Factoid

Required software

• Node.js >=6.3.0
• RethinkDB ^2.3.0

Configuration

The following environment variables can be used to configure the server:

General:

• NODE_ENV : the environment mode; either production or development (default)
• PORT : the port on which the server runs (default 3000)
• LOG_LEVEL : minimum log level; one of info (default), warn, error

Database:

• DB_NAME : name of the db (default factoid)
• DB_HOST : hostname or ip address of the database host (default localhost)
• DB_PORT : port where the db can be accessed (default 28015, the rethinkdb default)
• DB_USER : username if the db uses auth (undefined by default)
• DB_PASS : password if the db uses auth (undefined by default)
• DB_CERT : local file path to certificate (cert) file if the db uses ssl (undefined by default)

Services:

• DEFAULT_CACHE_SIZE : default max number of entries in each cache
• REACH_URL : full url of the reach textmining endpoint
• UNIPROT_URL : full url of uniprot query service
• UNIPROT_CACHE_SIZE : overrides default cache size for uniprot query cache

Run targets

• npm start : start the server
• npm stop : stop the server
• npm run build : build project
• npm run build-prod : build the project for production
• npm run bundle-profile : visualise the bundle dependencies
• npm run clean : clean the project
• npm run watch : watch mode (debug mode enabled, auto rebuild, livereload)
• npm test : run tests
• npm run lint : lint the project

Running via Docker

Build the container. Here, factoid is used as the container name.

cd factoid
docker build -t factoid .

Run the container:

docker run -it -p 12345:3000 -u "node" -e "NODE_ENV=production" -e "PORT=3000" --name "factoid" factoid

Or run with an env file that defines the environment variables:

docker run -it -p 12345:3000 -u "node" --env-file prod.env --name "factoid" factoid

Notes:

• The -it switches are necessary to make node respond to ctrl+c etc. in docker.
• The -p switch indicates that port 3000 on the container is mapped to port 12345 on the host. Without this switch, the server is inaccessible.
• The -u switch is used so that a non-root user is used inside the container.
• The -e switch is used to set environment variables. Alternatively use --env-file to use a file with the environment variables.
• References:
  • Dockerizing a Node.js web app
  • Documentation of docker-node
  • Docker CLI docs

Testing

All files /test will be run by Mocha. You can npm test to run all tests, or you can run mocha -g specific-test-name (prerequisite: npm install -g mocha) to run specific tests.

The tests expect rethinkdb to be running on localhost on the default port (28015).

Chai is included to make the tests easier to read and write.

Notes:

• The Syncher.synch() is setup separately for each test file and namespaced. The reason for this is that the tests need to be able to be run independently and previous Syncher.synch() calls from other files would otherwise conflict.
• Each test file should require('./util/conf') to make debugging with promises easier etc.

Publishing a release

1. Make sure the tests are passing: npm test
2. Make sure the linting is passing: npm run lint
3. Bump the version number with npm version, in accordance with semver. The version command in npm updates both package.json and git tags, but note that it uses a v prefix on the tags (e.g. v1.2.3).
4. For a bug fix / patch release, run npm version patch.
5. For a new feature release, run npm version minor.
6. For a breaking API change, run npm version major.
7. For a specific version number (e.g. 1.2.3), run npm version 1.2.3.
8. Push the release: git push origin --tags