cdd 0.0.1 → 0.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.md +74 -1
- data/Rakefile +6 -0
- data/lib/cdd/base.rb +13 -0
- data/lib/cdd/client.rb +2 -2
- data/lib/cdd/export.rb +25 -0
- data/lib/cdd/project.rb +2 -18
- data/lib/cdd/search.rb +27 -0
- data/lib/cdd/vault.rb +17 -12
- data/lib/cdd/version.rb +1 -1
- data/lib/cdd.rb +3 -0
- data/spec/cdd_spec.rb +125 -0
- data/spec/spec_helper.rb +7 -0
- metadata +12 -5
data/README.md
CHANGED
@@ -25,6 +25,7 @@ require 'cdd'
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cdd = CDD::Client.new(YOUR_TOKEN)
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```
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## Vaults
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Retrieve your vaults
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```ruby
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@@ -36,7 +37,8 @@ Returns a list of vault objects that look like:
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[{"name"=>"Your Vault Name", "id"=>1234}]
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```
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-
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## Projects
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Given a vault object, you can retrieve it's project list:
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```ruby
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projects = vaults.first.projects
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```
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[{"name"=>"Your Project Name", "id"=>1234}]
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```
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## Searches
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Given a vault object, you can retrieve it's searches list:
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```ruby
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projects = vaults.first.searches
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```
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Returns a list of searches objects that look like:
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```ruby
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[{"name"=>"Your Search Name", "id"=>1234}]
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```
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## Exporting
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With a ```Search``` object and one or more ```Project``` objects, you can export matching data.
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### Synchronous Export
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The simplest way to export data is using the ```Search#export``` method. The CDD API is asynchronous, this method wraps the API in a synchronous method. You can use in two ways:
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```ruby
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require 'cdd'
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cdd = CDD::Client.new(YOUR_TOKEN)
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vaults = cdd.vaults
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vault = vaults.first
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search = vault.searches.first
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projects = vault.projects
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data = search.export(projects, "csv") # The second parameter defaults to CSV and can be omitted.
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puts data
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```
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Or by using the block syntax, this time in SDF format:
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```ruby
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require 'cdd'
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cdd = CDD::Client.new(YOUR_TOKEN)
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vaults = cdd.vaults
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vault = vaults.first
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search = vault.searches.first
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projects = vault.projects
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search.export(projects, "sdf") do |data|
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puts data
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end
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```
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### Asynchronous Export
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The synchronous export method is provided as a courtesy. If you could be exporting any non-trivial amount of data, you should use the aynchronous method.
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To begin an export using the method ```Search#start_export```. This will return an ```Export``` object which can be polled or used to retrieve data.
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```ruby
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require 'cdd'
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cdd = CDD::Client.new(YOUR_TOKEN)
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vaults = cdd.vaults
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vault = vaults.first
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search = vault.searches.first
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projects = vault.projects
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export = search.start_export(projects, "sdf")
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export_state = export.poll
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puts export_state["status"]
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```
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When ```export.poll["status"] == "finished"``` the export is complete and can be downloaded. You retrieve the data with the following method:
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```ruby
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export.data
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```
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That will return a string containing either the CSV or SDF results.
