phenoscaperb 0.1.0

data/lib/phenoscaperb/constants.rb

@@ -0,0 +1,8 @@
+require 'net/http'
+
+NETWORKABLE_EXCEPTIONS = [Faraday::Error::ClientError,
+                          URI::InvalidURIError,
+                          Encoding::UndefinedConversionError,
+                          ArgumentError,
+                          NoMethodError,
+                          TypeError]

data/lib/phenoscaperb/error.rb

@@ -0,0 +1,22 @@
+module Phenoscape
+  # Custom error class for rescuing from all Phenoscape errors
+  class Error < StandardError; end
+
+  # Raised when Phenoscape returns the HTTP status code 400
+  class BadRequest < Error; end
+
+  # Raised when Phenoscape returns the HTTP status code 404
+  class NotFound < Error; end
+
+  # Raised when Phenoscape returns the HTTP status code 500
+  class InternalServerError < Error; end
+
+  # Raised when Phenoscape returns the HTTP status code 502
+  class BadGateway < Error; end
+
+  # Raised when Phenoscape returns the HTTP status code 503
+  class ServiceUnavailable < Error; end
+
+  # Raised when Phenoscape returns the HTTP status code 504
+  class GatewayTimeout < Error; end
+end

data/lib/phenoscaperb/faraday.rb

@@ -0,0 +1,71 @@
+require 'faraday'
+require 'multi_json'
+
+# @private
+module FaradayMiddleware
+  # @private
+  class RaiseHttpException < Faraday::Middleware
+    def call(env)
+      @app.call(env).on_complete do |response|
+        case response[:status].to_i
+        when 400
+          raise Phenoscape::BadRequest, error_message_400(response)
+        when 404
+          raise Phenoscape::NotFound, error_message_400(response)
+        when 500
+          raise Phenoscape::InternalServerError, error_message_500(response, "Something is technically wrong.")
+        when 502
+          raise Phenoscape::BadGateway, error_message_500(response, "The server returned an invalid or incomplete response.")
+        when 503
+          raise Phenoscape::ServiceUnavailable, error_message_500(response, "Crossref is rate limiting your requests.")
+        when 504
+          raise Phenoscape::GatewayTimeout, error_message_500(response, "504 Gateway Time-out")
+        end
+      end
+    end
+
+    def initialize(app)
+      super app
+      @parser = nil
+    end
+
+    private
+
+    def error_message_400(response)
+      "\n   #{response[:method].to_s.upcase} #{response[:url].to_s}\n   Status #{response[:status]}#{error_body(response[:body])}"
+    end
+
+    def error_body(body)
+      if not body.nil? and not body.empty? and body.kind_of?(String)
+        if is_json?(body)
+          body = ::MultiJson.load(body)
+          if body['message'].nil?
+            body = nil
+          elseif body['message'].length == 1
+            body = body['message']
+          else
+            body = body['message'].collect { |x| x['message'] }.join('; ')
+          end
+        end
+      end
+
+      if body.nil?
+        nil
+      else
+        ": #{body}"
+      end
+    end
+
+    def error_message_500(response, body=nil)
+      "#{response[:method].to_s.upcase} #{response[:url].to_s}: #{[response[:status].to_s + ':', body].compact.join(' ')}"
+    end
+
+    def is_json?(string)
+      MultiJson.load(string)
+      return true
+    rescue MultiJson::ParseError
+      return false
+    end
+
+  end
+end

data/lib/phenoscaperb/helpers/configuration.rb

@@ -0,0 +1,26 @@
+# taken from: https://viget.com/extend/easy-gem-configuration-variables-with-defaults
+module Configuration
+
+  def configuration
+    yield self
+  end
+
+  def define_setting(name, default = nil)
+    class_variable_set("@@#{name}", default)
+    define_class_method "#{name}=" do |value|
+      class_variable_set("@@#{name}", value)
+    end
+    define_class_method name do
+      class_variable_get("@@#{name}")
+    end
+  end
+
+  private
+
+  def define_class_method(name, &block)
+    (class << self; self; end).instance_eval do
+      define_method name, &block
+    end
+  end
+
+end

