Updates byebug (development) to latest version. Stubs all remaining s…

…hared test frameworks (and they run!).

Gemfile.lock

@@ -9,9 +9,10 @@ GEM
   remote: https://rubygems.org/
   specs:
     awesome_print (1.2.0)
-    byebug (3.1.2)
+    byebug (3.4.0)
       columnize (~> 0.8)
       debugger-linecache (~> 1.2)
+      slop (~> 3.6)
     columnize (0.8.9)
     debugger-linecache (1.2.0)
     diff-lcs (1.2.5)
@@ -30,6 +31,7 @@ GEM
     rspec-mocks (3.1.0)
       rspec-support (~> 3.1.0)
     rspec-support (3.1.0)
+    slop (3.6.0)
 
 PLATFORMS
   ruby
@@ -38,6 +40,6 @@ DEPENDENCIES
   awesome_print
   bark!
   bundler (~> 1.5)
-  byebug
+  byebug (~> 3.4)
   rake
   rspec (~> 3.1)

README.md

@@ -4,12 +4,14 @@ bark
 [![Continuous Integration Status][6]][7]
 [![Dependency Status][8]][9]
 
-Bark is a Ruby Gem wrapper on the [Open Tree of Life API][3]. It was written over the course of the [OpenTree hackathon][2]  At present it seeks to provide a simple wrapper over all of the API calls available, returning a native json object for each response. It also acts as a sanity checker on the API calls themselves, running a suite of unity tests shared by related wrappers in [Python][5] and [R][4].
+Bark is a Ruby Gem wrapper on the [Open Tree of Life API][3]. It was written over the course of the [OpenTree hackathon][2]  At present it seeks to provide a simple wrapper over all of the API calls available, returning a native json object for each response. It also acts as a sanity checker on the API calls themselves, running a suite of unit tests shared by related wrappers in [Python][5] and [R][4].
 
 ## Installation
 
 _Bark has not yet been published to a gem repo!_
 
+Bark is written targetting Ruby 2.1.x.
+
 Add this line to your application's Gemfile:
 
     gem 'bark'

bark.gemspec

@@ -25,7 +25,7 @@ Gem::Specification.new do |spec|
 
   spec.add_development_dependency "bundler", "~> 1.5"
   spec.add_development_dependency "rake"
-  spec.add_development_dependency "byebug"
+  spec.add_development_dependency "byebug", "~> 3.4"
   spec.add_development_dependency "rspec", '~> 3.1'
   spec.add_development_dependency "awesome_print"
 

lib/bark.rb

@@ -11,6 +11,10 @@
 require_relative 'bark/request'
 require_relative 'bark/request/studies'
 require_relative 'bark/request/tree_of_life'
+require_relative 'bark/request/graph_of_life'
+require_relative 'bark/request/tnrs'
+require_relative 'bark/request/taxonomy'
+
 require_relative 'bark/response'
 
 class Bark

lib/bark/request/graph_of_life.rb

@@ -0,0 +1,76 @@
+class Bark::Request::GraphOfLife < Bark::Request
+
+    API_VERSION = 'v2'  
+    SEARCH_BASE = [Bark::Request::BASE_URL, API_VERSION, 'graph'].join("/")  
+
+    # Method: {parameters} 
+    METHODS = { 
+      gol_about: %i{},
+      gol_source_tree: %i{},
+      gol_node_info: %i{}, #  tree_id "is superflous and can be ignored"
+    }
+
+    # node_ids or ott_ids are required in some cases, so this
+    # will have to be cased 
+    REQUIRED_PARAMS = {
+    }
+
+    mrp = {}
+
+    REQUIRED_PARAMS.each do |k,v|
+      v.each do |m|
+        mrp[m].push(k) if mrp[m] 
+        mrp[m] ||= [k]
+      end
+    end
+
+    METHODS_REQUIRED_PARAMS = mrp
+
+    def initialize(method: :tol_about, params: {})
+      assign_options(method: method, params: params)
+      build_uri if valid?
+    end
+
+    def assign_options(method: method, params: params)
+      @method = method
+      @params = params
+      @params ||= {}
+    end
+
+    def valid?
+      raise "Method #{@method} not recognized." if @method && !self.class::METHODS.keys.include?(@method)
+      !@method.nil? && params_are_supported? && has_required_params?
+    end
+
+    def has_required_params?
+      case @method
+      when :gol_of_life
+      end
+     return true
+    end
+
+    def json_payload
+      JSON.generate(@params)
+    end
+
+    private 
+
+    # TODO: this doesn't feel right (or could be generalized out to superclass)
+    def build_uri
+      @uri = URI( SEARCH_BASE + '/' + send("#{@method}_url") )
+    end
+
+    def gol_about_url
+     'about' 
+    end
+
+    def gol_source_tree_url
+     'source_tree'
+    end
+
+    def gol_node_info_url
+      'node_info' 
+    end 
+
+
+  end

