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
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
that sets up the application configuration.
We start off with
which could then
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.
Commits attempting to fix the issue
finally decouples `gn3.db_utils` completely from `flask.current_app` and makes the `sql_uri` argument mandatory.