Chemistry commons Notes

Database Management

Source chemistry commons

source /nfs/soft/anaconda3/bin/activate ~khtang/.conda/envs/chemcommons 

Import data from Spreadsheet

• • This will be deprecated once we switched to use postgres

bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx]

Export Chemistry Commons DB

Run this script to create a snapshot of the database and JSON files for Enumeration

 bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash export mem2 [destination]

Restore data from backup

psql -U commoner -d commons -p 5434 < [db_snapshot_file]

How to simulate disaster

Stop chemistry commons docker container

ssh epyc2
sudo docker stop chemcommons

Delete database and create

psql -h mem2 -U commoner -d excipients -p 5434 //psql console login
=> drop database commons;
=> create database commons;

Restore db

psql -U commoner -d commons -p 5434 < [db_snapshot_file]

Start CC docker container

ssh epyc2
sudo docker start chemcommons