cdd 0.0.1 → 0.0.2
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- 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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25
25
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cdd = CDD::Client.new(YOUR_TOKEN)
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26
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```
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27
27
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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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@@ -46,6 +48,77 @@ Returns a list of project objects that look like:
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[{"name"=>"Your Project Name", "id"=>1234}]
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```
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+
## Searches
|
52
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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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|
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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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|
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```ruby
|
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+
require 'cdd'
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|
85
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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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|
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+
### Asynchronous Export
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|
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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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|
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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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|
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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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|
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```ruby
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export.data
|
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```
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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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1
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+
module CDD
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2
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class Export < Base
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attr_accessor :format
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4
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attr_accessor :status
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5
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attr_accessor :search
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6
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attr_accessor :vault
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7
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|
8
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def poll
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9
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client.execute(poll_url)
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10
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end
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11
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|
12
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def poll_url
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13
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"/api/v1/vaults/#{vault.id}/export_progress/#{self.id}"
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14
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+
end
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15
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|
16
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def data
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17
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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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19
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end
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20
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|
21
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def data_url
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22
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"/api/v1/vaults/#{vault.id}/exports/#{id}"
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23
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end
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24
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end
|
25
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end
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data/lib/cdd/project.rb
CHANGED
@@ -1,22 +1,6 @@
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1
1
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module CDD
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2
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-
class Project
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3
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-
attr_accessor :id
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2
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+
class Project < Base
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4
3
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attr_accessor :name
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5
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-
attr_accessor :
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6
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-
|
7
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-
def initialize(client, options={})
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8
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-
self.client = client
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9
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-
options.each do |k,v|
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10
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-
self.send("#{k}=",v)
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11
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-
end
|
12
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-
end
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13
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-
|
14
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-
def projects
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15
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client.execute(projects_url)
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16
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-
end
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17
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-
|
18
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-
def projects_url
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19
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-
"/api/v1/vaults/#{self.id}/projects"
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20
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-
end
|
4
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attr_accessor :vault
|
21
5
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end
|
22
6
|
end
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data/lib/cdd/search.rb
ADDED
@@ -0,0 +1,27 @@
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1
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+
module CDD
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2
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+
class Search < Base
|
3
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attr_accessor :name
|
4
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+
attr_accessor :vault
|
5
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+
|
6
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+
def start_export(projects=[], format="csv")
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7
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project_ids = projects.collect { |p| p.id }
|
8
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+
params = { :search => self.id, :projects => project_ids }
|
9
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+
result = JSON.parse(RestClient.post("#{client.url}#{vault.export_url(format)}", params, { "X-CDD-Token" => client.token }))
|
10
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CDD::Export.new(client, { :search => self, :vault => vault, :format => format }.merge(result))
|
11
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+
end
|
12
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+
|
13
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+
def export(projects=[], format="csv", &block)
|
14
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e = start_export(projects, format)
|
15
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state = e.poll
|
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+
while ["new", "started", "starting"].include?(state["status"]) do
|
17
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state = e.poll
|
18
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+
end
|
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data = e.data
|
20
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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
|
25
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+
end
|
26
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+
end
|
27
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+
end
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data/lib/cdd/vault.rb
CHANGED
@@ -1,24 +1,29 @@
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1
1
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module CDD
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2
