# Coupling current_app and db_utils

## Tags

* assigned: fredm, aruni
* priority: high
* type: bug
* status: closed, completed, fixed
* keywords: bug, configurations

## Description

=> https://github.com/genenetwork/genenetwork3/commit/de20ab3834f2a84fd3f2ba9657650e28898e27f0 This commit
couples current_app into db_utils

db_utils is used in other scripts, such as `scripts/index-genenetwork` which are (arguably) not supposed to be aware of the application, which leads to
=>https://ci.genenetwork.org/jobs/genenetwork3-build-xapian-index/108 application context errors.

Unfortunately, the naive fix of simply reverting to using the configuration variable `SQL_URI` could lead to configuration differences between the application and the scripts that would rely on the gn3.settings.SQL_URI variable. This is due to
=> https://github.com/genenetwork/genenetwork3/blob/98e9726405df3cce81356534335259a446b0c458/gn3/app.py#L32-L43 this section
that sets up the application configuration.

We start off with
=> https://github.com/genenetwork/genenetwork3/blob/98e9726405df3cce81356534335259a446b0c458/gn3/app.py#L32 the default configuration values
which could then
=> https://github.com/genenetwork/genenetwork3/blob/98e9726405df3cce81356534335259a446b0c458/gn3/app.py#L35-L36 be overwritten
by any settings provided via the `GN3_CONF` variable.

The issue here is that the value in `gn3.settings` can be fetched from the shell environment variables, overwriting any default value in `gn3.settings` but that can then be overwritten by `GN3_CONF`. This implies that we need a more traceable configuration system.

The scripts that use the same configuration values as the application should probably be run as **flask CLI** commands, or have the configuration variable(s) provided to the script(s) directly via the CLI.

### Fix: Provide URI on the CLI

Commits attempting to fix the issue

=> https://github.com/genenetwork/genenetwork3/commit/d8c73f74a022540eec306399a4ad719089678579 in genenetwork3
=> https://github.com/genenetwork/genenetwork-machines/commit/1fc0198aaf595719e9e5f1a182731073458c449e in genenetwork-machines

=> https://github.com/genenetwork/genenetwork3/commit/dbf0f9f0d34c9969aa6ae76f556745a9eb122106 This commit
finally decouples `gn3.db_utils` completely from `flask.current_app` and makes the `sql_uri` argument mandatory.