Code to create the needed tables and other changes in the RNAcentral database for new imports
Based on the code originally developed by Blake Sweeney (https://github.com/blakesweeney/new-db-flow)
Usage: add-db.py [OPTIONS]
Quick utility to produce and run necessary SQL commands for adding a new
database in RNAcentral
Options:
--index INTEGER Enter the database index
--descr TEXT
--full_descr TEXT
--display_name TEXT
--db TEXT The database connection string. Taken from environment
if possible
--dry_run Render templates and print them, but dont change the
database
--print_rendered Print rendered templates
--help Show this message and exit.
NB: I have a file which I use to make the DB URL into an environment variable, so it doesn't get specified in the command
The tool can run in interactive mode, and will prompt you for the necessary information. When importing PLncDB I ran
python add-db.py --dry_run
And at the interactive prompt gave the following answers, and got the dictionary with the necessary information:
Enter the database short description: PLNCDB
Enter the database full description: PLncDB
Enter the database display name: PLncDB
{'index': 50, 'descr': 'PLNCDB', 'full_descr': 'PLncDB', 'display_name': 'PLncDB', 'timestamp': '2022-08-16T15:41:01.347640'}
Some bits of the info are autofilled, like the index which will just jump to the next available if you don't specify otherwise.
After that the rendered SQL is printed, since I did a dry run, and the program exits
Always do a dry run and inspect the SQL
After that, you can run again without --dry_run to make the changes in the database. I would reccomend still running with --print_rendered so you can inspect the SQL. The code will ask for confirmation before committing your changes to the database, and that should be it!