openbel-api 1.0.3-java → 1.0.4-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 25d2e441f67f4be259e2f3a594a66c1c6524c061
-  data.tar.gz: 2dde1eb0808d0f1ded754a447ca787c06e8196e7
+  metadata.gz: 00a36abdeadf9bbfeaf6bd2251e2f7cd32b051bf
+  data.tar.gz: 29e80343fd5d984c9df84266fe707ded3fc10658
 SHA512:
-  metadata.gz: f1564a9fa715f528b2dce42f4f6238fb78f15bced541a786eee8b7c595b325ce2d19a596fc07bab9e579976c560137ccb22bed17af2d1a00420462896e5d1f5f
-  data.tar.gz: 84721bf531574e8c9355a26246c7f039c8556f28a0f1914ae251609dbd7ded8792a4c7dd05f22cd825141abfbe4915cf72b1592f2b3c55c796746ca65fe99a4f
+  metadata.gz: 0f417e1ab2ae9a477ed14d4ce15fbc048b83ce31e0fb2254c02ad16f11d4f1e187e18c2011420abf589367e9dcdabb230866b21af71b1517b9c866d29564aa76
+  data.tar.gz: 5a9377f4e826f6287883c89b414f4b5df48f5872fb72569da9ec1c577dcb04f716a1e0241ff85cb3376e31e5b9b2d710929da3c13ff5a775f21a737aaffdd229

data/.gemspec

@@ -26,7 +26,7 @@ Gem::Specification.new do |spec|
                                  'README.md'
                                ].flatten!
   spec.executables           = Dir.glob('bin/*').map(&File.method(:basename))
-  spec.homepage              = 'https://github.com/OpenBEL/openbel-server'
+  spec.homepage              = 'https://github.com/OpenBEL/openbel-api'
   spec.require_paths         = ['app', 'lib']
   spec.platform              = 'java'
   spec.required_ruby_version = '>= 2.0.0'

data/CHANGELOG.md

@@ -3,6 +3,13 @@ All notable changes to openbel-api will be documented in this file. The curated
 
 This project adheres to [Semantic Versioning][Semantic Versioning].
 
+## [1.0.4][1.0.4] - 2016-12-28
+### Added
+- Docker containers for development and production use of OpenBEL
+
+### Changed
+- Converted authentication to use Keycloak Pubkey RSA256 Token authentication
+
 ## [1.0.1][1.0.1] - 2016-06-08
 ### Added
 - Renaming APIs and code on [new terminology][new terminology].
@@ -87,6 +94,7 @@ Datasets are stored with a URI computed from the scheme and host that is serving
   - Retrieve equivalent namespace values from the individual.
   - Retrieve orthologous namespace values from the individual.
 
+[1.0.4]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.2...1.0.4
 [1.0.1]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.2...1.0.1
 [1.0.0]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.2...1.0.0
 [0.6.2]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.1...0.6.2

data/INSTALL.md

@@ -1,19 +1,21 @@
-Install
-=======
+## Install
 
 This library requires [Ruby](https://www.ruby-lang.org) (**>= 2.0.0**).  See [how to install ruby](https://github.com/OpenBEL/bel.rb/blob/master/INSTALL_RUBY.md).
 
-Install from [RubyGems.org](http://rubygems.org/gems/bel)
+#### From RubyGems
+
+Install from [RubyGems.org](http://rubygems.org/gems/openbel-api)
 
 ```bash
-    gem install bel
+    gem install openbel-api
 ```
 
-Build from master branch
+Run with `openbel-api --file your_config.yml`
+
+You can obtain an example configuration file with `openbel-config`.
+
+#### On Docker
+
+Please see the DOCKER.md file for Docker instructions
 
-1. Obtain source for master branch.
-  - `git clone git@github.com:OpenBEL/bel.rb.git`
 
-2. Build
-  - `gem build bel.gemspec`
-  - `gem install bel-[VERSION].gem`

data/README.md

@@ -2,6 +2,7 @@
 
 The OpenBEL API provides RESTful API access to your BEL content. It is part of [OpenBEL Platform][OpenBEL Platform].
 
+
 ## Features
 
 - Nanopub Store
@@ -61,6 +62,8 @@ The OpenBEL API is built to run with [JRuby][JRuby] and [Java 8][Java 8].
 
