pedsnetdcc is a CLI tool for PEDSnet data coordinating center ETL tasks.
The prepdb subcommand creates a new database for a specific data model version, e.g. pedsnet_dcc_v23 for 2.3.0, and schemas within the database. It presupposes that the database has been initialized and the correct system users have been created using https://github.research.chop.edu/dbhi/pedsnet/tree/master/db/.
docker build -t pedsnetdcc .
docker run -it --rm --link pedsnet_postgres_1:db pedsnetdcc prepdb -v 2.3.0 -p postgresql://$USER@db/postgres
Breakdown:
The first line builds the pedsnetdcc image.
The second line creates and runs a container based on that image, and throws it away afterwards (--rm). The --link phrase connects the alias db (used later in the command) to the PEDSnet database container (pedsnet_postgres_1). pedsnetdcc is the name of the image. Everything from prepdb onward is the arguments passed to the pedsnetdcc command inside the container. This command requires that the $USER be a superuser in the database.
...
- If you are using
pedsnetdccinstalled via Python instead of using Docker, you might be interested in Click auto-completion: http://click.pocoo.org/5/bashcomplete/.