setup.py setup-db triggers file not found on first run of pgadmin4

[J0x90]

Please note that security bugs or issues should be reported to security@pgadmin.org.

Describe the bug

When attempting to run pgadmin4 with python (https://www.pgadmin.org/download/pgadmin-4-python/), I have observed that when entering the last command in the instructions, I get an error.
Command:
pgadmin4
Error:
FileNotFoundError: [Errno 2] No such file or directory: '/var/lib/pgadmin/pgadmin4.db' -> '/var/lib/pgadmin/pgadmin4.db.20240309203301'

Looking through the source code, it appears that when the sqlite db does not exist, the program flow eventually ends up executing
flask_migrate.upgrade(migration_folder) within db_upgrade.py

For example, below we see upgrade_db() is entered because this is not cli_mode, and the SQLITE_PATH doesn't exist.

    def run_migration_for_sqlite():
        with app.app_context():
            # Run migration for the first time i.e. create database
            # If version not available, user must have aborted. Tables are not
            # created and so its an empty db
            if not os.path.exists(SQLITE_PATH) or get_version() == -1:
                # If running in cli mode then don't try to upgrade, just raise
                # the exception
                if not cli_mode:
                    upgrade_db()
                else:
                    if not os.path.exists(SQLITE_PATH):
                        raise FileNotFoundError(
                            'SQLite database file "' + SQLITE_PATH +
                            '" does not exists.')
                    raise RuntimeError(
                        'The configuration database file is not valid.')

Next we see db_upgrade(app) is entered.

    def upgrade_db():
        """
        Execute the migrations.
        """
        try:
            db_upgrade(app)
            os.environ['CORRUPTED_DB_BACKUP_FILE'] = ''
        except Exception:
            app.logger.error('Database migration failed')
            app.logger.error(traceback.format_exc())
            backup_db_file()

Finally, we see flask_migrate

def db_upgrade(app):
    from pgadmin.utils import u_encode, fs_encoding
    with app.app_context():
        migration_folder = os.path.join(
            os.path.dirname(os.path.realpath(u_encode(__file__, fs_encoding))),
            os.pardir, os.pardir,
            'migrations'
        )
        flask_migrate.upgrade(migration_folder)

Are yall sure that flask_migrate.upgrade is the right command to be ran for a first run of pgadmin4. Aka, will this create and initialize the db, because it appears that it is throwing an error when the db doesn't exist initially.

To Reproduce

Steps to reproduce the behavior:

1. Open terminal on Debian12
2. Enter the following commands

sudo adduser pgadmin4
sudo usermod -aG sudo pgadmin4
su - pgadmin4
sudo apt install python3.11-venv -y
sudo mkdir /var/lib/pgadmin
sudo mkdir /var/log/pgadmin
sudo chown $USER /var/lib/pgadmin
sudo chown $USER /var/log/pgadmin
python3 -m venv pgadmin4
source pgadmin4/bin/activate
pip install pgadmin4
pgadmin4

4. See the error

Expected behavior

Successful installation.

Error message

If possible, include the full, unedited text of any error messages displayed.

FileNotFoundError: [Errno 2] No such file or directory: '/var/lib/pgadmin/pgadmin4.db' -> '/var/lib/pgadmin/pgadmin4.db.20240309203909'

Screenshots

If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Debian 12
• Version: Linux debian-s-2vcpu-4gb-120gb-intel-sfo3-01 6.1.0-9-amd64 ISSUE2277-Internal server error displayed if table name contains long character #1 SMP PREEMPT_DYNAMIC Debian 6.1.27-1 (2023-05-08) x86_64 GNU/Linux
• Mode: Server
• Browser (if running in server mode): NA
• Package type: Python

Additional context

Add any other context about the problem here.

[khushboovashi]

@J0x90,
There should be some permission issue, so the db file wasn't created for you.
Please provide the entire log file here.

[ShaheedHaque]

As per the thread at https://www.postgresql.org/message-id/CAHAc2je_TBjuZ86nBkAjjAmjgFmAhb03kLNaROSM7nxRoor1Zw%40mail.gmail.com, this problem occurs newly in flask-migrate 4.0.6. It looks as though the changes in miguelgrinberg/Flask-Migrate@6f3f889 introduce some new behaviour which I guess pgadmin4 does not yet support.

[adityatoshniwal]

The x-arg was optional previously. Looks like they made it mandatory. A breaking change was released with minor version number. Unfortunately, pgAdmin was released on 7th and Flask-Migrate on 9th.

[adityatoshniwal]

@J0x90 @ShaheedHaque Flask-Migrate has fixed the issue and released a new version - 4.0.7. Please upgrade your venv with latest Flask-Migrate

[ShaheedHaque]

Flask-migrate 4.0.7 does indeed fix the issue for me.