 ## Getting up and Running
 
+*See the DOCKER.md file instructions for using Docker (recommended).*
+
 ### Installation
 
 The OpenBEL API is packaged and installed as a Ruby gem. A Ruby gem is packed library or application that runs on the Ruby virtual machine. In this case OpenBEL API runs only on [JRuby][JRuby].
@@ -132,31 +135,48 @@ resource_search:
     database_file: 'biological-concepts-rdf.db'
 ```
 
-
 **Tip**
 You can obtain the latest Resource Search database (20150611) from the [OpenBEL build server][Resource Search 20150611].
 
-*Token-based authentication*
-The OpenBEL API is equipped to require authentication for specific API paths (e.g. nanopub, Datasets). The implementation uses [Auth0][Auth0] as a single sign-on service.
 
-By default authentication is disabled.
+## Enabling Authentication
 
-The default configuration is:
+The OpenBEL API uses *Token-based authentication* supported by Keycloak.
+The OpenBEL API is equipped to require authentication for specific API
+paths (e.g. nanopub, Datasets). The implementation uses [Keycloak][Keycloak]
+for a single sign-on service.
+
+By default, authentication is disabled.  The default configuration is:
 
 ```yaml
 # Set a secret used during session creation....
 session_secret: 'changeme'
 
-# User authentication using Auth0.
 auth:
+  # Controls whether the API requires authentication
   enabled: false
-  redirect: 'https://openbel.auth0.com/authorize?response_type=code&scope=openid%20profile&client_id=K4oAPUaROjbWWTCoAhf0nKYfTGsZWbHE'
-  default_connection: 'linkedin'
-  domain:   'openbel.auth0.com'
-  id:       'K4oAPUaROjbWWTCoAhf0nKYfTGsZWbHE'
-  # secret:   'auth0 client secret here'
+  # Used by the auth middleware to decode and verify the JWT
+  #secret:   'JWT secret here'
+
+# API Authentication is provided via JWTs from Keycloak
+#    see http://jwt.io/ and https://keycloak.org
+# auth:
+#   # Controls whether the API requires authentication
+#   enabled: true
+#   # Used by the auth middleware to decode and verify the JWT
+#   secret: |
+#     -----BEGIN PUBLIC KEY-----
+#     <keycloak_pub_key>
+#     -----END PUBLIC KEY-----
 ```
 
+An example
+The keycloak Pub Key can be found in the Admin console for Keycloak:
+
+1. Realm Settings
+1. Keys tab
+1. Public Key -> View
+
 ### Running the OpenBEL API
 
 The OpenBEL API can be run using the `openbel-api` command and passing a configuration file.
@@ -276,7 +296,7 @@ Built with collaboration and a lot of :heart: by the [OpenBEL][OpenBEL] communit
 [Upgrading]: https://github.com/OpenBEL/openbel-api/blob/master/UPGRADING.md
 [RubyGems]: https://rubygems.org
 [RDF]: http://www.w3.org/RDF/
-[Auth0]: https://auth0.com/
+[Keycloak]: https://http://www.keycloak.org/
 [Puma HTTP server]: http://puma.io/
 [Resource RDF 20150611]: http://build.openbel.org/browse/OR-RRD2/latestSuccessful/artifact
 [Resource Search 20150611]: http://build.openbel.org/browse/OR-RSD2/latestSuccessful/artifact

data/VERSION

@@ -1 +1 @@
-1.0.3
+1.0.4

data/app/openbel/api/app.rb

@@ -6,6 +6,7 @@ require 'bel_parser'
 
 require_relative 'util'
 
+require 'rack'
 require 'rack/cors'
 require 'sinatra/base'
 require "sinatra/cookies"

data/app/openbel/api/middleware/auth.rb

@@ -39,14 +39,17 @@ module OpenBEL
       token = token_param unless token_param.nil?
 
       secret = OpenBEL::Settings[:auth][:secret]
-      secret = Base64.decode64(secret)
+      pubkey = OpenSSL::PKey::RSA.new(secret)
+
+      # secret = Base64.decode64(secret)
+
       # whether we should verify the token
       verify = true
       # JWT options passed to decode
-      options = {}
+      options = { :algorithm => 'RS256' }
 
       begin
-        decoded_token = decode(token, secret, verify, options)
+        decoded_token = decode(token, pubkey, verify, options)
       rescue ::JWT::VerificationError => ve
         puts ve.inspect
         raise 'invalid authorization token'

data/app/openbel/api/routes/annotations.rb

@@ -27,6 +27,11 @@ module OpenBEL
         )
       end
 
+      configure :development do |config|
+        Annotations.reset!
+        use Rack::Reloader
+      end
+
       options '/api/annotations' do
         response.headers['Allow'] = 'OPTIONS,GET'
         status 200

data/app/openbel/api/routes/authenticate.rb

@@ -3,6 +3,11 @@ module OpenBEL
 
     class Authenticate < Base
 
+      configure :development do |config|
+        Authenticate.reset!
+        use Rack::Reloader
+      end
+
       get '/api/authentication-enabled' do
