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module OpenTox
# key: /datasets
# set: dataset uris
# key: /dataset/:dataset/compounds
# set: compound uris
# key: /dataset/:dataset/compound/:inchi/:feature_type
# 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)
if params[:name]
uri = RestClient.get File.join(@@config[:services]["opentox-dataset"], params[:name])
elsif params[:uri]
uri = params[:uri]
end
if RestClient.get uri
Dataset.new(uri)
else
nil
end
end
def import(params)
if params[:csv]
# RestClient seems not to work for file uploads
`curl -X POST -F "file=@#{params[:csv]};type=text/csv" -F compound_format=#{params[:compound_format]} -F feature_type=#{params[:feature_type]} #{@uri + '/import'}`
end
end
def add_features(features,feature_type)
#puts @uri
#puts feature_type
#puts features.to_yaml
HTTPClient.post @uri, {:feature_type => feature_type, :features => features.to_yaml}
#`curl -X POST -F feature_type="#{feature_type}" -F features="#{features.to_yaml}" #{@uri}`
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,feature_type)
#puts File.join(@uri, 'compound', compound.inchi, feature_type)
RestClient.get(File.join(@uri, 'compound', compound.inchi, feature_type)).split("\n")
end
# Get all features for a compound
def features(compound,feature_type)
feature_uris(compound,feature_type).collect{|uri| Feature.new(:uri => uri)}
end
# Delete a dataset
def delete
RestClient.delete @uri
end
end
end
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