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## Contributing
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1. Fork it
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data/Rakefile
CHANGED
data/lib/cdd/base.rb
ADDED
data/lib/cdd/client.rb
CHANGED
data/lib/cdd/export.rb
ADDED
@@ -0,0 +1,25 @@
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module CDD
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class Export < Base
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attr_accessor :format
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attr_accessor :status
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attr_accessor :search
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attr_accessor :vault
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def poll
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client.execute(poll_url)
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end
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def poll_url
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"/api/v1/vaults/#{vault.id}/export_progress/#{self.id}"
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end
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def data
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response = RestClient.get "#{client.url}#{data_url}", { :params => {}, "X-CDD-Token" => client.token }
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response.to_s if response
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end
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def data_url
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"/api/v1/vaults/#{vault.id}/exports/#{id}"
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end
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end
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end
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data/lib/cdd/project.rb
CHANGED
@@ -1,22 +1,6 @@
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module CDD
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class Project
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attr_accessor :id
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class Project < Base
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attr_accessor :name
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attr_accessor :
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def initialize(client, options={})
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self.client = client
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options.each do |k,v|
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self.send("#{k}=",v)
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end
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end
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def projects
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client.execute(projects_url)
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end
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def projects_url
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"/api/v1/vaults/#{self.id}/projects"
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end
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attr_accessor :vault
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end
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end
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data/lib/cdd/search.rb
ADDED
@@ -0,0 +1,27 @@
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module CDD
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class Search < Base
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attr_accessor :name
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attr_accessor :vault
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def start_export(projects=[], format="csv")
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project_ids = projects.collect { |p| p.id }
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params = { :search => self.id, :projects => project_ids }
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result = JSON.parse(RestClient.post("#{client.url}#{vault.export_url(format)}", params, { "X-CDD-Token" => client.token }))
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CDD::Export.new(client, { :search => self, :vault => vault, :format => format }.merge(result))
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end
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def export(projects=[], format="csv", &block)
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e = start_export(projects, format)
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state = e.poll
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while ["new", "started", "starting"].include?(state["status"]) do
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state = e.poll
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end
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data = e.data
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if block
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return block.call(data)
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else
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return data
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end
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end
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end
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end
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data/lib/cdd/vault.rb
CHANGED
@@ -1,24 +1,29 @@
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module CDD
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class Vault
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attr_accessor :id
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class Vault < Base
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attr_accessor :name
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attr_accessor :client
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def initialize(client, options={})
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self.client = client
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options.each do |k,v|
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self.send("#{k}=",v)
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end
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end
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def projects
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client.execute(projects_url).collect do |hash|
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CDD::Project.new(self.client, hash)
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@project ||= client.execute(projects_url).collect do |hash|
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CDD::Project.new(self.client, {:vault => self}.merge(hash))
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end
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end
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def projects_url
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"/api/v1/vaults/#{self.id}/projects"
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end
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def searches
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@searches ||= client.execute(searches_url).collect do |hash|
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CDD::Search.new(client, {:vault => self}.merge(hash))
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end
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end
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def searches_url
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"/api/v1/vaults/#{self.id}/searches"
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end
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def export_url(format="csv")
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"/api/v1/vaults/#{self.id}/exports.#{format}"
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end
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end
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end
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data/lib/cdd/version.rb
CHANGED
data/lib/cdd.rb
CHANGED
data/spec/cdd_spec.rb
ADDED
@@ -0,0 +1,125 @@
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require 'spec_helper'
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describe CDD do
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context "A default client" do
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context "when requesting vaults" do
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let(:token) { ENV["CDD_TOKEN_ID"] || "1234567890" }
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let(:client) { CDD::Client.new(token) }
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it "should have the correct vaults_url" do
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client.vaults_url.should == "/api/v1/vaults"
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end
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it "should call the default vaults url" do
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RestClient.should_receive(:get).with("https://app.collaborativedrug.com/api/v1/vaults", { :params=>{} , "X-CDD-Token" => token}).and_return(fake_response([{:id => "1234", :name => "Test Vault"}].to_json))
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client.vaults
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end
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context "when requesting vaults" do
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before(:all) do
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RestClient.stub(:get).with("https://app.collaborativedrug.com/api/v1/vaults", { :params=>{} , "X-CDD-Token" => token}).and_return(fake_response([{:id => "1234", :name => "Test Vault"}].to_json))
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end