         enabled = OpenBEL::Settings[:auth][:enabled]
         hdrs = {'Content-Type' => 'application/json'}

data/app/openbel/api/routes/datasets.rb

@@ -56,6 +56,11 @@ module OpenBEL
         @annotation_transform = AnnotationTransform.new(annotations)
       end
 
+      configure :development do |config|
+        Datasets.reset!
+        use Rack::Reloader
+      end
+
       # Hang on to the Rack IO in order to do unbuffered reads.
       # use Rack::Config do |env|
       #   env['rack.input'], env['data.input'] = StringIO.new, env['rack.input']

data/app/openbel/api/routes/expressions.rb

@@ -20,14 +20,27 @@ module OpenBEL
         @spec         = BELParser::Language.specification(bel_version)
 
         # RdfRepository using Jena.
-        @rr = BEL::RdfRepository.plugins[:jena].create_repository(
-          :tdb_directory => OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
-        )
+        tdb = OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
+        @rr = BEL::RdfRepository.plugins[:jena].create_repository(:tdb_directory => tdb)
 
         # Annotations using RdfRepository
         @annotations = BEL::Resource::Annotations.new(@rr)
         # Namespaces using RdfRepository
-        @namespaces = BEL::Resource::Namespaces.new(@rr)
+        @namespaces  = BEL::Resource::Namespaces.new(@rr)
+
+        @supported_namespaces = Hash[
+          @namespaces.each.map { |ns|
+            prefix = ns.prefix.first.upcase
+
+            [
+              prefix,
+              BELParser::Expression::Model::Namespace.new(
+                prefix,
+                ns.uri
+              )
+            ]
+          }
+        ]
 
         # Resource Search using SQLite.
         @search = BEL::Resource::Search.plugins[:sqlite].create_search(
@@ -36,11 +49,16 @@ module OpenBEL
 
         @expression_validator = BELParser::Expression::Validator.new(
           @spec,
-          BELParser::Resources::DEFAULT_NAMESPACES,
-          BELParser::Resource.default_uri_reader,
+          @supported_namespaces,
+          BELParser::Resource::JenaTDBReader.new(tdb),
           BELParser::Resource.default_url_reader)
       end
 
+      configure :development do |config|
+        Expressions.reset!
+        use Rack::Reloader
+      end
+
       options '/api/expressions/*/completions' do
         response.headers['Allow'] = 'OPTIONS,GET'
         status 200
@@ -177,7 +195,9 @@ module OpenBEL
         statement =
           BELParser::Expression.parse_statements(
             bel,
-            @spec)
+            @spec,
+            @supported_namespaces
+        )
         halt 404 unless statement
 
         response.headers['Content-Type'] = 'application/json'

data/app/openbel/api/routes/language.rb

@@ -18,6 +18,11 @@ module OpenBEL
         @spec       = BELParser::Language.specification(bel_version)
       end
 
+      configure :development do |config|
+        Language.reset!
+        use Rack::Reloader
+      end
+
       options '/api/language' do
         response.headers['Allow'] = 'OPTIONS,GET'
         status 200

data/app/openbel/api/routes/namespaces.rb

@@ -40,6 +40,11 @@ module OpenBEL
         )
       end
 
+      configure :development do |config|
+        Namespaces.reset!
+        use Rack::Reloader
+      end
+
       options '/api/namespaces' do
         response.headers['Allow'] = 'OPTIONS,GET'
         status 200

data/app/openbel/api/routes/nanopubs.rb

@@ -32,6 +32,11 @@ module OpenBEL
         @annotation_grouping_transform = AnnotationGroupingTransform.new
       end
 
+      configure :development do |config|
+        Nanopubs.reset!
+        use Rack::Reloader
+      end
+
       helpers do
 
         def stream_nanopub_objects(cursor)

data/app/openbel/api/routes/root.rb

@@ -3,6 +3,11 @@ module OpenBEL
 
     class Root < Base
 
+      configure :development do |config|
+        Root.reset!
+        use Rack::Reloader
+      end
+
       options '/api' do
         response.headers['Allow'] = 'OPTIONS,GET'
         status 200

data/app/openbel/api/routes/version.rb

@@ -16,6 +16,11 @@ module OpenBEL
       }
       DEFAULT_TYPE     = TEXT
 
+      configure :development do |config|
+        Version.reset!
+        use Rack::Reloader
+      end
+
       helpers do
         def requested_media_type
           if params && params[:format]

data/bin/setup-docker.sh

@@ -0,0 +1,62 @@
+#!/usr/bin/env bash
+
+# run via: bash <(curl -s https://raw.githubusercontent.com/OpenBEL/openbel-api/master/bin/setup-docker.sh)
+
