README-run-etl.md guidance

[billudada78]

The guidance indicates the following recommended database and schema set up:
"export OMOP_SCHEMA='omop'
export OMOP='host=localhost dbname=postgres user=postgres options=--search_path='$OMOP_SCHEMA
export MIMIC='host=localhost dbname=postgres user=postgres options=--search_path=mimiciii'"

Unfortunately, the MIMIC-III postgres guidance indicates to use "mimic" as the dbname. I found out rather late that postgresql does not allow for cross-database references. I would recommend to align the naming convention with the MIMIC-III guidance (https://mimic.physionet.org/tutorials/install-mimic-locally-ubuntu/#1-install-postgres) or to highlight to the user that they should ensure the same dbname is used for both the OMOP schema and the MIMIC-III schema.

[parisni]

hi
thanks for the feedback !
all those things (database, schema names) are configurable. BTW if this would help to have default dbname=mimic for end user, please propose a pull request and make sure all dbname and documentation are set accordingly.

[billudada78]

I am unsure whether it is better to update dbname to mimic in the defaults or to simply warn the user in the readme file. Currently, the readme states:
"This README will assume the following:

MIMIC-III v1.4 is available in the mimic database under the mimiciii schema"

The OMOP schema, though is pointed towards the postgres database in the readme:

"export OMOP='host=localhost dbname=postgres user=postgres options=--search_path='$OMOP_SCHEMA"

I suspect several of the scripts assume dbname to be postgres. The MIMIC websites guide only needs to be modified to state "use dbname=postgres from step 7 onwards" and to replace "mimic" with "postgres" in the instruction below:

"CREATE DATABASE mimic OWNER mimicuser;"

I believe this is easiest to remedy in this GitHub readme file rather than adjusting all of the scripts to point towards a unique dbname.

[parisni]

please take a look at https://github.com/MIT-LCP/mimic-omop/blob/master/Makefile
this is an alternative script used to do the etl.
If the documentation can be clarified then we will do so