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# pc.rb
# (P)hysico (C)hemical descriptor calculation
# Author: Andreas Maunz
# Get a list of OpenBabel algorithms
# @return [text/uri-list] URIs of OpenBabel algorithms
get '/pc' do
algorithms = YAML::load_file File.join(ENV['HOME'], ".opentox", "config", "pc_descriptors.yaml")
response['Content-Type'] = 'text/uri-list'
list = (algorithms.keys << "AllDescriptors").join("\n") + "\n"
case request.env['HTTP_ACCEPT']
when /text\/html/
content_type "text/html"
OpenTox.text_to_html list
else
content_type 'text/uri-list'
list
end
end
# Get RDF/XML representation of OpenBabel algorithm
# @return [application/rdf+xml] OWL-DL representation of OpenBabel algorithm
get '/pc/:descriptor' do
descriptors = YAML::load_file File.join(ENV['HOME'], ".opentox", "config", "pc_descriptors.yaml")
alg_params = [ { DC.description => "Dataset URI", OT.paramScope => "mandatory", DC.title => "dataset_uri" } ]
if params[:descriptor] != "AllDescriptors"
descriptors = descriptors[params[:descriptor]]
else
alg_params << { DC.description => "Descriptor Category, one or more of '#{descriptors.collect { |id, info| info[:category] }.uniq.sort.join(",")}'", OT.paramScope => "optional", DC.title => "category" }
alg_params << { DC.description => "Software Library, one or more of '#{descriptors.collect { |id, info| info[:lib] }.uniq.sort.join(",")}'", OT.paramScope => "optional", DC.title => "lib" }
descriptors = {:id => "AllDescriptors", :name => "All PC descriptors" }
end
if descriptors
# Contents
algorithm = OpenTox::Algorithm::Generic.new(url_for("/pc/#{params[:descriptor]}",:full))
algorithm.metadata = {
DC.title => params[:descriptor],
DC.creator => "andreas@maunz.de",
DC.description => descriptors[:name],
RDF.type => [OTA.DescriptorCalculation],
}
algorithm.metadata[OT.parameters] = alg_params
algorithm.metadata[DC.description] << (", category: " + descriptors[:category]) unless descriptors[:id] == "AllDescriptors"
algorithm.metadata[DC.description] << (", lib: " + descriptors[:lib]) unless descriptors[:id] == "AllDescriptors"
# Deliver
case request.env['HTTP_ACCEPT']
when /text\/html/
content_type "text/html"
OpenTox.text_to_html algorithm.to_yaml
when /yaml/
content_type "application/x-yaml"
algorithm.to_yaml
else
response['Content-Type'] = 'application/rdf+xml'
algorithm.to_rdfxml
end
else
raise OpenTox::NotFoundError.new "Unknown descriptor #{params[:descriptor]}."
end
end
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