frankfarrell / chembl

NEW: now "Big Life Science demo" not only Cheml but also Clinical Trials and PUBMED

KIBI ChEMBL DEMO II

The code in this repo can reproduce the second Kibi ChEMBL demo. This are the steps to reproduce the demo.

1. 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

2. pip install -r requirements.txt

3. 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

4. explore the data at your kibi instance: http://localhost:5606

5. 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 run dump_all.sh.