The code in this repo can reproduce the second Kibi ChEMBL demo. This are the steps to reproduce the demo.
-
Start up a kibi instance. E.g. using docker:
docker run -d -p 5606:5606 -p 9201:9220 --net=chembl --name chembl-kibi sirensolutions/kibi-community-standard:4.6.4
-
pip install -r requirements.txt
-
run
python import.py -es http://localhost:9201
using the port your elasticsearch instance is exposed to and wait for it to complete this will:- Download and extract the chembl dumps in SQLite format
- Query the database and generate the input json file in the
import
directory - Load the json in elasticsearch with the proper mapping
- Create the necessary index-pattern in kibi
-
explore the data at your kibi instance: http://localhost:5606
-
To persist the state of kibi you can run
dump_kibi.sh
. This requires elasticdump to be installed. To save the data and the kibi configuartion in a compressed file you can rundump_all.sh
.