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|
get '/?' do # get index of models
Dir["models/*"].collect{|model| url_for("/", :full) + File.basename(model,".yaml")}.sort.join("\n")
end
get '/:id/?' do
path = File.join("models",params[:id] + ".yaml")
if File.exists? path
send_file path
else
status 404
"Model #{params[:id]} does not exist."
end
end
delete '/:id/?' do
path = File.join("models",params[:id] + ".yaml")
if File.exists? path
File.delete path
"Model #{params[:id]} deleted."
else
status 404
"Model #{params[:id]} does not exist."
end
end
post '/?' do # create model
case request.content_type
when /application\/x-yaml|text\/yaml/
input = request.env["rack.input"].read
id = Dir["models/*"].collect{|model| File.basename(model,".yaml").to_i}.sort.last
if id.nil?
id = 1
else
id += 1
end
File.open(File.join("models",id.to_s + ".yaml"),"w+") { |f| f.write input }
url_for("/#{id}", :full)
else
halt 400, "MIME type \"#{request.content_type}\" not supported."
end
url_for("/#{id}", :full)
end
# PREDICTIONS
post '/:id/?' do # create prediction
storage = Redland::MemoryStore.new
parser = Redland::Parser.new
serializer = Redland::Serializer.new
path = File.join("models",params[:id] + ".yaml")
if !File.exists? path
status 404
"Model #{params[:id]} does not exist."
end
compound = OpenTox::Compound.new :uri => params[:compound_uri]
data = YAML.load_file path
# find database activities
if data[:activities][compound.uri]
output = Redland::Model.new storage
output.add Redland::Uri.new(compound.uri), Redland::Uri.new(data[:endpoint]), Redland::Literal.new(data[:activities][compound.uri].to_s)
response = serializer.model_to_string(Redland::Uri.new(url_for("/",:full)), output)
else
compound_matches = compound.match data[:features]
conf = 0.0
neighbors = []
classification = nil
data[:fingerprints].each do |uri,matches|
sim = weighted_tanimoto(compound_matches,matches,data[:p_values])
if sim > 0.3
neighbors << uri
case data[:activities][uri].to_s
when 'true'
puts "t: #{sim}"
conf += OpenTox::Utils.gauss(sim)
when 'false'
conf -= OpenTox::Utils.gauss(sim)
end
end
end
conf = conf/neighbors.size
if conf > 0.0
classification = true
elsif conf < 0.0
classification = false
end
output = Redland::Model.new storage
output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/classification",:full)), classification.to_s
output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/confidence",:full)), conf.to_s
neighbors.each do |neighbor|
output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/neighbor",:full)), Redland::Uri.new(neighbor)
end
response =serializer.model_to_string(Redland::Uri.new(url_for("/",:full)), output)
end
m = { :classification => classification,
:confidence => conf,
:neighbors => neighbors,
:features => compound_matches
}
puts m.to_yaml
response
end
def weighted_tanimoto(fp_a,fp_b,p)
common_features = fp_a & fp_b
all_features = fp_a + fp_b
common_p_sum = 0.0
if common_features.size > 0
common_features.each{|f| common_p_sum += p[f]}
all_p_sum = 0.0
all_features.each{|f| all_p_sum += p[f]}
common_p_sum/all_p_sum
else
0.0
end
end
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