run a few Dags randomly. We need rows in the Dag run and task instance (or whatever rows that references Dag using FK)

3. Go to the Shell tab in the breeze terminal

4. Run

uv pip install apache-airflow==3.2.0
uv run airflow db migrate

What

Move the UPDATE statements inside disable_sqlite_fkeys so PRAGMA foreign_keys=off executes before autobegin opens a transaction.

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[Lee-W]

@vatsrahul1001 It looks like we used the wrong approach for testing, and I applied the wrong constraint during RC1 testing. I didn't have time to test it on RC2 until it was released yesterday 🤦‍♂️

After running the following command we discussed, I found out there's no dag_run in the DB.

breeze start-airflow  --backend sqlite --load-example-dags --use-airflow-version 3.1.8
breeze start-airflow  --backend sqlite --load-example-dags

So here's what I do for verifying this PR is correct (how to reproduce was detailed in the description)

Step 1

breeze start-airflow  --backend sqlite --load-example-dags --use-airflow-version 3.1.8 --terminal-multiplexer tmux

Step 2

Run a few Dags randomly. We need rows in the Dag run and task instance (or whatever rows that reference Dag using FK)

Step 3

Run Ctrl-C/Cmd-C on all airflow components in breeze but don't run stop_airflow and don't exit tmux

Step 4

git chechout to v3.2.0

Step 5

Go into the breeze terminal again

airflow db migrate

Step 6

Restart all the components in breeze (use the previous command with ↑)

[Dev-iL]

Can we modify the migration test (or add a new regression test) to capture this sort of issues?