lib/bark/request/taxonomy.rb

@@ -0,0 +1,78 @@
+class Bark::Request::Taxonomy < Bark::Request
+
+    API_VERSION = 'v2'  
+    SEARCH_BASE = [Bark::Request::BASE_URL, API_VERSION, 'taxonomy'].join("/")  
+
+    # Method: {parameters} 
+    METHODS = { 
+      taxonomy_about: %i{},
+      taxonomy_lica: %i{},
+      taxonomy_subtree: %i{}, 
+      taxonomy_taxon: %i{}, 
+    }
+
+    REQUIRED_PARAMS = {
+    }
+
+    mrp = {}
+
+    REQUIRED_PARAMS.each do |k,v|
+      v.each do |m|
+        mrp[m].push(k) if mrp[m] 
+        mrp[m] ||= [k]
+      end
+    end
+
+    METHODS_REQUIRED_PARAMS = mrp
+
+    def initialize(method: :tol_about, params: {})
+      assign_options(method: method, params: params)
+      build_uri if valid?
+    end
+
+    def assign_options(method: method, params: params)
+      @method = method
+      @params = params
+      @params ||= {}
+    end
+
+    def valid?
+      raise "Method #{@method} not recognized." if @method && !self.class::METHODS.keys.include?(@method)
+      !@method.nil? && params_are_supported? && has_required_params?
+    end
+
+    def has_required_params?
+      case @method
+      when :taxonomy_about
+      end 
+      return true
+    end
+
+    def json_payload
+      JSON.generate(@params)
+    end
+
+    private 
+
+    # TODO: this doesn't feel right (or could be generalized out to superclass)
+    def build_uri
+      @uri = URI( SEARCH_BASE + '/' + send("#{@method}_url") )
+    end
+
+    def taxonomy_about_url
+      'about' 
+    end
+
+    def taxonomy_lica_url
+      'lica'
+    end
+
+    def taxonomy_subtree_url 
+      'subtree' 
+    end 
+
+    def taxonomy_taxon_url 
+      'taxon'
+    end
+
+  end

lib/bark/request/tnrs.rb

@@ -0,0 +1,75 @@
+class Bark::Request::Tnrs < Bark::Request
+
+    API_VERSION = 'v2'  
+    SEARCH_BASE = [Bark::Request::BASE_URL, API_VERSION, 'tnrs'].join("/")  
+
+    # Method: {parameters} 
+    METHODS = { 
+      tnrs_match_names: %i{},
+      tnrs_contexts: %i{},
+      tnrs_infer_context: %i{}, 
+    }
+
+    # node_ids or ott_ids are required in some cases, so this
+    # will have to be cased 
+    REQUIRED_PARAMS = {
+    }
+
+    mrp = {}
+
+    REQUIRED_PARAMS.each do |k,v|
+      v.each do |m|
+        mrp[m].push(k) if mrp[m] 
+        mrp[m] ||= [k]
+      end
+    end
+
+    METHODS_REQUIRED_PARAMS = mrp
+
+    def initialize(method: :tol_about, params: {})
+      assign_options(method: method, params: params)
+      build_uri if valid?
+    end
+
+    def assign_options(method: method, params: params)
+      @method = method
+      @params = params
+      @params ||= {}
+    end
+
+    def valid?
+      raise "Method #{@method} not recognized." if @method && !self.class::METHODS.keys.include?(@method)
+      !@method.nil? && params_are_supported? && has_required_params?
+    end
+
+    def has_required_params?
+     #case @method
+     #when :foo  
+     #end
+      return true
+    end
+
+    def json_payload
+      JSON.generate(@params)
+    end
+
+    private 
+
+    # TODO: this doesn't feel right (or could be generalized out to superclass)
+    def build_uri
+      @uri = URI( SEARCH_BASE + '/' + send("#{@method}_url") )
+    end
+
+    def tnrs_match_names_url 
+     'match_names' 
+    end
+
+    def tnrs_contexts_url
+     'contexts'
+    end
+
+    def tnrs_infer_context_url
+      'infer_context' 
+    end 
+
+  end