data/lib/phenoscaperb/request.rb

@@ -0,0 +1,74 @@
+require "faraday"
+require "multi_json"
+require "nokogiri"
+require "phenoscaperb/error"
+require "phenoscaperb/constants"
+require 'phenoscaperb/utils'
+require 'phenoscaperb/helpers/configuration'
+
+##
+# Phenoscape::Request
+#
+# Class to perform HTTP requests to the Phenoscape API
+module Phenoscape
+  class Request #:nodoc:
+
+    attr_accessor :endpt
+    attr_accessor :args
+    attr_accessor :verbose
+    attr_accessor :options
+    attr_accessor :ret
+    attr_accessor :acchd
+
+    def initialize(endpt, args, verbose, options, ret, acchd = "application/json")
+      self.endpt = endpt
+      self.args = args
+      self.verbose = verbose
+      self.options = options
+      self.ret = ret
+      self.acchd = acchd
+    end
+
+    def perform
+      if verbose
+        conn = Faraday.new(:url => Phenoscape.base_url, :request => self.options || []) do |f|
+          f.response :logger
+          f.use FaradayMiddleware::RaiseHttpException
+          f.options.params_encoder = Faraday::FlatParamsEncoder
+          f.adapter  Faraday.default_adapter
+        end
+      else
+        conn = Faraday.new(:url => Phenoscape.base_url, :request => self.options || []) do |f|
+          f.use FaradayMiddleware::RaiseHttpException
+          f.options.params_encoder = Faraday::FlatParamsEncoder
+          f.adapter  Faraday.default_adapter
+        end
+      end
+
+      conn.headers[:user_agent] = make_ua
+      conn.headers["X-USER-AGENT"] = make_ua
+      if !self.acchd.nil?
+        conn.headers["Accept"] = self.acchd
+      end
+
+      res = conn.get self.endpt, self.args
+      
+      if !res.headers['content-type'].match(/json/).nil?
+        out = MultiJson.load(res.body)
+      else  
+        case self.ret
+        when "hash"
+          out = Nokogiri::XML(res.body).to_hash
+        when "text"
+          out = res.body
+        when "noko"
+          out = Nokogiri::XML(res.body)
+        end
+      end
+
+      return out
+
+    end
+
+  end
+end

data/lib/phenoscaperb/utils.rb

@@ -0,0 +1,43 @@
+def make_ua
+	requa = 'Faraday/v' + Faraday::VERSION
+  habua = 'Phenoscaperb/v' + Phenoscape::VERSION
+  return requa + ' ' + habua
+end
+
+class Hash
+	def tostrings
+		Hash[self.map{|(k,v)| [k.to_s,v]}]
+	end
+end
+
+class Hash
+	def tosymbols
+		Hash[self.map{|(k,v)| [k.to_sym,v]}]
+	end
+end
+
+def check_data(x, y)
+  if len2(x) == 1
+    testdata = [x]
+  else
+    testdata = x
+  end
+
+  for z in testdata
+    if !y.include? z
+      raise z + ' is not one of the choices'
+    end
+  end
+end
+
+def len2(x)
+  if x.class == String
+    return [x].length
+  else
+    return x.length
+  end
+end
+
+def stop(x)
+  raise ArgumentError, x
+end

