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CDD - Collaborative Drug Discovery

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Collaborative Drug Discovery is a web based tool for storing and sharing pharmaceutical research. This is a ruby wrapper for their API.

CDD's API can be found here.

Installation

Add this line to your application's Gemfile:

gem 'cdd'

And then execute:

$ bundle

Or install it yourself as:

$ gem install cdd

Usage

Setup your client:

require 'cdd'
cdd = CDD::Client.new(YOUR_TOKEN)

Vaults

Retrieve your vaults

vaults = cdd.vaults

Returns a list of vault objects that look like:

[{"name"=>"Your Vault Name", "id"=>1234}]

Projects

Given a vault object, you can retrieve it's project list:

projects = vaults.first.projects

Returns a list of project objects that look like:

[{"name"=>"Your Project Name", "id"=>1234}]

DataSets

Given a vault object, you can retrieve it's available data sets:

data_sets = vaults.first.data_sets

Returns a list of data_set objects that look like:

[{"name"=>"Data Set X", "id"=>1234567}]

Searches

Given a vault object, you can retrieve it's searches list:

projects = vaults.first.searches

Returns a list of searches objects that look like:

[{"name"=>"Your Search Name", "id"=>1234}]

Exporting

With a Search object and one or more Project objects, you can export matching data.

Synchronous Export

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:

require 'cdd'

cdd = CDD::Client.new(YOUR_TOKEN)
vaults = cdd.vaults
vault = vaults.first
search = vault.searches.first
projects = vault.projects
data = search.export(projects, "csv") # The second parameter defaults to CSV and can be omitted.
puts data

Or by using the block syntax, this time in SDF format:

require 'cdd'

cdd = CDD::Client.new(YOUR_TOKEN)
vaults = cdd.vaults
vault = vaults.first
search = vault.searches.first
projects = vault.projects
search.export(projects, [], "sdf") do |data|
  puts data
end

Asynchronous Export

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.

In this example, we will use publicly accessible data sets, this should result in a larger result set (and why we are using the )

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.

require 'cdd'

cdd = CDD::Client.new(YOUR_TOKEN)
vaults = cdd.vaults
vault = vaults.first
search = vault.searches.first
projects = vault.projects
data_sets = vault.data_sets
export = search.start_export(projects, data_sets, "sdf")
export_state = export.poll
puts export_state["status"]

When export.poll["status"] == "finished" the export is complete and can be downloaded. You retrieve the data with the following method:

export.data

That will return a string containing either the CSV or SDF results.

Contributing

  1. Fork it
  2. Create your feature branch (git checkout -b my-new-feature)
  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