Allow psql port etc and update for current Pandas

[juliangilbey]

Hi,

Thanks for creating this tool!

After a fair amount of effort, I managed to get the MIMIC_Extract command: make build_curated_from_psql (in the utils directory) to work. The key issues were:

• I had used the https://github.com/MIT-LCP/mimic-code repository to build the PostgreSQL database for MIMIC-III (at least with some minor modifications described in Allow extra options to be passed to psql calls with MIMIC-III MIT-LCP/mimic-code#1195). But that meant that I had a new user and password and so on, but the MIMIC_Extract scripts could not handle this. So I have made some modifications to various scripts to allow for this. (There was also an issue that utils/setup_user_env.sh expected the password as the first argument, but it was never called with an argument by the other scripts.)
• The scripts were written for Pandas < 0.20, and several methods have been removed from Pandas >= 1.0. So I have updated the mimic_direct_extract.py script to handle modern versions of Pandas.
• The mimic-code concept scripts place the concepts in the public schema, but mimic_direct_extract.py only looked in mimiciii. So I have modified the code to change the search_path to include public.

I'm sorry that this is a rather big patch; it would have been nicer to split it into separate patches, but I couldn't work on either part without fixing the other.