data/lib/phenoscaperb/version.rb

@@ -0,0 +1,3 @@
+module Phenoscape
+  VERSION = "0.1.0"
+end

data/phenoscaperb.gemspec

@@ -0,0 +1,40 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'phenoscaperb/version'
+
+Gem::Specification.new do |s|
+  s.name        = 'phenoscaperb'
+  s.version     = Phenoscape::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.required_ruby_version = '>= 2.0'
+  s.date        = '2017-12-11'
+  s.summary     = "Phenoscape Client"
+  s.description = "Low Level Ruby Client for the Phenoscape API"
+  s.authors     = "Scott Chamberlain"
+  s.email       = 'myrmecocystus@gmail.com'
+  s.homepage    = 'https://github.com/sckott/phenoscaperb'
+  s.licenses    = 'MIT'
+
+  s.files = `git ls-files -z`.split("\x0").reject {|f| f.match(%r{^(test|spec|features)/}) }
+  s.require_paths = ["lib"]
+
+  s.bindir      = 'bin'
+  s.executables = ['ph']
+
+  s.add_development_dependency 'bundler', '~> 1.14', '>= 1.14.6'
+  s.add_development_dependency 'rake', '~> 12.0', '>= 12.0.0'
+  s.add_development_dependency 'test-unit', '~> 3.2', '>= 3.2.1'
+  s.add_development_dependency 'simplecov', '~> 0.14.1'
+  s.add_development_dependency 'codecov', '~> 0.1.10'
+  s.add_development_dependency 'json', '~> 2.0', '>= 2.0.3'
+  s.add_development_dependency 'vcr', '~> 3.0', '>= 3.0.3'
+  s.add_development_dependency 'webmock', '~> 2.3', '>= 2.3.2'
+
+  s.add_runtime_dependency 'faraday', '~> 0.12.0.1'
+  s.add_runtime_dependency 'faraday_middleware', '~> 0.11.0.1'
+  s.add_runtime_dependency 'thor', '~> 0.20.0'
+  s.add_runtime_dependency 'nokogiri', '~> 1.8', '>= 1.8.1'
+  s.add_runtime_dependency 'xml-to-hash', '~> 1.0', '>= 1.0.3'
+  s.add_runtime_dependency 'multi_json', '~> 1.12', '>= 1.12.1'
+end

metadata

@@ -0,0 +1,318 @@
+--- !ruby/object:Gem::Specification
+name: phenoscaperb
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Scott Chamberlain
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2017-12-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.14.6
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.14.6
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.0.0
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.2.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.2.1
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.14.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.14.1
+- !ruby/object:Gem::Dependency
+  name: codecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.10
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.10
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.3
+- !ruby/object:Gem::Dependency
+  name: vcr
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.3
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.3.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.3.2
+- !ruby/object:Gem::Dependency
+  name: faraday
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.12.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.12.0.1
+- !ruby/object:Gem::Dependency
+  name: faraday_middleware
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.11.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.11.0.1
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.20.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.20.0
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.1
+- !ruby/object:Gem::Dependency
+  name: xml-to-hash
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.3
+- !ruby/object:Gem::Dependency
+  name: multi_json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.12.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.12.1
+description: Low Level Ruby Client for the Phenoscape API
+email: myrmecocystus@gmail.com
+executables:
+- ph
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- CHANGELOG.md
+- CONDUCT.md
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.md
+- Rakefile
+- bin/ph
+- lib/phenoscaperb.rb
+- lib/phenoscaperb/Genes.rb
+- lib/phenoscaperb/Ontotrace.rb
+- lib/phenoscaperb/Studies.rb
+- lib/phenoscaperb/Taxa.rb
+- lib/phenoscaperb/Terms.rb
+- lib/phenoscaperb/constants.rb
+- lib/phenoscaperb/error.rb
+- lib/phenoscaperb/faraday.rb
+- lib/phenoscaperb/helpers/configuration.rb
+- lib/phenoscaperb/request.rb
+- lib/phenoscaperb/utils.rb
+- lib/phenoscaperb/version.rb
+- phenoscaperb.gemspec
+homepage: https://github.com/sckott/phenoscaperb
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '2.0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.13
+signing_key: 
+specification_version: 4
+summary: Phenoscape Client
+test_files: []