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# descriptors.rb
# Calculation of physico-chemical descriptors
# Author: Andreas Maunz, Christoph Helma
require 'openbabel'
module OpenTox
class Application < Service
before '/descriptor/:method/?' do
if request.get?
@algorithm = OpenTox::Algorithm::Descriptor.new @uri
@algorithm.parameters = [ {
RDF::DC.description => "Dataset URI",
RDF::OT.paramScope => "optional",
RDF::DC.title => "dataset_uri"
},{
RDF::DC.description => "Compound URI",
RDF::OT.paramScope => "optional",
RDF::DC.title => "compound_uri"
} ]
@algorithm.metadata = {
RDF.type => [RDF::OT.Algorithm, RDF::OTA.DescriptorCalculation],
}
end
end
get '/descriptor/?' do
render [ uri('/descriptor/physchem'), uri('/descriptor/smarts_match'), uri('/descriptor/smarts_count'), uri('/descriptor/lookup')].sort
end
get '/descriptor/smarts_match/?' do
@algorithm.parameters += [ {
RDF::DC.description => "SMARTS strings",
RDF::OT.paramScope => "mandatory",
RDF::DC.title => "descriptors"
} ]
@algorithm.metadata[RDF::DC.title] = "SMARTS matcher"
render @algorithm
end
get '/descriptor/smarts_count/?' do
@algorithm.parameters += [ {
RDF::DC.description => "Counts SMARTS matches",
RDF::OT.paramScope => "mandatory",
RDF::DC.title => "descriptors"
} ]
@algorithm.metadata[RDF::DC.title] = "SMARTS count"
render @algorithm
end
get '/descriptor/physchem/?' do
@algorithm.parameters += [ {
RDF::DC.description => "Physical-chemical descriptors (see #{File.join @uri, 'list'} for a list of supported parameters)",
RDF::OT.paramScope => "mandatory",
RDF::DC.title => "descriptors"
} ]
@algorithm.metadata[RDF::DC.title] = "Physical-chemical descriptors"
render @algorithm
end
get '/descriptor/physchem/list/?' do
response['Content-Type'] = 'text/plain'
OpenTox::Algorithm::Descriptor::DESCRIPTORS.collect{|k,v| "#{k}\t#{v}"}.join "\n"
end
get '/descriptor/physchem/unique/?' do
response['Content-Type'] = 'text/plain'
OpenTox::Algorithm::Descriptor::UNIQUEDESCRIPTORS.collect{|d| "#{d}\t#{OpenTox::Algorithm::Descriptor::DESCRIPTORS[d]}"}.join "\n"
end
get '/descriptor/lookup/?' do
@algorithm.parameters += [ {
RDF::DC.description => "Read feature values from a dataset",
RDF::OT.paramScope => "mandatory",
RDF::DC.title => "feature_dataset_uri"
} ]
@algorithm.metadata[RDF::DC.title] = "Dataset lookup"
render @algorithm
end
post '/descriptor/:method' do
if params[:method] == "physchem"
params[:descriptors] = OpenTox::Algorithm::Descriptor::UNIQUEDESCRIPTORS if !params[:descriptors] or params[:descriptors] == [""]
else
bad_request_error "Please provide 'descriptors' parameters.", @uri unless params[:descriptors]
end
if params[:compound_uri] # return json
@compounds = [params[:compound_uri]].flatten.collect{|u| OpenTox::Compound.new u}
result = OpenTox::Algorithm::Descriptor.send(params[:method].to_sym, @compounds, params[:descriptors])
Hash[result.map {|compound, v| [compound.uri, v] }].to_json
elsif params[:dataset_uri] # return dataset
task = OpenTox::Task.run("Calculating #{params[:method]} descriptors for dataset #{params[:dataset_uri]}.", @uri) do |task|
@compounds = OpenTox::Dataset.new(params[:dataset_uri]).compounds
result = OpenTox::Algorithm::Descriptor.send(params[:method].to_sym, @compounds, params[:descriptors])
internal_server_error "internal error: wrong num results" if (@compounds.size != result.size)
dataset = OpenTox::Dataset.new
dataset.metadata = {
RDF::DC.title => "Physico-chemical descriptors",
RDF::DC.creator => @uri,
RDF::OT.hasSource => @uri,
}
dataset.parameters = [
{ RDF::DC.title => "dataset_uri", RDF::OT.paramValue => params[:dataset_uri] },
{ RDF::DC.title => "descriptors", RDF::OT.paramValue => params[:descriptors] },
]
params[:method] == "smarts_match" ? feature_type = RDF::OT.NominalFeature : feature_type = RDF::OT.NumericFeature
#get descriptor names as returned from calculation (names may differ from params[:descriptors] because of CDK descriptors)
descriptors = []
result.each do |compound,values|
values.each do |desc,val|
descriptors << desc unless descriptors.include?(desc)
end
end
#try to preserve descriptor order
sorted_descriptors = []
params[:descriptors].each do |d|
sorted_descriptors << descriptors.delete(d) if descriptors.include?(d)
end
sorted_descriptors += descriptors
sorted_descriptors.each do |name|
dataset.features << OpenTox::Feature.find_or_create({
RDF::DC.title => name,
RDF.type => [RDF::OT.Feature, feature_type],
RDF::DC.description => OpenTox::Algorithm::Descriptor.description(name)
})
end
result.each do |compound,values|
dataset << ([compound] + sorted_descriptors.collect{|name| values[name]})
end
dataset.put
dataset.uri
end
response['Content-Type'] = 'text/uri-list'
halt 202,task.uri
else
bad_request_error "Please provide a dataset_uri or compound_uri parameter", @uri
end
end
end
end
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