genomelink-ruby 0.1.0

checksums.yaml

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data/.gitignore

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# byebug files
+.byebug*
+
+# ctags
+.tags*
+
+# rspec failure tracking
+.rspec_status

data/.rspec

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+--format documentation
+--color
+--require spec_helper

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.4.2
+before_install: gem install bundler -v 1.16.1

data/Gemfile

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+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in genomelink-ruby.gemspec
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    genomelink-ruby (0.1.0)
+      oauth2
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    byebug (9.1.0)
+    diff-lcs (1.3)
+    faraday (0.12.2)
+      multipart-post (>= 1.2, < 3)
+    jwt (1.5.6)
+    multi_json (1.13.1)
+    multi_xml (0.6.0)
+    multipart-post (2.0.0)
+    oauth2 (1.4.0)
+      faraday (>= 0.8, < 0.13)
+      jwt (~> 1.0)
+      multi_json (~> 1.3)
+      multi_xml (~> 0.5)
+      rack (>= 1.2, < 3)
+    rack (2.0.4)
+    rake (10.5.0)
+    rspec (3.7.0)
+      rspec-core (~> 3.7.0)
+      rspec-expectations (~> 3.7.0)
+      rspec-mocks (~> 3.7.0)
+    rspec-core (3.7.1)
+      rspec-support (~> 3.7.0)
+    rspec-expectations (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-mocks (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-support (3.7.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.16)
+  byebug
+  genomelink-ruby!
+  rake (~> 10.0)
+  rspec (~> 3.0)
+
+BUNDLED WITH
+   1.16.1

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2018 Ashwin Subramanian
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+
+# GENOME LINK Ruby Gem
+
+Ruby gem library to quickly get started with the GENOME LINK API. This supports both the authentication mechanisms, token based and OAuth 2.0.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'genomelink-ruby'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install genomelink-ruby
+
+## Usage/Examples
+Example Usage for calling the reports API with oAuth token
+```ruby
+2.4.2 :001 > require 'genomelink'
+ => true
+2.4.2 :002 > result = Genomelink::Report.fetch("eye-color","GENOMELINKTEST001")
+ => #<Genomelink::Report:0x00007f87b41fb010 @phenotype={"url_name"=>"eye-color", "display_name"=>"Genetic eye color", "category"=>"trait"}, @population="european", @scores=[{"score"=>0, "text"=>"Tend to not have brown eyes"}, {"score"=>1, "text"=>"Tend to not have brown eyes, slightly"}, {"score"=>2, "text"=>"Intermediate"}, {"score"=>3, "text"=>"Slight tendency for brown eyes"}, {"score"=>4, "text"=>"Stronger tendency for brown eyes"}], @summary={"score"=>0, "text"=>"Tend to not have brown eyes", "warnings"=>[]}>
+2.4.2 :003 > result.summary
+ => {"score"=>0, "text"=>"Tend to not have brown eyes", "warnings"=>[]}
+```
+
+Example Usage for oAuth -
+```ruby
+# To get the redirect URL :
+redirect_url = Genomelink::Oauth.authorization_url("report:eye-color")
+# Redirect user to the above URL.
+# After authentication user control reaches the callback URL with code.
+# Use the code from the parameters and request a token
+token = Genomelink::Oauth.get_token(params[:code])
+# This token can be used to call the reports API as given above.
+# Store this token and if it expired use the code again to get a new token.
+```
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment. To run only the unit tests, run the specs in `spec/unit`. The integration specs which reach out to genomelink are in `spec/integration`
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/s-ashwinkumar/genomelink-ruby. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "genomelink"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/genomelink-ruby.gemspec

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+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "genomelink/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "genomelink-ruby"
+  spec.version       = Genomelink::VERSION
+  spec.authors       = ["Ashwin Subramanian"]
+  spec.email         = ["s.ashwinkumar24902gmail.com"]
+
+  spec.summary       = %q{Ruby Gem to access genome link APIs}
+  spec.description   = %q{This is a ruby gem to access the genome link APIs. It inclides the API classes and the OAuth system.}
+  spec.license       = "MIT"
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.16"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "byebug"
+  spec.add_dependency "oauth2"
+end

data/lib/genomelink.rb

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+require "genomelink/version"
+require "genomelink/base"
+require "genomelink/reports"
+require "genomelink/oauth"
+
+module Genomelink
+  SITE = 'https://genomelink.io'.freeze
+  # Path for genomelinke oauth
+  OAUTH_PATH = "#{SITE}/oauth/authorize".freeze
+end

