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include OpenTox
require 'rack/cors'
#require_relative "helper.rb"
# add CORS support for swagger
use Rack::Cors do |config|
config.allow do |allow|
allow.origins '*'
allow.resource "/#{SERVICE}/*",
:methods => [:head, :get, :post, :put, :delete, :options],
:headers => :any,
:max_age => 0
end
end
before do
@accept = request.env['HTTP_ACCEPT']
response['Content-Type'] = @accept
end
# route to swagger API file
get "/api/api.json" do
response['Content-Type'] = "application/json"
api_file = File.join("api", "api.json")
bad_request_error "API Documentation in Swagger JSON is not implemented.", uri("/#{SERVICE}/api") unless File.exists?(api_file)
File.read(api_file)
end
# Get a list of all prediction models
# @param [Header] Accept one of text/uri-list,
# @return [text/uri-list] list of all prediction models
get "/model/?" do
models = OpenTox::Model::Prediction.all
case @accept
when "text/uri-list"
uri_list = models.collect{|model| uri("/model/#{model.model_id}")}
return uri_list.join("\n") + "\n"
when "application/json"
models = JSON.parse models.to_json
models.each_index do |idx|
models[idx][:URI] = uri("/model/#{models[idx]["model_id"]["$oid"]}")
models[idx][:crossvalidation_uri] = uri("/crossvalidation/#{models[idx]["crossvalidation_id"]["$oid"]}") if models[idx]["crossvalidation_id"]
end
return models.to_json
else
bad_request_error "Mime type #{@accept} is not supported."
end
end
get "/model/:id/?" do
model = OpenTox::Model::Lazar.find params[:id]
resource_not_found_error "Model with id: #{params[:id]} not found." unless model
model[:URI] = uri("/model/#{model.id}")
model[:neighbor_algorithm_parameters][:feature_dataset_uri] = uri("/dataset/#{model[:neighbor_algorithm_parameters][:feature_dataset_id]}") if model[:neighbor_algorithm_parameters][:feature_dataset_id]
model[:training_dataset_uri] = uri("/dataset/#{model.training_dataset_id}") if model.training_dataset_id
model[:prediction_feature_uri] = uri("/dataset/#{model.prediction_feature_id}") if model.prediction_feature_id
return model.to_json
end
post "/model/:id/?" do
identifier = params[:identifier].split(",")
begin
# get compound from SMILES
compounds = identifier.collect{ |i| Compound.from_smiles i.strip }
rescue
@error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
return @error_report
end
model = OpenTox::Model::Lazar.find params[:id]
batch = {}
compounds.each do |compound|
prediction = model.predict(compound)
batch[compound] = {:id => compound.id, :inchi => compound.inchi, :smiles => compound.smiles, :model => model, :prediction => prediction}
end
return batch.to_json
end
# Get a list of a single or all descriptors
# @param [Header] Accept one of text/plain, application/json
# @param [Path] Descriptor name (e.G.: Openbabel.HBA1)
# @return [text/plain, application/json] list of all prediction models
get "/algorithm/descriptor/?:descriptor?" do
case @accept
when "application/json"
return "#{JSON.pretty_generate OpenTox::Algorithm::Descriptor::DESCRIPTORS} " unless params[:descriptor]
return {params[:descriptor] => OpenTox::Algorithm::Descriptor.description(params[:descriptor])}.to_json
else
return OpenTox::Algorithm::Descriptor::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor]
return OpenTox::Algorithm::Descriptor.description params[:descriptor]
end
end
post "/algorithm/descriptor/?" do
bad_request_error "Missing Parameter " unless (params[:identifier] or params[:file]) and params[:descriptor]
descriptor = params['descriptor'].split(',')
if params[:file]
data = OpenTox::Dataset.from_csv_file params[:file][:tempfile]
else
data = OpenTox::Compound.from_smiles params[:identifier]
end
d = Algorithm::Descriptor.physchem data, descriptor
csv = d.to_csv
csv = "SMILES,#{params[:descriptor]}\n#{params[:identifier]},#{csv}" if params[:identifier]
case @accept
when "application/csv"
return csv
when "application/json"
lines = CSV.parse(csv)
keys = lines.delete lines.first
data = lines.collect{|values|Hash[keys.zip(values)]}
return JSON.pretty_generate(data)
end
end
get %r{/compound/(.+)} do |inchi|
bad_request_error "Input parameter #{inchi} is not an InChI" unless inchi.match(/^InChI=/)
compound = OpenTox::Compound.from_inchi URI.unescape(inchi)
response['Content-Type'] = @accept
case @accept
when "application/json"
return JSON.pretty_generate JSON.parse(compound.to_json)
when "chemical/x-daylight-smiles"
return compound.smiles
when "chemical/x-inchi"
return compound.inchi
when "chemical/x-mdl-sdfile"
return compound.sdf
when "chemical/x-mdl-molfile"
when "image/png"
return compound.png
when "image/svg+xml"
return compound.svg
when "text/plain"
return "#{compound.names}\n"
else
return compound.inspect
end
end
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