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|
['rubygems', 'rest_client', 'spork', 'environment'].each do |lib|
require lib
end
module OpenTox
class OpenTox
attr_reader :uri
# Escape all nonword characters
def uri_escape(string)
URI.escape(string, /[^\w]/)
end
# Returns true if object creation has finished (for asynchronous processes)
def finished?
YAML.load(RestClient.get(@uri))[:finished]
end
# Get the object name
def name
RestClient.get @uri + '/name'
end
# Deletes an object
def destroy
RestClient.delete @uri
end
end
class Compound < OpenTox
# Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc)
def initialize(params)
if params[:uri]
@uri = params[:uri].to_s
elsif params[:smiles]
@uri = RestClient.post @services['opentox-compound'] ,:smiles => uri_escape(params[:smiles])
elsif params[:name]
@uri = RestClient.post @services['opentox-compound'] ,:name => uri_escape(params[:name])
end
end
# Get the (canonical) smiles
def smiles
RestClient.get @uri
end
# Matchs a smarts string
def match?(smarts)
if RestClient.get(@uri + '/match/' + uri_escape(smarts)) == 'true'
true
else
false
end
end
# Match an array of smarts features, returns matching features
def match(smarts_features)
smarts_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact
end
end
class Feature < OpenTox
# Initialize with <tt>:uri => uri</tt>, or <tt>:name => name, :values => hash_of_property_names_and_values</tt>
def initialize(params)
if params[:uri]
@uri = params[:uri].to_s
else
@uri = @services['opentox-feature']+ uri_escape(params[:name])
params[:values].each do |k,v|
@uri += '/' + k.to_s + '/' + v.to_s
end
end
end
# Get the value of a property
def value(property)
RestClient.get @uri + '/' + property
end
end
class Dataset < OpenTox
# Initialize with <tt>:uri => uri</tt> or <tt>:name => name</tt> (creates a new dataset)
def initialize(params)
if params[:uri]
@uri = params[:uri].to_s
elsif params[:name] and params[:filename]
@uri = `curl -X POST -F file=@#{params[:filename]} -F name="#{params[:name]}" #{@services['opentox-dataset']}`
elsif params[:name]
@uri = RestClient.post @services['opentox-dataset'], :name => params[:name]
end
end
# Get all compounds from a dataset
def compounds
RestClient.get(@uri + '/compounds').split("\n").collect{ |c| Compound.new(:uri => c) }
end
# Get all compounds and features from a dataset, returns a hash with compound_uris as keys and arrays of feature_uris as values
def all_compounds_and_features_uris
YAML.load(RestClient.get(@uri + '/compounds/features'))
end
# Get all features from a dataset
def all_features
RestClient.get(@uri + '/features').split("\n").collect{|f| Feature.new(:uri => f)}
end
# Get all features for a compound
def features(compound)
RestClient.get(@uri + '/compound/' + uri_escape(compound.uri) + '/features').split("\n").collect{|f| Feature.new(:uri => f) }
end
# Add a compound and a feature to a dataset
def add(compound,feature)
RestClient.put @uri, :compound_uri => compound.uri, :feature_uri => feature.uri
end
# Tell the dataset that it is complete
def close
RestClient.put @uri, :finished => 'true'
end
end
class Fminer < OpenTox
# Create a new dataset with BBRC features
def initialize(training_dataset)
@dataset_uri = RestClient.post @services['opentox-fminer'], :dataset_uri => training_dataset.uri
end
def dataset
Dataset.new(:uri => @dataset_uri)
end
end
class Lazar < OpenTox
# Create a new prediction model from a dataset
def initialize(params)
if params[:uri]
@uri = params[:uri]
elsif params[:dataset_uri]
@uri = RestClient.post @services['opentox-lazar']+ 'models' , :dataset_uri => params[:dataset_uri]
end
end
# Predict a compound
def predict(compound)
LazarPrediction.new(:uri => RestClient.post(@uri, :compound_uri => compound.uri))
end
end
class LazarPrediction < OpenTox
def initialize(params)
if params[:uri]
@uri = params[:uri]
end
end
def classification
YAML.load(RestClient.get @uri)[:classification]
end
def confidence
YAML.load(RestClient.get @uri)[:confidence]
end
def neighbors
RestClient.get @uri + '/neighbors'
end
def features
RestClient.get @uri + '/features'
end
end
end
|
