assaydepot 0.0.2 → 0.0.3

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 5565b98889ea2e4abfde64c7a86b9f10bb7007d9
+  data.tar.gz: 3637b96d37f982f765c312d15cd1b98cbf2ad728
+SHA512:
+  metadata.gz: d465642914b663fec3017aa5c50e32a7b9a83eee1220a27a199f9f718ad5599fbfc8b4ede16c8596a5fe388d9900d9291e6e6bc7338e244f68dc9a0962f45a63
+  data.tar.gz: b9793e07b1c15fc4d53ac949c21b534a27bfcbf4c5f532baec682af4281c3b4a414b1df4727aedb0e1de555436335450205922d2d9d57c3b2dbbd3149a6e3d06

data/.travis.yml

@@ -0,0 +1,5 @@
+before_script:
+  - export ASSAYDEPOT_APP_ID=6hH3KQZz9oqR5lqtckyqfAUcyfNgHQ
+  - export ASSAYDEPOT_APP_SECRET=FDwDYchR220FSYDPtqS12e-P0pjx-7y_tbba3wyr-3VschLuVgpvOBBL
+script:
+  - bundle exec rake spec

data/LICENSE.md

@@ -0,0 +1,10 @@
+#The MIT License (MIT)
+
+Copyright (c) 2012 Assay Depot
+
+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

@@ -1,4 +1,4 @@
-# Assay Depot
+# Assay Depot ![Build Status](https://secure.travis-ci.org/assaydepot/assaydepot-rb.png) [![Code Climate](https://codeclimate.com/badge.png)](https://codeclimate.com/github/assaydepot/assaydepot-rb)
 
 Ruby interface for Assay Depot's online laboratory (http://www.assaydepot.com).
 
@@ -66,3 +66,7 @@ AssayDepot::Provider.get(providers.first["id"])
 3. Commit your changes (`git commit -am 'Added some feature'`)
 4. Push to the branch (`git push origin my-new-feature`)
 5. Create new Pull Request
+
+## License
+
+The Assay Depot Ruby SDK is released under the MIT license.

data/Rakefile

@@ -1,2 +1,8 @@
 #!/usr/bin/env rake
 require "bundler/gem_tasks"
+
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec)
+
+task :test => :spec
+task :default => :spec

data/assaydepot.gemspec

@@ -9,11 +9,15 @@ Gem::Specification.new do |gem|
   gem.homepage      = "https://github.com/assaydepot/assaydepot-rb"
 
   gem.add_dependency('json')
+  gem.add_development_dependency('rake')
+  gem.add_development_dependency('rspec')
+  gem.add_development_dependency('oauth2')
 
   gem.files         = `git ls-files`.split($\)
   gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
   gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
   gem.name          = "assaydepot"
   gem.require_paths = ["lib"]
+  
   gem.version       = AssayDepot::VERSION
 end

data/lib/assaydepot.rb

@@ -4,23 +4,4 @@ require "assaydepot/client"
 require "assaydepot/model"
 require "assaydepot/ware"
 require "assaydepot/provider"
-
-# Twitter.configure do |config|
-#   config.consumer_key = YOUR_CONSUMER_KEY
-#   config.consumer_secret = YOUR_CONSUMER_SECRET
-#   config.oauth_token = YOUR_OAUTH_TOKEN
-#   config.oauth_token_secret = YOUR_OAUTH_TOKEN_SECRET
-# end
-
-module AssayDepot
-  class << self
-    include AssayDepot::Configurable
-  end
-
-  # Delegate to a AssayDepot::Client
-  #
-  # @return [AssayDepot::Client]
-  def client
-    AssayDepot::Client.new(options)
-  end
-end
+require "assaydepot/core"

data/lib/assaydepot/client.rb

@@ -8,11 +8,11 @@ module AssayDepot
     end
 
     def search_url(params={})
-      "#{AssayDepot.url}/#{@search_type}.json?#{params.collect { |k,v| "#{k}=#{v.to_s.gsub(" ","+")}"}.join("&")}"
+      "#{AssayDepot.url}/#{@search_type}.json"
     end
 
     def get_url(id, params={})
-      "#{AssayDepot.url}/#{@search_type}/#{id}.json?#{params.collect { |k,v| "#{k}=#{v.to_s.gsub(" ","+")}"}.join("&")}"
+      "#{AssayDepot.url}/#{@search_type}/#{id}.json"
     end
 
     def search(query, facets, params={})
@@ -21,12 +21,16 @@ module AssayDepot
       facets.map do |name,value|
         params["facets[#{name}][]"] = value
       end
-      JSON.parse(open(search_url(params)).read)
+      execute(search_url, params)
     end
 
     def get(id, params={})
       params["access_token"] = AssayDepot.access_token
-      JSON.parse(open(get_url(id, params)).read)
+      execute(get_url(id), params)
+    end
+
+    def execute(url, params)
+      JSON.parse(open("#{url}?#{params.collect { |k,v| "#{k}=#{v.to_s.gsub(" ","+")}"}.join("&")}").read)
     end
   end
 end

data/lib/assaydepot/core.rb

@@ -0,0 +1,12 @@
+module AssayDepot
+  class << self
+    include ::AssayDepot::Configurable
+  end
+
+  # Delegate to a AssayDepot::Client
+  #
+  # @return [AssayDepot::Client]
+  def client
+    ::AssayDepot::Client.new(options)
+  end
+end

data/lib/assaydepot/model.rb

@@ -79,7 +79,7 @@ module AssayDepot
 
       def find(query)
         result = self.clone
-        result.search_query = search_query
+        result.search_query = query
         result
       end
 

