This is a webserver for gene set enrichment analysis on a very large gene set -- one constructed by extracting gene sets from PMC OA. The bot does the extraction weekly.
Rather than splitting up the meta and data APIs, all functionality is incorporated into a postgres database.
We use postgraphile to serve the database on a graphql endpoint -- this endpoint can then be used for all necessary functionality, including both metadata search, filtering, and enrichment analysis. For speed purposes, enrichment is done through a companion API written in rust, the database itself communicates with this API, it is transparent to the application or users of the database.
# prepare environment variables
cp .env.example .env
# review & edit .env
# start db
docker-compose up -d postgres
# create db/ensure it's fully migrated
dbmate up
# start companion API
docker-compose up -d enrich
# start app (production)
docker-compose up -d app
# start app (development)
npm run devPYTHONPATH=bot python -m helper ingest -i your-gmt.gmt
PYTHONPATH=bot python -m helper ingest-paper-info
PYTHONPATH=bot python -m helper ingest-gene-infoSee src/graphql/core.graphql
These can be tested/developed at http://localhost:3000/graphiql