A from-scratch rewrite of the Drug-Gene Interaction Database.
First, make sure you have all of the following installed:
Clone and enter the repository:
git clone https://github.com/dgidb/dgidb-v5
cd dgidb-v5
First, you may need to switch your Ruby version with RVM to match the version declared in the first few lines of the Gemfile. For example, to switch to version 3.0.4:
rvm install 3.0.4
rvm 3.0.4
From the repo root, enter the server subdirectory:
cd server
If RVM is properly installed, you should expect to encounter a warning message here:
RVM used your Gemfile for selecting Ruby, it is all fine - Heroku does that too,
you can ignore these warnings with 'rvm rvmrc warning ignore ./Gemfile'.
To ignore the warning for all files run 'rvm rvmrc warning ignore allGemfiles'.
Next, install Rails and other required gems with bundle
:
bundle install
The server will need a running Postgres instance. Postgres start commands may vary based on your OS and processor type. The following should work on M1 Macs:
pg_ctl -D /opt/homebrew/var/postgres start
# on older macs you may need to use a different path instead, eg "pg_ctl -D /usr/local/var/postgres start"
Database initialization utilities are in-progress, so for now, the easiest way to get a working database is to manually create it using the psql
command. First, enter the psql console:
psql -d postgres # if you are opening psql for the first time, you'll need to connect to the database 'postgres'
# should produce a prompt like the following:
# psql (14.2)
# Type "help" for help.
#
# jss009=#
Within the psql console, create the DGIdb database, then quit:
CREATE DATABASE dgidb;
\q
Next, back in the main shell, import a database dump file (ask on Slack if you need the latest file):
psql -d dgidb -f dgidb_dump_20220526.psql # provide path to data dump
That should take a few minutes. Finally, start the Rails server:
rails s
Navigate to localhost:3000/api/graphiql
in your browser. If the example query provided runs successfully, then you're all set.
Navigate to the /client directory:
# from dgidb-v5 root
cd client
Install dependencies with yarn:
yarn install
Start the client:
yarn start