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-
class Vault
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3
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-
attr_accessor :id
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2
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+
class Vault < Base
|
4
3
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attr_accessor :name
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5
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-
attr_accessor :client
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6
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-
|
7
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-
def initialize(client, options={})
|
8
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-
self.client = client
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9
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-
options.each do |k,v|
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10
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-
self.send("#{k}=",v)
|
11
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-
end
|
12
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-
end
|
13
4
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14
5
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def projects
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15
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-
client.execute(projects_url).collect do |hash|
|
16
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-
CDD::Project.new(self.client, hash)
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6
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+
@project ||= client.execute(projects_url).collect do |hash|
|
7
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+
CDD::Project.new(self.client, {:vault => self}.merge(hash))
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17
8
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end
|
18
9
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end
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10
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|
20
11
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def projects_url
|
21
12
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"/api/v1/vaults/#{self.id}/projects"
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22
13
|
end
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14
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+
|
15
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def searches
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16
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@searches ||= client.execute(searches_url).collect do |hash|
|
17
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CDD::Search.new(client, {:vault => self}.merge(hash))
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18
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+
end
|
19
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+
end
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20
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+
|
21
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def searches_url
|
22
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+
"/api/v1/vaults/#{self.id}/searches"
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23
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end
|
24
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+
|
25
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+
def export_url(format="csv")
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26
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+
"/api/v1/vaults/#{self.id}/exports.#{format}"
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27
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+
end
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23
28
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end
|
24
29
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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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|
1
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+
require 'spec_helper'
|
2
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+
|
3
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describe CDD do
|
4
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+
|
5
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context "A default client" do
|
6
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context "when requesting vaults" do
|
7
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let(:token) { ENV["CDD_TOKEN_ID"] || "1234567890" }
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8
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let(:client) { CDD::Client.new(token) }
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9
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+
|
10
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+
it "should have the correct vaults_url" do
|
11
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client.vaults_url.should == "/api/v1/vaults"
|
12
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+
end
|
13
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+
|
14
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it "should call the default vaults url" do
|
15
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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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16
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+
client.vaults
|
17
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+
end
|
18
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+
|
19
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+
context "when requesting vaults" do
|
20
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+
before(:all) do
|
21
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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))
|
22
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+
end
|
23
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+
let(:vaults) { client.vaults }
|
24
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+
|
25
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+
it "should return an array of vaults" do
|
26
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+
vaults.class.should == Array
|
27
|
+
vaults.first.class.should == CDD::Vault
|
28
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+
end
|
29
|
+
|
30
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+
context "the vault" do
|
31
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+
let(:vault) { vaults.first }
|
32
|
+
|
33
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+
it "should have the correct values" do
|
34
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+
vault.id.should == "1234"
|
35
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+
vault.name.should == "Test Vault"
|
36
|
+
end
|
37
|
+
|
38
|
+
it "should have the correct default export_url" do
|
39
|
+
vault.export_url.should == "/api/v1/vaults/#{vault.id}/exports.csv"
|
40
|
+
end
|
41
|
+
|
42
|
+
it "should have the correct csv export_url" do
|
43
|
+
vault.export_url("csv").should == "/api/v1/vaults/#{vault.id}/exports.csv"
|
44
|
+
end
|
45
|
+
|
46
|
+
it "should have the correct sdf export_url" do
|
47
|
+
vault.export_url("sdf").should == "/api/v1/vaults/#{vault.id}/exports.sdf"
|
48
|
+
end
|
49
|
+
|
50
|
+
it "should have the correct searches_url" do
|
51
|
+
vault.searches_url.should == "/api/v1/vaults/#{vault.id}/searches"
|
52
|
+
end
|
53
|
+
|
54
|
+
it "should call the default searches url" do
|
55
|
+
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))
|
56
|
+
vault.searches
|
57
|
+
end
|
58
|
+
|
59
|
+
context "when requesting searches" do
|
60
|
+
before(:all) do
|
61
|
+
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))
|
62
|
+
end
|
63
|
+
let(:searches) { vault.searches }
|
64
|
+
|
65
|
+
it "should return an array of searches" do
|
66
|
+
searches.class.should == Array
|
67
|
+
searches.first.class.should == CDD::Search
|
68
|
+
end
|
69
|
+
|
70
|
+
context "the search" do
|
71
|
+
let(:search) { searches.first }
|
72
|
+
|
73
|
+
it "should have the correct values" do
|
74
|
+
search.id.should == "12345"
|
75
|
+
search.name.should == "Test Search"
|
76
|
+
end
|
77
|
+
end
|
78
|
+
end
|
79
|
+
|
80
|
+
it "should have the correct projects_url" do
|
81
|
+
vaults.first.projects_url.should == "/api/v1/vaults/#{vaults.first.id}/projects"
|
82
|
+
end
|
83
|
+
|
84
|
+
it "should call the default projects url" do
|
85
|
+
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))
|
86
|
+
vault.projects
|
87
|
+
end
|
88
|
+
|
89
|
+
context "when requesting projects" do
|
90
|
+
before(:all) do
|
91
|
+
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))
|
92
|
+
end
|
93
|
+
let(:projects) { vault.projects }
|
94
|
+
|
95
|
+
it "should return an array of projects" do
|
96
|
+
projects.class.should == Array
|
97
|
+
projects.first.class.should == CDD::Project
|
98
|
+
end
|
99
|
+
|
100
|
+
context "the project" do
|
101
|
+
let(:project) { projects.first }
|
102
|
+
|
103
|
+
it "should have the correct values" do
|
104
|
+
project.id.should == "123456"
|
105
|
+
project.name.should == "Test Project"
|
106
|
+
end
|
107
|
+
end
|
108
|
+
end
|
109
|
+
end
|
110
|
+
end
|
111
|
+
end
|
112
|
+
end
|
113
|
+
|
114
|
+
context "A client with a custom url" do
|
115
|
+
context "when requesting vaults" do
|
116
|
+
let(:token) { ENV["CDD_TOKEN_ID"] || "1234567890" }
|
117
|
+
let(:client) { CDD::Client.new(token, :url => "http://example.com") }
|
118
|
+
|
119
|
+
it "should call the custom vaults url" do
|
120
|
+
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))
|
121
|
+
vaults = client.vaults
|
122
|
+
end
|
123
|
+
end
|
124
|
+
end
|
125
|
+
end
|
data/spec/spec_helper.rb
ADDED
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: cdd
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.2
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -9,7 +9,7 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2013-01-
|
12
|
+
date: 2013-01-19 00:00:00.000000000 Z
|
13
13
|
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
|