Signature Commons: Docker Compose

This configuration file is designed to make it easy to deploy the entire signature-commons software architecture on any cloud with docker-compose support.

It uses an nginx proxy to proxy connections from the outside world to the docker containers:

• maayanlab/signature-commons-metadata-api
• maayanlab/enrichmentapi

It can also optionally host the signature commons metadata database.

Using this repo

This is a mono-repo for all of the signature commons applications. It uses git submodules to organize the separate repositories into one and lerna for linking together javascript related dependencies. Cloning the repository and all the submodules can be done with:

git clone --recurse-submodules git@github.com:dcic/signature-commons.git

If you already have it cloned, you can get all the submodules with:

git submodule update --init --recursive

.env

Many aspects of the application can be configured via environment variables--copy .env.example to .env and modify as needed.

Refreshing APIs

Metadata DB: Trigger the API to refresh the cached views/indecies

docker-compose exec metadata-api /bin/bash -c "npx typeorm migration:revert && npx typeorm migration:run"

Data DB: Trigger the API to load the desired data.

# The variables here should be replaced with .env settings, `file` should be set with the file used during ingestion.
curl -H 'Content-Type: application/json' -H "Authorization: Token ${TOKEN}" -X POST 'http://localhost/enrichmentapi/api/v1/load' -d "{\"bucket\": \"${AWS_BUCKET}\", \"file\": \"${file}.so\", \"datasetname\": \"${file}\"}'

Performing ingestion

# Setup virtualenv
python3 -m venv venv
source venv/bin/activate

cd ingestion
pip install -r requirements.txt
python ingest.py