+hash docker 2>/dev/null || { echo >&2 "I require docker. Please install.  Aborting."; exit 1; }
+hash docker-compose 2>/dev/null || { echo >&2 "I require docker-compose. Please install.  Aborting."; exit 1; }
+
+
+ssh_status=$(ssh -o BatchMode=yes -o ConnectTimeout=5 git@github.com 2>&1)
+
+if [[ $ssh_status == *"successfully authenticated"* ]] ; then
+  clone_cmd="git clone git@github.com:OpenBEL/openbel-api.git";
+else
+  clone_cmd="git clone https://github.com/OpenBEL/openbel-api.git";
+fi
+
+if [ ! -d "openbel-api" ]; then
+    $clone_cmd
+else
+    cd openbel-api;
+    git pull;
+    cd ..;
+fi
+
+
+cd openbel-api
+git submodule update --init  # Update project submodules (in the ./subprojects directory)
+HOME=$(pwd)
+
+
+# Download and bunzip2 datasets
+if [ ! -d "$HOME/data/rdf_resources" ]; then
+    mkdir -p $HOME/data/rdf_resources
+    cd $HOME/data/rdf_resources
+    curl -O http://datasets.openbel.org/biological-concepts-rdf.db.bz2
+    bunzip2 biological-concepts-rdf.db.bz2
+fi
+
+if [ ! -d "$HOME/data/rdf_store" ]; then
+    mkdir -p $HOME/data
+    cd $HOME/data
+    curl -O http://datasets.openbel.org/rdf_store.tar.bz2
+    bunzip2 rdf_store.tar.bz2
+    tar xvf rdf_store.tar
+    rm rdf_store.tar
+fi
+
+cd $HOME
+
+if [ ! -f "$HOME/config/config.yml" ]; then
+    cp config/config.yml.example config/config.yml
+fi
+
+printf "Remember to configure config/config.yml\n\n"
+
+echo "To start the dev docker instance: "
+echo "  docker-compose build"
+echo "  docker-compose up"
+
+printf "\n\nTo run production docker: "
+echo "  docker-compose -f docker-compose-prod.yml build"
+echo "  docker-compose -f docker-compose-prod.yml up"

data/config/config.yml

@@ -8,7 +8,7 @@ bel:
   #     (BEL version 1.0 specification)
   #   2.0
   #     (BEL version 2.0 specification)
-  version: 2.0
+  version: 1.0
 
 # Storage of nanopubs through the Mongo database.
 nanopub_store:
@@ -16,8 +16,8 @@ nanopub_store:
 
     # The MongoDB host to connect to. For example if MongoDB's net.bindIp
     # setting is configured as 127.0.0.1 we should be able to connect using
-    # localhost.
-    host:                     'localhost'
+    # 'localhost'.  We use 'mongodb' for use in the docker-compose file.
+    host:                     'mongodb'
 
     # The default MongoDB port. Configured under MongoDB's `net.port` setting.
     port:                     27017
@@ -51,12 +51,12 @@ nanopub_store:
 # RDF dataset for BEL datasets, annotations, and namespaces using Apache Jena.
 resource_rdf:
   jena:
-    tdb_directory: 'biological-concepts-rdf'
+    tdb_directory: '/data/rdf_store'
 
 # Full-text search over annotation and namespace values using SQLite.
 resource_search:
   sqlite:
-    database_file: 'biological-concepts-rdf.db'
+    database_file: '/data/rdf_resources/biological-concepts-rdf.db'
 
 # Set a secret used during session creation....
 session_secret: 'changeme'
@@ -66,5 +66,8 @@ auth:
   # Controls whether the API requires authentication
   enabled: false
   # Used by the auth middleware to decode and verify the JWT
-  #secret:   'JWT secret here'
+  secret: |
+    -----BEGIN PUBLIC KEY-----
+    MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAu77nUtVw7SIIcUTSiStzMPB7BGB/9eS+CpppsUaiyZyWCXlrALT3YdqneSlpX4Ta+0wvhOkKQtoSS8dCH8GIi7esAmfdHetHfRgeDXHAlXo8HIzshUzODg3ysT7j+Ha3eJsO+LNS/omHDhsarP8Z2eThW876iKJCCc/mB76a6u1e4Id+52K5lG++m8Pn4Gs+cqd2sKUKcMJ9CkJ6dBIdGlXHMoOHj4C33SPrEG/vEBv5cu0l5PP3RiBAuaZHpLKzfIiaLOpj/k4dD/weVt5gwTIJn16AEgPD7173Xef0HgoPlQInDFrJwsGpYCnIPZWSxRbvjKkya2Auj0QZyMCrXwIDAQAB
+    -----END PUBLIC KEY-----
 

metadata

@@ -1,348 +1,348 @@
 --- !ruby/object:Gem::Specification
 name: openbel-api
 version: !ruby/object:Gem::Version
-  version: 1.0.3
+  version: 1.0.4
 platform: java
 authors:
 - Anthony Bargnesi
 - Nick Bargnesi
 - William Hayes
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
 date: 2016-03-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
+  name: bel
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
-  name: bel
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
 - !ruby/object:Gem::Dependency
+  name: json-ld
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: json-ld
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
+  name: rdf-json
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: rdf-json
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
+  name: rdf-rdfa
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: rdf-rdfa
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
+  name: rdf-rdfxml