spec/lib/request/graph_of_life_spec.rb

@@ -0,0 +1,44 @@
+require 'spec_helper'
+
+describe Bark::Request::GraphOfLife do
+
+ #context 'Ruby/Bark specific implementation' do
+ #  specify 'is written for an API_VERSION' do
+ #    expect( Bark::Request::TreeOfLife::API_VERSION).to eq('v2')
+ #  end
+
+ #  specify 'has an SEARCH_BASE' do
+ #    expect( Bark::Request::TreeOfLife::SEARCH_BASE).to eq('http://devapi.opentreeoflife.org/v2/tree_of_life')
+ #  end
+
+ #  specify 'reference methods by ot API wrapper shared name in METHODS' do 
+ #    expect( Bark::Request::TreeOfLife::METHODS.keys.sort).to eq(%i{tol_about tol_mrca tol_subtree tol_induced_tree}.sort)
+ #  end
+
+ #  context 'building a request URI' do
+ #    specify 'for find_tree_of_life'  do
+ #      a = Bark::Request::TreeOfLife.new(method: :tol_about)
+ #      expect(a.uri.to_s).to eq('http://devapi.opentreeoflife.org/v2/tree_of_life/about')
+ #    end
+
+ #    specify 'for matched_tree_of_life' do
+ #      a = Bark::Request::TreeOfLife.new(method: :tol_mrca)
+ #      expect(a.uri.to_s).to eq('http://devapi.opentreeoflife.org/v2/tree_of_life/mrca')
+ #    end
+ #  end
+
+ #  context 'basic use, for :about, in a response' do
+ #    specify 'works' do
+ #      a = Bark::Request::TreeOfLife.new(method: :tol_about, params: {})
+ #      b = Bark::Response.new(request: a)
+ #      expect(b.request_succeeded?).to be(true)
+ #      expect(b.json.keys.include?('root_node_id')).to be(true)
+ #    end
+ #  end
+
+    context 'shared tests' do
+      run_tests(Bark::Request::GraphOfLife, SharedTestsHelper::SHARED_TESTS['graph_of_life'])
+    end
+
+ # end
+end 

spec/lib/request/taxonomy_spec.rb

@@ -0,0 +1,44 @@
+require 'spec_helper'
+
+describe Bark::Request::Taxonomy do
+
+ #context 'Ruby/Bark specific implementation' do
+ #  specify 'is written for an API_VERSION' do
+ #    expect( Bark::Request::TreeOfLife::API_VERSION).to eq('v2')
+ #  end
+
+ #  specify 'has an SEARCH_BASE' do
+ #    expect( Bark::Request::TreeOfLife::SEARCH_BASE).to eq('http://devapi.opentreeoflife.org/v2/tree_of_life')
+ #  end
+
+ #  specify 'reference methods by ot API wrapper shared name in METHODS' do 
+ #    expect( Bark::Request::TreeOfLife::METHODS.keys.sort).to eq(%i{tol_about tol_mrca tol_subtree tol_induced_tree}.sort)
+ #  end
+
+ #  context 'building a request URI' do
+ #    specify 'for find_tree_of_life'  do
+ #      a = Bark::Request::TreeOfLife.new(method: :tol_about)
+ #      expect(a.uri.to_s).to eq('http://devapi.opentreeoflife.org/v2/tree_of_life/about')
+ #    end
+
+ #    specify 'for matched_tree_of_life' do
+ #      a = Bark::Request::TreeOfLife.new(method: :tol_mrca)
+ #      expect(a.uri.to_s).to eq('http://devapi.opentreeoflife.org/v2/tree_of_life/mrca')
+ #    end
+ #  end
+
+ #  context 'basic use, for :about, in a response' do
+ #    specify 'works' do
+ #      a = Bark::Request::TreeOfLife.new(method: :tol_about, params: {})
+ #      b = Bark::Response.new(request: a)
+ #      expect(b.request_succeeded?).to be(true)
+ #      expect(b.json.keys.include?('root_node_id')).to be(true)
+ #    end
+ #  end
+
+    context 'shared tests' do
+      run_tests(Bark::Request::Taxonomy, SharedTestsHelper::SHARED_TESTS['taxonomy'])
+    end
+
+ #  end
+end