data/lib/genomelink/base.rb

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+require 'oauth2'
+
+module Genomelink
+  class ConfigNotFound < StandardError; end
+  # The Base class for all of the other class.
+  # Let other classes inherit from here and put common methods here.
+  #
+  # @author [ashwin]
+  #
+  class Base
+    class << self
+      # Makes a get request to genomelink for the URL given and with the given token.
+      #  TODO : use meta programming and define all Restful methods.
+      # @param path [String] the path to hit for the request.
+      # @param token [String] the access token to be used.
+      #
+      # @return [Hash] The response Json parsed as a hash.
+      def get(path, token)
+        result = service(token).get do |req|
+          req.url path
+          req.headers['Authorization'] = "BEARER #{token}"
+        end
+        JSON.parse(result.body)
+      end
+
+      private
+
+      # gets a genomelink API service/client
+      # @param token [String] Access token.
+      #
+      # @return [OAuth2::AccessToken] An initialized AccessToken instance that acts as service client
+      def service(token)
+        @service ||= Faraday.new(url: SITE)
+      end
+    end
+
+    # A constructor to take a hash and assign it to the instance variables
+    # @param options = {} [Hash] Could by any class's hash, but the first level keys should be defined in the class
+    #
+    # @return [Subclass os Base] Returns object of any subclass like Report
+    def initialize(options = {})
+      options.each do |attribute, value|
+        instance_variable_set("@#{attribute}", value)
+      end
+    end
+  end
+end

data/lib/genomelink/genome.rb

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+module Genomelink
+  class Genome < Base
+  end
+end

data/lib/genomelink/oauth.rb

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+module Genomelink
+  # Oauth class to take care of the Oauth 2.0 with genomelink APIs
+  #
+  # @author [ashwin]
+  #
+  class Oauth < Base
+    class << self
+      # Used to get the redirect URL to Genomelink where user can authorize an app.
+      # @param scope [String] Space delimited list of scopes that specify what the user can access
+      #   EXAMPLE : "report:bmi report:longevity"
+      # This should be within the ones selected during the registering the client application.
+      #
+      # @return [String] URL where user needs to be redirected for authorization
+      def authorization_url(scope)
+        client.auth_code.authorize_url(redirect_uri: get_config('GENOMELINK_CALLBACK_URL'), scope: scope)
+      end
+
+      # [get_token description]
+      # @param auth_code [String] This is the code that is returned after use visits and authorizes on the authorization URL
+      #
+      # @return [String] Access token that can be used to access the genomelink API.
+      def get_token(auth_code)
+        client.auth_code.get_token(auth_code, redirect_uri: get_config('GENOMELINK_CALLBACK_URL')).token
+      end
+
+      private
+      # gets the Oauth Client object
+      #
+      # @return [OAuth2::Client] A Oauth Client object.
+      def client
+        @client ||= OAuth2::Client.new( get_config('GENOMELINK_CLIENT_ID'),
+          get_config('GENOMELINK_CLIENT_SECRET'),
+          :site => OAUTH_PATH
+        )
+      end
+
+      # gets a gicen env variable, checks for existence and throws exception if not present
+      # @param config_name [String] key of the env variable
+      #
+      # @return [String] value of the env variable
+      def get_config(config_name)
+        raise ConfigNotFound, "Environment variable #{config_name} not found !" unless ENV[config_name]
+        ENV[config_name]
+      end
+    end
+  end
+end

data/lib/genomelink/reports.rb

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+module Genomelink
+  # Report class to represent the reports API
+  #
+  # @author [ashwin]
+  #
+  class Report < Base
+    attr_accessor :summary, :phenotype, :population, :scores
+    class << self
+      # Method to get the report for a given trait.
+      # @param trait [String] A particular trait to fetch details for.
+      # @param token [Sting] Access token to be used.
+      #
+      # @return [Report] A report object with summary, phenotype, population and scores.
+      def fetch(trait, token)
+        new get(path_to_trait(trait), token)
+      end
+
+      private
+      # Method to return the path to hit to get report of a trait
+      # @param trait [String] A particular trait to fetch details for.
+      #
+      # @return [String] path for the URL/request
+      def path_to_trait(trait)
+        "/v1/reports/#{trait}?population=european"
+      end
+    end
+  end
+end

data/lib/genomelink/version.rb

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+module Genomelink
+  VERSION = "0.1.0"
+end

metadata

@@ -0,0 +1,132 @@
+--- !ruby/object:Gem::Specification
+name: genomelink-ruby
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Ashwin Subramanian
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2018-04-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: oauth2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: This is a ruby gem to access the genome link APIs. It inclides the API
+  classes and the OAuth system.
+email:
+- s.ashwinkumar24902gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- genomelink-ruby.gemspec
+- lib/genomelink.rb
+- lib/genomelink/base.rb
+- lib/genomelink/genome.rb
+- lib/genomelink/oauth.rb
+- lib/genomelink/reports.rb
+- lib/genomelink/version.rb
+homepage: 
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.14
+signing_key: 
+specification_version: 4
+summary: Ruby Gem to access genome link APIs
+test_files: []