shared: removed 'text()' from cursor.execute

[psaiz]

• closes https://github.com/zenodo/rdm-project/issues/197
  ❤️ Thank you for your contribution!

Description

Rolls back part of psaiz@5fc0fc9.
It looks like the connection.execute and cursor.execute expect different arguments. The former is a text, the latter a string.

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[psaiz]

This is the error that I got in invenio-stats before having this patch

dbapi_connection = <sqlite3.Connection object at 0x1178845e0>, connection_record = <sqlalchemy.pool.base._ConnectionRecord object at 0x11789bc90>

    def do_sqlite_connect(dbapi_connection, connection_record):
        """Ensure SQLite checks foreign key constraints.
    
        For further details see "Foreign key support" sections on
        https://docs.sqlalchemy.org/en/latest/dialects/sqlite.html#foreign-key-support
        """
        # Enable foreign key constraint checking
        cursor = dbapi_connection.cursor()
>       cursor.execute(text("PRAGMA foreign_keys=ON"))
E       TypeError: execute() argument 1 must be str, not TextClause

/usr/local/lib/python3.11/site-packages/invenio_db/shared.py:95: TypeError

I'm a bit confused why the error didn't appear on this module...

[utnapischtim]

@psaiz please check first your Sqlalchemy version. the TextClause will be used in the future, but old versions does not support it. Maybe you have the wrong SQLAlchemy version installed locally.

[psaiz]

Hi @utnapischtim,

Thanks for looking into this. I see this error in the pipelines of other modules that depend on invenio-db. It might be that invenio-db requires an old version of SQLAlchemy, and then this is still something that should be addressed in the invenio-db module

[utnapischtim]

@psaiz
I think there is another problem in the invenio-previewer package. Invenio-db works with the same installed SQLAlchemy version as invenio-previewer, for FlaskSQLAlchemy it is the same version too.

Further i don't think that invenio-db should handle that. Invenio-db is working as expected with the installed packages. Otherwise the error should also pop up in on the invenio-db tests. My problem with removing the compatibility with newer SQLAlchemy versions in invenio-db is that it would be a problem in the future so i think it is the better way to improve invenio-previewer first.

What i see too is that invenio-previewer is using sqlite, maybe that introduces a problem which is not tested in invenio-db.

Since the error is happening on doctest you could update those packages (e.g. Sphinx) first on invenio-previewer and see if that fixes the problem?

[ntarocco]

@utnapischtim it turned out that we were never testing sqlite here in invenio-db. In the PR below, we have added the sqlite tests in the CI matrix.
The change proposed by @psaiz is the one in the official documentation: https://docs.sqlalchemy.org/en/20/dialects/sqlite.html#foreign-key-support

Closing because superseded by: #171