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module OpenTox
# key: /datasets
# set: dataset uris
# key: /dataset/:dataset/compounds
# set: compound uris
# key: /dataset/:dataset/compound/:inchi
# set: feature uris
class Dataset < OpenTox
# Initialize with <tt>:uri => uri</tt> or <tt>:name => name</tt> (creates a new dataset)
def initialize(uri)
super(uri)
end
def self.create(params)
uri = RestClient.post File.join(@@config[:services]["opentox-dataset"],"datasets"), :name => params[:name]
Dataset.new(uri.to_s)
end
def self.find(params)
begin
if params[:name]
uri = File.join(@@config[:services]["opentox-dataset"], URI.encode(params[:name]))
elsif params[:uri]
uri = params[:uri]
end
RestClient.get uri # check if the resource is available
Dataset.new(uri) if uri
rescue
nil
end
end
def self.find_or_create(params)
self.create(params) unless self.find(params)
end
def import(params)
if params[:csv]
# RestClient seems not to work for file uploads
#RestClient.post @uri + '/import', :compound_format => params[:compound_format], :content_type => "text/csv", :file => File.new(params[:csv])
`curl -X POST -F "file=@#{params[:csv]};type=text/csv" -F compound_format=#{params[:compound_format]} #{@uri + '/import'}`
end
end
def add(features)
RestClient.post @uri, :features => features.to_yaml
end
# Get all compounds from a dataset
def compound_uris
RestClient.get(File.join(@uri, 'compounds')).split("\n")
end
def compounds
compound_uris.collect{|uri| Compound.new(:uri => uri)}
end
# Get all features for a compound
def feature_uris(compound)
uri = File.join(@uri, 'compound', CGI.escape(compound.inchi)) # URI.encode does not work here
RestClient.get(uri).split("\n")
end
# Get all features for a compound
def features(compound)
feature_uris(compound).collect{|uri| Feature.new(:uri => uri)}
end
def all_features
RestClient.get(File.join(@uri, 'features')).split("\n")
end
# Delete a dataset
def delete
RestClient.delete @uri
end
def tanimoto(dataset)
RestClient.get(File.join(@uri,'tanimoto',dataset.path))
end
def weighted_tanimoto(dataset)
RestClient.get(File.join(@uri,'weighted_tanimoto',dataset.path))
end
end
end
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