scientific_protocols 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
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+  data.tar.gz: a1004217252c2cab20a837495d5c4d3274e67332
+SHA512:
+  metadata.gz: 065e0ba01ef90d1bbd4e7b2b7d7bd204b1f47d3e315cbd21de3074922c0c38c2d282c4a32d725462209cb89b73196c7c4cdfa6bd144c2d30d84bba0bea634270
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/spec/fixtures/vcr_cassettes/
+/tmp/
+.idea/
+*.bundle
+*.so
+*.o
+*.a
+*.gem
+mkmf.log

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in scientificprotocols.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 David Iorns
+
+MIT License
+
+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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+# Scientific Protocols Ruby Client
+
+A Ruby wrapper for the Scientific Protocols API.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'scientific_protocols'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install scientific_protocols
+
+## Usage
+
+Get protocols.
+```
+protocols = ScientificProtocols.client.get_protocols
+
+protocols.each do |protocol|
+  puts protocol
+end
+```
+
+Get a protocol.
+```
+protocol = ScientificProtocols.client.get_protocol(id: 'beta-glactasidase-stain')
+
+puts protocol
+
+{
+   "id":"beta-glactasidase-stain",
+   "url":"https://www.scientificprotocols.org/api/v1/protocols/beta-glactasidase-stain",
+   "title":"Beta-Glactasidase Stain",
+   "description":"\r\n\r\n### Solutions\r\n\r\n1. Solution A\r\n...",
+   "gist_id":"315e630a1fe9fe6e9bab",
+   "html_url":"https://www.scientificprotocols.org/protocols/beta-glactasidase-stain",
+   "discussion_html_url":"https://www.scientificprotocols.org/protocols/beta-glactasidase-stain/discussion",
+   "tags":[
+      "Histology"
+   ],
+   "author":{
+      "username":"scientificprotocols",
+      "html_url":"https://www.scientificprotocols.org/users/scientificprotocols"
+   },
+   "created_at":"2014-07-09T18:59:17.254Z",
+   "updated_at":"2014-07-09T18:59:17.254Z"
+}
+```
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/scientificprotocols-ruby-client/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+

data/lib/scientificprotocols.rb

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+require 'scientificprotocols/version'
+
+module ScientificProtocols
+  autoload :Client, 'scientificprotocols/client'
+  autoload :DSL, 'scientificprotocols/dsl'
+  autoload :Resources, 'scientificprotocols/resources'
+  autoload :Errors, 'scientificprotocols/errors'
+  autoload :Utils, 'scientificprotocols/utils'
+
+  class << self
+    # @return [String]
+    attr_accessor :api_key
+    attr_accessor :logger
+  end
+
+  module_function
+
+  # @return [ScientificProtocols::Client]
+  def client
+    @client ||= Client.new()
+  end
+end

data/lib/scientificprotocols/client.rb

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+require 'faraday'
+require 'json'
+require 'openssl'
+require 'active_support/all'
+require 'scientificprotocols/dsl'
+require 'scientificprotocols/errors'
+require 'scientificprotocols/utils'
+
+module ScientificProtocols
+  class Client
+    include DSL
+    include Errors
+    include Utils
+
+    URL = 'https://www.scientificprotocols.org/api/v1/'
+    REQUESTS = [:get, :post, :put, :delete]
+    HEADERS = {'Accept' => 'application/json', 'Content-Type' => 'application/json'}
+
+    def initialize
+      # Setup HTTP request connection to Zenodo.
+      @connection ||= Faraday.new do |builder|
+        builder.request :multipart
+        builder.request :url_encoded
+        builder.response :logger
+        builder.adapter Faraday.default_adapter
+      end
+    end
+
+    # @param [:get, :post, :put, :delete] method.
+    # @param [String] path.
+    # @param [Hash] query (optional).
+    # @param [Hash] headers request headers (optional).
+    # @raise [ArgumentError] If the response is blank.
+    # @raise [ResourceNotFoundError] If the response code is 404.
+    # @raise [ClientError] If the response code is not in the success range.
+    # @return [Faraday::Response] server response.
+    def request(method, path, query = {}, headers = HEADERS)
+      raise ArgumentError, "Unsupported method #{method.inspect}. Only :get, :post, :put, :delete are allowed" unless REQUESTS.include?(method)
+
+      payload = nil
+      if query.present?
+        accept = headers.present? ? headers['Accept'] : nil
+        if accept.present? && accept == 'application/json'
+          payload = JSON.generate(query)
+        else
+          payload = query
+        end
+      end
+      response = @connection.run_request(method, "#{URL}#{path}", payload, headers)
+
+      case response.status.to_i
+        when 200..299
+          return response
+        when 404
+          raise ResourceNotFoundError.new(response: response)
+        else
+          raise ClientError.new(response: response)
+      end
+    end
+  end
+end

