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DEVELOPMENT.md

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DEVELOPMENT.md

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Development

Local

Developing on openbel-api requires the following system dependencies:

  • Git
  • Java 8 (JDK)
  • JRuby 9.x
  • MongoDB 3.2
  • SQLite 3.x

Setting up data:

  • To start you will have to obtain RDF resources and full-text search database containing biological concepts (e.g. annotations, namespaces). Obtain data from OpenBEL Build Server.

Then follow a few steps:

  1. Clone the openbel-api using Git.
  • git clone git@github.com:OpenBEL/openbel-api.git
  1. Change directory to the cloned repository.
  • cd openbel-api
  1. Clone submodules for local developement to the subprojects/ directory.
  • git submodule update
  1. Install bundle on JRuby.
  • jruby -S gem install bundler
  1. Install openbel-api dependencies using bundler.
  • jruby -S bundle install --path .gems
  • This ensures we isolate gem dependencies from other system gem paths.
  • Bundler saves this configuration so we don't need to specify --path again.
  1. Run bin/openbel-api using bundler.
  • jruby -S bundle exec bin/openbel-api --file config/config.yml

If all went well you should see:

Puma starting in single mode...
* Version 3.1.0 (jruby 2.3.1), codename: El Niño Winter Wonderland
* Min threads: 0, max threads: 16
* Environment: development
* Listening on tcp://0.0.0.0:9292
Use Ctrl-C to stop

On Docker

Please see the DOCKER.md file for guidance with Docker

Running Tests

API_ROOT_URL=https://pmi-openbel.sbvimprover.com/api rspec -fd spec/expression/*

You will need to install the hyperclient gem first with: gem install hyperclient