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let(:vaults) { client.vaults }
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it "should return an array of vaults" do
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vaults.class.should == Array
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vaults.first.class.should == CDD::Vault
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end
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context "the vault" do
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let(:vault) { vaults.first }
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it "should have the correct values" do
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vault.id.should == "1234"
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vault.name.should == "Test Vault"
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end
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it "should have the correct default export_url" do
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vault.export_url.should == "/api/v1/vaults/#{vault.id}/exports.csv"
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end
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it "should have the correct csv export_url" do
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vault.export_url("csv").should == "/api/v1/vaults/#{vault.id}/exports.csv"
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end
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it "should have the correct sdf export_url" do
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vault.export_url("sdf").should == "/api/v1/vaults/#{vault.id}/exports.sdf"
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end
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it "should have the correct searches_url" do
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vault.searches_url.should == "/api/v1/vaults/#{vault.id}/searches"
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end
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it "should call the default searches url" do
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RestClient.should_receive(:get).with("https://app.collaborativedrug.com/api/v1/vaults/#{vault.id}/searches", { :params=>{} , "X-CDD-Token" => token}).and_return(fake_response([{:id => "12345", :name => "Test Search"}].to_json))
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vault.searches
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end
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context "when requesting searches" do
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before(:all) do
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RestClient.stub(:get).with("https://app.collaborativedrug.com/api/v1/vaults/#{vault.id}/searches", { :params=>{} , "X-CDD-Token" => token}).and_return(fake_response([{:id => "12345", :name => "Test Search"}].to_json))
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end
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let(:searches) { vault.searches }
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it "should return an array of searches" do
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searches.class.should == Array
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searches.first.class.should == CDD::Search
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end
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context "the search" do
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let(:search) { searches.first }
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it "should have the correct values" do
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search.id.should == "12345"
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search.name.should == "Test Search"
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end
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end
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end
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it "should have the correct projects_url" do
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vaults.first.projects_url.should == "/api/v1/vaults/#{vaults.first.id}/projects"
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end
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it "should call the default projects url" do
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RestClient.should_receive(:get).with("https://app.collaborativedrug.com/api/v1/vaults/#{vaults.first.id}/projects", { :params=>{} , "X-CDD-Token" => token}).and_return(fake_response([{:id => "123456", :name => "Test Project"}].to_json))
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vault.projects
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end
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context "when requesting projects" do
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before(:all) do
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RestClient.stub(:get).with("https://app.collaborativedrug.com/api/v1/vaults/#{vaults.first.id}/projects", { :params=>{} , "X-CDD-Token" => token}).and_return(fake_response([{:id => "123456", :name => "Test Project"}].to_json))
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end
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let(:projects) { vault.projects }
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it "should return an array of projects" do
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projects.class.should == Array
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projects.first.class.should == CDD::Project
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end
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context "the project" do
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let(:project) { projects.first }
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it "should have the correct values" do
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project.id.should == "123456"
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project.name.should == "Test Project"
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end
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end
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end
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end
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end
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end
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end
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context "A client with a custom url" do
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context "when requesting vaults" do
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let(:token) { ENV["CDD_TOKEN_ID"] || "1234567890" }
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let(:client) { CDD::Client.new(token, :url => "http://example.com") }
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it "should call the custom vaults url" do
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RestClient.should_receive(:get).with("http://example.com/api/v1/vaults", { :params=>{} , "X-CDD-Token" => token}).and_return(fake_response([{:id => "1234", :name => "Test Vault"}].to_json))
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vaults = client.vaults
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end
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end
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end
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end
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data/spec/spec_helper.rb
ADDED
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: cdd
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3
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version: !ruby/object:Gem::Version
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version: 0.0.
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version: 0.0.2
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5
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prerelease:
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6
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platform: ruby
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7
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authors:
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@@ -9,7 +9,7 @@ authors:
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9
9
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2013-01-
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+
date: 2013-01-19 00:00:00.000000000 Z
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dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: json
|
@@ -89,10 +89,15 @@ files:
|
|
89
89
|
- Rakefile
|
90
90
|
- cdd.gemspec
|
91
91
|
- lib/cdd.rb
|
92
|
+
- lib/cdd/base.rb
|
92
93
|
- lib/cdd/client.rb
|
94
|
+
- lib/cdd/export.rb
|
93
95
|
- lib/cdd/project.rb
|
96
|
+
- lib/cdd/search.rb
|
94
97
|
- lib/cdd/vault.rb
|
95
98
|
- lib/cdd/version.rb
|
99
|
+
- spec/cdd_spec.rb
|
100
|
+
- spec/spec_helper.rb
|
96
101
|
homepage: http://github.com/cpetersen/cdd
|
97
102
|
licenses: []
|
98
103
|
post_install_message:
|
@@ -107,7 +112,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
107
112
|
version: '0'
|
108
113
|
segments:
|
109
114
|
- 0
|
110
|
-
hash:
|
115
|
+
hash: 3887554079488693763
|
111
116
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
112
117
|
none: false
|
113
118
|
requirements:
|
@@ -116,7 +121,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
116
121
|
version: '0'
|
117
122
|
segments:
|
118
123
|
- 0
|
119
|
-
hash:
|
124
|
+
hash: 3887554079488693763
|
120
125
|
requirements: []
|
121
126
|
rubyforge_project:
|
122
127
|
rubygems_version: 1.8.24
|
@@ -124,4 +129,6 @@ signing_key:
|
|
124
129
|
specification_version: 3
|
125
130
|
summary: Collaborative Drug Discovery is a web based tool for storing and sharing
|
126
131
|
pharmaceutical research. This is a ruby wrapper for their API.
|
127
|
-
test_files:
|
132
|
+
test_files:
|
133
|
+
- spec/cdd_spec.rb
|
134
|
+
- spec/spec_helper.rb
|