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module OpenTox
# Wrapper for OpenTox Algorithms
module Algorithm
include OpenTox
# Execute algorithm with parameters, please consult the OpenTox API and the webservice documentation for acceptable parameters
# @param [optional,Hash] params Algorithm parameters
# @param [optional,Boolean] wait set to false if method should return a task uri instead of the algorithm result
# @return [String] URI of new resource (dataset, model, ...)
def run params=nil, wait=true
uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list"}
wait_for_task uri if wait
end
class Generic
include OpenTox
include Algorithm
end
class Descriptor
include OpenTox
include Algorithm
[:smarts_match,:smarts_count,:physchem,:lookup].each do |descriptor|
Descriptor.define_singleton_method(descriptor) do |compounds,descriptors=nil|
descriptors = [descriptors] unless descriptors.is_a? Array
case compounds.class.to_s
when "Array"
klasses = compounds.collect{|c| c.class}.uniq
bad_request_error "First argument contains objects with a different class than OpenTox::Compound or OpenTox::Dataset #{klasses.inspect}" unless klasses.size == 1 and klasses.first == Compound
JSON.parse(Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s)).run(:compound_uri => compounds.collect{|c| c.uri}, :descriptors => descriptors))
when "OpenTox::Compound"
JSON.parse(Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s)).run(:compound_uri => compounds.uri, :descriptors => descriptors))
when "OpenTox::Dataset"
task_uri = Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s)).run(:dataset_uri => compounds.uri, :descriptors => descriptors)
Dataset.new(wait_for_task task_uri)
else
bad_request_error "First argument contains objects with a different class than OpenTox::Compound or OpenTox::Dataset"
end
end
end
# returns a hash, keys: physchem descriptors, values: their description
def self.physchem_descriptors
Hash[ RestClientWrapper.get(File.join(service_uri, "descriptor", "physchem", "list")).to_s.split("\n").collect{|l| l.split("\t")} ]
end
# returns array of "descriptor-values", as CDK descriptors calculate serveral values, e.g., ALOGP produces ALOGP.ALogP, ALOGP.ALogp2, ALOGP.AMR
def self.physchem_descriptor_values
RestClientWrapper.get(File.join(service_uri, "descriptor", "physchem", "list_values")).to_s.split("\n")
end
end
class Fminer
include OpenTox
include Algorithm
def self.bbrc params
Fminer.new(File.join(service_uri, "fminer", "bbrc")).run params
end
def self.last params
Fminer.new(File.join(service_uri, "fminer", "last")).run params
end
end
end
end
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