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: rdf-rdfxml
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
+  name: rdf-trig
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: rdf-trig
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
+  name: rdf-trix
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: rdf-trix
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
+  name: rdf-turtle
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: rdf-turtle
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
+  name: bel-search-sqlite
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
-  name: bel-search-sqlite
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
 - !ruby/object:Gem::Dependency
+  name: bel-rdf-jena
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
-  name: bel-rdf-jena
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
 - !ruby/object:Gem::Dependency
+  name: mongo
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.12.5
-  name: mongo
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.12.5
 - !ruby/object:Gem::Dependency
+  name: bson
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.12.5
-  name: bson
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.12.5
 - !ruby/object:Gem::Dependency
+  name: dot_hash
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.5.9
-  name: dot_hash
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.5.9
 - !ruby/object:Gem::Dependency
+  name: jrjackson
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.3.7
-  name: jrjackson
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.3.7
 - !ruby/object:Gem::Dependency
+  name: json_schema
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.10.0
-  name: json_schema
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.10.0
 - !ruby/object:Gem::Dependency
+  name: multi_json
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.11.2
-  name: multi_json
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.11.2
 - !ruby/object:Gem::Dependency
+  name: oat
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.4.6
-  name: oat
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.4.6
 - !ruby/object:Gem::Dependency
+  name: puma
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 3.1.0
-  name: puma
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 3.1.0
 - !ruby/object:Gem::Dependency
+  name: rack
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.6.4
-  name: rack
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.6.4
 - !ruby/object:Gem::Dependency
+  name: rack-cors
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.4.0
-  name: rack-cors
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.4.0
 - !ruby/object:Gem::Dependency
+  name: rack-handlers
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.7.0
-  name: rack-handlers
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.7.0
 - !ruby/object:Gem::Dependency
+  name: sinatra
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.4.6
-  name: sinatra
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.4.6
 - !ruby/object:Gem::Dependency
+  name: sinatra-contrib
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.4.6
-  name: sinatra-contrib
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.4.6
 - !ruby/object:Gem::Dependency
+  name: jwt
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.5.2
-  name: jwt
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
@@ -351,8 +351,9 @@ dependencies:
 description: The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.
 email: abargnesi@selventa.com
 executables:
-- openbel-config
 - openbel-api
+- openbel-config
+- setup-docker.sh
 extensions: []
 extra_rdoc_files: []
 files:
@@ -408,6 +409,7 @@ files:
 - app/openbel/api/version.rb
 - bin/openbel-api
 - bin/openbel-config
+- bin/setup-docker.sh
 - config/config.yml
 - config/server_config.rb
 - lib/openbel/api/cache/cache.rb
@@ -428,11 +430,11 @@ files:
 - lib/openbel/api/plugin/plugin_repository.rb
 - lib/openbel/api/storage/cache_proxy.rb
 - lib/openbel/api/storage/triple_storage.rb
-homepage: https://github.com/OpenBEL/openbel-server
+homepage: https://github.com/OpenBEL/openbel-api
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - app
@@ -448,9 +450,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project:
-rubygems_version: 2.6.4
-signing_key:
+rubyforge_project: 
+rubygems_version: 2.4.6
+signing_key: 
 specification_version: 4
 summary: The OpenBEL API provided over RESTful HTTP endpoints.
 test_files: []