DGIdb v5

A from-scratch rewrite of the Drug-Gene Interaction Database.

For developers

Initial dependencies

First, make sure you have all of the following installed:

• RVM -- choose the stable version
• PostgreSQL, either from here or here
• NPM/Node

Clone and enter the repository:

git clone https://github.com/dgidb/dgidb-v5
cd dgidb-v5

Server setup

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.

Data loading

To perform a data load from scratch, first run the reset task to provide a clean, seeded DB:

rake db:reset

Most DGIdb data comes from static files, typically called claims.tsv. The data loader classes expect server/lib/data/ to contain the following files:

lib/data
├── bader_lab
│   └── claims.tsv
├── cancer_commons
│   └── claims.tsv
├── caris_molecular_intelligence
│   └── claims.tsv
├── cgi
│   └── claims.tsv
├── chembl
│   └── chembl.db
├── clearity_foundation_biomarkers
│   └── claims.tsv
├── clearity_foundation_clinical_trial
│   └── claims.tsv
├── cosmic
│   └── claims.csv
├── dgene
│   └── claims.tsv
├── drugbank
│   └── claims.xml
├── dtc
│   └── claims.csv
├── ensembl
│   └── claims.tsv
├── entrez
│   └── claims.tsv
├── fda
│   └── claims.tsv
├── foundation_one_genes
│   └── claims.tsv
├── go
│   └── targets.tsv
├── guide_to_pharmacology
│   ├── interactions.csv
│   └── targets_and_families.csv
├── hingorani_casas
│   └── claims.tsv
├── hopkins_groom
│   └── claims.tsv
├── human_protein_atlas
│   └── claims.tsv
├── idg
│   ├── claims.json
│   └── claims.tsv
├── msk_impact
│   └── claims.tsv
├── my_cancer_genome
│   └── claims.tsv
├── my_cancer_genome_clinical_trial
│   └── claims.tsv
├── nci
│   ├── claims.tsv
│   └── claims.xml
├── oncokb
│   ├── drug_claim.csv
│   ├── gene_claim.csv
│   ├── gene_claim_aliases.csv
│   ├── interaction_claim.csv
│   ├── interaction_claim_attributes.csv
│   └── interaction_claim_links.csv
├── oncomine
│   └── claims.tsv
├── pharmgkb
│   └── claims.tsv
├── russ_lampel
│   └── claims.tsv
├── talc
│   └── claims.tsv
├── tdg_clinical_trial
│   ├── claims.tsv
├── tempus
│   └── claims.tsv
├── tend
│   └── claims.tsv
└── ttd
    └── claims.csv

First, load claims:

rake dgidb:import:all

Then, run grouping. By default, the groupers will expect a normalizer service to be running locally on port 8000; use the THERAPY_HOSTNAME and GENE_HOSTNAME environment variables to specify alternate hosts:

export THERAPY_HOSTNAME=http://localhost:7999  # no trailing backslash
rake dgidb:group:drugs
export GENE_HOSTNAME=http://localhost:7998  # no trailing backslash
rake dgidb:group:genes
rake dgidb:group:interactions

Finally, normalize remaining metadata:

rake dgidb:normalize:drug_approval_types
rake dgidb:normalize:drug_types
rake dgidb:normalize:populate_source_counters

Client setup

Navigate to the /client directory:

# from dgidb-v5 root
cd client

Install dependencies with yarn:

yarn install

Start the client:

yarn start

Frontend style is enforced by ESLint and Prettier. Conformance is ensured by pre-commit. Before your first commit, run

pre-commit install

In practice, Prettier will do most of the formatting work for you to be in accordance with ESLint. Run the following to autoformat a file:

yarn run prettier --write path/to/file