data/lib/assaydepot/provider.rb

@@ -1,6 +1,6 @@
 module AssayDepot
   class Provider
-    include Model
+    include ::AssayDepot::Model
 
     def self.search_type
       "providers"

data/lib/assaydepot/version.rb

@@ -1,3 +1,3 @@
 module AssayDepot
-  VERSION = "0.0.2"
+  VERSION = "0.0.3"
 end

data/lib/assaydepot/ware.rb

@@ -1,6 +1,6 @@
 module AssayDepot
   class Ware
-    include Model
+    include ::AssayDepot::Model
 
     def self.search_type
       "wares"

data/spec/assaydepot_spec.rb

@@ -0,0 +1,128 @@
+require 'oauth2'
+require 'assaydepot'
+
+describe AssayDepot do
+  let(:site) { "https://staging.assaydepot.com" }
+
+  context "when accessing the api via oauth2 client credentials" do
+    let(:client) { 
+      OAuth2::Client.new( ENV["ASSAYDEPOT_APP_ID"],
+                          ENV["ASSAYDEPOT_APP_SECRET"],
+                          :site => site)
+    }
+    let(:access_token) { client.client_credentials.get_token(:redirect_uri => 'http://localhost:4567/oauth2/callback') }
+    before(:all) do
+      AssayDepot.configure do |config|
+        config.access_token = access_token.token
+        config.url = "#{site}/api"
+      end
+    end
+
+    context "and searching for wares matching \"antibody\"" do
+      let(:wares) { AssayDepot::Ware.find("antibody") }
+
+      it "should return a Ware object" do
+        wares.class.should == AssayDepot::Ware
+      end
+
+      it "should return some wares" do
+        wares.total.should > 1
+      end
+
+      context "and getting the details for the first ware" do
+        let(:ware_result) { AssayDepot::Ware.get(wares.first["id"]) }
+
+        it "should have a ware" do
+          ware_result["ware"].should_not be_nil
+        end
+
+        it "should have a description" do
+          ware_result["ware"]["description"].should_not be_nil
+        end
+      end
+    end
+
+    context "when searching for wares of type CustomService" do
+      let(:wares) { AssayDepot::Ware.where(:ware_type => "CustomService") }
+      it "should return facets" do
+        wares.facets.should_not be_empty
+      end
+
+      it "should include the source facet" do
+        wares.facets.should include("source")
+      end
+
+      it "should include the ware_type facet" do
+        wares.facets.should include("ware_type")
+      end
+
+      it "should include the available_provider_names facet" do
+        wares.facets.should include("available_provider_names")
+      end
+
+      it "should include the certifications facet" do
+        wares.facets.should include("certifications")
+      end
+
+      it "should include the countries facet" do
+        wares.facets.should include("countries")
+      end
+
+      it "should include the protein_type facet" do
+        wares.facets.should include("protein_type")
+      end
+
+      it "should include the clonality facet" do
+        wares.facets.should include("clonality")
+      end
+
+      it "should include the cell_source facet" do
+        wares.facets.should include("cell_source")
+      end
+
+      it "should include the species facet" do
+        wares.facets.should include("species")
+      end
+
+      it "should include the tissue facet" do
+        wares.facets.should include("tissue")
+      end
+    end
+
+    context "when searching for wares using a chained query" do
+      let(:wares) { AssayDepot::Ware.where(:ware_type => "CustomService").where(:available_provider_names => "Assay Depot").page(2) }
+
+      it "should return wares" do
+        wares.total.should > 1
+      end
+
+      it "the ware's name should be available" do
+        wares.first["name"].should_not be_nil
+      end
+    end
+
+    context "and searching for providers that start with the letter a" do
+      let(:providers) { AssayDepot::Provider.where(:starts_with => "a").per_page(50) }
+ 
+      it "should return a Provider object" do
+        providers.class.should == AssayDepot::Provider
+      end
+
+      it "should return some providers" do
+        providers.total.should > 1
+      end
+
+      context "and getting the details for the first provider" do
+        let(:provider_result) { AssayDepot::Provider.get(providers.first["id"]) }
+
+        it "should have a provider" do
+          provider_result["provider"].should_not be_nil
+        end
+
+        it "should have a description" do
+          provider_result["provider"]["description"].should_not be_nil
+        end
+      end
+    end
+  end
+end

metadata

@@ -1,30 +1,69 @@
 --- !ruby/object:Gem::Specification
 name: assaydepot
 version: !ruby/object:Gem::Version
-  version: 0.0.2
-  prerelease: 
+  version: 0.0.3
 platform: ruby
 authors:
 - Christopher Petersen
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-09 00:00:00.000000000 Z
+date: 2015-08-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  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: rspec
+  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: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: This is the first version of Assay Depot's Ruby SDK. It provides read
@@ -36,40 +75,43 @@ extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- .travis.yml
 - Gemfile
-- LICENSE
+- LICENSE.md
 - README.md
 - Rakefile
 - assaydepot.gemspec
 - lib/assaydepot.rb
 - lib/assaydepot/client.rb
 - lib/assaydepot/configurable.rb
+- lib/assaydepot/core.rb
 - lib/assaydepot/model.rb
 - lib/assaydepot/provider.rb
 - lib/assaydepot/version.rb
 - lib/assaydepot/ware.rb
+- spec/assaydepot_spec.rb
 homepage: https://github.com/assaydepot/assaydepot-rb
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.4.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Provides read access to Assay Depot's Services and Vendors.
-test_files: []
+test_files:
+- spec/assaydepot_spec.rb

data/LICENSE

@@ -1,22 +0,0 @@
-Copyright (c) 2012 Christopher Petersen
-
-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.