data/lib/scientificprotocols/dsl.rb

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+require 'scientificprotocols'
+
+module ScientificProtocols
+  module DSL
+  end
+end
+
+require 'scientificprotocols/dsl/protocols'
+require 'scientificprotocols/utils'
+require 'mime-types'
+
+module ScientificProtocols
+  module DSL
+    include Protocols
+    include Utils
+  end
+end
+

data/lib/scientificprotocols/dsl/protocols.rb

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+require 'scientificprotocols/dsl'
+
+module ScientificProtocols
+  module DSL::Protocols
+    # GET /Protocols
+    # Get protocols.
+    # @return [Array, nil].
+    def get_protocols
+      Resources::Protocol.parse(request(:get, 'protocols/', nil, nil))
+    end
+
+    # GET /Protocol/{id}
+    # Get a protocol.
+    # @param [String] id A protocol's ID.
+    # @raise [ArgumentError] If the method arguments are blank.
+    # @return [ScientificProtocols::Resources::protocol, nil].
+    def get_protocol(id:)
+      raise ArgumentError, 'ID cannot be blank' if id.blank?
+      Resources::Protocol.parse(request(:get, "protocols/#{id}"))
+    end
+  end
+end

data/lib/scientificprotocols/errors.rb

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+require 'scientificprotocols'
+
+module ScientificProtocols
+  module Errors
+  end
+end
+
+require 'scientificprotocols/errors/resource_not_found_error'
+require 'scientificprotocols/errors/client_error'
+

data/lib/scientificprotocols/errors/client_error.rb

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+module ScientificProtocols
+  module Errors
+    class ClientError < StandardError
+      def initialize(response:)
+        @response = response
+      end
+    end
+  end
+end

data/lib/scientificprotocols/errors/resource_not_found_error.rb

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+require 'scientificprotocols/errors/client_error'
+
+module ScientificProtocols
+  module Errors
+    class ResourceNotFoundError < ClientError
+    end
+  end
+end

data/lib/scientificprotocols/resources.rb

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+require 'scientificprotocols'
+
+module ScientificProtocols
+  module Resources
+  end
+end
+
+require 'scientificprotocols/resources/object'
+require 'scientificprotocols/resources/protocol'
+

data/lib/scientificprotocols/resources/object.rb

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+require 'delegate'
+require 'json'
+require 'time'
+
+module ScientificProtocols
+  module Resources
+    class Object < SimpleDelegator
+      require 'scientificprotocols/resources/object/serializers'
+      require 'scientificprotocols/resources/object/attributes'
+
+      include Serializers
+      include Attributes
+
+      # Define common attributes, applicable to different resources
+      attribute :date_created_utc, Time
+      attribute :date_updated_utc, Time
+
+      def inspect
+        "#<#{self.class.name}:#{'0x00%x' % (object_id << 1)} #{inspect_attributes}>"
+      end
+
+      private
+
+      def inspect_attributes
+        attributes.map { |key, value| "@#{key}=#{value.inspect}" }.join(' ')
+      end
+    end
+  end
+end

