z0rde / ebi-ac-compounds-parser

ebi.ac.uk cli compound database parser

ebi.ac.uk compounds database parser

Parsing compounds data from ebi.ac.uk api to Postgres database. The goal was to keep it clean and minimal in modules, without using any unnecesary things like flask etc.

external modules used:

requests, for getting data from web api

rich, for printing it in table form

sqlalchemy for database access

How to use:

install with

docker-compose build

run with command line arguments:

sudo docker-compose run app [arguments...]

for example

sudo docker-compose run app get all

get - parse compound info to db

get all - get all compounds

show - display compound data from db

show all - display all gathered data

clear - erase the database

valid compound names are:

ADP, ATP, STI, ZID, DPM, XP9, 18W, 29P