data/lib/scientificprotocols/resources/object/attributes.rb

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+module ScientificProtocols::Resources::Object::Attributes
+  module ClassMethods
+    def attributes
+      @attributes ||=
+        begin
+          if superclass.respond_to?(:attributes)
+            superclass.attributes.dup
+          else
+            Hash.new { |hash, key| hash[key] = ::Object }
+          end
+        end
+    end
+
+    # @return [Module] module holding all attribute accessors
+    def attributes_module
+      @attributes_module ||= const_set(:AttributeMethods, Module.new)
+    end
+
+    def define_attribute_accessor(name, type = nil)
+      type ||= attributes[name.to_sym] || Object
+      attributes_module.send(:define_method, name) do
+        deserialize_attribute(name, type)
+      end
+    end
+
+    def attribute(name, type = String)
+      attributes[name] = type
+
+      define_attribute_accessor(name, type)
+    end
+
+    alias_method :has_many, :attribute
+  end
+
+  def self.included(base)
+    base.extend(ClassMethods)
+    super
+  end
+
+  def attributes
+    {}.tap do |result|
+      __getobj__.keys.each do |key|
+        attribute = key.to_s.downcase
+        result[attribute] = public_send(attribute)
+      end
+    end
+  end
+
+  def method_missing(name, *args, &block)
+    attribute = name.to_s.upcase
+    if __getobj__.key?(attribute)
+      self.class.define_attribute_accessor(name)
+      deserialize_attribute(name, self.class.attributes[name.to_sym])
+    else
+      super
+    end
+  end
+
+  private
+
+  def respond_to_missing?(name, include_all = false)
+    __getobj__.key?(name.to_s.upcase) || super(name, include_all)
+  end
+
+  # @param [String, Symbol] name
+  # @param [Class, #to_s] type
+  def deserialize_attribute(name, type)
+    raw = __getobj__[name.to_s.upcase]
+    self.class.serializer_for(type).deserialize(raw)
+  end
+end

data/lib/scientificprotocols/resources/object/serializers.rb

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+require 'logger'
+module ScientificProtocols
+  module Resources
+    class Object
+      module Serializers
+        module Object
+          def self.serialize(value)
+            value.to_s
+          end
+
+          def self.deserialize(value)
+            case value
+              when Array
+                value.map { |v| v.deep_transform_keys{ |key| key.downcase } }
+              when Hash
+                value.deep_transform_keys{ |key| key.downcase }
+              else
+                value
+            end
+          end
+        end
+
+        module Time
+          def self.serialize(value)
+            value.utc.xmlschema
+          end
+
+          def self.deserialize(value)
+            ::Time.parse(value)
+          end
+        end
+
+        module ClassMethods
+          # @return [Hash] corresponding serializers for different attributes
+          def serializers
+            @serializers ||= {}
+          end
+
+          # @param [String, Symbol] type type of attribute to be serialized or deserialized
+          # @return [#serialize, #deserialize] serializer for provided type
+          def serializer_for(type)
+            serializers[type] ||=
+              begin
+                class_symbol = type.to_s.to_sym
+                if type.respond_to?(:deserialize) && type.respond_to?(:serialize)
+                  type
+                elsif Serializers.constants.include?(class_symbol)
+                  Serializers.const_get(class_symbol)
+                elsif Resources.constants.include?(class_symbol)
+                  Resources.const_get(class_symbol)
+                else
+                  Serializers::Object
+                end
+              end
+          end
+
+          # Deserialize a Faraday response.
+          # @param [Faraday::Response] response.
+          # @raise [ArgumentError] If the response is blank.
+          # @return [Object, nil].
+          def deserialize(response)
+            raise ArgumentError, "Response cannot be blank" if response.blank?
+
+            attributes = response.body
+            begin
+              attributes = JSON.parse(response.body)
+              case attributes
+                when Array
+                  return attributes.map { |object| new(object) }
+                when Hash
+                  return new(attributes)
+              end
+            rescue JSON::ParserError
+              logger = Logger.new(STDOUT)
+              logger.error("Could not parse: #{response.body}")
+            end
+            nil
+          end
+
+          alias_method :parse, :deserialize
+
+          def serialize(object)
+            object.serialize
+          end
+        end
+
+        def self.included(base)
+          super
+          base.extend ClassMethods
+        end
+
+        def serialize
+          {}.tap do |result|
+            attributes.each do |name, value|
+              result[name.upcase] = self.class.serializer_for(name).serialize(value)
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/scientificprotocols/resources/protocol.rb

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+require 'scientificprotocols/resources/object'
+
+module ScientificProtocols
+  module Resources
+    class Protocol < ScientificProtocols::Resources::Object
+
+    end
+  end
+end

data/lib/scientificprotocols/utils.rb

@@ -0,0 +1,8 @@
+require 'scientificprotocols'
+
+module ScientificProtocols
+  module Utils
+  end
+end
+
+require 'scientificprotocols/utils/url_helper'

data/lib/scientificprotocols/utils/url_helper.rb

@@ -0,0 +1,17 @@
+module ScientificProtocols
+  module Utils
+    class UrlHelper
+      # Build a URL with a querystring containing optional params if supplied.
+      # @param [UrlHelper] path The name of the resource path as per the URL e.g. contacts.
+      # @param [Hash] params A hash of params we're turning into a querystring.
+      # @return [UrlHelper] The URL of the resource with required params.
+      def self.build_url(path:, params:)
+        params.delete_if {|k,v| v.blank?}
+        params = params.to_query
+        query = path
+        query << ('?' + params) unless params.blank?
+        query
+      end
+    end
+  end
+end

data/lib/scientificprotocols/version.rb

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+module ScientificProtocols
+  VERSION = '0.0.1'
+end

data/scientificprotocols.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'scientificprotocols/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'scientific_protocols'
+  spec.version       = ScientificProtocols::VERSION
+  spec.authors       = ['David Iorns']
+  spec.email         = ['david.iorns@gmail.com']
+  spec.summary       = %q{A Ruby wrapper for the Scientific Protocols API.}
+  spec.homepage      = 'https://www.scientificprotocols.org'
+  spec.license       = 'MIT'
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ['lib']
+
+  spec.add_dependency 'faraday'
+  spec.add_dependency 'activesupport'
+  spec.add_dependency 'mime-types'
+
+  spec.add_development_dependency 'bundler', '~> 1.7'
+  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'rspec', '~> 3.0.0'
+  spec.add_development_dependency 'webmock', '~> 1.18.0'
+  spec.add_development_dependency 'vcr'
+end

data/spec/scientificprotocols/client_spec.rb

@@ -0,0 +1,5 @@
+require 'spec_helper'
+
+describe ScientificProtocols::Client do
+  subject(:client) { ScientificProtocols::Client.new }
+end

data/spec/scientificprotocols/dsl/protocols_spec.rb

@@ -0,0 +1,23 @@
+require 'spec_helper'
+
+describe ScientificProtocols::DSL::Protocols do
+  # GET /protocols
+  describe '#get_protocols' do
+    it 'returns an array of protocols' do
+      VCR.use_cassette('get_protocols') do
+        protocols = ScientificProtocols.client.get_protocols
+        expect(protocols).to be_a(Array)
+        expect(protocols.first).to be_a(Protocol)
+      end
+    end
+  end
+  
+  # GET /protocols/{id}
+  describe '#get_protocol' do
+    it 'returns a protocol' do
+      VCR.use_cassette('get_protocol') do
+        expect(ScientificProtocols.client.get_protocol(id: 'beta-glactasidase-stain')).to be_a(Protocol)
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,9 @@
+require 'webmock/rspec'
+require 'scientificprotocols'
+require 'vcr'
+include ScientificProtocols::Resources
+
+VCR.configure do |c|
+  c.cassette_library_dir = 'spec/fixtures/vcr_cassettes'
+  c.hook_into :webmock
+end

metadata

@@ -0,0 +1,184 @@
+--- !ruby/object:Gem::Specification
+name: scientific_protocols
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- David Iorns
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-12-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: faraday
+  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'
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  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'
+- !ruby/object:Gem::Dependency
+  name: mime-types
+  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'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !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: 3.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.18.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.18.0
+- !ruby/object:Gem::Dependency
+  name: vcr
+  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'
+description: 
+email:
+- david.iorns@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/scientificprotocols.rb
+- lib/scientificprotocols/client.rb
+- lib/scientificprotocols/dsl.rb
+- lib/scientificprotocols/dsl/protocols.rb
+- lib/scientificprotocols/errors.rb
+- lib/scientificprotocols/errors/client_error.rb
+- lib/scientificprotocols/errors/resource_not_found_error.rb
+- lib/scientificprotocols/resources.rb
+- lib/scientificprotocols/resources/object.rb
+- lib/scientificprotocols/resources/object/attributes.rb
+- lib/scientificprotocols/resources/object/serializers.rb
+- lib/scientificprotocols/resources/protocol.rb
+- lib/scientificprotocols/utils.rb
+- lib/scientificprotocols/utils/url_helper.rb
+- lib/scientificprotocols/version.rb
+- scientificprotocols.gemspec
+- spec/scientificprotocols/client_spec.rb
+- spec/scientificprotocols/dsl/protocols_spec.rb
+- spec/spec_helper.rb
+homepage: https://www.scientificprotocols.org
+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: 2.4.4
+signing_key: 
+specification_version: 4
+summary: A Ruby wrapper for the Scientific Protocols API.
+test_files:
+- spec/scientificprotocols/client_spec.rb
+- spec/scientificprotocols/dsl/protocols_spec.rb
+- spec/spec_helper.rb
+has_rdoc: